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diff --git a/doc/doc2/Eqs/.log b/doc/doc2/Eqs/.log
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+This is TeX, Version 3.14159 (Web2C 7.4.5) (format=latex 2008.11.14) 27 AUG 2011 15:16
+**pair_sph_tait
+(/usr/share/texmf/tex/latex/tools/.tex
+LaTeX2e <2001/06/01>
+Babel <v3.7h> and hyphenation patterns for american, french, german, ngerman, n
+ohyphenation, loaded.
+File ignored)
+*
+(Please type a command or say `\end')
+*x
+
+! LaTeX Error: Missing \begin{document}.
+
+See the LaTeX manual or LaTeX Companion for explanation.
+Type H <return> for immediate help.
+ ...
+
+<*> x
+
+? x
+
+Here is how much of TeX's memory you used:
+ 6 strings out of 95847
+ 257 string characters out of 1195947
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+ 14 hyphenation exceptions out of 1000
+ 5i,0n,4p,93b,14s stack positions out of 1500i,500n,5000p,200000b,5000s
+No pages of output.
diff --git a/doc/doc2/Eqs/angle_charmm.jpg b/doc/doc2/Eqs/angle_charmm.jpg
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diff --git a/doc/doc2/Eqs/angle_charmm.tex b/doc/doc2/Eqs/angle_charmm.tex
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--- /dev/null
+++ b/doc/doc2/Eqs/angle_charmm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_class2.jpg b/doc/doc2/Eqs/angle_class2.jpg
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diff --git a/doc/doc2/Eqs/angle_class2.tex b/doc/doc2/Eqs/angle_class2.tex
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index 000000000..e5a542e87
--- /dev/null
+++ b/doc/doc2/Eqs/angle_class2.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & E_a + E_{bb} + E_{ba} \\
+ E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
+ E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
+ E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_cosine.jpg b/doc/doc2/Eqs/angle_cosine.jpg
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index 000000000..23b9b6431
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diff --git a/doc/doc2/Eqs/angle_cosine.tex b/doc/doc2/Eqs/angle_cosine.tex
new file mode 100644
index 000000000..e76667609
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [1 + \cos(\theta)]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_cosine_delta.jpg b/doc/doc2/Eqs/angle_cosine_delta.jpg
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diff --git a/doc/doc2/Eqs/angle_cosine_delta.tex b/doc/doc2/Eqs/angle_cosine_delta.tex
new file mode 100644
index 000000000..918e9e504
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine_delta.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [1 - \cos(\theta - \theta_0)]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_periodic.jpg b/doc/doc2/Eqs/angle_cosine_periodic.jpg
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index 000000000..a9d7d50cb
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diff --git a/doc/doc2/Eqs/angle_cosine_periodic.tex b/doc/doc2/Eqs/angle_cosine_periodic.tex
new file mode 100644
index 000000000..69aa1bba6
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine_periodic.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_shift.jpg b/doc/doc2/Eqs/angle_cosine_shift.jpg
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index 000000000..d9929939c
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diff --git a/doc/doc2/Eqs/angle_cosine_shift.tex b/doc/doc2/Eqs/angle_cosine_shift.tex
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index 000000000..e795d6bef
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine_shift.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_shift_exp.jpg b/doc/doc2/Eqs/angle_cosine_shift_exp.jpg
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index 000000000..294986de4
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diff --git a/doc/doc2/Eqs/angle_cosine_shift_exp.tex b/doc/doc2/Eqs/angle_cosine_shift_exp.tex
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index 000000000..4afa01356
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine_shift_exp.tex
@@ -0,0 +1,13 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E=-U_{min}
+\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
+\quad\mbox{with}\quad
+U(\theta,\theta_0)
+=-0.5 \left(1+\cos(\theta-\theta_0) \right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_squared.jpg b/doc/doc2/Eqs/angle_cosine_squared.jpg
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index 000000000..b992398b7
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diff --git a/doc/doc2/Eqs/angle_cosine_squared.tex b/doc/doc2/Eqs/angle_cosine_squared.tex
new file mode 100644
index 000000000..57ae47ae4
--- /dev/null
+++ b/doc/doc2/Eqs/angle_cosine_squared.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [\cos(\theta) - \cos(\theta_0)]^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_gamma.jpg b/doc/doc2/Eqs/angle_dipole_gamma.jpg
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index 000000000..4bf618e25
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diff --git a/doc/doc2/Eqs/angle_dipole_gamma.tex b/doc/doc2/Eqs/angle_dipole_gamma.tex
new file mode 100644
index 000000000..965b74ad9
--- /dev/null
+++ b/doc/doc2/Eqs/angle_dipole_gamma.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_potential.jpg b/doc/doc2/Eqs/angle_dipole_potential.jpg
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diff --git a/doc/doc2/Eqs/angle_dipole_potential.tex b/doc/doc2/Eqs/angle_dipole_potential.tex
new file mode 100644
index 000000000..8949835eb
--- /dev/null
+++ b/doc/doc2/Eqs/angle_dipole_potential.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\cos\gamma - \cos\gamma_0)^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_torque.jpg b/doc/doc2/Eqs/angle_dipole_torque.jpg
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index 000000000..996a9df3c
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diff --git a/doc/doc2/Eqs/angle_dipole_torque.tex b/doc/doc2/Eqs/angle_dipole_torque.tex
new file mode 100644
index 000000000..9527459fd
--- /dev/null
+++ b/doc/doc2/Eqs/angle_dipole_torque.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
+ \vec{r_{ij}} \times \vec{\mu_j}
+$$
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_fourier.jpg b/doc/doc2/Eqs/angle_fourier.jpg
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index 000000000..e748e6743
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diff --git a/doc/doc2/Eqs/angle_fourier.tex b/doc/doc2/Eqs/angle_fourier.tex
new file mode 100644
index 000000000..f7f76462e
--- /dev/null
+++ b/doc/doc2/Eqs/angle_fourier.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_fourier_simple.jpg b/doc/doc2/Eqs/angle_fourier_simple.jpg
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index 000000000..6c9297b97
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diff --git a/doc/doc2/Eqs/angle_fourier_simple.tex b/doc/doc2/Eqs/angle_fourier_simple.tex
new file mode 100644
index 000000000..3228315a1
--- /dev/null
+++ b/doc/doc2/Eqs/angle_fourier_simple.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [ 1.0 + c \cos ( n \theta) ]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/angle_harmonic.jpg b/doc/doc2/Eqs/angle_harmonic.jpg
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index 000000000..352be0b54
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diff --git a/doc/doc2/Eqs/angle_harmonic.tex b/doc/doc2/Eqs/angle_harmonic.tex
new file mode 100644
index 000000000..c566376b5
--- /dev/null
+++ b/doc/doc2/Eqs/angle_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\theta - \theta_0)^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_quartic.jpg b/doc/doc2/Eqs/angle_quartic.jpg
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index 000000000..744ce7a35
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diff --git a/doc/doc2/Eqs/angle_quartic.tex b/doc/doc2/Eqs/angle_quartic.tex
new file mode 100644
index 000000000..ff9ff9a7d
--- /dev/null
+++ b/doc/doc2/Eqs/angle_quartic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/bond_class2.jpg b/doc/doc2/Eqs/bond_class2.jpg
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index 000000000..493048100
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diff --git a/doc/doc2/Eqs/bond_class2.tex b/doc/doc2/Eqs/bond_class2.tex
new file mode 100644
index 000000000..0735b6102
--- /dev/null
+++ b/doc/doc2/Eqs/bond_class2.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_fene.jpg b/doc/doc2/Eqs/bond_fene.jpg
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index 000000000..e8b909c08
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diff --git a/doc/doc2/Eqs/bond_fene.tex b/doc/doc2/Eqs/bond_fene.tex
new file mode 100644
index 000000000..ec4dd8efa
--- /dev/null
+++ b/doc/doc2/Eqs/bond_fene.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
+ 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_fene_expand.jpg b/doc/doc2/Eqs/bond_fene_expand.jpg
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index 000000000..1d04acec3
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diff --git a/doc/doc2/Eqs/bond_fene_expand.tex b/doc/doc2/Eqs/bond_fene_expand.tex
new file mode 100644
index 000000000..5fd96e7ad
--- /dev/null
+++ b/doc/doc2/Eqs/bond_fene_expand.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = -0.5 K R_0^2
+ \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
+ 4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
+ \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
+ \Delta\right)}\right)^6 \right] + \epsilon
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/bond_harmonic.jpg b/doc/doc2/Eqs/bond_harmonic.jpg
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index 000000000..fe9ef5619
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diff --git a/doc/doc2/Eqs/bond_harmonic.tex b/doc/doc2/Eqs/bond_harmonic.tex
new file mode 100644
index 000000000..246108689
--- /dev/null
+++ b/doc/doc2/Eqs/bond_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (r - r_0)^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_harmonic_shift.jpg b/doc/doc2/Eqs/bond_harmonic_shift.jpg
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index 000000000..3e66d853a
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diff --git a/doc/doc2/Eqs/bond_harmonic_shift.tex b/doc/doc2/Eqs/bond_harmonic_shift.tex
new file mode 100644
index 000000000..3daa16724
--- /dev/null
+++ b/doc/doc2/Eqs/bond_harmonic_shift.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_harmonic_shift_cut.jpg b/doc/doc2/Eqs/bond_harmonic_shift_cut.jpg
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index 000000000..06640e4fe
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diff --git a/doc/doc2/Eqs/bond_harmonic_shift_cut.tex b/doc/doc2/Eqs/bond_harmonic_shift_cut.tex
new file mode 100644
index 000000000..3daa16724
--- /dev/null
+++ b/doc/doc2/Eqs/bond_harmonic_shift_cut.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_morse.jpg b/doc/doc2/Eqs/bond_morse.jpg
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index 000000000..6795c9e52
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diff --git a/doc/doc2/Eqs/bond_morse.tex b/doc/doc2/Eqs/bond_morse.tex
new file mode 100644
index 000000000..a0d7a8996
--- /dev/null
+++ b/doc/doc2/Eqs/bond_morse.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
+ E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_nonlinear.jpg b/doc/doc2/Eqs/bond_nonlinear.jpg
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index 000000000..0f18d8e73
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diff --git a/doc/doc2/Eqs/bond_nonlinear.tex b/doc/doc2/Eqs/bond_nonlinear.tex
new file mode 100644
index 000000000..b8cdc9616
--- /dev/null
+++ b/doc/doc2/Eqs/bond_nonlinear.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_quartic.jpg b/doc/doc2/Eqs/bond_quartic.jpg
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index 000000000..9d092883b
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diff --git a/doc/doc2/Eqs/bond_quartic.tex b/doc/doc2/Eqs/bond_quartic.tex
new file mode 100644
index 000000000..0d0cceb35
--- /dev/null
+++ b/doc/doc2/Eqs/bond_quartic.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
+ 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/box.jpg b/doc/doc2/Eqs/box.jpg
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diff --git a/doc/doc2/Eqs/box.tex b/doc/doc2/Eqs/box.tex
new file mode 100644
index 000000000..8442ea85b
--- /dev/null
+++ b/doc/doc2/Eqs/box.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+a &=& {\rm lx} \\
+b^2 &=& {\rm ly}^2 + {\rm xy}^2 \\
+c^2 &=& {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\
+\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
+\cos{\beta} &=& \frac{\rm xz}{c} \\
+\cos{\gamma} &=& \frac{\rm xy}{b} \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/box_inverse.jpg b/doc/doc2/Eqs/box_inverse.jpg
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index 000000000..5d0895b87
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diff --git a/doc/doc2/Eqs/box_inverse.tex b/doc/doc2/Eqs/box_inverse.tex
new file mode 100644
index 000000000..68994f286
--- /dev/null
+++ b/doc/doc2/Eqs/box_inverse.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+{\rm lx} &=& a \\
+{\rm xy} &=& b \cos{\gamma} \\
+{\rm xz} &=& c \cos{\beta}\\
+{\rm ly}^2 &=& b^2 - {\rm xy}^2 \\
+{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
+{\rm lz}^2 &=& c^2 - {\rm xz}^2 - {\rm yz}^2 \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/centro_symmetry.jpg b/doc/doc2/Eqs/centro_symmetry.jpg
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index 000000000..1e89d11a1
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diff --git a/doc/doc2/Eqs/centro_symmetry.tex b/doc/doc2/Eqs/centro_symmetry.tex
new file mode 100644
index 000000000..8d9a9a33e
--- /dev/null
+++ b/doc/doc2/Eqs/centro_symmetry.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/cna_cutoff1.jpg b/doc/doc2/Eqs/cna_cutoff1.jpg
new file mode 100644
index 000000000..fae5c6b63
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diff --git a/doc/doc2/Eqs/cna_cutoff1.tex b/doc/doc2/Eqs/cna_cutoff1.tex
new file mode 100644
index 000000000..782082bdf
--- /dev/null
+++ b/doc/doc2/Eqs/cna_cutoff1.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+ r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
+ r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
+ r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/cna_cutoff2.jpg b/doc/doc2/Eqs/cna_cutoff2.jpg
new file mode 100644
index 000000000..744b61e9b
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diff --git a/doc/doc2/Eqs/cna_cutoff2.tex b/doc/doc2/Eqs/cna_cutoff2.tex
new file mode 100644
index 000000000..7559441a2
--- /dev/null
+++ b/doc/doc2/Eqs/cna_cutoff2.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+ Rc + Rs > 2*{\rm cutoff}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_bar.jpg b/doc/doc2/Eqs/compute_fep_bar.jpg
new file mode 100644
index 000000000..772ec9c04
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diff --git a/doc/doc2/Eqs/compute_fep_bar.tex b/doc/doc2/Eqs/compute_fep_bar.tex
new file mode 100644
index 000000000..a40aa1c29
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_bar.tex
@@ -0,0 +1,7 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_fdti.jpg b/doc/doc2/Eqs/compute_fep_fdti.jpg
new file mode 100644
index 000000000..ae8de241c
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diff --git a/doc/doc2/Eqs/compute_fep_fdti.tex b/doc/doc2/Eqs/compute_fep_fdti.tex
new file mode 100644
index 000000000..fdea6faa3
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_fdti.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
+ A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
+\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
+ A(\lambda_i)}{\delta} \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_fep.jpg b/doc/doc2/Eqs/compute_fep_fep.jpg
new file mode 100644
index 000000000..d84a76b0d
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diff --git a/doc/doc2/Eqs/compute_fep_fep.tex b/doc/doc2/Eqs/compute_fep_fep.tex
new file mode 100644
index 000000000..718aad3c4
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_fep.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
+- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
+ U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_lambda.jpg b/doc/doc2/Eqs/compute_fep_lambda.jpg
new file mode 100644
index 000000000..5ef9e8b9f
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diff --git a/doc/doc2/Eqs/compute_fep_lambda.tex b/doc/doc2/Eqs/compute_fep_lambda.tex
new file mode 100644
index 000000000..08c8faaa3
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_lambda.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
+ \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_ti.jpg b/doc/doc2/Eqs/compute_fep_ti.jpg
new file mode 100644
index 000000000..6b0c8fdc1
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diff --git a/doc/doc2/Eqs/compute_fep_ti.tex b/doc/doc2/Eqs/compute_fep_ti.tex
new file mode 100644
index 000000000..6222dbd50
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_ti.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
+ U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
+\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
+ U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_u.jpg b/doc/doc2/Eqs/compute_fep_u.jpg
new file mode 100644
index 000000000..62df5dd0c
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diff --git a/doc/doc2/Eqs/compute_fep_u.tex b/doc/doc2/Eqs/compute_fep_u.tex
new file mode 100644
index 000000000..e847a9ac4
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_u.tex
@@ -0,0 +1,7 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_vol.jpg b/doc/doc2/Eqs/compute_fep_vol.jpg
new file mode 100644
index 000000000..a66facad3
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diff --git a/doc/doc2/Eqs/compute_fep_vol.tex b/doc/doc2/Eqs/compute_fep_vol.tex
new file mode 100644
index 000000000..0301e3978
--- /dev/null
+++ b/doc/doc2/Eqs/compute_fep_vol.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
+ \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
+\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_gyration.jpg b/doc/doc2/Eqs/compute_gyration.jpg
new file mode 100644
index 000000000..228544443
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diff --git a/doc/doc2/Eqs/compute_gyration.tex b/doc/doc2/Eqs/compute_gyration.tex
new file mode 100644
index 000000000..97204f1de
--- /dev/null
+++ b/doc/doc2/Eqs/compute_gyration.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/compute_msd_nongauss.jpg b/doc/doc2/Eqs/compute_msd_nongauss.jpg
new file mode 100644
index 000000000..d57f6a4af
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diff --git a/doc/doc2/Eqs/compute_msd_nongauss.tex b/doc/doc2/Eqs/compute_msd_nongauss.tex
new file mode 100644
index 000000000..168d8f72e
--- /dev/null
+++ b/doc/doc2/Eqs/compute_msd_nongauss.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_saed1.jpg b/doc/doc2/Eqs/compute_saed1.jpg
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index 000000000..6bad3a610
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diff --git a/doc/doc2/Eqs/compute_saed1.tex b/doc/doc2/Eqs/compute_saed1.tex
new file mode 100644
index 000000000..0db2f55ec
--- /dev/null
+++ b/doc/doc2/Eqs/compute_saed1.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ I=\frac{F^{*}F}{N}
+$$
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_saed2.jpg b/doc/doc2/Eqs/compute_saed2.jpg
new file mode 100644
index 000000000..2b3b0bc09
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diff --git a/doc/doc2/Eqs/compute_saed2.tex b/doc/doc2/Eqs/compute_saed2.tex
new file mode 100644
index 000000000..d00560233
--- /dev/null
+++ b/doc/doc2/Eqs/compute_saed2.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_saed3.jpg b/doc/doc2/Eqs/compute_saed3.jpg
new file mode 100644
index 000000000..1bbc92090
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diff --git a/doc/doc2/Eqs/compute_saed3.tex b/doc/doc2/Eqs/compute_saed3.tex
new file mode 100644
index 000000000..5988a620c
--- /dev/null
+++ b/doc/doc2/Eqs/compute_saed3.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
+a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_sna_atom1.jpg b/doc/doc2/Eqs/compute_sna_atom1.jpg
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index 000000000..fe4b641aa
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diff --git a/doc/doc2/Eqs/compute_sna_atom1.tex b/doc/doc2/Eqs/compute_sna_atom1.tex
new file mode 100644
index 000000000..93e2709bf
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom1.tex
@@ -0,0 +1,11 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom2.jpg b/doc/doc2/Eqs/compute_sna_atom2.jpg
new file mode 100644
index 000000000..7a4b2c211
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diff --git a/doc/doc2/Eqs/compute_sna_atom2.tex b/doc/doc2/Eqs/compute_sna_atom2.tex
new file mode 100644
index 000000000..98d8f2efa
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom2.tex
@@ -0,0 +1,11 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom3.jpg b/doc/doc2/Eqs/compute_sna_atom3.jpg
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index 000000000..41d6774e9
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diff --git a/doc/doc2/Eqs/compute_sna_atom3.tex b/doc/doc2/Eqs/compute_sna_atom3.tex
new file mode 100644
index 000000000..5e3212f7b
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom3.tex
@@ -0,0 +1,16 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
+
+\begin{equation}
+B_{j_1,j_2,j} = \\
+\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
+\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
+u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
+\end{equation}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom4.jpg b/doc/doc2/Eqs/compute_sna_atom4.jpg
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index 000000000..5d53943bf
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diff --git a/doc/doc2/Eqs/compute_sna_atom4.tex b/doc/doc2/Eqs/compute_sna_atom4.tex
new file mode 100644
index 000000000..3477d163e
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom4.tex
@@ -0,0 +1,14 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+\label{eqn:f_c}
+f_c(r) & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
+& = & 0, r > R_{ii'}
+\end{eqnarray*}
+
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom5.jpg b/doc/doc2/Eqs/compute_sna_atom5.jpg
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index 000000000..732731fe1
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diff --git a/doc/doc2/Eqs/compute_sna_atom5.tex b/doc/doc2/Eqs/compute_sna_atom5.tex
new file mode 100644
index 000000000..72f5a0fe7
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom5.tex
@@ -0,0 +1,12 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+
+\begin{equation}
+- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i}
+\end{equation}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom6.jpg b/doc/doc2/Eqs/compute_sna_atom6.jpg
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index 000000000..963dd8141
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diff --git a/doc/doc2/Eqs/compute_sna_atom6.tex b/doc/doc2/Eqs/compute_sna_atom6.tex
new file mode 100644
index 000000000..7da589548
--- /dev/null
+++ b/doc/doc2/Eqs/compute_sna_atom6.tex
@@ -0,0 +1,12 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+
+\begin{document}
+
+
+\begin{eqnarray*}
+- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/compute_xrd1.jpg b/doc/doc2/Eqs/compute_xrd1.jpg
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index 000000000..8432fad4a
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diff --git a/doc/doc2/Eqs/compute_xrd1.tex b/doc/doc2/Eqs/compute_xrd1.tex
new file mode 100644
index 000000000..6e749c768
--- /dev/null
+++ b/doc/doc2/Eqs/compute_xrd1.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ I=Lp(\theta)\frac{F^{*}F}{N}
+$$
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_xrd2.jpg b/doc/doc2/Eqs/compute_xrd2.jpg
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index 000000000..1bcf0494e
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diff --git a/doc/doc2/Eqs/compute_xrd2.tex b/doc/doc2/Eqs/compute_xrd2.tex
new file mode 100644
index 000000000..d00560233
--- /dev/null
+++ b/doc/doc2/Eqs/compute_xrd2.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_xrd3.jpg b/doc/doc2/Eqs/compute_xrd3.jpg
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index 000000000..19f7aa99b
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diff --git a/doc/doc2/Eqs/compute_xrd3.tex b/doc/doc2/Eqs/compute_xrd3.tex
new file mode 100644
index 000000000..da0254134
--- /dev/null
+++ b/doc/doc2/Eqs/compute_xrd3.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)}
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_xrd4.jpg b/doc/doc2/Eqs/compute_xrd4.jpg
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index 000000000..385bb1efd
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diff --git a/doc/doc2/Eqs/compute_xrd4.tex b/doc/doc2/Eqs/compute_xrd4.tex
new file mode 100644
index 000000000..d4deb7ca5
--- /dev/null
+++ b/doc/doc2/Eqs/compute_xrd4.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ \frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2}
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/compute_xrd5.jpg b/doc/doc2/Eqs/compute_xrd5.jpg
new file mode 100644
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diff --git a/doc/doc2/Eqs/compute_xrd5.tex b/doc/doc2/Eqs/compute_xrd5.tex
new file mode 100644
index 000000000..2d97a3288
--- /dev/null
+++ b/doc/doc2/Eqs/compute_xrd5.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4}
+a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/dihedral_charmm.jpg b/doc/doc2/Eqs/dihedral_charmm.jpg
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diff --git a/doc/doc2/Eqs/dihedral_charmm.tex b/doc/doc2/Eqs/dihedral_charmm.tex
new file mode 100644
index 000000000..c3d860b26
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_charmm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [ 1 + \cos (n \phi - d) ]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_class2.jpg b/doc/doc2/Eqs/dihedral_class2.jpg
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diff --git a/doc/doc2/Eqs/dihedral_class2.tex b/doc/doc2/Eqs/dihedral_class2.tex
new file mode 100644
index 000000000..02acc16fb
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_class2.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
+ E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
+ E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
+ E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
+ & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
+ E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
+ & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
+ E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
+ E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg b/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg
new file mode 100644
index 000000000..ea0a7550f
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diff --git a/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex b/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex
new file mode 100644
index 000000000..4afa01356
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex
@@ -0,0 +1,13 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E=-U_{min}
+\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
+\quad\mbox{with}\quad
+U(\theta,\theta_0)
+=-0.5 \left(1+\cos(\theta-\theta_0) \right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/dihedral_fourier.jpg b/doc/doc2/Eqs/dihedral_fourier.jpg
new file mode 100644
index 000000000..663ac17ee
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diff --git a/doc/doc2/Eqs/dihedral_fourier.tex b/doc/doc2/Eqs/dihedral_fourier.tex
new file mode 100644
index 000000000..960d3a8ea
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_fourier.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/dihedral_harmonic.jpg b/doc/doc2/Eqs/dihedral_harmonic.jpg
new file mode 100644
index 000000000..cb5c16a8c
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diff --git a/doc/doc2/Eqs/dihedral_harmonic.tex b/doc/doc2/Eqs/dihedral_harmonic.tex
new file mode 100644
index 000000000..9d02036fc
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [ 1 + d \cos (n \phi) ]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_helix.jpg b/doc/doc2/Eqs/dihedral_helix.jpg
new file mode 100644
index 000000000..01a0ec982
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diff --git a/doc/doc2/Eqs/dihedral_helix.tex b/doc/doc2/Eqs/dihedral_helix.tex
new file mode 100644
index 000000000..ae25776f2
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_helix.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
+ C [1 + \cos(\theta + \frac{\pi}{4})]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_multi_harmonic.jpg b/doc/doc2/Eqs/dihedral_multi_harmonic.jpg
new file mode 100644
index 000000000..d066cd212
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diff --git a/doc/doc2/Eqs/dihedral_multi_harmonic.tex b/doc/doc2/Eqs/dihedral_multi_harmonic.tex
new file mode 100644
index 000000000..819aa7c57
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_multi_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \sum_{n=1,5} A_n \cos^{n-1}(\phi)
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_nharmonic.jpg b/doc/doc2/Eqs/dihedral_nharmonic.jpg
new file mode 100644
index 000000000..4f4928bdd
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diff --git a/doc/doc2/Eqs/dihedral_nharmonic.tex b/doc/doc2/Eqs/dihedral_nharmonic.tex
new file mode 100644
index 000000000..57a1d2528
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_nharmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \sum_{n=1,n} A_n \cos^{n-1}(\phi)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/dihedral_opls.jpg b/doc/doc2/Eqs/dihedral_opls.jpg
new file mode 100644
index 000000000..0546aebfd
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diff --git a/doc/doc2/Eqs/dihedral_opls.tex b/doc/doc2/Eqs/dihedral_opls.tex
new file mode 100644
index 000000000..5e4aada53
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_opls.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] +
+ \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_quadratic.jpg b/doc/doc2/Eqs/dihedral_quadratic.jpg
new file mode 100644
index 000000000..8fb17622f
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diff --git a/doc/doc2/Eqs/dihedral_quadratic.tex b/doc/doc2/Eqs/dihedral_quadratic.tex
new file mode 100644
index 000000000..049e4b2ec
--- /dev/null
+++ b/doc/doc2/Eqs/dihedral_quadratic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\phi - \phi_0)^2
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/dihedral_sign.jpg b/doc/doc2/Eqs/dihedral_sign.jpg
new file mode 100644
index 000000000..8d8352e8f
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diff --git a/doc/doc2/Eqs/dreiding_hbond.jpg b/doc/doc2/Eqs/dreiding_hbond.jpg
new file mode 100644
index 000000000..76cc42a45
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diff --git a/doc/doc2/Eqs/eff_ECP1.jpg b/doc/doc2/Eqs/eff_ECP1.jpg
new file mode 100644
index 000000000..3b8a3f8ff
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diff --git a/doc/doc2/Eqs/eff_ECP1.tex b/doc/doc2/Eqs/eff_ECP1.tex
new file mode 100644
index 000000000..7eecad0b8
--- /dev/null
+++ b/doc/doc2/Eqs/eff_ECP1.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Pauli(ECP_s)}=p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right)
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/eff_ECP2.jpg b/doc/doc2/Eqs/eff_ECP2.jpg
new file mode 100644
index 000000000..195ed55e4
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diff --git a/doc/doc2/Eqs/eff_ECP2.tex b/doc/doc2/Eqs/eff_ECP2.tex
new file mode 100644
index 000000000..238fe2f4f
--- /dev/null
+++ b/doc/doc2/Eqs/eff_ECP2.tex
@@ -0,0 +1,8 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right]
+$$
+ \end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/eff_KE.jpg b/doc/doc2/Eqs/eff_KE.jpg
new file mode 100644
index 000000000..40eed0df6
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diff --git a/doc/doc2/Eqs/eff_KE.tex b/doc/doc2/Eqs/eff_KE.tex
new file mode 100644
index 000000000..9f9af2fa2
--- /dev/null
+++ b/doc/doc2/Eqs/eff_KE.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E_{KE} = \frac{\hbar^2 }{{m_{e} }}\sum\limits_i {\frac{3}{{2s_i^2 }}}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/eff_NN.jpg b/doc/doc2/Eqs/eff_NN.jpg
new file mode 100644
index 000000000..c3c52e19b
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diff --git a/doc/doc2/Eqs/eff_NN.tex b/doc/doc2/Eqs/eff_NN.tex
new file mode 100644
index 000000000..4f9bb6d13
--- /dev/null
+++ b/doc/doc2/Eqs/eff_NN.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E_{NN} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{{Z_i Z_j }}{{R_{ij} }}}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/eff_Ne.jpg b/doc/doc2/Eqs/eff_Ne.jpg
new file mode 100644
index 000000000..e23ceacc8
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diff --git a/doc/doc2/Eqs/eff_Ne.tex b/doc/doc2/Eqs/eff_Ne.tex
new file mode 100644
index 000000000..e6813b125
--- /dev/null
+++ b/doc/doc2/Eqs/eff_Ne.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Ne} = - \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i,j} {\frac{{Z_i }}{{R_{ij} }}Erf\left( {\frac{{\sqrt 2 R_{ij} }}{{s_j }}} \right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/eff_Pauli.jpg b/doc/doc2/Eqs/eff_Pauli.jpg
new file mode 100644
index 000000000..61bb8652e
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diff --git a/doc/doc2/Eqs/eff_Pauli.tex b/doc/doc2/Eqs/eff_Pauli.tex
new file mode 100644
index 000000000..b6b8070cc
--- /dev/null
+++ b/doc/doc2/Eqs/eff_Pauli.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E_{Pauli} = \sum\limits_{\sigma _i = \sigma _j } {E\left( { \uparrow \uparrow } \right)_{ij}} + \sum\limits_{\sigma _i \ne \sigma _j } {E\left( { \uparrow \downarrow } \right)_{ij}}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/eff_ee.jpg b/doc/doc2/Eqs/eff_ee.jpg
new file mode 100644
index 000000000..aef84d0fd
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diff --git a/doc/doc2/Eqs/eff_ee.tex b/doc/doc2/Eqs/eff_ee.tex
new file mode 100644
index 000000000..5d17e5557
--- /dev/null
+++ b/doc/doc2/Eqs/eff_ee.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E_{ee} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{1}{{r_{ij} }}Erf\left( {\frac{{\sqrt 2 r_{ij} }}{{\sqrt {s_i^2 + s_j^2 } }}} \right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/eff_energy_expression.gif b/doc/doc2/Eqs/eff_energy_expression.gif
new file mode 100644
index 000000000..70cc4ddbc
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diff --git a/doc/doc2/Eqs/eff_energy_expression.jpg b/doc/doc2/Eqs/eff_energy_expression.jpg
new file mode 100644
index 000000000..e06fe8ff2
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diff --git a/doc/doc2/Eqs/eff_energy_expression.tex b/doc/doc2/Eqs/eff_energy_expression.tex
new file mode 100644
index 000000000..f56380f64
--- /dev/null
+++ b/doc/doc2/Eqs/eff_energy_expression.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_box_relax1.jpg b/doc/doc2/Eqs/fix_box_relax1.jpg
new file mode 100644
index 000000000..d42552604
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diff --git a/doc/doc2/Eqs/fix_box_relax1.tex b/doc/doc2/Eqs/fix_box_relax1.tex
new file mode 100644
index 000000000..a33236066
--- /dev/null
+++ b/doc/doc2/Eqs/fix_box_relax1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E = U + P_t \left(V-V_0 \right) + E_{strain}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_box_relax2.jpg b/doc/doc2/Eqs/fix_box_relax2.jpg
new file mode 100644
index 000000000..8fac42e0f
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diff --git a/doc/doc2/Eqs/fix_box_relax2.tex b/doc/doc2/Eqs/fix_box_relax2.tex
new file mode 100644
index 000000000..bc9cddef4
--- /dev/null
+++ b/doc/doc2/Eqs/fix_box_relax2.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_gld1.jpg b/doc/doc2/Eqs/fix_gld1.jpg
new file mode 100644
index 000000000..d54ce57a6
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diff --git a/doc/doc2/Eqs/fix_gld1.tex b/doc/doc2/Eqs/fix_gld1.tex
new file mode 100644
index 000000000..baa0f32a5
--- /dev/null
+++ b/doc/doc2/Eqs/fix_gld1.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{align*}
+ &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
+ &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\
+ &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s)
+\end{align*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg
new file mode 100644
index 000000000..9d82b40ec
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex
new file mode 100755
index 000000000..4a6ca6fe0
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg b/doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg
new file mode 100644
index 000000000..d3149616c
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex b/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex
new file mode 100755
index 000000000..8433c9264
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg b/doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg
new file mode 100644
index 000000000..cd10239c9
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex b/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex
new file mode 100755
index 000000000..1af82c497
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg
new file mode 100644
index 000000000..0a1c10414
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex
new file mode 100755
index 000000000..41ca4674e
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= 0
+$$
+$$
+\partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right)
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_properties.jpg b/doc/doc2/Eqs/fix_lb_fluid_properties.jpg
new file mode 100644
index 000000000..3d70cd766
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_properties.tex b/doc/doc2/Eqs/fix_lb_fluid_properties.tex
new file mode 100755
index 000000000..fe1290be1
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_properties.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\rho = \displaystyle\sum\limits_{i} f_i
+$$
+$$
+\rho u_{\alpha} = \displaystyle\sum\limits_{i} f_i e_{i\alpha}
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_stress.jpg b/doc/doc2/Eqs/fix_lb_fluid_stress.jpg
new file mode 100644
index 000000000..8f730e9d7
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_stress.tex b/doc/doc2/Eqs/fix_lb_fluid_stress.tex
new file mode 100755
index 000000000..b4e098253
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_stress.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg b/doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg
new file mode 100644
index 000000000..1816317ee
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diff --git a/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex b/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex
new file mode 100755
index 000000000..d5925f213
--- /dev/null
+++ b/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\eta_{\alpha \beta \gamma \nu} = \eta\left[\delta_{\alpha \gamma}\delta_{\beta \nu} + \delta_{\alpha \nu}\delta_{\beta \gamma} - \frac{2}{3}\delta_{\alpha \beta}\delta_{\gamma \nu}\right] + \Lambda \delta_{\alpha \beta}\delta_{\gamma \nu}
+$$
+
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_nh1.jpg b/doc/doc2/Eqs/fix_nh1.jpg
new file mode 100644
index 000000000..db59dbc43
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diff --git a/doc/doc2/Eqs/fix_nh1.tex b/doc/doc2/Eqs/fix_nh1.tex
new file mode 100644
index 000000000..f6928495c
--- /dev/null
+++ b/doc/doc2/Eqs/fix_nh1.tex
@@ -0,0 +1,35 @@
+\documentclass[24pt]{article}
+
+\pagestyle{empty}
+\Huge
+
+\begin{document}
+
+\mathchardef\mhyphen="2D
+
+% The imaginary unit
+\providecommand*{\iu}%
+ {\ensuremath{{\rm i}}}
+
+
+\begin{eqnarray*}
+\exp \left(\iu{} L \Delta t \right) &=&ﾊ
+\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
+&&\times \left[
+\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right)
+\exp \left(\iu{} L_{\epsilon , 1} \frac{\Delta t}{n} \right)
+\exp \left(\iu{} L_1 \frac{\Delta t}{n} \right)
+\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right)
+\right]^n \\
+&&\times
+\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right)
+\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right) \\
+&&+ \mathcal{O} \left(\Delta t^3 \right)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_nphug.jpg b/doc/doc2/Eqs/fix_nphug.jpg
new file mode 100644
index 000000000..a3a67e7b7
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diff --git a/doc/doc2/Eqs/fix_nphug.tex b/doc/doc2/Eqs/fix_nphug.tex
new file mode 100644
index 000000000..4e162b69b
--- /dev/null
+++ b/doc/doc2/Eqs/fix_nphug.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_orient_fcc.jpg b/doc/doc2/Eqs/fix_orient_fcc.jpg
new file mode 100644
index 000000000..b22e6c9c2
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diff --git a/doc/doc2/Eqs/fix_orient_fcc.tex b/doc/doc2/Eqs/fix_orient_fcc.tex
new file mode 100644
index 000000000..5596848eb
--- /dev/null
+++ b/doc/doc2/Eqs/fix_orient_fcc.tex
@@ -0,0 +1,30 @@
+\newcommand{\br}{\mathbf{r}}
+
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+ \xi_{i} = \sum_{j=1}^{12} \left| \br_{j} - \br_{j}^{\rm I} \right|
+\end{equation}
+
+\begin{equation}
+ \xi_{\rm IJ} = \sum_{j=1}^{12} \left| \br_{j}^{\rm J} - \br_{j}^{\rm I} \right|
+\end{equation}
+
+\begin{eqnarray}
+ \xi_{\rm low} &=& {\rm cutlo} \, \xi_{\rm IJ} \\
+ \xi_{\rm high} &=& {\rm cuthi} \, \xi_{\rm IJ}
+\end{eqnarray}
+
+\begin{eqnarray}
+ \omega_{i} &=& \frac{\pi}{2}
+ \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \\
+ \mbox{\hspace*{72pt}} \nonumber \\
+ u_{i} &=& 0 \mbox{\hspace{84pt} for } \xi_{i} < \xi_{\rm low} \nonumber \\
+ &=& {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
+ \mbox{\hspace{10pt} for } \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \\
+ &=& {\rm dE} \mbox{\hspace{80pt} for } \xi_{\rm high} < \xi_{i}
+ \nonumber
+\end{eqnarray}
+\end{document}
diff --git a/doc/doc2/Eqs/fix_pimd.jpg b/doc/doc2/Eqs/fix_pimd.jpg
new file mode 100644
index 000000000..b6e8f5831
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diff --git a/doc/doc2/Eqs/fix_pimd.tex b/doc/doc2/Eqs/fix_pimd.tex
new file mode 100644
index 000000000..983fead8e
--- /dev/null
+++ b/doc/doc2/Eqs/fix_pimd.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ Z = \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ]
+$$
+
+$$
+ H_{eff} = \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff}
+$$
+
+$$
+ V_{eff} = \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_rattle_constraints.jpg b/doc/doc2/Eqs/fix_rattle_constraints.jpg
new file mode 100644
index 000000000..2ba86095c
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diff --git a/doc/doc2/Eqs/fix_rattle_constraints.tex b/doc/doc2/Eqs/fix_rattle_constraints.tex
new file mode 100644
index 000000000..daff0ce77
--- /dev/null
+++ b/doc/doc2/Eqs/fix_rattle_constraints.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+
+\begin{document}
+\begin{align*}
+\mathbf r^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= d^2_{ij} \quad \text{and} \\
+\mathbf v^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= 0, \label{eq:velcon}
+\end{align*}
+\end{document}
diff --git a/doc/doc2/Eqs/fix_rattle_rij.jpg b/doc/doc2/Eqs/fix_rattle_rij.jpg
new file mode 100644
index 000000000..b08e2fe02
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diff --git a/doc/doc2/Eqs/fix_rattle_rij.tex b/doc/doc2/Eqs/fix_rattle_rij.tex
new file mode 100644
index 000000000..fae0457c6
--- /dev/null
+++ b/doc/doc2/Eqs/fix_rattle_rij.tex
@@ -0,0 +1,8 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+\begin{document}
+$$
+ \mathbf r^{n+1}_{ij} = \mathbf r^n_j - \mathbf r^n_i
+$$
+\end{document}
+
diff --git a/doc/doc2/Eqs/fix_spring_rg.jpg b/doc/doc2/Eqs/fix_spring_rg.jpg
new file mode 100644
index 000000000..313844f55
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diff --git a/doc/doc2/Eqs/fix_spring_rg.tex b/doc/doc2/Eqs/fix_spring_rg.tex
new file mode 100644
index 000000000..b772aaf65
--- /dev/null
+++ b/doc/doc2/Eqs/fix_spring_rg.tex
@@ -0,0 +1,19 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+{R_G}^2 = \frac{1}{M}\sum_{i}^{N}{m_{i}\left( x_{i} -
+\frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)^{2}}
+$$
+
+$$
+ E = K\left( R_G - R_{G0} \right)^{2}
+$$
+
+$$
+F_{i} = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G}
+\right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fix_ti_rs_force.jpg b/doc/doc2/Eqs/fix_ti_rs_force.jpg
new file mode 100644
index 000000000..a09bcb66c
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diff --git a/doc/doc2/Eqs/fix_ti_rs_force.tex b/doc/doc2/Eqs/fix_ti_rs_force.tex
new file mode 100644
index 000000000..849c0ccc9
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_rs_force.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+ F_{\text{total}} = \lambda F_{\text{int}}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_1.jpg b/doc/doc2/Eqs/fix_ti_rs_function_1.jpg
new file mode 100644
index 000000000..478dc5781
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diff --git a/doc/doc2/Eqs/fix_ti_rs_function_1.tex b/doc/doc2/Eqs/fix_ti_rs_function_1.tex
new file mode 100644
index 000000000..033d8d755
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_rs_function_1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_2.jpg b/doc/doc2/Eqs/fix_ti_rs_function_2.jpg
new file mode 100644
index 000000000..4fbfe45c6
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diff --git a/doc/doc2/Eqs/fix_ti_rs_function_2.tex b/doc/doc2/Eqs/fix_ti_rs_function_2.tex
new file mode 100644
index 000000000..a1dd377dc
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_rs_function_2.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_3.jpg b/doc/doc2/Eqs/fix_ti_rs_function_3.jpg
new file mode 100644
index 000000000..94ab0f468
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diff --git a/doc/doc2/Eqs/fix_ti_rs_function_3.tex b/doc/doc2/Eqs/fix_ti_rs_function_3.tex
new file mode 100644
index 000000000..2d2790fa9
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_rs_function_3.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_force.jpg b/doc/doc2/Eqs/fix_ti_spring_force.jpg
new file mode 100644
index 000000000..347102b3e
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diff --git a/doc/doc2/Eqs/fix_ti_spring_force.tex b/doc/doc2/Eqs/fix_ti_spring_force.tex
new file mode 100644
index 000000000..0acd0e54a
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_spring_force.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+ F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_1.jpg b/doc/doc2/Eqs/fix_ti_spring_function_1.jpg
new file mode 100644
index 000000000..8d3c9a78e
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diff --git a/doc/doc2/Eqs/fix_ti_spring_function_1.tex b/doc/doc2/Eqs/fix_ti_spring_function_1.tex
new file mode 100644
index 000000000..0673410b0
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_spring_function_1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \lambda(\tau) = \tau
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_2.jpg b/doc/doc2/Eqs/fix_ti_spring_function_2.jpg
new file mode 100644
index 000000000..96a17e63e
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diff --git a/doc/doc2/Eqs/fix_ti_spring_function_2.tex b/doc/doc2/Eqs/fix_ti_spring_function_2.tex
new file mode 100644
index 000000000..f2cb51e47
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ti_spring_function_2.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_ttm.jpg b/doc/doc2/Eqs/fix_ttm.jpg
new file mode 100644
index 000000000..8d9fac3fe
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diff --git a/doc/doc2/Eqs/fix_ttm.tex b/doc/doc2/Eqs/fix_ttm.tex
new file mode 100644
index 000000000..d5a3238f8
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ttm.tex
@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ C_e \rho_e \frac{\partial T_e}{\partial t} =
+ \bigtriangledown (\kappa_e \bigtriangledown T_e) -
+ g_p (T_e - T_a) + g_s T_a'
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_ttm_blast.jpg b/doc/doc2/Eqs/fix_ttm_blast.jpg
new file mode 100644
index 000000000..d4ffe05f1
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diff --git a/doc/doc2/Eqs/fix_ttm_blast.tex b/doc/doc2/Eqs/fix_ttm_blast.tex
new file mode 100644
index 000000000..6871ed5cc
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ttm_blast.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion}
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_ttm_blast1.jpg b/doc/doc2/Eqs/fix_ttm_blast1.jpg
new file mode 100644
index 000000000..1106c627c
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diff --git a/doc/doc2/Eqs/fix_ttm_blast1.tex b/doc/doc2/Eqs/fix_ttm_blast1.tex
new file mode 100644
index 000000000..642afe430
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ttm_blast1.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ \nabla_x P_e = \left[\frac{C_e{}T_e(x)\lambda}{(x+\lambda)^2} + \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right]
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_ttm_ce.jpg b/doc/doc2/Eqs/fix_ttm_ce.jpg
new file mode 100644
index 000000000..4f439e31e
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diff --git a/doc/doc2/Eqs/fix_ttm_ce.tex b/doc/doc2/Eqs/fix_ttm_ce.tex
new file mode 100644
index 000000000..f787590b8
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ttm_ce.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_ttm_mod.jpg b/doc/doc2/Eqs/fix_ttm_mod.jpg
new file mode 100644
index 000000000..7cc67200f
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diff --git a/doc/doc2/Eqs/fix_ttm_mod.tex b/doc/doc2/Eqs/fix_ttm_mod.tex
new file mode 100644
index 000000000..d0a313e67
--- /dev/null
+++ b/doc/doc2/Eqs/fix_ttm_mod.tex
@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ C_e \rho_e \frac{\partial T_e}{\partial t} =
+ \bigtriangledown (\kappa_e \bigtriangledown T_e) -
+ g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
+$$
+
+\end{document}
+
+
+
+
diff --git a/doc/doc2/Eqs/fix_wall_colloid.jpg b/doc/doc2/Eqs/fix_wall_colloid.jpg
new file mode 100644
index 000000000..8168d3a79
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diff --git a/doc/doc2/Eqs/fix_wall_colloid.tex b/doc/doc2/Eqs/fix_wall_colloid.tex
new file mode 100644
index 000000000..3ed716c26
--- /dev/null
+++ b/doc/doc2/Eqs/fix_wall_colloid.tex
@@ -0,0 +1,14 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray}
+E &=& \epsilon \left[ \frac{\sigma^{6}}{7560}
+ \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) -
+ \frac{}{} \right. \nonumber \\
+ &&\qquad \left. \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
+ \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right]
+\qquad r < r_c \nonumber
+\end{eqnarray}
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_wall_harmonic.jpg b/doc/doc2/Eqs/fix_wall_harmonic.jpg
new file mode 100644
index 000000000..3c605690c
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diff --git a/doc/doc2/Eqs/fix_wall_harmonic.tex b/doc/doc2/Eqs/fix_wall_harmonic.tex
new file mode 100644
index 000000000..86dcb80a0
--- /dev/null
+++ b/doc/doc2/Eqs/fix_wall_harmonic.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \hspace{0.1cm} (r - r_c)^2 \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fix_wall_lj1043.jpg b/doc/doc2/Eqs/fix_wall_lj1043.jpg
new file mode 100644
index 000000000..303743bf3
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diff --git a/doc/doc2/Eqs/fix_wall_lj1043.tex b/doc/doc2/Eqs/fix_wall_lj1043.tex
new file mode 100644
index 000000000..8ef981ca9
--- /dev/null
+++ b/doc/doc2/Eqs/fix_wall_lj1043.tex
@@ -0,0 +1,12 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} -
+ \left(\frac{\sigma}{r}\right)^4 -
+ \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
+ \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fix_wall_lj93.jpg b/doc/doc2/Eqs/fix_wall_lj93.jpg
new file mode 100644
index 000000000..18e502cfb
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diff --git a/doc/doc2/Eqs/fix_wall_lj93.tex b/doc/doc2/Eqs/fix_wall_lj93.tex
new file mode 100644
index 000000000..7372e55c1
--- /dev/null
+++ b/doc/doc2/Eqs/fix_wall_lj93.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} -
+ \left(\frac{\sigma}{r}\right)^3 \right]
+ \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fld.jpg b/doc/doc2/Eqs/fld.jpg
new file mode 100644
index 000000000..3d80d436f
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diff --git a/doc/doc2/Eqs/fld.tex b/doc/doc2/Eqs/fld.tex
new file mode 100644
index 000000000..7c75cfbe6
--- /dev/null
+++ b/doc/doc2/Eqs/fld.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+F^{H} = -R_{FU}(U-U^{\infty}) + R_{FE}E^{\infty}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/fld2.jpg b/doc/doc2/Eqs/fld2.jpg
new file mode 100644
index 000000000..42de943c9
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diff --git a/doc/doc2/Eqs/fld2.tex b/doc/doc2/Eqs/fld2.tex
new file mode 100644
index 000000000..43adae11d
--- /dev/null
+++ b/doc/doc2/Eqs/fld2.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+-R_{FU}(U-U^{\infty}) = -R_{FE}E^{\infty} - F^{rest}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/heat_flux_J.jpg b/doc/doc2/Eqs/heat_flux_J.jpg
new file mode 100644
index 000000000..cf3e220ca
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diff --git a/doc/doc2/Eqs/heat_flux_J.tex b/doc/doc2/Eqs/heat_flux_J.tex
new file mode 100644
index 000000000..53c0ff494
--- /dev/null
+++ b/doc/doc2/Eqs/heat_flux_J.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mathbf{J} & = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
+& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \mathbf{v}_j \right) \mathbf{x}_{ij} \right] \\
+& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) \right) \mathbf{x}_{ij} \right]
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/heat_flux_k.jpg b/doc/doc2/Eqs/heat_flux_k.jpg
new file mode 100644
index 000000000..2fd4a19e5
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diff --git a/doc/doc2/Eqs/heat_flux_k.tex b/doc/doc2/Eqs/heat_flux_k.tex
new file mode 100644
index 000000000..a6aa2aeab
--- /dev/null
+++ b/doc/doc2/Eqs/heat_flux_k.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+\kappa = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0) J_x(t) \rangle \, dt
+= \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot \mathbf{J}(t) \rangle \, dt
+$$
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/improper_class2.jpg b/doc/doc2/Eqs/improper_class2.jpg
new file mode 100644
index 000000000..ca0604f8d
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diff --git a/doc/doc2/Eqs/improper_class2.tex b/doc/doc2/Eqs/improper_class2.tex
new file mode 100644
index 000000000..2c41df1a2
--- /dev/null
+++ b/doc/doc2/Eqs/improper_class2.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & E_i + E_{aa} \\
+ E_i & = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\
+ E_{aa} & = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\
+ & & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\
+ & & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3)
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/improper_cossq.jpg b/doc/doc2/Eqs/improper_cossq.jpg
new file mode 100644
index 000000000..bddcb3d86
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diff --git a/doc/doc2/Eqs/improper_cossq.tex b/doc/doc2/Eqs/improper_cossq.tex
new file mode 100644
index 000000000..27e79c7b1
--- /dev/null
+++ b/doc/doc2/Eqs/improper_cossq.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/improper_cvff.jpg b/doc/doc2/Eqs/improper_cvff.jpg
new file mode 100644
index 000000000..14be3ffa0
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diff --git a/doc/doc2/Eqs/improper_cvff.tex b/doc/doc2/Eqs/improper_cvff.tex
new file mode 100644
index 000000000..3a038b6b8
--- /dev/null
+++ b/doc/doc2/Eqs/improper_cvff.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [1 + d \cos (n \phi) ]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/improper_fourier.jpg b/doc/doc2/Eqs/improper_fourier.jpg
new file mode 100644
index 000000000..0a1b13baf
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diff --git a/doc/doc2/Eqs/improper_fourier.tex b/doc/doc2/Eqs/improper_fourier.tex
new file mode 100644
index 000000000..47ac58ef0
--- /dev/null
+++ b/doc/doc2/Eqs/improper_fourier.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/improper_harmonic.jpg b/doc/doc2/Eqs/improper_harmonic.jpg
new file mode 100644
index 000000000..c2c1eb466
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diff --git a/doc/doc2/Eqs/improper_harmonic.tex b/doc/doc2/Eqs/improper_harmonic.tex
new file mode 100644
index 000000000..c47020cf9
--- /dev/null
+++ b/doc/doc2/Eqs/improper_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\chi - \chi_0)^2
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/improper_ring.jpg b/doc/doc2/Eqs/improper_ring.jpg
new file mode 100644
index 000000000..81a79f7ce
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diff --git a/doc/doc2/Eqs/improper_ring.tex b/doc/doc2/Eqs/improper_ring.tex
new file mode 100644
index 000000000..b7bd553c3
--- /dev/null
+++ b/doc/doc2/Eqs/improper_ring.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = &\frac{1}{6} K \left(\Delta_{ijl} + \Delta_{ijk} + \Delta_{kjl} \right)^6 \\
+ \Delta_{ijl} & = & \cos{\theta_{ijl} - \cos{\theta_0}} \\
+ \Delta_{ijk} & = & \cos{\theta_{ijk} - \cos{\theta_0}} \\
+ \Delta_{kjl} & = & \cos{\theta_{kjl} - \cos{\theta_0}}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/improper_umbrella.jpg b/doc/doc2/Eqs/improper_umbrella.jpg
new file mode 100644
index 000000000..8d6cbf81e
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diff --git a/doc/doc2/Eqs/improper_umbrella.tex b/doc/doc2/Eqs/improper_umbrella.tex
new file mode 100644
index 000000000..755a6af07
--- /dev/null
+++ b/doc/doc2/Eqs/improper_umbrella.tex
@@ -0,0 +1,13 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E=\frac{1}{2}K\left( \frac{1+cos\omega_0}{sin\omega_0}\right) ^2 \left( cos\omega - cos\omega_0\right) \qquad \omega_0 \neq 0^o
+$$
+
+$$
+E=K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/min_energy.jpg b/doc/doc2/Eqs/min_energy.jpg
new file mode 100644
index 000000000..7925d268a
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diff --git a/doc/doc2/Eqs/min_energy.tex b/doc/doc2/Eqs/min_energy.tex
new file mode 100644
index 000000000..78f8cae11
--- /dev/null
+++ b/doc/doc2/Eqs/min_energy.tex
@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E(r_1,r_2, \ldots ,r_N) & = & \sum_{i,j} E_{\it pair}(r_i,r_j) +
+ \sum_{ij} E_{\it bond}(r_i,r_j) +
+ \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\
+ && \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) +
+ \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) +
+ \sum_i E_{\it fix}(r_i)
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_adp.jpg b/doc/doc2/Eqs/pair_adp.jpg
new file mode 100644
index 000000000..accae4716
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diff --git a/doc/doc2/Eqs/pair_adp.tex b/doc/doc2/Eqs/pair_adp.tex
new file mode 100644
index 000000000..07e441f3f
--- /dev/null
+++ b/doc/doc2/Eqs/pair_adp.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_i & = & F_\alpha \left( \sum_{j\neq i} \rho_\beta (r_{ij}) \right) + \frac{1}{2} \sum_{j\neq i}\phi_{\alpha\beta}(r_{ij})+ \frac{1}{2} \sum_s (\mu_i^s)^2 + \frac{1}{2} \sum_{s,t} (\lambda_i^{st})^2 - \frac{1}{6} \nu_i^2 \\
+%
+\mu_i^s & = & \sum_{j\neq i}u_{\alpha\beta}(r_{ij})r_{ij}^s\\
+%
+\lambda_i^{st} & = & \sum_{j\neq i}w_{\alpha\beta}(r_{ij})r_{ij}^sr_{ij}^t\\
+%
+\nu_i & = & \sum_s\lambda_i^{ss}
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_airebo.jpg b/doc/doc2/Eqs/pair_airebo.jpg
new file mode 100644
index 000000000..a3259879f
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diff --git a/doc/doc2/Eqs/pair_airebo.tex b/doc/doc2/Eqs/pair_airebo.tex
new file mode 100644
index 000000000..6c40b2ef5
--- /dev/null
+++ b/doc/doc2/Eqs/pair_airebo.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{1}{2} \sum_i \sum_{j \neq i}
+ \left[ E^{REBO}_{ij} + E^{LJ}_{ij} +
+ \sum_{k \neq i,j} \sum_{l \neq i,j,k} E^{TORSION}_{kijl} \right]
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_beck.jpg b/doc/doc2/Eqs/pair_beck.jpg
new file mode 100644
index 000000000..a6da8a87d
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diff --git a/doc/doc2/Eqs/pair_beck.tex b/doc/doc2/Eqs/pair_beck.tex
new file mode 100644
index 000000000..dde6b6ef5
--- /dev/null
+++ b/doc/doc2/Eqs/pair_beck.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E\left(r\right) = A \exp\left[-\alpha r - \beta r^6\right] -
+\frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right)
+ \qquad r < R_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_bop.jpg b/doc/doc2/Eqs/pair_bop.jpg
new file mode 100644
index 000000000..d1fbb14b0
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diff --git a/doc/doc2/Eqs/pair_bop.tex b/doc/doc2/Eqs/pair_bop.tex
new file mode 100644
index 000000000..371bc035f
--- /dev/null
+++ b/doc/doc2/Eqs/pair_bop.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left( r_{ij} \right) - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\sigma,ij} \left( r_{ij} \right) \cdot \Theta_{\sigma,ij} - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\pi,ij} \left( r_{ij} \right) \cdot \Theta_{\pi,ij} + U_{prom}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_born.jpg b/doc/doc2/Eqs/pair_born.jpg
new file mode 100644
index 000000000..5e6b6a729
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diff --git a/doc/doc2/Eqs/pair_born.tex b/doc/doc2/Eqs/pair_born.tex
new file mode 100644
index 000000000..9106b5e94
--- /dev/null
+++ b/doc/doc2/Eqs/pair_born.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E = A \exp \left(\frac{\sigma - r}{\rho} \right) -
+ \frac{C}{r^6} + \frac{D}{r^8} \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_buck.jpg b/doc/doc2/Eqs/pair_buck.jpg
new file mode 100644
index 000000000..aaa5f7659
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diff --git a/doc/doc2/Eqs/pair_buck.tex b/doc/doc2/Eqs/pair_buck.tex
new file mode 100644
index 000000000..ef15af690
--- /dev/null
+++ b/doc/doc2/Eqs/pair_buck.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = A e^{-r / \rho} - \frac{C}{r^6} \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_charmm.jpg b/doc/doc2/Eqs/pair_charmm.jpg
new file mode 100644
index 000000000..7d6c709ce
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diff --git a/doc/doc2/Eqs/pair_charmm.tex b/doc/doc2/Eqs/pair_charmm.tex
new file mode 100644
index 000000000..9544f01f0
--- /dev/null
+++ b/doc/doc2/Eqs/pair_charmm.tex
@@ -0,0 +1,22 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
+ & = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+ & = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+ E & = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
+ & = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+ & = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+ LJ(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] \\
+ C(r) & = & \frac{C q_i q_j}{ \epsilon r} \\
+ S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
+ \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
+ { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
+\end{eqnarray*}
+
+\end{document}
+
+
diff --git a/doc/doc2/Eqs/pair_class2.jpg b/doc/doc2/Eqs/pair_class2.jpg
new file mode 100644
index 000000000..abec072e7
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diff --git a/doc/doc2/Eqs/pair_class2.tex b/doc/doc2/Eqs/pair_class2.tex
new file mode 100644
index 000000000..e2acc00bb
--- /dev/null
+++ b/doc/doc2/Eqs/pair_class2.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
+ 3 \left(\frac{\sigma}{r}\right)^6 \right]
+ \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_cmm.jpg b/doc/doc2/Eqs/pair_cmm.jpg
new file mode 100644
index 000000000..1ec60f730
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diff --git a/doc/doc2/Eqs/pair_cmm.tex b/doc/doc2/Eqs/pair_cmm.tex
new file mode 100644
index 000000000..9bab1e900
--- /dev/null
+++ b/doc/doc2/Eqs/pair_cmm.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
+ \left(\frac{\sigma}{r}\right)^6 \right] &
+ \qquad r < r_c \\
+ E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^4 \right] &
+ \qquad r < r_c \\
+ E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] &
+ \qquad r < r_c
+\end{eqnarray*}
+\end{document}
diff --git a/doc/doc2/Eqs/pair_colloid_cc.jpg b/doc/doc2/Eqs/pair_colloid_cc.jpg
new file mode 100644
index 000000000..a64094dda
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diff --git a/doc/doc2/Eqs/pair_colloid_cc.tex b/doc/doc2/Eqs/pair_colloid_cc.tex
new file mode 100644
index 000000000..e1485d325
--- /dev/null
+++ b/doc/doc2/Eqs/pair_colloid_cc.tex
@@ -0,0 +1,31 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray}
+U_A &=& - \frac{A_{cc}}{6} \left[
+ \frac{2 a_1 a_2}{r^2-\left(a_1+a_2\right)^2}
+ + \frac{2 a_1 a_2}{r^2 - \left(a_1 - a_2\right)^2}
+ + \mathrm{ln}
+ \left(
+ \frac{r^2-\left(a_1+a_2\right)^2}{r^2-\left(a_1-a_2\right)^2}
+ \right)
+ \right] \nonumber \\
+\nonumber \\
+U_R &=& \frac{A_{cc}}{37800} \frac{\sigma^6}{r}
+\left[ \frac{}{} \right. \nonumber \\
+ &&\qquad \frac{r^2-7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
+ {\left(r-a_1-a_2\right)^7} \nonumber \\
+ &&\qquad +\frac{r^2+7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
+ {\left(r+a_1+a_2\right)^7} \nonumber \\
+ &&\qquad -\frac{r^2+7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
+ {\left(r+a_1-a_2\right)^7} \nonumber \\
+ &&\qquad \left. -\frac{r^2-7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
+ {\left(r-a_1+a_2\right)^7}
+ \right] \nonumber \\
+\nonumber \\
+U &=& U_A + U_R, \qquad r < r_c \nonumber
+\end{eqnarray}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_colloid_cs.jpg b/doc/doc2/Eqs/pair_colloid_cs.jpg
new file mode 100644
index 000000000..8f5948fa5
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diff --git a/doc/doc2/Eqs/pair_colloid_cs.tex b/doc/doc2/Eqs/pair_colloid_cs.tex
new file mode 100644
index 000000000..760215ee0
--- /dev/null
+++ b/doc/doc2/Eqs/pair_colloid_cs.tex
@@ -0,0 +1,12 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray}
+ U &=& \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3}
+ \left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6}
+ {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], ~~ r < r_c \nonumber
+\end{eqnarray}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_colloid_ss.jpg b/doc/doc2/Eqs/pair_colloid_ss.jpg
new file mode 100644
index 000000000..4ce19ba1e
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diff --git a/doc/doc2/Eqs/pair_colloid_ss.tex b/doc/doc2/Eqs/pair_colloid_ss.tex
new file mode 100644
index 000000000..1cc511ed0
--- /dev/null
+++ b/doc/doc2/Eqs/pair_colloid_ss.tex
@@ -0,0 +1,12 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray}
+ U &=& \frac{A_{ss}}{36} \left[ \left( \frac{\sigma}{r}
+ \right)^{12} - \left( \frac{ \sigma}{r} \right)^6 \right], ~~
+ r < r_c \nonumber
+\end{eqnarray}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_comb1.jpg b/doc/doc2/Eqs/pair_comb1.jpg
new file mode 100644
index 000000000..e0711ca97
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diff --git a/doc/doc2/Eqs/pair_comb1.tex b/doc/doc2/Eqs/pair_comb1.tex
new file mode 100644
index 000000000..aab7c8d2d
--- /dev/null
+++ b/doc/doc2/Eqs/pair_comb1.tex
@@ -0,0 +1,7 @@
+\documentclass[12pt]{article}
+\begin{document} \large
+\begin{eqnarray*}
+E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\
+&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\
+\end{eqnarray*}
+\end{document}
diff --git a/doc/doc2/Eqs/pair_comb2.jpg b/doc/doc2/Eqs/pair_comb2.jpg
new file mode 100644
index 000000000..8b0e5ba51
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diff --git a/doc/doc2/Eqs/pair_comb2.tex b/doc/doc2/Eqs/pair_comb2.tex
new file mode 100644
index 000000000..cd022cc7f
--- /dev/null
+++ b/doc/doc2/Eqs/pair_comb2.tex
@@ -0,0 +1,23 @@
+\documentclass[10pt]{article}
+
+\begin{document}
+
+\begin{table}[h]
+\begin{tabular}{|c|c|c|c|c|c|c|c|c|}
+\hline
+ & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ & $Zr$ \\ \hline
+$O$ & F & F & F & F & F & F & F & F\\ \hline
+$Cu$ & F & F & P & F & F & P & F & P \\ \hline
+$N$ & F & P & F & M & F & P & P & P \\ \hline
+$C$ & F & F & M & F & F & M & M & M \\ \hline
+$H$ & F & F & F & F & F & M & M & F \\ \hline
+$Ti$ & F & P & P & M & M & F & P & P \\ \hline
+$Zn$ & F & F & P & M & M & P & F & P \\ \hline
+$Zr$ & F & P & P & M & F & P & P & F \\ \hline
+\multicolumn{9}{l}{F: Fully optimized} \\
+\multicolumn{9}{l}{M: Only optimized for dimer molecule} \\
+\multicolumn{9}{l}{P: in Progress but have it from mixing rule} \\
+\end{tabular}
+\end{table}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_diel.jpg b/doc/doc2/Eqs/pair_coul_diel.jpg
new file mode 100644
index 000000000..70cb84f7a
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diff --git a/doc/doc2/Eqs/pair_coul_diel.tex b/doc/doc2/Eqs/pair_coul_diel.tex
new file mode 100644
index 000000000..f0b893d88
--- /dev/null
+++ b/doc/doc2/Eqs/pair_coul_diel.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\
+ \epsilon_D(r) & = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right)
+\end{eqnarray*}
+\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_dsf.jpg b/doc/doc2/Eqs/pair_coul_dsf.jpg
new file mode 100644
index 000000000..a891b3ad1
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diff --git a/doc/doc2/Eqs/pair_coul_dsf.tex b/doc/doc2/Eqs/pair_coul_dsf.tex
new file mode 100644
index 000000000..ec69680fc
--- /dev/null
+++ b/doc/doc2/Eqs/pair_coul_dsf.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+$$
+ E =
+ q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
+ \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_soft.jpg b/doc/doc2/Eqs/pair_coul_soft.jpg
new file mode 100644
index 000000000..dad9c745b
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diff --git a/doc/doc2/Eqs/pair_coul_soft.tex b/doc/doc2/Eqs/pair_coul_soft.tex
new file mode 100644
index 000000000..2ff42a25b
--- /dev/null
+++ b/doc/doc2/Eqs/pair_coul_soft.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[
+E = \lambda^n \frac{ C q_i q_j}{\epsilon
+\left[ \alpha_{\mathrm{C}} (1-\lambda)^2 + r^2 \right]^{1/2}} \qquad r < r_c
+\]
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_wolf.jpg b/doc/doc2/Eqs/pair_coul_wolf.jpg
new file mode 100644
index 000000000..fd64cb6c0
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diff --git a/doc/doc2/Eqs/pair_coul_wolf.tex b/doc/doc2/Eqs/pair_coul_wolf.tex
new file mode 100644
index 000000000..4a6592638
--- /dev/null
+++ b/doc/doc2/Eqs/pair_coul_wolf.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+$$
+ E_i = \frac{1}{2} \sum_{j \neq i}
+ \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+ \frac{1}{2} \sum_{j \neq i}
+ \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_coulomb.jpg b/doc/doc2/Eqs/pair_coulomb.jpg
new file mode 100644
index 000000000..39aaebac3
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diff --git a/doc/doc2/Eqs/pair_coulomb.tex b/doc/doc2/Eqs/pair_coulomb.tex
new file mode 100644
index 000000000..9dacdc1af
--- /dev/null
+++ b/doc/doc2/Eqs/pair_coulomb.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_cs.jpg b/doc/doc2/Eqs/pair_cs.jpg
new file mode 100644
index 000000000..b870a3bdf
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diff --git a/doc/doc2/Eqs/pair_cs.tex b/doc/doc2/Eqs/pair_cs.tex
new file mode 100644
index 000000000..b7eacb8d5
--- /dev/null
+++ b/doc/doc2/Eqs/pair_cs.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_debye.jpg b/doc/doc2/Eqs/pair_debye.jpg
new file mode 100644
index 000000000..42bcb5cc6
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diff --git a/doc/doc2/Eqs/pair_debye.tex b/doc/doc2/Eqs/pair_debye.tex
new file mode 100644
index 000000000..392a6516c
--- /dev/null
+++ b/doc/doc2/Eqs/pair_debye.tex
@@ -0,0 +1,8 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+$$
+ E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_dipole.jpg b/doc/doc2/Eqs/pair_dipole.jpg
new file mode 100644
index 000000000..e106c17c9
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diff --git a/doc/doc2/Eqs/pair_dipole.tex b/doc/doc2/Eqs/pair_dipole.tex
new file mode 100644
index 000000000..bc0ae82f8
--- /dev/null
+++ b/doc/doc2/Eqs/pair_dipole.tex
@@ -0,0 +1,38 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] \\
+E_{qq} & = & \frac{q_i q_j}{r} \\
+E_{qp} & = & \frac{q}{r^3} (p \bullet \vec{r}) \\
+E_{pp} & = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) -
+ \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})
+\end{eqnarray*}
+
+\begin{eqnarray*}
+F_{qq} & = & \frac{q_i q_j}{r^3} \vec{r} \\
+F_{qp} & = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5}
+ (\vec{p} \bullet \vec{r}) \vec{r} \\
+F_{pp} & = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} -
+ \frac{15}{r^7} (\vec{p_i} \bullet \vec{r})
+ (\vec{p_j} \bullet \vec{r}) \vec{r} +
+ \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} +
+ (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right]
+\end{eqnarray*}
+
+\begin{eqnarray*}
+T_{pq} = T_{ij} & = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\
+T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\
+T_{pp} = T_{ij} & = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) +
+ \frac{3}{r^5} (\vec{p_j} \bullet \vec{r})
+ (\vec{p_i} \times \vec{r}) \\
+T_{pp} = T_{ji} & = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) +
+ \frac{3}{r^5} (\vec{p_i} \bullet \vec{r})
+ (\vec{p_j} \times \vec{r}) \\
+\end{eqnarray*}
+
+\end{document}
+
+
diff --git a/doc/doc2/Eqs/pair_dipole_sf.jpg b/doc/doc2/Eqs/pair_dipole_sf.jpg
new file mode 100644
index 000000000..c59153455
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diff --git a/doc/doc2/Eqs/pair_dipole_sf.tex b/doc/doc2/Eqs/pair_dipole_sf.tex
new file mode 100644
index 000000000..c653a3774
--- /dev/null
+++ b/doc/doc2/Eqs/pair_dipole_sf.tex
@@ -0,0 +1,51 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{LJ} & = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} -
+ \left( \frac{\sigma}{r} \right)^{\!6} \right] +
+ \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} -
+ 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2}
+ - 7\left( \frac{\sigma}{r_c} \right)^{\!12} +
+ 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\
+E_{qq} & = & \frac{q_i q_j}{r}\left(1-\frac{r}{r_c}\right)^{\!2} \\
+E_{pq} & = & E_{ji} = -\frac{q}{r^3} \left[ 1 -
+ 3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\
+E_{qp} & = & E_{ij} = \frac{q}{r^3} \left[ 1 -
+ 3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\
+E_{pp} & = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
+ 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3}
+ (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5}
+ (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\
+\end{eqnarray*}
+
+\begin{eqnarray*}
+F_{LJ} & = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} -
+ 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} -
+ \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon
+ \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\
+F_{qq} & = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} -
+ \frac{1}{r_c^2}\right)\vec{r} \\
+F_{pq} &=& F_{ij } = -\frac{3q}{r^5} \left[ 1 -
+ \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} +
+ \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\
+F_{qp} &=& F_{ij} = \frac{3q}{r^5} \left[ 1 -
+ \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} -
+ \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\
+F_{pp} & = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right]
+ \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r})
+ (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\
+ & & \left[1 -
+ 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right]
+ \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r})
+ \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r})
+ (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} \\
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_dipole_sf2.jpg b/doc/doc2/Eqs/pair_dipole_sf2.jpg
new file mode 100644
index 000000000..b9e57becf
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diff --git a/doc/doc2/Eqs/pair_dipole_sf2.tex b/doc/doc2/Eqs/pair_dipole_sf2.tex
new file mode 100644
index 000000000..74758ba23
--- /dev/null
+++ b/doc/doc2/Eqs/pair_dipole_sf2.tex
@@ -0,0 +1,24 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+T_{pq} = T_{ij} & = & \frac{q_j}{r^3} \left[ 1 -
+ 3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\
+T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} \left[ 1 -
+ 3\left(\frac{r}{r_c}\right)^{\!2} +
+ 2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\
+T_{pp} = T_{ij} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
+ e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\
+ & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
+ 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r})
+ (\vec{p_i} \times \vec{r}) \\
+T_{pp} = T_{ji} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
+ 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\
+ & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
+ 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r})
+ (\vec{p_j} \times \vec{r}) \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_dpd.jpg b/doc/doc2/Eqs/pair_dpd.jpg
new file mode 100644
index 000000000..e9bb8a69a
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diff --git a/doc/doc2/Eqs/pair_dpd.tex b/doc/doc2/Eqs/pair_dpd.tex
new file mode 100644
index 000000000..ba47f0d6b
--- /dev/null
+++ b/doc/doc2/Eqs/pair_dpd.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ \vec{f} & = & (F^C + F^D + F^R) \hat{r_{ij}} \qquad \qquad r < r_c \\
+ F^C & = & A w(r) \\
+ F^D & = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v_{ij}}) \\
+ F^R & = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\
+ w(r) & = & 1 - r/r_c
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_eam.jpg b/doc/doc2/Eqs/pair_eam.jpg
new file mode 100644
index 000000000..95c86b4ce
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diff --git a/doc/doc2/Eqs/pair_eam.tex b/doc/doc2/Eqs/pair_eam.tex
new file mode 100644
index 000000000..2ea20b219
--- /dev/null
+++ b/doc/doc2/Eqs/pair_eam.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
+ \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_eam_fs.jpg b/doc/doc2/Eqs/pair_eam_fs.jpg
new file mode 100644
index 000000000..fa72f8fc7
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diff --git a/doc/doc2/Eqs/pair_eam_fs.tex b/doc/doc2/Eqs/pair_eam_fs.tex
new file mode 100644
index 000000000..32ca605e2
--- /dev/null
+++ b/doc/doc2/Eqs/pair_eam_fs.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E_i = F_\alpha \left(\sum_{j \neq i}\
+ \rho_{\alpha\beta} (r_{ij})\right) +
+ \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_edip.jpg b/doc/doc2/Eqs/pair_edip.jpg
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index 000000000..393328048
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diff --git a/doc/doc2/Eqs/pair_edip.tex b/doc/doc2/Eqs/pair_edip.tex
new file mode 100644
index 000000000..27f5dd9ee
--- /dev/null
+++ b/doc/doc2/Eqs/pair_edip.tex
@@ -0,0 +1,22 @@
+\documentclass[12pt]{article}
+
+\usepackage{amssymb,amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+E & = & \sum_{j \ne i} \phi_{2}(R_{ij}, Z_{i}) + \sum_{j \ne i} \sum_{k \ne i,k > j} \phi_{3}(R_{ij}, R_{ik}, Z_{i}) \\
+\phi_{2}(r, Z) & = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\
+\phi_{3}(R_{ij}, R_{ik}, Z_i) & = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\
+Z_i & = & \sum_{m \ne i} f(R_{im}) \qquad
+ f(r) = \begin{cases}
+ 1 & \quad r<c \\
+ \exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\
+ 0 & \quad r>a
+ \end{cases} \\
+h(l,Z) & = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\
+Q(Z) & = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z})
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/doc2/Eqs/pair_eim1.jpg b/doc/doc2/Eqs/pair_eim1.jpg
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index 000000000..c243120b2
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diff --git a/doc/doc2/Eqs/pair_eim1.tex b/doc/doc2/Eqs/pair_eim1.tex
new file mode 100644
index 000000000..bfa5b6ebc
--- /dev/null
+++ b/doc/doc2/Eqs/pair_eim1.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left(r_{ij}\right) + \sum_{i=1}^{N}E_i\left(q_i,\sigma_i\right)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_eim2.jpg b/doc/doc2/Eqs/pair_eim2.jpg
new file mode 100644
index 000000000..4896f658f
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diff --git a/doc/doc2/Eqs/pair_eim2.tex b/doc/doc2/Eqs/pair_eim2.tex
new file mode 100644
index 000000000..d8c418134
--- /dev/null
+++ b/doc/doc2/Eqs/pair_eim2.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+q_i & = & \sum_{j=i_1}^{i_N} \eta_{ji}\left(r_{ij}\right) \\
+\sigma_i & = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\
+E_i\left(q_i,\sigma_i\right) & = & \frac{1}{2} \cdot q_i \cdot \sigma_i
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_eim3.jpg b/doc/doc2/Eqs/pair_eim3.jpg
new file mode 100644
index 000000000..57366bc15
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diff --git a/doc/doc2/Eqs/pair_eim3.tex b/doc/doc2/Eqs/pair_eim3.tex
new file mode 100644
index 000000000..84343c6ac
--- /dev/null
+++ b/doc/doc2/Eqs/pair_eim3.tex
@@ -0,0 +1,25 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\phi_{ij}\left(r\right) = \left\{ \begin{array}{lr}
+\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\alpha_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)-\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\beta_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=1 \\
+\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\alpha_{ij}} -\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\beta_{ij}}\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=2
+\end{array}
+\right.
+\end{eqnarray*}
+
+$$
+\eta_{ji} = A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right)
+$$
+
+$$
+\psi_{ij}\left(r\right) = A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right)
+$$
+
+$$
+f_{c}\left(r,r_p,r_c\right) = 0.510204 erfc\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gauss.jpg b/doc/doc2/Eqs/pair_gauss.jpg
new file mode 100644
index 000000000..97c2f0ecb
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diff --git a/doc/doc2/Eqs/pair_gauss.tex b/doc/doc2/Eqs/pair_gauss.tex
new file mode 100644
index 000000000..ed38e1394
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gauss.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+$$
+ E = - A \exp(-B r^2) \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gauss_cut.jpg b/doc/doc2/Eqs/pair_gauss_cut.jpg
new file mode 100644
index 000000000..e47bb8cc0
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diff --git a/doc/doc2/Eqs/pair_gauss_cut.tex b/doc/doc2/Eqs/pair_gauss_cut.tex
new file mode 100644
index 000000000..5d0bb430f
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gauss_cut.tex
@@ -0,0 +1,8 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ E = & \frac{H}{\sigma_h\sqrt{2\pi}} \exp\left[-\frac{(r-r_{mh})^2}{2\sigma_h^2}\right]
+\end{eqnarray*}
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gayberne.jpg b/doc/doc2/Eqs/pair_gayberne.jpg
new file mode 100644
index 000000000..e9b1f3ca9
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diff --git a/doc/doc2/Eqs/pair_gayberne.tex b/doc/doc2/Eqs/pair_gayberne.tex
new file mode 100644
index 000000000..d3c199e82
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gayberne.tex
@@ -0,0 +1,14 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
+\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
+\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
+\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
+
+$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
+
+$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gayberne2.jpg b/doc/doc2/Eqs/pair_gayberne2.jpg
new file mode 100644
index 000000000..a4e6c6f70
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diff --git a/doc/doc2/Eqs/pair_gayberne2.tex b/doc/doc2/Eqs/pair_gayberne2.tex
new file mode 100644
index 000000000..6efb75577
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gayberne2.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b =
+\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot {
+\frac{c}{ a \cdot b } } $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gran_hertz.jpg b/doc/doc2/Eqs/pair_gran_hertz.jpg
new file mode 100644
index 000000000..733875fee
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diff --git a/doc/doc2/Eqs/pair_gran_hertz.tex b/doc/doc2/Eqs/pair_gran_hertz.tex
new file mode 100644
index 000000000..d6e09493b
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gran_hertz.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ F_{hz} = \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} F_{hk} =
+ \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}}
+ \Big[ (k_n \delta \mathbf{n}_{ij} -
+ m_{\mbox{\scriptsize{eff}}} \: \gamma_n \mathbf{ v}_n) -
+ (k_t \mathbf{ \Delta s}_t +
+ m_{\mbox{\scriptsize{eff}}} \: \gamma_t \mathbf{v}_t) \Big]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gran_hooke.jpg b/doc/doc2/Eqs/pair_gran_hooke.jpg
new file mode 100644
index 000000000..36f34db6c
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diff --git a/doc/doc2/Eqs/pair_gran_hooke.tex b/doc/doc2/Eqs/pair_gran_hooke.tex
new file mode 100644
index 000000000..e1901e66a
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gran_hooke.tex
@@ -0,0 +1,12 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ F_{hk} = (k_n \delta \mathbf{n}_{ij} -
+ m_{\mbox{\scriptsize{eff}}} \gamma_n\mathbf{ v}_n) -
+ (k_t \mathbf{ \Delta s}_t +
+ m_{\mbox{\scriptsize{eff}}} \gamma_t \mathbf{v}_t)
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_gromacs.jpg b/doc/doc2/Eqs/pair_gromacs.jpg
new file mode 100644
index 000000000..885c059e6
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diff --git a/doc/doc2/Eqs/pair_gromacs.tex b/doc/doc2/Eqs/pair_gromacs.tex
new file mode 100644
index 000000000..88dbe1590
--- /dev/null
+++ b/doc/doc2/Eqs/pair_gromacs.tex
@@ -0,0 +1,17 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] + S_{LJ}(r)
+ \qquad r < r_c \\
+E_C & = & \frac{C q_i q_j}{\epsilon r} + S_C(r) \qquad r < r_c \\
+S(r) & = & C \qquad r < r_1 \\
+S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad r_1 < r < r_c \\
+A & = & (-3 E'(r_c) + (r_c - r_1) E''(r_c))/(r_c - r_1)^2 \\
+B & = & (2 E'(r_c) - (r_c - r_1) E''(r_c))/(r_c - r_1)^3 \\
+C & = & -E(r_c) + \frac{1}{2} (r_c - r_1) E'(r_c) - \frac{1}{12} (r_c - r_1)^2 E''(r_c)) \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_hbond_dreiding.jpg b/doc/doc2/Eqs/pair_hbond_dreiding.jpg
new file mode 100644
index 000000000..b93044ed3
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diff --git a/doc/doc2/Eqs/pair_hbond_dreiding.tex b/doc/doc2/Eqs/pair_hbond_dreiding.tex
new file mode 100644
index 000000000..9663ee560
--- /dev/null
+++ b/doc/doc2/Eqs/pair_hbond_dreiding.tex
@@ -0,0 +1,18 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+\begin{eqnarray*}
+ E & = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\
+ & = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+ & = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+ LJ(r) & = & AR^{-12}-BR^{-10}cos^n\theta=
+ \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}-
+ 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\
+ Morse(r) & = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta=
+ D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)}
+ \right\rbrace cos^n\theta \\
+ S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
+ \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
+ { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
+\end{eqnarray*}
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lj.jpg b/doc/doc2/Eqs/pair_lj.jpg
new file mode 100644
index 000000000..49cf7f5eb
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diff --git a/doc/doc2/Eqs/pair_lj.tex b/doc/doc2/Eqs/pair_lj.tex
new file mode 100644
index 000000000..011fb8b76
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right]
+ \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lj96.jpg b/doc/doc2/Eqs/pair_lj96.jpg
new file mode 100644
index 000000000..6462de180
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diff --git a/doc/doc2/Eqs/pair_lj96.tex b/doc/doc2/Eqs/pair_lj96.tex
new file mode 100644
index 000000000..e97062489
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj96.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
+ \left(\frac{\sigma}{r}\right)^6 \right]
+ \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_cubic.jpg b/doc/doc2/Eqs/pair_lj_cubic.jpg
new file mode 100644
index 000000000..69ec4f6e8
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diff --git a/doc/doc2/Eqs/pair_lj_cubic.tex b/doc/doc2/Eqs/pair_lj_cubic.tex
new file mode 100644
index 000000000..e2e1b67dd
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_cubic.tex
@@ -0,0 +1,12 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E &=& u_{LJ}(r) \qquad r \leq r_s \\
+ &=& u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\
+ &=& 0 \qquad r > r_c
+\end{eqnarray*}
+
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_expand.jpg b/doc/doc2/Eqs/pair_lj_expand.jpg
new file mode 100644
index 000000000..e27481889
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diff --git a/doc/doc2/Eqs/pair_lj_expand.tex b/doc/doc2/Eqs/pair_lj_expand.tex
new file mode 100644
index 000000000..0aaa2f44d
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_expand.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} -
+ \left(\frac{\sigma}{r - \Delta}\right)^6 \right]
+ \qquad r < r_c + \Delta
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_lj_sf.jpg b/doc/doc2/Eqs/pair_lj_sf.jpg
new file mode 100644
index 000000000..a70224000
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diff --git a/doc/doc2/Eqs/pair_lj_sf.tex b/doc/doc2/Eqs/pair_lj_sf.tex
new file mode 100644
index 000000000..e78e2ca75
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_sf.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
+ E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
+ \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_smooth.jpg b/doc/doc2/Eqs/pair_lj_smooth.jpg
new file mode 100644
index 000000000..d380fd345
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diff --git a/doc/doc2/Eqs/pair_lj_smooth.tex b/doc/doc2/Eqs/pair_lj_smooth.tex
new file mode 100644
index 000000000..5aa5495c2
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_smooth.tex
@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right]
+ \qquad r < r_{in} \\
+ F & = & C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3
+ \qquad r_{in} < r < r_c
+\end{eqnarray*}
+
+\end{document}
+
+
diff --git a/doc/doc2/Eqs/pair_lj_smooth_linear.jpg b/doc/doc2/Eqs/pair_lj_smooth_linear.jpg
new file mode 100644
index 000000000..b0626abae
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diff --git a/doc/doc2/Eqs/pair_lj_smooth_linear.tex b/doc/doc2/Eqs/pair_lj_smooth_linear.tex
new file mode 100644
index 000000000..b8980f8d2
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_smooth_linear.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\phi\left(r\right) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+ \left(\frac{\sigma}{r}\right)^6 \right] \\
+E\left(r\right) & = & \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
+\end{eqnarray*}
+
+\end{document}
+
+
diff --git a/doc/doc2/Eqs/pair_lj_soft.jpg b/doc/doc2/Eqs/pair_lj_soft.jpg
new file mode 100644
index 000000000..856d6d5bb
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diff --git a/doc/doc2/Eqs/pair_lj_soft.tex b/doc/doc2/Eqs/pair_lj_soft.tex
new file mode 100644
index 000000000..e32f11f0a
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lj_soft.tex
@@ -0,0 +1,15 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\[
+E = \lambda^n 4 \epsilon
+\left\{
+ \frac{1}{ \left[ \alpha_{\mathrm{LJ}} (1-\lambda)^2 +
+ \left( \displaystyle\frac{r}{\sigma} \right)^6 \right]^2 } -
+ \frac{1}{ \alpha_{\mathrm{LJ}} (1-\lambda)^2 +
+ \left( \displaystyle\frac{r}{\sigma} \right)^6 }
+\right\} \qquad r < r_c
+ \]
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_lubricate.jpg b/doc/doc2/Eqs/pair_lubricate.jpg
new file mode 100644
index 000000000..560591765
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diff --git a/doc/doc2/Eqs/pair_lubricate.tex b/doc/doc2/Eqs/pair_lubricate.tex
new file mode 100644
index 000000000..c7e3dd96e
--- /dev/null
+++ b/doc/doc2/Eqs/pair_lubricate.tex
@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ W & = & - a_{sq} | (v_1 - v_2) \bullet \mathbf{nn} |^2 -
+ a_{sh} | (\omega_1 + \omega_2) \bullet
+ (\mathbf{I} - \mathbf{nn}) - 2 \Omega_N |^2 - \\
+ & & a_{pu} | (\omega_1 - \omega_2) \bullet (\mathbf{I} - \mathbf{nn}) |^2 -
+ a_{tw} | (\omega_1 - \omega_2) \bullet \mathbf{nn} |^2 \qquad r < r_c
+\end{eqnarray*}
+
+$$
+\Omega_N = \mathbf{n} \times (v_1 - v_2) / r
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_meam.jpg b/doc/doc2/Eqs/pair_meam.jpg
new file mode 100644
index 000000000..f6de50a99
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diff --git a/doc/doc2/Eqs/pair_meam.tex b/doc/doc2/Eqs/pair_meam.tex
new file mode 100644
index 000000000..cb9bb1702
--- /dev/null
+++ b/doc/doc2/Eqs/pair_meam.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \sum_i \left\{ F_i(\bar{\rho}_i)
+ + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\}
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_meam_spline.jpg b/doc/doc2/Eqs/pair_meam_spline.jpg
new file mode 100644
index 000000000..29f1c7254
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diff --git a/doc/doc2/Eqs/pair_meam_spline.tex b/doc/doc2/Eqs/pair_meam_spline.tex
new file mode 100644
index 000000000..55d42f801
--- /dev/null
+++ b/doc/doc2/Eqs/pair_meam_spline.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}),
+$$
+
+$$
+ \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_meam_sw_spline.jpg b/doc/doc2/Eqs/pair_meam_sw_spline.jpg
new file mode 100644
index 000000000..80078999d
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diff --git a/doc/doc2/Eqs/pair_meam_sw_spline.tex b/doc/doc2/Eqs/pair_meam_sw_spline.tex
new file mode 100644
index 000000000..28abc433b
--- /dev/null
+++ b/doc/doc2/Eqs/pair_meam_sw_spline.tex
@@ -0,0 +1,23 @@
+\documentclass[showpacs,amsmath,amssymb,prb]{revtex4}
+
+
+\usepackage{graphicx}
+\usepackage{dcolumn}
+\usepackage{bm}
+
+\newcommand{\etal}{{\em et al.}}
+\newcommand{\OO}{{\mathcal{O}}}
+\newtheorem{theorem}{Theorem}
+
+\begin{document}
+
+\begin{eqnarray}
+E & = & E_{MEAM} + E_{SW} \nonumber \\
+E_{MEAM} & = & \sum _{IJ} \phi (r_{IJ}) + \sum _{I} U(\rho _I) \nonumber \\
+E_{SW} & = & \sum _{I} \sum _{JK} F(r_{IJ}) \, F(r_{IK}) \, G(\cos(\theta _{JIK})) \nonumber \\
+\rho _I & = & \sum _J \rho(r_{IJ}) + \sum _{JK} f(r_{IJ}) \, f(r_{IK}) \, g(\cos(\theta _{JIK})) \nonumber
+\end{eqnarray}
+
+\end{document}
+
+
diff --git a/doc/doc2/Eqs/pair_mie.jpg b/doc/doc2/Eqs/pair_mie.jpg
new file mode 100644
index 000000000..05a8221a9
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diff --git a/doc/doc2/Eqs/pair_mie.tex b/doc/doc2/Eqs/pair_mie.tex
new file mode 100644
index 000000000..2702ce9bc
--- /dev/null
+++ b/doc/doc2/Eqs/pair_mie.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
+ \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_mie2.jpg b/doc/doc2/Eqs/pair_mie2.jpg
new file mode 100644
index 000000000..216ca1554
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diff --git a/doc/doc2/Eqs/pair_mie2.tex b/doc/doc2/Eqs/pair_mie2.tex
new file mode 100644
index 000000000..2ee9e9b34
--- /dev/null
+++ b/doc/doc2/Eqs/pair_mie2.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_morse.jpg b/doc/doc2/Eqs/pair_morse.jpg
new file mode 100644
index 000000000..5ebcdb2e1
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diff --git a/doc/doc2/Eqs/pair_morse.tex b/doc/doc2/Eqs/pair_morse.tex
new file mode 100644
index 000000000..21204daa2
--- /dev/null
+++ b/doc/doc2/Eqs/pair_morse.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
+ \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_nb3b_harmonic.jpg b/doc/doc2/Eqs/pair_nb3b_harmonic.jpg
new file mode 100644
index 000000000..c8d23da04
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diff --git a/doc/doc2/Eqs/pair_nb3b_harmonic.tex b/doc/doc2/Eqs/pair_nb3b_harmonic.tex
new file mode 100644
index 000000000..7f7aa8078
--- /dev/null
+++ b/doc/doc2/Eqs/pair_nb3b_harmonic.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = K (\theta - \theta_0)^2
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_nm.jpg b/doc/doc2/Eqs/pair_nm.jpg
new file mode 100644
index 000000000..1e7fe0981
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diff --git a/doc/doc2/Eqs/pair_nm.tex b/doc/doc2/Eqs/pair_nm.tex
new file mode 100644
index 000000000..4adf9331c
--- /dev/null
+++ b/doc/doc2/Eqs/pair_nm.tex
@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n -
+ n \left(\frac{r_0}{r}\right)^m \right] \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared.jpg b/doc/doc2/Eqs/pair_resquared.jpg
new file mode 100644
index 000000000..c290c68df
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diff --git a/doc/doc2/Eqs/pair_resquared.tex b/doc/doc2/Eqs/pair_resquared.tex
new file mode 100644
index 000000000..e5c758aec
--- /dev/null
+++ b/doc/doc2/Eqs/pair_resquared.tex
@@ -0,0 +1,7 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2 $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared2.jpg b/doc/doc2/Eqs/pair_resquared2.jpg
new file mode 100644
index 000000000..d2ed21a62
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diff --git a/doc/doc2/Eqs/pair_resquared2.tex b/doc/doc2/Eqs/pair_resquared2.tex
new file mode 100644
index 000000000..ff2c3ca74
--- /dev/null
+++ b/doc/doc2/Eqs/pair_resquared2.tex
@@ -0,0 +1,7 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3) $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared3.jpg b/doc/doc2/Eqs/pair_resquared3.jpg
new file mode 100644
index 000000000..3916062a1
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diff --git a/doc/doc2/Eqs/pair_resquared3.tex b/doc/doc2/Eqs/pair_resquared3.tex
new file mode 100644
index 000000000..136bcf73d
--- /dev/null
+++ b/doc/doc2/Eqs/pair_resquared3.tex
@@ -0,0 +1,7 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ A_{12} = \epsilon_{\mathrm{LJ}} $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared4.jpg b/doc/doc2/Eqs/pair_resquared4.jpg
new file mode 100644
index 000000000..79ad067fa
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diff --git a/doc/doc2/Eqs/pair_resquared4.tex b/doc/doc2/Eqs/pair_resquared4.tex
new file mode 100644
index 000000000..6efb75577
--- /dev/null
+++ b/doc/doc2/Eqs/pair_resquared4.tex
@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b =
+\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot {
+\frac{c}{ a \cdot b } } $$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_snap.jpg b/doc/doc2/Eqs/pair_snap.jpg
new file mode 100644
index 000000000..af48357b5
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diff --git a/doc/doc2/Eqs/pair_snap.tex b/doc/doc2/Eqs/pair_snap.tex
new file mode 100644
index 000000000..d0a17de1f
--- /dev/null
+++ b/doc/doc2/Eqs/pair_snap.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_soft.jpg b/doc/doc2/Eqs/pair_soft.jpg
new file mode 100644
index 000000000..e8a654e1e
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diff --git a/doc/doc2/Eqs/pair_soft.tex b/doc/doc2/Eqs/pair_soft.tex
new file mode 100644
index 000000000..c2db15c2e
--- /dev/null
+++ b/doc/doc2/Eqs/pair_soft.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = A \left[ 1 + \cos\left(\frac{\pi r}{r_c}\right) \right]
+ \qquad r < r_c
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_sph_ideal.jpg b/doc/doc2/Eqs/pair_sph_ideal.jpg
new file mode 100644
index 000000000..370b75fe9
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diff --git a/doc/doc2/Eqs/pair_sph_ideal.tex b/doc/doc2/Eqs/pair_sph_ideal.tex
new file mode 100644
index 000000000..91c64f00b
--- /dev/null
+++ b/doc/doc2/Eqs/pair_sph_ideal.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ p = (\gamma - 1) \rho e
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_sph_tait.jpg b/doc/doc2/Eqs/pair_sph_tait.jpg
new file mode 100644
index 000000000..8bbfe8051
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diff --git a/doc/doc2/Eqs/pair_sph_tait.tex b/doc/doc2/Eqs/pair_sph_tait.tex
new file mode 100644
index 000000000..4e1fa9cfe
--- /dev/null
+++ b/doc/doc2/Eqs/pair_sph_tait.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ p = B [(\frac{\rho}{\rho_0})^{\gamma} - 1]
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_srp1.jpg b/doc/doc2/Eqs/pair_srp1.jpg
new file mode 100644
index 000000000..bbbdc43e0
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diff --git a/doc/doc2/Eqs/pair_srp1.tex b/doc/doc2/Eqs/pair_srp1.tex
new file mode 100644
index 000000000..45aa005d8
--- /dev/null
+++ b/doc/doc2/Eqs/pair_srp1.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F^{SRP}_{ij} & = & C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_srp2.jpg b/doc/doc2/Eqs/pair_srp2.jpg
new file mode 100644
index 000000000..c5d20dc21
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diff --git a/doc/doc2/Eqs/pair_srp2.tex b/doc/doc2/Eqs/pair_srp2.tex
new file mode 100644
index 000000000..19cb19ae7
--- /dev/null
+++ b/doc/doc2/Eqs/pair_srp2.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F_{i1}^{SRP} & = & F^{SRP}_{ij}(L) \\
+ F_{i2}^{SRP} & = & F^{SRP}_{ij}(1-L)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_sw.jpg b/doc/doc2/Eqs/pair_sw.jpg
new file mode 100644
index 000000000..f60f07fd2
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diff --git a/doc/doc2/Eqs/pair_sw.tex b/doc/doc2/Eqs/pair_sw.tex
new file mode 100644
index 000000000..ebcc39d77
--- /dev/null
+++ b/doc/doc2/Eqs/pair_sw.tex
@@ -0,0 +1,18 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \sum_i \sum_{j > i} \phi_2 (r_{ij}) +
+ \sum_i \sum_{j \neq i} \sum_{k > j}
+ \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\
+ \phi_2(r_{ij}) & = & A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} -
+ (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right]
+ \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\
+ \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = & \lambda_{ijk} \epsilon_{ijk} \left[ \cos \theta_{ijk} -
+ \cos \theta_{0ijk} \right]^2
+ \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right)
+ \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff.jpg b/doc/doc2/Eqs/pair_tersoff.jpg
new file mode 100644
index 000000000..bd3e14719
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diff --git a/doc/doc2/Eqs/pair_tersoff_1.jpg b/doc/doc2/Eqs/pair_tersoff_1.jpg
new file mode 100644
index 000000000..79600b499
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diff --git a/doc/doc2/Eqs/pair_tersoff_1.tex b/doc/doc2/Eqs/pair_tersoff_1.tex
new file mode 100644
index 000000000..7d3471249
--- /dev/null
+++ b/doc/doc2/Eqs/pair_tersoff_1.tex
@@ -0,0 +1,24 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+ V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
+ f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
+ 1 & r < R - D \\
+ \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
+ R-D < r < R + D \\
+ 0 & r > R + D
+ \end{array} \right. \\
+ f_R(r) & = & A \exp (-\lambda_1 r) \\
+ f_A(r) & = & -B \exp (-\lambda_2 r) \\
+ b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
+ \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
+ \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
+ g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
+ \frac{c^2}{\left[ d^2 +
+ (\cos \theta - \cos \theta_0)^2\right]} \right)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff_2.jpg b/doc/doc2/Eqs/pair_tersoff_2.jpg
new file mode 100644
index 000000000..6cb8778a0
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diff --git a/doc/doc2/Eqs/pair_tersoff_2.tex b/doc/doc2/Eqs/pair_tersoff_2.tex
new file mode 100644
index 000000000..7b5beb8ef
--- /dev/null
+++ b/doc/doc2/Eqs/pair_tersoff_2.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\lambda_1^{i,j} &=& \frac{1}{2}(\lambda_1^i + \lambda_1^j)\\
+\lambda_2^{i,j} &=& \frac{1}{2}(\lambda_2^i + \lambda_2^j)\\
+A_{i,j} &=& (A_{i}A_{j})^{1/2}\\
+B_{i,j} &=& \chi_{ij}(B_{i}B_{j})^{1/2}\\
+R_{i,j} &=& (R_{i}R_{j})^{1/2}\\
+S_{i,j} &=& (S_{i}S_{j})^{1/2}\\
+\end{eqnarray*}
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_tersoff_mod.jpg b/doc/doc2/Eqs/pair_tersoff_mod.jpg
new file mode 100644
index 000000000..2618943d8
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diff --git a/doc/doc2/Eqs/pair_tersoff_mod.tex b/doc/doc2/Eqs/pair_tersoff_mod.tex
new file mode 100644
index 000000000..eafc4fdee
--- /dev/null
+++ b/doc/doc2/Eqs/pair_tersoff_mod.tex
@@ -0,0 +1,24 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+ V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
+ f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
+ 1 & r < R - D \\
+ \frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
+ R-D < r < R + D \\
+ 0 & r > R + D
+ \end{array} \right. \\
+ f_R(r) & = & A \exp (-\lambda_1 r) \\
+ f_A(r) & = & -B \exp (-\lambda_2 r) \\
+ b_{ij} & = & \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
+ \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
+ \exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
+ g(\theta) & = & c_1 + g_o(\theta) g_a(\theta) \\
+ g_o(\theta) & = & \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
+ g_a(\theta) & = & 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff_zbl.jpg b/doc/doc2/Eqs/pair_tersoff_zbl.jpg
new file mode 100644
index 000000000..20d60d225
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diff --git a/doc/doc2/Eqs/pair_tersoff_zbl.tex b/doc/doc2/Eqs/pair_tersoff_zbl.tex
new file mode 100644
index 000000000..902819aa1
--- /dev/null
+++ b/doc/doc2/Eqs/pair_tersoff_zbl.tex
@@ -0,0 +1,33 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+ V_{ij} & = & (1 - f_F(r_{ij})) V^{ZBL}_{ij} + f_F(r_{ij}) V^{Tersoff}_{ij} \\
+f_F(r_{ij}) & = & \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\
+ \\
+ \\
+ V^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r_{ij}} \phi(r_{ij}/a) \\
+ a & = & \frac{0.8854\,a_0}{Z_{1}^{0.23} + Z_{2}^{0.23}}\\
+ \phi(x) & = & 0.1818e^{-3.2x} + 0.5099e^{-0.9423x} + 0.2802e^{-0.4029x} + 0.02817e^{-0.2016x}\\
+ \\
+ \\
+ V^{Tersoff}_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
+ f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
+ 1 & r < R - D \\
+ \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
+ R-D < r < R + D \\
+ 0 & r > R + D
+ \end{array} \right. \\
+ f_R(r) & = & A \exp (-\lambda_1 r) \\
+ f_A(r) & = & -B \exp (-\lambda_2 r) \\
+ b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
+ \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
+ \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
+ g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
+ \frac{c^2}{\left[ d^2 +
+ (\cos \theta - \cos \theta_0)^2\right]} \right)
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_yukawa.jpg b/doc/doc2/Eqs/pair_yukawa.jpg
new file mode 100644
index 000000000..103edc604
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diff --git a/doc/doc2/Eqs/pair_yukawa.tex b/doc/doc2/Eqs/pair_yukawa.tex
new file mode 100644
index 000000000..382cf249a
--- /dev/null
+++ b/doc/doc2/Eqs/pair_yukawa.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_yukawa_colloid.jpg b/doc/doc2/Eqs/pair_yukawa_colloid.jpg
new file mode 100644
index 000000000..1d8362475
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diff --git a/doc/doc2/Eqs/pair_yukawa_colloid.tex b/doc/doc2/Eqs/pair_yukawa_colloid.tex
new file mode 100644
index 000000000..dbdbbcd14
--- /dev/null
+++ b/doc/doc2/Eqs/pair_yukawa_colloid.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/pair_zbl.jpg b/doc/doc2/Eqs/pair_zbl.jpg
new file mode 100644
index 000000000..88656af5e
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diff --git a/doc/doc2/Eqs/pair_zbl.tex b/doc/doc2/Eqs/pair_zbl.tex
new file mode 100644
index 000000000..3d68dbed2
--- /dev/null
+++ b/doc/doc2/Eqs/pair_zbl.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ E^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_i Z_j \,e^2}{r_{ij}} \phi(r_{ij}/a)+ S(r_{ij})\\
+ a & = & \frac{0.46850}{Z_{i}^{0.23} + Z_{j}^{0.23}}\\
+ \phi(x) & = & 0.18175e^{-3.19980x} + 0.50986e^{-0.94229x} + 0.28022e^{-0.40290x} + 0.02817e^{-0.20162x}\\
+ \end{eqnarray*}
+
+\end{document}
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diff --git a/doc/doc2/Eqs/pressure.tex b/doc/doc2/Eqs/pressure.tex
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--- /dev/null
+++ b/doc/doc2/Eqs/pressure.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
+$$
+
+\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pressure_tensor.jpg b/doc/doc2/Eqs/pressure_tensor.jpg
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--- /dev/null
+++ b/doc/doc2/Eqs/pressure_tensor.tex
@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} +
+ \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
+$$
+
+\end{document}
diff --git a/doc/doc2/Eqs/rotate.jpg b/doc/doc2/Eqs/rotate.jpg
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--- /dev/null
+++ b/doc/doc2/Eqs/rotate.tex
@@ -0,0 +1,26 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mathbf{x}
+ &=&
+\begin{pmatrix}
+\mathbf{a} &
+\mathbf{b} &
+\mathbf{c}
+\end{pmatrix}
+\cdot
+ \frac{1}{V}
+ \begin{pmatrix}
+\mathbf{B \times C} \\
+\mathbf{C \times A} \\
+\mathbf{A \times B}
+\end{pmatrix}
+\cdot
+\mathbf{X}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/doc2/Eqs/stress_tensor.jpg b/doc/doc2/Eqs/stress_tensor.jpg
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new file mode 100644
index 000000000..f0d046ca2
--- /dev/null
+++ b/doc/doc2/Eqs/stress_tensor.tex
@@ -0,0 +1,20 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+S_{ab} & = & - \left[ m v_a v_b +
+ \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) +
+ \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \right. \\
+&& \left. \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
+ r_{3_a} F_{3_b}) +
+ \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
+ r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \right. \\
+&& \left. \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} +
+ r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) +
+ {\rm Kspace}(r_{i_a},F_{i_b}) +
+ \sum_{n = 1}^{N_f} r_{i_a} F_{i_b} \right]
+\end{eqnarray*}
+
+\end{document}
+
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--- /dev/null
+++ b/doc/doc2/Eqs/transform.tex
@@ -0,0 +1,27 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+\begin{pmatrix}
+\mathbf{a} &
+\mathbf{b} &
+\mathbf{c}
+\end{pmatrix}
+& = &
+\begin{pmatrix}
+a_x & b_x & c_x \\
+0 & b_y & c_y \\
+0 & 0 & c_z \\
+\end{pmatrix} \\
+a_x &=& A \\
+b_x &=& \mathbf{B} \cdot \mathbf{\hat{A}} \quad = \quad B \cos{\gamma} \\
+b_y &=& |\mathbf{\hat{A}} \times \mathbf{B}| \quad = \quad B \sin{\gamma} \quad = \quad \sqrt{B^2 - {b_x}^2} \\
+c_x &=& \mathbf{C} \cdot \mathbf{\hat{A}} \quad = \quad C \cos{\beta} \\
+c_y &=& \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\
+c_z &=& |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2} \\
+\end{eqnarray*}
+
+\end{document}
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diff --git a/doc/doc2/Manual.html b/doc/doc2/Manual.html
new file mode 100644
index 000000000..828cd51e0
--- /dev/null
+++ b/doc/doc2/Manual.html
@@ -0,0 +1,478 @@
+<HTML>
+<!-- HTML_ONLY -->
+<HEAD>
+<TITLE>LAMMPS Users Manual</TITLE>
+<META NAME="docnumber" CONTENT="27 Jul 2015 version">
+<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
+<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
+</HEAD>
+
+<BODY>
+
+<!-- END_HTML_ONLY -->
+
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H1></H1>
+
+<CENTER><H3>LAMMPS Documentation
+</H3></CENTER>
+<CENTER><H4>27 Jul 2015 version
+</H4></CENTER>
+<H4>Version info:
+</H4>
+<P>The LAMMPS "version" is the date when it was released, such as 1 May
+2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
+feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
+the WWW site</A>. Each dated copy of LAMMPS contains all the
+features and bug-fixes up to and including that version date. The
+version date is printed to the screen and logfile every time you run
+LAMMPS. It is also in the file src/version.h and in the LAMMPS
+directory name created when you unpack a tarball, and at the top of
+the first page of the manual (this page).
+</P>
+<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
+describe the most current version of LAMMPS.
+
+<LI>If you browse the HTML doc pages included in your tarball, they
+describe the version you have.
+
+<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
+about once per month. This is because it is large, and we don't want
+it to be part of every patch.
+
+<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
+directory, which describes the internal structure and algorithms of
+LAMMPS.
+</UL>
+<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator.
+</P>
+<P>LAMMPS is a classical molecular dynamics simulation code designed to
+run efficiently on parallel computers. It was developed at Sandia
+National Laboratories, a US Department of Energy facility, with
+funding from the DOE. It is an open-source code, distributed freely
+under the terms of the GNU Public License (GPL).
+</P>
+<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
+Thompson, and Paul Crozier who can be contacted at
+sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
+http://lammps.sandia.gov has more information about the code and its
+uses.
+</P>
+
+
+
+
+<HR>
+
+<P>The LAMMPS documentation is organized into the following sections. If
+you find errors or omissions in this manual or have suggestions for
+useful information to add, please send an email to the developers so
+we can improve the LAMMPS documentation.
+</P>
+<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
+page</A> at Section_commands.html#comm since
+it gives quick access to documentation for all LAMMPS commands.
+</P>
+<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
+<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
+</P>
+<P><!-- RST
+</P>
+<P>.. toctree::
+ :maxdepth: 2
+ :numbered: // comment
+</P>
+<P> Section_intro
+ Section_start
+ Section_commands
+ Section_packages
+ Section_accelerate
+ Section_howto
+ Section_example
+ Section_perf
+ Section_tools
+ Section_modify
+ Section_python
+ Section_errors
+ Section_history
+</P>
+<P>Indices and tables
+==================
+</P>
+<P>* :ref:`genindex` // comment
+* :ref:`search` // comment
+</P>
+<P>END_RST -->
+</P>
+<OL><LI><!-- HTML_ONLY -->
+<A HREF = "Section_intro.html">Introduction</A>
+
+<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
+<BR>
+ 1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
+<BR>
+ 1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
+<BR>
+ 1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
+<BR>
+ 1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
+<BR></UL>
+<LI><A HREF = "Section_start.html">Getting started</A>
+
+<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
+<BR>
+ 2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
+<BR>
+ 2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
+<BR>
+ 2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
+<BR>
+ 2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
+<BR>
+ 2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
+<BR>
+ 2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
+<BR>
+ 2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
+<BR>
+ 2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
+<BR></UL>
+<LI><A HREF = "Section_commands.html">Commands</A>
+
+<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
+<BR>
+ 3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
+<BR>
+ 3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
+<BR>
+ 3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
+<BR>
+ 3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
+<BR></UL>
+<LI><A HREF = "Section_packages.html">Packages</A>
+
+<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
+<BR>
+ 4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
+<BR></UL>
+<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
+
+<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
+<BR>
+ 5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
+<BR>
+ 5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
+<BR>
+<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
+<BR>
+ 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
+<BR>
+ 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
+<BR>
+ 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
+<BR>
+ 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
+<BR>
+ 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
+<BR></UL>
+ 5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
+<BR></UL>
+<LI><A HREF = "Section_howto.html">How-to discussions</A>
+
+<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
+<BR>
+ 6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
+<BR>
+ 6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
+<BR>
+ 6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
+<BR>
+ 6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
+<BR>
+ 6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
+<BR>
+ 6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
+<BR>
+ 6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
+<BR>
+ 6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
+<BR>
+ 6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
+<BR>
+ 6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
+<BR>
+ 6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
+<BR>
+ 6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
+<BR>
+ 6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
+<BR>
+ 6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
+<BR>
+ 6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
+<BR>
+ 6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
+<BR>
+ 6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
+<BR>
+ 6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
+<BR>
+ 6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
+<BR>
+ 6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
+<BR>
+ 6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
+<BR>
+ 6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
+<BR>
+ 6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
+<BR>
+ 6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
+<BR>
+ 6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
+<BR>
+ 6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
+<BR></UL>
+<LI><A HREF = "Section_example.html">Example problems</A>
+
+<LI><A HREF = "Section_perf.html">Performance & scalability</A>
+
+<LI><A HREF = "Section_tools.html">Additional tools</A>
+
+<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
+
+<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
+<BR>
+ 10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
+<BR>
+ 10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
+<BR>
+ 10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
+<BR>
+ 10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
+<BR>
+ 10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
+<BR>
+ 10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
+<BR>
+ 10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
+<BR>
+ 10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
+<BR>
+ 10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
+<BR>
+ 10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
+<BR>
+ 10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
+<BR>
+ 10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
+<BR>
+ 10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
+<BR>
+ 10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
+<BR></UL>
+<LI><A HREF = "Section_python.html">Python interface</A>
+
+<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
+<BR>
+ 11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
+<BR>
+ 11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
+<BR>
+ 11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
+<BR>
+ 11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
+<BR>
+ 11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
+<BR>
+ 11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
+<BR>
+ 11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
+<BR></UL>
+<LI><A HREF = "Section_errors.html">Errors</A>
+
+<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
+<BR>
+ 12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
+<BR>
+ 12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
+<BR></UL>
+<LI><A HREF = "Section_history.html">Future and history</A>
+
+<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
+<BR>
+ 13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
+<BR></UL>
+
+</OL>
+
+
+
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+
+</HTML>
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+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{center}
+
+\large{Additional documentation for the Gay-Berne ellipsoidal potential \\
+ as implemented in LAMMPS}
+
+\end{center}
+
+\centerline{Mike Brown, Sandia National Labs, April 2007}
+
+\vspace{0.3in}
+
+The Gay-Berne anisotropic LJ interaction between pairs of dissimilar
+ellipsoidal particles is given by
+
+$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
+\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
+\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
+\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
+
+where $\mathbf{A}_1$ and $\mathbf{A}_2$ are the transformation
+matrices from the simulation box frame to the body frame and
+$\mathbf{r}_{12}$ is the center to center vector between the
+particles. $U_r$ controls the shifted distance dependent interaction
+based on the distance of closest approach of the two particles
+($h_{12}$) and the user-specified shift parameter gamma:
+
+$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
+
+$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
+
+Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be
+given by the ellipsoid radii. The $\eta$ orientation-dependent energy
+based on the user-specified exponent $\upsilon$ is given by
+
+$$ \eta_{12} = [ \frac{ 2 s_1 s_2 }{\det ( \mathbf{G}_{12} )}]^{
+\upsilon / 2 } , $$
+
+$$ s_i = [a_i b_i + c_i c_i][a_i b_i]^{ 1 / 2 }, $$
+
+and
+
+$$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 = \mathbf{G}_1 +
+\mathbf{G}_2. $$
+
+Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
+(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by
+the relative well depths (dimensionless energy scales
+inversely proportional to the well-depths of the respective
+orthogonal configurations of the interacting molecules). The
+$\chi$ orientation-dependent energy based on the user-specified
+exponent $\mu$ is given by
+
+$$ \chi_{12} = [2 \hat{\mathbf{r}}_{12}^T \mathbf{B}_{12}^{-1}
+\hat{\mathbf{r}}_{12}]^\mu, $$
+
+$$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
+
+and
+
+$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
+\mathbf{B}_2. $$
+
+Here, we use the distance of closest approach approximation given by the
+Perram reference, namely
+
+$$ h_{12} = r - \sigma_{12} ( \mathbf{A}_1, \mathbf{A}_2,
+\mathbf{r}_{12} ), $$
+
+$$ r = |\mathbf{r}_{12}|, $$
+
+and
+
+$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}_{12}^T
+\mathbf{G}_{12}^{-1} \hat{\mathbf{r}}_{12}.]^{ -1/2 } $$
+
+Forces and Torques: Because the analytic forces and torques have not
+been published for this potential, we list them here:
+
+$$ \mathbf{f} = - \eta_{12} ( U_r \cdot { \frac{\partial \chi_{12}
+}{\partial r} } + \chi_{12} \cdot { \frac{\partial U_r }{\partial r} }
+) $$
+
+where the derivative of $U_r$ is given by (see Allen reference)
+
+$$ \frac{\partial U_r }{\partial r} = \frac{ \partial U_{SLJ} }{
+\partial r } \hat{\mathbf{r}}_{12} + r^{-2} \frac{ \partial U_{SLJ} }{
+\partial \varphi } [ \mathbf{\kappa} - ( \mathbf{\kappa}^T \cdot
+\hat{\mathbf{r}}_{12}) \hat{\mathbf{r}}_{12} ], $$
+
+$$ \frac{ \partial U_{SLJ} }{ \partial \varphi } = 24 \epsilon ( 2
+\varrho^{13} - \varrho^7 ) \sigma_{12}^3 / 2 \sigma, $$
+
+$$ \frac{ \partial U_{SLJ} }{ \partial r } = 24 \epsilon ( 2
+\varrho^{13} - \varrho^7 ) / \sigma, $$
+
+and
+
+$$ \mathbf{\kappa} = \mathbf{G}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
+
+The derivate of the $\chi$ term is given by
+
+$$ \frac{\partial \chi_{12} }{\partial r} = - r^{-2} \cdot 4.0 \cdot [
+\mathbf{\iota} - ( \mathbf{\iota}^T \cdot \hat{\mathbf{r}}_{12} )
+\hat{\mathbf{r}}_{12} ] \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu
+}, $$
+
+and
+
+$$ \mathbf{\iota} = \mathbf{B}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
+
+The torque is given by:
+
+$$ \mathbf{\tau}_i = U_r \eta_{12} \frac{ \partial \chi_{12} }{
+\partial \mathbf{q}_i } + \chi_{12} ( U_r \frac{ \partial \eta_{12} }{
+\partial \mathbf{q}_i } + \eta_{12} \frac{ \partial U_r }{ \partial
+\mathbf{q}_i } ), $$
+
+$$ \frac{ \partial U_r }{ \partial \mathbf{q}_i } = \mathbf{A}_i \cdot
+(- \mathbf{\kappa}^T \cdot \mathbf{G}_i \times \mathbf{f}_k ), $$
+
+$$ \mathbf{f}_k = - r^{-2} \frac{ \delta U_{SLJ} }{ \delta \varphi }
+\mathbf{\kappa}, $$
+
+and
+
+$$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
+r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
+\times \mathbf{\iota} ). $$
+
+For the derivative of the $\eta$ term, we were unable to find a matrix
+expression due to the determinant. Let $a_{mi}$ be the mth row of the
+rotation matrix $A_i$. Then,
+
+$$ \frac{ \partial \eta_{12} }{ \partial \mathbf{q}_i } = \mathbf{A}_i
+\cdot \sum_m \mathbf{a}_{mi} \times \frac{ \partial \eta_{12} }{
+\partial \mathbf{a}_{mi} } = \mathbf{A}_i \cdot \sum_m \mathbf{a}_{mi}
+\times \mathbf{d}_{mi}, $$
+
+where $d_mi$ represents the mth row of a derivative matrix $D_i$,
+
+$$ \mathbf{D}_i = - \frac{1}{2} \cdot ( \frac{2s1s2}{\det (
+\mathbf{G}_{12} ) } )^{ \upsilon / 2 } \cdot {\frac{\upsilon}{\det (
+\mathbf{G}_{12} ) }} \cdot \mathbf{E}, $$
+
+where the matrix $E$ gives the derivate with respect to the rotation
+matrix,
+
+$$ \mathbf{E} = [ e_{my} ] = \frac{ \partial \eta_{12} }{ \partial
+\mathbf{A}_i }, $$
+
+and
+
+$$ e_{my} = \det ( \mathbf{G}_{12} ) \cdot \mbox{trace} [
+\mathbf{G}_{12}^{-1} \cdot ( \hat{\mathbf{p}}_y \otimes \mathbf{a}_m +
+\mathbf{a}_m \otimes \hat{\mathbf{p}}_y ) \cdot s_{mm}^2 ]. $$
+
+Here, $p_v$ is the unit vector for the axes in the lab frame $(p1=[1, 0,
+0], p2=[0, 1, 0], and p3=[0, 0, 1])$ and $s_{mm}$ gives the mth radius of
+the ellipsoid $i$.
+
+\end{document}
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diff --git a/doc/doc2/PDF/pair_resquared_extra.pdf b/doc/doc2/PDF/pair_resquared_extra.pdf
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diff --git a/doc/doc2/PDF/pair_resquared_extra.tex b/doc/doc2/PDF/pair_resquared_extra.tex
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+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{center}
+
+\large{Additional documentation for the RE-squared ellipsoidal potential \\
+ as implemented in LAMMPS}
+
+\end{center}
+
+\centerline{Mike Brown, Sandia National Labs, October 2007}
+
+\vspace{0.3in}
+
+Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be
+given by the ellipsoid radii. Let the relative energy matrices
+$\mathbf{E}_i = \mbox{diag} (\epsilon_{ia}, \epsilon_{ib},
+\epsilon_{ic})$ be given by the relative well depths
+(dimensionless energy scales inversely proportional to the well-depths
+of the respective orthogonal configurations of the interacting molecules).
+Let $\mathbf{A}_1$ and $\mathbf{A}_2$ be the transformation matrices
+from the simulation box frame to the body frame and $\mathbf{r}$
+be the center to center vector between the particles. Let $A_{12}$ be
+the Hamaker constant for the interaction given in LJ units by
+$A_{12}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2$.
+
+\vspace{0.3in}
+
+The RE-squared anisotropic interaction between pairs of
+ellipsoidal particles is given by
+
+$$ U=U_A+U_R, $$
+
+$$ U_\alpha=\frac{A_{12}}{m_\alpha}(\frac\sigma{h})^{n_\alpha}
+(1+o_\alpha\eta\chi\frac\sigma{h}) \times \prod_i{
+\frac{a_ib_ic_i}{(a_i+h/p_\alpha)(b_i+h/p_\alpha)(c_i+h/p_\alpha)}}, $$
+
+$$ m_A=-36, n_A=0, o_A=3, p_A=2, $$
+
+$$ m_R=2025, n_R=6, o_R=45/56, p_R=60^{1/3}, $$
+
+$$ \chi = 2 \hat{\mathbf{r}}^T \mathbf{B}^{-1}
+\hat{\mathbf{r}}, $$
+
+$$ \hat{\mathbf{r}} = { \mathbf{r} } / |\mathbf{r}|, $$
+
+$$ \mathbf{B} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 $$
+
+$$ \eta = \frac{ \det[\mathbf{S}_1]/\sigma_1^2+
+det[\mathbf{S}_2]/\sigma_2^2}{[\det[\mathbf{H}]/
+(\sigma_1+\sigma_2)]^{1/2}}, $$
+
+$$ \sigma_i = (\hat{\mathbf{r}}^T\mathbf{A}_i^T\mathbf{S}_i^{-2}
+\mathbf{A}_i\hat{\mathbf{r}})^{-1/2}, $$
+
+$$ \mathbf{H} = \frac{1}{\sigma_1}\mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\frac{1}{\sigma_2}\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
+
+
+Here, we use the distance of closest approach approximation given by the
+Perram reference, namely
+
+$$ h = |r| - \sigma_{12}, $$
+
+$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}^T
+\mathbf{G}^{-1} \hat{\mathbf{r}}]^{ -1/2 }, $$
+
+and
+
+$$ \mathbf{G} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
+
+\vspace{0.3in}
+
+The RE-squared anisotropic interaction between a
+ellipsoidal particle and a Lennard-Jones sphere is defined
+as the $\lim_{a_2->0}U$ under the constraints that
+$a_2=b_2=c_2$ and $\frac{4}{3}\pi a_2^3\rho=1$:
+
+$$ U_{\mathrm{elj}}=U_{A_{\mathrm{elj}}}+U_{R_{\mathrm{elj}}}, $$
+
+$$ U_{\alpha_{\mathrm{elj}}}=(\frac{3\sigma^3c_\alpha^3}
+{4\pi h_{\mathrm{elj}}^3})\frac{A_{12_{\mathrm{elj}}}}
+{m_\alpha}(\frac\sigma{h_{\mathrm{elj}}})^{n_\alpha}
+(1+o_\alpha\chi_{\mathrm{elj}}\frac\sigma{h_{\mathrm{elj}}}) \times
+\frac{a_1b_1c_1}{(a_1+h_{\mathrm{elj}}/p_\alpha)
+(b_1+h_{\mathrm{elj}}/p_\alpha)(c_1+h_{\mathrm{elj}}/p_\alpha)}, $$
+
+$$ A_{12_{\mathrm{elj}}}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3), $$
+
+with $h_{\mathrm{elj}}$ and $\chi_{\mathrm{elj}}$ calculated as above
+by replacing $B$ with $B_{\mathrm{elj}}$ and $G$ with $G_{\mathrm{elj}}$:
+
+$$ \mathbf{B}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + I, $$
+
+$$ \mathbf{G}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1.$$
+
+\vspace{0.3in}
+
+The interaction between two LJ spheres is calculated as:
+
+$$
+ U_{\mathrm{lj}} = 4 \epsilon \left[ \left(\frac{\sigma}{|\mathbf{r}|}\right)^{12} -
+ \left(\frac{\sigma}{|\mathbf{r}|}\right)^6 \right]
+$$
+
+\vspace{0.3in}
+
+The analytic derivatives are used for all force and torque calculation.
+
+\end{document}
diff --git a/doc/doc2/Scripts/correlate.py b/doc/doc2/Scripts/correlate.py
new file mode 100644
index 000000000..5a0aaaf2c
--- /dev/null
+++ b/doc/doc2/Scripts/correlate.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+"""
+ function:
+ parse the block of thermo data in a lammps logfile and perform auto- and
+ cross correlation of the specified column data. The total sum of the
+ correlation is also computed which can be converted to an integral by
+ multiplying by the timestep.
+ output:
+ standard output contains column data for the auto- & cross correlations
+ plus the total sum of each. Note, only the upper triangle of the
+ correlation matrix is computed.
+ usage:
+ correlate.py [-c col] <-c col2> <-s max_correlation_time> [logfile]
+"""
+import sys
+import re
+import array
+
+# parse command line
+
+maxCorrelationTime = 0
+cols = array.array("I")
+nCols = 0
+args = sys.argv[1:]
+index = 0
+while index < len(args):
+ arg = args[index]
+ index += 1
+ if (arg == "-c"):
+ cols.append(int(args[index])-1)
+ nCols += 1
+ index += 1
+ elif (arg == "-s"):
+ maxCorrelationTime = int(args[index])
+ index += 1
+ else :
+ filename = arg
+if (nCols < 1): raise RuntimeError, 'no data columns requested'
+data = [array.array("d")]
+for s in range(1,nCols) : data.append( array.array("d") )
+
+# read data block from log file
+
+start = False
+input = open(filename)
+nSamples = 0
+pattern = re.compile('\d')
+line = input.readline()
+while line :
+ columns = line.split()
+ if (columns and pattern.match(columns[0])) :
+ for i in range(nCols):
+ data[i].append( float(columns[cols[i]]) )
+ nSamples += 1
+ start = True
+ else :
+ if (start) : break
+ line = input.readline()
+print "# read :",nSamples," samples of ", nCols," data"
+if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
+
+# correlate and integrate
+
+correlationPairs = []
+for i in range(0,nCols):
+ for j in range(i,nCols): # note only upper triangle of the correlation matrix
+ correlationPairs.append([i,j])
+header = "# "
+for k in range(len(correlationPairs)):
+ i = str(correlationPairs[k][0]+1)
+ j = str(correlationPairs[k][1]+1)
+ header += " C"+i+j+" sum_C"+i+j
+print header
+nCorrelationPairs = len(correlationPairs)
+sum = [0.0] * nCorrelationPairs
+for s in range(maxCorrelationTime) :
+ correlation = [0.0] * nCorrelationPairs
+ nt = nSamples-s
+ for t in range(0,nt) :
+ for p in range(nCorrelationPairs):
+ i = correlationPairs[p][0]
+ j = correlationPairs[p][1]
+ correlation[p] += data[i][t]*data[j][s+t]
+ output = ""
+ for p in range(0,nCorrelationPairs):
+ correlation[p] /= nt
+ sum[p] += correlation[p]
+ output += str(correlation[p]) + " " + str(sum[p]) + " "
+ print output
diff --git a/doc/doc2/Section_accelerate.html b/doc/doc2/Section_accelerate.html
new file mode 100644
index 000000000..7a5b054aa
--- /dev/null
+++ b/doc/doc2/Section_accelerate.html
@@ -0,0 +1,401 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>5. Accelerating LAMMPS performance
+</H3>
+<P>This section describes various methods for improving LAMMPS
+performance for different classes of problems running on different
+kinds of machines.
+</P>
+<P>There are two thrusts to the discussion that follows. The
+first is using code options that implement alternate algorithms
+that can speed-up a simulation. The second is to use one
+of the several accelerator packages provided with LAMMPS that
+contain code optimized for certain kinds of hardware, including
+multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
+</P>
+<UL><LI>5.1 <A HREF = "#acc_1">Measuring performance</A>
+
+<LI>5.2 <A HREF = "#acc_2">Algorithms and code options to boost performace</A>
+
+<LI>5.3 <A HREF = "#acc_3">Accelerator packages with optimized styles</A>
+
+<UL><LI> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
+
+<LI> 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
+
+<LI> 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
+
+<LI> 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
+
+<LI> 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
+
+<LI> 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
+</UL>
+<LI>5.4 <A HREF = "#acc_4">Comparison of various accelerator packages</A>
+</UL>
+<P>The <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the LAMMPS
+web site gives performance results for the various accelerator
+packages discussed in Section 5.2, for several of the standard LAMMPS
+benchmark problems, as a function of problem size and number of
+compute nodes, on different hardware platforms.
+</P>
+<HR>
+
+<HR>
+
+<H4><A NAME = "acc_1"></A>5.1 Measuring performance
+</H4>
+<P>Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.
+</P>
+<P>The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run. There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.
+</P>
+<P>For the set of runs, look at the timing data printed to the screen and
+log file at the end of each LAMMPS run. <A HREF = "Section_start.html#start_8">This
+section</A> of the manual has an overview.
+</P>
+<P>Running on one (or a few processors) should give a good estimate of
+the serial performance and what portions of the timestep are taking
+the most time. Running the same problem on a few different processor
+counts should give an estimate of parallel scalability. I.e. if the
+simulation runs 16x faster on 16 processors, its 100% parallel
+efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
+</P>
+<P>The most important data to look at in the timing info is the timing
+breakdown and relative percentages. For example, trying different
+options for speeding up the long-range solvers will have little impact
+if they only consume 10% of the run time. If the pairwise time is
+dominating, you may want to look at GPU or OMP versions of the pair
+style, as discussed below. Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling. Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time. For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.
+</P>
+<P>Another important detail in the timing info are the histograms of
+atoms counts and neighbor counts. If these vary widely across
+processors, you have a load-imbalance issue. This often results in
+inaccurate relative timing data, because processors have to wait when
+communication occurs for other processors to catch up. Thus the
+reported times for "Communication" or "Other" may be higher than they
+really are, due to load-imbalance. If this is an issue, you can
+uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+LAMMPS, to obtain synchronized timings.
+</P>
+<HR>
+
+<H4><A NAME = "acc_2"></A>5.2 General strategies
+</H4>
+<P>NOTE: this section 5.2 is still a work in progress
+</P>
+<P>Here is a list of general ideas for improving simulation performance.
+Most of them are only applicable to certain models and certain
+bottlenecks in the current performance, so let the timing data you
+generate be your guide. It is hard, if not impossible, to predict how
+much difference these options will make, since it is a function of
+problem size, number of processors used, and your machine. There is
+no substitute for identifying performance bottlenecks, and trying out
+various options.
+</P>
+<UL><LI>rRESPA
+<LI>2-FFT PPPM
+<LI>Staggered PPPM
+<LI>single vs double PPPM
+<LI>partial charge PPPM
+<LI>verlet/split run style
+<LI>processor command for proc layout and numa layout
+<LI>load-balancing: balance and fix balance
+</UL>
+<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
+2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
+PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
+achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
+cost is the performance bottleneck (typically large problems running
+on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
+</P>
+<P>Staggered PPPM performs calculations using two different meshes, one
+shifted slightly with respect to the other. This can reduce force
+aliasing errors and increase the accuracy of the method, but also
+doubles the amount of work required. For high relative accuracy, using
+staggered PPPM allows one to half the mesh size in each dimension as
+compared to regular PPPM, which can give around a 4x speedup in the
+kspace time. However, for low relative accuracy, using staggered PPPM
+gives little benefit and can be up to 2x slower in the kspace
+time. For example, the rhodopsin benchmark was run on a single
+processor, and results for kspace time vs. relative accuracy for the
+different methods are shown in the figure below. For this system,
+staggered PPPM (using ik differentiation) becomes useful when using a
+relative accuracy of slightly greater than 1e-5 and above.
+</P>
+<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
+</CENTER>
+<P>IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
+accuracy of energy and pressure as it does in forces, so some caution
+must be used if energy and/or pressure are quantities of interest,
+such as when using a barostat.
+</P>
+<HR>
+
+<H4><A NAME = "acc_3"></A>5.3 Packages with optimized styles
+</H4>
+<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
+<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
+been added to LAMMPS, which will typically run faster than the
+standard non-accelerated versions. Some require appropriate hardware
+to be present on your system, e.g. GPUs or Intel Xeon Phi
+coprocessors.
+</P>
+<P>All of these commands are in packages provided with LAMMPS. An
+overview of packages is give in <A HREF = "Section_packages.html">Section
+packages</A>. These are the accelerator packages
+currently in LAMMPS, either as standard or user packages:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><A HREF = "accelerate_cuda.html">USER-CUDA</A> </TD><TD > for NVIDIA GPUs</TD></TR>
+<TR><TD ><A HREF = "accelerate_gpu.html">GPU</A> </TD><TD > for NVIDIA GPUs as well as OpenCL support</TD></TR>
+<TR><TD ><A HREF = "accelerate_intel.html">USER-INTEL</A> </TD><TD > for Intel CPUs and Intel Xeon Phi</TD></TR>
+<TR><TD ><A HREF = "accelerate_kokkos.html">KOKKOS</A> </TD><TD > for GPUs, Intel Xeon Phi, and OpenMP threading</TD></TR>
+<TR><TD ><A HREF = "accelerate_omp.html">USER-OMP</A> </TD><TD > for OpenMP threading</TD></TR>
+<TR><TD ><A HREF = "accelerate_opt.html">OPT</A> </TD><TD > generic CPU optimizations
+</TD></TR></TABLE></DIV>
+
+<P>Any accelerated style has the same name as the corresponding standard
+style, except that a suffix is appended. Otherwise, the syntax for
+the command that uses the style is identical, their functionality is
+the same, and the numerical results it produces should also be the
+same, except for precision and round-off effects.
+</P>
+<P>For example, all of these styles are accelerated variants of the
+Lennard-Jones <A HREF = "pair_lj.html">pair_style lj/cut</A>:
+</P>
+<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/intel</A>
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/kk</A>
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/omp</A>
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A>
+</UL>
+<P>To see what accelerate styles are currently available, see
+<A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the manual. The
+doc pages for individual commands (e.g. <A HREF = "pair_lj.html">pair lj/cut</A> or
+<A HREF = "fix_nve.html">fix nve</A>) also list any accelerated variants available
+for that style.
+</P>
+<P>To use an accelerator package in LAMMPS, and one or more of the styles
+it provides, follow these general steps. Details vary from package to
+package and are explained in the individual accelerator doc pages,
+listed above:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >build the accelerator library </TD><TD > only for USER-CUDA and GPU packages </TD></TR>
+<TR><TD >install the accelerator package </TD><TD > make yes-opt, make yes-user-intel, etc </TD></TR>
+<TR><TD >add compile/link flags to Makefile.machine </TD><TD > in src/MAKE, <br> only for USER-INTEL, KOKKOS, USER-OMP packages </TD></TR>
+<TR><TD >re-build LAMMPS </TD><TD > make machine </TD></TR>
+<TR><TD >run a LAMMPS simulation </TD><TD > lmp_machine < in.script </TD></TR>
+<TR><TD >enable the accelerator package </TD><TD > via "-c on" and "-k on" <A HREF = "Section_start.html#start_7">command-line switches</A>, <br> only for USER-CUDA and KOKKOS packages </TD></TR>
+<TR><TD >set any needed options for the package </TD><TD > via "-pk" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "package.html">package</A> command, <br> only if defaults need to be changed </TD></TR>
+<TR><TD >use accelerated styles in your input script </TD><TD > via "-sf" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "suffix.html">suffix</A> command
+</TD></TR></TABLE></DIV>
+
+<P>The first 4 steps can be done as a single command, using the
+src/Make.py tool. The Make.py tool is discussed in <A HREF = "Section_start.html#start_4">Section
+2.4</A> of the manual, and its use is
+illustrated in the individual accelerator sections. Typically these
+steps only need to be done once, to create an executable that uses one
+or more accelerator packages.
+</P>
+<P>The last 4 steps can all be done from the command-line when LAMMPS is
+launched, without changing your input script, as illustrated in the
+individual accelerator sections. Or you can add
+<A HREF = "package.html">package</A> and <A HREF = "suffix.html">suffix</A> commands to your input
+script.
+</P>
+<P>IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
+executable with all its accelerator packages installed. Note that the
+USER-INTEL and KOKKOS packages require you to choose one of their
+options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
+or Phi for KOKKOS. Here are the exceptions; you cannot build a single
+executable with:
+</P>
+<UL><LI>both the USER-INTEL Phi and KOKKOS Phi options
+<LI>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages
+</UL>
+<P>See the examples/accelerate/README and make.list files for sample
+Make.py commands that build LAMMPS with any or all of the accelerator
+packages. As an example, here is a command that builds with all the
+GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
+including settings to build the needed auxiliary USER-CUDA and GPU
+libraries for Kepler GPUs:
+</P>
+<PRE>Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 \ -kokkos cuda arch=35 lib-all file mpi
+</PRE>
+<P>The examples/accelerate directory also has input scripts that can be
+used with all of the accelerator packages. See its README file for
+details.
+</P>
+<P>Likewise, the bench directory has FERMI and KEPLER and PHI
+sub-directories with Make.py commands and input scripts for using all
+the accelerator packages on various machines. See the README files in
+those dirs.
+</P>
+<P>As mentioned above, the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark
+page</A> of the LAMMPS web site gives
+performance results for the various accelerator packages for several
+of the standard LAMMPS benchmark problems, as a function of problem
+size and number of compute nodes, on different hardware platforms.
+</P>
+<P>Here is a brief summary of what the various packages provide. Details
+are in the individual accelerator sections.
+</P>
+<UL><LI>Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
+packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
+depends on a variety of factors, discussed in the accelerator
+sections.
+
+<LI>Styles with an "intel" suffix are part of the USER-INTEL
+package. These styles support vectorized single and mixed precision
+calculations, in addition to full double precision. In extreme cases,
+this can provide speedups over 3.5x on CPUs. The package also
+supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
+coprocessors. This can result in additional speedup over 2x depending
+on the hardware configuration.
+
+<LI>Styles with a "kk" suffix are part of the KOKKOS package, and can be
+run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
+Xeon Phi in "native" mode. The speed-up depends on a variety of
+factors, as discussed on the KOKKOS accelerator page.
+
+<LI>Styles with an "omp" suffix are part of the USER-OMP package and allow
+a pair-style to be run in multi-threaded mode using OpenMP. This can
+be useful on nodes with high-core counts when using less MPI processes
+than cores is advantageous, e.g. when running with PPPM so that FFTs
+are run on fewer MPI processors or when the many MPI tasks would
+overload the available bandwidth for communication.
+
+<LI>Styles with an "opt" suffix are part of the OPT package and typically
+speed-up the pairwise calculations of your simulation by 5-25% on a
+CPU.
+</UL>
+<P>The individual accelerator package doc pages explain:
+</P>
+<UL><LI>what hardware and software the accelerated package requires
+<LI>how to build LAMMPS with the accelerated package
+<LI>how to run with the accelerated package either via command-line switches or modifying the input script
+<LI>speed-ups to expect
+<LI>guidelines for best performance
+<LI>restrictions
+</UL>
+<HR>
+
+<H4><A NAME = "acc_4"></A>5.4 Comparison of various accelerator packages
+</H4>
+<P>NOTE: this section still needs to be re-worked with additional KOKKOS
+and USER-INTEL information.
+</P>
+<P>The next section compares and contrasts the various accelerator
+options, since there are multiple ways to perform OpenMP threading,
+run on GPUs, and run on Intel Xeon Phi coprocessors.
+</P>
+<P>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
+hardware, but they do it in different ways.
+</P>
+<P>As a consequence, for a particular simulation on specific hardware,
+one package may be faster than the other. We give guidelines below,
+but the best way to determine which package is faster for your input
+script is to try both of them on your machine. See the benchmarking
+section below for examples where this has been done.
+</P>
+<P><B>Guidelines for using each package optimally:</B>
+</P>
+<UL><LI>The GPU package allows you to assign multiple CPUs (cores) to a single
+GPU (a common configuration for "hybrid" nodes that contain multicore
+CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
+package does not allow this; you can only use one CPU per GPU.
+
+<LI>The GPU package moves per-atom data (coordinates, forces)
+back-and-forth between the CPU and GPU every timestep. The USER-CUDA
+package only does this on timesteps when a CPU calculation is required
+(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
+can formulate your input script to only use GPU-ized fixes and
+computes, and avoid doing I/O too often (thermo output, dump file
+snapshots, restart files), then the data transfer cost of the
+USER-CUDA package can be very low, causing it to run faster than the
+GPU package.
+
+<LI>The GPU package is often faster than the USER-CUDA package, if the
+number of atoms per GPU is "small". The crossover point, in terms of
+atoms/GPU at which the USER-CUDA package becomes faster depends
+strongly on the pair style. For example, for a simple Lennard Jones
+system the crossover (in single precision) is often about 50K-100K
+atoms per GPU. When performing double precision calculations the
+crossover point can be significantly smaller.
+
+<LI>Both packages compute bonded interactions (bonds, angles, etc) on the
+CPU. This means a model with bonds will force the USER-CUDA package
+to transfer per-atom data back-and-forth between the CPU and GPU every
+timestep. If the GPU package is running with several MPI processes
+assigned to one GPU, the cost of computing the bonded interactions is
+spread across more CPUs and hence the GPU package can run faster.
+
+<LI>When using the GPU package with multiple CPUs assigned to one GPU, its
+performance depends to some extent on high bandwidth between the CPUs
+and the GPU. Hence its performance is affected if full 16 PCIe lanes
+are not available for each GPU. In HPC environments this can be the
+case if S2050/70 servers are used, where two devices generally share
+one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
+full 16 lanes to each of the PCIe 2.0 16x slots.
+</UL>
+<P><B>Differences between the two packages:</B>
+</P>
+<UL><LI>The GPU package accelerates only pair force, neighbor list, and PPPM
+calculations. The USER-CUDA package currently supports a wider range
+of pair styles and can also accelerate many fix styles and some
+compute styles, as well as neighbor list and PPPM calculations.
+
+<LI>The USER-CUDA package does not support acceleration for minimization.
+
+<LI>The USER-CUDA package does not support hybrid pair styles.
+
+<LI>The USER-CUDA package can order atoms in the neighbor list differently
+from run to run resulting in a different order for force accumulation.
+
+<LI>The USER-CUDA package has a limit on the number of atom types that can be
+used in a simulation.
+
+<LI>The GPU package requires neighbor lists to be built on the CPU when using
+exclusion lists or a triclinic simulation box.
+
+<LI>The GPU package uses more GPU memory than the USER-CUDA package. This
+is generally not a problem since typical runs are computation-limited
+rather than memory-limited.
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>The LAMMPS distribution has two directories with sample input scripts
+for the GPU and USER-CUDA packages.
+</P>
+<UL><LI>lammps/examples/gpu = GPU package files
+<LI>lammps/examples/USER/cuda = USER-CUDA package files
+</UL>
+<P>These contain input scripts for identical systems, so they can be used
+to benchmark the performance of both packages on your system.
+</P>
+</HTML>
diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html
new file mode 100644
index 000000000..ea033b22d
--- /dev/null
+++ b/doc/doc2/Section_commands.html
@@ -0,0 +1,661 @@
+<HTML>
+<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>3. Commands
+</H3>
+<P>This section describes how a LAMMPS input script is formatted and the
+input script commands used to define a LAMMPS simulation.
+</P>
+3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
+3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
+3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
+3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
+3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
+
+<HR>
+
+<HR>
+
+<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
+</H4>
+<P>LAMMPS executes by reading commands from a input script (text file),
+one line at a time. When the input script ends, LAMMPS exits. Each
+command causes LAMMPS to take some action. It may set an internal
+variable, read in a file, or run a simulation. Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+</P>
+<P>In many cases, the ordering of commands in an input script is not
+important. However the following rules apply:
+</P>
+<P>(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings. Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+</P>
+<PRE>timestep 0.5
+run 100
+run 100
+</PRE>
+<P>does something different than this sequence:
+</P>
+<PRE>run 100
+timestep 0.5
+run 100
+</PRE>
+<P>In the first case, the specified timestep (0.5 fmsec) is used for two
+simulations of 100 timesteps each. In the 2nd case, the default
+timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
+fmsec timestep is used for the 2nd one.
+</P>
+<P>(2) Some commands are only valid when they follow other commands. For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+</P>
+<P>(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect. For example, the
+<A HREF = "read_data.html">read_data</A> command initializes the system by setting
+up the simulation box and assigning atoms to processors. If default
+values are not desired, the <A HREF = "processors.html">processors</A> and
+<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+</P>
+<P>Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
+more information on what errors mean. The documentation for each
+command lists restrictions on how the command can be used.
+</P>
+<HR>
+
+<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
+</H4>
+<P>Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive. Command names are lower-case, as
+are specified command arguments. Upper case letters may be used in
+file names or user-chosen ID strings.
+</P>
+<P>Here is how each line in the input script is parsed by LAMMPS:
+</P>
+<P>(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line. The next line is
+concatenated to the previous line by removing the "&" character and
+line break. This allows long commands to be continued across two or
+more lines. See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+</P>
+<P>(2) All characters from the first "#" character onward are treated as
+comment and discarded. See an exception in (6). Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line. Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+</P>
+<P>(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string. See an exception in
+(6).
+</P>
+<P>If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets. If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
+"x".
+</P>
+<P>How the variable is converted to a text string depends on what style
+of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them. The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command. The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+</P>
+<P>As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an <A HREF = "variable.html">equal-style variable</A>. This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names. For example, these 3 input script lines:
+</P>
+<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete
+</PRE>
+<P>can be replaced by
+</P>
+<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+</PRE>
+<P>so that you do not have to define (or discard) a temporary variable X.
+</P>
+<P>Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+</P>
+<PRE>variable a equal 2
+variable b2 equal 4
+print "B2 = ${b$a}"
+</PRE>
+<P>Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+<A HREF = "variable.html">equal-style variable</A>.
+</P>
+<P>See the <A HREF = "variable.html">variable</A> command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+</P>
+<P>(4) The line is broken into "words" separated by whitespace (tabs,
+spaces). Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+</P>
+<P>(5) The first word is the command name. All successive words in the
+line are arguments.
+</P>
+<P>(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes. A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above. When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line. If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed. For example:
+</P>
+<PRE>print "Volume = $v"
+print 'Volume = $v'
+if "$<I>steps</I> > 1000" then quit
+variable a string "red green blue &
+ purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+"""
+</PRE>
+<P>In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+</P>
+<P>See the <A HREF = "dump_modify.html">dump modify format</A>, <A HREF = "print.html">print</A>,
+<A HREF = "if.html">if</A>, and <A HREF = "python.html">python</A> commands for examples.
+</P>
+<P>A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+</P>
+<P>IMPORTANT NOTE: If the argument is itself a command that requires a
+quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
+<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then single, double, or
+triple quotes can be nested in the usual manner. See the doc pages
+for those commands for examples. Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+</P>
+<HR>
+
+<H4><A NAME = "cmd_3"></A>3.3 Input script structure
+</H4>
+<P>This section describes the structure of a typical LAMMPS input script.
+The "examples" directory in the LAMMPS distribution contains many
+sample input scripts; the corresponding problems are discussed in
+<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
+WWW Site</A>.
+</P>
+<P>A LAMMPS input script typically has 4 parts:
+</P>
+<OL><LI>Initialization
+<LI>Atom definition
+<LI>Settings
+<LI>Run a simulation
+</OL>
+<P>The last 2 parts can be repeated as many times as desired. I.e. run a
+simulation, change some settings, run some more, etc. Each of the 4
+parts is now described in more detail. Remember that almost all the
+commands need only be used if a non-default value is desired.
+</P>
+<P>(1) Initialization
+</P>
+<P>Set parameters that need to be defined before atoms are created or
+read-in from a file.
+</P>
+<P>The relevant commands are <A HREF = "units.html">units</A>,
+<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
+<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
+<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
+</P>
+<P>If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
+<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
+<A HREF = "improper_style.html">improper_style</A>.
+</P>
+<P>(2) Atom definition
+</P>
+<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
+or restart file via the <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
+molecular topology information. Or create atoms on a lattice (with no
+molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
+<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
+<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
+duplicated to make a larger simulation using the
+<A HREF = "replicate.html">replicate</A> command.
+</P>
+<P>(3) Settings
+</P>
+<P>Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+</P>
+<P>Force field coefficients are set by these commands (they can also be
+set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
+<A HREF = "improper_coeff.html">improper_coeff</A>,
+<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
+<A HREF = "special_bonds.html">special_bonds</A>.
+</P>
+<P>Various simulation parameters are set by these commands:
+<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
+<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
+<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
+<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
+</P>
+<P>Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
+</P>
+<P>Various computations can be specified for execution during a
+simulation using the <A HREF = "compute.html">compute</A>,
+<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
+commands.
+</P>
+<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
+and <A HREF = "restart.html">restart</A> commands.
+</P>
+<P>(4) Run a simulation
+</P>
+<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
+command. Energy minimization (molecular statics) is performed using
+the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
+(replica-exchange) simulation can be run using the
+<A HREF = "temper.html">temper</A> command.
+</P>
+<HR>
+
+<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
+</H4>
+<P>This section lists all LAMMPS commands, grouped by category. The
+<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
+that some style options for some commands are part of specific LAMMPS
+packages, which means they cannot be used unless the package was
+included when LAMMPS was built. Not all packages are included in a
+default LAMMPS build. These dependencies are listed as Restrictions
+in the command's documentation.
+</P>
+<P>Initialization:
+</P>
+<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
+<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
+<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
+</P>
+<P>Atom definition:
+</P>
+<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
+<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
+<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
+</P>
+<P>Force fields:
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
+<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
+<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
+<A HREF = "dihedral_style.html">dihedral_style</A>,
+<A HREF = "improper_coeff.html">improper_coeff</A>,
+<A HREF = "improper_style.html">improper_style</A>,
+<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
+<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
+<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
+<A HREF = "special_bonds.html">special_bonds</A>
+</P>
+<P>Settings:
+</P>
+<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
+<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
+<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
+<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
+<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
+</P>
+<P>Fixes:
+</P>
+<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
+</P>
+<P>Computes:
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
+<A HREF = "uncompute.html">uncompute</A>
+</P>
+<P>Output:
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
+<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
+<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
+<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
+<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
+<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
+</P>
+<P>Actions:
+</P>
+<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
+<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
+<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
+<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
+</P>
+<P>Miscellaneous:
+</P>
+<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
+<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
+<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
+<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
+</P>
+<HR>
+
+<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
+</H4>
+<P>This section lists all LAMMPS commands alphabetically, with a separate
+listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
+section</A> lists the same commands, grouped by category. Note
+that some style options for some commands are part of specific LAMMPS
+packages, which means they cannot be used unless the package was
+included when LAMMPS was built. Not all packages are included in a
+default LAMMPS build. These dependencies are listed as Restrictions
+in the command's documentation.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "comm_modify.html">comm_modify</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "comm_style.html">comm_style</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_bonds.html">create_bonds</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "info.html">info</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "python.html">python</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional commands in USER packages, which can be used if
+<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Fix styles
+</H4>
+<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions of each style
+or click on the style itself for a full description. Some of the
+styles have accelerated versions, which can be used if LAMMPS is built
+with the <A HREF = "Section_accelerate.html">appropriate accelerated package</A>.
+This is indicated by additional letters in parenthesis: c = USER-CUDA,
+g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce (c)</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_atom_swap.html">atom/swap</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce (c)</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_chunk.html">ave/chunk</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo/weight</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d (c)</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze (c)</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity (co)</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin (k)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (o)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (co)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (co)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_qeq.html">qeq/dynamic</A></TD><TD ><A HREF = "fix_qeq.html">qeq/point</A></TD><TD ><A HREF = "fix_qeq.html">qeq/shielded</A></TD><TD ><A HREF = "fix_qeq.html">qeq/slater</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csld</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_tfmc.html">tfmc</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional fix styles in USER packages, which can be used if
+<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Compute styles
+</H4>
+<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
+each style or click on the style itself for a full description. Some
+of the styles have accelerated versions, which can be used if LAMMPS
+is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_angmom_chunk.html">angmom/chunk</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_chunk_atom.html">chunk/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional compute styles in USER packages, which can be
+used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Pair_style potentials
+</H4>
+<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
+potentials. Click on the style itself for a full description. Many
+of the styles have accelerated versions, which can be used if LAMMPS
+is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cs</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cs</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (gko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/cs</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/streitz</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (ko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgkot)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy (cgkot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgkot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgiko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (cko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (cko)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (o)</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional pair styles in USER packages, which can be used
+if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd (o)</A></TD><TD ><A HREF = "pair_edip.html">edip (o)</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (gko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Bond_style potentials
+</H4>
+<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
+potentials. Click on the style itself for a full description. Some
+of the styles have accelerated versions, which can be used if LAMMPS
+is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "bond_none.html">none</A></TD><TD ><A HREF = "bond_hybrid.html">hybrid</A></TD><TD ><A HREF = "bond_class2.html">class2 (o)</A></TD><TD ><A HREF = "bond_fene.html">fene (ko)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "bond_fene_expand.html">fene/expand (o)</A></TD><TD ><A HREF = "bond_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "bond_morse.html">morse (o)</A></TD><TD ><A HREF = "bond_nonlinear.html">nonlinear (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "bond_quartic.html">quartic (o)</A></TD><TD ><A HREF = "bond_table.html">table (o)</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional bond styles in USER packages, which can be used
+if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift (o)</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut (o)</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Angle_style potentials
+</H4>
+<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
+angle potentials. Click on the style itself for a full description.
+Some of the styles have accelerated versions, which can be used if
+LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "angle_none.html">none</A></TD><TD ><A HREF = "angle_hybrid.html">hybrid</A></TD><TD ><A HREF = "angle_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "angle_class2.html">class2 (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "angle_cosine.html">cosine (o)</A></TD><TD ><A HREF = "angle_cosine_delta.html">cosine/delta (o)</A></TD><TD ><A HREF = "angle_cosine_periodic.html">cosine/periodic (o)</A></TD><TD ><A HREF = "angle_cosine_squared.html">cosine/squared (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "angle_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "angle_table.html">table (o)</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional angle styles in USER packages, which can be used
+if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "angle_cosine_shift.html">cosine/shift (o)</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "angle_dipole.html">dipole (o)</A></TD><TD ><A HREF = "angle_fourier.html">fourier (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "angle_fourier_simple.html">fourier/simple (o)</A></TD><TD ><A HREF = "angle_quartic.html">quartic (o)</A></TD><TD ><A HREF = "angle_sdk.html">sdk</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Dihedral_style potentials
+</H4>
+<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
+of dihedral potentials. Click on the style itself for a full
+description. Some of the styles have accelerated versions, which can
+be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "dihedral_none.html">none</A></TD><TD ><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD ><A HREF = "dihedral_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "dihedral_class2.html">class2 (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "dihedral_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "dihedral_helix.html">helix (o)</A></TD><TD ><A HREF = "dihedral_multi_harmonic.html">multi/harmonic (o)</A></TD><TD ><A HREF = "dihedral_opls.html">opls (ko)</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional dihedral styles in USER packages, which can be
+used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier (o)</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic (o)</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table (o)</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Improper_style potentials
+</H4>
+<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
+of improper potentials. Click on the style itself for a full
+description. Some of the styles have accelerated versions, which can
+be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "improper_none.html">none</A></TD><TD ><A HREF = "improper_hybrid.html">hybrid</A></TD><TD ><A HREF = "improper_class2.html">class2 (o)</A></TD><TD ><A HREF = "improper_cvff.html">cvff (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "improper_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "improper_umbrella.html">umbrella (o)</A>
+</TD></TR></TABLE></DIV>
+
+<P>These are additional improper styles in USER packages, which can be
+used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
+package</A>.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq (o)</A></TD><TD ><A HREF = "improper_fourier.html">fourier (o)</A></TD><TD ><A HREF = "improper_ring.html">ring (o)</A>
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<H4>Kspace solvers
+</H4>
+<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
+Kspace solvers. Click on the style itself for a full description.
+Some of the styles have accelerated versions, which can be used if
+LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
+package</A>. This is indicated by additional
+letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald (o)</A></TD><TD ><A HREF = "kspace_style.html">ewald/disp</A></TD><TD ><A HREF = "kspace_style.html">msm (o)</A></TD><TD ><A HREF = "kspace_style.html">msm/cg (o)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm (cgo)</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg (o)</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/tip4p (o)</A>
+</TD></TR></TABLE></DIV>
+
+</HTML>
diff --git a/doc/doc2/Section_errors.html b/doc/doc2/Section_errors.html
new file mode 100644
index 000000000..0e72c3dd0
--- /dev/null
+++ b/doc/doc2/Section_errors.html
@@ -0,0 +1,11168 @@
+<HTML>
+<CENTER><A HREF = "Section_python.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_history.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>12. Errors
+</H3>
+<P>This section describes the errors you can encounter when using LAMMPS,
+either conceptually, or as printed out by the program.
+</P>
+12.1 <A HREF = "#err_1">Common problems</A><BR>
+12.2 <A HREF = "#err_2">Reporting bugs</A><BR>
+12.3 <A HREF = "#err_3">Error & warning messages</A> <BR>
+
+<HR>
+
+<HR>
+
+<A NAME = "err_1"></A><H4>12.1 Common problems
+</H4>
+<P>If two LAMMPS runs do not produce the same answer on different
+machines or different numbers of processors, this is typically not a
+bug. In theory you should get identical answers on any number of
+processors and on any machine. In practice, numerical round-off can
+cause slight differences and eventual divergence of molecular dynamics
+phase space trajectories within a few 100s or few 1000s of timesteps.
+However, the statistical properties of the two runs (e.g. average
+energy or temperature) should still be the same.
+</P>
+<P>If the <A HREF = "velocity.html">velocity</A> command is used to set initial atom
+velocities, a particular atom can be assigned a different velocity
+when the problem is run on a different number of processors or on
+different machines. If this happens, the phase space trajectories of
+the two simulations will rapidly diverge. See the discussion of the
+<I>loop</I> option in the <A HREF = "velocity.html">velocity</A> command for details and
+options that avoid this issue.
+</P>
+<P>Similarly, the <A HREF = "create_atoms.html">create_atoms</A> command generates a
+lattice of atoms. For the same physical system, the ordering and
+numbering of atoms by atom ID may be different depending on the number
+of processors.
+</P>
+<P>Some commands use random number generators which may be setup to
+produce different random number streams on each processor and hence
+will produce different effects when run on different numbers of
+processors. A commonly-used example is the <A HREF = "fix_langevin.html">fix
+langevin</A> command for thermostatting.
+</P>
+<P>A LAMMPS simulation typically has two stages, setup and run. Most
+LAMMPS errors are detected at setup time; others like a bond
+stretching too far may not occur until the middle of a run.
+</P>
+<P>LAMMPS tries to flag errors and print informative error messages so
+you can fix the problem. Of course, LAMMPS cannot figure out your
+physics or numerical mistakes, like choosing too big a timestep,
+specifying erroneous force field coefficients, or putting 2 atoms on
+top of each other! If you run into errors that LAMMPS doesn't catch
+that you think it should flag, please send an email to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
+</P>
+<P>If you get an error message about an invalid command in your input
+script, you can determine what command is causing the problem by
+looking in the log.lammps file or using the <A HREF = "echo.html">echo command</A>
+to see it on the screen. If you get an error like "Invalid ...
+style", with ... being fix, compute, pair, etc, it means that you
+mistyped the style name or that the command is part of an optional
+package which was not compiled into your executable. The list of
+available styles in your executable can be listed by using <A HREF = "Section_start.html#start_7">the -h
+command-line argument</A>. The installation
+and compilation of optional packages is explained in the <A HREF = "Section_start.html#start_3">installation
+instructions</A>.
+</P>
+<P>For a given command, LAMMPS expects certain arguments in a specified
+order. If you mess this up, LAMMPS will often flag the error, but it
+may also simply read a bogus argument and assign a value that is
+valid, but not what you wanted. E.g. trying to read the string "abc"
+as an integer value of 0. Careful reading of the associated doc page
+for the command should allow you to fix these problems. Note that
+some commands allow for variables to be specified in place of numeric
+constants so that the value can be evaluated and change over the
+course of a run. This is typically done with the syntax <I>v_name</I> for
+a parameter, where name is the name of the variable. This is only
+allowed if the command documentation says it is.
+</P>
+<P>Generally, LAMMPS will print a message to the screen and logfile and
+exit gracefully when it encounters a fatal error. Sometimes it will
+print a WARNING to the screen and logfile and continue on; you can
+decide if the WARNING is important or not. A WARNING message that is
+generated in the middle of a run is only printed to the screen, not to
+the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
+crashes or hangs without spitting out an error message first then it
+could be a bug (see <A HREF = "#err_2">this section</A>) or one of the following
+cases:
+</P>
+<P>LAMMPS runs in the available memory a processor allows to be
+allocated. Most reasonable MD runs are compute limited, not memory
+limited, so this shouldn't be a bottleneck on most platforms. Almost
+all large memory allocations in the code are done via C-style malloc's
+which will generate an error message if you run out of memory.
+Smaller chunks of memory are allocated via C++ "new" statements. If
+you are unlucky you could run out of memory just when one of these
+small requests is made, in which case the code will crash or hang (in
+parallel), since LAMMPS doesn't trap on those errors.
+</P>
+<P>Illegal arithmetic can cause LAMMPS to run slow or crash. This is
+typically due to invalid physics and numerics that your simulation is
+computing. If you see wild thermodynamic values or NaN values in your
+LAMMPS output, something is wrong with your simulation. If you
+suspect this is happening, it is a good idea to print out
+thermodynamic info frequently (e.g. every timestep) via the
+<A HREF = "thermo.html">thermo</A> so you can monitor what is happening.
+Visualizing the atom movement is also a good idea to insure your model
+is behaving as you expect.
+</P>
+<P>In parallel, one way LAMMPS can hang is due to how different MPI
+implementations handle buffering of messages. If the code hangs
+without an error message, it may be that you need to specify an MPI
+setting or two (usually via an environment variable) to enable
+buffering or boost the sizes of messages that can be buffered.
+</P>
+<HR>
+
+<A NAME = "err_2"></A><H4>12.2 Reporting bugs
+</H4>
+<P>If you are confident that you have found a bug in LAMMPS, follow these
+steps.
+</P>
+<P>Check the <A HREF = "http://lammps.sandia.gov/bug.html">New features and bug
+fixes</A> section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
+site</A> to see if the bug has already been reported or fixed or the
+<A HREF = "http://lammps.sandia.gov/unbug.html">Unfixed bug</A> to see if a fix is
+pending.
+</P>
+<P>Check the <A HREF = "http://lammps.sandia.gov/mail.html">mailing list</A>
+to see if it has been discussed before.
+</P>
+<P>If not, send an email to the mailing list describing the problem with
+any ideas you have as to what is causing it or where in the code the
+problem might be. The developers will ask for more info if needed,
+such as an input script or data files.
+</P>
+<P>The most useful thing you can do to help us fix the bug is to isolate
+the problem. Run it on the smallest number of atoms and fewest number
+of processors and with the simplest input script that reproduces the
+bug and try to identify what command or combination of commands is
+causing the problem.
+</P>
+<P>As a last resort, you can send an email directly to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
+</P>
+<HR>
+
+<H4><A NAME = "err_3"></A>12.3 Error & warning messages
+</H4>
+<P>These are two alphabetic lists of the <A HREF = "#error">ERROR</A> and
+<A HREF = "#warn">WARNING</A> messages LAMMPS prints out and the reason why. If the
+explanation here is not sufficient, the documentation for the
+offending command may help.
+Error and warning messages also list the source file and line number
+where the error was generated. For example, this message
+</P>
+<P>ERROR: Illegal velocity command (velocity.cpp:78)
+</P>
+<P>means that line #78 in the file src/velocity.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+</P>
+<P>Note that error messages from <A HREF = "Section_start.html#start_3">user-contributed
+packages</A> are not listed here. If such an
+error occurs and is not self-explanatory, you'll need to look in the
+source code or contact the author of the package.
+</P>
+<H4><A NAME = "error"></A>Errors:
+</H4>
+<DL>
+
+<DT><I>1-3 bond count is inconsistent</I>
+
+<DD>An inconsistency was detected when computing the number of 1-3
+neighbors for each atom. This likely means something is wrong with
+the bond topologies you have defined.
+
+<DT><I>1-4 bond count is inconsistent</I>
+
+<DD>An inconsistency was detected when computing the number of 1-4
+neighbors for each atom. This likely means something is wrong with
+the bond topologies you have defined.
+
+<DT><I>Accelerator sharing is not currently supported on system</I>
+
+<DD>Multiple MPI processes cannot share the accelerator on your
+system. For NVIDIA GPUs, see the nvidia-smi command to change this
+setting.
+
+<DT><I>All angle coeffs are not set</I>
+
+<DD>All angle coefficients must be set in the data file or by the
+angle_coeff command before running a simulation.
+
+<DT><I>All atoms of a swapped type must have the same charge.</I>
+
+<DD>Self-explanatory.
+
+<DT><I>All bond coeffs are not set</I>
+
+<DD>All bond coefficients must be set in the data file or by the
+bond_coeff command before running a simulation.
+
+<DT><I>All dihedral coeffs are not set</I>
+
+<DD>All dihedral coefficients must be set in the data file or by the
+dihedral_coeff command before running a simulation.
+
+<DT><I>All improper coeffs are not set</I>
+
+<DD>All improper coefficients must be set in the data file or by the
+improper_coeff command before running a simulation.
+
+<DT><I>All masses are not set</I>
+
+<DD>For atom styles that define masses for each atom type, all masses must
+be set in the data file or by the mass command before running a
+simulation. They must also be set before using the velocity
+command.
+
+<DT><I>All mol IDs should be set for fix gcmc group atoms</I>
+
+<DD>The molecule flag is on, yet not all molecule ids in the fix group
+have been set to non-zero positive values by the user. This is an
+error since all atoms in the fix gcmc group are eligible for deletion,
+rotation, and translation and therefore must have valid molecule ids.
+
+<DT><I>All pair coeffs are not set</I>
+
+<DD>All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+<DT><I>All read_dump x,y,z fields must be specified for scaled, triclinic coords</I>
+
+<DD>For triclinic boxes and scaled coordinates you must specify all 3 of
+the x,y,z fields, else LAMMPS cannot reconstruct the unscaled
+coordinates.
+
+<DT><I>All universe/uloop variables must have same # of values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>All variables in next command must be same style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Angle atom missing in delete_bonds</I>
+
+<DD>The delete_bonds command cannot find one or more atoms in a particular
+angle on a particular processor. The pairwise cutoff is too short or
+the atoms are too far apart to make a valid angle.
+
+<DT><I>Angle atom missing in set command</I>
+
+<DD>The set command cannot find one or more atoms in a particular angle on
+a particular processor. The pairwise cutoff is too short or the atoms
+are too far apart to make a valid angle.
+
+<DT><I>Angle atoms %d %d %d missing on proc %d at step %ld</I>
+
+<DD>One or more of 3 atoms needed to compute a particular angle are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the angle has blown apart and an atom is
+too far away.
+
+<DT><I>Angle atoms missing on proc %d at step %ld</I>
+
+<DD>One or more of 3 atoms needed to compute a particular angle are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the angle has blown apart and an atom is
+too far away.
+
+<DT><I>Angle coeff for hybrid has invalid style</I>
+
+<DD>Angle style hybrid uses another angle style as one of its
+coefficients. The angle style used in the angle_coeff command or read
+from a restart file is not recognized.
+
+<DT><I>Angle coeffs are not set</I>
+
+<DD>No angle coefficients have been assigned in the data file or via the
+angle_coeff command.
+
+<DT><I>Angle extent > half of periodic box length</I>
+
+<DD>This error was detected by the neigh_modify check yes setting. It is
+an error because the angle atoms are so far apart it is ambiguous how
+it should be defined.
+
+<DT><I>Angle potential must be defined for SHAKE</I>
+
+<DD>When shaking angles, an angle_style potential must be used.
+
+<DT><I>Angle style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Angle style hybrid cannot have none as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Angle style hybrid cannot use same angle style twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Angle table must range from 0 to 180 degrees</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Angle table parameters did not set N</I>
+
+<DD>List of angle table parameters must include N setting.
+
+<DT><I>Angle_coeff command before angle_style is defined</I>
+
+<DD>Coefficients cannot be set in the data file or via the angle_coeff
+command until an angle_style has been assigned.
+
+<DT><I>Angle_coeff command before simulation box is defined</I>
+
+<DD>The angle_coeff command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Angle_coeff command when no angles allowed</I>
+
+<DD>The chosen atom style does not allow for angles to be defined.
+
+<DT><I>Angle_style command when no angles allowed</I>
+
+<DD>The chosen atom style does not allow for angles to be defined.
+
+<DT><I>Angles assigned incorrectly</I>
+
+<DD>Angles read in from the data file were not assigned correctly to
+atoms. This means there is something invalid about the topology
+definitions.
+
+<DT><I>Angles defined but no angle types</I>
+
+<DD>The data file header lists angles but no angle types.
+
+<DT><I>Append boundary must be shrink/minimum</I>
+
+<DD>The boundary style of the face where atoms are added
+must be of type m (shrink/minimum).
+
+<DT><I>Arccos of invalid value in variable formula</I>
+
+<DD>Argument of arccos() must be between -1 and 1.
+
+<DT><I>Arcsin of invalid value in variable formula</I>
+
+<DD>Argument of arcsin() must be between -1 and 1.
+
+<DT><I>Assigning body parameters to non-body atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Assigning ellipsoid parameters to non-ellipsoid atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Assigning line parameters to non-line atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Assigning tri parameters to non-tri atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom ID is negative</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom ID is too big</I>
+
+<DD>The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
+setting in your Makefile. See Section_start 2.2 of the manual for
+more details.
+
+<DT><I>Atom ID is zero</I>
+
+<DD>Either all atoms IDs must be zero or none of them.
+
+<DT><I>Atom IDs must be consecutive for velocity create loop all</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom IDs must be used for molecular systems</I>
+
+<DD>Atom IDs are used to identify and find partner atoms in bonds.
+
+<DT><I>Atom count changed in fix neb</I>
+
+<DD>This is not allowed in a NEB calculation.
+
+<DT><I>Atom count is inconsistent, cannot write data file</I>
+
+<DD>The sum of atoms across processors does not equal the global number
+of atoms. Probably some atoms have been lost.
+
+<DT><I>Atom count is inconsistent, cannot write restart file</I>
+
+<DD>Sum of atoms across processors does not equal initial total count.
+This is probably because you have lost some atoms.
+
+<DT><I>Atom in too many rigid bodies - boost MAXBODY</I>
+
+<DD>Fix poems has a parameter MAXBODY (in fix_poems.cpp) which determines
+the maximum number of rigid bodies a single atom can belong to (i.e. a
+multibody joint). The bodies you have defined exceed this limit.
+
+<DT><I>Atom sort did not operate correctly</I>
+
+<DD>This is an internal LAMMPS error. Please report it to the
+developers.
+
+<DT><I>Atom sorting has bin size = 0.0</I>
+
+<DD>The neighbor cutoff is being used as the bin size, but it is zero.
+Thus you must explicitly list a bin size in the atom_modify sort
+command or turn off sorting.
+
+<DT><I>Atom style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom style hybrid cannot use same atom style twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom style template molecule must have atom types</I>
+
+<DD>The defined molecule(s) does not specify atom types.
+
+<DT><I>Atom style was redefined after using fix property/atom</I>
+
+<DD>This is not allowed.
+
+<DT><I>Atom vector in equal-style variable formula</I>
+
+<DD>Atom vectors generate one value per atom which is not allowed
+in an equal-style variable.
+
+<DT><I>Atom-style variable in equal-style variable formula</I>
+
+<DD>Atom-style variables generate one value per atom which is not allowed
+in an equal-style variable.
+
+<DT><I>Atom_modify id command after simulation box is defined</I>
+
+<DD>The atom_modify id command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Atom_modify map command after simulation box is defined</I>
+
+<DD>The atom_modify map command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Atom_modify sort and first options cannot be used together</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom_style command after simulation box is defined</I>
+
+<DD>The atom_style command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Atom_style line can only be used in 2d simulations</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom_style tri can only be used in 3d simulations</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atomfile variable could not read values</I>
+
+<DD>Check the file assigned to the variable.
+
+<DT><I>Atomfile variable in equal-style variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atomfile-style variable in equal-style variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Attempt to pop empty stack in fix box/relax</I>
+
+<DD>Internal LAMMPS error. Please report it to the developers.
+
+<DT><I>Attempt to push beyond stack limit in fix box/relax</I>
+
+<DD>Internal LAMMPS error. Please report it to the developers.
+
+<DT><I>Attempting to rescale a 0.0 temperature</I>
+
+<DD>Cannot rescale a temperature that is already 0.0.
+
+<DT><I>Bad FENE bond</I>
+
+<DD>Two atoms in a FENE bond have become so far apart that the bond cannot
+be computed.
+
+<DT><I>Bad TIP4P angle type for PPPM/TIP4P</I>
+
+<DD>Specified angle type is not valid.
+
+<DT><I>Bad TIP4P angle type for PPPMDisp/TIP4P</I>
+
+<DD>Specified angle type is not valid.
+
+<DT><I>Bad TIP4P bond type for PPPM/TIP4P</I>
+
+<DD>Specified bond type is not valid.
+
+<DT><I>Bad TIP4P bond type for PPPMDisp/TIP4P</I>
+
+<DD>Specified bond type is not valid.
+
+<DT><I>Bad fix ID in fix append/atoms command</I>
+
+<DD>The value of the fix_id for keyword spatial must start with the suffix
+f_.
+
+<DT><I>Bad grid of processors</I>
+
+<DD>The 3d grid of processors defined by the processors command does not
+match the number of processors LAMMPS is being run on.
+
+<DT><I>Bad kspace_modify kmax/ewald parameter</I>
+
+<DD>Kspace_modify values for the kmax/ewald keyword must be integers > 0
+
+<DT><I>Bad kspace_modify slab parameter</I>
+
+<DD>Kspace_modify value for the slab/volume keyword must be >= 2.0.
+
+<DT><I>Bad matrix inversion in mldivide3</I>
+
+<DD>This error should not occur unless the matrix is badly formed.
+
+<DT><I>Bad principal moments</I>
+
+<DD>Fix rigid did not compute the principal moments of inertia of a rigid
+group of atoms correctly.
+
+<DT><I>Bad quadratic solve for particle/line collision</I>
+
+<DD>This is an internal error. It should nornally not occur.
+
+<DT><I>Bad quadratic solve for particle/tri collision</I>
+
+<DD>This is an internal error. It should nornally not occur.
+
+<DT><I>Bad real space Coulomb cutoff in fix tune/kspace</I>
+
+<DD>Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
+the Newton-Rhaphson method, but found a non-positive or NaN cutoff
+
+<DT><I>Balance command before simulation box is defined</I>
+
+<DD>The balance command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Balance produced bad splits</I>
+
+<DD>This should not occur. It means two or more cutting plane locations
+are on top of each other or out of order. Report the problem to the
+developers.
+
+<DT><I>Balance rcb cannot be used with comm_style brick</I>
+
+<DD>Comm_style tiled must be used instead.
+
+<DT><I>Balance shift string is invalid</I>
+
+<DD>The string can only contain the characters "x", "y", or "z".
+
+<DT><I>Bias compute does not calculate a velocity bias</I>
+
+<DD>The specified compute must compute a bias for temperature.
+
+<DT><I>Bias compute does not calculate temperature</I>
+
+<DD>The specified compute must compute temperature.
+
+<DT><I>Bias compute group does not match compute group</I>
+
+<DD>The specified compute must operate on the same group as the parent
+compute.
+
+<DT><I>Big particle in fix srd cannot be point particle</I>
+
+<DD>Big particles must be extended spheriods or ellipsoids.
+
+<DT><I>Bigint setting in lmptype.h is invalid</I>
+
+<DD>Size of bigint is less than size of tagint.
+
+<DT><I>Bigint setting in lmptype.h is not compatible</I>
+
+<DD>Format of bigint stored in restart file is not consistent with LAMMPS
+version you are running. See the settings in src/lmptype.h
+
+<DT><I>Bitmapped lookup tables require int/float be same size</I>
+
+<DD>Cannot use pair tables on this machine, because of word sizes. Use
+the pair_modify command with table 0 instead.
+
+<DT><I>Bitmapped table in file does not match requested table</I>
+
+<DD>Setting for bitmapped table in pair_coeff command must match table
+in file exactly.
+
+<DT><I>Bitmapped table is incorrect length in table file</I>
+
+<DD>Number of table entries is not a correct power of 2.
+
+<DT><I>Bond and angle potentials must be defined for TIP4P</I>
+
+<DD>Cannot use TIP4P pair potential unless bond and angle potentials
+are defined.
+
+<DT><I>Bond atom missing in box size check</I>
+
+<DD>The 2nd atoms needed to compute a particular bond is missing on this
+processor. Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away.
+
+<DT><I>Bond atom missing in delete_bonds</I>
+
+<DD>The delete_bonds command cannot find one or more atoms in a particular
+bond on a particular processor. The pairwise cutoff is too short or
+the atoms are too far apart to make a valid bond.
+
+<DT><I>Bond atom missing in image check</I>
+
+<DD>The 2nd atom in a particular bond is missing on this processor.
+Typically this is because the pairwise cutoff is set too short or the
+bond has blown apart and an atom is too far away.
+
+<DT><I>Bond atom missing in set command</I>
+
+<DD>The set command cannot find one or more atoms in a particular bond on
+a particular processor. The pairwise cutoff is too short or the atoms
+are too far apart to make a valid bond.
+
+<DT><I>Bond atoms %d %d missing on proc %d at step %ld</I>
+
+<DD>The 2nd atom needed to compute a particular bond is missing on this
+processor. Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away.
+
+<DT><I>Bond atoms missing on proc %d at step %ld</I>
+
+<DD>The 2nd atom needed to compute a particular bond is missing on this
+processor. Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away.
+
+<DT><I>Bond coeff for hybrid has invalid style</I>
+
+<DD>Bond style hybrid uses another bond style as one of its coefficients.
+The bond style used in the bond_coeff command or read from a restart
+file is not recognized.
+
+<DT><I>Bond coeffs are not set</I>
+
+<DD>No bond coefficients have been assigned in the data file or via the
+bond_coeff command.
+
+<DT><I>Bond extent > half of periodic box length</I>
+
+<DD>This error was detected by the neigh_modify check yes setting. It is
+an error because the bond atoms are so far apart it is ambiguous how
+it should be defined.
+
+<DT><I>Bond potential must be defined for SHAKE</I>
+
+<DD>Cannot use fix shake unless bond potential is defined.
+
+<DT><I>Bond style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Bond style hybrid cannot have none as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Bond style hybrid cannot use same bond style twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Bond style quartic cannot be used with 3,4-body interactions</I>
+
+<DD>No angle, dihedral, or improper styles can be defined when using
+bond style quartic.
+
+<DT><I>Bond style quartic cannot be used with atom style template</I>
+
+<DD>This bond style can change the bond topology which is not
+allowed with this atom style.
+
+<DT><I>Bond style quartic requires special_bonds = 1,1,1</I>
+
+<DD>This is a restriction of the current bond quartic implementation.
+
+<DT><I>Bond table parameters did not set N</I>
+
+<DD>List of bond table parameters must include N setting.
+
+<DT><I>Bond table values are not increasing</I>
+
+<DD>The values in the tabulated file must be monotonically increasing.
+
+<DT><I>BondAngle coeff for hybrid angle has invalid format</I>
+
+<DD>No "ba" field should appear in data file entry.
+
+<DT><I>BondBond coeff for hybrid angle has invalid format</I>
+
+<DD>No "bb" field should appear in data file entry.
+
+<DT><I>Bond_coeff command before bond_style is defined</I>
+
+<DD>Coefficients cannot be set in the data file or via the bond_coeff
+command until an bond_style has been assigned.
+
+<DT><I>Bond_coeff command before simulation box is defined</I>
+
+<DD>The bond_coeff command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Bond_coeff command when no bonds allowed</I>
+
+<DD>The chosen atom style does not allow for bonds to be defined.
+
+<DT><I>Bond_style command when no bonds allowed</I>
+
+<DD>The chosen atom style does not allow for bonds to be defined.
+
+<DT><I>Bonds assigned incorrectly</I>
+
+<DD>Bonds read in from the data file were not assigned correctly to atoms.
+This means there is something invalid about the topology definitions.
+
+<DT><I>Bonds defined but no bond types</I>
+
+<DD>The data file header lists bonds but no bond types.
+
+<DT><I>Both restart files must use % or neither</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Both restart files must use MPI-IO or neither</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Both sides of boundary must be periodic</I>
+
+<DD>Cannot specify a boundary as periodic only on the lo or hi side. Must
+be periodic on both sides.
+
+<DT><I>Boundary command after simulation box is defined</I>
+
+<DD>The boundary command cannot be used after a read_data, read_restart,
+or create_box command.
+
+<DT><I>Box bounds are invalid</I>
+
+<DD>The box boundaries specified in the read_data file are invalid. The
+lo value must be less than the hi value for all 3 dimensions.
+
+<DT><I>Box command after simulation box is defined</I>
+
+<DD>The box command cannot be used after a read_data, read_restart, or
+create_box command.
+
+<DT><I>CPU neighbor lists must be used for ellipsoid/sphere mix.</I>
+
+<DD>When using Gay-Berne or RE-squared pair styles with both ellipsoidal and
+spherical particles, the neighbor list must be built on the CPU
+
+<DT><I>Can not specify Pxy/Pxz/Pyz in fix box/relax with non-triclinic box</I>
+
+<DD>Only triclinic boxes can be used with off-diagonal pressure components.
+See the region prism command for details.
+
+<DT><I>Can not specify Pxy/Pxz/Pyz in fix nvt/npt/nph with non-triclinic box</I>
+
+<DD>Only triclinic boxes can be used with off-diagonal pressure components.
+See the region prism command for details.
+
+<DT><I>Can only use -plog with multiple partitions</I>
+
+<DD>Self-explanatory. See doc page discussion of command-line switches.
+
+<DT><I>Can only use -pscreen with multiple partitions</I>
+
+<DD>Self-explanatory. See doc page discussion of command-line switches.
+
+<DT><I>Can only use NEB with 1-processor replicas</I>
+
+<DD>This is current restriction for NEB as implemented in LAMMPS.
+
+<DT><I>Can only use TAD with 1-processor replicas for NEB</I>
+
+<DD>This is current restriction for NEB as implemented in LAMMPS.
+
+<DT><I>Cannot (yet) do analytic differentiation with pppm/gpu</I>
+
+<DD>This is a current restriction of this command.
+
+<DT><I>Cannot (yet) use 'electron' units with dipoles</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use Ewald with triclinic box and slab correction</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use K-space slab correction with compute group/group for triclinic systems</I>
+
+<DD>This option is not yet supported.
+
+<DT><I>Cannot (yet) use MSM with 2d simulation</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use PPPM with triclinic box and TIP4P</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use PPPM with triclinic box and slab correction</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use kspace slab correction with long-range dipoles and non-neutral systems or per-atom energy</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use kspace_modify diff ad with compute group/group</I>
+
+<DD>This option is not yet supported.
+
+<DT><I>Cannot (yet) use kspace_style pppm/stagger with triclinic systems</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Cannot (yet) use molecular templates with Kokkos</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)</I>
+
+<DD>Single precision cannot be used with MSM.
+
+<DT><I>Cannot add atoms to fix move variable</I>
+
+<DD>Atoms can not be added afterwards to this fix option.
+
+<DT><I>Cannot append atoms to a triclinic box</I>
+
+<DD>The simulation box must be defined with edges alligned with the
+Cartesian axes.
+
+<DT><I>Cannot balance in z dimension for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot change box ortho/triclinic with certain fixes defined</I>
+
+<DD>This is because those fixes store the shape of the box. You need to
+use unfix to discard the fix, change the box, then redefine a new
+fix.
+
+<DT><I>Cannot change box ortho/triclinic with dumps defined</I>
+
+<DD>This is because some dumps store the shape of the box. You need to
+use undump to discard the dump, change the box, then redefine a new
+dump.
+
+<DT><I>Cannot change box tilt factors for orthogonal box</I>
+
+<DD>Cannot use tilt factors unless the simulation box is non-orthogonal.
+
+<DT><I>Cannot change box to orthogonal when tilt is non-zero</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot change box z boundary to nonperiodic for a 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot change dump_modify every for dump dcd</I>
+
+<DD>The frequency of writing dump dcd snapshots cannot be changed.
+
+<DT><I>Cannot change dump_modify every for dump xtc</I>
+
+<DD>The frequency of writing dump xtc snapshots cannot be changed.
+
+<DT><I>Cannot change timestep once fix srd is setup</I>
+
+<DD>This is because various SRD properties depend on the timestep
+size.
+
+<DT><I>Cannot change timestep with fix pour</I>
+
+<DD>This is because fix pour pre-computes the time delay for particles to
+fall out of the insertion volume due to gravity.
+
+<DT><I>Cannot change to comm_style brick from tiled layout</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot change_box after reading restart file with per-atom info</I>
+
+<DD>This is because the restart file info cannot be migrated with the
+atoms. You can get around this by performing a 0-timestep run which
+will assign the restart file info to actual atoms.
+
+<DT><I>Cannot change_box in xz or yz for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot change_box in z dimension for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot clear group all</I>
+
+<DD>This operation is not allowed.
+
+<DT><I>Cannot close restart file - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot compute initial g_ewald_disp</I>
+
+<DD>LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
+factor that partitions the computation between real space and k-space
+for Disptersion interactions.
+
+<DT><I>Cannot create an atom map unless atoms have IDs</I>
+
+<DD>The simulation requires a mapping from global atom IDs to local atoms,
+but the atoms that have been defined have no IDs.
+
+<DT><I>Cannot create atoms with undefined lattice</I>
+
+<DD>Must use the lattice command before using the create_atoms
+command.
+
+<DT><I>Cannot create/grow a vector/array of pointers for %s</I>
+
+<DD>LAMMPS code is making an illegal call to the templated memory
+allocaters, to create a vector or array of pointers.
+
+<DT><I>Cannot create_atoms after reading restart file with per-atom info</I>
+
+<DD>The per-atom info was stored to be used when by a fix that you may
+re-define. If you add atoms before re-defining the fix, then there
+will not be a correct amount of per-atom info.
+
+<DT><I>Cannot create_box after simulation box is defined</I>
+
+<DD>A simulation box can only be defined once.
+
+<DT><I>Cannot currently use pair reax with pair hybrid</I>
+
+<DD>This is not yet supported.
+
+<DT><I>Cannot currently use pppm/gpu with fix balance.</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete group all</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete group currently used by a compute</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete group currently used by a dump</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete group currently used by a fix</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete group currently used by atom_modify first</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete_atoms bond yes for non-molecular systems</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot delete_atoms mol yes for non-molecular systems</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot displace_atoms after reading restart file with per-atom info</I>
+
+<DD>This is because the restart file info cannot be migrated with the
+atoms. You can get around this by performing a 0-timestep run which
+will assign the restart file info to actual atoms.
+
+<DT><I>Cannot do GCMC on atoms in atom_modify first group</I>
+
+<DD>This is a restriction due to the way atoms are organized in a list to
+enable the atom_modify first command.
+
+<DT><I>Cannot do atom/swap on atoms in atom_modify first group</I>
+
+<DD>This is a restriction due to the way atoms are organized in a list to
+enable the atom_modify first command.
+
+<DT><I>Cannot dump sort on atom IDs with no atom IDs defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot dump sort when multiple dump files are written</I>
+
+<DD>In this mode, each processor dumps its atoms to a file, so
+no sorting is allowed.
+
+<DT><I>Cannot embed Python when also extending Python with LAMMPS</I>
+
+<DD>When running LAMMPS via Python through the LAMMPS library interface
+you cannot also user the input script python command.
+
+<DT><I>Cannot evaporate atoms in atom_modify first group</I>
+
+<DD>This is a restriction due to the way atoms are organized in
+a list to enable the atom_modify first command.
+
+<DT><I>Cannot find create_bonds group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot find delete_bonds group ID</I>
+
+<DD>Group ID used in the delete_bonds command does not exist.
+
+<DT><I>Cannot find specified group ID for core particles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot find specified group ID for shell particles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot have both pair_modify shift and tail set to yes</I>
+
+<DD>These 2 options are contradictory.
+
+<DT><I>Cannot intersect groups using a dynamic group</I>
+
+<DD>This operation is not allowed.
+
+<DT><I>Cannot mix molecular and molecule template atom styles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open -reorder file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open ADP potential file %s</I>
+
+<DD>The specified ADP potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open AIREBO potential file %s</I>
+
+<DD>The specified AIREBO potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open BOP potential file %s</I>
+
+<DD>The specified BOP potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open COMB potential file %s</I>
+
+<DD>The specified COMB potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open COMB3 lib.comb3 file</I>
+
+<DD>The COMB3 library file cannot be opened. Check that the path and name
+are correct.
+
+<DT><I>Cannot open COMB3 potential file %s</I>
+
+<DD>The specified COMB3 potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open EAM potential file %s</I>
+
+<DD>The specified EAM potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open EIM potential file %s</I>
+
+<DD>The specified EIM potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open LCBOP potential file %s</I>
+
+<DD>The specified LCBOP potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open MEAM potential file %s</I>
+
+<DD>The specified MEAM potential file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open SNAP coefficient file %s</I>
+
+<DD>The specified SNAP coefficient file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open SNAP parameter file %s</I>
+
+<DD>The specified SNAP parameter file cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open Stillinger-Weber potential file %s</I>
+
+<DD>The specified SW potential file cannot be opened. Check that the path
+and name are correct.
+
+<DT><I>Cannot open Tersoff potential file %s</I>
+
+<DD>The specified potential file cannot be opened. Check that the path
+and name are correct.
+
+<DT><I>Cannot open balance output file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open coul/streitz potential file %s</I>
+
+<DD>The specified coul/streitz potential file cannot be opened. Check
+that the path and name are correct.
+
+<DT><I>Cannot open custom file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open data file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open dir to search for restart file</I>
+
+<DD>Using a "*" in the name of the restart file will open the current
+directory to search for matching file names.
+
+<DT><I>Cannot open dump file</I>
+
+<DD>The output file for the dump command cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open dump file %s</I>
+
+<DD>The output file for the dump command cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Cannot open file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct. If the file is a compressed file, also check that the gzip
+executable can be found and run.
+
+<DT><I>Cannot open file variable file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix ave/chunk file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix ave/correlate file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix ave/histo file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix ave/spatial file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix ave/time file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix balance output file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open fix poems file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix print file %s</I>
+
+<DD>The output file generated by the fix print command cannot be opened
+
+<DT><I>Cannot open fix qeq parameter file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix qeq/comb file %s</I>
+
+<DD>The output file for the fix qeq/combs command cannot be opened.
+Check that the path and name are correct.
+
+<DT><I>Cannot open fix reax/bonds file %s</I>
+
+<DD>The output file for the fix reax/bonds command cannot be opened.
+Check that the path and name are correct.
+
+<DT><I>Cannot open fix rigid infile %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix rigid restart file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix rigid/small infile %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open fix tmd file %s</I>
+
+<DD>The output file for the fix tmd command cannot be opened. Check that
+the path and name are correct.
+
+<DT><I>Cannot open fix ttm file %s</I>
+
+<DD>The output file for the fix ttm command cannot be opened. Check that
+the path and name are correct.
+
+<DT><I>Cannot open gzipped file</I>
+
+<DD>LAMMPS was compiled without support for reading and writing gzipped
+files through a pipeline to the gzip program with -DLAMMPS_GZIP.
+
+<DT><I>Cannot open input script %s</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open log.cite file</I>
+
+<DD>This file is created when you use some LAMMPS features, to indicate
+what paper you should cite on behalf of those who implemented
+the feature. Check that you have write priveleges into the directory
+you are running in.
+
+<DT><I>Cannot open log.lammps for writing</I>
+
+<DD>The default LAMMPS log file cannot be opened. Check that the
+directory you are running in allows for files to be created.
+
+<DT><I>Cannot open logfile</I>
+
+<DD>The LAMMPS log file named in a command-line argument cannot be opened.
+Check that the path and name are correct.
+
+<DT><I>Cannot open logfile %s</I>
+
+<DD>The LAMMPS log file specified in the input script cannot be opened.
+Check that the path and name are correct.
+
+<DT><I>Cannot open molecule file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct.
+
+<DT><I>Cannot open nb3b/harmonic potential file %s</I>
+
+<DD>The specified potential file cannot be opened. Check that the path
+and name are correct.
+
+<DT><I>Cannot open pair_write file</I>
+
+<DD>The specified output file for pair energies and forces cannot be
+opened. Check that the path and name are correct.
+
+<DT><I>Cannot open print file %s</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open processors output file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open restart file %s</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot open restart file for reading - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot open restart file for writing - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot open screen file</I>
+
+<DD>The screen file specified as a command-line argument cannot be
+opened. Check that the directory you are running in allows for files
+to be created.
+
+<DT><I>Cannot open universe log file</I>
+
+<DD>For a multi-partition run, the master log file cannot be opened.
+Check that the directory you are running in allows for files to be
+created.
+
+<DT><I>Cannot open universe screen file</I>
+
+<DD>For a multi-partition run, the master screen file cannot be opened.
+Check that the directory you are running in allows for files to be
+created.
+
+<DT><I>Cannot read from restart file - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot read_data add and merge</I>
+
+<DD>These options are not yet supported.
+
+<DT><I>Cannot read_data after simulation box is defined</I>
+
+<DD>The read_data command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Cannot read_restart after simulation box is defined</I>
+
+<DD>The read_restart command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Cannot redefine variable as a different style</I>
+
+<DD>An equal-style variable can be re-defined but only if it was
+originally an equal-style variable.
+
+<DT><I>Cannot replicate 2d simulation in z dimension</I>
+
+<DD>The replicate command cannot replicate a 2d simulation in the z
+dimension.
+
+<DT><I>Cannot replicate with fixes that store atom quantities</I>
+
+<DD>Either fixes are defined that create and store atom-based vectors or a
+restart file was read which included atom-based vectors for fixes.
+The replicate command cannot duplicate that information for new atoms.
+You should use the replicate command before fixes are applied to the
+system.
+
+<DT><I>Cannot reset timestep with a dynamic region defined</I>
+
+<DD>Dynamic regions (see the region command) have a time dependence.
+Thus you cannot change the timestep when one or more of these
+are defined.
+
+<DT><I>Cannot reset timestep with a time-dependent fix defined</I>
+
+<DD>You cannot reset the timestep when a fix that keeps track of elapsed
+time is in place.
+
+<DT><I>Cannot run 2d simulation with nonperiodic Z dimension</I>
+
+<DD>Use the boundary command to make the z dimension periodic in order to
+run a 2d simulation.
+
+<DT><I>Cannot set bond topology types for atom style template</I>
+
+<DD>The bond, angle, etc types cannot be changed for this atom style since
+they are static settings in the molecule template files.
+
+<DT><I>Cannot set both respa pair and inner/middle/outer</I>
+
+<DD>In the rRESPA integrator, you must compute pairwise potentials either
+all together (pair), or in pieces (inner/middle/outer). You can't do
+both.
+
+<DT><I>Cannot set dump_modify flush for dump xtc</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set mass for this atom style</I>
+
+<DD>This atom style does not support mass settings for each atom type.
+Instead they are defined on a per-atom basis in the data file.
+
+<DT><I>Cannot set meso_rho for this atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set non-zero image flag for non-periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set non-zero z velocity for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set quaternion for atom that has none</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set respa middle without inner/outer</I>
+
+<DD>In the rRESPA integrator, you must define both a inner and outer
+setting in order to use a middle setting.
+
+<DT><I>Cannot set restart file size - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot set temperature for fix rigid/nph</I>
+
+<DD>The temp keyword cannot be specified.
+
+<DT><I>Cannot set theta for atom that is not a line</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot set this attribute for this atom style</I>
+
+<DD>The attribute being set does not exist for the defined atom style.
+
+<DT><I>Cannot set variable z velocity for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot skew triclinic box in z for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot subtract groups using a dynamic group</I>
+
+<DD>This operation is not allowed.
+
+<DT><I>Cannot union groups using a dynamic group</I>
+
+<DD>This operation is not allowed.
+
+<DT><I>Cannot use -cuda on and -kokkos on together</I>
+
+<DD>This is not allowed since both packages can use GPUs.
+
+<DT><I>Cannot use -cuda on without USER-CUDA installed</I>
+
+<DD>The USER-CUDA package must be installed via "make yes-user-cuda"
+before LAMMPS is built.
+
+<DT><I>Cannot use -kokkos on without KOKKOS installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use -reorder after -partition</I>
+
+<DD>Self-explanatory. See doc page discussion of command-line switches.
+
+<DT><I>Cannot use Ewald with 2d simulation</I>
+
+<DD>The kspace style ewald cannot be used in 2d simulations. You can use
+2d Ewald in a 3d simulation; see the kspace_modify command.
+
+<DT><I>Cannot use Ewald/disp solver on system with no charge, dipole, or LJ particles</I>
+
+<DD>No atoms in system have a non-zero charge or dipole, or are LJ
+particles. Change charges/dipoles or change options of the kspace
+solver/pair style.
+
+<DT><I>Cannot use EwaldDisp with 2d simulation</I>
+
+<DD>This is a current restriction of this command.
+
+<DT><I>Cannot use GPU package with USER-CUDA package enabled</I>
+
+<DD>You cannot use both the GPU and USER-CUDA packages
+together. Use one or the other.
+
+<DT><I>Cannot use Kokkos pair style with rRESPA inner/middle</I>
+
+<DD>rRESPA inner/middle options are not yet supported by Kokkos.
+
+<DT><I>Cannot use NEB unless atom map exists</I>
+
+<DD>Use the atom_modify command to create an atom map.
+
+<DT><I>Cannot use NEB with a single replica</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use NEB with atom_modify sort enabled</I>
+
+<DD>This is current restriction for NEB implemented in LAMMPS.
+
+<DT><I>Cannot use PPPM with 2d simulation</I>
+
+<DD>The kspace style pppm cannot be used in 2d simulations. You can use
+2d PPPM in a 3d simulation; see the kspace_modify command.
+
+<DT><I>Cannot use PPPMDisp with 2d simulation</I>
+
+<DD>The kspace style pppm/disp cannot be used in 2d simulations. You can
+use 2d pppm/disp in a 3d simulation; see the kspace_modify command.
+
+<DT><I>Cannot use PRD with a changing box</I>
+
+<DD>The current box dimensions are not copied between replicas
+
+<DT><I>Cannot use PRD with a time-dependent fix defined</I>
+
+<DD>PRD alters the timestep in ways that will mess up these fixes.
+
+<DT><I>Cannot use PRD with a time-dependent region defined</I>
+
+<DD>PRD alters the timestep in ways that will mess up these regions.
+
+<DT><I>Cannot use PRD with atom_modify sort enabled</I>
+
+<DD>This is a current restriction of PRD. You must turn off sorting,
+which is enabled by default, via the atom_modify command.
+
+<DT><I>Cannot use PRD with multi-processor replicas unless atom map exists</I>
+
+<DD>Use the atom_modify command to create an atom map.
+
+<DT><I>Cannot use TAD unless atom map exists for NEB</I>
+
+<DD>See atom_modify map command to set this.
+
+<DT><I>Cannot use TAD with a single replica for NEB</I>
+
+<DD>NEB requires multiple replicas.
+
+<DT><I>Cannot use TAD with atom_modify sort enabled for NEB</I>
+
+<DD>This is a current restriction of NEB.
+
+<DT><I>Cannot use a damped dynamics min style with fix box/relax</I>
+
+<DD>This is a current restriction in LAMMPS. Use another minimizer
+style.
+
+<DT><I>Cannot use a damped dynamics min style with per-atom DOF</I>
+
+<DD>This is a current restriction in LAMMPS. Use another minimizer
+style.
+
+<DT><I>Cannot use append/atoms in periodic dimension</I>
+
+<DD>The boundary style of the face where atoms are added can not be of
+type p (periodic).
+
+<DT><I>Cannot use atomfile-style variable unless atom map exists</I>
+
+<DD>Self-explanatory. See the atom_modify command to create a map.
+
+<DT><I>Cannot use both com and bias with compute temp/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use chosen neighbor list style with buck/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with coul/cut/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with coul/dsf/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with coul/wolf/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with lj/cut/coul/cut/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with lj/cut/coul/long/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with lj/cut/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use chosen neighbor list style with pair eam/kk</I>
+
+<DD>That style is not supported by Kokkos.
+
+<DT><I>Cannot use compute chunk/atom bin z for 2d model</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use compute cluster/atom unless atoms have IDs</I>
+
+<DD>Atom IDs are used to identify clusters.
+
+<DT><I>Cannot use create_atoms rotate unless single style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use create_bonds unless atoms have IDs</I>
+
+<DD>This command requires a mapping from global atom IDs to local atoms,
+but the atoms that have been defined have no IDs.
+
+<DT><I>Cannot use create_bonds with non-molecular system</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use cwiggle in variable formula between runs</I>
+
+<DD>This is a function of elapsed time.
+
+<DT><I>Cannot use delete_atoms bond yes with atom_style template</I>
+
+<DD>This is because the bonds for that atom style are hardwired in the
+molecule template.
+
+<DT><I>Cannot use delete_atoms unless atoms have IDs</I>
+
+<DD>Your atoms do not have IDs, so the delete_atoms command cannot be
+used.
+
+<DT><I>Cannot use delete_bonds with non-molecular system</I>
+
+<DD>Your choice of atom style does not have bonds.
+
+<DT><I>Cannot use dump_modify fileper without % in dump file name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use dump_modify nfile without % in dump file name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use dynamic group with fix adapt atom</I>
+
+<DD>This is not yet supported.
+
+<DT><I>Cannot use fix TMD unless atom map exists</I>
+
+<DD>Using this fix requires the ability to lookup an atom index, which is
+provided by an atom map. An atom map does not exist (by default) for
+non-molecular problems. Using the atom_modify map command will force
+an atom map to be created.
+
+<DT><I>Cannot use fix ave/spatial z for 2 dimensional model</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix bond/break with non-molecular systems</I>
+
+<DD>Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify.
+
+<DT><I>Cannot use fix bond/create with non-molecular systems</I>
+
+<DD>Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify.
+
+<DT><I>Cannot use fix bond/swap with non-molecular systems</I>
+
+<DD>Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify.
+
+<DT><I>Cannot use fix box/relax on a 2nd non-periodic dimension</I>
+
+<DD>When specifying an off-diagonal pressure component, the 2nd of the two
+dimensions must be periodic. E.g. if the xy component is specified,
+then the y dimension must be periodic.
+
+<DT><I>Cannot use fix box/relax on a non-periodic dimension</I>
+
+<DD>When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+<DT><I>Cannot use fix box/relax with both relaxation and scaling on a tilt factor</I>
+
+<DD>When specifying scaling on a tilt factor component, that component can not
+also be controlled by the barostat. E.g. if scalexy yes is specified and
+also keyword tri or xy, this is wrong.
+
+<DT><I>Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension</I>
+
+<DD>When specifying scaling on a tilt factor component, the 2nd of the two
+dimensions must be periodic. E.g. if the xy component is specified,
+then the y dimension must be periodic.
+
+<DT><I>Cannot use fix deform on a shrink-wrapped boundary</I>
+
+<DD>The x, y, z options cannot be applied to shrink-wrapped
+dimensions.
+
+<DT><I>Cannot use fix deform tilt on a shrink-wrapped 2nd dim</I>
+
+<DD>This is because the shrink-wrapping will change the value
+of the strain implied by the tilt factor.
+
+<DT><I>Cannot use fix deform trate on a box with zero tilt</I>
+
+<DD>The trate style alters the current strain.
+
+<DT><I>Cannot use fix deposit rigid and not molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix deposit rigid and shake</I>
+
+<DD>These two attributes are conflicting.
+
+<DT><I>Cannot use fix deposit shake and not molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix enforce2d with 3d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix gcmc in a 2d simulation</I>
+
+<DD>Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc
+are allowed.
+
+<DT><I>Cannot use fix gcmc shake and not molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix msst without per-type mass defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix npt and fix deform on same component of stress tensor</I>
+
+<DD>This would be changing the same box dimension twice.
+
+<DT><I>Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension</I>
+
+<DD>When specifying an off-diagonal pressure component, the 2nd of the two
+dimensions must be periodic. E.g. if the xy component is specified,
+then the y dimension must be periodic.
+
+<DT><I>Cannot use fix nvt/npt/nph on a non-periodic dimension</I>
+
+<DD>When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+<DT><I>Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension</I>
+
+<DD>The 2nd dimension in the barostatted tilt factor must be periodic.
+
+<DT><I>Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension</I>
+
+<DD>The 2nd dimension in the barostatted tilt factor must be periodic.
+
+<DT><I>Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension</I>
+
+<DD>The 2nd dimension in the barostatted tilt factor must be periodic.
+
+<DT><I>Cannot use fix pour rigid and not molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix pour rigid and shake</I>
+
+<DD>These two attributes are conflicting.
+
+<DT><I>Cannot use fix pour shake and not molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix pour with triclinic box</I>
+
+<DD>This option is not yet supported.
+
+<DT><I>Cannot use fix press/berendsen and fix deform on same component of stress tensor</I>
+
+<DD>These commands both change the box size/shape, so you cannot use both
+together.
+
+<DT><I>Cannot use fix press/berendsen on a non-periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix press/berendsen with triclinic box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix reax/bonds without pair_style reax</I>
+
+<DD>Self-explantory.
+
+<DT><I>Cannot use fix rigid npt/nph and fix deform on same component of stress tensor</I>
+
+<DD>This would be changing the same box dimension twice.
+
+<DT><I>Cannot use fix rigid npt/nph on a non-periodic dimension</I>
+
+<DD>When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+<DT><I>Cannot use fix rigid/small npt/nph on a non-periodic dimension</I>
+
+<DD>When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+<DT><I>Cannot use fix shake with non-molecular system</I>
+
+<DD>Your choice of atom style does not have bonds.
+
+<DT><I>Cannot use fix ttm with 2d simulation</I>
+
+<DD>This is a current restriction of this fix due to the grid it creates.
+
+<DT><I>Cannot use fix ttm with triclinic box</I>
+
+<DD>This is a current restriction of this fix due to the grid it creates.
+
+<DT><I>Cannot use fix tune/kspace without a kspace style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix tune/kspace without a pair style</I>
+
+<DD>This fix (tune/kspace) can only be used when a pair style has been specified.
+
+<DT><I>Cannot use fix wall in periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall zlo/zhi for a 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall/reflect in periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall/reflect zlo/zhi for a 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall/srd in periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall/srd more than once</I>
+
+<DD>Nor is their a need to since multiple walls can be specified
+in one command.
+
+<DT><I>Cannot use fix wall/srd without fix srd</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix wall/srd zlo/zhi for a 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix_deposit unless atoms have IDs</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use fix_pour unless atoms have IDs</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use include command within an if command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use lines with fix srd unless overlap is set</I>
+
+<DD>This is because line segements are connected to each other.
+
+<DT><I>Cannot use multiple fix wall commands with pair brownian</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use multiple fix wall commands with pair lubricate</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use multiple fix wall commands with pair lubricate/poly</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use multiple fix wall commands with pair lubricateU</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use neigh_modify exclude with GPU neighbor builds</I>
+
+<DD>This is a current limitation of the GPU implementation
+in LAMMPS.
+
+<DT><I>Cannot use neighbor bins - box size << cutoff</I>
+
+<DD>Too many neighbor bins will be created. This typically happens when
+the simulation box is very small in some dimension, compared to the
+neighbor cutoff. Use the "nsq" style instead of "bin" style.
+
+<DT><I>Cannot use newton pair with beck/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with born/coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with born/coul/wolf/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with born/gpu pair style</I>
+
+<DD>Self-explantory.
+
+<DT><I>Cannot use newton pair with buck/coul/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with buck/coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with buck/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with colloid/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with coul/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with coul/debye/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with coul/dsf/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with dipole/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with dpd/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with dpd/tstat/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with eam/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with gauss/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with gayberne/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/charmm/coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/class2/coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/class2/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/coul/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/coul/debye/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/coul/dsf/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/coul/long/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/coul/msm/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/expand/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj/gromacs/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with lj96/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with mie/cut/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with morse/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with resquared/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with soft/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with table/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with yukawa/colloid/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use newton pair with yukawa/gpu pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use non-zero forces in an energy minimization</I>
+
+<DD>Fix setforce cannot be used in this manner. Use fix addforce
+instead.
+
+<DT><I>Cannot use non-zero z offset in read_data for 2d simulation</I>
+
+<DD>The offset option is not yet supported.
+
+<DT><I>Cannot use nonperiodic boundares with fix ttm</I>
+
+<DD>This fix requires a fully periodic simulation box.
+
+<DT><I>Cannot use nonperiodic boundaries with Ewald</I>
+
+<DD>For kspace style ewald, all 3 dimensions must have periodic boundaries
+unless you use the kspace_modify command to define a 2d slab with a
+non-periodic z dimension.
+
+<DT><I>Cannot use nonperiodic boundaries with EwaldDisp</I>
+
+<DD>For kspace style ewald/disp, all 3 dimensions must have periodic
+boundaries unless you use the kspace_modify command to define a 2d
+slab with a non-periodic z dimension.
+
+<DT><I>Cannot use nonperiodic boundaries with PPPM</I>
+
+<DD>For kspace style pppm, all 3 dimensions must have periodic boundaries
+unless you use the kspace_modify command to define a 2d slab with a
+non-periodic z dimension.
+
+<DT><I>Cannot use nonperiodic boundaries with PPPMDisp</I>
+
+<DD>For kspace style pppm/disp, all 3 dimensions must have periodic
+boundaries unless you use the kspace_modify command to define a 2d
+slab with a non-periodic z dimension.
+
+<DT><I>Cannot use order greater than 8 with pppm/gpu.</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use package gpu neigh yes with triclinic box</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Cannot use pair hybrid with GPU neighbor list builds</I>
+
+<DD>Neighbor list builds must be done on the CPU for this pair style.
+
+<DT><I>Cannot use pair tail corrections with 2d simulations</I>
+
+<DD>The correction factors are only currently defined for 3d systems.
+
+<DT><I>Cannot use processors part command without using partitions</I>
+
+<DD>See the command-line -partition switch.
+
+<DT><I>Cannot use ramp in variable formula between runs</I>
+
+<DD>This is because the ramp() function is time dependent.
+
+<DT><I>Cannot use region INF or EDGE when box does not exist</I>
+
+<DD>Regions that extend to the box boundaries can only be used after the
+create_box command has been used.
+
+<DT><I>Cannot use set atom with no atom IDs defined</I>
+
+<DD>Atom IDs are not defined, so they cannot be used to identify an atom.
+
+<DT><I>Cannot use set mol with no molecule IDs defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use swiggle in variable formula between runs</I>
+
+<DD>This is a function of elapsed time.
+
+<DT><I>Cannot use tris with fix srd unless overlap is set</I>
+
+<DD>This is because triangles are connected to each other.
+
+<DT><I>Cannot use variable energy with constant efield in fix efield</I>
+
+<DD>LAMMPS computes the energy itself when the E-field is constant.
+
+<DT><I>Cannot use variable energy with constant force in fix addforce</I>
+
+<DD>This is because for constant force, LAMMPS can compute the change
+in energy directly.
+
+<DT><I>Cannot use variable every setting for dump dcd</I>
+
+<DD>The format of DCD dump files requires snapshots be output
+at a constant frequency.
+
+<DT><I>Cannot use variable every setting for dump xtc</I>
+
+<DD>The format of this file requires snapshots at regular intervals.
+
+<DT><I>Cannot use vdisplace in variable formula between runs</I>
+
+<DD>This is a function of elapsed time.
+
+<DT><I>Cannot use velocity bias command without temp keyword</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use velocity create loop all unless atoms have IDs</I>
+
+<DD>Atoms in the simulation to do not have IDs, so this style
+of velocity creation cannot be performed.
+
+<DT><I>Cannot use wall in periodic dimension</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use write_restart fileper without % in restart file name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot use write_restart nfile without % in restart file name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot wiggle and shear fix wall/gran</I>
+
+<DD>Cannot specify both options at the same time.
+
+<DT><I>Cannot write to restart file - MPI error: %s</I>
+
+<DD>This error was generated by MPI when reading/writing an MPI-IO restart
+file.
+
+<DT><I>Cannot yet use KSpace solver with grid with comm style tiled</I>
+
+<DD>This is current restriction in LAMMPS.
+
+<DT><I>Cannot yet use comm_style tiled with multi-mode comm</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot yet use comm_style tiled with triclinic box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot yet use fix bond/break with this improper style</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Cannot yet use fix bond/create with this improper style</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Cannot zero Langevin force of 0 atoms</I>
+
+<DD>The group has zero atoms, so you cannot request its force
+be zeroed.
+
+<DT><I>Cannot zero gld force for zero atoms</I>
+
+<DD>There are no atoms currently in the group.
+
+<DT><I>Cannot zero momentum of no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Change_box command before simulation box is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Change_box volume used incorrectly</I>
+
+<DD>The "dim volume" option must be used immediately following one or two
+settings for "dim1 ..." (and optionally "dim2 ...") and must be for a
+different dimension, i.e. dim != dim1 and dim != dim2.
+
+<DT><I>Chunk/atom compute does not exist for compute angmom/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute com/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute gyration/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute inertia/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute msd/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute omega/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute property/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute temp/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute torque/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for compute vcm/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Chunk/atom compute does not exist for fix ave/chunk</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Comm tiled invalid index in box drop brick</I>
+
+<DD>Internal error check in comm_style tiled which should not occur.
+Contact the developers.
+
+<DT><I>Comm tiled mis-match in box drop brick</I>
+
+<DD>Internal error check in comm_style tiled which should not occur.
+Contact the developers.
+
+<DT><I>Comm_modify group != atom_modify first group</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Communication cutoff for comm_style tiled cannot exceed periodic box length</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Communication cutoff too small for SNAP micro load balancing</I>
+
+<DD>This can happen if you change the neighbor skin after your pair_style
+command or if your box dimensions grow during a run. You can set the
+cutoff explicitly via the comm_modify cutoff command.
+
+<DT><I>Compute %s does not allow use of dynamic group</I>
+
+<DD>Dynamic groups have not yet been enabled for this compute.
+
+<DT><I>Compute ID for compute chunk/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for compute reduce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for compute slice does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/chunk does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/correlate does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/histo does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/spatial does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix ave/time does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix store/state does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID for fix vector does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ID must be alphanumeric or underscore characters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute angle/local used when angles are not allowed</I>
+
+<DD>The atom style does not support angles.
+
+<DT><I>Compute angmom/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute body/local requires atom style body</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute bond/local used when bonds are not allowed</I>
+
+<DD>The atom style does not support bonds.
+
+<DT><I>Compute centro/atom requires a pair style be defined</I>
+
+<DD>This is because the computation of the centro-symmetry values
+uses a pairwise neighbor list.
+
+<DT><I>Compute chunk/atom compute array is accessed out-of-range</I>
+
+<DD>The index for the array is out of bounds.
+
+<DT><I>Compute chunk/atom compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom compute does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom compute does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom fix array is accessed out-of-range</I>
+
+<DD>the index for the array is out of bounds.
+
+<DT><I>Compute chunk/atom fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom fix does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom fix does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom for triclinic boxes requires units reduced</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom ids once but nchunk is not once</I>
+
+<DD>You cannot assign chunks IDs to atom permanently if the number of
+chunks may change.
+
+<DT><I>Compute chunk/atom molecule for non-molecular system</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom stores no IDs for compute property/chunk</I>
+
+<DD>It will only store IDs if its compress option is enabled.
+
+<DT><I>Compute chunk/atom stores no coord1 for compute property/chunk</I>
+
+<DD>Only certain binning options for comptue chunk/atom store coordinates.
+
+<DT><I>Compute chunk/atom stores no coord2 for compute property/chunk</I>
+
+<DD>Only certain binning options for comptue chunk/atom store coordinates.
+
+<DT><I>Compute chunk/atom stores no coord3 for compute property/chunk</I>
+
+<DD>Only certain binning options for comptue chunk/atom store coordinates.
+
+<DT><I>Compute chunk/atom variable is not atom-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute chunk/atom without bins cannot use discard mixed</I>
+
+<DD>That discard option only applies to the binning styles.
+
+<DT><I>Compute cluster/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Cannot identify clusters beyond cutoff.
+
+<DT><I>Compute cluster/atom requires a pair style be defined</I>
+
+<DD>This is so that the pair style defines a cutoff distance which
+is used to find clusters.
+
+<DT><I>Compute cna/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Self-explantory.
+
+<DT><I>Compute cna/atom requires a pair style be defined</I>
+
+<DD>Self-explantory.
+
+<DT><I>Compute com/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute contact/atom requires a pair style be defined</I>
+
+<DD>Self-explantory.
+
+<DT><I>Compute contact/atom requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute coord/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Cannot compute coordination at distances longer than the pair cutoff,
+since those atoms are not in the neighbor list.
+
+<DT><I>Compute coord/atom requires a pair style be defined</I>
+
+<DD>Self-explantory.
+
+<DT><I>Compute damage/atom requires peridynamic potential</I>
+
+<DD>Damage is a Peridynamic-specific metric. It requires you
+to be running a Peridynamics simulation.
+
+<DT><I>Compute dihedral/local used when dihedrals are not allowed</I>
+
+<DD>The atom style does not support dihedrals.
+
+<DT><I>Compute dilatation/atom cannot be used with this pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute dilatation/atom requires Peridynamic pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute does not allow an extra compute or fix to be reset</I>
+
+<DD>This is an internal LAMMPS error. Please report it to the
+developers.
+
+<DT><I>Compute erotate/asphere requires atom style ellipsoid or line or tri</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute erotate/asphere requires extended particles</I>
+
+<DD>This compute cannot be used with point paritlces.
+
+<DT><I>Compute erotate/rigid with non-rigid fix-ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute erotate/sphere requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute erotate/sphere/atom requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute event/displace has invalid fix event assigned</I>
+
+<DD>This is an internal LAMMPS error. Please report it to the
+developers.
+
+<DT><I>Compute group/group group ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute gyration/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute heat/flux compute ID does not compute ke/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute heat/flux compute ID does not compute pe/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute heat/flux compute ID does not compute stress/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute improper/local used when impropers are not allowed</I>
+
+<DD>The atom style does not support impropers.
+
+<DT><I>Compute inertia/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute ke/rigid with non-rigid fix-ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute msd/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute msd/chunk nchunk is not static</I>
+
+<DD>This is required because the MSD cannot be computed consistently if
+the number of chunks is changing. Compute chunk/atom allows setting
+nchunk to be static.
+
+<DT><I>Compute nve/asphere requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute nvt/nph/npt asphere requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute omega/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute pair must use group all</I>
+
+<DD>Pair styles accumlate energy on all atoms.
+
+<DT><I>Compute pe must use group all</I>
+
+<DD>Energies computed by potentials (pair, bond, etc) are computed on all
+atoms.
+
+<DT><I>Compute plasticity/atom cannot be used with this pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute plasticity/atom requires Peridynamic pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute pressure must use group all</I>
+
+<DD>Virial contributions computed by potentials (pair, bond, etc) are
+computed on all atoms.
+
+<DT><I>Compute pressure requires temperature ID to include kinetic energy</I>
+
+<DD>The keflag cannot be used unless a temperature compute is provided.
+
+<DT><I>Compute pressure temperature ID does not compute temperature</I>
+
+<DD>The compute ID assigned to a pressure computation must compute
+temperature.
+
+<DT><I>Compute property/atom floating point vector does not exist</I>
+
+<DD>The command is accessing a vector added by the fix property/atom
+command, that does not exist.
+
+<DT><I>Compute property/atom for atom property that isn't allocated</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute property/atom integer vector does not exist</I>
+
+<DD>The command is accessing a vector added by the fix property/atom
+command, that does not exist.
+
+<DT><I>Compute property/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute property/local cannot use these inputs together</I>
+
+<DD>Only inputs that generate the same number of datums can be used
+togther. E.g. bond and angle quantities cannot be mixed.
+
+<DT><I>Compute property/local does not (yet) work with atom_style template</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute property/local for property that isn't allocated</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute rdf requires a pair style be defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce compute array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Compute reduce compute calculates global values</I>
+
+<DD>A compute that calculates peratom or local values is required.
+
+<DT><I>Compute reduce compute does not calculate a local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce compute does not calculate a local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce compute does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce fix array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Compute reduce fix calculates global values</I>
+
+<DD>A fix that calculates peratom or local values is required.
+
+<DT><I>Compute reduce fix does not calculate a local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce fix does not calculate a local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce fix does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce replace requires min or max mode</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute reduce variable is not atom-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice compute array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Compute slice compute does not calculate a global array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice compute does not calculate a global vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice compute does not calculate global vector or array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice compute vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Compute slice fix array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Compute slice fix does not calculate a global array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice fix does not calculate a global vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice fix does not calculate global vector or array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute slice fix vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Compute sna/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute sna/atom requires a pair style be defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute snad/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute snad/atom requires a pair style be defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute snav/atom cutoff is longer than pairwise cutoff</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute snav/atom requires a pair style be defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute stress/atom temperature ID does not compute temperature</I>
+
+<DD>The specified compute must compute temperature.
+
+<DT><I>Compute temp/asphere requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute temp/asphere requires extended particles</I>
+
+<DD>This compute cannot be used with point paritlces.
+
+<DT><I>Compute temp/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute temp/cs requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Compute temp/cs used when bonds are not allowed</I>
+
+<DD>This compute only works on pairs of bonded particles.
+
+<DT><I>Compute temp/partial cannot use vz for 2d systemx</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute temp/profile cannot bin z for 2d systems</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute temp/profile cannot use vz for 2d systemx</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute temp/sphere requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ti kspace style does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ti pair style does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute ti tail when pair style does not compute tail corrections</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute torque/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Compute used in dump between runs is not current</I>
+
+<DD>The compute was not invoked on the current timestep, therefore it
+cannot be used in a dump between runs.
+
+<DT><I>Compute used in variable between runs is not current</I>
+
+<DD>Computes cannot be invoked by a variable in between runs. Thus they
+must have been evaluated on the last timestep of the previous run in
+order for their value(s) to be accessed. See the doc page for the
+variable command for more info.
+
+<DT><I>Compute used in variable thermo keyword between runs is not current</I>
+
+<DD>Some thermo keywords rely on a compute to calculate their value(s).
+Computes cannot be invoked by a variable in between runs. Thus they
+must have been evaluated on the last timestep of the previous run in
+order for their value(s) to be accessed. See the doc page for the
+variable command for more info.
+
+<DT><I>Compute vcm/chunk does not use chunk/atom compute</I>
+
+<DD>The style of the specified compute is not chunk/atom.
+
+<DT><I>Computed temperature for fix temp/berendsen cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Computed temperature for fix temp/rescale cannot be 0.0</I>
+
+<DD>Cannot rescale the temperature to a new value if the current
+temperature is 0.0.
+
+<DT><I>Core/shell partner atom not found</I>
+
+<DD>Could not find one of the atoms in the bond pair.
+
+<DT><I>Core/shell partners were not all found</I>
+
+<DD>Could not find or more atoms in the bond pairs.
+
+<DT><I>Could not adjust g_ewald_6</I>
+
+<DD>The Newton-Raphson solver failed to converge to a good value for
+g_ewald. This error should not occur for typical problems. Please
+send an email to the developers.
+
+<DT><I>Could not compute g_ewald</I>
+
+<DD>The Newton-Raphson solver failed to converge to a good value for
+g_ewald. This error should not occur for typical problems. Please
+send an email to the developers.
+
+<DT><I>Could not compute grid size</I>
+
+<DD>The code is unable to compute a grid size consistent with the desired
+accuracy. This error should not occur for typical problems. Please
+send an email to the developers.
+
+<DT><I>Could not compute grid size for Coulomb interaction</I>
+
+<DD>The code is unable to compute a grid size consistent with the desired
+accuracy. This error should not occur for typical problems. Please
+send an email to the developers.
+
+<DT><I>Could not compute grid size for Dispersion</I>
+
+<DD>The code is unable to compute a grid size consistent with the desired
+accuracy. This error should not occur for typical problems. Please
+send an email to the developers.
+
+<DT><I>Could not create 3d FFT plan</I>
+
+<DD>The FFT setup for the PPPM solver failed, typically due
+to lack of memory. This is an unusual error. Check the
+size of the FFT grid you are requesting.
+
+<DT><I>Could not create 3d grid of processors</I>
+
+<DD>The specified constraints did not allow a Px by Py by Pz grid to be
+created where Px * Py * Pz = P = total number of processors.
+
+<DT><I>Could not create 3d remap plan</I>
+
+<DD>The FFT setup in pppm failed.
+
+<DT><I>Could not create Python function arguments</I>
+
+<DD>This is an internal Python error, possibly because the number
+of inputs to the function is too large.
+
+<DT><I>Could not create numa grid of processors</I>
+
+<DD>The specified constraints did not allow this style of grid to be
+created. Usually this is because the total processor count is not a
+multiple of the cores/node or the user specified processor count is >
+1 in one of the dimensions.
+
+<DT><I>Could not create twolevel 3d grid of processors</I>
+
+<DD>The specified constraints did not allow this style of grid to be
+created.
+
+<DT><I>Could not evaluate Python function input variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find Python function</I>
+
+<DD>The provided Python code was run successfully, but it not
+define a callable function with the required name.
+
+<DT><I>Could not find atom_modify first group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find change_box group ID</I>
+
+<DD>Group ID used in the change_box command does not exist.
+
+<DT><I>Could not find compute ID for PRD</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute ID for TAD</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute ID for temperature bias</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute ID to delete</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute displace/atom fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute event/displace fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute heat/flux compute ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute msd fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute pressure temperature ID</I>
+
+<DD>The compute ID for calculating temperature does not exist.
+
+<DT><I>Could not find compute stress/atom temperature ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute vacf fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute/voronoi surface group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find compute_modify ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find custom per-atom property ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find delete_atoms group ID</I>
+
+<DD>Group ID used in the delete_atoms command does not exist.
+
+<DT><I>Could not find delete_atoms region ID</I>
+
+<DD>Region ID used in the delete_atoms command does not exist.
+
+<DT><I>Could not find displace_atoms group ID</I>
+
+<DD>Group ID used in the displace_atoms command does not exist.
+
+<DT><I>Could not find dump custom compute ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump custom fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump custom variable name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump group ID</I>
+
+<DD>A group ID used in the dump command does not exist.
+
+<DT><I>Could not find dump local compute ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump local fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump modify compute ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump modify custom atom floating point property ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump modify custom atom integer property ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump modify fix ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find dump modify variable name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix ID to delete</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix adapt storage fix ID</I>
+
+<DD>This should not happen unless you explicitly deleted
+a secondary fix that fix adapt created internally.
+
+<DT><I>Could not find fix gcmc exclusion group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix gcmc rotation group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix group ID</I>
+
+<DD>A group ID used in the fix command does not exist.
+
+<DT><I>Could not find fix msst compute ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix poems group ID</I>
+
+<DD>A group ID used in the fix poems command does not exist.
+
+<DT><I>Could not find fix recenter group ID</I>
+
+<DD>A group ID used in the fix recenter command does not exist.
+
+<DT><I>Could not find fix rigid group ID</I>
+
+<DD>A group ID used in the fix rigid command does not exist.
+
+<DT><I>Could not find fix srd group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find fix_modify ID</I>
+
+<DD>A fix ID used in the fix_modify command does not exist.
+
+<DT><I>Could not find fix_modify pressure ID</I>
+
+<DD>The compute ID for computing pressure does not exist.
+
+<DT><I>Could not find fix_modify temperature ID</I>
+
+<DD>The compute ID for computing temperature does not exist.
+
+<DT><I>Could not find group clear group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find group delete group ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find set group ID</I>
+
+<DD>Group ID specified in set command does not exist.
+
+<DT><I>Could not find thermo compute ID</I>
+
+<DD>Compute ID specified in thermo_style command does not exist.
+
+<DT><I>Could not find thermo custom compute ID</I>
+
+<DD>The compute ID needed by thermo style custom to compute a requested
+quantity does not exist.
+
+<DT><I>Could not find thermo custom fix ID</I>
+
+<DD>The fix ID needed by thermo style custom to compute a requested
+quantity does not exist.
+
+<DT><I>Could not find thermo custom variable name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find thermo fix ID</I>
+
+<DD>Fix ID specified in thermo_style command does not exist.
+
+<DT><I>Could not find thermo variable name</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not find thermo_modify pressure ID</I>
+
+<DD>The compute ID needed by thermo style custom to compute pressure does
+not exist.
+
+<DT><I>Could not find thermo_modify temperature ID</I>
+
+<DD>The compute ID needed by thermo style custom to compute temperature does
+not exist.
+
+<DT><I>Could not find undump ID</I>
+
+<DD>A dump ID used in the undump command does not exist.
+
+<DT><I>Could not find velocity group ID</I>
+
+<DD>A group ID used in the velocity command does not exist.
+
+<DT><I>Could not find velocity temperature ID</I>
+
+<DD>The compute ID needed by the velocity command to compute temperature
+does not exist.
+
+<DT><I>Could not find/initialize a specified accelerator device</I>
+
+<DD>Could not initialize at least one of the devices specified for the gpu
+package
+
+<DT><I>Could not grab element entry from EIM potential file</I>
+
+<DD>Self-explanatory
+
+<DT><I>Could not grab global entry from EIM potential file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not grab pair entry from EIM potential file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Could not initialize embedded Python</I>
+
+<DD>The main module in Python was not accessible.
+
+<DT><I>Could not open Python file</I>
+
+<DD>The specified file of Python code cannot be opened. Check that the
+path and name are correct.
+
+<DT><I>Could not process Python file</I>
+
+<DD>The Python code in the specified file was not run sucessfully by
+Python, probably due to errors in the Python code.
+
+<DT><I>Could not process Python string</I>
+
+<DD>The Python code in the here string was not run sucessfully by Python,
+probably due to errors in the Python code.
+
+<DT><I>Coulomb PPPMDisp order has been reduced below minorder</I>
+
+<DD>The default minimum order is 2. This can be reset by the
+kspace_modify minorder command.
+
+<DT><I>Coulomb cut not supported in pair_style buck/long/coul/coul</I>
+
+<DD>Must use long-range Coulombic interactions.
+
+<DT><I>Coulomb cut not supported in pair_style lj/long/coul/long</I>
+
+<DD>Must use long-range Coulombic interactions.
+
+<DT><I>Coulomb cut not supported in pair_style lj/long/tip4p/long</I>
+
+<DD>Must use long-range Coulombic interactions.
+
+<DT><I>Coulomb cutoffs of pair hybrid sub-styles do not match</I>
+
+<DD>If using a Kspace solver, all Coulomb cutoffs of long pair styles must
+be the same.
+
+<DT><I>Coulombic cut not supported in pair_style lj/long/dipole/long</I>
+
+<DD>Must use long-range Coulombic interactions.
+
+<DT><I>Cound not find dump_modify ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Create_atoms command before simulation box is defined</I>
+
+<DD>The create_atoms command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Create_atoms molecule has atom IDs, but system does not</I>
+
+<DD>The atom_style id command can be used to force atom IDs to be stored.
+
+<DT><I>Create_atoms molecule must have atom types</I>
+
+<DD>The defined molecule does not specify atom types.
+
+<DT><I>Create_atoms molecule must have coordinates</I>
+
+<DD>The defined molecule does not specify coordinates.
+
+<DT><I>Create_atoms region ID does not exist</I>
+
+<DD>A region ID used in the create_atoms command does not exist.
+
+<DT><I>Create_bonds command before simulation box is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Create_bonds command requires no kspace_style be defined</I>
+
+<DD>This is so that atom pairs that are already bonded to not appear
+in the neighbor list.
+
+<DT><I>Create_bonds command requires special_bonds 1-2 weights be 0.0</I>
+
+<DD>This is so that atom pairs that are already bonded to not appear in
+the neighbor list.
+
+<DT><I>Create_bonds max distance > neighbor cutoff</I>
+
+<DD>Can only create bonds for atom pairs that will be in neighbor list.
+
+<DT><I>Create_bonds requires a pair style be defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Create_box region ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Create_box region does not support a bounding box</I>
+
+<DD>Not all regions represent bounded volumes. You cannot use
+such a region with the create_box command.
+
+<DT><I>Custom floating point vector for fix store/state does not exist</I>
+
+<DD>The command is accessing a vector added by the fix property/atom
+command, that does not exist.
+
+<DT><I>Custom integer vector for fix store/state does not exist</I>
+
+<DD>The command is accessing a vector added by the fix property/atom
+command, that does not exist.
+
+<DT><I>Custom per-atom property ID is not floating point</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Custom per-atom property ID is not integer</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cut-offs missing in pair_style lj/long/dipole/long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cutoffs missing in pair_style buck/long/coul/long</I>
+
+<DD>Self-exlanatory.
+
+<DT><I>Cutoffs missing in pair_style lj/long/coul/long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cyclic loop in joint connections</I>
+
+<DD>Fix poems cannot (yet) work with coupled bodies whose joints connect
+the bodies in a ring (or cycle).
+
+<DT><I>Degenerate lattice primitive vectors</I>
+
+<DD>Invalid set of 3 lattice vectors for lattice command.
+
+<DT><I>Delete region ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Delete_atoms command before simulation box is defined</I>
+
+<DD>The delete_atoms command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Delete_atoms cutoff > max neighbor cutoff</I>
+
+<DD>Can only delete atoms in atom pairs that will be in neighbor list.
+
+<DT><I>Delete_atoms requires a pair style be defined</I>
+
+<DD>This is because atom deletion within a cutoff uses a pairwise
+neighbor list.
+
+<DT><I>Delete_bonds command before simulation box is defined</I>
+
+<DD>The delete_bonds command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Delete_bonds command with no atoms existing</I>
+
+<DD>No atoms are yet defined so the delete_bonds command cannot be used.
+
+<DT><I>Delta_mu not allowed when not using semi-grand in fix atom/swap command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Deposition region extends outside simulation box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Did not assign all atoms correctly</I>
+
+<DD>Atoms read in from a data file were not assigned correctly to
+processors. This is likely due to some atom coordinates being
+outside a non-periodic simulation box.
+
+<DT><I>Did not assign all restart atoms correctly</I>
+
+<DD>Atoms read in from the restart file were not assigned correctly to
+processors. This is likely due to some atom coordinates being outside
+a non-periodic simulation box. Normally this should not happen. You
+may wish to use the "remap" option on the read_restart command to see
+if this helps.
+
+<DT><I>Did not find all elements in MEAM library file</I>
+
+<DD>The requested elements were not found in the MEAM file.
+
+<DT><I>Did not find fix shake partner info</I>
+
+<DD>Could not find bond partners implied by fix shake command. This error
+can be triggered if the delete_bonds command was used before fix
+shake, and it removed bonds without resetting the 1-2, 1-3, 1-4
+weighting list via the special keyword.
+
+<DT><I>Did not find keyword in table file</I>
+
+<DD>Keyword used in pair_coeff command was not found in table file.
+
+<DT><I>Did not set pressure for fix rigid/nph</I>
+
+<DD>The press keyword must be specified.
+
+<DT><I>Did not set temp for fix rigid/nvt/small</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Did not set temp or press for fix rigid/npt/small</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Did not set temperature for fix rigid/nvt</I>
+
+<DD>The temp keyword must be specified.
+
+<DT><I>Did not set temperature or pressure for fix rigid/npt</I>
+
+<DD>The temp and press keywords must be specified.
+
+<DT><I>Dihedral atom missing in delete_bonds</I>
+
+<DD>The delete_bonds command cannot find one or more atoms in a particular
+dihedral on a particular processor. The pairwise cutoff is too short
+or the atoms are too far apart to make a valid dihedral.
+
+<DT><I>Dihedral atom missing in set command</I>
+
+<DD>The set command cannot find one or more atoms in a particular dihedral
+on a particular processor. The pairwise cutoff is too short or the
+atoms are too far apart to make a valid dihedral.
+
+<DT><I>Dihedral atoms %d %d %d %d missing on proc %d at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular dihedral are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the dihedral has blown apart and an atom is
+too far away.
+
+<DT><I>Dihedral atoms missing on proc %d at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular dihedral are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the dihedral has blown apart and an atom is
+too far away.
+
+<DT><I>Dihedral charmm is incompatible with Pair style</I>
+
+<DD>Dihedral style charmm must be used with a pair style charmm
+in order for the 1-4 epsilon/sigma parameters to be defined.
+
+<DT><I>Dihedral coeff for hybrid has invalid style</I>
+
+<DD>Dihedral style hybrid uses another dihedral style as one of its
+coefficients. The dihedral style used in the dihedral_coeff command
+or read from a restart file is not recognized.
+
+<DT><I>Dihedral coeffs are not set</I>
+
+<DD>No dihedral coefficients have been assigned in the data file or via
+the dihedral_coeff command.
+
+<DT><I>Dihedral style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dihedral style hybrid cannot have none as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dihedral style hybrid cannot use same dihedral style twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dihedral/improper extent > half of periodic box length</I>
+
+<DD>This error was detected by the neigh_modify check yes setting. It is
+an error because the dihedral atoms are so far apart it is ambiguous
+how it should be defined.
+
+<DT><I>Dihedral_coeff command before dihedral_style is defined</I>
+
+<DD>Coefficients cannot be set in the data file or via the dihedral_coeff
+command until an dihedral_style has been assigned.
+
+<DT><I>Dihedral_coeff command before simulation box is defined</I>
+
+<DD>The dihedral_coeff command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Dihedral_coeff command when no dihedrals allowed</I>
+
+<DD>The chosen atom style does not allow for dihedrals to be defined.
+
+<DT><I>Dihedral_style command when no dihedrals allowed</I>
+
+<DD>The chosen atom style does not allow for dihedrals to be defined.
+
+<DT><I>Dihedrals assigned incorrectly</I>
+
+<DD>Dihedrals read in from the data file were not assigned correctly to
+atoms. This means there is something invalid about the topology
+definitions.
+
+<DT><I>Dihedrals defined but no dihedral types</I>
+
+<DD>The data file header lists dihedrals but no dihedral types.
+
+<DT><I>Dimension command after simulation box is defined</I>
+
+<DD>The dimension command cannot be used after a read_data,
+read_restart, or create_box command.
+
+<DT><I>Dispersion PPPMDisp order has been reduced below minorder</I>
+
+<DD>The default minimum order is 2. This can be reset by the
+kspace_modify minorder command.
+
+<DT><I>Displace_atoms command before simulation box is defined</I>
+
+<DD>The displace_atoms command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Distance must be > 0 for compute event/displace</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Divide by 0 in influence function</I>
+
+<DD>This should not normally occur. It is likely a problem with your
+model.
+
+<DT><I>Divide by 0 in influence function of pair peri/lps</I>
+
+<DD>This should not normally occur. It is likely a problem with your
+model.
+
+<DT><I>Divide by 0 in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Domain too large for neighbor bins</I>
+
+<DD>The domain has become extremely large so that neighbor bins cannot be
+used. Most likely, one or more atoms have been blown out of the
+simulation box to a great distance.
+
+<DT><I>Double precision is not supported on this accelerator</I>
+
+<DD>Self-explanatory
+
+<DT><I>Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump cfg arguments must start with 'mass type xs ys zs' or 'mass type xsu ysu zsu'</I>
+
+<DD>This is a requirement of the CFG output format. See the dump cfg doc
+page for more details.
+
+<DT><I>Dump cfg requires one snapshot per file</I>
+
+<DD>Use the wildcard "*" character in the filename.
+
+<DT><I>Dump custom and fix not computed at compatible times</I>
+
+<DD>The fix must produce per-atom quantities on timesteps that dump custom
+needs them.
+
+<DT><I>Dump custom compute does not calculate per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom compute does not calculate per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom compute does not compute per-atom info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom fix does not compute per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom fix does not compute per-atom info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom fix does not compute per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump custom variable is not atom-style variable</I>
+
+<DD>Only atom-style variables generate per-atom quantities, needed for
+dump output.
+
+<DT><I>Dump dcd of non-matching # of atoms</I>
+
+<DD>Every snapshot written by dump dcd must contain the same # of atoms.
+
+<DT><I>Dump dcd requires sorting by atom ID</I>
+
+<DD>Use the dump_modify sort command to enable this.
+
+<DT><I>Dump every variable returned a bad timestep</I>
+
+<DD>The variable must return a timestep greater than the current timestep.
+
+<DT><I>Dump file MPI-IO output not allowed with % in filename</I>
+
+<DD>This is because a % signifies one file per processor and MPI-IO
+creates one large file for all processors.
+
+<DT><I>Dump file does not contain requested snapshot</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump file is incorrectly formatted</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump image bond not allowed with no bond types</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump image cannot perform sorting</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump image persp option is not yet supported</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump image requires one snapshot per file</I>
+
+<DD>Use a "*" in the filename.
+
+<DT><I>Dump local and fix not computed at compatible times</I>
+
+<DD>The fix must produce per-atom quantities on timesteps that dump local
+needs them.
+
+<DT><I>Dump local attributes contain no compute or fix</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local cannot sort by atom ID</I>
+
+<DD>This is because dump local does not really dump per-atom info.
+
+<DT><I>Dump local compute does not calculate local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local compute does not calculate local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local compute does not compute local info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local count is not consistent across input fields</I>
+
+<DD>Every column of output must be the same length.
+
+<DT><I>Dump local fix does not compute local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local fix does not compute local info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local fix does not compute local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump local fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify bcolor not allowed with no bond types</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify bdiam not allowed with no bond types</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify compute ID does not compute per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify compute ID does not compute per-atom info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify compute ID does not compute per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify compute ID vector is not large enough</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify element names do not match atom types</I>
+
+<DD>Number of element names must equal number of atom types.
+
+<DT><I>Dump modify fix ID does not compute per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify fix ID does not compute per-atom info</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify fix ID does not compute per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify fix ID vector is not large enough</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump modify variable is not atom-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump sort column is invalid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump xtc requires sorting by atom ID</I>
+
+<DD>Use the dump_modify sort command to enable this.
+
+<DT><I>Dump_modify buffer yes not allowed for this style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump_modify format string is too short</I>
+
+<DD>There are more fields to be dumped in a line of output than your
+format string specifies.
+
+<DT><I>Dump_modify region ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dumping an atom property that isn't allocated</I>
+
+<DD>The chosen atom style does not define the per-atom quantity being
+dumped.
+
+<DT><I>Duplicate fields in read_dump command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Duplicate particle in PeriDynamic bond - simulation box is too small</I>
+
+<DD>This is likely because your box length is shorter than 2 times
+the bond length.
+
+<DT><I>Electronic temperature dropped below zero</I>
+
+<DD>Something has gone wrong with the fix ttm electron temperature model.
+
+<DT><I>Empty brackets in variable</I>
+
+<DD>There is no variable syntax that uses empty brackets. Check
+the variable doc page.
+
+<DT><I>Energy was not tallied on needed timestep</I>
+
+<DD>You are using a thermo keyword that requires potentials to
+have tallied energy, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+<DT><I>Epsilon or sigma reference not set by pair style in PPPMDisp</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Epsilon or sigma reference not set by pair style in ewald/n</I>
+
+<DD>The pair style is not providing the needed epsilon or sigma values.
+
+<DT><I>Error in vdw spline: inner radius > outer radius</I>
+
+<DD>A pre-tabulated spline is invalid. Likely a problem with the
+potential parameters.
+
+<DT><I>Failed to allocate %ld bytes for array %s</I>
+
+<DD>Your LAMMPS simulation has run out of memory. You need to run a
+smaller simulation or on more processors.
+
+<DT><I>Failed to open FFmpeg pipeline to file %s</I>
+
+<DD>The specified file cannot be opened. Check that the path and name are
+correct and writable and that the FFmpeg executable can be found and run.
+
+<DT><I>Failed to reallocate %ld bytes for array %s</I>
+
+<DD>Your LAMMPS simulation has run out of memory. You need to run a
+smaller simulation or on more processors.
+
+<DT><I>Fewer SRD bins than processors in some dimension</I>
+
+<DD>This is not allowed. Make your SRD bin size smaller.
+
+<DT><I>File variable could not read value</I>
+
+<DD>Check the file assigned to the variable.
+
+<DT><I>Final box dimension due to fix deform is < 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix %s does not allow use of dynamic group</I>
+
+<DD>Dynamic groups have not yet been enabled for this fix.
+
+<DT><I>Fix ID for compute chunk/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for compute erotate/rigid does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for compute ke/rigid does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for compute reduce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for compute slice does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/chunk does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/correlate does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/histo does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/spatial does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix ave/time does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for fix store/state does not exist</I>
+
+<DD>Self-explanatory
+
+<DT><I>Fix ID for fix vector does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for read_data does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID for velocity does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ID must be alphanumeric or underscore characters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix SRD: bad bin assignment for SRD advection</I>
+
+<DD>Something has gone wrong in your SRD model; try using more
+conservative settings.
+
+<DT><I>Fix SRD: bad search bin assignment</I>
+
+<DD>Something has gone wrong in your SRD model; try using more
+conservative settings.
+
+<DT><I>Fix SRD: bad stencil bin for big particle</I>
+
+<DD>Something has gone wrong in your SRD model; try using more
+conservative settings.
+
+<DT><I>Fix SRD: too many big particles in bin</I>
+
+<DD>Reset the ATOMPERBIN parameter at the top of fix_srd.cpp
+to a larger value, and re-compile the code.
+
+<DT><I>Fix SRD: too many walls in bin</I>
+
+<DD>This should not happen unless your system has been setup incorrectly.
+
+<DT><I>Fix adapt interface to this pair style not supported</I>
+
+<DD>New coding for the pair style would need to be done.
+
+<DT><I>Fix adapt kspace style does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix adapt pair style does not exist</I>
+
+<DD>Self-explanatory
+
+<DT><I>Fix adapt pair style param not supported</I>
+
+<DD>The pair style does not know about the parameter you specified.
+
+<DT><I>Fix adapt requires atom attribute charge</I>
+
+<DD>The atom style being used does not specify an atom charge.
+
+<DT><I>Fix adapt requires atom attribute diameter</I>
+
+<DD>The atom style being used does not specify an atom diameter.
+
+<DT><I>Fix adapt type pair range is not valid for pair hybrid sub-style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix append/atoms requires a lattice be defined</I>
+
+<DD>Use the lattice command for this purpose.
+
+<DT><I>Fix ave/atom compute array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/atom compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/atom compute does not calculate a per-atom vector</I>
+
+<DD>A compute used by fix ave/atom must generate per-atom values.
+
+<DT><I>Fix ave/atom compute does not calculate per-atom values</I>
+
+<DD>A compute used by fix ave/atom must generate per-atom values.
+
+<DT><I>Fix ave/atom fix array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/atom fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/atom fix does not calculate a per-atom vector</I>
+
+<DD>A fix used by fix ave/atom must generate per-atom values.
+
+<DT><I>Fix ave/atom fix does not calculate per-atom values</I>
+
+<DD>A fix used by fix ave/atom must generate per-atom values.
+
+<DT><I>Fix ave/atom variable is not atom-style variable</I>
+
+<DD>A variable used by fix ave/atom must generate per-atom values.
+
+<DT><I>Fix ave/chunk compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk compute does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk compute does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk does not use chunk/atom compute</I>
+
+<DD>The specified conpute is not for a compute chunk/atom command.
+
+<DT><I>Fix ave/chunk fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk fix does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk fix does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/chunk variable is not atom-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/correlate compute does not calculate a scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/correlate compute does not calculate a vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/correlate compute vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/correlate fix does not calculate a scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/correlate fix does not calculate a vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/correlate fix vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/correlate variable is not equal-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo cannot input local values in scalar mode</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo cannot input per-atom values in scalar mode</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a global array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a global scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a global vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate local values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a global array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a global scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a global vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a local array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a local vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate a per-atom vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate local values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix does not calculate per-atom values</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo input is invalid compute</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo input is invalid fix</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo input is invalid variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/histo inputs are not all global, peratom, or local</I>
+
+<DD>All inputs in a single fix ave/histo command must be of the
+same style.
+
+<DT><I>Fix ave/spatial compute does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/spatial compute does not calculate a per-atom vector</I>
+
+<DD>A compute used by fix ave/spatial must generate per-atom values.
+
+<DT><I>Fix ave/spatial compute does not calculate per-atom values</I>
+
+<DD>A compute used by fix ave/spatial must generate per-atom values.
+
+<DT><I>Fix ave/spatial compute vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/spatial fix does not calculate a per-atom array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/spatial fix does not calculate a per-atom vector</I>
+
+<DD>A fix used by fix ave/spatial must generate per-atom values.
+
+<DT><I>Fix ave/spatial fix does not calculate per-atom values</I>
+
+<DD>A fix used by fix ave/spatial must generate per-atom values.
+
+<DT><I>Fix ave/spatial fix vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/spatial for triclinic boxes requires units reduced</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/spatial settings invalid with changing box size</I>
+
+<DD>If the box size changes, only the units reduced option can be
+used.
+
+<DT><I>Fix ave/spatial variable is not atom-style variable</I>
+
+<DD>A variable used by fix ave/spatial must generate per-atom values.
+
+<DT><I>Fix ave/time cannot set output array intensive/extensive from these inputs</I>
+
+<DD>One of more of the vector inputs has individual elements which are
+flagged as intensive or extensive. Such an input cannot be flagged as
+all intensive/extensive when turned into an array by fix ave/time.
+
+<DT><I>Fix ave/time cannot use variable with vector mode</I>
+
+<DD>Variables produce scalar values.
+
+<DT><I>Fix ave/time columns are inconsistent lengths</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time compute array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Fix ave/time compute does not calculate a scalar</I>
+
+<DD>Self-explantory.
+
+<DT><I>Fix ave/time compute does not calculate a vector</I>
+
+<DD>Self-explantory.
+
+<DT><I>Fix ave/time compute does not calculate an array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time compute vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/time fix array cannot be variable length</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time fix array is accessed out-of-range</I>
+
+<DD>An index for the array is out of bounds.
+
+<DT><I>Fix ave/time fix does not calculate a scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time fix does not calculate a vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time fix does not calculate an array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time fix vector cannot be variable length</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ave/time fix vector is accessed out-of-range</I>
+
+<DD>The index for the vector is out of bounds.
+
+<DT><I>Fix ave/time variable is not equal-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix balance rcb cannot be used with comm_style brick</I>
+
+<DD>Comm_style tiled must be used instead.
+
+<DT><I>Fix balance shift string is invalid</I>
+
+<DD>The string can only contain the characters "x", "y", or "z".
+
+<DT><I>Fix bond/break needs ghost atoms from further away</I>
+
+<DD>This is because the fix needs to walk bonds to a certain distance to
+acquire needed info, The comm_modify cutoff command can be used to
+extend the communication range.
+
+<DT><I>Fix bond/create angle type is invalid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix bond/create cutoff is longer than pairwise cutoff</I>
+
+<DD>This is not allowed because bond creation is done using the
+pairwise neighbor list.
+
+<DT><I>Fix bond/create dihedral type is invalid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix bond/create improper type is invalid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix bond/create induced too many angles/dihedrals/impropers per atom</I>
+
+<DD>See the read_data command for info on setting the "extra angle per
+atom", etc header values to allow for additional angles, etc to be
+formed.
+
+<DT><I>Fix bond/create needs ghost atoms from further away</I>
+
+<DD>This is because the fix needs to walk bonds to a certain distance to
+acquire needed info, The comm_modify cutoff command can be used to
+extend the communication range.
+
+<DT><I>Fix bond/swap cannot use dihedral or improper styles</I>
+
+<DD>These styles cannot be defined when using this fix.
+
+<DT><I>Fix bond/swap requires pair and bond styles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix bond/swap requires special_bonds = 0,1,1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix box/relax generated negative box length</I>
+
+<DD>The pressure being applied is likely too large. Try applying
+it incrementally, to build to the high pressure.
+
+<DT><I>Fix command before simulation box is defined</I>
+
+<DD>The fix command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Fix deform cannot use yz variable with xy</I>
+
+<DD>The yz setting cannot be a variable if xy deformation is also
+specified. This is because LAMMPS cannot determine if the yz setting
+will induce a box flip which would be invalid if xy is also changing.
+
+<DT><I>Fix deform is changing yz too much with xy</I>
+
+<DD>When both yz and xy are changing, it induces changes in xz if the
+box must flip from one tilt extreme to another. Thus it is not
+allowed for yz to grow so much that a flip is induced.
+
+<DT><I>Fix deform tilt factors require triclinic box</I>
+
+<DD>Cannot deform the tilt factors of a simulation box unless it
+is a triclinic (non-orthogonal) box.
+
+<DT><I>Fix deform volume setting is invalid</I>
+
+<DD>Cannot use volume style unless other dimensions are being controlled.
+
+<DT><I>Fix deposit and fix rigid/small not using same molecule template ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix deposit and fix shake not using same molecule template ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix deposit molecule must have atom types</I>
+
+<DD>The defined molecule does not specify atom types.
+
+<DT><I>Fix deposit molecule must have coordinates</I>
+
+<DD>The defined molecule does not specify coordinates.
+
+<DT><I>Fix deposit molecule template ID must be same as atom_style template ID</I>
+
+<DD>When using atom_style template, you cannot deposit molecules that are
+not in that template.
+
+<DT><I>Fix deposit region cannot be dynamic</I>
+
+<DD>Only static regions can be used with fix deposit.
+
+<DT><I>Fix deposit region does not support a bounding box</I>
+
+<DD>Not all regions represent bounded volumes. You cannot use
+such a region with the fix deposit command.
+
+<DT><I>Fix deposit shake fix does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix efield requires atom attribute q or mu</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Fix efield with dipoles cannot use atom-style variables</I>
+
+<DD>This option is not supported.
+
+<DT><I>Fix evaporate molecule requires atom attribute molecule</I>
+
+<DD>The atom style being used does not define a molecule ID.
+
+<DT><I>Fix external callback function not set</I>
+
+<DD>This must be done by an external program in order to use this fix.
+
+<DT><I>Fix for fix ave/atom not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/atom is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix ave/chunk not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/chunk is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix ave/correlate not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/correlate
+is requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix ave/histo not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/histo is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix ave/spatial not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/spatial is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix ave/time not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix ave/time
+is requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix store/state not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix store/state
+is requesting a value on a non-allowed timestep.
+
+<DT><I>Fix for fix vector not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Fix vector is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix freeze requires atom attribute torque</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Fix gcmc and fix shake not using same molecule template ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gcmc cannot exchange individual atoms belonging to a molecule</I>
+
+<DD>This is an error since you should not delete only one atom of a
+molecule. The user has specified atomic (non-molecular) gas
+exchanges, but an atom belonging to a molecule could be deleted.
+
+<DT><I>Fix gcmc does not (yet) work with atom_style template</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gcmc molecule command requires that atoms have molecule attributes</I>
+
+<DD>Should not choose the gcmc molecule feature if no molecules are being
+simulated. The general molecule flag is off, but gcmc's molecule flag
+is on.
+
+<DT><I>Fix gcmc molecule must have atom types</I>
+
+<DD>The defined molecule does not specify atom types.
+
+<DT><I>Fix gcmc molecule must have coordinates</I>
+
+<DD>The defined molecule does not specify coordinates.
+
+<DT><I>Fix gcmc molecule template ID must be same as atom_style template ID</I>
+
+<DD>When using atom_style template, you cannot insert molecules that are
+not in that template.
+
+<DT><I>Fix gcmc ran out of available atom IDs</I>
+
+<DD>See the setting for tagint in the src/lmptype.h file.
+
+<DT><I>Fix gcmc ran out of available molecule IDs</I>
+
+<DD>See the setting for tagint in the src/lmptype.h file.
+
+<DT><I>Fix gcmc region cannot be dynamic</I>
+
+<DD>Only static regions can be used with fix gcmc.
+
+<DT><I>Fix gcmc region does not support a bounding box</I>
+
+<DD>Not all regions represent bounded volumes. You cannot use
+such a region with the fix gcmc command.
+
+<DT><I>Fix gcmc region extends outside simulation box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gcmc shake fix does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld c coefficients must be >= 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld needs more prony series coefficients</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld prony terms must be > 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld series type must be pprony for now</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld start temperature must be >= 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld stop temperature must be >= 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix gld tau coefficients must be > 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix heat group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix heat kinetic energy of an atom went negative</I>
+
+<DD>This will cause the velocity rescaling about to be performed by fix
+heat to be invalid.
+
+<DT><I>Fix heat kinetic energy went negative</I>
+
+<DD>This will cause the velocity rescaling about to be performed by fix
+heat to be invalid.
+
+<DT><I>Fix in variable not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. The variable is
+requesting the values on a non-allowed timestep.
+
+<DT><I>Fix langevin angmom is not yet implemented with kokkos</I>
+
+<DD>This option is not yet available.
+
+<DT><I>Fix langevin angmom requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix langevin angmom requires extended particles</I>
+
+<DD>This fix option cannot be used with point paritlces.
+
+<DT><I>Fix langevin omega is not yet implemented with kokkos</I>
+
+<DD>This option is not yet available.
+
+<DT><I>Fix langevin omega requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix langevin omega requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Fix langevin period must be > 0.0</I>
+
+<DD>The time window for temperature relaxation must be > 0
+
+<DT><I>Fix langevin variable returned negative temperature</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix momentum group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix move cannot define z or vz variable for 2d problem</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix move cannot rotate aroung non z-axis for 2d problem</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix move cannot set linear z motion for 2d problem</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix move cannot set wiggle z motion for 2d problem</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix msst compute ID does not compute potential energy</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix msst compute ID does not compute pressure</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix msst compute ID does not compute temperature</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix msst requires a periodic box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix msst tscale must satisfy 0 <= tscale < 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state</I>
+
+<DD>Self-explanatory. The change in the box tilt is too extreme
+on a short timescale.
+
+<DT><I>Fix nve/asphere requires extended particles</I>
+
+<DD>This fix can only be used for particles with a shape setting.
+
+<DT><I>Fix nve/asphere/noforce requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/asphere/noforce requires extended particles</I>
+
+<DD>One of the particles is not an ellipsoid.
+
+<DT><I>Fix nve/body requires atom style body</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/body requires bodies</I>
+
+<DD>This fix can only be used for particles that are bodies.
+
+<DT><I>Fix nve/line can only be used for 2d simulations</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/line requires atom style line</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/line requires line particles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/sphere requires atom attribute mu</I>
+
+<DD>An atom style with this attribute is needed.
+
+<DT><I>Fix nve/sphere requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/sphere requires extended particles</I>
+
+<DD>This fix can only be used for particles of a finite size.
+
+<DT><I>Fix nve/tri can only be used for 3d simulations</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/tri requires atom style tri</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nve/tri requires tri particles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nvt/nph/npt asphere requires extended particles</I>
+
+<DD>The shape setting for a particle in the fix group has shape = 0.0,
+which means it is a point particle.
+
+<DT><I>Fix nvt/nph/npt sphere requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nvt/npt/nph damping parameters must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nvt/npt/nph dilate group ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix nvt/sphere requires extended particles</I>
+
+<DD>This fix can only be used for particles of a finite size.
+
+<DT><I>Fix orient/fcc file open failed</I>
+
+<DD>The fix orient/fcc command could not open a specified file.
+
+<DT><I>Fix orient/fcc file read failed</I>
+
+<DD>The fix orient/fcc command could not read the needed parameters from a
+specified file.
+
+<DT><I>Fix orient/fcc found self twice</I>
+
+<DD>The neighbor lists used by fix orient/fcc are messed up. If this
+error occurs, it is likely a bug, so send an email to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
+
+<DT><I>Fix peri neigh does not exist</I>
+
+<DD>Somehow a fix that the pair style defines has been deleted.
+
+<DT><I>Fix pour and fix rigid/small not using same molecule template ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour and fix shake not using same molecule template ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour insertion count per timestep is 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour molecule must have atom types</I>
+
+<DD>The defined molecule does not specify atom types.
+
+<DT><I>Fix pour molecule must have coordinates</I>
+
+<DD>The defined molecule does not specify coordinates.
+
+<DT><I>Fix pour molecule template ID must be same as atom style template ID</I>
+
+<DD>When using atom_style template, you cannot pour molecules that are
+not in that template.
+
+<DT><I>Fix pour polydisperse fractions do not sum to 1.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour region ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour region cannot be dynamic</I>
+
+<DD>Only static regions can be used with fix pour.
+
+<DT><I>Fix pour region does not support a bounding box</I>
+
+<DD>Not all regions represent bounded volumes. You cannot use
+such a region with the fix pour command.
+
+<DT><I>Fix pour requires atom attributes radius, rmass</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Fix pour rigid fix does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix pour shake fix does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix press/berendsen damping parameters must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix property/atom cannot specify mol twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix property/atom cannot specify q twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix property/atom mol when atom_style already has molecule attribute</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix property/atom q when atom_style already has charge attribute</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix property/atom vector name already exists</I>
+
+<DD>The name for an integer or floating-point vector must be unique.
+
+<DT><I>Fix qeq has negative upper Taper radius cutoff</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/comb group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/comb requires atom attribute q</I>
+
+<DD>An atom style with charge must be used to perform charge equilibration.
+
+<DT><I>Fix qeq/dynamic group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/dynamic requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/point group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/point has insufficient QEq matrix size</I>
+
+<DD>Occurs when number of neighbor atoms for an atom increased too much
+during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
+recompile.
+
+<DT><I>Fix qeq/point requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/shielded group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/shielded has insufficient QEq matrix size</I>
+
+<DD>Occurs when number of neighbor atoms for an atom increased too much
+during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
+recompile.
+
+<DT><I>Fix qeq/shielded requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/slater could not extract params from pair coul/streitz</I>
+
+<DD>This should not happen unless pair coul/streitz has been altered.
+
+<DT><I>Fix qeq/slater group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq/slater has insufficient QEq matrix size</I>
+
+<DD>Occurs when number of neighbor atoms for an atom increased too much
+during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
+recompile.
+
+<DT><I>Fix qeq/slater requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix reax/bonds numbonds > nsbmax_most</I>
+
+<DD>The limit of the number of bonds expected by the ReaxFF force field
+was exceeded.
+
+<DT><I>Fix recenter group has no atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix restrain requires an atom map, see atom_modify</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid atom has non-zero image flag in a non-periodic dimension</I>
+
+<DD>Image flags for non-periodic dimensions should not be set.
+
+<DT><I>Fix rigid file has no lines</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid langevin period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid molecule requires atom attribute molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid npt/nph dilate group ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid npt/nph does not yet allow triclinic box</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Fix rigid npt/nph period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid npt/small t_chain should not be less than 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid npt/small t_order must be 3 or 5</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid nvt/npt/nph damping parameters must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid nvt/small t_chain should not be less than 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid nvt/small t_iter should not be less than 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid nvt/small t_order must be 3 or 5</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid xy torque cannot be on for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid z force cannot be on for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/npt period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/npt temperature order must be 3 or 5</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/npt/small period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/nvt period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/nvt temperature order must be 3 or 5</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/nvt/small period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small atom has non-zero image flag in a non-periodic dimension</I>
+
+<DD>Image flags for non-periodic dimensions should not be set.
+
+<DT><I>Fix rigid/small langevin period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small molecule must have atom types</I>
+
+<DD>The defined molecule does not specify atom types.
+
+<DT><I>Fix rigid/small molecule must have coordinates</I>
+
+<DD>The defined molecule does not specify coordinates.
+
+<DT><I>Fix rigid/small npt/nph period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small nvt/npt/nph damping parameters must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small nvt/npt/nph dilate group ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small requires an atom map, see atom_modify</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid/small requires atom attribute molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rigid: Bad principal moments</I>
+
+<DD>The principal moments of inertia computed for a rigid body
+are not within the required tolerances.
+
+<DT><I>Fix shake cannot be used with minimization</I>
+
+<DD>Cannot use fix shake while doing an energy minimization since
+it turns off bonds that should contribute to the energy.
+
+<DT><I>Fix shake molecule template must have shake info</I>
+
+<DD>The defined molecule does not specify SHAKE information.
+
+<DT><I>Fix spring couple group ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix srd can only currently be used with comm_style brick</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Fix srd lamda must be >= 0.6 of SRD grid size</I>
+
+<DD>This is a requirement for accuracy reasons.
+
+<DT><I>Fix srd no-slip requires atom attribute torque</I>
+
+<DD>This is because the SRD collisions will impart torque to the solute
+particles.
+
+<DT><I>Fix srd requires SRD particles all have same mass</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix srd requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Fix srd requires newton pair on</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix store/state compute array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix store/state compute does not calculate a per-atom array</I>
+
+<DD>The compute calculates a per-atom vector.
+
+<DT><I>Fix store/state compute does not calculate a per-atom vector</I>
+
+<DD>The compute calculates a per-atom vector.
+
+<DT><I>Fix store/state compute does not calculate per-atom values</I>
+
+<DD>Computes that calculate global or local quantities cannot be used
+with fix store/state.
+
+<DT><I>Fix store/state fix array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix store/state fix does not calculate a per-atom array</I>
+
+<DD>The fix calculates a per-atom vector.
+
+<DT><I>Fix store/state fix does not calculate a per-atom vector</I>
+
+<DD>The fix calculates a per-atom array.
+
+<DT><I>Fix store/state fix does not calculate per-atom values</I>
+
+<DD>Fixes that calculate global or local quantities cannot be used with
+fix store/state.
+
+<DT><I>Fix store/state for atom property that isn't allocated</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix store/state variable is not atom-style variable</I>
+
+<DD>Only atom-style variables calculate per-atom quantities.
+
+<DT><I>Fix temp/berendsen period must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix temp/berendsen variable returned negative temperature</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix temp/csvr is not compatible with fix shake</I>
+
+<DD>These two commands cannot currently be used toghether.
+
+<DT><I>Fix temp/csvr variable returned negative temperature</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix temp/rescale variable returned negative temperature</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix tfmc displacement length must be > 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix tfmc is not compatible with fix shake</I>
+
+<DD>These two commands cannot currently be used together.
+
+<DT><I>Fix tfmc temperature must be > 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix thermal/conductivity swap value must be positive</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix tmd must come after integration fixes</I>
+
+<DD>Any fix tmd command must appear in the input script after all time
+integration fixes (nve, nvt, npt). See the fix tmd documentation for
+details.
+
+<DT><I>Fix ttm electron temperatures must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm electronic_density must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm electronic_specific_heat must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm electronic_thermal_conductivity must be >= 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm gamma_p must be > 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm gamma_s must be >= 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm number of nodes must be > 0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix ttm v_0 must be >= 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix used in compute chunk/atom not computed at compatible time</I>
+
+<DD>The chunk/atom compute cannot query the output of the fix on a timestep
+it is needed.
+
+<DT><I>Fix used in compute reduce not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Compute reduce is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix used in compute slice not computed at compatible time</I>
+
+<DD>Fixes generate their values on specific timesteps. Compute slice is
+requesting a value on a non-allowed timestep.
+
+<DT><I>Fix vector cannot set output array intensive/extensive from these inputs</I>
+
+<DD>The inputs to the command have conflicting intensive/extensive attributes.
+You need to use more than one fix vector command.
+
+<DT><I>Fix vector compute does not calculate a scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector compute does not calculate a vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector fix does not calculate a scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector fix does not calculate a vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix vector variable is not equal-style variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix viscosity swap value must be positive</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix viscosity vtarget value must be positive</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix wall cutoff <= 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix wall/colloid requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix wall/colloid requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Fix wall/gran is incompatible with Pair style</I>
+
+<DD>Must use a granular pair style to define the parameters needed for
+this fix.
+
+<DT><I>Fix wall/gran requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix wall/piston command only available at zlo</I>
+
+<DD>The face keyword must be zlo.
+
+<DT><I>Fix wall/region colloid requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix wall/region colloid requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Fix wall/region cutoff <= 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix_modify pressure ID does not compute pressure</I>
+
+<DD>The compute ID assigned to the fix must compute pressure.
+
+<DT><I>Fix_modify temperature ID does not compute temperature</I>
+
+<DD>The compute ID assigned to the fix must compute temperature.
+
+<DT><I>For triclinic deformation, specified target stress must be hydrostatic</I>
+
+<DD>Triclinic pressure control is allowed using the tri keyword, but
+non-hydrostatic pressure control can not be used in this case.
+
+<DT><I>Found no restart file matching pattern</I>
+
+<DD>When using a "*" in the restart file name, no matching file was found.
+
+<DT><I>GPU library not compiled for this accelerator</I>
+
+<DD>Self-explanatory.
+
+<DT><I>GPU package does not (yet) work with atom_style template</I>
+
+<DD>Self-explanatory.
+
+<DT><I>GPU particle split must be set to 1 for this pair style.</I>
+
+<DD>For this pair style, you cannot run part of the force calculation on
+the host. See the package command.
+
+<DT><I>GPU split param must be positive for hybrid pair styles</I>
+
+<DD>See the package gpu command.
+
+<DT><I>Ghost velocity forward comm not yet implemented with Kokkos</I>
+
+<DD>This is a current restriction.
+
+<DT><I>Gmask function in equal-style variable formula</I>
+
+<DD>Gmask is per-atom operation.
+
+<DT><I>Gravity changed since fix pour was created</I>
+
+<DD>The gravity vector defined by fix gravity must be static.
+
+<DT><I>Gravity must point in -y to use with fix pour in 2d</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Gravity must point in -z to use with fix pour in 3d</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Grmask function in equal-style variable formula</I>
+
+<DD>Grmask is per-atom operation.
+
+<DT><I>Group ID does not exist</I>
+
+<DD>A group ID used in the group command does not exist.
+
+<DT><I>Group ID in variable formula does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Group all cannot be made dynamic</I>
+
+<DD>This operation is not allowed.
+
+<DT><I>Group command before simulation box is defined</I>
+
+<DD>The group command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Group dynamic cannot reference itself</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Group dynamic parent group cannot be dynamic</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Group dynamic parent group does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Group region ID does not exist</I>
+
+<DD>A region ID used in the group command does not exist.
+
+<DT><I>If read_dump purges it cannot replace or trim</I>
+
+<DD>These operations are not compatible. See the read_dump doc
+page for details.
+
+<DT><I>Illegal ... command</I>
+
+<DD>Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+<DT><I>Illegal COMB parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal COMB3 parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal Stillinger-Weber parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal Tersoff parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal compute voronoi/atom command (occupation and (surface or edges))</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Illegal coul/streitz parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal dump_modify sfactor value (must be > 0.0)</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Illegal dump_modify tfactor value (must be > 0.0)</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Illegal fix gcmc gas mass <= 0</I>
+
+<DD>The computed mass of the designated gas molecule or atom type was less
+than or equal to zero.
+
+<DT><I>Illegal fix tfmc random seed</I>
+
+<DD>Seeds can only be nonzero positive integers.
+
+<DT><I>Illegal fix wall/piston velocity</I>
+
+<DD>The piston velocity must be positive.
+
+<DT><I>Illegal integrate style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Illegal nb3b/harmonic parameter</I>
+
+<DD>One or more of the coefficients defined in the potential file is
+invalid.
+
+<DT><I>Illegal number of angle table entries</I>
+
+<DD>There must be at least 2 table entries.
+
+<DT><I>Illegal number of bond table entries</I>
+
+<DD>There must be at least 2 table entries.
+
+<DT><I>Illegal number of pair table entries</I>
+
+<DD>There must be at least 2 table entries.
+
+<DT><I>Illegal simulation box</I>
+
+<DD>The lower bound of the simulation box is greater than the upper bound.
+
+<DT><I>Imageint setting in lmptype.h is invalid</I>
+
+<DD>Imageint must be as large or larger than smallint.
+
+<DT><I>Imageint setting in lmptype.h is not compatible</I>
+
+<DD>Format of imageint stored in restart file is not consistent with
+LAMMPS version you are running. See the settings in src/lmptype.h
+
+<DT><I>Improper atom missing in delete_bonds</I>
+
+<DD>The delete_bonds command cannot find one or more atoms in a particular
+improper on a particular processor. The pairwise cutoff is too short
+or the atoms are too far apart to make a valid improper.
+
+<DT><I>Improper atom missing in set command</I>
+
+<DD>The set command cannot find one or more atoms in a particular improper
+on a particular processor. The pairwise cutoff is too short or the
+atoms are too far apart to make a valid improper.
+
+<DT><I>Improper atoms %d %d %d %d missing on proc %d at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular improper are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the improper has blown apart and an atom is
+too far away.
+
+<DT><I>Improper atoms missing on proc %d at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular improper are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the improper has blown apart and an atom is
+too far away.
+
+<DT><I>Improper coeff for hybrid has invalid style</I>
+
+<DD>Improper style hybrid uses another improper style as one of its
+coefficients. The improper style used in the improper_coeff command
+or read from a restart file is not recognized.
+
+<DT><I>Improper coeffs are not set</I>
+
+<DD>No improper coefficients have been assigned in the data file or via
+the improper_coeff command.
+
+<DT><I>Improper style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Improper style hybrid cannot have none as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Improper style hybrid cannot use same improper style twice</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Improper_coeff command before improper_style is defined</I>
+
+<DD>Coefficients cannot be set in the data file or via the improper_coeff
+command until an improper_style has been assigned.
+
+<DT><I>Improper_coeff command before simulation box is defined</I>
+
+<DD>The improper_coeff command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Improper_coeff command when no impropers allowed</I>
+
+<DD>The chosen atom style does not allow for impropers to be defined.
+
+<DT><I>Improper_style command when no impropers allowed</I>
+
+<DD>The chosen atom style does not allow for impropers to be defined.
+
+<DT><I>Impropers assigned incorrectly</I>
+
+<DD>Impropers read in from the data file were not assigned correctly to
+atoms. This means there is something invalid about the topology
+definitions.
+
+<DT><I>Impropers defined but no improper types</I>
+
+<DD>The data file header lists improper but no improper types.
+
+<DT><I>Incomplete use of variables in create_atoms command</I>
+
+<DD>The var and set options must be used together.
+
+<DT><I>Inconsistent iparam/jparam values in fix bond/create command</I>
+
+<DD>If itype and jtype are the same, then their maxbond and newtype
+settings must also be the same.
+
+<DT><I>Inconsistent line segment in data file</I>
+
+<DD>The end points of the line segment are not equal distances from the
+center point which is the atom coordinate.
+
+<DT><I>Inconsistent triangle in data file</I>
+
+<DD>The centroid of the triangle as defined by the corner points is not
+the atom coordinate.
+
+<DT><I>Inconsistent use of finite-size particles by molecule template molecules</I>
+
+<DD>Not all of the molecules define a radius for their constituent
+particles.
+
+<DT><I>Incorrect # of floating-point values in Bodies section of data file</I>
+
+<DD>See doc page for body style.
+
+<DT><I>Incorrect # of integer values in Bodies section of data file</I>
+
+<DD>See doc page for body style.
+
+<DT><I>Incorrect %s format in data file</I>
+
+<DD>A section of the data file being read by fix property/atom does
+not have the correct number of values per line.
+
+<DT><I>Incorrect SNAP parameter file</I>
+
+<DD>The file cannot be parsed correctly, check its internal syntax.
+
+<DT><I>Incorrect args for angle coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect args for bond coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect args for dihedral coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect args for improper coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect args for pair coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect args in pair_style command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Incorrect atom format in data file</I>
+
+<DD>Number of values per atom line in the data file is not consistent with
+the atom style.
+
+<DT><I>Incorrect atom format in neb file</I>
+
+<DD>The number of fields per line is not what expected.
+
+<DT><I>Incorrect bonus data format in data file</I>
+
+<DD>See the read_data doc page for a description of how various kinds of
+bonus data must be formatted for certain atom styles.
+
+<DT><I>Incorrect boundaries with slab Ewald</I>
+
+<DD>Must have periodic x,y dimensions and non-periodic z dimension to use
+2d slab option with Ewald.
+
+<DT><I>Incorrect boundaries with slab EwaldDisp</I>
+
+<DD>Must have periodic x,y dimensions and non-periodic z dimension to use
+2d slab option with Ewald.
+
+<DT><I>Incorrect boundaries with slab PPPM</I>
+
+<DD>Must have periodic x,y dimensions and non-periodic z dimension to use
+2d slab option with PPPM.
+
+<DT><I>Incorrect boundaries with slab PPPMDisp</I>
+
+<DD>Must have periodic x,y dimensions and non-periodic z dimension to use
+2d slab option with pppm/disp.
+
+<DT><I>Incorrect element names in ADP potential file</I>
+
+<DD>The element names in the ADP file do not match those requested.
+
+<DT><I>Incorrect element names in EAM potential file</I>
+
+<DD>The element names in the EAM file do not match those requested.
+
+<DT><I>Incorrect format in COMB potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in COMB3 potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in MEAM potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in SNAP coefficient file</I>
+
+<DD>Incorrect number of words per line in the coefficient file.
+
+<DT><I>Incorrect format in SNAP parameter file</I>
+
+<DD>Incorrect number of words per line in the parameter file.
+
+<DT><I>Incorrect format in Stillinger-Weber potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in TMD target file</I>
+
+<DD>Format of file read by fix tmd command is incorrect.
+
+<DT><I>Incorrect format in Tersoff potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in coul/streitz potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect format in nb3b/harmonic potential file</I>
+
+<DD>Incorrect number of words per line in the potential file.
+
+<DT><I>Incorrect integer value in Bodies section of data file</I>
+
+<DD>See doc page for body style.
+
+<DT><I>Incorrect multiplicity arg for dihedral coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect rigid body format in fix rigid file</I>
+
+<DD>The number of fields per line is not what expected.
+
+<DT><I>Incorrect rigid body format in fix rigid/small file</I>
+
+<DD>The number of fields per line is not what expected.
+
+<DT><I>Incorrect sign arg for dihedral coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Incorrect velocity format in data file</I>
+
+<DD>Each atom style defines a format for the Velocity section
+of the data file. The read-in lines do not match.
+
+<DT><I>Incorrect weight arg for dihedral coefficients</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Index between variable brackets must be positive</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Indexed per-atom vector in variable formula without atom map</I>
+
+<DD>Accessing a value from an atom vector requires the ability to lookup
+an atom index, which is provided by an atom map. An atom map does not
+exist (by default) for non-molecular problems. Using the atom_modify
+map command will force an atom map to be created.
+
+<DT><I>Initial temperatures not all set in fix ttm</I>
+
+<DD>Self-explantory.
+
+<DT><I>Input line quote not followed by whitespace</I>
+
+<DD>An end quote must be followed by whitespace.
+
+<DT><I>Insertion region extends outside simulation box</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Insufficient Jacobi rotations for POEMS body</I>
+
+<DD>Eigensolve for rigid body was not sufficiently accurate.
+
+<DT><I>Insufficient Jacobi rotations for body nparticle</I>
+
+<DD>Eigensolve for rigid body was not sufficiently accurate.
+
+<DT><I>Insufficient Jacobi rotations for rigid body</I>
+
+<DD>Eigensolve for rigid body was not sufficiently accurate.
+
+<DT><I>Insufficient Jacobi rotations for rigid molecule</I>
+
+<DD>Eigensolve for rigid body was not sufficiently accurate.
+
+<DT><I>Insufficient Jacobi rotations for triangle</I>
+
+<DD>The calculation of the intertia tensor of the triangle failed. This
+should not happen if it is a reasonably shaped triangle.
+
+<DT><I>Insufficient memory on accelerator</I>
+
+<DD>There is insufficient memory on one of the devices specified for the gpu
+package
+
+<DT><I>Internal error in atom_style body</I>
+
+<DD>This error should not occur. Contact the developers.
+
+<DT><I>Invalid -reorder N value</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid Boolean syntax in if command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid Kokkos command-line args</I>
+
+<DD>Self-explanatory. See Section 2.7 of the manual for details.
+
+<DT><I>Invalid LAMMPS restart file</I>
+
+<DD>The file does not appear to be a LAMMPS restart file since
+it doesn't contain the correct magic string at the beginning.
+
+<DT><I>Invalid REAX atom type</I>
+
+<DD>There is a mis-match between LAMMPS atom types and the elements
+listed in the ReaxFF force field file.
+
+<DT><I>Invalid angle table length</I>
+
+<DD>Length must be 2 or greater.
+
+<DT><I>Invalid angle type in Angles section of data file</I>
+
+<DD>Angle type must be positive integer and within range of specified angle
+types.
+
+<DT><I>Invalid angle type in Angles section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid angle type index for fix shake</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid args for non-hybrid pair coefficients</I>
+
+<DD>"NULL" is only supported in pair_coeff calls when using pair hybrid
+
+<DT><I>Invalid argument to factorial %d</I>
+
+<DD>N must be >= 0 and <= 167, otherwise the factorial result is too
+large.
+
+<DT><I>Invalid atom ID in %s section of data file</I>
+
+<DD>An atom in a section of the data file being read by fix property/atom
+has an invalid atom ID that is <= 0 or > the maximum existing atom ID.
+
+<DT><I>Invalid atom ID in Angles section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Angles section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom ID in Atoms section of data file</I>
+
+<DD>Atom IDs must be positive integers.
+
+<DT><I>Invalid atom ID in Bodies section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Bonds section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Bonds section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom ID in Bonus section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Dihedrals section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Impropers section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in Velocities section of data file</I>
+
+<DD>Atom IDs must be positive integers and within range of defined
+atoms.
+
+<DT><I>Invalid atom ID in dihedrals section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom ID in impropers section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom ID in variable file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom IDs in neb file</I>
+
+<DD>An ID in the file was not found in the system.
+
+<DT><I>Invalid atom diameter in molecule file</I>
+
+<DD>Diameters must be >= 0.0.
+
+<DT><I>Invalid atom mass for fix shake</I>
+
+<DD>Mass specified in fix shake command must be > 0.0.
+
+<DT><I>Invalid atom mass in molecule file</I>
+
+<DD>Masses must be > 0.0.
+
+<DT><I>Invalid atom type in Atoms section of data file</I>
+
+<DD>Atom types must range from 1 to specified # of types.
+
+<DT><I>Invalid atom type in create_atoms command</I>
+
+<DD>The create_box command specified the range of valid atom types.
+An invalid type is being requested.
+
+<DT><I>Invalid atom type in create_atoms mol command</I>
+
+<DD>The atom types in the defined molecule are added to the value
+specified in the create_atoms command, as an offset. The final value
+for each atom must be between 1 to N, where N is the number of atom
+types.
+
+<DT><I>Invalid atom type in fix atom/swap command</I>
+
+<DD>The atom type specified in the atom/swap command does not exist.
+
+<DT><I>Invalid atom type in fix bond/create command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom type in fix deposit command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom type in fix deposit mol command</I>
+
+<DD>The atom types in the defined molecule are added to the value
+specified in the create_atoms command, as an offset. The final value
+for each atom must be between 1 to N, where N is the number of atom
+types.
+
+<DT><I>Invalid atom type in fix gcmc command</I>
+
+<DD>The atom type specified in the gcmc command does not exist.
+
+<DT><I>Invalid atom type in fix gcmc mol command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom type in fix pour command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid atom type in fix pour mol command</I>
+
+<DD>The atom types in the defined molecule are added to the value
+specified in the create_atoms command, as an offset. The final value
+for each atom must be between 1 to N, where N is the number of atom
+types.
+
+<DT><I>Invalid atom type in molecule file</I>
+
+<DD>Atom types must range from 1 to specified # of types.
+
+<DT><I>Invalid atom type in neighbor exclusion list</I>
+
+<DD>Atom types must range from 1 to Ntypes inclusive.
+
+<DT><I>Invalid atom type index for fix shake</I>
+
+<DD>Atom types must range from 1 to Ntypes inclusive.
+
+<DT><I>Invalid atom types in pair_write command</I>
+
+<DD>Atom types must range from 1 to Ntypes inclusive.
+
+<DT><I>Invalid atom vector in variable formula</I>
+
+<DD>The atom vector is not recognized.
+
+<DT><I>Invalid atom_style body command</I>
+
+<DD>No body style argument was provided.
+
+<DT><I>Invalid atom_style command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid attribute in dump custom command</I>
+
+<DD>Self-explantory.
+
+<DT><I>Invalid attribute in dump local command</I>
+
+<DD>Self-explantory.
+
+<DT><I>Invalid attribute in dump modify command</I>
+
+<DD>Self-explantory.
+
+<DT><I>Invalid basis setting in create_atoms command</I>
+
+<DD>The basis index must be between 1 to N where N is the number of basis
+atoms in the lattice. The type index must be between 1 to N where N
+is the number of atom types.
+
+<DT><I>Invalid basis setting in fix append/atoms command</I>
+
+<DD>The basis index must be between 1 to N where N is the number of basis
+atoms in the lattice. The type index must be between 1 to N where N
+is the number of atom types.
+
+<DT><I>Invalid bin bounds in compute chunk/atom</I>
+
+<DD>The lo/hi values are inconsistent.
+
+<DT><I>Invalid bin bounds in fix ave/spatial</I>
+
+<DD>The lo/hi values are inconsistent.
+
+<DT><I>Invalid body nparticle command</I>
+
+<DD>Arguments in atom-style command are not correct.
+
+<DT><I>Invalid bond table length</I>
+
+<DD>Length must be 2 or greater.
+
+<DT><I>Invalid bond type in Bonds section of data file</I>
+
+<DD>Bond type must be positive integer and within range of specified bond
+types.
+
+<DT><I>Invalid bond type in Bonds section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid bond type in create_bonds command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid bond type in fix bond/break command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid bond type in fix bond/create command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid bond type index for fix shake</I>
+
+<DD>Self-explanatory. Check the fix shake command in the input script.
+
+<DT><I>Invalid coeffs for this dihedral style</I>
+
+<DD>Cannot set class 2 coeffs in data file for this dihedral style.
+
+<DT><I>Invalid color in dump_modify command</I>
+
+<DD>The specified color name was not in the list of recognized colors.
+See the dump_modify doc page.
+
+<DT><I>Invalid color map min/max values</I>
+
+<DD>The min/max values are not consistent with either each other or
+with values in the color map.
+
+<DT><I>Invalid command-line argument</I>
+
+<DD>One or more command-line arguments is invalid. Check the syntax of
+the command you are using to launch LAMMPS.
+
+<DT><I>Invalid compute ID in variable formula</I>
+
+<DD>The compute is not recognized.
+
+<DT><I>Invalid create_atoms rotation vector for 2d model</I>
+
+<DD>The rotation vector can only have a z component.
+
+<DT><I>Invalid custom OpenCL parameter string.</I>
+
+<DD>There are not enough or too many parameters in the custom string for package
+GPU.
+
+<DT><I>Invalid cutoff in comm_modify command</I>
+
+<DD>Specified cutoff must be >= 0.0.
+
+<DT><I>Invalid cutoffs in pair_write command</I>
+
+<DD>Inner cutoff must be larger than 0.0 and less than outer cutoff.
+
+<DT><I>Invalid d1 or d2 value for pair colloid coeff</I>
+
+<DD>Neither d1 or d2 can be < 0.
+
+<DT><I>Invalid data file section: Angle Coeffs</I>
+
+<DD>Atom style does not allow angles.
+
+<DT><I>Invalid data file section: AngleAngle Coeffs</I>
+
+<DD>Atom style does not allow impropers.
+
+<DT><I>Invalid data file section: AngleAngleTorsion Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: AngleTorsion Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Angles</I>
+
+<DD>Atom style does not allow angles.
+
+<DT><I>Invalid data file section: Bodies</I>
+
+<DD>Atom style does not allow bodies.
+
+<DT><I>Invalid data file section: Bond Coeffs</I>
+
+<DD>Atom style does not allow bonds.
+
+<DT><I>Invalid data file section: BondAngle Coeffs</I>
+
+<DD>Atom style does not allow angles.
+
+<DT><I>Invalid data file section: BondBond Coeffs</I>
+
+<DD>Atom style does not allow angles.
+
+<DT><I>Invalid data file section: BondBond13 Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Bonds</I>
+
+<DD>Atom style does not allow bonds.
+
+<DT><I>Invalid data file section: Dihedral Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Dihedrals</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Ellipsoids</I>
+
+<DD>Atom style does not allow ellipsoids.
+
+<DT><I>Invalid data file section: EndBondTorsion Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Improper Coeffs</I>
+
+<DD>Atom style does not allow impropers.
+
+<DT><I>Invalid data file section: Impropers</I>
+
+<DD>Atom style does not allow impropers.
+
+<DT><I>Invalid data file section: Lines</I>
+
+<DD>Atom style does not allow lines.
+
+<DT><I>Invalid data file section: MiddleBondTorsion Coeffs</I>
+
+<DD>Atom style does not allow dihedrals.
+
+<DT><I>Invalid data file section: Triangles</I>
+
+<DD>Atom style does not allow triangles.
+
+<DT><I>Invalid delta_conf in tad command</I>
+
+<DD>The value must be between 0 and 1 inclusive.
+
+<DT><I>Invalid density in Atoms section of data file</I>
+
+<DD>Density value cannot be <= 0.0.
+
+<DT><I>Invalid density in set command</I>
+
+<DD>Density must be > 0.0.
+
+<DT><I>Invalid diameter in set command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid dihedral type in Dihedrals section of data file</I>
+
+<DD>Dihedral type must be positive integer and within range of specified
+dihedral types.
+
+<DT><I>Invalid dihedral type in dihedrals section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid dipole length in set command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid displace_atoms rotate axis for 2d</I>
+
+<DD>Axis must be in z direction.
+
+<DT><I>Invalid dump dcd filename</I>
+
+<DD>Filenames used with the dump dcd style cannot be binary or compressed
+or cause multiple files to be written.
+
+<DT><I>Invalid dump frequency</I>
+
+<DD>Dump frequency must be 1 or greater.
+
+<DT><I>Invalid dump image element name</I>
+
+<DD>The specified element name was not in the standard list of elements.
+See the dump_modify doc page.
+
+<DT><I>Invalid dump image filename</I>
+
+<DD>The file produced by dump image cannot be binary and must
+be for a single processor.
+
+<DT><I>Invalid dump image persp value</I>
+
+<DD>Persp value must be >= 0.0.
+
+<DT><I>Invalid dump image theta value</I>
+
+<DD>Theta must be between 0.0 and 180.0 inclusive.
+
+<DT><I>Invalid dump image zoom value</I>
+
+<DD>Zoom value must be > 0.0.
+
+<DT><I>Invalid dump movie filename</I>
+
+<DD>The file produced by dump movie cannot be binary or compressed
+and must be a single file for a single processor.
+
+<DT><I>Invalid dump xtc filename</I>
+
+<DD>Filenames used with the dump xtc style cannot be binary or compressed
+or cause multiple files to be written.
+
+<DT><I>Invalid dump xyz filename</I>
+
+<DD>Filenames used with the dump xyz style cannot be binary or cause files
+to be written by each processor.
+
+<DT><I>Invalid dump_modify threshhold operator</I>
+
+<DD>Operator keyword used for threshold specification in not recognized.
+
+<DT><I>Invalid entry in -reorder file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid fix ID in variable formula</I>
+
+<DD>The fix is not recognized.
+
+<DT><I>Invalid fix ave/time off column</I>
+
+<DD>Self-explantory.
+
+<DT><I>Invalid fix box/relax command for a 2d simulation</I>
+
+<DD>Fix box/relax styles involving the z dimension cannot be used in
+a 2d simulation.
+
+<DT><I>Invalid fix box/relax command pressure settings</I>
+
+<DD>If multiple dimensions are coupled, those dimensions must be specified.
+
+<DT><I>Invalid fix box/relax pressure settings</I>
+
+<DD>Settings for coupled dimensions must be the same.
+
+<DT><I>Invalid fix nvt/npt/nph command for a 2d simulation</I>
+
+<DD>Cannot control z dimension in a 2d model.
+
+<DT><I>Invalid fix nvt/npt/nph command pressure settings</I>
+
+<DD>If multiple dimensions are coupled, those dimensions must be
+specified.
+
+<DT><I>Invalid fix nvt/npt/nph pressure settings</I>
+
+<DD>Settings for coupled dimensions must be the same.
+
+<DT><I>Invalid fix press/berendsen for a 2d simulation</I>
+
+<DD>The z component of pressure cannot be controlled for a 2d model.
+
+<DT><I>Invalid fix press/berendsen pressure settings</I>
+
+<DD>Settings for coupled dimensions must be the same.
+
+<DT><I>Invalid fix qeq parameter file</I>
+
+<DD>Element index > number of atom types.
+
+<DT><I>Invalid fix rigid npt/nph command for a 2d simulation</I>
+
+<DD>Cannot control z dimension in a 2d model.
+
+<DT><I>Invalid fix rigid npt/nph command pressure settings</I>
+
+<DD>If multiple dimensions are coupled, those dimensions must be
+specified.
+
+<DT><I>Invalid fix rigid/small npt/nph command for a 2d simulation</I>
+
+<DD>Cannot control z dimension in a 2d model.
+
+<DT><I>Invalid fix rigid/small npt/nph command pressure settings</I>
+
+<DD>If multiple dimensions are coupled, those dimensions must be
+specified.
+
+<DT><I>Invalid flag in force field section of restart file</I>
+
+<DD>Unrecognized entry in restart file.
+
+<DT><I>Invalid flag in header section of restart file</I>
+
+<DD>Unrecognized entry in restart file.
+
+<DT><I>Invalid flag in peratom section of restart file</I>
+
+<DD>The format of this section of the file is not correct.
+
+<DT><I>Invalid flag in type arrays section of restart file</I>
+
+<DD>Unrecognized entry in restart file.
+
+<DT><I>Invalid format in Bodies section of data file</I>
+
+<DD>The specified number of integer or floating point values does not
+appear.
+
+<DT><I>Invalid frequency in temper command</I>
+
+<DD>Nevery must be > 0.
+
+<DT><I>Invalid group ID in neigh_modify command</I>
+
+<DD>A group ID used in the neigh_modify command does not exist.
+
+<DT><I>Invalid group function in variable formula</I>
+
+<DD>Group function is not recognized.
+
+<DT><I>Invalid group in comm_modify command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid image up vector</I>
+
+<DD>Up vector cannot be (0,0,0).
+
+<DT><I>Invalid immediate variable</I>
+
+<DD>Syntax of immediate value is incorrect.
+
+<DT><I>Invalid improper type in Impropers section of data file</I>
+
+<DD>Improper type must be positive integer and within range of specified
+improper types.
+
+<DT><I>Invalid improper type in impropers section of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid index for non-body particles in compute body/local command</I>
+
+<DD>Only indices 1,2,3 can be used for non-body particles.
+
+<DT><I>Invalid index in compute body/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in angle table parameters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in bond table parameters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute angle/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute bond/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute dihedral/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute improper/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute pair/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute property/atom command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute property/chunk command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in compute property/local command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in dump cfg command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid keyword in pair table parameters</I>
+
+<DD>Keyword used in list of table parameters is not recognized.
+
+<DT><I>Invalid length in set command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid mass in set command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid mass line in data file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid mass value</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid math function in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid math/group/special function in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid option in lattice command for non-custom style</I>
+
+<DD>Certain lattice keywords are not supported unless the
+lattice style is "custom".
+
+<DT><I>Invalid order of forces within respa levels</I>
+
+<DD>For respa, ordering of force computations within respa levels must
+obey certain rules. E.g. bonds cannot be compute less frequently than
+angles, pairwise forces cannot be computed less frequently than
+kspace, etc.
+
+<DT><I>Invalid pair table cutoff</I>
+
+<DD>Cutoffs in pair_coeff command are not valid with read-in pair table.
+
+<DT><I>Invalid pair table length</I>
+
+<DD>Length of read-in pair table is invalid
+
+<DT><I>Invalid param file for fix qeq/shielded</I>
+
+<DD>Invalid value of gamma.
+
+<DT><I>Invalid param file for fix qeq/slater</I>
+
+<DD>Zeta value is 0.0.
+
+<DT><I>Invalid partitions in processors part command</I>
+
+<DD>Valid partitions are numbered 1 to N and the sender and receiver
+cannot be the same partition.
+
+<DT><I>Invalid python command</I>
+
+<DD>Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+<DT><I>Invalid radius in Atoms section of data file</I>
+
+<DD>Radius must be >= 0.0.
+
+<DT><I>Invalid random number seed in fix ttm command</I>
+
+<DD>Random number seed must be > 0.
+
+<DT><I>Invalid random number seed in set command</I>
+
+<DD>Random number seed must be > 0.
+
+<DT><I>Invalid replace values in compute reduce</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid rigid body ID in fix rigid file</I>
+
+<DD>The ID does not match the number of an existing ID of rigid bodies
+that are defined by the fix rigid command.
+
+<DT><I>Invalid rigid body ID in fix rigid/small file</I>
+
+<DD>The ID does not match the number of an existing ID of rigid bodies
+that are defined by the fix rigid/small command.
+
+<DT><I>Invalid run command N value</I>
+
+<DD>The number of timesteps must fit in a 32-bit integer. If you want to
+run for more steps than this, perform multiple shorter runs.
+
+<DT><I>Invalid run command start/stop value</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid run command upto value</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid seed for Marsaglia random # generator</I>
+
+<DD>The initial seed for this random number generator must be a positive
+integer less than or equal to 900 million.
+
+<DT><I>Invalid seed for Park random # generator</I>
+
+<DD>The initial seed for this random number generator must be a positive
+integer.
+
+<DT><I>Invalid shake angle type in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shake atom in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shake bond type in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shake flag in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shape in Ellipsoids section of data file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shape in Triangles section of data file</I>
+
+<DD>Two or more of the triangle corners are duplicate points.
+
+<DT><I>Invalid shape in set command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid shear direction for fix wall/gran</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid special atom index in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid special function in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid style in pair_write command</I>
+
+<DD>Self-explanatory. Check the input script.
+
+<DT><I>Invalid syntax in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid t_event in prd command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid t_event in tad command</I>
+
+<DD>The value must be greater than 0.
+
+<DT><I>Invalid template atom in Atoms section of data file</I>
+
+<DD>The atom indices must be between 1 to N, where N is the number of
+atoms in the template molecule the atom belongs to.
+
+<DT><I>Invalid template index in Atoms section of data file</I>
+
+<DD>The template indices must be between 1 to N, where N is the number of
+molecules in the template.
+
+<DT><I>Invalid thermo keyword in variable formula</I>
+
+<DD>The keyword is not recognized.
+
+<DT><I>Invalid threads_per_atom specified.</I>
+
+<DD>For 3-body potentials on the GPU, the threads_per_atom setting cannot be
+greater than 4 for NVIDIA GPUs.
+
+<DT><I>Invalid timestep reset for fix ave/atom</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid timestep reset for fix ave/chunk</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid timestep reset for fix ave/correlate</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid timestep reset for fix ave/histo</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid timestep reset for fix ave/spatial</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid timestep reset for fix ave/time</I>
+
+<DD>Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+<DT><I>Invalid tmax in tad command</I>
+
+<DD>The value must be greater than 0.0.
+
+<DT><I>Invalid type for mass set</I>
+
+<DD>Mass command must set a type from 1-N where N is the number of atom
+types.
+
+<DT><I>Invalid use of library file() function</I>
+
+<DD>This function is called thru the library interface. This
+error should not occur. Contact the developers if it does.
+
+<DT><I>Invalid value in set command</I>
+
+<DD>The value specified for the setting is invalid, likely because it is
+too small or too large.
+
+<DT><I>Invalid variable evaluation in variable formula</I>
+
+<DD>A variable used in a formula could not be evaluated.
+
+<DT><I>Invalid variable in next command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invalid variable name</I>
+
+<DD>Variable name used in an input script line is invalid.
+
+<DT><I>Invalid variable name in variable formula</I>
+
+<DD>Variable name is not recognized.
+
+<DT><I>Invalid variable style in special function next</I>
+
+<DD>Only file-style or atomfile-style variables can be used with next().
+
+<DT><I>Invalid variable style with next command</I>
+
+<DD>Variable styles <I>equal</I> and <I>world</I> cannot be used in a next
+command.
+
+<DT><I>Invalid volume in set command</I>
+
+<DD>Volume must be > 0.0.
+
+<DT><I>Invalid wiggle direction for fix wall/gran</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invoked angle equil angle on angle style none</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invoked angle single on angle style none</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invoked bond equil distance on bond style none</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invoked bond single on bond style none</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Invoked pair single on pair style none</I>
+
+<DD>A command (e.g. a dump) attempted to invoke the single() function on a
+pair style none, which is illegal. You are probably attempting to
+compute per-atom quantities with an undefined pair style.
+
+<DT><I>Invoking coulombic in pair style lj/coul requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Invoking coulombic in pair style lj/long/dipole/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>KIM neighbor iterator exceeded range</I>
+
+<DD>This should not happen. It likely indicates a bug
+in the KIM implementation of the interatomic potential
+where it is requesting neighbors incorrectly.
+
+<DT><I>KOKKOS package does not yet support comm_style tiled</I>
+
+<DD>Self-explanatory.
+
+<DT><I>KOKKOS package requires a kokkos enabled atom_style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>KSpace accuracy must be > 0</I>
+
+<DD>The kspace accuracy designated in the input must be greater than zero.
+
+<DT><I>KSpace accuracy too large to estimate G vector</I>
+
+<DD>Reduce the accuracy request or specify gwald explicitly
+via the kspace_modify command.
+
+<DT><I>KSpace accuracy too low</I>
+
+<DD>Requested accuracy must be less than 1.0.
+
+<DT><I>KSpace solver requires a pair style</I>
+
+<DD>No pair style is defined.
+
+<DT><I>KSpace style does not yet support triclinic geometries</I>
+
+<DD>The specified kspace style does not allow for non-orthogonal
+simulation boxes.
+
+<DT><I>KSpace style has not yet been set</I>
+
+<DD>Cannot use kspace_modify command until a kspace style is set.
+
+<DT><I>KSpace style is incompatible with Pair style</I>
+
+<DD>Setting a kspace style requires that a pair style with matching
+long-range Coulombic or dispersion components be used.
+
+<DT><I>Keyword %s in MEAM parameter file not recognized</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Kspace style does not support compute group/group</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Kspace style pppm/disp/tip4p requires newton on</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Kspace style pppm/tip4p requires newton on</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Kspace style requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Kspace_modify eigtol must be smaller than one</I>
+
+<DD>Self-explanatory.
+
+<DT><I>LAMMPS is not built with Python embedded</I>
+
+<DD>This is done by including the PYTHON package before LAMMPS is built.
+This is required to use python-style variables.
+
+<DT><I>LAMMPS unit_style lj not supported by KIM models</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>LJ6 off not supported in pair_style buck/long/coul/long</I>
+
+<DD>Self-exlanatory.
+
+<DT><I>Label wasn't found in input script</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Lattice orient vectors are not orthogonal</I>
+
+<DD>The three specified lattice orientation vectors must be mutually
+orthogonal.
+
+<DT><I>Lattice orient vectors are not right-handed</I>
+
+<DD>The three specified lattice orientation vectors must create a
+right-handed coordinate system such that a1 cross a2 = a3.
+
+<DT><I>Lattice primitive vectors are collinear</I>
+
+<DD>The specified lattice primitive vectors do not for a unit cell with
+non-zero volume.
+
+<DT><I>Lattice settings are not compatible with 2d simulation</I>
+
+<DD>One or more of the specified lattice vectors has a non-zero z
+component.
+
+<DT><I>Lattice spacings are invalid</I>
+
+<DD>Each x,y,z spacing must be > 0.
+
+<DT><I>Lattice style incompatible with simulation dimension</I>
+
+<DD>2d simulation can use sq, sq2, or hex lattice. 3d simulation can use
+sc, bcc, or fcc lattice.
+
+<DT><I>Log of zero/negative value in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Lost atoms via balance: original %ld current %ld</I>
+
+<DD>This should not occur. Report the problem to the developers.
+
+<DT><I>Lost atoms: original %ld current %ld</I>
+
+<DD>Lost atoms are checked for each time thermo output is done. See the
+thermo_modify lost command for options. Lost atoms usually indicate
+bad dynamics, e.g. atoms have been blown far out of the simulation
+box, or moved futher than one processor's sub-domain away before
+reneighboring.
+
+<DT><I>MEAM library error %d</I>
+
+<DD>A call to the MEAM Fortran library returned an error.
+
+<DT><I>MPI_LMP_BIGINT and bigint in lmptype.h are not compatible</I>
+
+<DD>The size of the MPI datatype does not match the size of a bigint.
+
+<DT><I>MPI_LMP_TAGINT and tagint in lmptype.h are not compatible</I>
+
+<DD>The size of the MPI datatype does not match the size of a tagint.
+
+<DT><I>MSM can only currently be used with comm_style brick</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>MSM grid is too large</I>
+
+<DD>The global MSM grid is larger than OFFSET in one or more dimensions.
+OFFSET is currently set to 16384. You likely need to decrease the
+requested accuracy.
+
+<DT><I>MSM order must be 4, 6, 8, or 10</I>
+
+<DD>This is a limitation of the MSM implementation in LAMMPS:
+the MSM order can only be 4, 6, 8, or 10.
+
+<DT><I>Mass command before simulation box is defined</I>
+
+<DD>The mass command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Matrix factorization to split dispersion coefficients failed</I>
+
+<DD>This should not normally happen. Contact the developers.
+
+<DT><I>Min_style command before simulation box is defined</I>
+
+<DD>The min_style command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Minimization could not find thermo_pe compute</I>
+
+<DD>This compute is created by the thermo command. It must have been
+explicitly deleted by a uncompute command.
+
+<DT><I>Minimize command before simulation box is defined</I>
+
+<DD>The minimize command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Mismatched brackets in variable</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Mismatched compute in variable formula</I>
+
+<DD>A compute is referenced incorrectly or a compute that produces per-atom
+values is used in an equal-style variable formula.
+
+<DT><I>Mismatched fix in variable formula</I>
+
+<DD>A fix is referenced incorrectly or a fix that produces per-atom
+values is used in an equal-style variable formula.
+
+<DT><I>Mismatched variable in variable formula</I>
+
+<DD>A variable is referenced incorrectly or an atom-style variable that
+produces per-atom values is used in an equal-style variable
+formula.
+
+<DT><I>Modulo 0 in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule IDs too large for compute chunk/atom</I>
+
+<DD>The IDs must not be larger than can be stored in a 32-bit integer
+since chunk IDs are 32-bit integers.
+
+<DT><I>Molecule file has angles but no nangles setting</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file has bonds but no nbonds setting</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file has bonds but no special flags</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file has dihedrals but no ndihedrals setting</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file has impropers but no nimpropers setting</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file has special flags but no bonds</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file needs both Special Bond sections</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file shake flags not before shake atoms</I>
+
+<DD>The order of the two sections is important.
+
+<DT><I>Molecule file shake flags not before shake bonds</I>
+
+<DD>The order of the two sections is important.
+
+<DT><I>Molecule file shake info is incomplete</I>
+
+<DD>All 3 SHAKE sections are needed.
+
+<DT><I>Molecule file special list does not match special count</I>
+
+<DD>The number of values in an atom's special list does not match count.
+
+<DT><I>Molecule file z center-of-mass must be 0.0 for 2d</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule file z coord must be 0.0 for 2d</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for atom_style template does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for create_atoms does not exist</I>
+
+<DD>Self-explantory.
+
+<DT><I>Molecule template ID for fix deposit does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for fix gcmc does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for fix pour does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for fix rigid/small does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID for fix shake does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule template ID must be alphanumeric or underscore characters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule toplogy/atom exceeds system topology/atom</I>
+
+<DD>The number of bonds, angles, etc per-atom in the molecule exceeds the
+system setting. See the create_box command for how to specify these
+values.
+
+<DT><I>Molecule topology type exceeds system topology type</I>
+
+<DD>The number of bond, angle, etc types in the molecule exceeds the
+system setting. See the create_box command for how to specify these
+values.
+
+<DT><I>More than one fix deform</I>
+
+<DD>Only one fix deform can be defined at a time.
+
+<DT><I>More than one fix freeze</I>
+
+<DD>Only one of these fixes can be defined, since the granular pair
+potentials access it.
+
+<DT><I>More than one fix shake</I>
+
+<DD>Only one fix shake can be defined.
+
+<DT><I>Must define angle_style before Angle Coeffs</I>
+
+<DD>Must use an angle_style command before reading a data file that
+defines Angle Coeffs.
+
+<DT><I>Must define angle_style before BondAngle Coeffs</I>
+
+<DD>Must use an angle_style command before reading a data file that
+defines Angle Coeffs.
+
+<DT><I>Must define angle_style before BondBond Coeffs</I>
+
+<DD>Must use an angle_style command before reading a data file that
+defines Angle Coeffs.
+
+<DT><I>Must define bond_style before Bond Coeffs</I>
+
+<DD>Must use a bond_style command before reading a data file that
+defines Bond Coeffs.
+
+<DT><I>Must define dihedral_style before AngleAngleTorsion Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines AngleAngleTorsion Coeffs.
+
+<DT><I>Must define dihedral_style before AngleTorsion Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines AngleTorsion Coeffs.
+
+<DT><I>Must define dihedral_style before BondBond13 Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines BondBond13 Coeffs.
+
+<DT><I>Must define dihedral_style before Dihedral Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines Dihedral Coeffs.
+
+<DT><I>Must define dihedral_style before EndBondTorsion Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines EndBondTorsion Coeffs.
+
+<DT><I>Must define dihedral_style before MiddleBondTorsion Coeffs</I>
+
+<DD>Must use a dihedral_style command before reading a data file that
+defines MiddleBondTorsion Coeffs.
+
+<DT><I>Must define improper_style before AngleAngle Coeffs</I>
+
+<DD>Must use an improper_style command before reading a data file that
+defines AngleAngle Coeffs.
+
+<DT><I>Must define improper_style before Improper Coeffs</I>
+
+<DD>Must use an improper_style command before reading a data file that
+defines Improper Coeffs.
+
+<DT><I>Must define pair_style before Pair Coeffs</I>
+
+<DD>Must use a pair_style command before reading a data file that defines
+Pair Coeffs.
+
+<DT><I>Must define pair_style before PairIJ Coeffs</I>
+
+<DD>Must use a pair_style command before reading a data file that defines
+PairIJ Coeffs.
+
+<DT><I>Must have more than one processor partition to temper</I>
+
+<DD>Cannot use the temper command with only one processor partition. Use
+the -partition command-line option.
+
+<DT><I>Must read Atoms before Angles</I>
+
+<DD>The Atoms section of a data file must come before an Angles section.
+
+<DT><I>Must read Atoms before Bodies</I>
+
+<DD>The Atoms section of a data file must come before a Bodies section.
+
+<DT><I>Must read Atoms before Bonds</I>
+
+<DD>The Atoms section of a data file must come before a Bonds section.
+
+<DT><I>Must read Atoms before Dihedrals</I>
+
+<DD>The Atoms section of a data file must come before a Dihedrals section.
+
+<DT><I>Must read Atoms before Ellipsoids</I>
+
+<DD>The Atoms section of a data file must come before a Ellipsoids
+section.
+
+<DT><I>Must read Atoms before Impropers</I>
+
+<DD>The Atoms section of a data file must come before an Impropers
+section.
+
+<DT><I>Must read Atoms before Lines</I>
+
+<DD>The Atoms section of a data file must come before a Lines section.
+
+<DT><I>Must read Atoms before Triangles</I>
+
+<DD>The Atoms section of a data file must come before a Triangles section.
+
+<DT><I>Must read Atoms before Velocities</I>
+
+<DD>The Atoms section of a data file must come before a Velocities
+section.
+
+<DT><I>Must set both respa inner and outer</I>
+
+<DD>Cannot use just the inner or outer option with respa without using the
+other.
+
+<DT><I>Must set number of threads via package omp command</I>
+
+<DD>Because you are using the USER-OMP package, set the number of threads
+via its settings, not by the pair_style snap nthreads setting.
+
+<DT><I>Must shrink-wrap piston boundary</I>
+
+<DD>The boundary style of the face where the piston is applied must be of
+type s (shrink-wrapped).
+
+<DT><I>Must specify a region in fix deposit</I>
+
+<DD>The region keyword must be specified with this fix.
+
+<DT><I>Must specify a region in fix pour</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must specify at least 2 types in fix atom/swap command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM</I>
+
+<DD>The kspace scalar pressure option cannot (yet) be used with rRESPA.
+
+<DT><I>Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm</I>
+
+<DD>Otherwise MSM will compute only a scalar pressure. See the kspace_modify
+command for details on this setting.
+
+<DT><I>Must use 'kspace_modify pressure/scalar no' to obtain per-atom virial with kspace_style MSM</I>
+
+<DD>The kspace scalar pressure option cannot be used to obtain per-atom virial.
+
+<DT><I>Must use 'kspace_modify pressure/scalar no' with GPU MSM Pair styles</I>
+
+<DD>The kspace scalar pressure option is not (yet) compatible with GPU MSM Pair styles.
+
+<DT><I>Must use 'kspace_modify pressure/scalar no' with kspace_style msm/cg</I>
+
+<DD>The kspace scalar pressure option is not compatible with kspace_style msm/cg.
+
+<DT><I>Must use -in switch with multiple partitions</I>
+
+<DD>A multi-partition simulation cannot read the input script from stdin.
+The -in command-line option must be used to specify a file.
+
+<DT><I>Must use a block or cylinder region with fix pour</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use a block region with fix pour for 2d simulations</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use a bond style with TIP4P potential</I>
+
+<DD>TIP4P potentials assume bond lengths in water are constrained
+by a fix shake command.
+
+<DT><I>Must use a molecular atom style with fix poems molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use a z-axis cylinder region with fix pour</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use an angle style with TIP4P potential</I>
+
+<DD>TIP4P potentials assume angles in water are constrained by a fix shake
+command.
+
+<DT><I>Must use atom map style array with Kokkos</I>
+
+<DD>See the atom_modify map command.
+
+<DT><I>Must use atom style with molecule IDs with fix bond/swap</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use pair_style comb or comb3 with fix qeq/comb</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Must use variable energy with fix addforce</I>
+
+<DD>Must define an energy vartiable when applyting a dynamic
+force during minimization.
+
+<DT><I>Must use variable energy with fix efield</I>
+
+<DD>You must define an energy when performing a minimization with a
+variable E-field.
+
+<DT><I>NEB command before simulation box is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>NEB requires damped dynamics minimizer</I>
+
+<DD>Use a different minimization style.
+
+<DT><I>NEB requires use of fix neb</I>
+
+<DD>Self-explanatory.
+
+<DT><I>NL ramp in wall/piston only implemented in zlo for now</I>
+
+<DD>The ramp keyword can only be used for piston applied to face zlo.
+
+<DT><I>Need ntypes-1 delta_mu values in fix atom/swap command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Needed bonus data not in data file</I>
+
+<DD>Some atom styles require bonus data. See the read_data doc page for
+details.
+
+<DT><I>Needed molecular topology not in data file</I>
+
+<DD>The header of the data file indicated bonds, angles, etc would be
+included, but they are not present.
+
+<DT><I>Neigh_modify exclude molecule requires atom attribute molecule</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Neigh_modify include group != atom_modify first group</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Neighbor delay must be 0 or multiple of every setting</I>
+
+<DD>The delay and every parameters set via the neigh_modify command are
+inconsistent. If the delay setting is non-zero, then it must be a
+multiple of the every setting.
+
+<DT><I>Neighbor include group not allowed with ghost neighbors</I>
+
+<DD>This is a current restriction within LAMMPS.
+
+<DT><I>Neighbor list overflow, boost neigh_modify one</I>
+
+<DD>There are too many neighbors of a single atom. Use the neigh_modify
+command to increase the max number of neighbors allowed for one atom.
+You may also want to boost the page size.
+
+<DT><I>Neighbor multi not yet enabled for ghost neighbors</I>
+
+<DD>This is a current restriction within LAMMPS.
+
+<DT><I>Neighbor multi not yet enabled for granular</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Neighbor multi not yet enabled for rRESPA</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Neighbor page size must be >= 10x the one atom setting</I>
+
+<DD>This is required to prevent wasting too much memory.
+
+<DT><I>New atom IDs exceed maximum allowed ID</I>
+
+<DD>See the setting for tagint in the src/lmptype.h file.
+
+<DT><I>New bond exceeded bonds per atom in create_bonds</I>
+
+<DD>See the read_data command for info on setting the "extra bond per
+atom" header value to allow for additional bonds to be formed.
+
+<DT><I>New bond exceeded bonds per atom in fix bond/create</I>
+
+<DD>See the read_data command for info on setting the "extra bond per
+atom" header value to allow for additional bonds to be formed.
+
+<DT><I>New bond exceeded special list size in fix bond/create</I>
+
+<DD>See the special_bonds extra command for info on how to leave space in
+the special bonds list to allow for additional bonds to be formed.
+
+<DT><I>Newton bond change after simulation box is defined</I>
+
+<DD>The newton command cannot be used to change the newton bond value
+after a read_data, read_restart, or create_box command.
+
+<DT><I>Next command must list all universe and uloop variables</I>
+
+<DD>This is to insure they stay in sync.
+
+<DT><I>No Kspace style defined for compute group/group</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No OpenMP support compiled in</I>
+
+<DD>An OpenMP flag is set, but LAMMPS was not built with
+OpenMP support.
+
+<DT><I>No angle style is defined for compute angle/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No angles allowed with this atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No atom count in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No atoms in data file</I>
+
+<DD>The header of the data file indicated that atoms would be included,
+but they are not present.
+
+<DT><I>No basis atoms in lattice</I>
+
+<DD>Basis atoms must be defined for lattice style user.
+
+<DT><I>No bodies allowed with this atom style</I>
+
+<DD>Self-explanatory. Check data file.
+
+<DT><I>No bond style is defined for compute bond/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No bonds allowed with this atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No box information in dump. You have to use 'box no'</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No dihedral style is defined for compute dihedral/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No dihedrals allowed with this atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No dump custom arguments specified</I>
+
+<DD>The dump custom command requires that atom quantities be specified to
+output to dump file.
+
+<DT><I>No dump local arguments specified</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No ellipsoids allowed with this atom style</I>
+
+<DD>Self-explanatory. Check data file.
+
+<DT><I>No fix gravity defined for fix pour</I>
+
+<DD>Gravity is required to use fix pour.
+
+<DT><I>No improper style is defined for compute improper/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No impropers allowed with this atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No input values for fix ave/spatial</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No lines allowed with this atom style</I>
+
+<DD>Self-explanatory. Check data file.
+
+<DT><I>No matching element in ADP potential file</I>
+
+<DD>The ADP potential file does not contain elements that match the
+requested elements.
+
+<DT><I>No matching element in EAM potential file</I>
+
+<DD>The EAM potential file does not contain elements that match the
+requested elements.
+
+<DT><I>No molecule topology allowed with atom style template</I>
+
+<DD>The data file cannot specify the number of bonds, angles, etc,
+because this info if inferred from the molecule templates.
+
+<DT><I>No overlap of box and region for create_atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No pair coul/streitz for fix qeq/slater</I>
+
+<DD>These commands must be used together.
+
+<DT><I>No pair hbond/dreiding coefficients set</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No pair style defined for compute group/group</I>
+
+<DD>Cannot calculate group interactions without a pair style defined.
+
+<DT><I>No pair style is defined for compute pair/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No pair style is defined for compute property/local</I>
+
+<DD>Self-explanatory.
+
+<DT><I>No rigid bodies defined</I>
+
+<DD>The fix specification did not end up defining any rigid bodies.
+
+<DT><I>No triangles allowed with this atom style</I>
+
+<DD>Self-explanatory. Check data file.
+
+<DT><I>Non digit character between brackets in variable</I>
+
+<DD>Self-explantory.
+
+<DT><I>Non integer # of swaps in temper command</I>
+
+<DD>Swap frequency in temper command must evenly divide the total # of
+timesteps.
+
+<DT><I>Non-numeric box dimensions - simulation unstable</I>
+
+<DD>The box size has apparently blown up.
+
+<DT><I>Not all atom IDs are 0</I>
+
+<DD>Either all atoms IDs must be zero or none of them.
+
+<DT><I>Nprocs not a multiple of N for -reorder</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Number of core atoms != number of shell atoms</I>
+
+<DD>There must be a one-to-one pairing of core and shell atoms.
+
+<DT><I>Numeric index is out of bounds</I>
+
+<DD>A command with an argument that specifies an integer or range of
+integers is using a value that is less than 1 or greater than the
+maximum allowed limit.
+
+<DT><I>One or more atoms belong to multiple rigid bodies</I>
+
+<DD>Two or more rigid bodies defined by the fix rigid command cannot
+contain the same atom.
+
+<DT><I>One or zero atoms in rigid body</I>
+
+<DD>Any rigid body defined by the fix rigid command must contain 2 or more
+atoms.
+
+<DT><I>Only 2 types allowed when not using semi-grand in fix atom/swap command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Only one cut-off allowed when requesting all long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Only one cutoff allowed when requesting all long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Only zhi currently implemented for fix append/atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Out of range atoms - cannot compute MSM</I>
+
+<DD>One or more atoms are attempting to map their charge to a MSM grid point
+that is not owned by a processor. This is likely for one of two
+reasons, both of them bad. First, it may mean that an atom near the
+boundary of a processor's sub-domain has moved more than 1/2 the
+<A HREF = "neighbor.html">neighbor skin distance</A> without neighbor lists being
+rebuilt and atoms being migrated to new processors. This also means
+you may be missing pairwise interactions that need to be computed.
+The solution is to change the re-neighboring criteria via the
+<A HREF = "neigh_modify">neigh_modify</A> command. The safest settings are "delay 0
+every 1 check yes". Second, it may mean that an atom has moved far
+outside a processor's sub-domain or even the entire simulation box.
+This indicates bad physics, e.g. due to highly overlapping atoms, too
+large a timestep, etc.
+
+<DT><I>Out of range atoms - cannot compute PPPM</I>
+
+<DD>One or more atoms are attempting to map their charge to a PPPM grid
+point that is not owned by a processor. This is likely for one of two
+reasons, both of them bad. First, it may mean that an atom near the
+boundary of a processor's sub-domain has moved more than 1/2 the
+<A HREF = "neighbor.html">neighbor skin distance</A> without neighbor lists being
+rebuilt and atoms being migrated to new processors. This also means
+you may be missing pairwise interactions that need to be computed.
+The solution is to change the re-neighboring criteria via the
+<A HREF = "neigh_modify">neigh_modify</A> command. The safest settings are "delay 0
+every 1 check yes". Second, it may mean that an atom has moved far
+outside a processor's sub-domain or even the entire simulation box.
+This indicates bad physics, e.g. due to highly overlapping atoms, too
+large a timestep, etc.
+
+<DT><I>Out of range atoms - cannot compute PPPMDisp</I>
+
+<DD>One or more atoms are attempting to map their charge to a PPPM grid
+point that is not owned by a processor. This is likely for one of two
+reasons, both of them bad. First, it may mean that an atom near the
+boundary of a processor's sub-domain has moved more than 1/2 the
+<A HREF = "neighbor.html">neighbor skin distance</A> without neighbor lists being
+rebuilt and atoms being migrated to new processors. This also means
+you may be missing pairwise interactions that need to be computed.
+The solution is to change the re-neighboring criteria via the
+<A HREF = "neigh_modify">neigh_modify</A> command. The safest settings are "delay 0
+every 1 check yes". Second, it may mean that an atom has moved far
+outside a processor's sub-domain or even the entire simulation box.
+This indicates bad physics, e.g. due to highly overlapping atoms, too
+large a timestep, etc.
+
+<DT><I>Overflow of allocated fix vector storage</I>
+
+<DD>This should not normally happen if the fix correctly calculated
+how long the vector will grow to. Contact the developers.
+
+<DT><I>Overlapping large/large in pair colloid</I>
+
+<DD>This potential is infinite when there is an overlap.
+
+<DT><I>Overlapping small/large in pair colloid</I>
+
+<DD>This potential is infinite when there is an overlap.
+
+<DT><I>POEMS fix must come before NPT/NPH fix</I>
+
+<DD>NPT/NPH fix must be defined in input script after all poems fixes,
+else the fix contribution to the pressure virial is incorrect.
+
+<DT><I>PPPM can only currently be used with comm_style brick</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>PPPM grid is too large</I>
+
+<DD>The global PPPM grid is larger than OFFSET in one or more dimensions.
+OFFSET is currently set to 4096. You likely need to decrease the
+requested accuracy.
+
+<DT><I>PPPM grid stencil extends beyond nearest neighbor processor</I>
+
+<DD>This is not allowed if the kspace_modify overlap setting is no.
+
+<DT><I>PPPM order < minimum allowed order</I>
+
+<DD>The default minimum order is 2. This can be reset by the
+kspace_modify minorder command.
+
+<DT><I>PPPM order cannot be < 2 or > than %d</I>
+
+<DD>This is a limitation of the PPPM implementation in LAMMPS.
+
+<DT><I>PPPMDisp Coulomb grid is too large</I>
+
+<DD>The global PPPM grid is larger than OFFSET in one or more dimensions.
+OFFSET is currently set to 4096. You likely need to decrease the
+requested accuracy.
+
+<DT><I>PPPMDisp Dispersion grid is too large</I>
+
+<DD>The global PPPM grid is larger than OFFSET in one or more dimensions.
+OFFSET is currently set to 4096. You likely need to decrease the
+requested accuracy.
+
+<DT><I>PPPMDisp can only currently be used with comm_style brick</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>PPPMDisp coulomb order cannot be greater than %d</I>
+
+<DD>This is a limitation of the PPPM implementation in LAMMPS.
+
+<DT><I>PPPMDisp used but no parameters set, for further information please see the pppm/disp documentation</I>
+
+<DD>An efficient and accurate usage of the pppm/disp requires settings via the kspace_modify command. Please see the pppm/disp documentation for further instructions.
+
+<DT><I>PRD command before simulation box is defined</I>
+
+<DD>The prd command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>PRD nsteps must be multiple of t_event</I>
+
+<DD>Self-explanatory.
+
+<DT><I>PRD t_corr must be multiple of t_event</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Package command after simulation box is defined</I>
+
+<DD>The package command cannot be used afer a read_data, read_restart, or
+create_box command.
+
+<DT><I>Package cuda command without USER-CUDA package enabled</I>
+
+<DD>The USER-CUDA package must be installed via "make yes-user-cuda"
+before LAMMPS is built, and the "-c on" must be used to enable the
+package.
+
+<DT><I>Package gpu command without GPU package installed</I>
+
+<DD>The GPU package must be installed via "make yes-gpu" before LAMMPS is
+built.
+
+<DT><I>Package intel command without USER-INTEL package installed</I>
+
+<DD>The USER-INTEL package must be installed via "make yes-user-intel"
+before LAMMPS is built.
+
+<DT><I>Package kokkos command without KOKKOS package enabled</I>
+
+<DD>The KOKKOS package must be installed via "make yes-kokkos" before
+LAMMPS is built, and the "-k on" must be used to enable the package.
+
+<DT><I>Package omp command without USER-OMP package installed</I>
+
+<DD>The USER-OMP package must be installed via "make yes-user-omp" before
+LAMMPS is built.
+
+<DT><I>Pair body requires atom style body</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair body requires body style nparticle</I>
+
+<DD>This pair style is specific to the nparticle body style.
+
+<DT><I>Pair brownian requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair brownian requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Pair brownian requires monodisperse particles</I>
+
+<DD>All particles must be the same finite size.
+
+<DT><I>Pair brownian/poly requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair brownian/poly requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Pair brownian/poly requires newton pair off</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair coeff for hybrid has invalid style</I>
+
+<DD>Style in pair coeff must have been listed in pair_style command.
+
+<DT><I>Pair coul/wolf requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair cutoff < Respa interior cutoff</I>
+
+<DD>One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+<DT><I>Pair dipole/cut requires atom attributes q, mu, torque</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair dipole/cut/gpu requires atom attributes q, mu, torque</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair dipole/long requires atom attributes q, mu, torque</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair distance < table inner cutoff</I>
+
+<DD>Two atoms are closer together than the pairwise table allows.
+
+<DT><I>Pair distance > table outer cutoff</I>
+
+<DD>Two atoms are further apart than the pairwise table allows.
+
+<DT><I>Pair dpd requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair gayberne epsilon a,b,c coeffs are not all set</I>
+
+<DD>Each atom type involved in pair_style gayberne must
+have these 3 coefficients set at least once.
+
+<DT><I>Pair gayberne requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair gayberne requires atoms with same type have same shape</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair gayberne/gpu requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair gayberne/gpu requires atoms with same type have same shape</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair granular requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair granular requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair granular with shear history requires newton pair off</I>
+
+<DD>This is a current restriction of the implementation of pair
+granular styles with history.
+
+<DT><I>Pair hybrid sub-style does not support single call</I>
+
+<DD>You are attempting to invoke a single() call on a pair style
+that doesn't support it.
+
+<DT><I>Pair hybrid sub-style is not used</I>
+
+<DD>No pair_coeff command used a sub-style specified in the pair_style
+command.
+
+<DT><I>Pair inner cutoff < Respa interior cutoff</I>
+
+<DD>One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+<DT><I>Pair inner cutoff >= Pair outer cutoff</I>
+
+<DD>The specified cutoffs for the pair style are inconsistent.
+
+<DT><I>Pair line/lj requires atom style line</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair lj/long/dipole/long requires atom attributes mu, torque</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair lubricate requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair lubricate requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair lubricate requires monodisperse particles</I>
+
+<DD>All particles must be the same finite size.
+
+<DT><I>Pair lubricate/poly requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair lubricate/poly requires extended particles</I>
+
+<DD>One of the particles has radius 0.0.
+
+<DT><I>Pair lubricate/poly requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair lubricate/poly requires newton pair off</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair lubricateU requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair lubricateU requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair lubricateU requires monodisperse particles</I>
+
+<DD>All particles must be the same finite size.
+
+<DT><I>Pair lubricateU/poly requires ghost atoms store velocity</I>
+
+<DD>Use the comm_modify vel yes command to enable this.
+
+<DT><I>Pair lubricateU/poly requires newton pair off</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair peri lattice is not identical in x, y, and z</I>
+
+<DD>The lattice defined by the lattice command must be cubic.
+
+<DT><I>Pair peri requires a lattice be defined</I>
+
+<DD>Use the lattice command for this purpose.
+
+<DT><I>Pair peri requires an atom map, see atom_modify</I>
+
+<DD>Even for atomic systems, an atom map is required to find Peridynamic
+bonds. Use the atom_modify command to define one.
+
+<DT><I>Pair resquared epsilon a,b,c coeffs are not all set</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair resquared epsilon and sigma coeffs are not all set</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair resquared requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair resquared requires atoms with same type have same shape</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair resquared/gpu requires atom style ellipsoid</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair resquared/gpu requires atoms with same type have same shape</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style AIREBO requires atom IDs</I>
+
+<DD>This is a requirement to use the AIREBO potential.
+
+<DT><I>Pair style AIREBO requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the AIREBO
+potential.
+
+<DT><I>Pair style BOP requires atom IDs</I>
+
+<DD>This is a requirement to use the BOP potential.
+
+<DT><I>Pair style BOP requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the BOP
+potential.
+
+<DT><I>Pair style COMB requires atom IDs</I>
+
+<DD>This is a requirement to use the AIREBO potential.
+
+<DT><I>Pair style COMB requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style COMB requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the COMB
+potential.
+
+<DT><I>Pair style COMB3 requires atom IDs</I>
+
+<DD>This is a requirement to use the COMB3 potential.
+
+<DT><I>Pair style COMB3 requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style COMB3 requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the COMB3
+potential.
+
+<DT><I>Pair style LCBOP requires atom IDs</I>
+
+<DD>This is a requirement to use the LCBOP potential.
+
+<DT><I>Pair style LCBOP requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the Tersoff
+potential.
+
+<DT><I>Pair style MEAM requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the MEAM
+potential.
+
+<DT><I>Pair style SNAP requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the SNAP
+potential.
+
+<DT><I>Pair style Stillinger-Weber requires atom IDs</I>
+
+<DD>This is a requirement to use the SW potential.
+
+<DT><I>Pair style Stillinger-Weber requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the SW
+potential.
+
+<DT><I>Pair style Tersoff requires atom IDs</I>
+
+<DD>This is a requirement to use the Tersoff potential.
+
+<DT><I>Pair style Tersoff requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use the Tersoff
+potential.
+
+<DT><I>Pair style bop requires comm ghost cutoff at least 3x larger than %g</I>
+
+<DD>Use the communicate ghost command to set this. See the pair bop
+doc page for more details.
+
+<DT><I>Pair style born/coul/long requires atom attribute q</I>
+
+<DD>An atom style that defines this attribute must be used.
+
+<DT><I>Pair style born/coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style born/coul/wolf requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style buck/coul/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style buck/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style buck/coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style buck/long/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style coul/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style coul/cut/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style coul/debye/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style coul/dsf requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style coul/dsf/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style coul/streitz requires atom attribute q</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style does not have extra field requested by compute pair/local</I>
+
+<DD>The pair style does not support the pN value requested by the compute
+pair/local command.
+
+<DT><I>Pair style does not support bond_style quartic</I>
+
+<DD>The pair style does not have a single() function, so it can
+not be invoked by bond_style quartic.
+
+<DT><I>Pair style does not support compute group/group</I>
+
+<DD>The pair_style does not have a single() function, so it cannot be
+invokded by the compute group/group command.
+
+<DT><I>Pair style does not support compute pair/local</I>
+
+<DD>The pair style does not have a single() function, so it can
+not be invoked by compute pair/local.
+
+<DT><I>Pair style does not support compute property/local</I>
+
+<DD>The pair style does not have a single() function, so it can
+not be invoked by fix bond/swap.
+
+<DT><I>Pair style does not support fix bond/swap</I>
+
+<DD>The pair style does not have a single() function, so it can
+not be invoked by fix bond/swap.
+
+<DT><I>Pair style does not support pair_write</I>
+
+<DD>The pair style does not have a single() function, so it can
+not be invoked by pair write.
+
+<DT><I>Pair style does not support rRESPA inner/middle/outer</I>
+
+<DD>You are attempting to use rRESPA options with a pair style that
+does not support them.
+
+<DT><I>Pair style granular with history requires atoms have IDs</I>
+
+<DD>Atoms in the simulation do not have IDs, so history effects
+cannot be tracked by the granular pair potential.
+
+<DT><I>Pair style hbond/dreiding requires an atom map, see atom_modify</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style hbond/dreiding requires atom IDs</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style hbond/dreiding requires molecular system</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style hbond/dreiding requires newton pair on</I>
+
+<DD>See the newton command for details.
+
+<DT><I>Pair style hybrid cannot have hybrid as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style hybrid cannot have none as an argument</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style is incompatible with TIP4P KSpace style</I>
+
+<DD>The pair style does not have the requires TIP4P settings.
+
+<DT><I>Pair style lj/charmm/coul/charmm requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style lj/charmm/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style lj/charmm/coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/class2/coul/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/class2/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/class2/coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/cut/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/debye/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/dsf requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style lj/cut/coul/dsf/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/coul/long/gpu requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/tip4p/cut requires atom IDs</I>
+
+<DD>This is a requirement to use this potential.
+
+<DT><I>Pair style lj/cut/tip4p/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style lj/cut/tip4p/cut requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use this
+potential.
+
+<DT><I>Pair style lj/cut/tip4p/long requires atom IDs</I>
+
+<DD>There are no atom IDs defined in the system and the TIP4P potential
+requires them to find O,H atoms with a water molecule.
+
+<DT><I>Pair style lj/cut/tip4p/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style lj/cut/tip4p/long requires newton pair on</I>
+
+<DD>This is because the computation of constraint forces within a water
+molecule adds forces to atoms owned by other processors.
+
+<DT><I>Pair style lj/gromacs/coul/gromacs requires atom attribute q</I>
+
+<DD>An atom_style with this attribute is needed.
+
+<DT><I>Pair style lj/long/dipole/long does not currently support respa</I>
+
+<DD>This feature is not yet supported.
+
+<DT><I>Pair style lj/long/tip4p/long requires atom IDs</I>
+
+<DD>There are no atom IDs defined in the system and the TIP4P potential
+requires them to find O,H atoms with a water molecule.
+
+<DT><I>Pair style lj/long/tip4p/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style lj/long/tip4p/long requires newton pair on</I>
+
+<DD>This is because the computation of constraint forces within a water
+molecule adds forces to atoms owned by other processors.
+
+<DT><I>Pair style nb3b/harmonic requires atom IDs</I>
+
+<DD>This is a requirement to use this potential.
+
+<DT><I>Pair style nb3b/harmonic requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use this potential.
+
+<DT><I>Pair style nm/cut/coul/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style nm/cut/coul/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style peri requires atom style peri</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style reax requires atom IDs</I>
+
+<DD>This is a requirement to use the ReaxFF potential.
+
+<DT><I>Pair style reax requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style reax requires newton pair on</I>
+
+<DD>This is a requirement to use the ReaxFF potential.
+
+<DT><I>Pair style requires a KSpace style</I>
+
+<DD>No kspace style is defined.
+
+<DT><I>Pair style requires use of kspace_style ewald/disp</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair style sw/gpu requires atom IDs</I>
+
+<DD>This is a requirement to use this potential.
+
+<DT><I>Pair style sw/gpu requires newton pair off</I>
+
+<DD>See the newton command. This is a restriction to use this potential.
+
+<DT><I>Pair style tip4p/cut requires atom IDs</I>
+
+<DD>This is a requirement to use this potential.
+
+<DT><I>Pair style tip4p/cut requires atom attribute q</I>
+
+<DD>The atom style defined does not have this attribute.
+
+<DT><I>Pair style tip4p/cut requires newton pair on</I>
+
+<DD>See the newton command. This is a restriction to use this potential.
+
+<DT><I>Pair style tip4p/long requires atom IDs</I>
+
+<DD>There are no atom IDs defined in the system and the TIP4P potential
+requires them to find O,H atoms with a water molecule.
+
+<DT><I>Pair style tip4p/long requires atom attribute q</I>
+
+<DD>The atom style defined does not have these attributes.
+
+<DT><I>Pair style tip4p/long requires newton pair on</I>
+
+<DD>This is because the computation of constraint forces within a water
+molecule adds forces to atoms owned by other processors.
+
+<DT><I>Pair table cutoffs must all be equal to use with KSpace</I>
+
+<DD>When using pair style table with a long-range KSpace solver, the
+cutoffs for all atom type pairs must all be the same, since the
+long-range solver starts at that cutoff.
+
+<DT><I>Pair table parameters did not set N</I>
+
+<DD>List of pair table parameters must include N setting.
+
+<DT><I>Pair tersoff/zbl requires metal or real units</I>
+
+<DD>This is a current restriction of this pair potential.
+
+<DT><I>Pair tri/lj requires atom style tri</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair yukawa/colloid requires atom style sphere</I>
+
+<DD>Self-explantory.
+
+<DT><I>Pair yukawa/colloid requires atoms with same type have same radius</I>
+
+<DD>Self-explantory.
+
+<DT><I>Pair yukawa/colloid/gpu requires atom style sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>PairKIM only works with 3D problems</I>
+
+<DD>This is a current limitation.
+
+<DT><I>Pair_coeff command before pair_style is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair_coeff command before simulation box is defined</I>
+
+<DD>The pair_coeff command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Pair_modify command before pair_style is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair_write command before pair_style is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Particle on or inside fix wall surface</I>
+
+<DD>Particles must be "exterior" to the wall in order for energy/force to
+be calculated.
+
+<DT><I>Particle on or inside surface of region used in fix wall/region</I>
+
+<DD>Particles must be "exterior" to the region surface in order for
+energy/force to be calculated.
+
+<DT><I>Per-atom compute in equal-style variable formula</I>
+
+<DD>Equal-style variables cannot use per-atom quantities.
+
+<DT><I>Per-atom energy was not tallied on needed timestep</I>
+
+<DD>You are using a thermo keyword that requires potentials to
+have tallied energy, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+<DT><I>Per-atom fix in equal-style variable formula</I>
+
+<DD>Equal-style variables cannot use per-atom quantities.
+
+<DT><I>Per-atom virial was not tallied on needed timestep</I>
+
+<DD>You are using a thermo keyword that requires potentials to have
+tallied the virial, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+<DT><I>Per-processor system is too big</I>
+
+<DD>The number of owned atoms plus ghost atoms on a single
+processor must fit in 32-bit integer.
+
+<DT><I>Potential energy ID for fix neb does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Potential energy ID for fix nvt/nph/npt does not exist</I>
+
+<DD>A compute for potential energy must be defined.
+
+<DT><I>Potential file has duplicate entry</I>
+
+<DD>The potential file has more than one entry for the same element.
+
+<DT><I>Potential file is missing an entry</I>
+
+<DD>The potential file does not have a needed entry.
+
+<DT><I>Power by 0 in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure ID for fix box/relax does not exist</I>
+
+<DD>The compute ID needed to compute pressure for the fix does not
+exist.
+
+<DT><I>Pressure ID for fix modify does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure ID for fix npt/nph does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure ID for fix press/berendsen does not exist</I>
+
+<DD>The compute ID needed to compute pressure for the fix does not
+exist.
+
+<DT><I>Pressure ID for fix rigid npt/nph does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure ID for thermo does not exist</I>
+
+<DD>The compute ID needed to compute pressure for thermodynamics does not
+exist.
+
+<DT><I>Pressure control can not be used with fix nvt</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control can not be used with fix nvt/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control can not be used with fix nvt/sllod</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control can not be used with fix nvt/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix nph</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix nph/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix nph/small</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix nph/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix nphug</I>
+
+<DD>A pressure control keyword (iso, aniso, tri, x, y, or z) must be
+provided.
+
+<DT><I>Pressure control must be used with fix npt</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix npt/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pressure control must be used with fix npt/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Processor count in z must be 1 for 2d simulation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Processor partitions do not match number of allocated processors</I>
+
+<DD>The total number of processors in all partitions must match the number
+of processors LAMMPS is running on.
+
+<DT><I>Processors command after simulation box is defined</I>
+
+<DD>The processors command cannot be used after a read_data, read_restart,
+or create_box command.
+
+<DT><I>Processors custom grid file is inconsistent</I>
+
+<DD>The vales in the custom file are not consistent with the number of
+processors you are running on or the Px,Py,Pz settings of the
+processors command. Or there was not a setting for every processor.
+
+<DT><I>Processors grid numa and map style are incompatible</I>
+
+<DD>Using numa for gstyle in the processors command requires using
+cart for the map option.
+
+<DT><I>Processors part option and grid style are incompatible</I>
+
+<DD>Cannot use gstyle numa or custom with the part option.
+
+<DT><I>Processors twogrid requires proc count be a multiple of core count</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pstart and Pstop must have the same value</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Python function evaluation failed</I>
+
+<DD>The Python function did not run succesfully and/or did not return a
+value (if it is supposed to return a value). This is probably due to
+some error condition in the function.
+
+<DT><I>Python function is not callable</I>
+
+<DD>The provided Python code was run successfully, but it not
+define a callable function with the required name.
+
+<DT><I>Python invoke of undefined function</I>
+
+<DD>Cannot invoke a function that has not been previously defined.
+
+<DT><I>Python variable does not match Python function</I>
+
+<DD>This matching is defined by the python-style variable and the python
+command.
+
+<DT><I>Python variable has no function</I>
+
+<DD>No python command was used to define the function associated with the
+python-style variable.
+
+<DT><I>QEQ with 'newton pair off' not supported</I>
+
+<DD>See the newton command. This is a restriction to use the QEQ fixes.
+
+<DT><I>R0 < 0 for fix spring command</I>
+
+<DD>Equilibrium spring length is invalid.
+
+<DT><I>RATTLE coordinate constraints are not satisfied up to desired tolerance</I>
+
+<DD>Self-explanatory.
+
+<DT><I>RATTLE determinant = 0.0</I>
+
+<DD>The determinant of the matrix being solved for a single cluster
+specified by the fix rattle command is numerically invalid.
+
+<DT><I>RATTLE failed</I>
+
+<DD>Certain constraints were not satisfied.
+
+<DT><I>RATTLE velocity constraints are not satisfied up to desired tolerance</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Read dump of atom property that isn't allocated</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Read rerun dump file timestep > specified stop</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Read restart MPI-IO input not allowed with % in filename</I>
+
+<DD>This is because a % signifies one file per processor and MPI-IO
+creates one large file for all processors.
+
+<DT><I>Read_data shrink wrap did not assign all atoms correctly</I>
+
+<DD>This is typically because the box-size specified in the data file is
+large compared to the actual extent of atoms in a shrink-wrapped
+dimension. When LAMMPS shrink-wraps the box atoms will be lost if the
+processor they are re-assigned to is too far away. Choose a box
+size closer to the actual extent of the atoms.
+
+<DT><I>Read_dump command before simulation box is defined</I>
+
+<DD>The read_dump command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Read_dump field not found in dump file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Read_dump triclinic status does not match simulation</I>
+
+<DD>Both the dump snapshot and the current LAMMPS simulation must
+be using either an orthogonal or triclinic box.
+
+<DT><I>Read_dump xyz fields do not have consistent scaling/wrapping</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Reading from MPI-IO filename when MPIIO package is not installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Reax_defs.h setting for NATDEF is too small</I>
+
+<DD>Edit the setting in the ReaxFF library and re-compile the
+library and re-build LAMMPS.
+
+<DT><I>Reax_defs.h setting for NNEIGHMAXDEF is too small</I>
+
+<DD>Edit the setting in the ReaxFF library and re-compile the
+library and re-build LAMMPS.
+
+<DT><I>Receiving partition in processors part command is already a receiver</I>
+
+<DD>Cannot specify a partition to be a receiver twice.
+
+<DT><I>Region ID for compute chunk/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for compute reduce/region does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for compute temp/region does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for dump custom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix addforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix atom/swap does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix ave/spatial does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix aveforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix deposit does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix efield does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix evaporate does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix gcmc does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix heat does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix setforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for fix wall/region does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID for group dynamic does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region ID in variable formula does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region cannot have 0 length rotation vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region for fix oneway does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region intersect region ID does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Region union or intersect cannot be dynamic</I>
+
+<DD>The sub-regions can be dynamic, but not the combined region.
+
+<DT><I>Region union region ID does not exist</I>
+
+<DD>One or more of the region IDs specified by the region union command
+does not exist.
+
+<DT><I>Replacing a fix, but new style != old style</I>
+
+<DD>A fix ID can be used a 2nd time, but only if the style matches the
+previous fix. In this case it is assumed you with to reset a fix's
+parameters. This error may mean you are mistakenly re-using a fix ID
+when you do not intend to.
+
+<DT><I>Replicate command before simulation box is defined</I>
+
+<DD>The replicate command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Replicate did not assign all atoms correctly</I>
+
+<DD>Atoms replicated by the replicate command were not assigned correctly
+to processors. This is likely due to some atom coordinates being
+outside a non-periodic simulation box.
+
+<DT><I>Replicated system atom IDs are too big</I>
+
+<DD>See the setting for tagint in the src/lmptype.h file.
+
+<DT><I>Replicated system is too big</I>
+
+<DD>See the setting for bigint in the src/lmptype.h file.
+
+<DT><I>Required border comm not yet implemented with Kokkos</I>
+
+<DD>There are various limitations in the communication options supported
+by Kokkos.
+
+<DT><I>Rerun command before simulation box is defined</I>
+
+<DD>The rerun command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Rerun dump file does not contain requested snapshot</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Resetting timestep size is not allowed with fix move</I>
+
+<DD>This is because fix move is moving atoms based on elapsed time.
+
+<DT><I>Respa inner cutoffs are invalid</I>
+
+<DD>The first cutoff must be <= the second cutoff.
+
+<DT><I>Respa levels must be >= 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Respa middle cutoffs are invalid</I>
+
+<DD>The first cutoff must be <= the second cutoff.
+
+<DT><I>Restart file MPI-IO output not allowed with % in filename</I>
+
+<DD>This is because a % signifies one file per processor and MPI-IO
+creates one large file for all processors.
+
+<DT><I>Restart file byte ordering is not recognized</I>
+
+<DD>The file does not appear to be a LAMMPS restart file since it doesn't
+contain a recognized byte-orderomg flag at the beginning.
+
+<DT><I>Restart file byte ordering is swapped</I>
+
+<DD>The file was written on a machine with different byte-ordering than
+the machine you are reading it on. Convert it to a text data file
+instead, on the machine you wrote it on.
+
+<DT><I>Restart file incompatible with current version</I>
+
+<DD>This is probably because you are trying to read a file created with a
+version of LAMMPS that is too old compared to the current version.
+Use your older version of LAMMPS and convert the restart file
+to a data file.
+
+<DT><I>Restart file is a MPI-IO file</I>
+
+<DD>The file is inconsistent with the filename you specified for it.
+
+<DT><I>Restart file is a multi-proc file</I>
+
+<DD>The file is inconsistent with the filename you specified for it.
+
+<DT><I>Restart file is not a MPI-IO file</I>
+
+<DD>The file is inconsistent with the filename you specified for it.
+
+<DT><I>Restart file is not a multi-proc file</I>
+
+<DD>The file is inconsistent with the filename you specified for it.
+
+<DT><I>Restart variable returned a bad timestep</I>
+
+<DD>The variable must return a timestep greater than the current timestep.
+
+<DT><I>Restrain atoms %d %d %d %d missing on proc %d at step %ld</I>
+
+<DD>The 4 atoms in a restrain dihedral specified by the fix restrain
+command are not all accessible to a processor. This probably means an
+atom has moved too far.
+
+<DT><I>Restrain atoms %d %d %d missing on proc %d at step %ld</I>
+
+<DD>The 3 atoms in a restrain angle specified by the fix restrain
+command are not all accessible to a processor. This probably means an
+atom has moved too far.
+
+<DT><I>Restrain atoms %d %d missing on proc %d at step %ld</I>
+
+<DD>The 2 atoms in a restrain bond specified by the fix restrain
+command are not all accessible to a processor. This probably means an
+atom has moved too far.
+
+<DT><I>Reuse of compute ID</I>
+
+<DD>A compute ID cannot be used twice.
+
+<DT><I>Reuse of dump ID</I>
+
+<DD>A dump ID cannot be used twice.
+
+<DT><I>Reuse of molecule template ID</I>
+
+<DD>The template IDs must be unique.
+
+<DT><I>Reuse of region ID</I>
+
+<DD>A region ID cannot be used twice.
+
+<DT><I>Rigid body atoms %d %d missing on proc %d at step %ld</I>
+
+<DD>This means that an atom cannot find the atom that owns the rigid body
+it is part of, or vice versa. The solution is to use the communicate
+cutoff command to insure ghost atoms are acquired from far enough away
+to encompass the max distance printed when the fix rigid/small command
+was invoked.
+
+<DT><I>Rigid body has degenerate moment of inertia</I>
+
+<DD>Fix poems will only work with bodies (collections of atoms) that have
+non-zero principal moments of inertia. This means they must be 3 or
+more non-collinear atoms, even with joint atoms removed.
+
+<DT><I>Rigid fix must come before NPT/NPH fix</I>
+
+<DD>NPT/NPH fix must be defined in input script after all rigid fixes,
+else the rigid fix contribution to the pressure virial is
+incorrect.
+
+<DT><I>Rmask function in equal-style variable formula</I>
+
+<DD>Rmask is per-atom operation.
+
+<DT><I>Run command before simulation box is defined</I>
+
+<DD>The run command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Run command start value is after start of run</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Run command stop value is before end of run</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Run_style command before simulation box is defined</I>
+
+<DD>The run_style command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>SRD bin size for fix srd differs from user request</I>
+
+<DD>Fix SRD had to adjust the bin size to fit the simulation box. See the
+cubic keyword if you want this message to be an error vs warning.
+
+<DT><I>SRD bins for fix srd are not cubic enough</I>
+
+<DD>The bin shape is not within tolerance of cubic. See the cubic
+keyword if you want this message to be an error vs warning.
+
+<DT><I>SRD particle %d started inside big particle %d on step %ld bounce %d</I>
+
+<DD>See the inside keyword if you want this message to be an error vs
+warning.
+
+<DT><I>SRD particle %d started inside wall %d on step %ld bounce %d</I>
+
+<DD>See the inside keyword if you want this message to be an error vs
+warning.
+
+<DT><I>Same dimension twice in fix ave/spatial</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Sending partition in processors part command is already a sender</I>
+
+<DD>Cannot specify a partition to be a sender twice.
+
+<DT><I>Set command before simulation box is defined</I>
+
+<DD>The set command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Set command floating point vector does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Set command integer vector does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Set command with no atoms existing</I>
+
+<DD>No atoms are yet defined so the set command cannot be used.
+
+<DT><I>Set region ID does not exist</I>
+
+<DD>Region ID specified in set command does not exist.
+
+<DT><I>Shake angles have different bond types</I>
+
+<DD>All 3-atom angle-constrained SHAKE clusters specified by the fix shake
+command that are the same angle type, must also have the same bond
+types for the 2 bonds in the angle.
+
+<DT><I>Shake atoms %d %d %d %d missing on proc %d at step %ld</I>
+
+<DD>The 4 atoms in a single shake cluster specified by the fix shake
+command are not all accessible to a processor. This probably means
+an atom has moved too far.
+
+<DT><I>Shake atoms %d %d %d missing on proc %d at step %ld</I>
+
+<DD>The 3 atoms in a single shake cluster specified by the fix shake
+command are not all accessible to a processor. This probably means
+an atom has moved too far.
+
+<DT><I>Shake atoms %d %d missing on proc %d at step %ld</I>
+
+<DD>The 2 atoms in a single shake cluster specified by the fix shake
+command are not all accessible to a processor. This probably means
+an atom has moved too far.
+
+<DT><I>Shake cluster of more than 4 atoms</I>
+
+<DD>A single cluster specified by the fix shake command can have no more
+than 4 atoms.
+
+<DT><I>Shake clusters are connected</I>
+
+<DD>A single cluster specified by the fix shake command must have a single
+central atom with up to 3 other atoms bonded to it.
+
+<DT><I>Shake determinant = 0.0</I>
+
+<DD>The determinant of the matrix being solved for a single cluster
+specified by the fix shake command is numerically invalid.
+
+<DT><I>Shake fix must come before NPT/NPH fix</I>
+
+<DD>NPT fix must be defined in input script after SHAKE fix, else the
+SHAKE fix contribution to the pressure virial is incorrect.
+
+<DT><I>Shear history overflow, boost neigh_modify one</I>
+
+<DD>There are too many neighbors of a single atom. Use the neigh_modify
+command to increase the max number of neighbors allowed for one atom.
+You may also want to boost the page size.
+
+<DT><I>Small to big integers are not sized correctly</I>
+
+<DD>This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
+as defined in src/lmptype.h are not what is expected. Contact
+the developers if this occurs.
+
+<DT><I>Smallint setting in lmptype.h is invalid</I>
+
+<DD>It has to be the size of an integer.
+
+<DT><I>Smallint setting in lmptype.h is not compatible</I>
+
+<DD>Smallint stored in restart file is not consistent with LAMMPS version
+you are running.
+
+<DT><I>Special list size exceeded in fix bond/create</I>
+
+<DD>See the read_data command for info on setting the "extra special per
+atom" header value to allow for additional special values to be
+stored.
+
+<DT><I>Specified processors != physical processors</I>
+
+<DD>The 3d grid of processors defined by the processors command does not
+match the number of processors LAMMPS is being run on.
+
+<DT><I>Specified target stress must be uniaxial or hydrostatic</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Sqrt of negative value in variable formula</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Substitution for illegal variable</I>
+
+<DD>Input script line contained a variable that could not be substituted
+for.
+
+<DT><I>Support for writing images in JPEG format not included</I>
+
+<DD>LAMMPS was not built with the -DLAMMPS_JPEG switch in the Makefile.
+
+<DT><I>Support for writing images in PNG format not included</I>
+
+<DD>LAMMPS was not built with the -DLAMMPS_PNG switch in the Makefile.
+
+<DT><I>Support for writing movies not included</I>
+
+<DD>LAMMPS was not built with the -DLAMMPS_FFMPEG switch in the Makefile
+
+<DT><I>System in data file is too big</I>
+
+<DD>See the setting for bigint in the src/lmptype.h file.
+
+<DT><I>System is not charge neutral, net charge = %g</I>
+
+<DD>The total charge on all atoms on the system is not 0.0, which
+is not valid for the long-range Coulombic solvers.
+
+<DT><I>TAD nsteps must be multiple of t_event</I>
+
+<DD>Self-explanatory.
+
+<DT><I>TIP4P hydrogen has incorrect atom type</I>
+
+<DD>The TIP4P pairwise computation found an H atom whose type does not
+agree with the specified H type.
+
+<DT><I>TIP4P hydrogen is missing</I>
+
+<DD>The TIP4P pairwise computation failed to find the correct H atom
+within a water molecule.
+
+<DT><I>TMD target file did not list all group atoms</I>
+
+<DD>The target file for the fix tmd command did not list all atoms in the
+fix group.
+
+<DT><I>Tad command before simulation box is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Tagint setting in lmptype.h is invalid</I>
+
+<DD>Tagint must be as large or larger than smallint.
+
+<DT><I>Tagint setting in lmptype.h is not compatible</I>
+
+<DD>Format of tagint stored in restart file is not consistent with LAMMPS
+version you are running. See the settings in src/lmptype.h
+
+<DT><I>Target pressure for fix rigid/nph cannot be < 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target pressure for fix rigid/npt/small cannot be < 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target temperature for fix nvt/npt/nph cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target temperature for fix rigid/npt cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target temperature for fix rigid/npt/small cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target temperature for fix rigid/nvt cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Target temperature for fix rigid/nvt/small cannot be 0.0</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temper command before simulation box is defined</I>
+
+<DD>The temper command cannot be used before a read_data, read_restart, or
+create_box command.
+
+<DT><I>Temperature ID for fix bond/swap does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix box/relax does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix nvt/npt does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix press/berendsen does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix rigid nvt/npt/nph does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix temp/berendsen does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix temp/csvr does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature ID for fix temp/rescale does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control can not be used with fix nph</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control can not be used with fix nph/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control can not be used with fix nph/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix nphug</I>
+
+<DD>The temp keyword must be provided.
+
+<DT><I>Temperature control must be used with fix npt</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix npt/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix npt/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix nvt</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix nvt/asphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix nvt/sllod</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must be used with fix nvt/sphere</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature control must not be used with fix nph/small</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Temperature for fix nvt/sllod does not have a bias</I>
+
+<DD>The specified compute must compute temperature with a bias.
+
+<DT><I>Tempering could not find thermo_pe compute</I>
+
+<DD>This compute is created by the thermo command. It must have been
+explicitly deleted by a uncompute command.
+
+<DT><I>Tempering fix ID is not defined</I>
+
+<DD>The fix ID specified by the temper command does not exist.
+
+<DT><I>Tempering temperature fix is not valid</I>
+
+<DD>The fix specified by the temper command is not one that controls
+temperature (nvt or langevin).
+
+<DT><I>Test_descriptor_string already allocated</I>
+
+<DD>This is an internal error. Contact the developers.
+
+<DT><I>The package gpu command is required for gpu styles</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo and fix not computed at compatible times</I>
+
+<DD>Fixes generate values on specific timesteps. The thermo output
+does not match these timesteps.
+
+<DT><I>Thermo compute array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo compute does not compute array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo compute does not compute scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo compute does not compute vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo custom variable cannot be indexed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo custom variable is not equal-style variable</I>
+
+<DD>Only equal-style variables can be output with thermodynamics, not
+atom-style variables.
+
+<DT><I>Thermo every variable returned a bad timestep</I>
+
+<DD>The variable must return a timestep greater than the current timestep.
+
+<DT><I>Thermo fix array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo fix does not compute array</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo fix does not compute scalar</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo fix does not compute vector</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo keyword in variable requires thermo to use/init pe</I>
+
+<DD>You are using a thermo keyword in a variable that requires
+potential energy to be calculated, but your thermo output
+does not use it. Add it to your thermo output.
+
+<DT><I>Thermo keyword in variable requires thermo to use/init press</I>
+
+<DD>You are using a thermo keyword in a variable that requires pressure to
+be calculated, but your thermo output does not use it. Add it to your
+thermo output.
+
+<DT><I>Thermo keyword in variable requires thermo to use/init temp</I>
+
+<DD>You are using a thermo keyword in a variable that requires temperature
+to be calculated, but your thermo output does not use it. Add it to
+your thermo output.
+
+<DT><I>Thermo style does not use press</I>
+
+<DD>Cannot use thermo_modify to set this parameter since the thermo_style
+is not computing this quantity.
+
+<DT><I>Thermo style does not use temp</I>
+
+<DD>Cannot use thermo_modify to set this parameter since the thermo_style
+is not computing this quantity.
+
+<DT><I>Thermo_modify every variable returned a bad timestep</I>
+
+<DD>The returned timestep is less than or equal to the current timestep.
+
+<DT><I>Thermo_modify int format does not contain d character</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Thermo_modify pressure ID does not compute pressure</I>
+
+<DD>The specified compute ID does not compute pressure.
+
+<DT><I>Thermo_modify temperature ID does not compute temperature</I>
+
+<DD>The specified compute ID does not compute temperature.
+
+<DT><I>Thermo_style command before simulation box is defined</I>
+
+<DD>The thermo_style command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>This variable thermo keyword cannot be used between runs</I>
+
+<DD>Keywords that refer to time (such as cpu, elapsed) do not
+make sense in between runs.
+
+<DT><I>Threshhold for an atom property that isn't allocated</I>
+
+<DD>A dump threshhold has been requested on a quantity that is
+not defined by the atom style used in this simulation.
+
+<DT><I>Timestep must be >= 0</I>
+
+<DD>Specified timestep is invalid.
+
+<DT><I>Too big a problem to use velocity create loop all</I>
+
+<DD>The system size must fit in a 32-bit integer to use this option.
+
+<DT><I>Too big a timestep</I>
+
+<DD>Specified timestep is too large.
+
+<DT><I>Too big a timestep for dump dcd</I>
+
+<DD>The timestep must fit in a 32-bit integer to use this dump style.
+
+<DT><I>Too big a timestep for dump xtc</I>
+
+<DD>The timestep must fit in a 32-bit integer to use this dump style.
+
+<DT><I>Too few bits for lookup table</I>
+
+<DD>Table size specified via pair_modify command does not work with your
+machine's floating point representation.
+
+<DT><I>Too many -pk arguments in command line</I>
+
+<DD>The string formed by concatenating the arguments is too long. Use a
+package command in the input script instead.
+
+<DT><I>Too many MSM grid levels</I>
+
+<DD>The max number of MSM grid levels is hardwired to 10.
+
+<DT><I>Too many args in variable function</I>
+
+<DD>More args are used than any variable function allows.
+
+<DT><I>Too many atom pairs for pair bop</I>
+
+<DD>The number of atomic pairs exceeds the expected number. Check your
+atomic structure to ensure that it is realistic.
+
+<DT><I>Too many atom sorting bins</I>
+
+<DD>This is likely due to an immense simulation box that has blown up
+to a large size.
+
+<DT><I>Too many atom triplets for pair bop</I>
+
+<DD>The number of three atom groups for angle determinations exceeds the
+expected number. Check your atomic structrure to ensure that it is
+realistic.
+
+<DT><I>Too many atoms for dump dcd</I>
+
+<DD>The system size must fit in a 32-bit integer to use this dump
+style.
+
+<DT><I>Too many atoms for dump xtc</I>
+
+<DD>The system size must fit in a 32-bit integer to use this dump
+style.
+
+<DT><I>Too many atoms to dump sort</I>
+
+<DD>Cannot sort when running with more than 2^31 atoms.
+
+<DT><I>Too many exponent bits for lookup table</I>
+
+<DD>Table size specified via pair_modify command does not work with your
+machine's floating point representation.
+
+<DT><I>Too many groups</I>
+
+<DD>The maximum number of atom groups (including the "all" group) is
+given by MAX_GROUP in group.cpp and is 32.
+
+<DT><I>Too many iterations</I>
+
+<DD>You must use a number of iterations that fit in a 32-bit integer
+for minimization.
+
+<DT><I>Too many lines in one body in data file - boost MAXBODY</I>
+
+<DD>MAXBODY is a setting at the top of the src/read_data.cpp file.
+Set it larger and re-compile the code.
+
+<DT><I>Too many local+ghost atoms for neighbor list</I>
+
+<DD>The number of nlocal + nghost atoms on a processor
+is limited by the size of a 32-bit integer with 2 bits
+removed for masking 1-2, 1-3, 1-4 neighbors.
+
+<DT><I>Too many mantissa bits for lookup table</I>
+
+<DD>Table size specified via pair_modify command does not work with your
+machine's floating point representation.
+
+<DT><I>Too many masses for fix shake</I>
+
+<DD>The fix shake command cannot list more masses than there are atom
+types.
+
+<DT><I>Too many molecules for fix poems</I>
+
+<DD>The limit is 2^31 = ~2 billion molecules.
+
+<DT><I>Too many molecules for fix rigid</I>
+
+<DD>The limit is 2^31 = ~2 billion molecules.
+
+<DT><I>Too many neighbor bins</I>
+
+<DD>This is likely due to an immense simulation box that has blown up
+to a large size.
+
+<DT><I>Too many timesteps</I>
+
+<DD>The cummulative timesteps must fit in a 64-bit integer.
+
+<DT><I>Too many timesteps for NEB</I>
+
+<DD>You must use a number of timesteps that fit in a 32-bit integer
+for NEB.
+
+<DT><I>Too many total atoms</I>
+
+<DD>See the setting for bigint in the src/lmptype.h file.
+
+<DT><I>Too many total bits for bitmapped lookup table</I>
+
+<DD>Table size specified via pair_modify command is too large. Note that
+a value of N generates a 2^N size table.
+
+<DT><I>Too much buffered per-proc info for dump</I>
+
+<DD>The size of the buffered string must fit in a 32-bit integer for a
+dump.
+
+<DT><I>Too much per-proc info for dump</I>
+
+<DD>Number of local atoms times number of columns must fit in a 32-bit
+integer for dump.
+
+<DT><I>Tree structure in joint connections</I>
+
+<DD>Fix poems cannot (yet) work with coupled bodies whose joints connect
+the bodies in a tree structure.
+
+<DT><I>Triclinic box skew is too large</I>
+
+<DD>The displacement in a skewed direction must be less than half the box
+length in that dimension. E.g. the xy tilt must be between -half and
++half of the x box length. This constraint can be relaxed by using
+the box tilt command.
+
+<DT><I>Tried to convert a double to int, but input_double > INT_MAX</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Trying to build an occasional neighbor list before initialization completed</I>
+
+<DD>This is not allowed. Source code caller needs to be modified.
+
+<DT><I>Two fix ave commands using same compute chunk/atom command in incompatible ways</I>
+
+<DD>They are both attempting to "lock" the chunk/atom command so that the
+chunk assignments persist for some number of timesteps, but are doing
+it in different ways.
+
+<DT><I>Two groups cannot be the same in fix spring couple</I>
+
+<DD>Self-explanatory.
+
+<DT><I>USER-CUDA mode requires CUDA variant of min style</I>
+
+<DD>CUDA mode is enabled, so the min style must include a cuda suffix.
+
+<DT><I>USER-CUDA mode requires CUDA variant of run style</I>
+
+<DD>CUDA mode is enabled, so the run style must include a cuda suffix.
+
+<DT><I>USER-CUDA package does not yet support comm_style tiled</I>
+
+<DD>Self-explanatory.
+
+<DT><I>USER-CUDA package requires a cuda enabled atom_style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unable to initialize accelerator for use</I>
+
+<DD>There was a problem initializing an accelerator for the gpu package
+
+<DT><I>Unbalanced quotes in input line</I>
+
+<DD>No matching end double quote was found following a leading double
+quote.
+
+<DT><I>Unexpected end of -reorder file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unexpected end of AngleCoeffs section</I>
+
+<DD>Read a blank line.
+
+<DT><I>Unexpected end of BondCoeffs section</I>
+
+<DD>Read a blank line.
+
+<DT><I>Unexpected end of DihedralCoeffs section</I>
+
+<DD>Read a blank line.
+
+<DT><I>Unexpected end of ImproperCoeffs section</I>
+
+<DD>Read a blank line.
+
+<DT><I>Unexpected end of PairCoeffs section</I>
+
+<DD>Read a blank line.
+
+<DT><I>Unexpected end of custom file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unexpected end of data file</I>
+
+<DD>LAMMPS hit the end of the data file while attempting to read a
+section. Something is wrong with the format of the data file.
+
+<DT><I>Unexpected end of dump file</I>
+
+<DD>A read operation from the file failed.
+
+<DT><I>Unexpected end of fix rigid file</I>
+
+<DD>A read operation from the file failed.
+
+<DT><I>Unexpected end of fix rigid/small file</I>
+
+<DD>A read operation from the file failed.
+
+<DT><I>Unexpected end of molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unexpected end of neb file</I>
+
+<DD>A read operation from the file failed.
+
+<DT><I>Units command after simulation box is defined</I>
+
+<DD>The units command cannot be used after a read_data, read_restart, or
+create_box command.
+
+<DT><I>Universe/uloop variable count < # of partitions</I>
+
+<DD>A universe or uloop style variable must specify a number of values >= to the
+number of processor partitions.
+
+<DT><I>Unknown angle style</I>
+
+<DD>The choice of angle style is unknown.
+
+<DT><I>Unknown atom style</I>
+
+<DD>The choice of atom style is unknown.
+
+<DT><I>Unknown body style</I>
+
+<DD>The choice of body style is unknown.
+
+<DT><I>Unknown bond style</I>
+
+<DD>The choice of bond style is unknown.
+
+<DT><I>Unknown command: %s</I>
+
+<DD>The command is not known to LAMMPS. Check the input script.
+
+<DT><I>Unknown compute style</I>
+
+<DD>The choice of compute style is unknown.
+
+<DT><I>Unknown dihedral style</I>
+
+<DD>The choice of dihedral style is unknown.
+
+<DT><I>Unknown dump reader style</I>
+
+<DD>The choice of dump reader style via the format keyword is unknown.
+
+<DT><I>Unknown dump style</I>
+
+<DD>The choice of dump style is unknown.
+
+<DT><I>Unknown error in GPU library</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unknown fix style</I>
+
+<DD>The choice of fix style is unknown.
+
+<DT><I>Unknown identifier in data file: %s</I>
+
+<DD>A section of the data file cannot be read by LAMMPS.
+
+<DT><I>Unknown improper style</I>
+
+<DD>The choice of improper style is unknown.
+
+<DT><I>Unknown keyword in thermo_style custom command</I>
+
+<DD>One or more specified keywords are not recognized.
+
+<DT><I>Unknown kspace style</I>
+
+<DD>The choice of kspace style is unknown.
+
+<DT><I>Unknown pair style</I>
+
+<DD>The choice of pair style is unknown.
+
+<DT><I>Unknown pair_modify hybrid sub-style</I>
+
+<DD>The choice of sub-style is unknown.
+
+<DT><I>Unknown region style</I>
+
+<DD>The choice of region style is unknown.
+
+<DT><I>Unknown section in molecule file</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unknown table style in angle style table</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unknown table style in bond style table</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unknown table style in pair_style command</I>
+
+<DD>Style of table is invalid for use with pair_style table command.
+
+<DT><I>Unknown unit_style</I>
+
+<DD>Self-explanatory. Check the input script or data file.
+
+<DT><I>Unrecognized lattice type in MEAM file 1</I>
+
+<DD>The lattice type in an entry of the MEAM library file is not
+valid.
+
+<DT><I>Unrecognized lattice type in MEAM file 2</I>
+
+<DD>The lattice type in an entry of the MEAM parameter file is not
+valid.
+
+<DT><I>Unrecognized pair style in compute pair command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Unrecognized virial argument in pair_style command</I>
+
+<DD>Only two options are supported: LAMMPSvirial and KIMvirial
+
+<DT><I>Unsupported mixing rule in kspace_style ewald/disp</I>
+
+<DD>Only geometric mixing is supported.
+
+<DT><I>Unsupported order in kspace_style ewald/disp</I>
+
+<DD>Only 1/r^6 dispersion or dipole terms are supported.
+
+<DT><I>Unsupported order in kspace_style pppm/disp, pair_style %s</I>
+
+<DD>Only pair styles with 1/r and 1/r^6 dependence are currently supported.
+
+<DT><I>Using fix nvt/sllod with inconsistent fix deform remap option</I>
+
+<DD>Fix nvt/sllod requires that deforming atoms have a velocity profile
+provided by "remap v" as a fix deform option.
+
+<DT><I>Using fix nvt/sllod with no fix deform defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using fix srd with inconsistent fix deform remap option</I>
+
+<DD>When shearing the box in an SRD simulation, the remap v option for fix
+deform needs to be used.
+
+<DT><I>Using pair lubricate with inconsistent fix deform remap option</I>
+
+<DD>Must use remap v option with fix deform with this pair style.
+
+<DT><I>Using pair lubricate/poly with inconsistent fix deform remap option</I>
+
+<DD>If fix deform is used, the remap v option is required.
+
+<DT><I>Using suffix cuda without USER-CUDA package enabled</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using suffix gpu without GPU package installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using suffix intel without USER-INTEL package installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using suffix kk without KOKKOS package enabled</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using suffix omp without USER-OMP package installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable ID in variable formula does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable atom ID is too large</I>
+
+<DD>Specified ID is larger than the maximum allowed atom ID.
+
+<DT><I>Variable evaluation before simulation box is defined</I>
+
+<DD>Cannot evaluate a compute or fix or atom-based value in a variable
+before the simulation has been setup.
+
+<DT><I>Variable evaluation in fix wall gave bad value</I>
+
+<DD>The returned value for epsilon or sigma < 0.0.
+
+<DT><I>Variable evaluation in region gave bad value</I>
+
+<DD>Variable returned a radius < 0.0.
+
+<DT><I>Variable for compute ti is invalid style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable for create_atoms is invalid style</I>
+
+<DD>The variables must be equal-style variables.
+
+<DT><I>Variable for dump every is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for dump image center is invalid style</I>
+
+<DD>Must be an equal-style variable.
+
+<DT><I>Variable for dump image persp is invalid style</I>
+
+<DD>Must be an equal-style variable.
+
+<DT><I>Variable for dump image phi is invalid style</I>
+
+<DD>Must be an equal-style variable.
+
+<DT><I>Variable for dump image theta is invalid style</I>
+
+<DD>Must be an equal-style variable.
+
+<DT><I>Variable for dump image zoom is invalid style</I>
+
+<DD>Must be an equal-style variable.
+
+<DT><I>Variable for fix adapt is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix addforce is invalid style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable for fix aveforce is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix deform is invalid style</I>
+
+<DD>The variable must be an equal-style variable.
+
+<DT><I>Variable for fix efield is invalid style</I>
+
+<DD>The variable must be an equal- or atom-style variable.
+
+<DT><I>Variable for fix gravity is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix heat is invalid style</I>
+
+<DD>Only equal-style or atom-style variables can be used.
+
+<DT><I>Variable for fix indent is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix indent is not equal style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix langevin is invalid style</I>
+
+<DD>It must be an equal-style variable.
+
+<DT><I>Variable for fix move is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix setforce is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix temp/berendsen is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix temp/csvr is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix temp/rescale is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix wall is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix wall/reflect is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for fix wall/srd is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for group dynamic is invalid style</I>
+
+<DD>The variable must be an atom-style variable.
+
+<DT><I>Variable for group is invalid style</I>
+
+<DD>Only atom-style variables can be used.
+
+<DT><I>Variable for region cylinder is invalid style</I>
+
+<DD>Only equal-style varaibles are allowed.
+
+<DT><I>Variable for region is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for region is not equal style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable for region sphere is invalid style</I>
+
+<DD>Only equal-style varaibles are allowed.
+
+<DT><I>Variable for restart is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for set command is invalid style</I>
+
+<DD>Only atom-style variables can be used.
+
+<DT><I>Variable for thermo every is invalid style</I>
+
+<DD>Only equal-style variables can be used.
+
+<DT><I>Variable for velocity set is invalid style</I>
+
+<DD>Only atom-style variables can be used.
+
+<DT><I>Variable for voronoi radius is not atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable formula compute array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable formula compute vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable formula fix array is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable formula fix vector is accessed out-of-range</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable has circular dependency</I>
+
+<DD>A circular dependency is when variable "a" in used by variable "b" and
+variable "b" is also used by varaible "a". Circular dependencies with
+longer chains of dependence are also not allowed.
+
+<DT><I>Variable name between brackets must be alphanumeric or underscore characters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for compute chunk/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for compute reduce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for compute ti does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for create_atoms does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump every does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump image center does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump image persp does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump image phi does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump image theta does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for dump image zoom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix adapt does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix addforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/atom does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/chunk does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/correlate does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/histo does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/spatial does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix ave/time does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix aveforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix deform does not exist</I>
+
+<DD>Self-explantory.
+
+<DT><I>Variable name for fix efield does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix gravity does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix heat does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix indent does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix langevin does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix move does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix setforce does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix store/state does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix temp/berendsen does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix temp/csvr does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix temp/rescale does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix vector does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix wall does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix wall/reflect does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for fix wall/srd does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for group does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for group dynamic does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for region cylinder does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for region does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for region sphere does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for restart does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for set command does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for thermo every does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for velocity set does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name for voronoi radius does not exist</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable name must be alphanumeric or underscore characters</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Variable uses atom property that isn't allocated</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Velocity command before simulation box is defined</I>
+
+<DD>The velocity command cannot be used before a read_data, read_restart,
+or create_box command.
+
+<DT><I>Velocity command with no atoms existing</I>
+
+<DD>A velocity command has been used, but no atoms yet exist.
+
+<DT><I>Velocity ramp in z for a 2d problem</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Velocity rigid used with non-rigid fix-ID</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Velocity temperature ID does calculate a velocity bias</I>
+
+<DD>The specified compute must compute a bias for temperature.
+
+<DT><I>Velocity temperature ID does not compute temperature</I>
+
+<DD>The compute ID given to the velocity command must compute
+temperature.
+
+<DT><I>Verlet/split can only currently be used with comm_style brick</I>
+
+<DD>This is a current restriction in LAMMPS.
+
+<DT><I>Verlet/split does not yet support TIP4P</I>
+
+<DD>This is a current limitation.
+
+<DT><I>Verlet/split requires 2 partitions</I>
+
+<DD>See the -partition command-line switch.
+
+<DT><I>Verlet/split requires Rspace partition layout be multiple of Kspace partition layout in each dim</I>
+
+<DD>This is controlled by the processors command.
+
+<DT><I>Verlet/split requires Rspace partition size be multiple of Kspace partition size</I>
+
+<DD>This is so there is an equal number of Rspace processors for every
+Kspace processor.
+
+<DT><I>Virial was not tallied on needed timestep</I>
+
+<DD>You are using a thermo keyword that requires potentials to
+have tallied the virial, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+<DT><I>Voro++ error: narea and neigh have a different size</I>
+
+<DD>This error is returned by the Voro++ library.
+
+<DT><I>Wall defined twice in fix wall command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Wall defined twice in fix wall/reflect command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Wall defined twice in fix wall/srd command</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Water H epsilon must be 0.0 for pair style lj/cut/tip4p/cut</I>
+
+<DD>This is because LAMMPS does not compute the Lennard-Jones interactions
+with these particles for efficiency reasons.
+
+<DT><I>Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long</I>
+
+<DD>This is because LAMMPS does not compute the Lennard-Jones interactions
+with these particles for efficiency reasons.
+
+<DT><I>Water H epsilon must be 0.0 for pair style lj/long/tip4p/long</I>
+
+<DD>This is because LAMMPS does not compute the Lennard-Jones interactions
+with these particles for efficiency reasons.
+
+<DT><I>World variable count doesn't match # of partitions</I>
+
+<DD>A world-style variable must specify a number of values equal to the
+number of processor partitions.
+
+<DT><I>Write_data command before simulation box is defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Write_restart command before simulation box is defined</I>
+
+<DD>The write_restart command cannot be used before a read_data,
+read_restart, or create_box command.
+
+<DT><I>Writing to MPI-IO filename when MPIIO package is not installed</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Zero length rotation vector with displace_atoms</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Zero length rotation vector with fix move</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Zero-length lattice orient vector</I>
+
+<DD>Self-explanatory.
+
+
+</DL>
+<H4><A NAME = "warn"></A>Warnings:
+</H4>
+<DL>
+
+<DT><I>Adjusting Coulombic cutoff for MSM, new cutoff = %g</I>
+
+<DD>The adjust/cutoff command is turned on and the Coulombic cutoff has been
+adjusted to match the user-specified accuracy.
+
+<DT><I>Angle atoms missing at step %ld</I>
+
+<DD>One or more of 3 atoms needed to compute a particular angle are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the angle has blown apart and an atom is
+too far away.
+
+<DT><I>Angle style in data file differs from currently defined angle style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Atom style in data file differs from currently defined atom style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Bond atom missing in box size check</I>
+
+<DD>The 2nd atoms needed to compute a particular bond is missing on this
+processor. Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away.
+
+<DT><I>Bond atom missing in image check</I>
+
+<DD>The 2nd atom in a particular bond is missing on this processor.
+Typically this is because the pairwise cutoff is set too short or the
+bond has blown apart and an atom is too far away.
+
+<DT><I>Bond atoms missing at step %ld</I>
+
+<DD>The 2nd atom needed to compute a particular bond is missing on this
+processor. Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away.
+
+<DT><I>Bond style in data file differs from currently defined bond style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Bond/angle/dihedral extent > half of periodic box length</I>
+
+<DD>This is a restriction because LAMMPS can be confused about which image
+of an atom in the bonded interaction is the correct one to use.
+"Extent" in this context means the maximum end-to-end length of the
+bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
+length, multiplying by the number of bonds in the interaction (e.g. 3
+for a dihedral) and adding a small amount of stretch.
+
+<DT><I>Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero</I>
+
+<DD>Self-explantory.
+
+<DT><I>Cannot count rigid body degrees-of-freedom before bodies are fully initialized</I>
+
+<DD>This means the temperature associated with the rigid bodies may be
+incorrect on this timestep.
+
+<DT><I>Cannot count rigid body degrees-of-freedom before bodies are initialized</I>
+
+<DD>This means the temperature associated with the rigid bodies may be
+incorrect on this timestep.
+
+<DT><I>Cannot include log terms without 1/r terms; setting flagHI to 1</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Cannot include log terms without 1/r terms; setting flagHI to 1.</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Charges are set, but coulombic solver is not used</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Charges did not converge at step %ld: %lg</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Communication cutoff is too small for SNAP micro load balancing, increased to %lf</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Compute cna/atom cutoff may be too large to find ghost atom neighbors</I>
+
+<DD>The neighbor cutoff used may not encompass enough ghost atoms
+to perform this operation correctly.
+
+<DT><I>Computing temperature of portions of rigid bodies</I>
+
+<DD>The group defined by the temperature compute does not encompass all
+the atoms in one or more rigid bodies, so the change in
+degrees-of-freedom for the atoms in those partial rigid bodies will
+not be accounted for.
+
+<DT><I>Create_bonds max distance > minimum neighbor cutoff</I>
+
+<DD>This means atom pairs for some atom types may not be in the neighbor
+list and thus no bond can be created between them.
+
+<DT><I>Delete_atoms cutoff > minimum neighbor cutoff</I>
+
+<DD>This means atom pairs for some atom types may not be in the neighbor
+list and thus an atom in that pair cannot be deleted.
+
+<DT><I>Dihedral atoms missing at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular dihedral are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the dihedral has blown apart and an atom is
+too far away.
+
+<DT><I>Dihedral problem</I>
+
+<DD>Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry.
+
+<DT><I>Dihedral problem: %d %ld %d %d %d %d</I>
+
+<DD>Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry.
+
+<DT><I>Dihedral style in data file differs from currently defined dihedral style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Dump dcd/xtc timestamp may be wrong with fix dt/reset</I>
+
+<DD>If the fix changes the timestep, the dump dcd file will not
+reflect the change.
+
+<DT><I>Estimated error in splitting of dispersion coeffs is %g</I>
+
+<DD>Error is greater than 0.0001 percent.
+
+<DT><I>Ewald/disp Newton solver failed, using old method to estimate g_ewald</I>
+
+<DD>Self-explanatory. Choosing a different cutoff value may help.
+
+<DT><I>FENE bond too long</I>
+
+<DD>A FENE bond has stretched dangerously far. It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+<DT><I>FENE bond too long: %ld %d %d %g</I>
+
+<DD>A FENE bond has stretched dangerously far. It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+<DT><I>FENE bond too long: %ld %g</I>
+
+<DD>A FENE bond has stretched dangerously far. It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up.
+
+<DT><I>Fix SRD walls overlap but fix srd overlap not set</I>
+
+<DD>You likely want to set this in your input script.
+
+<DT><I>Fix bond/swap will ignore defined angles</I>
+
+<DD>See the doc page for fix bond/swap for more info on this
+restriction.
+
+<DT><I>Fix evaporate may delete atom with non-zero molecule ID</I>
+
+<DD>This is probably an error, since you should not delete only one atom
+of a molecule.
+
+<DT><I>Fix gcmc using full_energy option</I>
+
+<DD>Fix gcmc has automatically turned on the full_energy option since it
+is required for systems like the one specified by the user. User input
+included one or more of the following: kspace, triclinic, a hybrid
+pair style, an eam pair style, or no "single" function for the pair
+style.
+
+<DT><I>Fix move does not update angular momentum</I>
+
+<DD>Atoms store this quantity, but fix move does not (yet) update it.
+
+<DT><I>Fix move does not update quaternions</I>
+
+<DD>Atoms store this quantity, but fix move does not (yet) update it.
+
+<DT><I>Fix qeq CG convergence failed (%g) after %d iterations at %ld step</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix qeq has non-zero lower Taper radius cutoff</I>
+
+<DD>Absolute value must be <= 0.01.
+
+<DT><I>Fix qeq has very low Taper radius cutoff</I>
+
+<DD>Value should typically be >= 5.0.
+
+<DT><I>Fix qeq/dynamic tolerance may be too small for damped dynamics</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Fix rattle should come after all other integration fixes</I>
+
+<DD>This fix is designed to work after all other integration fixes change
+atom positions. Thus it should be the last integration fix specified.
+If not, it will not satisfy the desired constraints as well as it
+otherwise would.
+
+<DT><I>Fix recenter should come after all other integration fixes</I>
+
+<DD>Other fixes may change the position of the center-of-mass, so
+fix recenter should come last.
+
+<DT><I>Fix srd SRD moves may trigger frequent reneighboring</I>
+
+<DD>This is because the SRD particles may move long distances.
+
+<DT><I>Fix srd grid size > 1/4 of big particle diameter</I>
+
+<DD>This may cause accuracy problems.
+
+<DT><I>Fix srd particle moved outside valid domain</I>
+
+<DD>This may indicate a problem with your simulation parameters.
+
+<DT><I>Fix srd particles may move > big particle diameter</I>
+
+<DD>This may cause accuracy problems.
+
+<DT><I>Fix srd viscosity < 0.0 due to low SRD density</I>
+
+<DD>This may cause accuracy problems.
+
+<DT><I>Fix thermal/conductivity comes before fix ave/spatial</I>
+
+<DD>The order of these 2 fixes in your input script is such that fix
+thermal/conductivity comes first. If you are using fix ave/spatial to
+measure the temperature profile induced by fix viscosity, then this
+may cause a glitch in the profile since you are averaging immediately
+after swaps have occurred. Flipping the order of the 2 fixes
+typically helps.
+
+<DT><I>Fix viscosity comes before fix ave/spatial</I>
+
+<DD>The order of these 2 fixes in your input script is such that
+fix viscosity comes first. If you are using fix ave/spatial
+to measure the velocity profile induced by fix viscosity, then
+this may cause a glitch in the profile since you are averaging
+immediately after swaps have occurred. Flipping the order
+of the 2 fixes typically helps.
+
+<DT><I>Fixes cannot send data in Kokkos communication, switching to classic communication</I>
+
+<DD>This is current restriction with Kokkos.
+
+<DT><I>For better accuracy use 'pair_modify table 0'</I>
+
+<DD>The user-specified force accuracy cannot be achieved unless the table
+feature is disabled by using 'pair_modify table 0'.
+
+<DT><I>Geometric mixing assumed for 1/r^6 coefficients</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Group for fix_modify temp != fix group</I>
+
+<DD>The fix_modify command is specifying a temperature computation that
+computes a temperature on a different group of atoms than the fix
+itself operates on. This is probably not what you want to do.
+
+<DT><I>H matrix size has been exceeded: m_fill=%d H.m=%d\n</I>
+
+<DD>This is the size of the matrix.
+
+<DT><I>Improper atoms missing at step %ld</I>
+
+<DD>One or more of 4 atoms needed to compute a particular improper are
+missing on this processor. Typically this is because the pairwise
+cutoff is set too short or the improper has blown apart and an atom is
+too far away.
+
+<DT><I>Improper problem: %d %ld %d %d %d %d</I>
+
+<DD>Conformation of the 4 listed improper atoms is extreme; you may want
+to check your simulation geometry.
+
+<DT><I>Improper style in data file differs from currently defined improper style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Inconsistent image flags</I>
+
+<DD>The image flags for a pair on bonded atoms appear to be inconsistent.
+Inconsistent means that when the coordinates of the two atoms are
+unwrapped using the image flags, the two atoms are far apart.
+Specifically they are further apart than half a periodic box length.
+Or they are more than a box length apart in a non-periodic dimension.
+This is usually due to the initial data file not having correct image
+flags for the 2 atoms in a bond that straddles a periodic boundary.
+They should be different by 1 in that case. This is a warning because
+inconsistent image flags will not cause problems for dynamics or most
+LAMMPS simulations. However they can cause problems when such atoms
+are used with the fix rigid or replicate commands.
+
+<DT><I>KIM Model does not provide `energy'; Potential energy will be zero</I>
+
+<DD>Self-explanatory.
+
+<DT><I>KIM Model does not provide `forces'; Forces will be zero</I>
+
+<DD>Self-explanatory.
+
+<DT><I>KIM Model does not provide `particleEnergy'; energy per atom will be zero</I>
+
+<DD>Self-explanatory.
+
+<DT><I>KIM Model does not provide `particleVirial'; virial per atom will be zero</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Kspace_modify slab param < 2.0 may cause unphysical behavior</I>
+
+<DD>The kspace_modify slab parameter should be larger to insure periodic
+grids padded with empty space do not overlap.
+
+<DT><I>Less insertions than requested</I>
+
+<DD>The fix pour command was unsuccessful at finding open space
+for as many particles as it tried to insert.
+
+<DT><I>Library error in lammps_gather_atoms</I>
+
+<DD>This library function cannot be used if atom IDs are not defined
+or are not consecutively numbered.
+
+<DT><I>Library error in lammps_scatter_atoms</I>
+
+<DD>This library function cannot be used if atom IDs are not defined or
+are not consecutively numbered, or if no atom map is defined. See the
+atom_modify command for details about atom maps.
+
+<DT><I>Lost atoms via change_box: original %ld current %ld</I>
+
+<DD>The command options you have used caused atoms to be lost.
+
+<DT><I>Lost atoms via displace_atoms: original %ld current %ld</I>
+
+<DD>The command options you have used caused atoms to be lost.
+
+<DT><I>Lost atoms: original %ld current %ld</I>
+
+<DD>Lost atoms are checked for each time thermo output is done. See the
+thermo_modify lost command for options. Lost atoms usually indicate
+bad dynamics, e.g. atoms have been blown far out of the simulation
+box, or moved futher than one processor's sub-domain away before
+reneighboring.
+
+<DT><I>MSM mesh too small, increasing to 2 points in each direction</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Mismatch between velocity and compute groups</I>
+
+<DD>The temperature computation used by the velocity command will not be
+on the same group of atoms that velocities are being set for.
+
+<DT><I>Mixing forced for lj coefficients</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Molecule attributes do not match system attributes</I>
+
+<DD>An attribute is specified (e.g. diameter, charge) that is
+not defined for the specified atom style.
+
+<DT><I>Molecule has bond topology but no special bond settings</I>
+
+<DD>This means the bonded atoms will not be excluded in pair-wise
+interactions.
+
+<DT><I>Molecule template for create_atoms has multiple molecules</I>
+
+<DD>The create_atoms command will only create molecules of a single type,
+i.e. the first molecule in the template.
+
+<DT><I>Molecule template for fix gcmc has multiple molecules</I>
+
+<DD>The fix gcmc command will only create molecules of a single type,
+i.e. the first molecule in the template.
+
+<DT><I>Molecule template for fix shake has multiple molecules</I>
+
+<DD>The fix shake command will only recoginze molecules of a single
+type, i.e. the first molecule in the template.
+
+<DT><I>More than one compute centro/atom</I>
+
+<DD>It is not efficient to use compute centro/atom more than once.
+
+<DT><I>More than one compute cluster/atom</I>
+
+<DD>It is not efficient to use compute cluster/atom more than once.
+
+<DT><I>More than one compute cna/atom defined</I>
+
+<DD>It is not efficient to use compute cna/atom more than once.
+
+<DT><I>More than one compute contact/atom</I>
+
+<DD>It is not efficient to use compute contact/atom more than once.
+
+<DT><I>More than one compute coord/atom</I>
+
+<DD>It is not efficient to use compute coord/atom more than once.
+
+<DT><I>More than one compute damage/atom</I>
+
+<DD>It is not efficient to use compute ke/atom more than once.
+
+<DT><I>More than one compute dilatation/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>More than one compute erotate/sphere/atom</I>
+
+<DD>It is not efficient to use compute erorate/sphere/atom more than once.
+
+<DT><I>More than one compute ke/atom</I>
+
+<DD>It is not efficient to use compute ke/atom more than once.
+
+<DT><I>More than one compute plasticity/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>More than one compute sna/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>More than one compute snad/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>More than one compute snav/atom</I>
+
+<DD>Self-explanatory.
+
+<DT><I>More than one fix poems</I>
+
+<DD>It is not efficient to use fix poems more than once.
+
+<DT><I>More than one fix rigid</I>
+
+<DD>It is not efficient to use fix rigid more than once.
+
+<DT><I>Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies</I>
+
+<DD>This is because excluding specific pair interactions also excludes
+them from long-range interactions which may not be the desired effect.
+The special_bonds command handles this consistently by insuring
+excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
+consistently by both the short-range pair style and the long-range
+solver. This is not done for exclusions of charged atom pairs via the
+neigh_modify exclude command.
+
+<DT><I>New thermo_style command, previous thermo_modify settings will be lost</I>
+
+<DD>If a thermo_style command is used after a thermo_modify command, the
+settings changed by the thermo_modify command will be reset to their
+default values. This is because the thermo_modify commmand acts on
+the currently defined thermo style, and a thermo_style command creates
+a new style.
+
+<DT><I>No Kspace calculation with verlet/split</I>
+
+<DD>The 2nd partition performs a kspace calculation so the kspace_style
+command must be used.
+
+<DT><I>No automatic unit conversion to XTC file format conventions possible for units lj</I>
+
+<DD>This means no scaling will be performed.
+
+<DT><I>No fixes defined, atoms won't move</I>
+
+<DD>If you are not using a fix like nve, nvt, npt then atom velocities and
+coordinates will not be updated during timestepping.
+
+<DT><I>No joints between rigid bodies, use fix rigid instead</I>
+
+<DD>The bodies defined by fix poems are not connected by joints. POEMS
+will integrate the body motion, but it would be more efficient to use
+fix rigid.
+
+<DT><I>Not using real units with pair reax</I>
+
+<DD>This is most likely an error, unless you have created your own ReaxFF
+parameter file in a different set of units.
+
+<DT><I>Number of MSM mesh points changed to be a multiple of 2</I>
+
+<DD>MSM requires that the number of grid points in each direction be a multiple
+of two and the number of grid points in one or more directions have been
+adjusted to meet this requirement.
+
+<DT><I>OMP_NUM_THREADS environment is not set.</I>
+
+<DD>This environment variable must be set appropriately to use the
+USER-OMP pacakge.
+
+<DT><I>One or more atoms are time integrated more than once</I>
+
+<DD>This is probably an error since you typically do not want to
+advance the positions or velocities of an atom more than once
+per timestep.
+
+<DT><I>One or more chunks do not contain all atoms in molecule</I>
+
+<DD>This may not be what you intended.
+
+<DT><I>One or more dynamic groups may not be updated at correct point in timestep</I>
+
+<DD>If there are other fixes that act immediately after the intitial stage
+of time integration within a timestep (i.e. after atoms move), then
+the command that sets up the dynamic group should appear after those
+fixes. This will insure that dynamic group assignements are made
+after all atoms have moved.
+
+<DT><I>One or more respa levels compute no forces</I>
+
+<DD>This is computationally inefficient.
+
+<DT><I>Pair COMB charge %.10f with force %.10f hit max barrier</I>
+
+<DD>Something is possibly wrong with your model.
+
+<DT><I>Pair COMB charge %.10f with force %.10f hit min barrier</I>
+
+<DD>Something is possibly wrong with your model.
+
+<DT><I>Pair brownian needs newton pair on for momentum conservation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair dpd needs newton pair on for momentum conservation</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Pair dsmc: num_of_collisions > number_of_A</I>
+
+<DD>Collision model in DSMC is breaking down.
+
+<DT><I>Pair dsmc: num_of_collisions > number_of_B</I>
+
+<DD>Collision model in DSMC is breaking down.
+
+<DT><I>Pair style in data file differs from currently defined pair style</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Particle deposition was unsuccessful</I>
+
+<DD>The fix deposit command was not able to insert as many atoms as
+needed. The requested volume fraction may be too high, or other atoms
+may be in the insertion region.
+
+<DT><I>Proc sub-domain size < neighbor skin, could lead to lost atoms</I>
+
+<DD>The decomposition of the physical domain (likely due to load
+balancing) has led to a processor's sub-domain being smaller than the
+neighbor skin in one or more dimensions. Since reneighboring is
+triggered by atoms moving the skin distance, this may lead to lost
+atoms, if an atom moves all the way across a neighboring processor's
+sub-domain before reneighboring is triggered.
+
+<DT><I>Reducing PPPM order b/c stencil extends beyond nearest neighbor processor</I>
+
+<DD>This may lead to a larger grid than desired. See the kspace_modify overlap
+command to prevent changing of the PPPM order.
+
+<DT><I>Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor</I>
+
+<DD>This may lead to a larger grid than desired. See the kspace_modify overlap
+command to prevent changing of the PPPM order.
+
+<DT><I>Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor</I>
+
+<DD>This may lead to a larger grid than desired. See the kspace_modify overlap
+command to prevent changing of the PPPM order.
+
+<DT><I>Replacing a fix, but new group != old group</I>
+
+<DD>The ID and style of a fix match for a fix you are changing with a fix
+command, but the new group you are specifying does not match the old
+group.
+
+<DT><I>Replicating in a non-periodic dimension</I>
+
+<DD>The parameters for a replicate command will cause a non-periodic
+dimension to be replicated; this may cause unwanted behavior.
+
+<DT><I>Resetting reneighboring criteria during PRD</I>
+
+<DD>A PRD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes. Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation.
+
+<DT><I>Resetting reneighboring criteria during TAD</I>
+
+<DD>A TAD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes. Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation.
+
+<DT><I>Resetting reneighboring criteria during minimization</I>
+
+<DD>Minimization requires that neigh_modify settings be delay = 0, every =
+1, check = yes. Since these settings were not in place, LAMMPS
+changed them and will restore them to their original values after the
+minimization.
+
+<DT><I>Restart file used different # of processors</I>
+
+<DD>The restart file was written out by a LAMMPS simulation running on a
+different number of processors. Due to round-off, the trajectories of
+your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors.
+
+<DT><I>Restart file used different 3d processor grid</I>
+
+<DD>The restart file was written out by a LAMMPS simulation running on a
+different 3d grid of processors. Due to round-off, the trajectories
+of your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors.
+
+<DT><I>Restart file used different boundary settings, using restart file values</I>
+
+<DD>Your input script cannot change these restart file settings.
+
+<DT><I>Restart file used different newton bond setting, using restart file value</I>
+
+<DD>The restart file value will override the setting in the input script.
+
+<DT><I>Restart file used different newton pair setting, using input script value</I>
+
+<DD>The input script value will override the setting in the restart file.
+
+<DT><I>Restrain problem: %d %ld %d %d %d %d</I>
+
+<DD>Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry.
+
+<DT><I>Running PRD with only one replica</I>
+
+<DD>This is allowed, but you will get no parallel speed-up.
+
+<DT><I>SRD bin shifting turned on due to small lamda</I>
+
+<DD>This is done to try to preserve accuracy.
+
+<DT><I>SRD bin size for fix srd differs from user request</I>
+
+<DD>Fix SRD had to adjust the bin size to fit the simulation box. See the
+cubic keyword if you want this message to be an error vs warning.
+
+<DT><I>SRD bins for fix srd are not cubic enough</I>
+
+<DD>The bin shape is not within tolerance of cubic. See the cubic
+keyword if you want this message to be an error vs warning.
+
+<DT><I>SRD particle %d started inside big particle %d on step %ld bounce %d</I>
+
+<DD>See the inside keyword if you want this message to be an error vs
+warning.
+
+<DT><I>SRD particle %d started inside wall %d on step %ld bounce %d</I>
+
+<DD>See the inside keyword if you want this message to be an error vs
+warning.
+
+<DT><I>Shake determinant < 0.0</I>
+
+<DD>The determinant of the quadratic equation being solved for a single
+cluster specified by the fix shake command is numerically suspect. LAMMPS
+will set it to 0.0 and continue.
+
+<DT><I>Should not allow rigid bodies to bounce off relecting walls</I>
+
+<DD>LAMMPS allows this, but their dynamics are not computed correctly.
+
+<DT><I>Should not use fix nve/limit with fix shake</I>
+
+<DD>This will lead to invalid constraint forces in the SHAKE computation.
+
+<DT><I>Simulations might be very slow because of large number of structure factors</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Slab correction not needed for MSM</I>
+
+<DD>Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
+
+<DT><I>System is not charge neutral, net charge = %g</I>
+
+<DD>The total charge on all atoms on the system is not 0.0, which
+is not valid for the long-range Coulombic solvers.
+
+<DT><I>Table inner cutoff >= outer cutoff</I>
+
+<DD>You specified an inner cutoff for a Coulombic table that is longer
+than the global cutoff. Probably not what you wanted.
+
+<DT><I>Temperature for MSST is not for group all</I>
+
+<DD>User-assigned temperature to MSST fix does not compute temperature for
+all atoms. Since MSST computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by MSST could be inaccurate.
+
+<DT><I>Temperature for NPT is not for group all</I>
+
+<DD>User-assigned temperature to NPT fix does not compute temperature for
+all atoms. Since NPT computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by NPT could be inaccurate.
+
+<DT><I>Temperature for fix modify is not for group all</I>
+
+<DD>The temperature compute is being used with a pressure calculation
+which does operate on group all, so this may be inconsistent.
+
+<DT><I>Temperature for thermo pressure is not for group all</I>
+
+<DD>User-assigned temperature to thermo via the thermo_modify command does
+not compute temperature for all atoms. Since thermo computes a global
+pressure, the kinetic energy contribution from the temperature is
+assumed to also be for all atoms. Thus the pressure printed by thermo
+could be inaccurate.
+
+<DT><I>The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015</I>
+
+<DD>Self-explanatory.
+
+<DT><I>The minimizer does not re-orient dipoles when using fix efield</I>
+
+<DD>This means that only the atom coordinates will be minimized,
+not the orientation of the dipoles.
+
+<DT><I>Too many common neighbors in CNA %d times</I>
+
+<DD>More than the maximum # of neighbors was found multiple times. This
+was unexpected.
+
+<DT><I>Too many inner timesteps in fix ttm</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Too many neighbors in CNA for %d atoms</I>
+
+<DD>More than the maximum # of neighbors was found multiple times. This
+was unexpected.
+
+<DT><I>Triclinic box skew is large</I>
+
+<DD>The displacement in a skewed direction is normally required to be less
+than half the box length in that dimension. E.g. the xy tilt must be
+between -half and +half of the x box length. You have relaxed the
+constraint using the box tilt command, but the warning means that a
+LAMMPS simulation may be inefficient as a result.
+
+<DT><I>Use special bonds = 0,1,1 with bond style fene</I>
+
+<DD>Most FENE models need this setting for the special_bonds command.
+
+<DT><I>Use special bonds = 0,1,1 with bond style fene/expand</I>
+
+<DD>Most FENE models need this setting for the special_bonds command.
+
+<DT><I>Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions</I>
+
+<DD>This is likely not what you want to do. The exclusion settings will
+eliminate neighbors in the neighbor list, which the manybody potential
+needs to calculated its terms correctly.
+
+<DT><I>Using compute temp/deform with inconsistent fix deform remap option</I>
+
+<DD>Fix nvt/sllod assumes deforming atoms have a velocity profile provided
+by "remap v" or "remap none" as a fix deform option.
+
+<DT><I>Using compute temp/deform with no fix deform defined</I>
+
+<DD>This is probably an error, since it makes little sense to use
+compute temp/deform in this case.
+
+<DT><I>Using fix srd with box deformation but no SRD thermostat</I>
+
+<DD>The deformation will heat the SRD particles so this can
+be dangerous.
+
+<DT><I>Using kspace solver on system with no charge</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using largest cut-off for lj/long/dipole/long long long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using largest cutoff for buck/long/coul/long</I>
+
+<DD>Self-exlanatory.
+
+<DT><I>Using largest cutoff for lj/long/coul/long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using largest cutoff for pair_style lj/long/tip4p/long</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using package gpu without any pair style defined</I>
+
+<DD>Self-explanatory.
+
+<DT><I>Using pair tail corrections with nonperiodic system</I>
+
+<DD>This is probably a bogus thing to do, since tail corrections are
+computed by integrating the density of a periodic system out to
+infinity.
+
+
+</DL>
+</HTML>
diff --git a/doc/doc2/Section_example.html b/doc/doc2/Section_example.html
new file mode 100644
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+++ b/doc/doc2/Section_example.html
@@ -0,0 +1,126 @@
+<HTML>
+<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>7. Example problems
+</H3>
+<P>The LAMMPS distribution includes an examples sub-directory with
+several sample problems. Each problem is in a sub-directory of its
+own. Most are 2d models so that they run quickly, requiring at most a
+couple of minutes to run on a desktop machine. Each problem has an
+input script (in.*) and produces a log file (log.*) and dump file
+(dump.*) when it runs. Some use a data file (data.*) of initial
+coordinates as additional input. A few sample log file outputs on
+different machines and different numbers of processors are included in
+the directories to compare your answers to. E.g. a log file like
+log.crack.foo.P means it ran on P processors of machine "foo".
+</P>
+<P>For examples that use input data files, many of them were produced by
+<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
+<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
+documentation and provided with the LAMMPS distribution.
+</P>
+<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
+text dump file will be produced, which can be animated by various
+<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
+also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
+Tools</A> section of the LAMMPS documentation.
+</P>
+<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
+script, and assuming you have built LAMMPS with a JPG library, JPG
+snapshot images will be produced when the simulation runs. They can
+be quickly post-processed into a movie using commands described on the
+<A HREF = "dump_image.html">dump image</A> doc page.
+</P>
+<P>Animations of many of these examples can be viewed on the Movies
+section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
+</P>
+<P>These are the sample problems in the examples sub-directories:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
+<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
+<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
+<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
+<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
+<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
+<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
+<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
+<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
+<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
+<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
+<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
+<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
+<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
+<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
+<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
+<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
+<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
+<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
+<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
+<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
+<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
+<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
+<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
+<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
+<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
+<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
+<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
+<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
+<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
+<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
+<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
+<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
+<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
+<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
+<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
+<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
+<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
+<TR><TD >tri</TD><TD > triangular particles in rigid bodies
+</TD></TR></TABLE></DIV>
+
+<P>Here is how you might run and visualize one of the sample problems:
+</P>
+<PRE>cd indent
+cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
+lmp_linux < in.indent # run the problem
+</PRE>
+<P>Running the simulation produces the files <I>dump.indent</I> and
+<I>log.lammps</I>. You can visualize the dump file as follows:
+</P>
+<PRE>../../tools/xmovie/xmovie -scale dump.indent
+</PRE>
+<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
+script a series of JPG images will be produced by the run. These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools. See the
+<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
+Imagemagick command would create a GIF file suitable for viewing in a
+browser.
+</P>
+<PRE>% convert -loop 1 *.jpg foo.gif
+</PRE>
+<HR>
+
+<P>There is also a COUPLE directory with examples of how to use LAMMPS as
+a library, either by itself or in tandem with another code or library.
+See the COUPLE/README file to get started.
+</P>
+<P>There is also an ELASTIC directory with an example script for
+computing elastic constants, using a zero temperature Si example. See
+the in.elastic file for more info.
+</P>
+<P>There is also a USER directory which contains subdirectories of
+user-provided examples for user packages. See the README files in
+those directories for more info. See the
+<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
+packages.
+</P>
+</HTML>
diff --git a/doc/doc2/Section_history.html b/doc/doc2/Section_history.html
new file mode 100644
index 000000000..d827db95e
--- /dev/null
+++ b/doc/doc2/Section_history.html
@@ -0,0 +1,129 @@
+<HTML>
+<CENTER><A HREF = "Section_errors.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Manual.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>13. Future and history
+</H3>
+<P>This section lists features we plan to add to LAMMPS, features of
+previous versions of LAMMPS, and features of other parallel molecular
+dynamics codes our group has distributed.
+</P>
+13.1 <A HREF = "#hist_1">Coming attractions</A><BR>
+13.2 <A HREF = "#hist_2">Past versions</A> <BR>
+
+<HR>
+
+<HR>
+
+<H4><A NAME = "hist_1"></A>13.1 Coming attractions
+</H4>
+<P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the
+LAMMPS WWW page gives a list of features we are hoping to add to
+LAMMPS in the future, including contact names of individuals you can
+email if you are interested in contributing to the developement or
+would be a future user of that feature.
+</P>
+<P>You can also send <A HREF = "http://lammps.sandia.gov/authors.html">email to the
+developers</A> if you want to add
+your wish to the list.
+</P>
+<HR>
+
+<H4><A NAME = "hist_2"></A>13.2 Past versions
+</H4>
+<P>LAMMPS development began in the mid 1990s under a cooperative research
+& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
+and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
+to develop a large-scale parallel classical MD code; the coding effort
+was led by Steve Plimpton at Sandia.
+</P>
+<P>After the CRADA ended, a final F77 version, LAMMPS 99, was
+released. As development of LAMMPS continued at Sandia, its memory
+management was converted to F90; a final F90 version was released as
+LAMMPS 2001.
+</P>
+<P>The current LAMMPS is a rewrite in C++ and was first publicly released
+as an open source code in 2004. It includes many new features beyond
+those in LAMMPS 99 or 2001. It also includes features from older
+parallel MD codes written at Sandia, namely ParaDyn, Warp, and
+GranFlow (see below).
+</P>
+<P>In late 2006 we began merging new capabilities into LAMMPS that were
+developed by Aidan Thompson at Sandia for his MD code GRASP, which has
+a parallel framework similar to LAMMPS. Most notably, these have
+included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
+and the associated charge-equilibration routines needed for ReaxFF.
+</P>
+<P>The <A HREF = "http://lammps.sandia.gov/history.html">History link</A> on the
+LAMMPS WWW page gives a timeline of features added to the
+C++ open-source version of LAMMPS over the last several years.
+</P>
+<P>These older codes are available for download from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
+site</A>, except for Warp & GranFlow which were primarily used
+internally. A brief listing of their features is given here.
+</P>
+<P>LAMMPS 2001
+</P>
+<UL><LI> F90 + MPI
+<LI> dynamic memory
+<LI> spatial-decomposition parallelism
+<LI> NVE, NVT, NPT, NPH, rRESPA integrators
+<LI> LJ and Coulombic pairwise force fields
+<LI> all-atom, united-atom, bead-spring polymer force fields
+<LI> CHARMM-compatible force fields
+<LI> class 2 force fields
+<LI> 3d/2d Ewald & PPPM
+<LI> various force and temperature constraints
+<LI> SHAKE
+<LI> Hessian-free truncated-Newton minimizer
+<LI> user-defined diagnostics
+</UL>
+<P>LAMMPS 99
+</P>
+<UL><LI> F77 + MPI
+<LI> static memory allocation
+<LI> spatial-decomposition parallelism
+<LI> most of the LAMMPS 2001 features with a few exceptions
+<LI> no 2d Ewald & PPPM
+<LI> molecular force fields are missing a few CHARMM terms
+<LI> no SHAKE
+</UL>
+<P>Warp
+</P>
+<UL><LI> F90 + MPI
+<LI> spatial-decomposition parallelism
+<LI> embedded atom method (EAM) metal potentials + LJ
+<LI> lattice and grain-boundary atom creation
+<LI> NVE, NVT integrators
+<LI> boundary conditions for applying shear stresses
+<LI> temperature controls for actively sheared systems
+<LI> per-atom energy and centro-symmetry computation and output
+</UL>
+<P>ParaDyn
+</P>
+<UL><LI> F77 + MPI
+<LI> atom- and force-decomposition parallelism
+<LI> embedded atom method (EAM) metal potentials
+<LI> lattice atom creation
+<LI> NVE, NVT, NPT integrators
+<LI> all serial DYNAMO features for controls and constraints
+</UL>
+<P>GranFlow
+</P>
+<UL><LI> F90 + MPI
+<LI> spatial-decomposition parallelism
+<LI> frictional granular potentials
+<LI> NVE integrator
+<LI> boundary conditions for granular flow and packing and walls
+<LI> particle insertion
+</UL>
+</HTML>
diff --git a/doc/doc2/Section_howto.html b/doc/doc2/Section_howto.html
new file mode 100644
index 000000000..86ba13791
--- /dev/null
+++ b/doc/doc2/Section_howto.html
@@ -0,0 +1,2800 @@
+<HTML>
+<CENTER><A HREF = "Section_accelerate.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_example.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>6. How-to discussions
+</H3>
+<P>This section describes how to perform common tasks using LAMMPS.
+</P>
+6.1 <A HREF = "#howto_1">Restarting a simulation</A><BR>
+6.2 <A HREF = "#howto_2">2d simulations</A><BR>
+6.3 <A HREF = "#howto_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
+6.4 <A HREF = "#howto_4">Running multiple simulations from one input script</A><BR>
+6.5 <A HREF = "#howto_5">Multi-replica simulations</A><BR>
+6.6 <A HREF = "#howto_6">Granular models</A><BR>
+6.7 <A HREF = "#howto_7">TIP3P water model</A><BR>
+6.8 <A HREF = "#howto_8">TIP4P water model</A><BR>
+6.9 <A HREF = "#howto_9">SPC water model</A><BR>
+6.10 <A HREF = "#howto_10">Coupling LAMMPS to other codes</A><BR>
+6.11 <A HREF = "#howto_11">Visualizing LAMMPS snapshots</A><BR>
+6.12 <A HREF = "#howto_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
+6.13 <A HREF = "#howto_13">NEMD simulations</A><BR>
+6.14 <A HREF = "#howto_14">Finite-size spherical and aspherical particles</A><BR>
+6.15 <A HREF = "#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
+6.16 <A HREF = "#howto_16">Thermostatting, barostatting and computing temperature</A><BR>
+6.17 <A HREF = "#howto_17">Walls</A><BR>
+6.18 <A HREF = "#howto_18">Elastic constants</A><BR>
+6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
+6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
+6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
+6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
+6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A><BR>
+6.24 <A HREF = "#howto_24">Setting parameters for the kspace_style pppm/disp command</A><BR>
+6.25 <A HREF = "#howto_25">Polarizable models</A><BR>
+6.26 <A HREF = "#howto_26">Adiabatic core/shell model</A><BR>
+6.27 <A HREF = "#howto_27">Drude induced dipoles</A> <BR>
+
+<P>The example input scripts included in the LAMMPS distribution and
+highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
+setup and run various kinds of simulations.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "howto_1"></A><H4>6.1 Restarting a simulation
+</H4>
+<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
+<A HREF = "run.html">run</A> commands can be used in the same input script. Each
+run will continue from where the previous run left off. Or binary
+restart files can be saved to disk using the <A HREF = "restart.html">restart</A>
+command. At a later time, these binary files can be read via a
+<A HREF = "read_restart.html">read_restart</A> command in a new script. Or they can
+be converted to text data files using the <A HREF = "Section_start.html#start_7">-r command-line
+switch</A> and read by a
+<A HREF = "read_data.html">read_data</A> command in a new script.
+</P>
+<P>Here we give examples of 2 scripts that read either a binary restart
+file or a converted data file and then issue a new run command to
+continue where the previous run left off. They illustrate what
+settings must be made in the new script. Details are discussed in the
+documentation for the <A HREF = "read_restart.html">read_restart</A> and
+<A HREF = "read_data.html">read_data</A> commands.
+</P>
+<P>Look at the <I>in.chain</I> input script provided in the <I>bench</I> directory
+of the LAMMPS distribution to see the original script that these 2
+scripts are based on. If that script had the line
+</P>
+<PRE>restart 50 tmp.restart
+</PRE>
+<P>added to it, it would produce 2 binary restart files (tmp.restart.50
+and tmp.restart.100) as it ran.
+</P>
+<P>This script could be used to read the 1st restart file and re-run the
+last 50 timesteps:
+</P>
+<PRE>read_restart tmp.restart.50
+</PRE>
+<PRE>neighbor 0.4 bin
+neigh_modify every 1 delay 1
+</PRE>
+<PRE>fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297
+</PRE>
+<PRE>timestep 0.012
+</PRE>
+<PRE>run 50
+</PRE>
+<P>Note that the following commands do not need to be repeated because
+their settings are included in the restart file: <I>units, atom_style,
+special_bonds, pair_style, bond_style</I>. However these commands do
+need to be used, since their settings are not in the restart file:
+<I>neighbor, fix, timestep</I>.
+</P>
+<P>If you actually use this script to perform a restarted run, you will
+notice that the thermodynamic data match at step 50 (if you also put a
+"thermo 50" command in the original script), but do not match at step
+100. This is because the <A HREF = "fix_langevin.html">fix langevin</A> command
+uses random numbers in a way that does not allow for perfect restarts.
+</P>
+<P>As an alternate approach, the restart file could be converted to a data
+file as follows:
+</P>
+<PRE>lmp_g++ -r tmp.restart.50 tmp.restart.data
+</PRE>
+<P>Then, this script could be used to re-run the last 50 steps:
+</P>
+<PRE>units lj
+atom_style bond
+pair_style lj/cut 1.12
+pair_modify shift yes
+bond_style fene
+special_bonds 0.0 1.0 1.0
+</PRE>
+<PRE>read_data tmp.restart.data
+</PRE>
+<PRE>neighbor 0.4 bin
+neigh_modify every 1 delay 1
+</PRE>
+<PRE>fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297
+</PRE>
+<PRE>timestep 0.012
+</PRE>
+<PRE>reset_timestep 50
+run 50
+</PRE>
+<P>Note that nearly all the settings specified in the original <I>in.chain</I>
+script must be repeated, except the <I>pair_coeff</I> and <I>bond_coeff</I>
+commands since the new data file lists the force field coefficients.
+Also, the <A HREF = "reset_timestep.html">reset_timestep</A> command is used to tell
+LAMMPS the current timestep. This value is stored in restart files,
+but not in data files.
+</P>
+<HR>
+
+<A NAME = "howto_2"></A><H4>6.2 2d simulations
+</H4>
+<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
+</P>
+<P>Make the simulation box periodic in z via the <A HREF = "boundary.html">boundary</A>
+command. This is the default.
+</P>
+<P>If using the <A HREF = "create_box.html">create box</A> command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+</P>
+<PRE><A HREF = "create_box.html">create box</A> 1 -10 10 -10 10 -0.25 0.25
+</PRE>
+<P>If using the <A HREF = "read_data.html">read data</A> command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create_box command settings just described. For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+</P>
+<P>Use the <A HREF = "fix_enforce2d.html">fix enforce2d</A> command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep. The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+</P>
+<P>Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+</P>
+<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
+spheres, as opposed to point particles. In 2d, the particles will
+still be spheres, not disks, meaning their moment of inertia will be
+the same as in 3d.
+</P>
+<HR>
+
+<A NAME = "howto_3"></A><H4>6.3 CHARMM, AMBER, and DREIDING force fields
+</H4>
+<P>A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system. Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly
+used in the CHARMM, AMBER, and DREIDING force fields. Setting
+coefficients is done in the input data file via the
+<A HREF = "read_data.html">read_data</A> command or in the input script with
+commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
+<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">Section_tools</A>
+for additional tools that can use CHARMM or AMBER to assign force
+field coefficients and convert their output into LAMMPS input.
+</P>
+<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
+field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
+field.
+</P>
+
+
+
+
+<P>These style choices compute force field formulas that are consistent
+with common options in CHARMM or AMBER. See each command's
+documentation for the formula it computes.
+</P>
+<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
+<LI><A HREF = "angle_charmm.html">angle_style</A> charmm
+<LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
+<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm
+<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm/implicit
+<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/long
+</UL>
+<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
+<LI><A HREF = "special_bonds.html">special_bonds</A> amber
+</UL>
+<P>DREIDING is a generic force field developed by the <A HREF = "http://www.wag.caltech.edu">Goddard
+group</A> at Caltech and is useful for
+predicting structures and dynamics of organic, biological and
+main-group inorganic molecules. The philosophy in DREIDING is to use
+general force constants and geometry parameters based on simple
+hybridization considerations, rather than individual force constants
+and geometric parameters that depend on the particular combinations of
+atoms involved in the bond, angle, or torsion terms. DREIDING has an
+<A HREF = "pair_hbond_dreiding.html">explicit hydrogen bond term</A> to describe
+interactions involving a hydrogen atom on very electronegative atoms
+(N, O, F).
+</P>
+<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
+</P>
+<P>These style choices compute force field formulas that are consistent
+with the DREIDING force field. See each command's
+documentation for the formula it computes.
+</P>
+<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
+<LI><A HREF = "bond_morse.html">bond_style</A> morse
+</UL>
+<UL><LI><A HREF = "angle_harmonic.html">angle_style</A> harmonic
+<LI><A HREF = "angle_cosine.html">angle_style</A> cosine
+<LI><A HREF = "angle_cosine_periodic.html">angle_style</A> cosine/periodic
+</UL>
+<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
+<LI><A HREF = "improper_umbrella.html">improper_style</A> umbrella
+</UL>
+<UL><LI><A HREF = "pair_buck.html">pair_style</A> buck
+<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/cut
+<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/long
+<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut
+<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/cut
+<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/long
+</UL>
+<UL><LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/lj
+<LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/morse
+</UL>
+<UL><LI><A HREF = "special_bonds.html">special_bonds</A> dreiding
+</UL>
+<HR>
+
+<A NAME = "howto_4"></A><H4>6.4 Running multiple simulations from one input script
+</H4>
+<P>This can be done in several ways. See the documentation for
+individual commands for more details on how these examples work.
+</P>
+<P>If "multiple simulations" means continue a previous simulation for
+more timesteps, then you simply use the <A HREF = "run.html">run</A> command
+multiple times. For example, this script
+</P>
+<PRE>units lj
+atom_style atomic
+read_data data.lj
+run 10000
+run 10000
+run 10000
+run 10000
+run 10000
+</PRE>
+<P>would run 5 successive simulations of the same system for a total of
+50,000 timesteps.
+</P>
+<P>If you wish to run totally different simulations, one after the other,
+the <A HREF = "clear.html">clear</A> command can be used in between them to
+re-initialize LAMMPS. For example, this script
+</P>
+<PRE>units lj
+atom_style atomic
+read_data data.lj
+run 10000
+clear
+units lj
+atom_style atomic
+read_data data.lj.new
+run 10000
+</PRE>
+<P>would run 2 independent simulations, one after the other.
+</P>
+<P>For large numbers of independent simulations, you can use
+<A HREF = "variable.html">variables</A> and the <A HREF = "next.html">next</A> and
+<A HREF = "jump.html">jump</A> commands to loop over the same input script
+multiple times with different settings. For example, this
+script, named in.polymer
+</P>
+<PRE>variable d index run1 run2 run3 run4 run5 run6 run7 run8
+shell cd $d
+read_data data.polymer
+run 10000
+shell cd ..
+clear
+next d
+jump in.polymer
+</PRE>
+<P>would run 8 simulations in different directories, using a data.polymer
+file in each directory. The same concept could be used to run the
+same system at 8 different temperatures, using a temperature variable
+and storing the output in different log and dump files, for example
+</P>
+<PRE>variable a loop 8
+variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
+log log.$a
+read data.polymer
+velocity all create $t 352839
+fix 1 all nvt $t $t 100.0
+dump 1 all atom 1000 dump.$a
+run 100000
+clear
+next t
+next a
+jump in.polymer
+</PRE>
+<P>All of the above examples work whether you are running on 1 or
+multiple processors, but assumed you are running LAMMPS on a single
+partition of processors. LAMMPS can be run on multiple partitions via
+the "-partition" command-line switch as described in <A HREF = "Section_start.html#start_7">this
+section</A> of the manual.
+</P>
+<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
+scripts could be used if the "index" and "loop" variables were
+replaced with <I>universe</I>-style variables, as described in the
+<A HREF = "variable.html">variable</A> command. Also, the "next t" and "next a"
+commands would need to be replaced with a single "next a t" command.
+With these modifications, the 8 simulations of each script would run
+on the 3 partitions one after the other until all were finished.
+Initially, 3 simulations would be started simultaneously, one on each
+partition. When one finished, that partition would then start
+the 4th simulation, and so forth, until all 8 were completed.
+</P>
+<HR>
+
+<A NAME = "howto_5"></A><H4>6.5 Multi-replica simulations
+</H4>
+<P>Several commands in LAMMPS run mutli-replica simulations, meaning
+that multiple instances (replicas) of your simulation are run
+simultaneously, with small amounts of data exchanged between replicas
+periodically.
+</P>
+<P>These are the relevant commands:
+</P>
+<UL><LI><A HREF = "neb.html">neb</A> for nudged elastic band calculations
+<LI><A HREF = "prd.html">prd</A> for parallel replica dynamics
+<LI><A HREF = "tad.html">tad</A> for temperature accelerated dynamics
+<LI><A HREF = "temper.html">temper</A> for parallel tempering
+<LI><A HREF = "fix_pimd.html">fix pimd</A> for path-integral molecular dynamics (PIMD)
+</UL>
+<P>NEB is a method for finding transition states and barrier energies.
+PRD and TAD are methods for performing accelerated dynamics to find
+and perform infrequent events. Parallel tempering or replica exchange
+runs different replicas at a series of temperature to facilitate
+rare-event sampling.
+</P>
+<P>These commands can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P>PIMD runs different replicas whose individual particles are coupled
+together by springs to model a system or ring-polymers.
+</P>
+<P>This commands can only be used if LAMMPS was built with the USER-MISC
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P>In all these cases, you must run with one or more processors per
+replica. The processors assigned to each replica are determined at
+run-time by using the <A HREF = "Section_start.html#start_7">-partition command-line
+switch</A> to launch LAMMPS on multiple
+partitions, which in this context are the same as replicas. E.g.
+these commands:
+</P>
+<PRE>mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
+</PRE>
+<P>would each run 8 replicas, on either 16 or 8 processors. Note the use
+of the <A HREF = "Section_start.html#start_7">-in command-line switch</A> to specify
+the input script which is required when running in multi-replica mode.
+</P>
+<P>Also note that with MPI installed on a machine (e.g. your desktop),
+you can run on more (virtual) processors than you have physical
+processors. Thus the above commands could be run on a
+single-processor (or few-processor) desktop so that you can run
+a multi-replica simulation on more replicas than you have
+physical processors.
+</P>
+<HR>
+
+<A NAME = "howto_6"></A><H4>6.6 Granular models
+</H4>
+<P>Granular system are composed of spherical particles with a diameter,
+as opposed to point particles. This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+</P>
+<P>To run a simulation of a granular model, you will want to use
+the following commands:
+</P>
+<UL><LI><A HREF = "atom_style.html">atom_style sphere</A>
+<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
+<LI><A HREF = "fix_gravity.html">fix gravity</A>
+</UL>
+<P>This compute
+</P>
+<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
+</UL>
+<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#howto_15">output with
+thermodynamic info</A>.
+</P>
+<P>Use one of these 3 pair potentials, which compute forces and torques
+between interacting pairs of particles:
+</P>
+<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history
+<LI><A HREF = "pair_style.html">pair_style</A> gran/no_history
+<LI><A HREF = "pair_style.html">pair_style</A> gran/hertzian
+</UL>
+<P>These commands implement fix options specific to granular systems:
+</P>
+<UL><LI><A HREF = "fix_freeze.html">fix freeze</A>
+<LI><A HREF = "fix_pour.html">fix pour</A>
+<LI><A HREF = "fix_viscous.html">fix viscous</A>
+<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A>
+</UL>
+<P>The fix style <I>freeze</I> zeroes both the force and torque of frozen
+atoms, and should be used for granular system instead of the fix style
+<I>setforce</I>.
+</P>
+<P>For computational efficiency, you can eliminate needless pairwise
+computations between frozen atoms by using this command:
+</P>
+<UL><LI><A HREF = "neigh_modify.html">neigh_modify</A> exclude
+</UL>
+<HR>
+
+<A NAME = "howto_7"></A><H4>6.7 TIP3P water model
+</H4>
+<P>The TIP3P water model as implemented in CHARMM
+<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
+used.
+</P>
+<P>These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
+cutoff. The K values can be used if a flexible TIP3P model (without
+fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
+set to 0.0, it corresponds to the original 1983 TIP3P model
+<A HREF = "#Jorgensen">(Jorgensen)</A>.
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -0.834<BR>
+H charge = 0.417<BR>
+LJ epsilon of OO = 0.1521<BR>
+LJ sigma of OO = 3.1507<BR>
+LJ epsilon of HH = 0.0460<BR>
+LJ sigma of HH = 0.4000<BR>
+LJ epsilon of OH = 0.0836<BR>
+LJ sigma of OH = 1.7753<BR>
+K of OH bond = 450<BR>
+r0 of OH bond = 0.9572<BR>
+K of HOH angle = 55<BR>
+theta of HOH angle = 104.52 <BR>
+</P>
+<P>These are the parameters to use for TIP3P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS), see <A HREF = "#Price">(Price)</A> for
+details:
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -0.830<BR>
+H charge = 0.415<BR>
+LJ epsilon of OO = 0.102<BR>
+LJ sigma of OO = 3.188<BR>
+LJ epsilon, sigma of OH, HH = 0.0<BR>
+K of OH bond = 450<BR>
+r0 of OH bond = 0.9572<BR>
+K of HOH angle = 55<BR>
+theta of HOH angle = 104.52 <BR>
+</P>
+<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
+models</A>.
+</P>
+<HR>
+
+<A NAME = "howto_8"></A><H4>6.8 TIP4P water model
+</H4>
+<P>The four-point TIP4P rigid water model extends the traditional
+three-point TIP3P model by adding an additional site, usually
+massless, where the charge associated with the oxygen atom is placed.
+This site M is located at a fixed distance away from the oxygen along
+the bisector of the HOH bond angle. A bond style of <I>harmonic</I> and an
+angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
+</P>
+<P>A TIP4P model is run with LAMMPS using either this command
+for a cutoff model:
+</P>
+<P><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A>
+</P>
+<P>or these two commands for a long-range model:
+</P>
+<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A>
+<LI><A HREF = "kspace_style.html">kspace_style pppm/tip4p</A>
+</UL>
+<P>For both models, the bond lengths and bond angles should be held fixed
+using the <A HREF = "fix_shake.html">fix shake</A> command.
+</P>
+<P>These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP4P model with a cutoff
+<A HREF = "#Jorgensen">(Jorgensen)</A>. Note that the OM distance is specified in
+the <A HREF = "pair_style.html">pair_style</A> command, not as part of the pair
+coefficients.
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -1.040<BR>
+H charge = 0.520<BR>
+r0 of OH bond = 0.9572<BR>
+theta of HOH angle = 104.52 <BR>
+OM distance = 0.15<BR>
+LJ epsilon of O-O = 0.1550<BR>
+LJ sigma of O-O = 3.1536<BR>
+LJ epsilon, sigma of OH, HH = 0.0<BR>
+Coulombic cutoff = 8.5 <BR>
+</P>
+<P>For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+http://dx.doi.org/10.1063/1.1931662) these values can be used:
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -1.1794<BR>
+H charge = 0.5897<BR>
+r0 of OH bond = 0.9572<BR>
+theta of HOH angle = 104.52<BR>
+OM distance = 0.1577<BR>
+LJ epsilon of O-O = 0.21084<BR>
+LJ sigma of O-O = 3.1668<BR>
+LJ epsilon, sigma of OH, HH = 0.0<BR>
+Coulombic cutoff = 8.5 <BR>
+</P>
+<P>For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+http://dx.doi.org/10.1063/1.2121687), these values can be used:
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -1.1128<BR>
+H charge = 0.5564<BR>
+r0 of OH bond = 0.9572<BR>
+theta of HOH angle = 104.52<BR>
+OM distance = 0.1546<BR>
+LJ epsilon of O-O = 0.1852<BR>
+LJ sigma of O-O = 3.1589<BR>
+LJ epsilon, sigma of OH, HH = 0.0<BR>
+Coulombic cutoff = 8.5 <BR>
+</P>
+<P>These are the parameters to use for TIP4P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS):
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -1.0484<BR>
+H charge = 0.5242<BR>
+r0 of OH bond = 0.9572<BR>
+theta of HOH angle = 104.52<BR>
+OM distance = 0.1250<BR>
+LJ epsilon of O-O = 0.16275<BR>
+LJ sigma of O-O = 3.16435<BR>
+LJ epsilon, sigma of OH, HH = 0.0 <BR>
+</P>
+<P>Note that the when using the TIP4P pair style, the neighobr list
+cutoff for Coulomb interactions is effectively extended by a distance
+2 * (OM distance), to account for the offset distance of the
+fictitious charges on O atoms in water molecules. Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2*(OM distance), to shrink the size of the neighbor list.
+This leads to slightly larger cost for the long-range calculation, so
+you can test the trade-off for your model. The OM distance and the LJ
+and Coulombic cutoffs are set in the <A HREF = "pair_lj.html">pair_style
+lj/cut/tip4p/long</A> command.
+</P>
+<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
+models</A>.
+</P>
+<HR>
+
+<A NAME = "howto_9"></A><H4>6.9 SPC water model
+</H4>
+<P>The SPC water model specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
+used.
+</P>
+<P>These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid SPC model.
+</P>
+<P>O mass = 15.9994<BR>
+H mass = 1.008<BR>
+O charge = -0.820<BR>
+H charge = 0.410<BR>
+LJ epsilon of OO = 0.1553<BR>
+LJ sigma of OO = 3.166<BR>
+LJ epsilon, sigma of OH, HH = 0.0<BR>
+r0 of OH bond = 1.0<BR>
+theta of HOH angle = 109.47 <BR>
+</P>
+<P>Note that as originally proposed, the SPC model was run with a 9
+Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
+with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
+any of the parameters above, though it becomes a different model in
+that mode of usage.
+</P>
+<P>The SPC/E (extended) water model is the same, except
+the partial charge assignemnts change:
+</P>
+<P>O charge = -0.8476<BR>
+H charge = 0.4238 <BR>
+</P>
+<P>See the <A HREF = "#Berendsen">(Berendsen)</A> reference for more details on both
+the SPC and SPC/E models.
+</P>
+<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
+models</A>.
+</P>
+<HR>
+
+<A NAME = "howto_10"></A><H4>6.10 Coupling LAMMPS to other codes
+</H4>
+<P>LAMMPS is designed to allow it to be coupled to other codes. For
+example, a quantum mechanics code might compute forces on a subset of
+atoms and pass those forces to LAMMPS. Or a continuum finite element
+(FE) simulation might use atom positions as boundary conditions on FE
+nodal points, compute a FE solution, and return interpolated forces on
+MD atoms.
+</P>
+<P>LAMMPS can be coupled to other codes in at least 3 ways. Each has
+advantages and disadvantages, which you'll have to think about in the
+context of your application.
+</P>
+<P>(1) Define a new <A HREF = "fix.html">fix</A> command that calls the other code. In
+this scenario, LAMMPS is the driver code. During its timestepping,
+the fix is invoked, and can make library calls to the other code,
+which has been linked to LAMMPS as a library. This is the way the
+<A HREF = "http://www.rpi.edu/~anderk5/lab">POEMS</A> package that performs constrained rigid-body motion on
+groups of atoms is hooked to LAMMPS. See the
+<A HREF = "fix_poems.html">fix_poems</A> command for more details. See <A HREF = "Section_modify.html">this
+section</A> of the documentation for info on how to add
+a new fix to LAMMPS.
+</P>
+
+
+<P>(2) Define a new LAMMPS command that calls the other code. This is
+conceptually similar to method (1), but in this case LAMMPS and the
+other code are on a more equal footing. Note that now the other code
+is not called during the timestepping of a LAMMPS run, but between
+runs. The LAMMPS input script can be used to alternate LAMMPS runs
+with calls to the other code, invoked via the new command. The
+<A HREF = "run.html">run</A> command facilitates this with its <I>every</I> option, which
+makes it easy to run a few steps, invoke the command, run a few steps,
+invoke the command, etc.
+</P>
+<P>In this scenario, the other code can be called as a library, as in
+(1), or it could be a stand-alone code, invoked by a system() call
+made by the command (assuming your parallel machine allows one or more
+processors to start up another program). In the latter case the
+stand-alone code could communicate with LAMMPS thru files that the
+command writes and reads.
+</P>
+<P>See <A HREF = "Section_modify.html">Section_modify</A> of the documentation for how
+to add a new command to LAMMPS.
+</P>
+<P>(3) Use LAMMPS as a library called by another code. In this case the
+other code is the driver and calls LAMMPS as needed. Or a wrapper
+code could link and call both LAMMPS and another code as libraries.
+Again, the <A HREF = "run.html">run</A> command has options that allow it to be
+invoked with minimal overhead (no setup or clean-up) if you wish to do
+multiple short runs, driven by another program.
+</P>
+<P>Examples of driver codes that call LAMMPS as a library are included in
+the examples/COUPLE directory of the LAMMPS distribution; see
+examples/COUPLE/README for more details:
+</P>
+<UL><LI>simple: simple driver programs in C++ and C which invoke LAMMPS as a
+library
+
+<LI>lammps_quest: coupling of LAMMPS and <A HREF = "http://dft.sandia.gov/Quest">Quest</A>, to run classical
+MD with quantum forces calculated by a density functional code
+
+<LI>lammps_spparks: coupling of LAMMPS and <A HREF = "http://www.sandia.gov/~sjplimp/spparks.html">SPPARKS</A>, to couple
+a kinetic Monte Carlo model for grain growth using MD to calculate
+strain induced across grain boundaries
+</UL>
+
+
+
+
+<P><A HREF = "Section_start.html#start_5">This section</A> of the documentation
+describes how to build LAMMPS as a library. Once this is done, you
+can interface with LAMMPS either via C++, C, Fortran, or Python (or
+any other language that supports a vanilla C-like interface). For
+example, from C++ you could create one (or more) "instances" of
+LAMMPS, pass it an input script to process, or execute individual
+commands, all by invoking the correct class methods in LAMMPS. From C
+or Fortran you can make function calls to do the same things. See
+<A HREF = "Section_python.html">Section_python</A> of the manual for a description
+of the Python wrapper provided with LAMMPS that operates through the
+LAMMPS library interface.
+</P>
+<P>The files src/library.cpp and library.h contain the C-style interface
+to LAMMPS. See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
+manual for a description of the interface and how to extend it for
+your needs.
+</P>
+<P>Note that the lammps_open() function that creates an instance of
+LAMMPS takes an MPI communicator as an argument. This means that
+instance of LAMMPS will run on the set of processors in the
+communicator. Thus the calling code can run LAMMPS on all or a subset
+of processors. For example, a wrapper script might decide to
+alternate between LAMMPS and another code, allowing them both to run
+on all the processors. Or it might allocate half the processors to
+LAMMPS and half to the other code and run both codes simultaneously
+before syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+</P>
+<HR>
+
+<A NAME = "howto_11"></A><H4>6.11 Visualizing LAMMPS snapshots
+</H4>
+<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
+simulations can be visualized (and analyzed) in a variety of ways.
+</P>
+<P>LAMMPS snapshots are created by the <A HREF = "dump.html">dump</A> command which can
+create files in several formats. The native LAMMPS dump format is a
+text file (see "dump atom" or "dump custom") which can be visualized
+by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
+LAMMPS package. This produces simple, fast 2d projections of 3d
+systems, and can be useful for rapid debugging of simulation geometry
+and atom trajectories.
+</P>
+<P>Several programs included with LAMMPS as auxiliary tools can convert
+native LAMMPS dump files to other formats. See the
+<A HREF = "Section_tools.html">Section_tools</A> doc page for details. The first is
+the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
+lammps2pdb Perl script which converts LAMMPS dump files into PDB
+files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
+converts LAMMPS dump files into Accelrys' Insight MD program files.
+The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
+LAMMPS dump files into CFG files which can be read into the
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
+</P>
+<P>A Python-based toolkit distributed by our group can read native LAMMPS
+dump files, including custom dump files with additional columns of
+user-specified atom information, and convert them to various formats
+or pipe them into visualization software directly. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
+WWW site</A> for details. Specifically, Pizza.py can convert
+LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
+Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
+RasMol visualization programs. Pizza.py has tools that do interactive
+3d OpenGL visualization and one that creates SVG images of dump file
+snapshots.
+</P>
+<P>LAMMPS can create XYZ files directly (via "dump xyz") which is a
+simple text-based file format used by many visualization programs
+including <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
+</P>
+<P>LAMMPS can create DCD files directly (via "dump dcd") which can be
+read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> in conjunction with a CHARMM PSF file. Using this
+form of output avoids the need to convert LAMMPS snapshots to PDB
+files. See the <A HREF = "dump.html">dump</A> command for more information on DCD
+files.
+</P>
+<P>LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
+file format which can also be read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> for visualization.
+See the <A HREF = "dump.html">dump</A> command for more information on XTC files.
+</P>
+
+
+
+
+
+
+
+
+<HR>
+
+<A NAME = "howto_12"></A><H4>6.12 Triclinic (non-orthogonal) simulation boxes
+</H4>
+<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
+particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
+conditions of the box (periodic, non-periodic, etc). The orthogonal
+box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
+starting from the origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> =
+(0,yhi-ylo,0); <B>c</B> = (0,0,zhi-zlo). The 6 parameters
+(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
+is created, e.g. by the <A HREF = "create_box.html">create_box</A> or
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
+where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
+parameters, as well as lx,ly,lz, can be output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command.
+</P>
+<P>LAMMPS also allows simulations to be performed in triclinic
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
+triclinic symmetry. The parallelepiped has its "origin" at
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
+origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> = (xy,yhi-ylo,0); <B>c</B> =
+(xz,yz,zhi-zlo). <I>xy,xz,yz</I> can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped. In LAMMPS the triclinic
+simulation box edge vectors <B>a</B>, <B>b</B>, and <B>c</B> cannot be arbitrary
+vectors. As indicated, <B>a</B> must lie on the positive x axis. <B>b</B> must
+lie in the xy plane, with strictly positive y component. <B>c</B> may have
+any orientation with strictly positive z component. The requirement
+that <B>a</B>, <B>b</B>, and <B>c</B> have strictly positive x, y, and z components,
+respectively, ensures that <B>a</B>, <B>b</B>, and <B>c</B> form a complete
+right-handed basis. These restrictions impose no loss of generality,
+since it is possible to rotate/invert any set of 3 crystal basis
+vectors so that they conform to the restrictions.
+</P>
+<P>For example, assume that the 3 vectors <B>A</B>,<B>B</B>,<B>C</B> are the edge
+vectors of a general parallelepiped, where there is no restriction on
+<B>A</B>,<B>B</B>,<B>C</B> other than they form a complete right-handed basis i.e.
+<B>A</B> x <B>B</B> . <B>C</B> > 0. The equivalent LAMMPS <B>a</B>,<B>b</B>,<B>c</B> are a linear
+rotation of <B>A</B>, <B>B</B>, and <B>C</B> and can be computed as follows:
+</P>
+<CENTER><IMG SRC = "Eqs/transform.jpg">
+</CENTER>
+<P>where A = |<B>A</B>| indicates the scalar length of <B>A</B>. The ^ hat symbol
+indicates the corresponding unit vector. <I>beta</I> and <I>gamma</I> are angles
+between the vectors described below. Note that by construction,
+<B>a</B>, <B>b</B>, and <B>c</B> have strictly positive x, y, and z components, respectively.
+If it should happen that
+<B>A</B>, <B>B</B>, and <B>C</B> form a left-handed basis, then the above equations
+are not valid for <B>c</B>. In this case, it is necessary
+to first apply an inversion. This can be achieved
+by interchanging two basis vectors or by changing the sign of one of them.
+</P>
+<P>For consistency, the same rotation/inversion applied to the basis vectors
+must also be applied to atom positions, velocities,
+and any other vector quantities.
+This can be conveniently achieved by first converting to
+fractional coordinates in the
+old basis and then converting to distance coordinates in the new basis.
+The transformation is given by the following equation:
+</P>
+<CENTER><IMG SRC = "Eqs/rotate.jpg">
+</CENTER>
+<P>where <I>V</I> is the volume of the box, <B>X</B> is the original vector quantity and
+<B>x</B> is the vector in the LAMMPS basis.
+</P>
+<P>There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary. Some commands that work
+with triclinic boxes, e.g. the <A HREF = "fix_deform.html">fix deform</A> and <A HREF = "fix_nh.html">fix
+npt</A> commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions. See the command doc pages
+for details.
+</P>
+<P>The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
+time the simluation box is created. This happens in one of 3 ways.
+If the <A HREF = "create_box.html">create_box</A> command is used with a region of
+style <I>prism</I>, then a triclinic box is setup. See the
+<A HREF = "region.html">region</A> command for details. If the
+<A HREF = "read_data.html">read_data</A> command is used to define the simulation
+box, and the header of the data file contains a line with the "xy xz
+yz" keyword, then a triclinic box is setup. See the
+<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
+<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
+was written from a simulation using a triclinic box, then a triclinic
+box will be setup for the restarted simulation.
+</P>
+<P>Note that you can define a triclinic box with all 3 tilt factors =
+0.0, so that it is initially orthogonal. This is necessary if the box
+will become non-orthogonal, e.g. due to the <A HREF = "fix_nh.html">fix npt</A> or
+<A HREF = "fix_deform.html">fix deform</A> commands. Alternatively, you can use the
+<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
+orthogonal to triclinic and vice versa.
+</P>
+<P>As with orthogonal boxes, LAMMPS defines triclinic box size parameters
+lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
+The 9 parameters, as well as lx,ly,lz, can be output via the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.
+</P>
+<P>To avoid extremely tilted boxes (which would be computationally
+inefficient), LAMMPS normally requires that no tilt factor can skew
+the box more than half the distance of the parallel box length, which
+is the 1st dimension in the tilt factor (x for xz). This is required
+both when the simulation box is created, e.g. via the
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> commands,
+as well as when the box shape changes dynamically during a simulation,
+e.g. via the <A HREF = "fix_deform.html">fix deform</A> or <A HREF = "fix_nh.html">fix npt</A>
+commands.
+</P>
+<P>For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5. Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are geometrically all equivalent. If the box tilt exceeds this
+limit during a dynamics run (e.g. via the <A HREF = "fix_deform.html">fix deform</A>
+command), then the box is "flipped" to an equivalent shape with a tilt
+factor within the bounds, so the run can continue. See the <A HREF = "fix_deform.html">fix
+deform</A> doc page for further details.
+</P>
+<P>One exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic. In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity. In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient, due to the highly skewed simulation box.
+</P>
+<P>The limitation on not creating a simulation box with a tilt factor
+skewing the box more than half the distance of the parallel box length
+can be overridden via the <A HREF = "box.html">box</A> command. Setting the <I>tilt</I>
+keyword to <I>large</I> allows any tilt factors to be specified.
+</P>
+<P>Box flips that may occur using the <A HREF = "fix_deform.html">fix deform</A> or
+<A HREF = "fix_nh.html">fix npt</A> commands can be turned off using the <I>flip no</I>
+option with either of the commands.
+</P>
+<P>Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+</P>
+<P>Triclinic crystal structures are often defined using three lattice
+constants <I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and
+<I>gamma</I>. Note that in this nomenclature, the a, b, and c lattice
+constants are the scalar lengths of the edge vectors <B>a</B>, <B>b</B>, and <B>c</B>
+defined above. The relationship between these 6 quantities
+(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
+</P>
+<CENTER><IMG SRC = "Eqs/box.jpg">
+</CENTER>
+<P>The inverse relationship can be written as follows:
+</P>
+<CENTER><IMG SRC = "Eqs/box_inverse.jpg">
+</CENTER>
+<P>The values of <I>a</I>, <I>b</I>, <I>c</I> , <I>alpha</I>, <I>beta</I> , and <I>gamma</I> can be printed
+out or accessed by computes using the
+<A HREF = "thermo_style.html">thermo_style custom</A> keywords
+<I>cella</I>, <I>cellb</I>, <I>cellc</I>, <I>cellalpha</I>, <I>cellbeta</I>, <I>cellgamma</I>,
+respectively.
+</P>
+<P>As discussed on the <A HREF = "dump.html">dump</A> command doc page, when the BOX
+BOUNDS for a snapshot is written to a dump file for a triclinic box,
+an orthogonal bounding box which encloses the triclinic simulation box
+is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
+box, formatted as follows:
+</P>
+<PRE>ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+</PRE>
+<P>This bounding box is convenient for many visualization programs and is
+calculated from the 9 triclinic box parameters
+(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
+</P>
+<PRE>xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+ylo_bound = ylo + MIN(0.0,yz)
+yhi_bound = yhi + MAX(0.0,yz)
+zlo_bound = zlo
+zhi_bound = zhi
+</PRE>
+<P>These formulas can be inverted if you need to convert the bounding box
+back into the triclinic box parameters, e.g. xlo = xlo_bound -
+MIN(0.0,xy,xz,xy+xz).
+</P>
+<P>One use of triclinic simulation boxes is to model solid-state crystals
+with triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be
+used with non-orthogonal basis vectors to define a lattice that will
+tile a triclinic simulation box via the
+<A HREF = "create_atoms.html">create_atoms</A> command.
+</P>
+<P>A second use is to run Parinello-Rahman dyanamics via the <A HREF = "fix_nh.html">fix
+npt</A> command, which will adjust the xy, xz, yz tilt
+factors to compensate for off-diagonal components of the pressure
+tensor. The analalog for an <A HREF = "minimize.html">energy minimization</A> is
+the <A HREF = "fix_box_relax.html">fix box/relax</A> command.
+</P>
+<P>A third use is to shear a bulk solid to study the response of the
+material. The <A HREF = "fix_deform.html">fix deform</A> command can be used for
+this purpose. It allows dynamic control of the xy, xz, yz tilt
+factors as a simulation runs. This is discussed in the next section
+on non-equilibrium MD (NEMD) simulations.
+</P>
+<HR>
+
+<A NAME = "howto_13"></A><H4>6.13 NEMD simulations
+</H4>
+<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
+used to measure a fluid's rheological properties such as viscosity.
+In LAMMPS, such simulations can be performed by first setting up a
+non-orthogonal simulation box (see the preceding Howto section).
+</P>
+<P>A shear strain can be applied to the simulation box at a desired
+strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
+<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
+the sheared fluid and integrate the SLLOD equations of motion for the
+system. Fix nvt/sllod uses <A HREF = "compute_temp_deform.html">compute
+temp/deform</A> to compute a thermal temperature
+by subtracting out the streaming velocity of the shearing atoms. The
+velocity profile or other properties of the fluid can be monitored via
+the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
+</P>
+<P>As discussed in the previous section on non-orthogonal simulation
+boxes, the amount of tilt or skew that can be applied is limited by
+LAMMPS for computational efficiency to be 1/2 of the parallel box
+length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
+a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
+deform</A> command, when the tilt value reaches a limit,
+the box is flipped to the opposite limit which is an equivalent tiling
+of periodic space. The strain rate can then continue to change as
+before. In a long NEMD simulation these box re-shaping events may
+occur many times.
+</P>
+<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
+deform</A> should be set to "remap v", since that is what
+<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
+profile consistent with the applied shear strain rate.
+</P>
+<P>An alternative method for calculating viscosities is provided via the
+<A HREF = "fix_viscosity.html">fix viscosity</A> command.
+</P>
+<HR>
+
+<A NAME = "howto_14"></A><H4>6.14 Finite-size spherical and aspherical particles
+</H4>
+<P>Typical MD models treat atoms or particles as point masses. Sometimes
+it is desirable to have a model with finite-size particles such as
+spheroids or ellipsoids or generalized aspherical bodies. The
+difference is that such particles have a moment of inertia, rotational
+energy, and angular momentum. Rotation is induced by torque coming
+from interactions with other particles.
+</P>
+<P>LAMMPS has several options for running simulations with these kinds of
+particles. The following aspects are discussed in turn:
+</P>
+<UL><LI>atom styles
+<LI>pair potentials
+<LI>time integration
+<LI>computes, thermodynamics, and dump output
+<LI>rigid bodies composed of finite-size particles
+</UL>
+<P>Example input scripts for these kinds of models are in the body,
+colloid, dipole, ellipse, line, peri, pour, and tri directories of the
+<A HREF = "Section_example.html">examples directory</A> in the LAMMPS distribution.
+</P>
+<H5>Atom styles
+</H5>
+<P>There are several <A HREF = "atom_style.html">atom styles</A> that allow for
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
+tri, peri, and body.
+</P>
+<P>The sphere style defines particles that are spheriods and each
+particle can have a unique diameter and mass (or density). These
+particles store an angular velocity (omega) and can be acted upon by
+torque. The "set" command can be used to modify the diameter and mass
+of individual particles, after then are created.
+</P>
+<P>The dipole style does not actually define finite-size particles, but
+is often used in conjunction with spherical particles, via a command
+like
+</P>
+<PRE>atom_style hybrid sphere dipole
+</PRE>
+<P>This is because when dipoles interact with each other, they induce
+torques, and a particle must be finite-size (i.e. have a moment of
+inertia) in order to respond and rotate. See the <A HREF = "atom_style.html">atom_style
+dipole</A> command for details. The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+</P>
+<P>The ellipsoid style defines particles that are ellipsoids and thus can
+be aspherical. Each particle has a shape, specified by 3 diameters,
+and mass (or density). These particles store an angular momentum and
+their orientation (quaternion), and can be acted upon by torque. They
+do not store an angular velocity (omega), which can be in a different
+direction than angular momentum, rather they compute it as needed.
+The "set" command can be used to modify the diameter, orientation, and
+mass of individual particles, after then are created. It also has a
+brief explanation of what quaternions are.
+</P>
+<P>The line style defines line segment particles with two end points and
+a mass (or density). They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
+</P>
+<P>The tri style defines triangular particles with three corner points
+and a mass (or density). They can be used in 3d simulations, and they
+can be joined together to form rigid bodies which represent arbitrary
+particles with a triangulated surface.
+</P>
+<P>The peri style is used with <A HREF = "pair_peri.html">Peridynamic models</A> and
+defines particles as having a volume, that is used internally in the
+<A HREF = "pair_peri.html">pair_style peri</A> potentials.
+</P>
+<P>The body style allows for definition of particles which can represent
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc. The body style
+is discussed in more detail on the <A HREF = "body.html">body</A> doc page.
+</P>
+<P>Note that if one of these atom styles is used (or multiple styles via
+the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
+the system are required to be finite-size or aspherical.
+</P>
+<P>For example, in the ellipsoid style, if the 3 shape parameters are set
+to the same value, the particle will be a sphere rather than an
+ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
+diameter is set to 0.0, it will be a point particle. In the line or
+tri style, if the lineflag or triflag is specified as 0, then it
+will be a point particle.
+</P>
+<P>Some of the pair styles used to compute pairwise interactions between
+finite-size particles also compute the correct interaction with point
+particles as well, e.g. the interaction between a point particle and a
+finite-size particle or between two point particles. If necessary,
+<A HREF = "pair_hybrid.html">pair_style hybrid</A> can be used to insure the correct
+interactions are computed for the appropriate style of interactions.
+Likewise, using groups to partition particles (ellipsoids versus
+spheres versus point particles) will allow you to use the appropriate
+time integrators and temperature computations for each class of
+particles. See the doc pages for various commands for details.
+</P>
+<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses. This means they have the same moment of inertia as the 3d
+object. When temperature is computed, the correct degrees of freedom
+are used for rotation in a 2d versus 3d system.
+</P>
+<H5>Pair potentials
+</H5>
+<P>When a system with finite-size particles is defined, the particles
+will only rotate and experience torque if the force field computes
+such interactions. These are the various <A HREF = "pair_style.html">pair
+styles</A> that generate torque:
+</P>
+<UL><LI><A HREF = "pair_gran.html">pair_style gran/history</A>
+<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A>
+<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
+<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
+<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
+<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
+<LI><A HREF = "pair_brownian.html">pair_style brownian</A>
+<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
+<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A>
+<LI><A HREF = "pair_tri_lj.html">pair_style tri/lj</A>
+<LI><A HREF = "pair_body.html">pair_style body</A>
+</UL>
+<P>The granular pair styles are used with spherical particles. The
+dipole pair style is used with the dipole atom style, which could be
+applied to spherical or ellipsoidal particles. The GayBerne and
+REsquared potentials require ellipsoidal particles, though they will
+also work if the 3 shape parameters are the same (a sphere). The
+Brownian and lubrication potentials are used with spherical particles.
+The line, tri, and body potentials are used with line segment,
+triangular, and body particles respectively.
+</P>
+<H5>Time integration
+</H5>
+<P>There are several fixes that perform time integration on finite-size
+spherical particles, meaning the integrators update the rotational
+orientation and angular velocity or angular momentum of the particles:
+</P>
+<UL><LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
+<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
+<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
+</UL>
+<P>Likewise, there are 3 fixes that perform time integration on
+ellipsoidal particles:
+</P>
+<UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
+<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
+<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
+</UL>
+<P>The advantage of these fixes is that those which thermostat the
+particles include the rotational degrees of freedom in the temperature
+calculation and thermostatting. The <A HREF = "fix_langevin">fix langevin</A>
+command can also be used with its <I>omgea</I> or <I>angmom</I> options to
+thermostat the rotational degrees of freedom for spherical or
+ellipsoidal particles. Other thermostatting fixes only operate on the
+translational kinetic energy of finite-size particles.
+</P>
+<P>These fixes perform constant NVE time integration on line segment,
+triangular, and body particles:
+</P>
+<UL><LI><A HREF = "fix_nve_line.html">fix nve/line</A>
+<LI><A HREF = "fix_nve_tri.html">fix nve/tri</A>
+<LI><A HREF = "fix_nve_body.html">fix nve/body</A>
+</UL>
+<P>Note that for mixtures of point and finite-size particles, these
+integration fixes can only be used with <A HREF = "group.html">groups</A> which
+contain finite-size particles.
+</P>
+<H5>Computes, thermodynamics, and dump output
+</H5>
+<P>There are several computes that calculate the temperature or
+rotational energy of spherical or ellipsoidal particles:
+</P>
+<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
+<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
+<LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
+<LI><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
+</UL>
+<P>These include rotational degrees of freedom in their computation. If
+you wish the thermodynamic output of temperature or pressure to use
+one of these computes (e.g. for a system entirely composed of
+finite-size particles), then the compute can be defined and the
+<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by default
+thermodynamic quantities will be calculated with a temperature that
+only includes translational degrees of freedom. See the
+<A HREF = "thermo_style.html">thermo_style</A> command for details.
+</P>
+<P>These commands can be used to output various attributes of finite-size
+particles:
+</P>
+<UL><LI><A HREF = "dump.html">dump custom</A>
+<LI><A HREF = "compute_property_atom.html">compute property/atom</A>
+<LI><A HREF = "dump.html">dump local</A>
+<LI><A HREF = "compute_body_local.html">compute body/local</A>
+</UL>
+<P>Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
+</P>
+<H5>Rigid bodies composed of finite-size particles
+</H5>
+<P>The <A HREF = "fix_rigid.html">fix rigid</A> command treats a collection of
+particles as a rigid body, computes its inertia tensor, sums the total
+force and torque on the rigid body each timestep due to forces on its
+constituent particles, and integrates the motion of the rigid body.
+</P>
+<P>If any of the constituent particles of a rigid body are finite-size
+particles (spheres or ellipsoids or line segments or triangles), then
+their contribution to the inertia tensor of the body is different than
+if they were point particles. This means the rotational dynamics of
+the rigid body will be different. Thus a model of a dimer is
+different if the dimer consists of two point masses versus two
+spheroids, even if the two particles have the same mass. Finite-size
+particles that experience torque due to their interaction with other
+particles will also impart that torque to a rigid body they are part
+of.
+</P>
+<P>See the "fix rigid" command for example of complex rigid-body models
+it is possible to define in LAMMPS.
+</P>
+<P>Note that the <A HREF = "fix_shake.html">fix shake</A> command can also be used to
+treat 2, 3, or 4 particles as a rigid body, but it always assumes the
+particles are point masses.
+</P>
+<P>Also note that body particles cannot be modeled with the <A HREF = "fix_rigid.html">fix
+rigid</A> command. Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles. Individual body partices are typically treated
+as rigid bodies, and their motion integrated with a command like <A HREF = "fix_nve_body.html">fix
+nve/body</A>. Interactions between pairs of body
+particles are computed via a command like <A HREF = "pair_body.html">pair_style
+body</A>.
+</P>
+<HR>
+
+<A NAME = "howto_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
+</H4>
+<P>There are four basic kinds of LAMMPS output:
+</P>
+<UL><LI><A HREF = "thermo_style.html">Thermodynamic output</A>, which is a list
+of quantities printed every few timesteps to the screen and logfile.
+
+<LI><A HREF = "dump.html">Dump files</A>, which contain snapshots of atoms and various
+per-atom values and are written at a specified frequency.
+
+<LI>Certain fixes can output user-specified quantities to files: <A HREF = "fix_ave_time.html">fix
+ave/time</A> for time averaging, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> for spatial averaging, and <A HREF = "fix_print.html">fix
+print</A> for single-line output of
+<A HREF = "variable.html">variables</A>. Fix print can also output to the
+screen.
+
+<LI><A HREF = "restart.html">Restart files</A>.
+</UL>
+<P>A simulation prints one set of thermodynamic output and (optionally)
+restart files. It can generate any number of dump files and fix
+output files, depending on what <A HREF = "dump.html">dump</A> and <A HREF = "fix.html">fix</A>
+commands you specify.
+</P>
+<P>As discussed below, LAMMPS gives you a variety of ways to determine
+what quantities are computed and printed when the thermodynamics,
+dump, or fix commands listed above perform output. Throughout this
+discussion, note that users can also <A HREF = "Section_modify.html">add their own computes and fixes
+to LAMMPS</A> which can then generate values that can
+then be output with these commands.
+</P>
+<P>The following sub-sections discuss different LAMMPS command related
+to output and the kind of data they operate on and produce:
+</P>
+<UL><LI><A HREF = "#global">Global/per-atom/local data</A>
+<LI><A HREF = "#scalar">Scalar/vector/array data</A>
+<LI><A HREF = "#thermo">Thermodynamic output</A>
+<LI><A HREF = "#dump">Dump file output</A>
+<LI><A HREF = "#fixoutput">Fixes that write output files</A>
+<LI><A HREF = "#computeoutput">Computes that process output quantities</A>
+<LI><A HREF = "#fixoutput">Fixes that process output quantities</A>
+<LI><A HREF = "#compute">Computes that generate values to output</A>
+<LI><A HREF = "#fix">Fixes that generate values to output</A>
+<LI><A HREF = "#variable">Variables that generate values to output</A>
+<LI><A HREF = "#table">Summary table of output options and data flow between commands</A>
+</UL>
+<H5><A NAME = "global"></A>Global/per-atom/local data
+</H5>
+<P>Various output-related commands work with three different styles of
+data: global, per-atom, or local. A global datum is one or more
+system-wide values, e.g. the temperature of the system. A per-atom
+datum is one or more values per atom, e.g. the kinetic energy of each
+atom. Local datums are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances.
+</P>
+<H5><A NAME = "scalar"></A>Scalar/vector/array data
+</H5>
+<P>Global, per-atom, and local datums can each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values. The
+doc page for a "compute" or "fix" or "variable" that generates data
+will specify both the style and kind of data it produces, e.g. a
+per-atom vector.
+</P>
+<P>When a quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID in this case is the ID of a compute. The leading
+"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
+<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
+<TR><TD >c_ID[I][J] </TD><TD > one element of array
+</TD></TR></TABLE></DIV>
+
+<P>In other words, using one bracket reduces the dimension of the data
+once (vector -> scalar, array -> vector). Using two brackets reduces
+the dimension twice (array -> scalar). Thus a command that uses
+scalar values as input can typically also process elements of a vector
+or array.
+</P>
+<H5><A NAME = "thermo"></A>Thermodynamic output
+</H5>
+<P>The frequency and format of thermodynamic output is set by the
+<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
+<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
+<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values
+are calculated and written out. Pre-defined keywords can be specified
+(e.g. press, etotal, etc). Three additional kinds of keywords can
+also be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A>
+or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
+output. In each case, the compute, fix, or variable must generate
+global values for input to the <A HREF = "dump.html">thermo_style custom</A>
+command.
+</P>
+<P>Note that thermodynamic output values can be "extensive" or
+"intensive". The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature). The
+setting for <A HREF = "thermo_modify.html">thermo_modify norm</A> determines whether
+extensive quantities are normalized or not. Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details. <A HREF = "variable.html">Equal-style variables</A> produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+</P>
+<H5><A NAME = "dump"></A>Dump file output
+</H5>
+<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
+<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
+pre-defined formats (dump atom, dump xtc, etc).
+</P>
+<P>There is also a <A HREF = "dump.html">dump custom</A> format where the user
+specifies what values are output with each atom. Pre-defined atom
+attributes can be specified (id, x, fx, etc). Three additional kinds
+of keywords can also be specified (c_ID, f_ID, v_name), where a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
+provides the values to be output. In each case, the compute, fix, or
+variable must generate per-atom values for input to the <A HREF = "dump.html">dump
+custom</A> command.
+</P>
+<P>There is also a <A HREF = "dump.html">dump local</A> format where the user specifies
+what local values to output. A pre-defined index keyword can be
+specified to enumuerate the local values. Two additional kinds of
+keywords can also be specified (c_ID, f_ID), where a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
+provides the values to be output. In each case, the compute or fix
+must generate local values for input to the <A HREF = "dump.html">dump local</A>
+command.
+</P>
+<H5><A NAME = "fixoutput"></A>Fixes that write output files
+</H5>
+<P>Several fixes take various quantities as input and can write output
+files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
+<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>, and <A HREF = "fix_print.html">fix
+print</A>.
+</P>
+<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables direct output to
+a file and/or time-averaging of global scalars or vectors. The user
+specifies one or more quantities as input. These can be global
+<A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or
+<A HREF = "variable.html">variables</A> of any style except the atom style which
+produces per-atom values. Since a variable can refer to keywords used
+by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or
+press) and individual per-atom values, a wide variety of quantities
+can be time averaged and/or output in this way. If the inputs are one
+or more scalar values, then the fix generate a global scalar or vector
+of output. If the inputs are one or more vector values, then the fix
+generates a global vector or array of output. The time-averaged
+output of this fix can also be used as input to other output commands.
+</P>
+<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables direct
+output to a file of spatial-averaged per-atom quantities like those
+output in dump files, within 1d layers of the simulation box. The
+per-atom quantities can be atom density (mass or number) or atom
+attributes such as position, velocity, force. They can also be
+per-atom quantities calculated by a <A HREF = "compute.html">compute</A>, by a
+<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
+spatial-averaged output of this fix can also be used as input to other
+output commands.
+</P>
+<P>The <A HREF = "fix_ave_histo.html">fix ave/histo</A> command enables direct output
+to a file of histogrammed quantities, which can be global or per-atom
+or local quantities. The histogram output of this fix can also be
+used as input to other output commands.
+</P>
+<P>The <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command enables direct
+output to a file of time-correlated quantities, which can be global
+scalars. The correlation matrix output of this fix can also be used
+as input to other output commands.
+</P>
+<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output
+written to the screen and log file or to a separate file, periodically
+during a running simulation. The line can contain one or more
+<A HREF = "variable.html">variable</A> values for any style variable except the atom
+style). As explained above, variables themselves can contain
+references to global values generated by <A HREF = "thermo_style.html">thermodynamic
+keywords</A>, <A HREF = "compute.html">computes</A>,
+<A HREF = "fix.html">fixes</A>, or other <A HREF = "variable.html">variables</A>, or to per-atom
+values for a specific atom. Thus the <A HREF = "fix_print.html">fix print</A>
+command is a means to output a wide variety of quantities separate
+from normal thermodynamic or dump file output.
+</P>
+<H5><A NAME = "computeoutput"></A>Computes that process output quantities
+</H5>
+<P>The <A HREF = "compute_reduce.html">compute reduce</A> and <A HREF = "compute_reduce.html">compute
+reduce/region</A> commands take one or more per-atom
+or local vector quantities as inputs and "reduce" them (sum, min, max,
+ave) to scalar quantities. These are produced as output values which
+can be used as input to other output commands.
+</P>
+<P>The <A HREF = "compute_slice.html">compute slice</A> command take one or more global
+vector or array quantities as inputs and extracts a subset of their
+values to create a new vector or array. These are produced as output
+values which can be used as input to other output commands.
+</P>
+<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a
+list of one or more pre-defined atom attributes (id, x, fx, etc) and
+stores the values in a per-atom vector or array. These are produced
+as output values which can be used as input to other output commands.
+The list of atom attributes is the same as for the <A HREF = "dump.html">dump
+custom</A> command.
+</P>
+<P>The <A HREF = "compute_property_local.html">compute property/local</A> command takes
+a list of one or more pre-defined local attributes (bond info, angle
+info, etc) and stores the values in a local vector or array. These
+are produced as output values which can be used as input to other
+output commands.
+</P>
+<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
+</H5>
+<P>The <A HREF = "fix_vector.html">fix vector</A> command can create global vectors as
+output from global scalars as input, accumulating them one element at
+a time.
+</P>
+<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
+of per-atom vectors. The per-atom quantities can be atom attributes
+such as position, velocity, force. They can also be per-atom
+quantities calculated by a <A HREF = "compute.html">compute</A>, by a
+<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
+time-averaged per-atom output of this fix can be used as input to
+other output commands.
+</P>
+<P>The <A HREF = "fix_store_state.html">fix store/state</A> command can archive one or
+more per-atom attributes at a particular time, so that the old values
+can be used in a future calculation or output. The list of atom
+attributes is the same as for the <A HREF = "dump.html">dump custom</A> command,
+including per-atom quantities calculated by a <A HREF = "compute.html">compute</A>,
+by a <A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>.
+The output of this fix can be used as input to other output commands.
+</P>
+<H5><A NAME = "compute"></A>Computes that generate values to output
+</H5>
+<P>Every <A HREF = "compute.html">compute</A> in LAMMPS produces either global or
+per-atom or local values. The values can be scalars or vectors or
+arrays of data. These values can be output using the other commands
+described in this section. The doc page for each compute command
+describes what it produces. Computes that produce per-atom or local
+values have the word "atom" or "local" in their style name. Computes
+without the word "atom" or "local" produce global values.
+</P>
+<H5><A NAME = "fix"></A>Fixes that generate values to output
+</H5>
+<P>Some <A HREF = "fix.html">fixes</A> in LAMMPS produces either global or per-atom or
+local values which can be accessed by other commands. The values can
+be scalars or vectors or arrays of data. These values can be output
+using the other commands described in this section. The doc page for
+each fix command tells whether it produces any output quantities and
+describes them.
+</P>
+<H5><A NAME = "variable"></A>Variables that generate values to output
+</H5>
+<P>Every <A HREF = "variable.html">variables</A> defined in an input script generates
+either a global scalar value or a per-atom vector (only atom-style
+variables) when it is accessed. The formulas used to define equal-
+and atom-style variables can contain references to the thermodynamic
+keywords and to global and per-atom data generated by computes, fixes,
+and other variables. The values generated by variables can be output
+using the other commands described in this section.
+</P>
+<H5><A NAME = "table"></A>Summary table of output options and data flow between commands
+</H5>
+<P>This table summarizes the various commands that can be used for
+generating output from LAMMPS. Each command produces output data of
+some kind and/or writes data to a file. Most of the commands can take
+data from other commands as input. Thus you can link many of these
+commands together in pipeline form, where data produced by one command
+is used as input to another command and eventually written to the
+screen or to a file. Note that to hook two commands together the
+output and input data types must match, e.g. global/per-atom/local
+data and scalar/vector/array data.
+</P>
+<P>Also note that, as described above, when a command takes a scalar as
+input, that could be an element of a vector or array. Likewise a
+vector input could be a column of an array.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "dump.html">dump local</A></TD><TD > local vectors</TD><TD > dump file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_print.html">fix print</A></TD><TD > global scalar from variable</TD><TD > screen, file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "print.html">print</A></TD><TD > global scalar from variable</TD><TD > screen</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "compute_slice.html">compute slice</A></TD><TD > global vectors/arrays</TD><TD > global vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_vector.html">fix vector</A></TD><TD > global scalars</TD><TD > global vector</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_ave_histo.html">fix ave/histo</A></TD><TD > global/per-atom/local scalars and vectors</TD><TD > global array, file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_ave_correlate.html">fix ave/correlate</A></TD><TD > global scalars</TD><TD > global array, file</TD><TD ></TD></TR>
+<TR><TD ><A HREF = "fix_store_state.html">fix store/state</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
+<TR><TD >
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "howto_16"></A><H4>6.16 Thermostatting, barostatting, and computing temperature
+</H4>
+<P>Thermostatting means controlling the temperature of particles in an MD
+simulation. Barostatting means controlling the pressure. Since the
+pressure includes a kinetic component due to particle velocities, both
+these operations require calculation of the temperature. Typically a
+target temperature (T) and/or pressure (P) is specified by the user,
+and the thermostat or barostat attempts to equilibrate the system to
+the requested T and/or P.
+</P>
+<P>Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant). Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motiion of particles) and its thermal velocity. The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+</P>
+<P>LAMMPS has several options for computing temperatures, any of which
+can be used in thermostatting and barostatting. These <A HREF = "compute.html">compute
+commands</A> calculate temperature, and the <A HREF = "compute_pressure.html">compute
+pressure</A> command calculates pressure.
+</P>
+<UL><LI><A HREF = "compute_temp.html">compute temp</A>
+<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
+<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
+<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
+<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
+<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
+<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
+<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
+<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
+</UL>
+<P>All but the first 3 calculate velocity biases directly (e.g. advection
+velocities) that are removed when computing the thermal temperature.
+<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
+temp/asphere</A> compute kinetic energy for
+finite-size particles that includes rotational degrees of freedom.
+They both allow for velocity biases indirectly, via an optional extra
+argument, another temperature compute that subtracts a velocity bias.
+This allows the translational velocity of spherical or aspherical
+particles to be adjusted in prescribed ways.
+</P>
+<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
+case by a pair style. Several thermostatting fixes are available:
+Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
+(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
+can be invoked via the <I>dpd/tstat</I> pair style:
+</P>
+<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
+<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
+<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
+<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
+<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
+<LI><A HREF = "fix_temp_csvr.html">fix temp/csvr</A>
+<LI><A HREF = "fix_langevin.html">fix langevin</A>
+<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
+<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
+</UL>
+<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
+particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion. See the <A HREF = "#howto_13">NEMD
+simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
+nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
+nvt/asphere</A> thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+</P>
+<P>DPD thermostatting alters pairwise interactions in a manner analagous
+to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>Any of the thermostatting fixes can use temperature computes that
+remove bias which has two effects. First, the current calculated
+temperature, which is compared to the requested target temperature, is
+caluclated with the velocity bias removed. Second, the thermostat
+adjusts only the thermal temperature component of the particle's
+velocities, which are the velocities with the bias removed. The
+removed bias is then added back to the adjusted velocities. See the
+doc pages for the individual fixes and for the
+<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
+a temperature compute to a thermostatting fix. For example, you can
+apply a thermostat to only the x and z components of velocity by using
+it in conjunction with <A HREF = "compute_temp_partial.html">compute
+temp/partial</A>. Of you could thermostat only
+the thermal temperature of a streaming flow of particles without
+affecting the streaming velocity, by using <A HREF = "compute_temp_profile.html">compute
+temp/profile</A>.
+</P>
+<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
+they update the velocities and positions of particles due to forces
+and velocities respectively. The other thermostat fixes only adjust
+velocities; they do NOT perform time integration updates. Thus they
+should be used in conjunction with a constant NVE integration fix such
+as these:
+</P>
+<UL><LI><A HREF = "fix_nve.html">fix nve</A>
+<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
+<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
+</UL>
+<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+</P>
+<UL><LI><A HREF = "fix_nh.html">fix npt</A>
+<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
+<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
+<LI><A HREF = "fix_nh.html">fix nph</A>
+<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
+</UL>
+<P>The <A HREF = "fix_nh.html">fix npt</A> commands include a Nose-Hoover thermostat
+and barostat. <A HREF = "fix_nh.html">Fix nph</A> is just a Nose/Hoover barostat;
+it does no thermostatting. Both <A HREF = "fix_nh.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
+press/bernendsen</A> can be used in conjunction
+with any of the thermostatting fixes.
+</P>
+<P>As with the thermostats, <A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_nh.html">fix
+nph</A> only use translational motion of the particles in
+computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
+npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
+npt/asphere</A> thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+</P>
+<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
+pressure</A> compute to calculate a current
+pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
+temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
+pressure</A> command), which is used to calculated
+the kinetic componenet of the pressure. The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic componenet which contributes to the current
+pressure. See the doc pages for the individual fixes and for the
+<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+</P>
+<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_nh.html">fix
+npt</A> and <A HREF = "fix_nh.html">fix nph</A>) perform time
+integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
+so it should be used with one of the constant NVE fixes or with one of
+the NVT fixes.
+</P>
+<P>Finally, thermodynamic output, which can be setup via the
+<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
+and pressure values. As explained on the doc page for the
+<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
+setup by the thermo command itself. They are NOT the ones associated
+with any thermostatting or barostatting fix you have defined or with
+any compute that calculates a temperature or pressure. Thus if you
+want to view these values of T and P, you need to specify them
+explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
+you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
+re-define what temperature or pressure compute is used for default
+thermodynamic output.
+</P>
+<HR>
+
+<A NAME = "howto_17"></A><H4>6.17 Walls
+</H4>
+<P>Walls in an MD simulation are typically used to bound particle motion,
+i.e. to serve as a boundary condition.
+</P>
+<P>Walls in LAMMPS can be of rough (made of particles) or idealized
+surfaces. Ideal walls can be smooth, generating forces only in the
+normal direction, or frictional, generating forces also in the
+tangential direction.
+</P>
+<P>Rough walls, built of particles, can be created in various ways. The
+particles themselves can be generated like any other particle, via the
+<A HREF = "lattice.html">lattice</A> and <A HREF = "create_atoms.html">create_atoms</A> commands,
+or read in via the <A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Their motion can be constrained by many different commands, so that
+they do not move at all, move together as a group at constant velocity
+or in response to a net force acting on them, move in a prescribed
+fashion (e.g. rotate around a point), etc. Note that if a time
+integration fix like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nvt</A>
+is not used with the group that contains wall particles, their
+positions and velocities will not be updated.
+</P>
+<UL><LI><A HREF = "fix_aveforce.html">fix aveforce</A> - set force on particles to average value, so they move together
+<LI><A HREF = "fix_setforce.html">fix setforce</A> - set force on particles to a value, e.g. 0.0
+<LI><A HREF = "fix_freeze.html">fix freeze</A> - freeze particles for use as granular walls
+<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - advect particles by their velocity, but without force
+<LI><A HREF = "fix_move.html">fix move</A> - prescribe motion of particles by a linear velocity, oscillation, rotation, variable
+</UL>
+<P>The <A HREF = "fix_move.html">fix move</A> command offers the most generality, since
+the motion of individual particles can be specified with
+<A HREF = "variable.html">variable</A> formula which depends on time and/or the
+particle position.
+</P>
+<P>For rough walls, it may be useful to turn off pairwise interactions
+between wall particles via the <A HREF = "neigh_modify.html">neigh_modify
+exclude</A> command.
+</P>
+<P>Rough walls can also be created by specifying frozen particles that do
+not move and do not interact with mobile particles, and then tethering
+other particles to the fixed particles, via a <A HREF = "bond_style.html">bond</A>.
+The bonded particles do interact with other mobile particles.
+</P>
+<P>Idealized walls can be specified via several fix commands. <A HREF = "fix_wall_gran.html">Fix
+wall/gran</A> creates frictional walls for use with
+granular particles; all the other commands create smooth walls.
+</P>
+<UL><LI><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> - reflective flat walls
+<LI><A HREF = "fix_wall.html">fix wall/lj93</A> - flat walls, with Lennard-Jones 9/3 potential
+<LI><A HREF = "fix_wall.html">fix wall/lj126</A> - flat walls, with Lennard-Jones 12/6 potential
+<LI><A HREF = "fix_wall.html">fix wall/colloid</A> - flat walls, with <A HREF = "pair_colloid.html">pair_style colloid</A> potential
+<LI><A HREF = "fix_wall.html">fix wall/harmonic</A> - flat walls, with repulsive harmonic spring potential
+<LI><A HREF = "fix_wall_region.html">fix wall/region</A> - use region surface as wall
+<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - flat or curved walls with <A HREF = "pair_gran.html">pair_style granular</A> potential
+</UL>
+<P>The <I>lj93</I>, <I>lj126</I>, <I>colloid</I>, and <I>harmonic</I> styles all allow the
+flat walls to move with a constant velocity, or oscillate in time.
+The <A HREF = "fix_wall_region.html">fix wall/region</A> command offers the most
+generality, since the region surface is treated as a wall, and the
+geometry of the region can be a simple primitive volume (e.g. a
+sphere, or cube, or plane), or a complex volume made from the union
+and intersection of primitive volumes. <A HREF = "region.html">Regions</A> can also
+specify a volume "interior" or "exterior" to the specified primitive
+shape or <I>union</I> or <I>intersection</I>. <A HREF = "region.html">Regions</A> can also be
+"dynamic" meaning they move with constant velocity, oscillate, or
+rotate.
+</P>
+<P>The only frictional idealized walls currently in LAMMPS are flat or
+curved surfaces specified by the <A HREF = "fix_wall_gran.html">fix wall/gran</A>
+command. At some point we plan to allow regoin surfaces to be used as
+frictional walls, as well as triangulated surfaces.
+</P>
+<HR>
+
+<A NAME = "howto_18"></A><H4>6.18 Elastic constants
+</H4>
+<P>Elastic constants characterize the stiffness of a material. The formal
+definition is provided by the linear relation that holds between the
+stress and strain tensors in the limit of infinitesimal deformation.
+In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
+the repeated indices imply summation. s_ij are the elements of the
+symmetric stress tensor. e_kl are the elements of the symmetric strain
+tensor. C_ijkl are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has 3^4=81 elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
+is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
+derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
+most 7*6/2 = 21 distinct elements.
+</P>
+<P>At zero temperature, it is easy to estimate these derivatives by
+deforming the simulation box in one of the six directions using the
+<A HREF = "change_box.html">change_box</A> command and measuring the change in the
+stress tensor. A general-purpose script that does this is given in the
+examples/elastic directory described in <A HREF = "Section_example.html">this
+section</A>.
+</P>
+<P>Calculating elastic constants at finite temperature is more
+challenging, because it is necessary to run a simulation that perfoms
+time averages of differential properties. One way to do this is to
+measure the change in average stress tensor in an NVT simulations when
+the cell volume undergoes a finite deformation. In order to balance
+the systematic and statistical errors in this method, the magnitude of
+the deformation must be chosen judiciously, and care must be taken to
+fully equilibrate the deformed cell before sampling the stress
+tensor. Another approach is to sample the triclinic cell fluctuations
+that occur in an NPT simulation. This method can also be slow to
+converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
+</P>
+<HR>
+
+<A NAME = "howto_19"></A><H4>6.19 Library interface to LAMMPS
+</H4>
+<P>As described in <A HREF = "Section_start.html#start_5">Section_start 5</A>, LAMMPS
+can be built as a library, so that it can be called by another code,
+used in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other
+codes, or driven through a <A HREF = "Section_python.html">Python interface</A>.
+</P>
+<P>All of these methodologies use a C-style interface to LAMMPS that is
+provided in the files src/library.cpp and src/library.h. The
+functions therein have a C-style argument list, but contain C++ code
+you could write yourself in a C++ application that was invoking LAMMPS
+directly. The C++ code in the functions illustrates how to invoke
+internal LAMMPS operations. Note that LAMMPS classes are defined
+within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
+application.
+</P>
+<P>Library.cpp contains these 4 functions:
+</P>
+<PRE>void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_close(void *)
+void lammps_file(void *, char *)
+char *lammps_command(void *, char *)
+</PRE>
+<P>The lammps_open() function is used to initialize LAMMPS, passing in a
+list of strings as if they were <A HREF = "Section_start.html#start_7">command-line
+arguments</A> when LAMMPS is run in
+stand-alone mode from the command line, and a MPI communicator for
+LAMMPS to run under. It returns a ptr to the LAMMPS object that is
+created, and which is used in subsequent library calls. The
+lammps_open() function can be called multiple times, to create
+multiple instances of LAMMPS.
+</P>
+<P>LAMMPS will run on the set of processors in the communicator. This
+means the calling code can run LAMMPS on all or a subset of
+processors. For example, a wrapper script might decide to alternate
+between LAMMPS and another code, allowing them both to run on all the
+processors. Or it might allocate half the processors to LAMMPS and
+half to the other code and run both codes simultaneously before
+syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+</P>
+<P>The lammps_close() function is used to shut down an instance of LAMMPS
+and free all its memory.
+</P>
+<P>The lammps_file() and lammps_command() functions are used to pass a
+file or string to LAMMPS as if it were an input script or single
+command in an input script. Thus the calling code can read or
+generate a series of LAMMPS commands one line at a time and pass it
+thru the library interface to setup a problem and then run it,
+interleaving the lammps_command() calls with other calls to extract
+information from LAMMPS, perform its own operations, or call another
+code's library.
+</P>
+<P>Other useful functions are also included in library.cpp. For example:
+</P>
+<PRE>void *lammps_extract_global(void *, char *)
+void *lammps_extract_atom(void *, char *)
+void *lammps_extract_compute(void *, char *, int, int)
+void *lammps_extract_fix(void *, char *, int, int, int, int)
+void *lammps_extract_variable(void *, char *, char *)
+int lammps_set_variable(void *, char *, char *)
+int lammps_get_natoms(void *)
+void lammps_get_coords(void *, double *)
+void lammps_put_coords(void *, double *)
+</PRE>
+<P>These can extract various global or per-atom quantities from LAMMPS as
+well as values calculated by a compute, fix, or variable. The
+"set_variable" function can set an existing string-style variable to a
+new value, so that subsequent LAMMPS commands can access the variable.
+The "get" and "put" operations can retrieve and reset atom
+coordinates. See the library.cpp file and its associated header file
+library.h for details.
+</P>
+<P>The key idea of the library interface is that you can write any
+functions you wish to define how your code talks to LAMMPS and add
+them to src/library.cpp and src/library.h, as well as to the <A HREF = "Section_python.html">Python
+interface</A>. The routines you add can access or
+change any LAMMPS data you wish. The examples/COUPLE and python
+directories have example C++ and C and Python codes which show how a
+driver code can link to LAMMPS as a library, run LAMMPS on a subset of
+processors, grab data from LAMMPS, change it, and put it back into
+LAMMPS.
+</P>
+<HR>
+
+<A NAME = "howto_20"></A><H4>6.20 Calculating thermal conductivity
+</H4>
+<P>The thermal conductivity kappa of a material can be measured in at
+least 4 ways using various options in LAMMPS. See the examples/KAPPA
+directory for scripts that implement the 4 methods discussed here for
+a simple Lennard-Jones fluid model. Also, see <A HREF = "Section_howto.html#howto_21">this
+section</A> of the manual for an analogous
+discussion for viscosity.
+</P>
+<P>The thermal conducitivity tensor kappa is a measure of the propensity
+of a material to transmit heat energy in a diffusive manner as given
+by Fourier's law
+</P>
+<P>J = -kappa grad(T)
+</P>
+<P>where J is the heat flux in units of energy per area per time and
+grad(T) is the spatial gradient of temperature. The thermal
+conductivity thus has units of energy per distance per time per degree
+K and is often approximated as an isotropic quantity, i.e. as a
+scalar.
+</P>
+<P>The first method is to setup two thermostatted regions at opposite
+ends of a simulation box, or one in the middle and one at the end of a
+periodic box. By holding the two regions at different temperatures
+with a <A HREF = "Section_howto.html#howto_13">thermostatting fix</A>, the energy
+added to the hot region should equal the energy subtracted from the
+cold region and be proportional to the heat flux moving between the
+regions. See the paper by <A HREF = "#Ikeshoji">Ikeshoji and Hafskjold</A> for
+details of this idea. Note that thermostatting fixes such as <A HREF = "fix_nh.html">fix
+nvt</A>, <A HREF = "fix_langevin.html">fix langevin</A>, and <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A> store the cumulative energy they
+add/subtract.
+</P>
+<P>Alternatively, as a second method, the <A HREF = "fix_heat.html">fix heat</A>
+command can used in place of thermostats on each of two regions to
+add/subtract specified amounts of energy to both regions. In both
+cases, the resulting temperatures of the two regions can be monitored
+with the "compute temp/region" command and the temperature profile of
+the intermediate region can be monitored with the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> and <A HREF = "compute_ke_atom.html">compute
+ke/atom</A> commands.
+</P>
+<P>The third method is to perform a reverse non-equilibrium MD simulation
+using the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
+command which implements the rNEMD algorithm of Muller-Plathe.
+Kinetic energy is swapped between atoms in two different layers of the
+simulation box. This induces a temperature gradient between the two
+layers which can be monitored with the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> and <A HREF = "compute_ke_atom.html">compute
+ke/atom</A> commands. The fix tallies the
+cumulative energy transfer that it performs. See the <A HREF = "fix_thermal_conductivity.html">fix
+thermal/conductivity</A> command for
+details.
+</P>
+<P>The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the heat flux
+to kappa. The heat flux can be calculated from the fluctuations of
+per-atom potential and kinetic energies and per-atom stress tensor in
+a steady-state equilibrated simulation. This is in contrast to the
+two preceding non-equilibrium methods, where energy flows continuously
+between hot and cold regions of the simulation box.
+</P>
+<P>The <A HREF = "compute_heat_flux.html">compute heat/flux</A> command can calculate
+the needed heat flux and describes how to implement the Green_Kubo
+formalism using additional LAMMPS commands, such as the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A> command to calculate the needed
+auto-correlation. See the doc page for the <A HREF = "compute_heat_flux.html">compute
+heat/flux</A> command for an example input script
+that calculates the thermal conductivity of solid Ar via the GK
+formalism.
+</P>
+<HR>
+
+<A NAME = "howto_21"></A><H4>6.21 Calculating viscosity
+</H4>
+<P>The shear viscosity eta of a fluid can be measured in at least 4 ways
+using various options in LAMMPS. See the examples/VISCOSITY directory
+for scripts that implement the 4 methods discussed here for a simple
+Lennard-Jones fluid model. Also, see <A HREF = "Section_howto.html#howto_20">this
+section</A> of the manual for an analogous
+discussion for thermal conductivity.
+</P>
+<P>Eta is a measure of the propensity of a fluid to transmit momentum in
+a direction perpendicular to the direction of velocity or momentum
+flow. Alternatively it is the resistance the fluid has to being
+sheared. It is given by
+</P>
+<P>J = -eta grad(Vstream)
+</P>
+<P>where J is the momentum flux in units of momentum per area per time.
+and grad(Vstream) is the spatial gradient of the velocity of the fluid
+moving in another direction, normal to the area through which the
+momentum flows. Viscosity thus has units of pressure-time.
+</P>
+<P>The first method is to perform a non-equlibrium MD (NEMD) simulation
+by shearing the simulation box via the <A HREF = "fix_deform.html">fix deform</A>
+command, and using the <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command to
+thermostat the fluid via the SLLOD equations of motion.
+Alternatively, as a second method, one or more moving walls can be
+used to shear the fluid in between them, again with some kind of
+thermostat that modifies only the thermal (non-shearing) components of
+velocity to prevent the fluid from heating up.
+</P>
+<P>In both cases, the velocity profile setup in the fluid by this
+procedure can be monitored by the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> command, which determines
+grad(Vstream) in the equation above. E.g. the derivative in the
+y-direction of the Vx component of fluid motion or grad(Vstream) =
+dVx/dy. The Pxy off-diagonal component of the pressure or stress
+tensor, as calculated by the <A HREF = "compute_pressure.html">compute pressure</A>
+command, can also be monitored, which is the J term in the equation
+above. See <A HREF = "Section_howto.html#howto_13">this section</A> of the manual
+for details on NEMD simulations.
+</P>
+<P>The third method is to perform a reverse non-equilibrium MD simulation
+using the <A HREF = "fix_viscosity.html">fix viscosity</A> command which implements
+the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
+swapped between atoms in two different layers of the simulation box in
+a different dimension. This induces a velocity gradient which can be
+monitored with the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
+The fix tallies the cummulative momentum transfer that it performs.
+See the <A HREF = "fix_viscosity.html">fix viscosity</A> command for details.
+</P>
+<P>The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the
+stress/pressure tensor to eta. This can be done in a steady-state
+equilibrated simulation which is in contrast to the two preceding
+non-equilibrium methods, where momentum flows continuously through the
+simulation box.
+</P>
+<P>Here is an example input script that calculates the viscosity of
+liquid Ar via the GK formalism:
+</P>
+<PRE># Sample LAMMPS input script for viscosity of liquid Ar
+</PRE>
+<PRE>units real
+variable T equal 86.4956
+variable V equal vol
+variable dt equal 4.0
+variable p equal 400 # correlation length
+variable s equal 5 # sample interval
+variable d equal $p*$s # dump interval
+</PRE>
+<PRE># convert from LAMMPS real units to SI
+</PRE>
+<PRE>variable kB equal 1.3806504e-23 # [J/K/</B> Boltzmann
+variable atm2Pa equal 101325.0
+variable A2m equal 1.0e-10
+variable fs2s equal 1.0e-15
+variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
+</PRE>
+<PRE># setup problem
+</PRE>
+<PRE>dimension 3
+boundary p p p
+lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+region box block 0 4 0 4 0 4
+create_box 1 box
+create_atoms 1 box
+mass 1 39.948
+pair_style lj/cut 13.0
+pair_coeff * * 0.2381 3.405
+timestep ${dt}
+thermo $d
+</PRE>
+<PRE># equilibration and thermalization
+</PRE>
+<PRE>velocity all create $T 102486 mom yes rot yes dist gaussian
+fix NVT all nvt temp $T $T 10 drag 0.2
+run 8000
+</PRE>
+<PRE># viscosity calculation, switch to NVE if desired
+</PRE>
+<PRE>#unfix NVT
+#fix NVE all nve
+</PRE>
+<PRE>reset_timestep 0
+variable pxy equal pxy
+variable pxz equal pxz
+variable pyz equal pyz
+fix SS all ave/correlate $s $p $d &
+ v_pxy v_pxz v_pyz type auto file S0St.dat ave running
+variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
+variable v11 equal trap(f_SS[3])*${scale}
+variable v22 equal trap(f_SS[4])*${scale}
+variable v33 equal trap(f_SS[5])*${scale}
+thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
+run 100000
+variable v equal (v_v11+v_v22+v_v33)/3.0
+variable ndens equal count(all)/vol
+print "average viscosity: $v [Pa.s/</B> @ $T K, ${ndens} /A^3"
+</PRE>
+<HR>
+
+<A NAME = "howto_22"></A><H4>6.22 Calculating a diffusion coefficient
+</H4>
+<P>The diffusion coefficient D of a material can be measured in at least
+2 ways using various options in LAMMPS. See the examples/DIFFUSE
+directory for scripts that implement the 2 methods discussed here for
+a simple Lennard-Jones fluid model.
+</P>
+<P>The first method is to measure the mean-squared displacement (MSD) of
+the system, via the <A HREF = "compute_msd.html">compute msd</A> command. The slope
+of the MSD versus time is proportional to the diffusion coefficient.
+The instantaneous MSD values can be accumulated in a vector via the
+<A HREF = "fix_vector.html">fix vector</A> command, and a line fit to the vector to
+compute its slope via the <A HREF = "variable.html">variable slope</A> function, and
+thus extract D.
+</P>
+<P>The second method is to measure the velocity auto-correlation function
+(VACF) of the system, via the <A HREF = "compute_vacf.html">compute vacf</A>
+command. The time-integral of the VACF is proportional to the
+diffusion coefficient. The instantaneous VACF values can be
+accumulated in a vector via the <A HREF = "fix_vector.html">fix vector</A> command,
+and time integrated via the <A HREF = "variable.html">variable trap</A> function,
+and thus extract D.
+</P>
+<HR>
+
+<A NAME = "howto_23"></A><H4>6.23 Using chunks to calculate system properties
+</H4>
+<P>In LAMMS, "chunks" are collections of atoms, as defined by the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command, which assigns
+each atom to a chunk ID (or to no chunk at all). The number of chunks
+and the assignment of chunk IDs to atoms can be static or change over
+time. Examples of "chunks" are molecules or spatial bins or atoms
+with similar values (e.g. coordination number or potential energy).
+</P>
+<P>The per-atom chunk IDs can be used as input to two other kinds of
+commands, to calculate various properties of a system:
+</P>
+<UL><LI><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
+<LI>any of the <A HREF = "compute.html">compute */chunk</A> commands
+</UL>
+<P>Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed. Then some examples are given of how to compute different
+properties with chunk commands.
+</P>
+<H5>Compute chunk/atom command:
+</H5>
+<P>This compute can assign atoms to chunks of various styles. Only atoms
+in the specified group and optional specified region are assigned to a
+chunk. Here are some possible chunk definitions:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >atoms in same molecule </TD><TD > chunk ID = molecule ID </TD></TR>
+<TR><TD >atoms of same atom type </TD><TD > chunk ID = atom type </TD></TR>
+<TR><TD >all atoms with same atom property (charge, radius, etc) </TD><TD > chunk ID = output of compute property/atom </TD></TR>
+<TR><TD >atoms in same cluster </TD><TD > chunk ID = output of <A HREF = "compute_cluster_atom.html">compute cluster/atom</A> command </TD></TR>
+<TR><TD >atoms in same spatial bin </TD><TD > chunk ID = bin ID </TD></TR>
+<TR><TD >atoms in same rigid body </TD><TD > chunk ID = molecule ID used to define rigid bodies </TD></TR>
+<TR><TD >atoms with similar potential energy </TD><TD > chunk ID = output of <A HREF = "compute_pe_atom.html">compute pe/atom</A> </TD></TR>
+<TR><TD >atoms with same local defect structure </TD><TD > chunk ID = output of <A HREF = "compute_centro_atom.html">compute centro/atom</A> or <A HREF = "compute_coord_atom.html">compute coord/atom</A> command
+</TD></TR></TABLE></DIV>
+
+<P>Note that chunk IDs are integer values, so for atom properties or
+computes that produce a floating point value, they will be truncated
+to an integer. You could also use the compute in a variable that
+scales the floating point value to spread it across multiple intergers.
+</P>
+<P>Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+</P>
+<P>This compute also calculates the number of chunks <I>Nchunk</I>, which is
+used by other commands to tally per-chunk data. <I>Nchunk</I> can be a
+static value or change over time (e.g. the number of clusters). The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+</P>
+<P>Note that this compute allows the per-atom output of other
+<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
+<A HREF = "variable.html">variables</A> to be used to define chunk IDs for each
+atom. This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID. See
+<A HREF = "Section_modify.html">Section_modify</A> of the documentation for how to
+do this. You can also define a <A HREF = "variable.html">per-atom variable</A> in
+the input script that uses a formula to generate a chunk ID for each
+atom.
+</P>
+<H5>Fix ave/chunk command:
+</H5>
+<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command as input. For each chunk,
+it then sums one or more specified per-atom values over the atoms in
+each chunk. The per-atom values can be any atom property, such as
+velocity, force, charge, potential energy, kinetic energy, stress,
+etc. Additional keywords are defined for per-chunk properties like
+density and temperature. More generally any per-atom value generated
+by other <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and <A HREF = "variable.html">per-atom
+variables</A>, can be summed over atoms in each chunk.
+</P>
+<P>Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file. The
+fix produces a global array as output with one row of values per
+chunk.
+</P>
+<H5>Compute */chunk commands:
+</H5>
+<P>Currently the following computes operate on chunks of atoms to produce
+per-chunk values.
+</P>
+<UL><LI><A HREF = "compute_com_chunk.html">compute com/chunk</A>
+<LI><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
+<LI><A HREF = "compute_inertia_chunk.html">compute inertia/chunk</A>
+<LI><A HREF = "compute_msd_chunk.html">compute msd/chunk</A>
+<LI><A HREF = "compute_property_chunk.html">compute property/chunk</A>
+<LI><A HREF = "compute_temp_chunk.html">compute temp/chunk</A>
+<LI><A HREF = "compute_vcm_chunk.html">compute torque/chunk</A>
+<LI><A HREF = "compute_vcm_chunk.html">compute vcm/chunk</A>
+</UL>
+<P>They each take the ID of a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command as input. As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, temperature, torque,
+and velocity of center-of-mass for each chunk of atoms. The <A HREF = "compute_property_chunk.html">compute
+property/chunk</A> command can tally the
+count of atoms in each chunk and extract other per-chunk properties.
+</P>
+<P>The reason these various calculations are not part of the <A HREF = "fix_ave_chunk.html">fix
+ave/chunk command</A>, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk. For example, many of them require calculation
+of a center of mass, which requires summing mass*position over the
+atoms and then dividing by summed mass.
+</P>
+<P>All of these computes produce a global vector or global array as
+output, wih one or more values per chunk. They can be used
+in various ways:
+</P>
+<UL><LI>As input to the <A HREF = "fix_ave_time.html">fix ave/time</A> command, which can
+write the values to a file and optionally time average them.
+
+<LI>As input to the <A HREF = "fix_ave_histo.html">fix ave/histo</A> command to
+histogram values across chunks. E.g. a histogram of cluster sizes or
+molecule diffusion rates.
+
+<LI>As input to special functions of <A HREF = "variable.html">equal-style
+variables</A>, like sum() and max(). E.g. to find the
+largest cluster or fastest diffusing molecule.
+</UL>
+<H5>Example calculations with chunks
+</H5>
+<P>Here are eaxmples using chunk commands to calculate various
+properties:
+</P>
+<P>(1) Average velocity in each of 1000 2d spatial bins:
+</P>
+<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
+fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
+</PRE>
+<P>(2) Temperature in each spatial bin, after subtracting a flow
+velocity:
+</P>
+<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
+compute vbias all temp/profile 1 0 0 y 10
+fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
+</PRE>
+<P>(3) Center of mass of each molecule:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P>(4) Total force on each molecule and ave/max across all molecules:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1<B>2</B>)
+variable xmax equal max(f_1<B>2</B>)
+thermo 1000
+thermo_style custom step temp v_xave v_xmax
+</PRE>
+<P>(5) Histogram of cluster sizes:
+</P>
+<PRE>compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
+</PRE>
+<HR>
+
+<A NAME = "howto_24"></A><H4>6.24 Setting parameters for the <A HREF = "kspace_style.html">kspace_style pppm/disp</A> command
+</H4>
+<P>The PPPM method computes interactions by splitting the pair potential
+into two parts, one of which is computed in a normal pairwise fashion,
+the so-called real-space part, and one of which is computed using the
+Fourier transform, the so called reciprocal-space or kspace part. For
+both parts, the potential is not computed exactly but is approximated.
+Thus, there is an error in both parts of the computation, the
+real-space and the kspace error. The just mentioned facts are true
+both for the PPPM for Coulomb as well as dispersion interactions. The
+deciding difference - and also the reason why the parameters for
+pppm/disp have to be selected with more care - is the impact of the
+errors on the results: The kspace error of the PPPM for Coulomb and
+dispersion interaction and the real-space error of the PPPM for
+Coulomb interaction have the character of noise. In contrast, the
+real-space error of the PPPM for dispersion has a clear physical
+interpretation: the underprediction of cohesion. As a consequence, the
+real-space error has a much stronger effect than the kspace error on
+simulation results for pppm/disp. Parameters must thus be chosen in a
+way that this error is much smaller than the kspace error.
+</P>
+<P>When using pppm/disp and not making any specifications on the PPPM
+parameters via the kspace modify command, parameters will be tuned
+such that the real-space error and the kspace error are equal. This
+will result in simulations that are either inaccurate or slow, both of
+which is not desirable. For selecting parameters for the pppm/disp
+that provide fast and accurate simulations, there are two approaches,
+which both have their up- and downsides.
+</P>
+<P>The first approach is to set desired real-space an kspace accuracies
+via the <I>kspace_modify force/disp/real</I> and <I>kspace_modify
+force/disp/kspace</I> commands. Note that the accuracies have to be
+specified in force units and are thus dependend on the chosen unit
+settings. For real units, 0.0001 and 0.002 seem to provide reasonable
+accurate and efficient computations for the real-space and kspace
+accuracies. 0.002 and 0.05 work well for most systems using lj
+units. PPPM parameters will be generated based on the desired
+accuracies. The upside of this approach is that it usually provides a
+good set of parameters and will work for both the <I>kspace_modify diff
+ad</I> and <I>kspace_modify diff ik</I> options. The downside of the method
+is that setting the PPPM parameters will take some time during the
+initialization of the simulation.
+</P>
+<P>The second approach is to set the parameters for the pppm/disp
+explicitly using the <I>kspace_modify mesh/disp</I>, <I>kspace_modify
+order/disp</I>, and <I>kspace_modify gewald/disp</I> commands. This approach
+requires a more experienced user who understands well the impact of
+the choice of parameters on the simulation accuracy and
+performance. This approach provides a fast initialization of the
+simulation. However, it is sensitive to errors: A combination of
+parameters that will perform well for one system might result in
+far-from-optimal conditions for other simulations. For example,
+parametes that provide accurate and fast computations for
+all-atomistic force fields can provide insufficient accuracy or
+united-atomistic force fields (which is related to that the latter
+typically have larger dispersion coefficients).
+</P>
+<P>To avoid inaccurate or inefficient simulations, the pppm/disp stops
+simulations with an error message if no action is taken to control the
+PPPM parameters. If the automatic parameter generation is desired and
+real-space and kspace accuracies are desired to be equal, this error
+message can be suppressed using the <I>kspace_modify disp/auto yes</I>
+command.
+</P>
+<P>A reasonable approach that combines the upsides of both methods is to
+make the first run using the <I>kspace_modify force/disp/real</I> and
+<I>kspace_modify force/disp/kspace</I> commands, write down the PPPM
+parameters from the outut, and specify these parameters using the
+second approach in subsequent runs (which have the same composition,
+force field, and approximately the same volume).
+</P>
+<P>Concerning the performance of the pppm/disp there are two more things
+to consider. The first is that when using the pppm/disp, the cutoff
+parameter does no longer affect the accuracy of the simulation
+(subject to that gewald/disp is adjusted when changing the cutoff).
+The performance can thus be increased by examining different values
+for the cutoff parameter. A lower bound for the cutoff is only set by
+the truncation error of the repulsive term of pair potentials.
+</P>
+<P>The second is that the mixing rule of the pair style has an impact on
+the computation time when using the pppm/disp. Fastest computations
+are achieved when using the geometric mixing rule. Using the
+arithmetic mixing rule substantially increases the computational cost.
+The computational overhead can be reduced using the <I>kspace_modify
+mix/disp geom</I> and <I>kspace_modify splittol</I> commands. The first
+command simply enforces geometric mixing of the dispersion
+coeffiecients in kspace computations. This introduces some error in
+the computations but will also significantly speed-up the
+simulations. The second keyword sets the accuracy with which the
+dispersion coefficients are approximated using a matrix factorization
+approach. This may result in better accuracy then using the first
+command, but will usually also not provide an equally good increase of
+efficiency.
+</P>
+<P>Finally, pppm/disp can also be used when no mixing rules apply.
+This can be achieved using the <I>kspace_modify mix/disp none</I> command.
+Note that the code does not check automatically whether any mixing
+rule is fulfilled. If mixing rules do not apply, the user will have
+to specify this command explicitly.
+</P>
+<HR>
+
+<A NAME = "howto_25"></A><H4>6.25 Polarizable models
+</H4>
+<P>In polarizable force fields the charge distributions in molecules and
+materials respond to their electrostatic environements. Polarizable
+systems can be simulated in LAMMPS using three methods:
+</P>
+<UL><LI>the fluctuating charge method, implemented in the <A HREF = "fix_qeq.html">QEQ</A>
+package,
+
+<LI>the adiabatic core-shell method, implemented in the
+<A HREF = "#howto_26">CORESHELL</A> package,
+
+<LI>the thermalized Drude dipole method, implemented in the
+<A HREF = "#howto_27">USER-DRUDE</A> package.
+</UL>
+<P>The fluctuating charge method calculates instantaneous charges on
+interacting atoms based on the electronegativity equalization
+principle. It is implemented in the <A HREF = "fix_qeq.html">fix qeq</A> which is
+available in several variants. It is a relatively efficient technique
+since no additional particles are introduced. This method allows for
+charge transfer between molecules or atom groups. However, because the
+charges are located at the interaction sites, off-plane components of
+polarization cannot be represented in planar molecules or atom groups.
+</P>
+<P>The two other methods share the same basic idea: polarizable atoms are
+split into one core atom and one satellite particle (called shell or
+Drude particle) attached to it by a harmonic spring. Both atoms bear
+a charge and they represent collectively an induced electric dipole.
+These techniques are computationally more expensive than the QEq
+method because of additional particles and bonds. These two
+charge-on-spring methods differ in certain features, with the
+core-shell model being normally used for ionic/crystalline materials,
+whereas the so-called Drude model is normally used for molecular
+systems and fluid states.
+</P>
+<P>The core-shell model is applicable to crystalline materials where the
+high symmetry around each site leads to stable trajectories of the
+core-shell pairs. However, bonded atoms in molecules can be so close
+that a core would interact too strongly or even capture the Drude
+particle of a neighbor. The Drude dipole model is relatively more
+complex in order to remediate this and other issues. Specifically, the
+Drude model includes specific thermostating of the core-Drude pairs
+and short-range damping of the induced dipoles.
+</P>
+<P>The three polarization methods can be implemented through a
+self-consistent calculation of charges or induced dipoles at each
+timestep. In the fluctuating charge scheme this is done by the matrix
+inversion method in <A HREF = "fix_qeq.html">fix qeq/point</A>, but for core-shell
+or Drude-dipoles the relaxed-dipoles technique would require an slow
+iterative procedure. These self-consistent solutions yield accurate
+trajectories since the additional degrees of freedom representing
+polarization are massless. An alternative is to attribute a mass to
+the additional degrees of freedom and perform time integration using
+an extended Lagrangian technique. For the fluctuating charge scheme
+this is done by <A HREF = "fix_qeq.html">fix qeq/dynamic</A>, and for the
+charge-on-spring models by the methods outlined in the next two
+sections. The assignment of masses to the additional degrees of
+freedom can lead to unphysical trajectories if care is not exerted in
+choosing the parameters of the poarizable models and the simulation
+conditions.
+</P>
+<P>In the core-shell model the vibration of the shells is kept faster
+than the ionic vibrations to mimic the fast response of the
+polarizable electrons. But in molecular systems thermalizing the
+core-Drude pairs at temperatures comparable to the rest of the
+simulation leads to several problems (kinetic energy transfer, too
+short a timestep, etc.) In order to avoid these problems the relative
+motion of the Drude particles with respect to their cores is kept
+"cold" so the vibration of the core-Drude pairs is very slow,
+approaching the self-consistent regime. In both models the
+temperature is regulated using the velocities of the center of mass of
+core+shell (or Drude) pairs, but in the Drude model the actual
+relative core-Drude particle motion is thermostated separately as
+well.
+</P>
+<HR>
+
+<A NAME = "howto_26"></A><H4>6.26 Adiabatic core/shell model
+</H4>
+<P>The adiabatic core-shell model by <A HREF = "#MitchellFinchham">Mitchell and
+Finchham</A> is a simple method for adding
+polarizability to a system. In order to mimic the electron shell of
+an ion, a satellite particle is attached to it. This way the ions are
+split into a core and a shell where the latter is meant to react to
+the electrostatic environment inducing polarizability.
+</P>
+<P>Technically, shells are attached to the cores by a spring force f =
+k*r where k is a parametrized spring constant and r is the distance
+between the core and the shell. The charges of the core and the shell
+add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
+similar fashion the mass of the ion is distributed on the core and the
+shell with the core having the larger mass.
+</P>
+<P>To run this model in LAMMPS, <A HREF = "atom_style.html">atom_style</A> <I>full</I> can
+be used since atom charge and bonds are needed. Each kind of
+core/shell pair requires two atom types and a bond type. The core and
+shell of a core/shell pair should be bonded to each other with a
+harmonic bond that provides the spring force. For example, a data file
+for NaCl, as found in examples/coreshell, has this format:
+</P>
+<PRE>432 atoms # core and shell atoms
+216 bonds # number of core/shell springs
+</PRE>
+<PRE>4 atom types # 2 cores and 2 shells for Na and Cl
+2 bond types
+</PRE>
+<PRE>0.0 24.09597 xlo xhi
+0.0 24.09597 ylo yhi
+0.0 24.09597 zlo zhi
+</PRE>
+<PRE>Masses # core/shell mass ratio = 0.1
+</PRE>
+<PRE>1 20.690784 # Na core
+2 31.90500 # Cl core
+3 2.298976 # Na shell
+4 3.54500 # Cl shell
+</PRE>
+<PRE>Atoms
+</PRE>
+<PRE>1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
+2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
+3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
+4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
+(...)
+</PRE>
+<PRE>Bonds # Bond topology for spring forces
+</PRE>
+<PRE>1 2 1 2 # spring for core/shell pair 1
+2 2 3 4 # spring for core/shell pair 2
+(...)
+</PRE>
+<P>Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
+defined between the shells. Coulombic interactions are defined
+between all cores and shells. If desired, additional bonds can be
+specified between cores.
+</P>
+<P>The <A HREF = "special_bonds.html">special_bonds</A> command should be used to
+turn-off the Coulombic interaction within core/shell pairs, since that
+interaction is set by the bond spring. This is done using the
+<A HREF = "special_bonds.html">special_bonds</A> command with a 1-2 weight = 0.0,
+which is the default value.
+</P>
+<P>Since the core/shell model permits distances of r = 0.0 between the
+core and shell, a pair style with a "cs" suffix needs to be used to
+implement a valid long-range Coulombic correction. Several such pair
+styles are provided in the CORESHELL package. See <A HREF = "pair_cs.html">this doc
+page</A> for details. All of the core/shell enabled pair
+styles require the use of a long-range Coulombic solver, as specified
+by the <A HREF = "kspace_style.html">kspace_style</A> command. Either the PPPM or
+Ewald solvers can be used.
+</P>
+<P>For the NaCL example problem, these pair style and bond style settings
+are used:
+</P>
+<PRE>pair_style born/coul/long/cs 20.0 20.0
+pair_coeff * * 0.0 1.000 0.00 0.00 0.00
+pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
+pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
+pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+</PRE>
+<PRE>bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+</PRE>
+<P>When running dynamics with the adiabatic core/shell model, the
+following issues should be considered. Since the relative motion of
+the core and shell particles corresponds to the polarization, typical
+thermostats can alter the polarization behaviour, meaining the shell
+will not react freely to its electrostatic environment. Therefore
+it's typically desirable to decouple the relative motion of the
+core/shell pair, which is an imaginary degree of freedom, from the
+real physical system. To do that, the <A HREF = "compute_temp_cs.html">compute
+temp/cs</A> command can be used, in conjunction with
+any of the thermostat fixes, such as <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin">fix
+langevin</A>. This compute uses the center-of-mass velocity
+of the core/shell pairs to calculate a temperature, and insures that
+velocity is what is rescaled for thermostatting purposes. The
+<A HREF = "compute_temp_cs.html">compute temp/cs</A> command requires input of two
+groups, one for the core atoms, another for the shell atoms. These
+can be defined using the <A HREF = "group.html">group <I>type</I></A> command. Note that
+to perform thermostatting using this definition of temperature, the
+<A HREF = "fix_modify.html">fix modify temp</A> command should be used to assign the
+comptue to the thermostat fix. Likewise the <A HREF = "thermo_modify.html">thermo_modify
+temp</A> command can be used to make this temperature
+be output for the overall system.
+</P>
+<P>For the NaCl example, this can be done as follows:
+</P>
+<PRE>group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
+fix thermostatequ all nve # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ # output of center-of-mass derived temperature
+</PRE>
+<P>When intializing the velocities of a system with core/shell pairs, it
+is also desirable to not introduce energy into the relative motion of
+the core/shell particles, but only assign a center-of-mass velocity to
+the pairs. This can be done by using the <I>bias</I> keyword of the
+<A HREF = "velocity.html">velocity create</A> command and assigning the <A HREF = "compute_temp_cs.html">compute
+temp/cs</A> command to the <I>temp</I> keyword of the
+<A HREF = "velocity.html">velocity</A> commmand, e.g.
+</P>
+<PRE>velocity all create 1427 134 bias yes temp CSequ
+velocity all scale 1427 temp CSequ
+</PRE>
+<P>It is important to note that the polarizability of the core/shell
+pairs is based on their relative motion. Therefore the choice of
+spring force and mass ratio need to ensure much faster relative motion
+of the 2 atoms within the core/shell pair than their center-of-mass
+velocity. This allow the shells to effectively react instantaneously
+to the electrostatic environment. This fast movement also limits the
+timestep size that can be used.
+</P>
+<P>Additionally, the mass mismatch of the core and shell particles means
+that only a small amount of energy is transfered to the decoupled
+imaginary degrees of freedom. However, this transfer will typically
+lead to a a small drift in total energy over time. This internal
+energy can be monitored using the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
+temp/chunk</A> commands. The internal kinetic
+energies of each core/shell pair can then be summed using the sum()
+special functino of the <A HREF = "variable.html">variable</A> command. Or they can
+be time/averaged and output using the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command. To use these commands, each core/shell pair must be defined
+as a "chunk". If each core/shell pair is defined as its own molecule,
+the molecule ID can be used to define the chunks. If cores are bonded
+to each other to form larger molecules, then another way to define the
+chunks is to use the <A HREF = "fix_property_atom.html">fix property/atom</A> to
+assign a core/shell ID to each atom via a special field in the data
+file read by the <A HREF = "read_data.html">read_data</A> command. This field can
+then be accessed by the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command, to use as input to
+the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command to define the
+core/shell pairs as chunks.
+</P>
+<P>For example,
+</P>
+<PRE>fix csinfo all property/atom i_CSID # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
+compute prop all property/atom i_CSID
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
+</PRE>
+<P>The additional section in the date file would be formatted like this:
+</P>
+<PRE>CS-Info # header of additional section
+</PRE>
+<PRE>1 1 # column 1 = atom ID, column 2 = core/shell ID
+2 1
+3 2
+4 2
+5 3
+6 3
+7 4
+8 4
+(...)
+</PRE>
+<HR>
+
+<A NAME = "howto_27"></A><H4>6.27 Drude induced dipoles
+</H4>
+<P>The thermalized Drude model, similarly to the <A HREF = "#howto_26">core-shell</A>
+model, representes induced dipoles by a pair of charges (the core atom
+and the Drude particle) connected by a harmonic spring. The Drude
+model has a number of features aimed at its use in molecular systems
+(<A HREF = "#Lamoureux">Lamoureux and Roux</A>):
+</P>
+<UL><LI>Thermostating of the additional degrees of freedom associated with the
+induced dipoles at very low temperature, in terms of the reduced
+coordinates of the Drude particles with respect to their cores. This
+makes the trajectory close to that of relaxed induced dipoles.
+
+<LI>Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
+pair represents a single (polarizable) atom, so the special screening
+factors in a covalent structure should be the same for the core and
+the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
+special neighbor relations from their respective cores.
+
+<LI>Stabilization of the interactions between induced dipoles. Drude
+dipoles on covalently bonded atoms interact too strongly due to the
+short distances, so an atom may capture the Drude particle of a
+neighbor, or the induced dipoles within the same molecule may align
+too much. To avoid this, damping at short range can be done by Thole
+functions (for which there are physical grounds). This Thole damping
+is applied to the point charges composing the induced dipole (the
+charge of the Drude particle and the opposite charge on the core, not
+to the total charge of the core atom).
+</UL>
+<P>A detailed tutorial covering the usage of Drude induced dipoles in
+LAMMPS is <A HREF = "tutorial_drude.html">available here</A>.
+</P>
+<P>As with the core-shell model, the cores and Drude particles should
+appear in the data file as standard atoms. The same holds for the
+springs between them, which are described by standard harmonic bonds.
+The nature of the atoms (core, Drude particle or non-polarizable) is
+specified via the <A HREF = "fix_drude.html">fix drude</A> command. The special
+list of neighbors is automatically refactored to account for the
+equivalence of core and Drude particles as regards special 1-2 to 1-4
+screening. It may be necessary to use the <I>extra</I> keyword of the
+<A HREF = "special_bonds.html">special_bonds</A> command. If using <A HREF = "fix_shake.html">fix
+shake</A>, make sure no Drude particle is in this fix
+group.
+</P>
+<P>There are two ways to thermostat the Drude particles at a low
+temperature: use either <A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
+for a Langevin thermostat, or <A HREF = "fix_drude_transform.html">fix
+drude/transform/*</A> for a Nose-Hoover
+thermostat. The former requires use of the command <A HREF = "comm_modify.html">comm_modify vel
+yes</A>. The latter requires two separate integration
+fixes like <I>nvt</I> or <I>npt</I>. The correct temperatures of the reduced
+degrees of freedom can be calculated using the <A HREF = "compute_temp_drude.html">compute
+temp/drude</A>. This requires also to use the
+command <I>comm_modify vel yes</I>.
+</P>
+<P>Short-range damping of the induced dipole interactions can be achieved
+using Thole functions through the the <A HREF = "pair_thole.html">pair style
+thole</A> in <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
+with a Coulomb pair style. It may be useful to use <I>coul/long/cs</I> or
+similar from the CORESHELL package if the core and Drude particle come
+too close, which can cause numerical issues.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "Berendsen"></A>
+
+<P><B>(Berendsen)</B> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+6269-6271 (1987).
+</P>
+<A NAME = "Cornell"></A>
+
+<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+</P>
+<A NAME = "Horn"></A>
+
+<P><B>(Horn)</B> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
+J Chem Phys, 120, 9665 (2004).
+</P>
+<A NAME = "Ikeshoji"></A>
+
+<P><B>(Ikeshoji)</B> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
+(1994).
+</P>
+<A NAME = "MacKerell"></A>
+
+<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+</P>
+<A NAME = "Mayo"></A>
+
+<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+</P>
+<A NAME = "Jorgensen"></A>
+
+<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+</P>
+<A NAME = "Price"></A>
+
+<P><B>(Price)</B> Price and Brooks, J Chem Phys, 121, 10096 (2004).
+</P>
+<A NAME = "Shinoda"></A>
+
+<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+</P>
+<A NAME = "MitchellFinchham"></A>
+
+<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+</P>
+<A NAME = "Lamoureux"></A>
+
+<P><B>(Lamoureux and Roux)</B> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
+</P>
+</HTML>
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+<HTML>
+<CENTER><A HREF = "Manual.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_start.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>1. Introduction
+</H3>
+<P>This section provides an overview of what LAMMPS can and can't do,
+describes what it means for LAMMPS to be an open-source code, and
+acknowledges the funding and people who have contributed to LAMMPS
+over the years.
+</P>
+1.1 <A HREF = "#intro_1">What is LAMMPS</A><BR>
+1.2 <A HREF = "#intro_2">LAMMPS features</A><BR>
+1.3 <A HREF = "#intro_3">LAMMPS non-features</A><BR>
+1.4 <A HREF = "#intro_4">Open source distribution</A><BR>
+1.5 <A HREF = "#intro_5">Acknowledgments and citations</A> <BR>
+
+<HR>
+
+<HR>
+
+<A NAME = "intro_1"></A><H4>1.1 What is LAMMPS
+</H4>
+<P>LAMMPS is a classical molecular dynamics code that models an ensemble
+of particles in a liquid, solid, or gaseous state. It can model
+atomic, polymeric, biological, metallic, granular, and coarse-grained
+systems using a variety of force fields and boundary conditions.
+</P>
+<P>For examples of LAMMPS simulations, see the Publications page of the
+<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
+</P>
+<P>LAMMPS runs efficiently on single-processor desktop or laptop
+machines, but is designed for parallel computers. It will run on any
+parallel machine that compiles C++ and supports the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPI</A>
+message-passing library. This includes distributed- or shared-memory
+parallel machines and Beowulf-style clusters.
+</P>
+
+
+<P>LAMMPS can model systems with only a few particles up to millions or
+billions. See <A HREF = "Section_perf.html">Section_perf</A> for information on
+LAMMPS performance and scalability, or the Benchmarks section of the
+<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
+</P>
+<P>LAMMPS is a freely-available open-source code, distributed under the
+terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
+modify the code however you wish. See <A HREF = "#intro_4">this section</A> for a
+brief discussion of the open-source philosophy.
+</P>
+
+
+<P>LAMMPS is designed to be easy to modify or extend with new
+capabilities, such as new force fields, atom types, boundary
+conditions, or diagnostics. See <A HREF = "Section_modify.html">Section_modify</A>
+for more details.
+</P>
+<P>The current version of LAMMPS is written in C++. Earlier versions
+were written in F77 and F90. See
+<A HREF = "Section_history.html">Section_history</A> for more information on
+different versions. All versions can be downloaded from the <A HREF = "http://lammps.sandia.gov">LAMMPS
+WWW Site</A>.
+</P>
+<P>LAMMPS was originally developed under a US Department of Energy CRADA
+(Cooperative Research and Development Agreement) between two DOE labs
+and 3 companies. It is distributed by <A HREF = "http://www.sandia.gov">Sandia National Labs</A>.
+See <A HREF = "#intro_5">this section</A> for more information on LAMMPS funding and
+individuals who have contributed to LAMMPS.
+</P>
+
+
+<P>In the most general sense, LAMMPS integrates Newton's equations of
+motion for collections of atoms, molecules, or macroscopic particles
+that interact via short- or long-range forces with a variety of
+initial and/or boundary conditions. For computational efficiency
+LAMMPS uses neighbor lists to keep track of nearby particles. The
+lists are optimized for systems with particles that are repulsive at
+short distances, so that the local density of particles never becomes
+too large. On parallel machines, LAMMPS uses spatial-decomposition
+techniques to partition the simulation domain into small 3d
+sub-domains, one of which is assigned to each processor. Processors
+communicate and store "ghost" atom information for atoms that border
+their sub-domain. LAMMPS is most efficient (in a parallel sense) for
+systems whose particles fill a 3d rectangular box with roughly uniform
+density. Papers with technical details of the algorithms used in
+LAMMPS are listed in <A HREF = "#intro_5">this section</A>.
+</P>
+<HR>
+
+<A NAME = "intro_2"></A><H4>1.2 LAMMPS features
+</H4>
+<P>This section highlights LAMMPS features, with pointers to specific
+commands which give more details. If LAMMPS doesn't have your
+favorite interatomic potential, boundary condition, or atom type, see
+<A HREF = "Section_modify.html">Section_modify</A>, which describes how you can add
+it to LAMMPS.
+</P>
+<H5>General features
+</H5>
+<UL><LI> runs on a single processor or in parallel
+<LI> distributed-memory message-passing parallelism (MPI)
+<LI> spatial-decomposition of simulation domain for parallelism
+<LI> open-source distribution
+<LI> highly portable C++
+<LI> optional libraries used: MPI and single-processor FFT
+<LI> GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
+<LI> easy to extend with new features and functionality
+<LI> runs from an input script
+<LI> syntax for defining and using variables and formulas
+<LI> syntax for looping over runs and breaking out of loops
+<LI> run one or multiple simulations simultaneously (in parallel) from one script
+<LI> build as library, invoke LAMMPS thru library interface or provided Python wrapper
+<LI> couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
+</UL>
+<H5>Particle and model types
+</H5>
+<P>(<A HREF = "atom_style.html">atom style</A> command)
+</P>
+<UL><LI> atoms
+<LI> coarse-grained particles (e.g. bead-spring polymers)
+<LI> united-atom polymers or organic molecules
+<LI> all-atom polymers, organic molecules, proteins, DNA
+<LI> metals
+<LI> granular materials
+<LI> coarse-grained mesoscale models
+<LI> finite-size spherical and ellipsoidal particles
+<LI> finite-size line segment (2d) and triangle (3d) particles
+<LI> point dipole particles
+<LI> rigid collections of particles
+<LI> hybrid combinations of these
+</UL>
+<H5>Force fields
+</H5>
+<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
+<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
+<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
+commands)
+</P>
+<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
+<LI> charged pairwise potentials: Coulombic, point-dipole
+<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
+<LI> long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
+<LI> polarization models: <A HREF = "fix_qeq.html">QEq</A>, <A HREF = "Section_howto.html#howto_26">core/shell model</A>, <A HREF = "Section_howto.html#howto_27">Drude dipole model</A>
+<LI> charge equilibration (QEq via dynamic, point, shielded, Slater methods)
+<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
+<LI> mesoscopic potentials: granular, Peridynamics, SPH
+<LI> electron force field (eFF, AWPMD)
+<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
+<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS)
+<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
+<LI> improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
+<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
+<LI> water potentials: TIP3P, TIP4P, SPC
+<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
+<LI> force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
+<LI> access to <A HREF = "http://openkim.org">KIM archive</A> of potentials via <A HREF = "pair_kim.html">pair kim</A>
+<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
+<LI> overlaid potentials: superposition of multiple pair potentials
+</UL>
+<H5>Atom creation
+</H5>
+<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
+<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
+<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
+</P>
+<UL><LI> read in atom coords from files
+<LI> create atoms on one or more lattices (e.g. grain boundaries)
+<LI> delete geometric or logical groups of atoms (e.g. voids)
+<LI> replicate existing atoms multiple times
+<LI> displace atoms
+</UL>
+<H5>Ensembles, constraints, and boundary conditions
+</H5>
+<P>(<A HREF = "fix.html">fix</A> command)
+</P>
+<UL><LI> 2d or 3d systems
+<LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains
+<LI> constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
+<LI> thermostatting options for groups and geometric regions of atoms
+<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
+<LI> simulation box deformation (tensile and shear)
+<LI> harmonic (umbrella) constraint forces
+<LI> rigid body constraints
+<LI> SHAKE bond and angle constraints
+<LI> Monte Carlo bond breaking, formation, swapping
+<LI> atom/molecule insertion and deletion
+<LI> walls of various kinds
+<LI> non-equilibrium molecular dynamics (NEMD)
+<LI> variety of additional boundary conditions and constraints
+</UL>
+<H5>Integrators
+</H5>
+<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
+</P>
+<UL><LI> velocity-Verlet integrator
+<LI> Brownian dynamics
+<LI> rigid body integration
+<LI> energy minimization via conjugate gradient or steepest descent relaxation
+<LI> rRESPA hierarchical timestepping
+<LI> rerun command for post-processing of dump files
+</UL>
+<H5>Diagnostics
+</H5>
+<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
+</UL>
+<H5>Output
+</H5>
+<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
+</P>
+<UL><LI> log file of thermodynamic info
+<LI> text dump files of atom coords, velocities, other per-atom quantities
+<LI> binary restart files
+<LI> parallel I/O of dump and restart files
+<LI> per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
+<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
+<LI> spatial and time averaging of per-atom quantities
+<LI> time averaging of system-wide quantities
+<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
+</UL>
+<H5>Multi-replica models
+</H5>
+<P><A HREF = "neb.html">nudged elastic band</A>
+<A HREF = "prd.html">parallel replica dynamics</A>
+<A HREF = "tad.html">temperature accelerated dynamics</A>
+<A HREF = "temper.html">parallel tempering</A>
+</P>
+<H5>Pre- and post-processing
+</H5>
+<UL><LI>Various pre- and post-processing serial tools are packaged
+with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
+
+<LI>Our group has also written and released a separate toolkit called
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations. Pizza.py is
+written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
+Pizza.py WWW site</A>.
+</UL>
+
+
+
+
+<H5>Specialized features
+</H5>
+<P>These are LAMMPS capabilities which you may not think of as typical
+molecular dynamics options:
+</P>
+<UL><LI><A HREF = "balance.html">static</A> and <A HREF = "fix_balance.html">dynamic load-balancing</A>
+<LI><A HREF = "body.html">generalized aspherical particles</A>
+<LI><A HREF = "fix_srd.html">stochastic rotation dynamics (SRD)</A>
+<LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
+<LI>calculate <A HREF = "compute_xrd.html">virtual diffraction patterns</A>
+<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
+<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
+<LI><A HREF = "fix_qmmm.html">QM/MM coupling</A>
+<LI><A HREF = "fix_ipi.html">path-integral molecular dynamics (PIMD)</A> and <A HREF = "fix_pimd.html">this as well</A>
+<LI>Monte Carlo via <A HREF = "fix_gcmc.html">GCMC</A> and <A HREF = "fix_tfmc.html">tfMC</A> and <A HREF = "fix_swap.html">atom swapping</A>
+<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
+<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
+<LI><A HREF = "fix_lb_fluid.html">Lattice Boltzmann fluid</A>
+<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
+<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
+</UL>
+<HR>
+
+<A NAME = "intro_3"></A><H4>1.3 LAMMPS non-features
+</H4>
+<P>LAMMPS is designed to efficiently compute Newton's equations of motion
+for a system of interacting particles. Many of the tools needed to
+pre- and post-process the data for such simulations are not included
+in the LAMMPS kernel for several reasons:
+</P>
+<UL><LI>the desire to keep LAMMPS simple
+<LI>they are not parallel operations
+<LI>other codes already do them
+<LI>limited development resources
+</UL>
+<P>Specifically, LAMMPS itself does not:
+</P>
+<UL><LI>run thru a GUI
+<LI>build molecular systems
+<LI>assign force-field coefficients automagically
+<LI>perform sophisticated analyses of your MD simulation
+<LI>visualize your MD simulation
+<LI>plot your output data
+</UL>
+<P>A few tools for pre- and post-processing tasks are provided as part of
+the LAMMPS package; they are described in <A HREF = "Section_tools.html">this
+section</A>. However, many people use other codes or
+write their own tools for these tasks.
+</P>
+<P>As noted above, our group has also written and released a separate
+toolkit called <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
+bullets. It provides tools for doing setup, analysis, plotting, and
+visualization for LAMMPS simulations. Pizza.py is written in
+<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
+site</A>.
+</P>
+<P>LAMMPS requires as input a list of initial atom coordinates and types,
+molecular topology information, and force-field coefficients assigned
+to all atoms and bonds. LAMMPS will not build molecular systems and
+assign force-field parameters for you.
+</P>
+<P>For atomic systems LAMMPS provides a <A HREF = "create_atoms.html">create_atoms</A>
+command which places atoms on solid-state lattices (fcc, bcc,
+user-defined, etc). Assigning small numbers of force field
+coefficients can be done via the <A HREF = "pair_coeff.html">pair coeff</A>, <A HREF = "bond_coeff.html">bond
+coeff</A>, <A HREF = "angle_coeff.html">angle coeff</A>, etc commands.
+For molecular systems or more complicated simulation geometries, users
+typically use another code as a builder and convert its output to
+LAMMPS input format, or write their own code to generate atom
+coordinate and molecular topology for LAMMPS to read in.
+</P>
+<P>For complicated molecular systems (e.g. a protein), a multitude of
+topology information and hundreds of force-field coefficients must
+typically be specified. We suggest you use a program like
+<A HREF = "http://www.scripps.edu/brooks">CHARMM</A> or <A HREF = "http://amber.scripps.edu">AMBER</A> or other molecular builders to setup
+such problems and dump its information to a file. You can then
+reformat the file as LAMMPS input. Some of the tools in <A HREF = "Section_tools.html">this
+section</A> can assist in this process.
+</P>
+<P>Similarly, LAMMPS creates output files in a simple format. Most users
+post-process these files with their own analysis tools or re-format
+them for input into other programs, including visualization packages.
+If you are convinced you need to compute something on-the-fly as
+LAMMPS runs, see <A HREF = "Section_modify.html">Section_modify</A> for a discussion
+of how you can use the <A HREF = "dump.html">dump</A> and <A HREF = "compute.html">compute</A> and
+<A HREF = "fix.html">fix</A> commands to print out data of your choosing. Keep in
+mind that complicated computations can slow down the molecular
+dynamics timestepping, particularly if the computations are not
+parallel, so it is often better to leave such analysis to
+post-processing codes.
+</P>
+<P>A very simple (yet fast) visualizer is provided with the LAMMPS
+package - see the <A HREF = "Section_tools.html#xmovie">xmovie</A> tool in <A HREF = "Section_tools.html">this
+section</A>. It creates xyz projection views of
+atomic coordinates and animates them. We find it very useful for
+debugging purposes. For high-quality visualization we recommend the
+following packages:
+</P>
+<UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
+<LI><A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
+<LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
+<LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
+<LI><A HREF = "http://www.openrasmol.org">RasMol</A>
+</UL>
+<P>Other features that LAMMPS does not yet (and may never) support are
+discussed in <A HREF = "Section_history.html">Section_history</A>.
+</P>
+<P>Finally, these are freely-available molecular dynamics codes, most of
+them parallel, which may be well-suited to the problems you want to
+model. They can also be used in conjunction with LAMMPS to perform
+complementary modeling tasks.
+</P>
+<UL><LI><A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
+<LI><A HREF = "http://amber.scripps.edu">AMBER</A>
+<LI><A HREF = "http://www.ks.uiuc.edu/Research/namd/">NAMD</A>
+<LI><A HREF = "http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</A>
+<LI><A HREF = "http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</A>
+<LI><A HREF = "http://dasher.wustl.edu/tinker">Tinker</A>
+</UL>
+
+
+
+
+
+
+
+
+
+
+
+
+<P>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
+modeling biological molecules. CHARMM and AMBER use
+atom-decomposition (replicated-data) strategies for parallelism; NAMD
+and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
+Tinker is a serial code. DL_POLY includes potentials for a variety of
+biological and non-biological materials; both a replicated-data and
+spatial-decomposition version exist.
+</P>
+<HR>
+
+<A NAME = "intro_4"></A><H4>1.4 Open source distribution
+</H4>
+<P>LAMMPS comes with no warranty of any kind. As each source file states
+in its header, it is a copyrighted code that is distributed free-of-
+charge, under the terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A> (GPL). This
+is often referred to as open-source distribution - see
+<A HREF = "http://www.gnu.org">www.gnu.org</A> or <A HREF = "http://www.opensource.org">www.opensource.org</A> for more
+details. The legal text of the GPL is in the LICENSE file that is
+included in the LAMMPS distribution.
+</P>
+
+
+
+
+<P>Here is a summary of what the GPL means for LAMMPS users:
+</P>
+<P>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+choose, including for commercial purposes.
+</P>
+<P>(2) If you distribute a modified version of LAMMPS, it must remain
+open-source, meaning you distribute it under the terms of the GPL.
+You should clearly annotate such a code as a derivative version of
+LAMMPS.
+</P>
+<P>(3) If you release any code that includes LAMMPS source code, then it
+must also be open-sourced, meaning you distribute it under the terms
+of the GPL.
+</P>
+<P>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
+source file headers (including the copyright and GPL notices) should
+remain part of the code.
+</P>
+<P>In the spirit of an open-source code, these are various ways you can
+contribute to making LAMMPS better. You can send email to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A> on any of these
+items.
+</P>
+<UL><LI>Point prospective users to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Mention it in
+talks or link to it from your WWW site.
+
+<LI>If you find an error or omission in this manual or on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
+Site</A>, or have a suggestion for something to clarify or include,
+send an email to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
+
+<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">Section_errors 2</A>
+describes how to report it.
+
+<LI>If you publish a paper using LAMMPS results, send the citation (and
+any cool pictures or movies if you like) to add to the Publications,
+Pictures, and Movies pages of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>, with links
+and attributions back to you.
+
+<LI>Create a new Makefile.machine that can be added to the src/MAKE
+directory.
+
+<LI>The tools sub-directory of the LAMMPS distribution has various
+stand-alone codes for pre- and post-processing of LAMMPS data. More
+details are given in <A HREF = "Section_tools.html">Section_tools</A>. If you write
+a new tool that users will find useful, it can be added to the LAMMPS
+distribution.
+
+<LI>LAMMPS is designed to be easy to extend with new code for features
+like potentials, boundary conditions, diagnostic computations, etc.
+<A HREF = "Section_modify.html">This section</A> gives details. If you add a
+feature of general interest, it can be added to the LAMMPS
+distribution.
+
+<LI>The Benchmark page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> lists LAMMPS
+performance on various platforms. The files needed to run the
+benchmarks are part of the LAMMPS distribution. If your machine is
+sufficiently different from those listed, your timing data can be
+added to the page.
+
+<LI>You can send feedback for the User Comments page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
+Site</A>. It might be added to the page. No promises.
+
+<LI>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
+Leave on desk. VISA also accepted. Chocolate chip cookies
+encouraged.
+</UL>
+<HR>
+
+<H4><A NAME = "intro_5"></A>1.5 Acknowledgments and citations
+</H4>
+<P>LAMMPS development has been funded by the <A HREF = "http://www.doe.gov">US Department of
+Energy</A> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
+programs and its <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and <A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices.
+</P>
+<P>Specifically, work on the latest version was funded in part by the US
+Department of Energy's Genomics:GTL program
+(<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the <A HREF = "http://www.genomes2life.org">project</A>, "Carbon
+Sequestration in Synechococcus Sp.: From Molecular Machines to
+Hierarchical Modeling".
+</P>
+
+
+
+
+
+
+
+
+
+
+<P>The following paper describe the basic parallel algorithms used in
+LAMMPS. If you use LAMMPS results in your published work, please cite
+this paper and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
+(http://lammps.sandia.gov):
+</P>
+<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
+Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
+</P>
+<P>Other papers describing specific algorithms used in LAMMPS are listed
+under the <A HREF = "http://lammps.sandia.gov/cite.html">Citing LAMMPS link</A> of
+the LAMMPS WWW page.
+</P>
+<P>The <A HREF = "http://lammps.sandia.gov/papers.html">Publications link</A> on the
+LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
+not listed there for some reason, feel free to send us the info. If
+the simulations in your paper produced cool pictures or animations,
+we'll be pleased to add them to the
+<A HREF = "http://lammps.sandia.gov/pictures.html">Pictures</A> or
+<A HREF = "http://lammps.sandia.gov/movies.html">Movies</A> pages of the LAMMPS WWW
+site.
+</P>
+<P>The core group of LAMMPS developers is at Sandia National Labs:
+</P>
+<UL><LI>Steve Plimpton, sjplimp at sandia.gov
+<LI>Aidan Thompson, athomps at sandia.gov
+<LI>Paul Crozier, pscrozi at sandia.gov
+</UL>
+<P>The following folks are responsible for significant contributions to
+the code, or other aspects of the LAMMPS development effort. Many of
+the packages they have written are somewhat unique to LAMMPS and the
+code would not be as general-purpose as it is without their expertise
+and efforts.
+</P>
+<UL><LI>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
+<LI>Roy Pollock (LLNL), Ewald and PPPM solvers
+<LI>Mike Brown (ORNL), brownw at ornl.gov, GPU package
+<LI>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
+<LI>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
+<LI>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
+<LI>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
+<LI>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
+<LI>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
+<LI>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
+<LI>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
+<LI>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
+<LI>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package
+</UL>
+<P>As discussed in <A HREF = "Section_history.html">Section_history</A>, LAMMPS
+originated as a cooperative project between DOE labs and industrial
+partners. Folks involved in the design and testing of the original
+version of LAMMPS were the following:
+</P>
+<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
+<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
+<LI>Steve Lustig (Dupont)
+<LI>Jim Belak (LLNL)
+</UL>
+</HTML>
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+<HTML>
+<CENTER> <A HREF = "Section_tools.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_python.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>10. Modifying & extending LAMMPS
+</H3>
+<P>This section describes how to customize LAMMPS by modifying
+and extending its source code.
+</P>
+10.1 <A HREF = "#mod_1">Atom styles</A><BR>
+10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
+10.3 <A HREF = "#mod_3">Compute styles</A><BR>
+10.4 <A HREF = "#mod_4">Dump styles</A><BR>
+10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
+10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
+10.7 <A HREF = "mod_7">Input script commands</A><BR>
+10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
+10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
+10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
+10.11 <A HREF = "#mod_11">Region styles</A><BR>
+10.12 <A HREF = "#mod_12">Body styles</A><BR>
+10.13 <A HREF = "#mod_13">Thermodynamic output options</A><BR>
+10.14 <A HREF = "#mod_14">Variable options</A><BR>
+10.15 <A HREF = "#mod_15">Submitting new features for inclusion in LAMMPS</A> <BR>
+
+<P>LAMMPS is designed in a modular fashion so as to be easy to modify and
+extend with new functionality. In fact, about 75% of its source code
+is files added in this fashion.
+</P>
+<P>In this section, changes and additions users can make are listed along
+with minimal instructions. If you add a new feature to LAMMPS and
+think it will be of interest to general users, we encourage you to
+submit it to the developers for inclusion in the released version of
+LAMMPS. Information about how to do this is provided
+<A HREF = "#mod_14">below</A>.
+</P>
+<P>The best way to add a new feature is to find a similar feature in
+LAMMPS and look at the corresponding source and header files to figure
+out what it does. You will need some knowledge of C++ to be able to
+understand the hi-level structure of LAMMPS and its class
+organization, but functions (class methods) that do actual
+computations are written in vanilla C-style code and operate on simple
+C-style data structures (vectors and arrays).
+</P>
+<P>Most of the new features described in this section require you to
+write a new C++ derived class (except for exceptions described below,
+where you can make small edits to existing files). Creating a new
+class requires 2 files, a source code file (*.cpp) and a header file
+(*.h). The derived class must provide certain methods to work as a
+new option. Depending on how different your new feature is compared
+to existing features, you can either derive from the base class
+itself, or from a derived class that already exists. Enabling LAMMPS
+to invoke the new class is as simple as putting the two source
+files in the src dir and re-building LAMMPS.
+</P>
+<P>The advantage of C++ and its object-orientation is that all the code
+and variables needed to define the new feature are in the 2 files you
+write, and thus shouldn't make the rest of LAMMPS more complex or
+cause side-effect bugs.
+</P>
+<P>Here is a concrete example. Suppose you write 2 files pair_foo.cpp
+and pair_foo.h that define a new class PairFoo that computes pairwise
+potentials described in the classic 1997 <A HREF = "#Foo">paper</A> by Foo, et al.
+If you wish to invoke those potentials in a LAMMPS input script with a
+command like
+</P>
+<PRE>pair_style foo 0.1 3.5
+</PRE>
+<P>then your pair_foo.h file should be structured as follows:
+</P>
+<PRE>#ifdef PAIR_CLASS
+PairStyle(foo,PairFoo)
+#else
+...
+(class definition for PairFoo)
+...
+#endif
+</PRE>
+<P>where "foo" is the style keyword in the pair_style command, and
+PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
+files.
+</P>
+<P>When you re-build LAMMPS, your new pairwise potential becomes part of
+the executable and can be invoked with a pair_style command like the
+example above. Arguments like 0.1 and 3.5 can be defined and
+processed by your new class.
+</P>
+<P>As illustrated by this pairwise example, many kinds of options are
+referred to in the LAMMPS documentation as the "style" of a particular
+command.
+</P>
+<P>The instructions below give the header file for the base class that
+these styles are derived from. Public variables in that file are ones
+used and set by the derived classes which are also used by the base
+class. Sometimes they are also used by the rest of LAMMPS. Virtual
+functions in the base class header file which are set = 0 are ones you
+must define in your new derived class to give it the functionality
+LAMMPS expects. Virtual functions that are not set to 0 are functions
+you can optionally define.
+</P>
+<P>Additionally, new output options can be added directly to the
+thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
+below.
+</P>
+<P>Here are additional guidelines for modifying LAMMPS and adding new
+functionality:
+</P>
+<UL><LI>Think about whether what you want to do would be better as a pre- or
+post-processing step. Many computations are more easily and more
+quickly done that way.
+
+<LI>Don't do anything within the timestepping of a run that isn't
+parallel. E.g. don't accumulate a bunch of data on a single processor
+and analyze it. You run the risk of seriously degrading the parallel
+efficiency.
+
+<LI>If your new feature reads arguments or writes output, make sure you
+follow the unit conventions discussed by the <A HREF = "units.html">units</A>
+command.
+
+<LI>If you add something you think is truly useful and doesn't impact
+LAMMPS performance when it isn't used, send an email to the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. We might be
+interested in adding it to the LAMMPS distribution. See further
+details on this at the bottom of this page.
+</UL>
+<HR>
+
+<HR>
+
+<A NAME = "mod_1"></A><H4>10.1 Atom styles
+</H4>
+<P>Classes that define an <A HREF = "atom_style.html">atom style</A> are derived from
+the AtomVec class and managed by the Atom class. The atom style
+determines what attributes are associated with an atom. A new atom
+style can be created if one of the existing atom styles does not
+define all the attributes you need to store and communicate with
+atoms.
+</P>
+<P>Atom_vec_atomic.cpp is a simple example of an atom style.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See atom_vec.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >init</TD><TD > one time setup (optional)</TD></TR>
+<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths (required)</TD></TR>
+<TR><TD >grow_reset</TD><TD > make array pointers in Atom and AtomVec classes consistent (required)</TD></TR>
+<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations (required)</TD></TR>
+<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep (required)</TD></TR>
+<TR><TD >pack_comm_vel</TD><TD > add velocity info to communication buffer (required)</TD></TR>
+<TR><TD >pack_comm_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
+<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
+<TR><TD >unpack_comm_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces (required)</TD></TR>
+<TR><TD >pack_reverse_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
+<TR><TD >unpack_reverse_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds (required)</TD></TR>
+<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer (required)</TD></TR>
+<TR><TD >pack_border_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
+<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
+<TR><TD >unpack_border_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
+<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor (required)</TD></TR>
+<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
+<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms (required)</TD></TR>
+<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer (required)</TD></TR>
+<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer (required)</TD></TR>
+<TR><TD >create_atom</TD><TD > create an individual atom of this style (required)</TD></TR>
+<TR><TD >data_atom</TD><TD > parse an atom line from the data file (required)</TD></TR>
+<TR><TD >data_atom_hybrid</TD><TD > parse additional atom info unique to this atom style (optional)</TD></TR>
+<TR><TD >data_vel</TD><TD > parse one line of velocity information from data file (optional)</TD></TR>
+<TR><TD >data_vel_hybrid</TD><TD > parse additional velocity data unique to this atom style (optional)</TD></TR>
+<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays (required)
+</TD></TR></TABLE></DIV>
+
+<P>The constructor of the derived class sets values for several variables
+that you must set when defining a new atom style, which are documented
+in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
+the word "customize" and you will find locations you will need to
+modify.
+</P>
+<P>IMPORTANT NOTE: It is possible to add some attributes, such as a
+molecule ID, to atom styles that do not have them via the <A HREF = "fix_property_atom.html">fix
+property/atom</A> command. This command also
+allows new custom attributes consisting of extra integer or
+floating-point values to be added to atoms. See the <A HREF = "fix_property_atom.html">fix
+property/atom</A> doc page for examples of cases
+where this is useful and details on how to initialize, access, and
+output the custom values.
+</P>
+<P>New <A HREF = "pair_style.html">pair styles</A>, <A HREF = "fix.html">fixes</A>, or
+<A HREF = "compute.html">computes</A> can be added to LAMMPS, as discussed below.
+The code for these classes can use the per-atom properties defined by
+fix property/atom. The Atom class has a find_custom() method that is
+useful in this context:
+</P>
+<PRE>int index = atom->find_custom(char *name, int &flag);
+</PRE>
+<P>The "name" of a custom attribute, as specified in the <A HREF = "fix_property_atom.html">fix
+property/atom</A> command, is checked to verify
+that it exists and its index is returned. The method also sets flag =
+0/1 depending on whether it is an integer or floating-point attribute.
+The vector of values associated with the attribute can then be
+accessed using the returned index as
+</P>
+<PRE>int *ivector = atom->ivector[index];
+double *dvector = atom->dvector[index];
+</PRE>
+<P>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
+which store the attributes of individual atoms.
+</P>
+<HR>
+
+<A NAME = "mod_2"></A><H4>10.2 Bond, angle, dihedral, improper potentials
+</H4>
+<P>Classes that compute molecular interactions are derived from the Bond,
+Angle, Dihedral, and Improper classes. New styles can be created to
+add new potentials to LAMMPS.
+</P>
+<P>Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
+the harmonic forms of the angle, dihedral, and improper style
+commands.
+</P>
+<P>Here is a brief description of common methods you define in your
+new derived class. See bond.h, angle.h, dihedral.h, and improper.h
+for details and specific additional methods.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >init</TD><TD > check if all coefficients are set, calls <I>init_style</I> (optional)</TD></TR>
+<TR><TD >init_style</TD><TD > check if style specific conditions are met (optional)</TD></TR>
+<TR><TD >compute</TD><TD > compute the molecular interactions (required)</TD></TR>
+<TR><TD >settings</TD><TD > apply global settings for all types (optional)</TD></TR>
+<TR><TD >coeff</TD><TD > set coefficients for one type (required)</TD></TR>
+<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE (required, bond only)</TD></TR>
+<TR><TD >equilibrium_angle</TD><TD > opening of angle, used by SHAKE (required, angle only)</TD></TR>
+<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files (required)</TD></TR>
+<TR><TD >single</TD><TD > force and energy of a single bond or angle (required, bond or angle only)</TD></TR>
+<TR><TD >memory_usage</TD><TD > tally memory allocated by the style (optional)
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_3"></A><H4>10.3 Compute styles
+</H4>
+<P>Classes that compute scalar and vector quantities like temperature
+and the pressure tensor, as well as classes that compute per-atom
+quantities like kinetic energy and the centro-symmetry parameter
+are derived from the Compute class. New styles can be created
+to add new calculations to LAMMPS.
+</P>
+<P>Compute_temp.cpp is a simple example of computing a scalar
+temperature. Compute_ke_atom.cpp is a simple example of computing
+per-atom kinetic energy.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See compute.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >init</TD><TD > perform one time setup (required)</TD></TR>
+<TR><TD >init_list</TD><TD > neighbor list setup, if needed (optional)</TD></TR>
+<TR><TD >compute_scalar</TD><TD > compute a scalar quantity (optional)</TD></TR>
+<TR><TD >compute_vector</TD><TD > compute a vector of quantities (optional)</TD></TR>
+<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom (optional)</TD></TR>
+<TR><TD >compute_local</TD><TD > compute one or more quantities per processor (optional)</TD></TR>
+<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate (optional)</TD></TR>
+<TR><TD >unpack_comm</TD><TD > unpack the buffer (optional)</TD></TR>
+<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate (optional)</TD></TR>
+<TR><TD >unpack_reverse</TD><TD > unpack the buffer (optional)</TD></TR>
+<TR><TD >remove_bias</TD><TD > remove velocity bias from one atom (optional)</TD></TR>
+<TR><TD >remove_bias_all</TD><TD > remove velocity bias from all atoms in group (optional)</TD></TR>
+<TR><TD >restore_bias</TD><TD > restore velocity bias for one atom after remove_bias (optional)</TD></TR>
+<TR><TD >restore_bias_all</TD><TD > same as before, but for all atoms in group (optional)</TD></TR>
+<TR><TD >memory_usage</TD><TD > tally memory usage (optional)
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_4"></A><H4>10.4 Dump styles
+</H4>
+<A NAME = "mod_5"></A><H4>10.5 Dump custom output options
+</H4>
+<P>Classes that dump per-atom info to files are derived from the Dump
+class. To dump new quantities or in a new format, a new derived dump
+class can be added, but it is typically simpler to modify the
+DumpCustom class contained in the dump_custom.cpp file.
+</P>
+<P>Dump_atom.cpp is a simple example of a derived dump class.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See dump.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >write_header</TD><TD > write the header section of a snapshot of atoms</TD></TR>
+<TR><TD >count</TD><TD > count the number of lines a processor will output</TD></TR>
+<TR><TD >pack</TD><TD > pack a proc's output data into a buffer</TD></TR>
+<TR><TD >write_data</TD><TD > write a proc's data to a file
+</TD></TR></TABLE></DIV>
+
+<P>See the <A HREF = "dump.html">dump</A> command and its <I>custom</I> style for a list of
+keywords for atom information that can already be dumped by
+DumpCustom. It includes options to dump per-atom info from Compute
+classes, so adding a new derived Compute class is one way to calculate
+new quantities to dump.
+</P>
+<P>Alternatively, you can add new keywords to the dump custom command.
+Search for the word "customize" in dump_custom.cpp to see the
+half-dozen or so locations where code will need to be added.
+</P>
+<HR>
+
+<A NAME = "mod_6"></A><H4>10.6 Fix styles
+</H4>
+<P>In LAMMPS, a "fix" is any operation that is computed during
+timestepping that alters some property of the system. Essentially
+everything that happens during a simulation besides force computation,
+neighbor list construction, and output, is a "fix". This includes
+time integration (update of coordinates and velocities), force
+constraints or boundary conditions (SHAKE or walls), and diagnostics
+(compute a diffusion coefficient). New styles can be created to add
+new options to LAMMPS.
+</P>
+<P>Fix_setforce.cpp is a simple example of setting forces on atoms to
+prescribed values. There are dozens of fix options already in LAMMPS;
+choose one as a template that is similar to what you want to
+implement.
+</P>
+<P>Here is a brief description of methods you can define in your new
+derived class. See fix.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep (required)</TD></TR>
+<TR><TD >init</TD><TD > initialization before a run (optional)</TD></TR>
+<TR><TD >setup_pre_exchange</TD><TD > called before atom exchange in setup (optional)</TD></TR>
+<TR><TD >setup_pre_force</TD><TD > called before force computation in setup (optional)</TD></TR>
+<TR><TD >setup</TD><TD > called immediately before the 1st timestep and after forces are computed (optional)</TD></TR>
+<TR><TD >min_setup_pre_force</TD><TD > like setup_pre_force, but for minimizations instead of MD runs (optional)</TD></TR>
+<TR><TD >min_setup</TD><TD > like setup, but for minimizations instead of MD runs (optional)</TD></TR>
+<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep (optional)</TD></TR>
+<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps (optional)</TD></TR>
+<TR><TD >pre_neighbor</TD><TD > called before neighbor list build (optional)</TD></TR>
+<TR><TD >pre_force</TD><TD > called before pair & molecular forces are computed (optional)</TD></TR>
+<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed and communicated (optional)</TD></TR>
+<TR><TD >final_integrate</TD><TD > called at end of each timestep (optional)</TD></TR>
+<TR><TD >end_of_step</TD><TD > called at very end of timestep (optional)</TD></TR>
+<TR><TD >write_restart</TD><TD > dumps fix info to restart file (optional)</TD></TR>
+<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix (optional)</TD></TR>
+<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix (optional)</TD></TR>
+<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor (optional)</TD></TR>
+<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer (optional)</TD></TR>
+<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer (optional)</TD></TR>
+<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file (optional)</TD></TR>
+<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer (optional)</TD></TR>
+<TR><TD >size_restart</TD><TD > size of atom's data (optional)</TD></TR>
+<TR><TD >maxsize_restart</TD><TD > max size of atom's data (optional)</TD></TR>
+<TR><TD >setup_pre_force_respa</TD><TD > same as setup_pre_force, but for rRESPA (optional)</TD></TR>
+<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA (optional)</TD></TR>
+<TR><TD >post_integrate_respa</TD><TD > called after the first half integration step is done in rRESPA (optional)</TD></TR>
+<TR><TD >pre_force_respa</TD><TD > same as pre_force, but for rRESPA (optional)</TD></TR>
+<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA (optional)</TD></TR>
+<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA (optional)</TD></TR>
+<TR><TD >min_pre_force</TD><TD > called after pair & molecular forces are computed in minimizer (optional)</TD></TR>
+<TR><TD >min_post_force</TD><TD > called after pair & molecular forces are computed and communicated in minmizer (optional)</TD></TR>
+<TR><TD >min_store</TD><TD > store extra data for linesearch based minimization on a LIFO stack (optional)</TD></TR>
+<TR><TD >min_pushstore</TD><TD > push the minimization LIFO stack one element down (optional)</TD></TR>
+<TR><TD >min_popstore</TD><TD > pop the minimization LIFO stack one element up (optional)</TD></TR>
+<TR><TD >min_clearstore</TD><TD > clear minimization LIFO stack (optional)</TD></TR>
+<TR><TD >min_step</TD><TD > reset or move forward on line search minimization (optional)</TD></TR>
+<TR><TD >min_dof</TD><TD > report number of degrees of freedom <I>added</I> by this fix in minimization (optional)</TD></TR>
+<TR><TD >max_alpha</TD><TD > report maximum allowed step size during linesearch minimization (optional)</TD></TR>
+<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity (optional)</TD></TR>
+<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity (optional)</TD></TR>
+<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
+<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
+<TR><TD >dof</TD><TD > report number of degrees of freedom <I>removed</I> by this fix during MD (optional)</TD></TR>
+<TR><TD >compute_scalar</TD><TD > return a global scalar property that the fix computes (optional)</TD></TR>
+<TR><TD >compute_vector</TD><TD > return a component of a vector property that the fix computes (optional)</TD></TR>
+<TR><TD >compute_array</TD><TD > return a component of an array property that the fix computes (optional)</TD></TR>
+<TR><TD >deform</TD><TD > called when the box size is changed (optional)</TD></TR>
+<TR><TD >reset_target</TD><TD > called when a change of the target temperature is requested during a run (optional)</TD></TR>
+<TR><TD >reset_dt</TD><TD > is called when a change of the time step is requested during a run (optional)</TD></TR>
+<TR><TD >modify_param</TD><TD > called when a fix_modify request is executed (optional)</TD></TR>
+<TR><TD >memory_usage</TD><TD > report memory used by fix (optional)</TD></TR>
+<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output (optional)
+</TD></TR></TABLE></DIV>
+
+<P>Typically, only a small fraction of these methods are defined for a
+particular fix. Setmask is mandatory, as it determines when the fix
+will be invoked during the timestep. Fixes that perform time
+integration (<I>nve</I>, <I>nvt</I>, <I>npt</I>) implement initial_integrate() and
+final_integrate() to perform velocity Verlet updates. Fixes that
+constrain forces implement post_force().
+</P>
+<P>Fixes that perform diagnostics typically implement end_of_step(). For
+an end_of_step fix, one of your fix arguments must be the variable
+"nevery" which is used to determine when to call the fix and you must
+set this variable in the constructor of your fix. By convention, this
+is the first argument the fix defines (after the ID, group-ID, style).
+</P>
+<P>If the fix needs to store information for each atom that persists from
+timestep to timestep, it can manage that memory and migrate the info
+with the atoms as they move from processors to processor by
+implementing the grow_arrays, copy_arrays, pack_exchange, and
+unpack_exchange methods. Similarly, the pack_restart and
+unpack_restart methods can be implemented to store information about
+the fix in restart files. If you wish an integrator or force
+constraint fix to work with rRESPA (see the <A HREF = "run_style.html">run_style</A>
+command), the initial_integrate, post_force_integrate, and
+final_integrate_respa methods can be implemented. The thermo method
+enables a fix to contribute values to thermodynamic output, as printed
+quantities and/or to be summed to the potential energy of the system.
+</P>
+<HR>
+
+<A NAME = "mod_7"></A><H4>10.7 Input script commands
+</H4>
+<P>New commands can be added to LAMMPS input scripts by adding new
+classes that have a "command" method. For example, the create_atoms,
+read_data, velocity, and run commands are all implemented in this
+fashion. When such a command is encountered in the LAMMPS input
+script, LAMMPS simply creates a class with the corresponding name,
+invokes the "command" method of the class, and passes it the arguments
+from the input script. The command method can perform whatever
+operations it wishes on LAMMPS data structures.
+</P>
+<P>The single method your new class must define is as follows:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >command</TD><TD > operations performed by the new command
+</TD></TR></TABLE></DIV>
+
+<P>Of course, the new class can define other methods and variables as
+needed.
+</P>
+<HR>
+
+<A NAME = "mod_8"></A><H4>10.8 Kspace computations
+</H4>
+<P>Classes that compute long-range Coulombic interactions via K-space
+representations (Ewald, PPPM) are derived from the KSpace class. New
+styles can be created to add new K-space options to LAMMPS.
+</P>
+<P>Ewald.cpp is an example of computing K-space interactions.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See kspace.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >init</TD><TD > initialize the calculation before a run</TD></TR>
+<TR><TD >setup</TD><TD > computation before the 1st timestep of a run</TD></TR>
+<TR><TD >compute</TD><TD > every-timestep computation</TD></TR>
+<TR><TD >memory_usage</TD><TD > tally of memory usage
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_9"></A><H4>10.9 Minimization styles
+</H4>
+<P>Classes that perform energy minimization derived from the Min class.
+New styles can be created to add new minimization algorithms to
+LAMMPS.
+</P>
+<P>Min_cg.cpp is an example of conjugate gradient minimization.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See min.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >init</TD><TD > initialize the minimization before a run</TD></TR>
+<TR><TD >run</TD><TD > perform the minimization</TD></TR>
+<TR><TD >memory_usage</TD><TD > tally of memory usage
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_10"></A><H4>10.10 Pairwise potentials
+</H4>
+<P>Classes that compute pairwise interactions are derived from the Pair
+class. In LAMMPS, pairwise calculation include manybody potentials
+such as EAM or Tersoff where particles interact without a static bond
+topology. New styles can be created to add new pair potentials to
+LAMMPS.
+</P>
+<P>Pair_lj_cut.cpp is a simple example of a Pair class, though it
+includes some optional methods to enable its use with rRESPA.
+</P>
+<P>Here is a brief description of the class methods in pair.h:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >compute</TD><TD > workhorse routine that computes pairwise interactions</TD></TR>
+<TR><TD >settings</TD><TD > reads the input script line with arguments you define</TD></TR>
+<TR><TD >coeff</TD><TD > set coefficients for one i,j type pair</TD></TR>
+<TR><TD >init_one</TD><TD > perform initialization for one i,j type pair</TD></TR>
+<TR><TD >init_style</TD><TD > initialization specific to this pair style</TD></TR>
+<TR><TD >write & read_restart</TD><TD > write/read i,j pair coeffs to restart files</TD></TR>
+<TR><TD >write & read_restart_settings</TD><TD > write/read global settings to restart files</TD></TR>
+<TR><TD >single</TD><TD > force and energy of a single pairwise interaction between 2 atoms</TD></TR>
+<TR><TD >compute_inner/middle/outer</TD><TD > versions of compute used by rRESPA
+</TD></TR></TABLE></DIV>
+
+<P>The inner/middle/outer routines are optional.
+</P>
+<HR>
+
+<A NAME = "mod_11"></A><H4>10.11 Region styles
+</H4>
+<P>Classes that define geometric regions are derived from the Region
+class. Regions are used elsewhere in LAMMPS to group atoms, delete
+atoms to create a void, insert atoms in a specified region, etc. New
+styles can be created to add new region shapes to LAMMPS.
+</P>
+<P>Region_sphere.cpp is an example of a spherical region.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See region.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >match</TD><TD > determine whether a point is in the region
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_12"></A><H4>10.11 Body styles
+</H4>
+<P>Classes that define body particles are derived from the Body class.
+Body particles can represent complex entities, such as surface meshes
+of discrete points, collections of sub-particles, deformable objects,
+etc.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A> of the manual for
+an overview of using body particles and the <A HREF = "body.html">body</A> doc page
+for details on the various body styles LAMMPS supports. New styles
+can be created to add new kinds of body particles to LAMMPS.
+</P>
+<P>Body_nparticle.cpp is an example of a body particle that is treated as
+a rigid body containing N sub-particles.
+</P>
+<P>Here is a brief description of methods you define in your new derived
+class. See body.h for details.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >data_body</TD><TD > process a line from the Bodies section of a data file</TD></TR>
+<TR><TD >noutrow</TD><TD > number of sub-particles output is generated for</TD></TR>
+<TR><TD >noutcol</TD><TD > number of values per-sub-particle output is generated for</TD></TR>
+<TR><TD >output</TD><TD > output values for the Mth sub-particle</TD></TR>
+<TR><TD >pack_comm_body</TD><TD > body attributes to communicate every timestep</TD></TR>
+<TR><TD >unpack_comm_body</TD><TD > unpacking of those attributes</TD></TR>
+<TR><TD >pack_border_body</TD><TD > body attributes to communicate when reneighboring is done</TD></TR>
+<TR><TD >unpack_border_body</TD><TD > unpacking of those attributes
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<A NAME = "mod_13"></A><H4>10.13 Thermodynamic output options
+</H4>
+<P>There is one class that computes and prints thermodynamic information
+to the screen and log file; see the file thermo.cpp.
+</P>
+<P>There are two styles defined in thermo.cpp: "one" and "multi". There
+is also a flexible "custom" style which allows the user to explicitly
+list keywords for quantities to print when thermodynamic info is
+output. See the <A HREF = "thermo_style.html">thermo_style</A> command for a list
+of defined quantities.
+</P>
+<P>The thermo styles (one, multi, etc) are simply lists of keywords.
+Adding a new style thus only requires defining a new list of keywords.
+Search for the word "customize" with references to "thermo style" in
+thermo.cpp to see the two locations where code will need to be added.
+</P>
+<P>New keywords can also be added to thermo.cpp to compute new quantities
+for output. Search for the word "customize" with references to
+"keyword" in thermo.cpp to see the several locations where code will
+need to be added.
+</P>
+<P>Note that the <A HREF = "thermo.html">thermo_style custom</A> command already allows
+for thermo output of quantities calculated by <A HREF = "fix.html">fixes</A>,
+<A HREF = "compute.html">computes</A>, and <A HREF = "variable.html">variables</A>. Thus, it may
+be simpler to compute what you wish via one of those constructs, than
+by adding a new keyword to the thermo command.
+</P>
+<HR>
+
+<A NAME = "mod_14"></A><H4>10.14 Variable options
+</H4>
+<P>There is one class that computes and stores <A HREF = "variable.html">variable</A>
+information in LAMMPS; see the file variable.cpp. The value
+associated with a variable can be periodically printed to the screen
+via the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</A>, or
+<A HREF = "thermo_style.html">thermo_style custom</A> commands. Variables of style
+"equal" can compute complex equations that involve the following types
+of arguments:
+</P>
+<PRE>thermo keywords = ke, vol, atoms, ...
+other variables = v_a, v_myvar, ...
+math functions = div(x,y), mult(x,y), add(x,y), ...
+group functions = mass(group), xcm(group,x), ...
+atom values = x[123], y[3], vx[34], ...
+compute values = c_mytemp[0], c_thermo_press[3], ...
+</PRE>
+<P>Adding keywords for the <A HREF = "thermo_style.html">thermo_style custom</A> command
+(which can then be accessed by variables) was discussed
+<A HREF = "Section_modify.html#thermo">here</A> on this page.
+</P>
+<P>Adding a new math function of one or two arguments can be done by
+editing one section of the Variable::evaulate() method. Search for
+the word "customize" to find the appropriate location.
+</P>
+<P>Adding a new group function can be done by editing one section of the
+Variable::evaulate() method. Search for the word "customize" to find
+the appropriate location. You may need to add a new method to the
+Group class as well (see the group.cpp file).
+</P>
+<P>Accessing a new atom-based vector can be done by editing one section
+of the Variable::evaulate() method. Search for the word "customize"
+to find the appropriate location.
+</P>
+<P>Adding new <A HREF = "compute.html">compute styles</A> (whose calculated values can
+then be accessed by variables) was discussed
+<A HREF = "Section_modify.html#compute">here</A> on this page.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "mod_15"></A><H4>10.15 Submitting new features for inclusion in LAMMPS
+</H4>
+<P>We encourage users to submit new features to <A HREF = "http://lammps.sandia.gov/authors.html">the
+developers</A> that they add to
+LAMMPS, especially if you think they will be of interest to other
+users. If they are broadly useful we may add them as core files to
+LAMMPS or as part of a <A HREF = "Section_start.html#start_3">standard package</A>.
+Else we will add them as a user-contributed file or package. Examples
+of user packages are in src sub-directories that start with USER. The
+USER-MISC package is simply a collection of (mostly) unrelated single
+files, which is the simplest way to have your contribution quickly
+added to the LAMMPS distribution. You can see a list of the both
+standard and user packages by typing "make package" in the LAMMPS src
+directory.
+</P>
+<P>Note that by providing us the files to release, you are agreeing to
+make them open-source, i.e. we can release them under the terms of the
+GPL, used as a license for the rest of LAMMPS. See <A HREF = "Section_intro.html#intro_4">Section
+1.4</A> for details.
+</P>
+<P>With user packages and files, all we are really providing (aside from
+the fame and fortune that accompanies having your name in the source
+code and on the <A HREF = "http://lammps.sandia.gov/authors.html">Authors page</A>
+of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A>), is a means for you to distribute your
+work to the LAMMPS user community, and a mechanism for others to
+easily try out your new feature. This may help you find bugs or make
+contact with new collaborators. Note that you're also implicitly
+agreeing to support your code which means answer questions, fix bugs,
+and maintain it if LAMMPS changes in some way that breaks it (an
+unusual event).
+</P>
+<P>NOTE: If you prefer to actively develop and support your add-on
+feature yourself, then you may wish to make it available for download
+from your own website, as a user package that LAMMPS users can add to
+their copy of LAMMPS. See the <A HREF = "http://lammps.sandia.gov/offsite.html">Offsite LAMMPS packages and
+tools</A> page of the LAMMPS web
+site for examples of groups that do this. We are happy to advertise
+your package and web site from that page. Simply email the
+<A HREF = "http://lammps.sandia.gov/authors.html">developers</A> with info about
+your package and we will post it there.
+</P>
+<P>The previous sections of this doc page describe how to add new "style"
+files of various kinds to LAMMPS. Packages are simply collections of
+one or more new class files which are invoked as a new style within a
+LAMMPS input script. If designed correctly, these additions typically
+do not require changes to the main core of LAMMPS; they are simply
+add-on files. If you think your new feature requires non-trivial
+changes in core LAMMPS files, you'll need to <A HREF = "http://lammps.sandia.gov/authors.html">communicate with the
+developers</A>, since we may or may
+not want to make those changes. An example of a trivial change is
+making a parent-class method "virtual" when you derive a new child
+class from it.
+</P>
+<P>Here are the steps you need to follow to submit a single file or user
+package for our consideration. Following these steps will save both
+you and us time. See existing files in packages in the src dir for
+examples.
+</P>
+<UL><LI>All source files you provide must compile with the most current
+version of LAMMPS.
+
+<LI>If you want your file(s) to be added to main LAMMPS or one of its
+standard packages, then it needs to be written in a style compatible
+with other LAMMPS source files. This is so the developers can
+understand it and hopefully maintain it. This basically means that
+the code accesses data structures, performs its operations, and is
+formatted similar to other LAMMPS source files, including the use of
+the error class for error and warning messages.
+
+<LI>If you want your contribution to be added as a user-contributed
+feature, and it's a single file (actually a *.cpp and *.h file) it can
+rapidly be added to the USER-MISC directory. Send us the one-line
+entry to add to the USER-MISC/README file in that dir, along with the
+2 source files. You can do this multiple times if you wish to
+contribute several individual features.
+
+<LI>If you want your contribution to be added as a user-contribution and
+it is several related featues, it is probably best to make it a user
+package directory with a name like USER-FOO. In addition to your new
+files, the directory should contain a README text file. The README
+should contain your name and contact information and a brief
+description of what your new package does. If your files depend on
+other LAMMPS style files also being installed (e.g. because your file
+is a derived class from the other LAMMPS class), then an Install.sh
+file is also needed to check for those dependencies. See other README
+and Install.sh files in other USER directories as examples. Send us a
+tarball of this USER-FOO directory.
+
+<LI>Your new source files need to have the LAMMPS copyright, GPL notice,
+and your name and email address at the top, like other
+user-contributed LAMMPS source files. They need to create a class
+that is inside the LAMMPS namespace. If the file is for one of the
+USER packages, including USER-MISC, then we are not as picky about the
+coding style (see above). I.e. the files do not need to be in the
+same stylistic format and syntax as other LAMMPS files, though that
+would be nice for developers as well as users who try to read your
+code.
+
+<LI>You must also create a documentation file for each new command or
+style you are adding to LAMMPS. This will be one file for a
+single-file feature. For a package, it might be several files. These
+are simple text files which we auto-convert to HTML. Thus they must
+be in the same format as other *.txt files in the lammps/doc directory
+for similar commands and styles; use one or more of them as a starting
+point. As appropriate, the text files can include links to equations
+(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
+files), or figures (see doc/JPG for examples), or even additional PDF
+files with further details (see doc/PDF for examples). The doc page
+should also include literature citations as appropriate; see the
+bottom of doc/fix_nh.txt for examples and the earlier part of the same
+file for how to format the cite itself. The "Restrictions" section of
+the doc page should indicate that your command is only available if
+LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
+See other user package doc files for examples of how to do this. The
+txt2html tool we use to convert to HTML can be downloaded from <A HREF = "http://www.sandia.gov/~sjplimp/download.html">this
+site</A>, so you can perform
+the HTML conversion yourself to proofread your doc page.
+
+<LI>For a new package (or even a single command) you can include one or
+more example scripts. These should run in no more than 1 minute, even
+on a single processor, and not require large data files as input. See
+directories under examples/USER for examples of input scripts other
+users provided for their packages.
+
+<LI>If there is a paper of yours describing your feature (either the
+algorithm/science behind the feature itself, or its initial usage, or
+its implementation in LAMMPS), you can add the citation to the *.cpp
+source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
+A LaTeX citation is stored in a variable at the top of the file and a
+single line of code that references the variable is added to the
+constructor of the class. Whenever a user invokes your feature from
+their input script, this will cause LAMMPS to output the citation to a
+log.cite file and prompt the user to examine the file. Note that you
+should only use this for a paper you or your group authored.
+E.g. adding a cite in the code for a paper by Nose and Hoover if you
+write a fix that implements their integrator is not the intended
+usage. That kind of citation should just be in the doc page you
+provide.
+</UL>
+<P>Finally, as a general rule-of-thumb, the more clear and
+self-explanatory you make your doc and README files, and the easier
+you make it for people to get started, e.g. by providing example
+scripts, the more likely it is that users will try out your new
+feature.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "Foo"></A>
+
+<P><B>(Foo)</B> Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).
+</P>
+</HTML>
diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html
new file mode 100644
index 000000000..4b9bd9275
--- /dev/null
+++ b/doc/doc2/Section_packages.html
@@ -0,0 +1,665 @@
+<HTML>
+<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>4. Packages
+</H3>
+<P>This section gives a quick overview of the add-on packages that extend
+LAMMPS functionality.
+</P>
+4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
+4.2 <A HREF = "#pkg_2">User packages</A> <BR>
+
+<P>LAMMPS includes many optional packages, which are groups of files that
+enable a specific set of features. For example, force fields for
+molecular systems or granular systems are in packages. You can see
+the list of all packages by typing "make package" from within the src
+directory of the LAMMPS distribution.
+</P>
+<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
+details on how to include/exclude specific packages as part of the
+LAMMPS build process, and for more details about the differences
+between standard packages and user packages in LAMMPS.
+</P>
+<P>Below, the packages currently availabe in LAMMPS are listed. For
+standard packages, just a one-line description is given. For user
+packages, more details are provided.
+</P>
+<HR>
+
+<HR>
+
+<H4><A NAME = "pkg_1"></A>4.1 Standard packages
+</H4>
+<P>The current list of standard packages is as follows:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
+<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
+<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
+<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR>
+<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
+<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
+<TR ALIGN="center"><TD >PYTHON</TD><TD > embed Python code in an input script</TD><TD > -</TD><TD > <A HREF = "python.html">python</A></TD><TD > python</TD><TD > lib/python</TD></TR>
+<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
+<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</TD></TR>
+<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >
+</TD></TR></TABLE></DIV>
+
+<P>The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+</P>
+<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
+Jonathan Higdon's group at UIUC.
+</P>
+<P>(2) The OPT package was created by James Fischer (High Performance
+Technologies), David Richie, and Vincent Natoli (Stone Ridge
+Technolgy).
+</P>
+<P>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
+and Ellad Tadmor (U Minn).
+</P>
+<P>(4) The KOKKOS package was created primarily by Christian Trott
+(Sandia). It uses the Kokkos library which was developed by Carter
+Edwards, Christian, and collaborators at Sandia.
+</P>
+<P>The "Doc page" column links to either a portion of the
+<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
+command implemented as part of the package.
+</P>
+<P>The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory.
+</P>
+<P>The "Library" column lists an external library which must be built
+first and which LAMMPS links to when it is built. If it is listed as
+lib/package, then the code for the library is under the lib directory
+of the LAMMPS distribution. See the lib/package/README file for info
+on how to build the library. If it is not listed as lib/package, then
+it is a third-party library not included in the LAMMPS distribution.
+See the src/package/README or src/package/Makefile.lammps file for
+info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section
+start</A> of the manual also gives details
+on how to build LAMMPS with both kinds of auxiliary libraries.
+</P>
+<HR>
+
+<HR>
+
+<H4><A NAME = "pkg_2"></A>4.2 User packages
+</H4>
+<P>The current list of user-contributed packages is as follows:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
+<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
+<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
+<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
+<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
+<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
+<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
+<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QUIP/libatoms interface</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "pair_quip.html">pair_style quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
+<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >
+</TD></TR></TABLE></DIV>
+
+
+
+
+
+
+
+
+
+
+
+<P>The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+</P>
+<P>If the Library is not listed as lib/package, then it is a third-party
+library not included in the LAMMPS distribution. See the
+src/package/Makefile.lammps file for info on where to download the
+library from.
+</P>
+<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
+Jon Zimmerman (Sandia).
+</P>
+<P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
+the colvars module library written by Giacomo Fiorin (Temple U) and
+Jerome Henin (LISM, Marseille, France).
+</P>
+<P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
+Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
+(U Blaise Pascal).
+</P>
+<P>The "Doc page" column links to either a portion of the
+<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
+command implemented as part of the package, or to additional
+documentation provided witht he package.
+</P>
+<P>The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory. USER/cuda
+refers to the examples/USER/cuda directory.
+</P>
+<P>The "Library" column lists an external library which must be built
+first and which LAMMPS links to when it is built. If it is listed as
+lib/package, then the code for the library is under the lib directory
+of the LAMMPS distribution. See the lib/package/README file for info
+on how to build the library. If it is not listed as lib/package, then
+it is a third-party library not included in the LAMMPS distribution.
+See the src/package/Makefile.lammps file for info on where to download
+the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
+manual also gives details on how to build LAMMPS with both kinds of
+auxiliary libraries.
+</P>
+<P>More details on each package, from the USER-*/README file is given
+below.
+</P>
+<HR>
+
+<H4>USER-ATC package
+</H4>
+<P>This package implements a "fix atc" command which can be used in a
+LAMMPS input script. This fix can be employed to either do concurrent
+coupling of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.
+</P>
+<P>See the doc page for the fix atc command to get started. At the
+bottom of the doc page are many links to additional documentation
+contained in the doc/USER/atc directory.
+</P>
+<P>There are example scripts for using this package in examples/USER/atc.
+</P>
+<P>This package uses an external library in lib/atc which must be
+compiled before making LAMMPS. See the lib/atc/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The primary people who created this package are Reese Jones (rjones at
+sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
+Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
+you have questions.
+</P>
+<HR>
+
+<H4>USER-AWPMD package
+</H4>
+<P>This package contains a LAMMPS implementation of the Antisymmetrized
+Wave Packet Molecular Dynamics (AWPMD) method.
+</P>
+<P>See the doc page for the pair_style awpmd/cut command to get started.
+</P>
+<P>There are example scripts for using this package in examples/USER/awpmd.
+</P>
+<P>This package uses an external library in lib/awpmd which must be
+compiled before making LAMMPS. See the lib/awpmd/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The person who created this package is Ilya Valuev at the JIHT in
+Russia (valuev at physik.hu-berlin.de). Contact him directly if you
+have questions.
+</P>
+<HR>
+
+<H4>USER-CG-CMM package
+</H4>
+<P>This package implements 3 commands which can be used in a LAMMPS input
+script:
+</P>
+<UL><LI>pair_style lj/sdk
+<LI>pair_style lj/sdk/coul/long
+<LI>angle_style sdk
+</UL>
+<P>These styles allow coarse grained MD simulations with the
+parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
+(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
+and charged amino acids.
+</P>
+<P>See the doc pages for these commands for details.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/cg-cmm.
+</P>
+<P>This is the second generation implementation reducing the the clutter
+of the previous version. For many systems with electrostatics, it will
+be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
+instead of the combined lj/sdk/coul/long style. since the number of
+charged atom types is usually small. For any other coulomb
+interactions this is now required. To exploit this property, the use
+of the kspace_style pppm/cg is recommended over regular pppm. For all
+new styles, input file backward compatibility is provided. The old
+implementation is still available through appending the /old
+suffix. These will be discontinued and removed after the new
+implementation has been fully validated.
+</P>
+<P>The current version of this package should be considered beta
+quality. The CG potentials work correctly for "normal" situations, but
+have not been testing with all kinds of potential parameters and
+simulation systems.
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-COLVARS package
+</H4>
+<P>This package implements the "fix colvars" command which can be
+used in a LAMMPS input script.
+</P>
+<P>This fix allows to use "collective variables" to implement
+Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
+Sampling and Restraints. This code consists of two parts:
+</P>
+<UL><LI>A portable collective variable module library written and maintained
+<LI>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
+<LI>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
+<LI>the directory lib/colvars and needs to be compiled first. The colvars
+<LI>fix and an interface layer, exchanges information between LAMMPS and
+<LI>the collective variable module.
+</UL>
+<P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/colvars
+</P>
+<P>This is a very new interface that does not yet support all
+features in the module and will see future optimizations
+and improvements. The colvars module library is also available
+in NAMD has been thoroughly used and tested there. Bugs and
+problems are likely due to the interface layers code.
+Thus the current version of this package should be considered
+beta quality.
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-CUDA package
+</H4>
+<P>This package provides acceleration of various LAMMPS pair styles, fix
+styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
+GPUs.
+</P>
+<P>See this section of the manual to get started:
+</P>
+<P><A HREF = "Section_accelerate.html#acc_7">Section_accelerate</A>
+</P>
+<P>There are example scripts for using this package in
+examples/USER/cuda.
+</P>
+<P>This package uses an external library in lib/cuda which must be
+compiled before making LAMMPS. See the lib/cuda/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The person who created this package is Christian Trott at the
+University of Technology Ilmenau, Germany (christian.trott at
+tu-ilmenau.de). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-DIFFRACTION package
+</H4>
+<P>This package contains the commands neeed to calculate x-ray and
+electron diffraction intensities based on kinematic diffraction
+theory.
+</P>
+<P>See these doc pages and their related commands to get started:
+</P>
+<UL><LI><A HREF = "compute_xrd.html">compute xrd</A>
+<LI><A HREF = "compute_saed.html">compute saed</A>
+<LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A>
+</UL>
+<P>The person who created this package is Shawn P. Coleman
+(shawn.p.coleman8.ctr at mail.mil) while at the University of
+Arkansas. Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-DRUDE package
+</H4>
+<P>This package implements methods for simulating polarizable systems
+in LAMMPS using thermalized Drude oscillators.
+</P>
+<P>See these doc pages and their related commands to get started:
+</P>
+<UL><LI><A HREF = "tutorial_drude.html">Drude tutorial</A>
+<LI><A HREF = "fix_drude.html">fix drude</A>
+<LI><A HREF = "compute_temp_drude.html">compute temp/drude</A>
+<LI><A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
+<LI><A HREF = "fix_drude_transform.html">fix drude/transform/...</A>
+<LI><A HREF = "pair_thole.html">pair thole</A>
+</UL>
+<P>There are auxiliary tools for using this package in tools/drude.
+</P>
+<P>The person who created this package is Alain Dequidt at Universite
+Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
+Contact him directly if you have questions. Co-authors: Julien Devemy,
+Agilio Padua.
+</P>
+<HR>
+
+<H4>USER-EFF package
+</H4>
+<P>This package contains a LAMMPS implementation of the electron Force
+Field (eFF) currently under development at Caltech, as described in
+A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
+2010. The eFF potential was first introduced by Su and Goddard, in
+2007.
+</P>
+<P>eFF can be viewed as an approximation to QM wave packet dynamics and
+Fermionic molecular dynamics, combining the ability of electronic
+structure methods to describe atomic structure, bonding, and chemistry
+in materials, and of plasma methods to describe nonequilibrium
+dynamics of large systems with a large number of highly excited
+electrons. We classify it as a mixed QM-classical approach rather than
+a conventional force field method, which introduces QM-based terms (a
+spin-dependent repulsion term to account for the Pauli exclusion
+principle and the electron wavefunction kinetic energy associated with
+the Heisenberg principle) that reduce, along with classical
+electrostatic terms between nuclei and electrons, to the sum of a set
+of effective pairwise potentials. This makes eFF uniquely suited to
+simulate materials over a wide range of temperatures and pressures
+where electronically excited and ionized states of matter can occur
+and coexist.
+</P>
+<P>The necessary customizations to the LAMMPS core are in place to
+enable the correct handling of explicit electron properties during
+minimization and dynamics.
+</P>
+<P>See the doc page for the pair_style eff/cut command to get started.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/eff.
+</P>
+<P>There are auxiliary tools for using this package in tools/eff.
+</P>
+<P>The person who created this package is Andres Jaramillo-Botero at
+CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
+have questions.
+</P>
+<HR>
+
+<H4>USER-FEP package
+</H4>
+<P>This package provides methods for performing free energy perturbation
+simulations with soft-core pair potentials in LAMMPS.
+</P>
+<P>See these doc pages and their related commands to get started:
+</P>
+<UL><LI><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>
+<LI><A HREF = "compute_fep.html">compute fep</A>
+<LI><A HREF = "pair_lj_soft.html">soft pair styles</A>
+</UL>
+<P>The person who created this package is Agilio Padua at Universite
+Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
+Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-INTEL package
+</H4>
+<P>This package provides options for performing neighbor list and
+non-bonded force calculations in single, mixed, or double precision
+and also a capability for accelerating calculations with an
+Intel(R) Xeon Phi(TM) coprocessor.
+</P>
+<P>See this section of the manual to get started:
+</P>
+<P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A>
+</P>
+<P>The person who created this package is W. Michael Brown at Intel
+(michael.w.brown at intel.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-LB package
+</H4>
+<P>This package contains a LAMMPS implementation of a background
+Lattice-Boltzmann fluid, which can be used to model MD particles
+influenced by hydrodynamic forces.
+</P>
+<P>See this doc page and its related commands to get started:
+</P>
+<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>
+</P>
+<P>The people who created this package are Frances Mackay (fmackay at
+uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
+Western Ontario. Contact them directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-MISC package
+</H4>
+<P>The files in this package are a potpourri of (mostly) unrelated
+features contributed to LAMMPS by users. Each feature is a single
+pair of files (*.cpp and *.h).
+</P>
+<P>More information about each feature can be found by reading its doc
+page in the LAMMPS doc directory. The doc page which lists all LAMMPS
+input script commands is as follows:
+</P>
+<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
+</P>
+<P>User-contributed features are listed at the bottom of the fix,
+compute, pair, etc sections.
+</P>
+<P>The list of features and author of each is given in the
+src/USER-MISC/README file.
+</P>
+<P>You should contact the author directly if you have specific questions
+about the feature or its coding.
+</P>
+<HR>
+
+<H4>USER-MOLFILE package
+</H4>
+<P>This package contains a dump molfile command which uses molfile
+plugins that are bundled with the
+<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and
+analysis program, to enable LAMMPS to dump its information in formats
+compatible with various molecular simulation tools.
+</P>
+<P>The package only provides the interface code, not the plugins. These
+can be obtained from a VMD installation which has to match the
+platform that you are using to compile LAMMPS for. By adding plugins
+to VMD, support for new file formats can be added to LAMMPS (or VMD or
+other programs that use them) without having to recompile the
+application itself.
+</P>
+<P>See this doc page to get started:
+</P>
+<P><A HREF = "dump_molfile.html#acc_5">dump molfile</A>
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-OMP package
+</H4>
+<P>This package provides OpenMP multi-threading support and
+other optimizations of various LAMMPS pair styles, dihedral
+styles, and fix styles.
+</P>
+<P>See this section of the manual to get started:
+</P>
+<P><A HREF = "Section_accelerate.html#acc_5">Section_accelerate</A>
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-PHONON package
+</H4>
+<P>This package contains a fix phonon command that calculates dynamical
+matrices, which can then be used to compute phonon dispersion
+relations, directly from molecular dynamics simulations.
+</P>
+<P>See this doc page to get started:
+</P>
+<P><A HREF = "fix_phonon.html">fix phonon</A>
+</P>
+<P>The person who created this package is Ling-Ti Kong (konglt at
+sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
+if you have questions.
+</P>
+<HR>
+
+<H4>USER-QMMM package
+</H4>
+<P>This package provides a fix qmmm command which allows LAMMPS to be
+used in a QM/MM simulation, currently only in combination with pw.x
+code from the <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> package.
+</P>
+
+
+<P>The current implementation only supports an ONIOM style mechanical
+coupling to the Quantum ESPRESSO plane wave DFT package.
+Electrostatic coupling is in preparation and the interface has been
+written in a manner that coupling to other QM codes should be possible
+without changes to LAMMPS itself.
+</P>
+<P>See this doc page to get started:
+</P>
+<P><A HREF = "fix_qmmm.html">fix qmmm</A>
+</P>
+<P>as well as the lib/qmmm/README file.
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-QTB package
+</H4>
+<P>This package provides a self-consistent quantum treatment of the
+vibrational modes in a classical molecular dynamics simulation. By
+coupling the MD simulation to a colored thermostat, it introduces zero
+point energy into the system, alter the energy power spectrum and the
+heat capacity towards their quantum nature. This package could be of
+interest if one wants to model systems at temperatures lower than
+their classical limits or when temperatures ramp up across the
+classical limits in the simulation.
+</P>
+<P>See these two doc pages to get started:
+</P>
+<P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a
+colored thermostat and can be used with other time integration schemes
+like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>.
+</P>
+<P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a
+multi-scale shock technique simulation by coupling the quantum thermal
+bath with the shocked system.
+</P>
+<P>The person who created this package is Yuan Shen (sy0302 at
+stanford.edu) at Stanford University. Contact him directly if you
+have questions.
+</P>
+<HR>
+
+<H4>USER-REAXC package
+</H4>
+<P>This package contains a implementation for LAMMPS of the ReaxFF force
+field. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. It was originally developed by Adri van Duin and the Goddard
+group at CalTech.
+</P>
+<P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
+C, should give identical or very similar results to pair_style reax,
+which is a ReaxFF implementation on top of a Fortran library, a
+version of which library was originally authored by Adri van Duin.
+</P>
+<P>The reax/c version should be somewhat faster and more scalable,
+particularly with respect to the charge equilibration calculation. It
+should also be easier to build and use since there are no complicating
+issues with Fortran memory allocation or linking to a Fortran library.
+</P>
+<P>For technical details about this implemention of ReaxFF, see
+this paper:
+</P>
+<P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
+and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
+S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
+</P>
+<P>See the doc page for the pair_style reax/c command for details
+of how to use it in LAMMPS.
+</P>
+<P>The person who created this package is Hasan Metin Aktulga (hmaktulga
+at lbl.gov), while at Purdue University. Contact him directly, or
+Aidan Thompson at Sandia (athomps at sandia.gov), if you have
+questions.
+</P>
+<HR>
+
+<H4>USER-SPH package
+</H4>
+<P>This package implements smoothed particle hydrodynamics (SPH) in
+LAMMPS. Currently, the package has the following features:
+</P>
+<P>* Tait, ideal gas, Lennard-Jones equation of states, full support for
+ complete (i.e. internal-energy dependent) equations of state
+* plain or Monaghans XSPH integration of the equations of motion
+* density continuity or density summation to propagate the density field
+* commands to set internal energy and density of particles from the
+ input script
+* output commands to access internal energy and density for dumping and
+ thermo output
+</P>
+<P>See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
+</P>
+<P>There are example scripts for using this package in examples/USER/sph.
+</P>
+<P>The person who created this package is Georg Ganzenmuller at the
+Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
+Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
+you have questions.
+</P>
+</HTML>
diff --git a/doc/doc2/Section_perf.html b/doc/doc2/Section_perf.html
new file mode 100644
index 000000000..330d99407
--- /dev/null
+++ b/doc/doc2/Section_perf.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "Section_example.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_tools.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>8. Performance & scalability
+</H3>
+<P>LAMMPS performance on several prototypical benchmarks and machines is
+discussed on the Benchmarks page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> where
+CPU timings and parallel efficiencies are listed. Here, the
+benchmarks are described briefly and some useful rules of thumb about
+their performance are highlighted.
+</P>
+<P>These are the 5 benchmark problems:
+</P>
+<OL><LI>LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
+neighbors per atom), NVE integration
+
+<LI>Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
+pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
+atom), NVE integration
+
+<LI>EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
+neighbors per atom), NVE integration
+
+<LI>Chute = granular chute flow, frictional history potential with 1.1
+sigma cutoff (7 neighbors per atom), NVE integration
+
+<LI>Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
+field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
+particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
+integration
+</OL>
+<P>The input files for running the benchmarks are included in the LAMMPS
+distribution, as are sample output files. Each of the 5 problems has
+32,000 atoms and runs for 100 timesteps. Each can be run as a serial
+benchmarks (on one processor) or in parallel. In parallel, each
+benchmark can be run as a fixed-size or scaled-size problem. For
+fixed-size benchmarking, the same 32K atom problem is run on various
+numbers of processors. For scaled-size benchmarking, the model size
+is increased with the number of processors. E.g. on 8 processors, a
+256K-atom problem is run; on 1024 processors, a 32-million atom
+problem is run, etc.
+</P>
+<P>A useful metric from the benchmarks is the CPU cost per atom per
+timestep. Since LAMMPS performance scales roughly linearly with
+problem size and timesteps, the run time of any problem using the same
+model (atom style, force field, cutoff, etc) can then be estimated.
+For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler
+under Red Hat Linux), the CPU run-time in seconds/atom/timestep for
+the 5 problems is
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD ALIGN ="right">Problem:</TD><TD > LJ</TD><TD > Chain</TD><TD > EAM</TD><TD > Chute</TD><TD > Rhodopsin</TD></TR>
+<TR ALIGN="center"><TD ALIGN ="right">CPU/atom/step:</TD><TD > 4.55E-6</TD><TD > 2.18E-6</TD><TD > 9.38E-6</TD><TD > 2.18E-6</TD><TD > 1.11E-4</TD></TR>
+<TR ALIGN="center"><TD ALIGN ="right">Ratio to LJ:</TD><TD > 1.0</TD><TD > 0.48</TD><TD > 2.06</TD><TD > 0.48</TD><TD > 24.5
+</TD></TR></TABLE></DIV>
+
+<P>The ratios mean that if the atomic LJ system has a normalized cost of
+1.0, the bead-spring chains and granular systems run 2x faster, while
+the EAM metal and solvated protein models run 2x and 25x slower
+respectively. The bulk of these cost differences is due to the
+expense of computing a particular pairwise force field for a given
+number of neighbors per atom.
+</P>
+<P>Performance on a parallel machine can also be predicted from the
+one-processor timings if the parallel efficiency can be estimated.
+The communication bandwidth and latency of a particular parallel
+machine affects the efficiency. On most machines LAMMPS will give
+fixed-size parallel efficiencies on these benchmarks above 50% so long
+as the atoms/processor count is a few 100 or greater - i.e. on 64 to
+128 processors. Likewise, scaled-size parallel efficiencies will
+typically be 80% or greater up to very large processor counts. The
+benchmark data on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> gives specific examples on
+some different machines, including a run of 3/4 of a billion LJ atoms
+on 1500 processors that ran at 85% parallel efficiency.
+</P>
+</HTML>
diff --git a/doc/doc2/Section_python.html b/doc/doc2/Section_python.html
new file mode 100644
index 000000000..c89503510
--- /dev/null
+++ b/doc/doc2/Section_python.html
@@ -0,0 +1,792 @@
+<HTML>
+<CENTER><A HREF = "Section_modify.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_errors.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>11. Python interface to LAMMPS
+</H3>
+<P>LAMMPS can work together with Python in two ways. First, Python can
+wrap LAMMPS through the <A HREF = "Section_howto.html#howto_19">LAMMPS library
+interface</A>, so that a Python script can
+create one or more instances of LAMMPS and launch one or more
+simulations. In Python lingo, this is "extending" Python with LAMMPS.
+</P>
+<P>Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
+script can invoke Python code, and pass information back-and-forth
+between the input script and Python functions you write. The Python
+code can also callback to LAMMPS to query or change its attributes.
+In Python lingo, this is "embedding" Python in LAMMPS.
+</P>
+<P>This section describes how to do both.
+</P>
+<UL><LI>11.1 <A HREF = "#py_1">Overview of running LAMMPS from Python</A>
+<LI>11.2 <A HREF = "#py_2">Overview of using Python from a LAMMPS script</A>
+<LI>11.3 <A HREF = "#py_3">Building LAMMPS as a shared library</A>
+<LI>11.4 <A HREF = "#py_4">Installing the Python wrapper into Python</A>
+<LI>11.5 <A HREF = "#py_5">Extending Python with MPI to run in parallel</A>
+<LI>11.6 <A HREF = "#py_6">Testing the Python-LAMMPS interface</A>
+<LI>11.7 <A HREF = "#py_7">Using LAMMPS from Python</A>
+<LI>11.8 <A HREF = "#py_8">Example Python scripts that use LAMMPS</A>
+</UL>
+<P>If you are not familiar with it, <A HREF = "http://www.python.org">Python</A> is a
+powerful scripting and programming language which can essentially do
+anything that faster, lower-level languages like C or C++ can do, but
+typically with much fewer lines of code. When used in embedded mode,
+Python can perform operations that the simplistic LAMMPS input script
+syntax cannot. Python can be also be used as a "glue" language to
+drive a program through its library interface, or to hook multiple
+pieces of software together, such as a simulation package plus a
+visualization package, or to run a coupled multiscale or multiphysics
+model.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the manual and
+the couple directory of the distribution for more ideas about coupling
+LAMMPS to other codes. See <A HREF = "Section_howto.html#howto_19">Section_howto
+19</A> for a description of the LAMMPS
+library interface provided in src/library.cpp and src/library.h, and
+how to extend it for your needs. As described below, that interface
+is what is exposed to Python either when calling LAMMPS from Python or
+when calling Python from a LAMMPS input script and then calling back
+to LAMMPS from Python code. The library interface is designed to be
+easy to add functions to. Thus the Python interface to LAMMPS is also
+easy to extend as well.
+</P>
+<P>If you create interesting Python scripts that run LAMMPS or
+interesting Python functions that can be called from a LAMMPS input
+script, that you think would be useful to other users, please <A HREF = "http://lammps.sandia.gov/authors.html">email
+them to the developers</A>. We can
+include them in the LAMMPS distribution.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "py_1"></A><H4>11.1 Overview of running LAMMPS from Python
+</H4>
+<P>The LAMMPS distribution includes a python directory with all you need
+to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS
+library interface, with one wrapper function per LAMMPS library
+function. This file makes it is possible to do the following either
+from a Python script, or interactively from a Python prompt: create
+one or more instances of LAMMPS, invoke LAMMPS commands or give it an
+input script, run LAMMPS incrementally, extract LAMMPS results, an
+modify internal LAMMPS variables. From a Python script you can do
+this in serial or parallel. Running Python interactively in parallel
+does not generally work, unless you have a version of Python that
+extends standard Python to enable multiple instances of Python to read
+what you type.
+</P>
+<P>To do all of this, you must first build LAMMPS as a shared library,
+then insure that your Python can find the python/lammps.py file and
+the shared library. These steps are explained in subsequent sections
+11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a
+parallel Python program and how to test that you are ready to use
+LAMMPS from Python. Section 11.7 lists all the functions in the
+current LAMMPS library interface and how to call them from Python.
+</P>
+<P>Section 11.8 gives some examples of coupling LAMMPS to other tools via
+Python. For example, LAMMPS can easily be coupled to a GUI or other
+visualization tools that display graphs or animations in real time as
+LAMMPS runs. Examples of such scripts are inlcluded in the python
+directory.
+</P>
+<P>Two advantages of using Python to run LAMMPS are how concise the
+language is, and that it can be run interactively, enabling rapid
+development and debugging of programs. If you use it to mostly invoke
+costly operations within LAMMPS, such as running a simulation for a
+reasonable number of timesteps, then the overhead cost of invoking
+LAMMPS thru Python will be negligible.
+</P>
+<P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
+"ctypes" package in Python, which auto-generates the interface code
+needed between Python and a set of C interface routines for a library.
+Ctypes is part of standard Python for versions 2.5 and later. You can
+check which version of Python you have installed, by simply typing
+"python" at a shell prompt.
+</P>
+<HR>
+
+<A NAME = "py_2"></A><H4>11.2 Overview of using Python from a LAMMPS script
+</H4>
+<P>IMPORTANT NOTE: It is not currently possible to use the
+<A HREF = "python.html">python</A> command described in this section with Python 3,
+only with Python 2. The C API changed from Python 2 to 3 and the
+LAMMPS code is not compatible with both.
+</P>
+<P>LAMMPS has a <A HREF = "python.html">python</A> command which can be used in an
+input script to define and execute a Python function that you write
+the code for. The Python function can also be assigned to a LAMMPS
+python-style variable via the <A HREF = "variable.html">variable</A> command. Each
+time the variable is evaluated, either in the LAMMPS input script
+itself, or by another LAMMPS command that uses the variable, this will
+trigger the Python function to be invoked.
+</P>
+<P>The Python code for the function can be included directly in the input
+script or in an auxiliary file. The function can have arguments which
+are mapped to LAMMPS variables (also defined in the input script) and
+it can return a value to a LAMMPS variable. This is thus a mechanism
+for your input script to pass information to a piece of Python code,
+ask Python to execute the code, and return information to your input
+script.
+</P>
+<P>Note that a Python function can be arbitrarily complex. It can import
+other Python modules, instantiate Python classes, call other Python
+functions, etc. The Python code that you provide can contain more
+code than the single function. It can contain other functions or
+Python classes, as well as global variables or other mechanisms for
+storing state between calls from LAMMPS to the function.
+</P>
+<P>The Python function you provide can consist of "pure" Python code that
+only performs operations provided by standard Python. However, the
+Python function can also "call back" to LAMMPS through its
+Python-wrapped library interface, in the manner described in the
+previous section 11.1. This means it can issue LAMMPS input script
+commands or query and set internal LAMMPS state. As an example, this
+can be useful in an input script to create a more complex loop with
+branching logic, than can be created using the simple looping and
+brancing logic enabled by the <A HREF = "next.html">next</A> and <A HREF = "if.html">if</A>
+commands.
+</P>
+<P>See the <A HREF = "python.html">python</A> doc page and the <A HREF = "variable.html">variable</A>
+doc page for its python-style variables for more info, including
+examples of Python code you can write for both pure Python operations
+and callbacks to LAMMPS.
+</P>
+<P>To run pure Python code from LAMMPS, you only need to build LAMMPS
+with the PYTHON package installed:
+</P>
+<P>make yes-python
+make machine
+</P>
+<P>Note that this will link LAMMPS with the Python library on your
+system, which typically requires several auxiliary system libraries to
+also be linked. The list of these libraries and the paths to find
+them are specified in the lib/python/Makefile.lammps file. You need
+to insure that file contains the correct information for your version
+of Python and your machine to successfully build LAMMPS. See the
+lib/python/README file for more info.
+</P>
+<P>If you want to write Python code with callbacks to LAMMPS, then you
+must also follow the steps overviewed in the preceeding section (11.1)
+for running LAMMPS from Python. I.e. you must build LAMMPS as a
+shared library and insure that Python can find the python/lammps.py
+file and the shared library.
+</P>
+<HR>
+
+<A NAME = "py_3"></A><H4>11.3 Building LAMMPS as a shared library
+</H4>
+<P>Instructions on how to build LAMMPS as a shared library are given in
+<A HREF = "Section_start.html#start_5">Section_start 5</A>. A shared library is one
+that is dynamically loadable, which is what Python requires to wrap
+LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
+</P>
+<P>>From the src directory, type
+</P>
+<PRE>make foo mode=shlib
+</PRE>
+<P>where foo is the machine target name, such as linux or g++ or serial.
+This should create the file liblammps_foo.so in the src directory, as
+well as a soft link liblammps.so, which is what the Python wrapper will
+load by default. Note that if you are building multiple machine
+versions of the shared library, the soft link is always set to the
+most recently built version.
+</P>
+<P>If this fails, see <A HREF = "Section_start.html#start_5">Section_start 5</A> for
+more details, especially if your LAMMPS build uses auxiliary libraries
+like MPI or FFTW which may not be built as shared libraries on your
+system.
+</P>
+<HR>
+
+<A NAME = "py_4"></A><H4>11.4 Installing the Python wrapper into Python
+</H4>
+<P>For Python to invoke LAMMPS, there are 2 files it needs to know about:
+</P>
+<UL><LI>python/lammps.py
+<LI>src/liblammps.so
+</UL>
+<P>Lammps.py is the Python wrapper on the LAMMPS library interface.
+Liblammps.so is the shared LAMMPS library that Python loads, as
+described above.
+</P>
+<P>You can insure Python can find these files in one of two ways:
+</P>
+<UL><LI>set two environment variables
+<LI>run the python/install.py script
+</UL>
+<P>If you set the paths to these files as environment variables, you only
+have to do it once. For the csh or tcsh shells, add something like
+this to your ~/.cshrc file, one line for each of the two files:
+</P>
+<PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python
+setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
+</PRE>
+<P>If you use the python/install.py script, you need to invoke it every
+time you rebuild LAMMPS (as a shared library) or make changes to the
+python/lammps.py file.
+</P>
+<P>You can invoke install.py from the python directory as
+</P>
+<PRE>% python install.py [libdir] [pydir]
+</PRE>
+<P>The optional libdir is where to copy the LAMMPS shared library to; the
+default is /usr/local/lib. The optional pydir is where to copy the
+lammps.py file to; the default is the site-packages directory of the
+version of Python that is running the install script.
+</P>
+<P>Note that libdir must be a location that is in your default
+LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a
+location that Python looks in by default for imported modules, like
+its site-packages dir. If you want to copy these files to
+non-standard locations, such as within your own user space, you will
+need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
+accordingly, as above.
+</P>
+<P>If the install.py script does not allow you to copy files into system
+directories, prefix the python command with "sudo". If you do this,
+make sure that the Python that root runs is the same as the Python you
+run. E.g. you may need to do something like
+</P>
+<PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir]
+</PRE>
+<P>You can also invoke install.py from the make command in the src
+directory as
+</P>
+<PRE>% make install-python
+</PRE>
+<P>In this mode you cannot append optional arguments. Again, you may
+need to prefix this with "sudo". In this mode you cannot control
+which Python is invoked by root.
+</P>
+<P>Note that if you want Python to be able to load different versions of
+the LAMMPS shared library (see <A HREF = "#py_5">this section</A> below), you will
+need to manually copy files like liblammps_g++.so into the appropriate
+system directory. This is not needed if you set the LD_LIBRARY_PATH
+environment variable as described above.
+</P>
+<HR>
+
+<A NAME = "py_5"></A><H4>11.5 Extending Python with MPI to run in parallel
+</H4>
+<P>If you wish to run LAMMPS in parallel from Python, you need to extend
+your Python with an interface to MPI. This also allows you to
+make MPI calls directly from Python in your script, if you desire.
+</P>
+<P>There are several Python packages available that purport to wrap MPI
+as a library and allow MPI functions to be called from Python.
+</P>
+<P>These include
+</P>
+<UL><LI><A HREF = "http://pympi.sourceforge.net/">pyMPI</A>
+<LI><A HREF = "http://code.google.com/p/maroonmpi/">maroonmpi</A>
+<LI><A HREF = "http://code.google.com/p/mpi4py/">mpi4py</A>
+<LI><A HREF = "http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16">myMPI</A>
+<LI><A HREF = "http://code.google.com/p/pypar">Pypar</A>
+</UL>
+<P>All of these except pyMPI work by wrapping the MPI library and
+exposing (some portion of) its interface to your Python script. This
+means Python cannot be used interactively in parallel, since they do
+not address the issue of interactive input to multiple instances of
+Python running on different processors. The one exception is pyMPI,
+which alters the Python interpreter to address this issue, and (I
+believe) creates a new alternate executable (in place of "python"
+itself) as a result.
+</P>
+<P>In principle any of these Python/MPI packages should work to invoke
+LAMMPS in parallel and to make MPI calls themselves from a Python
+script which is itself running in parallel. However, when I
+downloaded and looked at a few of them, their documentation was
+incomplete and I had trouble with their installation. It's not clear
+if some of the packages are still being actively developed and
+supported.
+</P>
+<P>The one I recommend, since I have successfully used it with LAMMPS, is
+Pypar. Pypar requires the ubiquitous <A HREF = "http://numpy.scipy.org">Numpy
+package</A> be installed in your Python. After
+launching python, type
+</P>
+<PRE>import numpy
+</PRE>
+<P>to see if it is installed. If not, here is how to install it (version
+1.3.0b1 as of April 2009). Unpack the numpy tarball and from its
+top-level directory, type
+</P>
+<PRE>python setup.py build
+sudo python setup.py install
+</PRE>
+<P>The "sudo" is only needed if required to copy Numpy files into your
+Python distribution's site-packages directory.
+</P>
+<P>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
+and from its "source" directory, type
+</P>
+<PRE>python setup.py build
+sudo python setup.py install
+</PRE>
+<P>Again, the "sudo" is only needed if required to copy Pypar files into
+your Python distribution's site-packages directory.
+</P>
+<P>If you have successully installed Pypar, you should be able to run
+Python and type
+</P>
+<PRE>import pypar
+</PRE>
+<P>without error. You should also be able to run python in parallel
+on a simple test script
+</P>
+<PRE>% mpirun -np 4 python test.py
+</PRE>
+<P>where test.py contains the lines
+</P>
+<PRE>import pypar
+print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
+</PRE>
+<P>and see one line of output for each processor you run on.
+</P>
+<P>IMPORTANT NOTE: To use Pypar and LAMMPS in parallel from Python, you
+must insure both are using the same version of MPI. If you only have
+one MPI installed on your system, this is not an issue, but it can be
+if you have multiple MPIs. Your LAMMPS build is explicit about which
+MPI it is using, since you specify the details in your lo-level
+src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find
+information about the MPI it uses to build against. And it tries to
+load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
+the MPI library that LAMMPS is using. If you have problems running
+both Pypar and LAMMPS together, this is an issue you may need to
+address, e.g. by moving other MPI installations so that Pypar finds
+the right one.
+</P>
+<HR>
+
+<A NAME = "py_6"></A><H4>11.6 Testing the Python-LAMMPS interface
+</H4>
+<P>To test if LAMMPS is callable from Python, launch Python interactively
+and type:
+</P>
+<PRE>>>> from lammps import lammps
+>>> lmp = lammps()
+</PRE>
+<P>If you get no errors, you're ready to use LAMMPS from Python. If the
+2nd command fails, the most common error to see is
+</P>
+<PRE>OSError: Could not load LAMMPS dynamic library
+</PRE>
+<P>which means Python was unable to load the LAMMPS shared library. This
+typically occurs if the system can't find the LAMMPS shared library or
+one of the auxiliary shared libraries it depends on, or if something
+about the library is incompatible with your Python. The error message
+should give you an indication of what went wrong.
+</P>
+<P>You can also test the load directly in Python as follows, without
+first importing from the lammps.py file:
+</P>
+<PRE>>>> from ctypes import CDLL
+>>> CDLL("liblammps.so")
+</PRE>
+<P>If an error occurs, carefully go thru the steps in <A HREF = "Section_start.html#start_5">Section_start
+5</A> and above about building a shared
+library and about insuring Python can find the necessary two files
+it needs.
+</P>
+<H5><B>Test LAMMPS and Python in serial:</B>
+</H5>
+<P>To run a LAMMPS test in serial, type these lines into Python
+interactively from the bench directory:
+</P>
+<PRE>>>> from lammps import lammps
+>>> lmp = lammps()
+>>> lmp.file("in.lj")
+</PRE>
+<P>Or put the same lines in the file test.py and run it as
+</P>
+<PRE>% python test.py
+</PRE>
+<P>Either way, you should see the results of running the in.lj benchmark
+on a single processor appear on the screen, the same as if you had
+typed something like:
+</P>
+<PRE>lmp_g++ < in.lj
+</PRE>
+<H5><B>Test LAMMPS and Python in parallel:</B>
+</H5>
+<P>To run LAMMPS in parallel, assuming you have installed the
+<A HREF = "http://datamining.anu.edu.au/~ole/pypar">Pypar</A> package as discussed
+above, create a test.py file containing these lines:
+</P>
+<PRE>import pypar
+from lammps import lammps
+lmp = lammps()
+lmp.file("in.lj")
+print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
+pypar.finalize()
+</PRE>
+<P>You can then run it in parallel as:
+</P>
+<PRE>% mpirun -np 4 python test.py
+</PRE>
+<P>and you should see the same output as if you had typed
+</P>
+<PRE>% mpirun -np 4 lmp_g++ < in.lj
+</PRE>
+<P>Note that if you leave out the 3 lines from test.py that specify Pypar
+commands you will instantiate and run LAMMPS independently on each of
+the P processors specified in the mpirun command. In this case you
+should get 4 sets of output, each showing that a LAMMPS run was made
+on a single processor, instead of one set of output showing that
+LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
+means that Pypar is not working correctly.
+</P>
+<P>Also note that once you import the PyPar module, Pypar initializes MPI
+for you, and you can use MPI calls directly in your Python script, as
+described in the Pypar documentation. The last line of your Python
+script should be pypar.finalize(), to insure MPI is shut down
+correctly.
+</P>
+<H5><B>Running Python scripts:</B>
+</H5>
+<P>Note that any Python script (not just for LAMMPS) can be invoked in
+one of several ways:
+</P>
+<PRE>% python foo.script
+% python -i foo.script
+% foo.script
+</PRE>
+<P>The last command requires that the first line of the script be
+something like this:
+</P>
+<PRE>#!/usr/local/bin/python
+#!/usr/local/bin/python -i
+</PRE>
+<P>where the path points to where you have Python installed, and that you
+have made the script file executable:
+</P>
+<PRE>% chmod +x foo.script
+</PRE>
+<P>Without the "-i" flag, Python will exit when the script finishes.
+With the "-i" flag, you will be left in the Python interpreter when
+the script finishes, so you can type subsequent commands. As
+mentioned above, you can only run Python interactively when running
+Python on a single processor, not in parallel.
+</P>
+<HR>
+
+<HR>
+
+<A NAME = "py_7"></A><H4>11.7 Using LAMMPS from Python
+</H4>
+<P>As described above, the Python interface to LAMMPS consists of a
+Python "lammps" module, the source code for which is in
+python/lammps.py, which creates a "lammps" object, with a set of
+methods that can be invoked on that object. The sample Python code
+below assumes you have first imported the "lammps" module in your
+Python script, as follows:
+</P>
+<PRE>from lammps import lammps
+</PRE>
+<P>These are the methods defined by the lammps module. If you look at
+the files src/library.cpp and src/library.h you will see that they
+correspond one-to-one with calls you can make to the LAMMPS library
+from a C++ or C or Fortran program.
+</P>
+<PRE>lmp = lammps() # create a LAMMPS object using the default liblammps.so library
+lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object
+lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
+lmp = lammps("",list) # ditto, with command-line args, e.g. list = ["-echo","screen"]
+lmp = lammps("g++",list)
+</PRE>
+<PRE>lmp.close() # destroy a LAMMPS object
+</PRE>
+<PRE>lmp.file(file) # run an entire input script, file = "in.lj"
+lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
+</PRE>
+<PRE>xlo = lmp.extract_global(name,type) # extract a global quantity
+ # name = "boxxlo", "nlocal", etc
+ # type = 0 = int
+ # 1 = double
+</PRE>
+<PRE>coords = lmp.extract_atom(name,type) # extract a per-atom quantity
+ # name = "x", "type", etc
+ # type = 0 = vector of ints
+ # 1 = array of ints
+ # 2 = vector of doubles
+ # 3 = array of doubles
+</PRE>
+<PRE>eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
+v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
+ # id = ID of compute or fix
+ # style = 0 = global data
+ # 1 = per-atom data
+ # 2 = local data
+ # type = 0 = scalar
+ # 1 = vector
+ # 2 = array
+ # i,j = indices of value in global vector or array
+</PRE>
+<PRE>var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
+ # name = name of variable
+ # group = group ID (ignored for equal-style variables)
+ # flag = 0 = equal-style variable
+ # 1 = atom-style variable
+</PRE>
+<PRE>flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
+natoms = lmp.get_natoms() # total # of atoms as int
+data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
+ # name = "x", "charge", "type", etc
+ # count = # of per-atom values, 1 or 3, etc
+lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
+ # name = "x", "charge", "type", etc
+ # count = # of per-atom values, 1 or 3, etc
+</PRE>
+<HR>
+
+<P>IMPORTANT NOTE: Currently, the creation of a LAMMPS object from within
+lammps.py does not take an MPI communicator as an argument. There
+should be a way to do this, so that the LAMMPS instance runs on a
+subset of processors if desired, but I don't know how to do it from
+Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the
+processors. If someone figures out how to do this with one or more of
+the Python wrappers for MPI, like Pypar, please let us know and we
+will amend these doc pages.
+</P>
+<P>The lines
+</P>
+<PRE>from lammps import lammps
+lmp = lammps()
+</PRE>
+<P>create an instance of LAMMPS, wrapped in a Python class by the lammps
+Python module, and return an instance of the Python class as lmp. It
+is used to make all subequent calls to the LAMMPS library.
+</P>
+<P>Additional arguments can be used to tell Python the name of the shared
+library to load or to pass arguments to the LAMMPS instance, the same
+as if LAMMPS were launched from a command-line prompt.
+</P>
+<P>If the ptr argument is set like this:
+</P>
+<PRE>lmp = lammps(ptr=lmpptr)
+</PRE>
+<P>then lmpptr must be an argument passed to Python via the LAMMPS
+<A HREF = "python.html">python</A> command, when it is used to define a Python
+function that is invoked by the LAMMPS input script. This mode of
+using Python with LAMMPS is described above in 11.2. The variable
+lmpptr refers to the instance of LAMMPS that called the embedded
+Python interpreter. Using it as an argument to lammps() allows the
+returned Python class instance "lmp" to make calls to that instance of
+LAMMPS. See the <A HREF = "python.html">python</A> command doc page for examples
+using this syntax.
+</P>
+<P>Note that you can create multiple LAMMPS objects in your Python
+script, and coordinate and run multiple simulations, e.g.
+</P>
+<PRE>from lammps import lammps
+lmp1 = lammps()
+lmp2 = lammps()
+lmp1.file("in.file1")
+lmp2.file("in.file2")
+</PRE>
+<P>The file() and command() methods allow an input script or single
+commands to be invoked.
+</P>
+<P>The extract_global(), extract_atom(), extract_compute(),
+extract_fix(), and extract_variable() methods return values or
+pointers to data structures internal to LAMMPS.
+</P>
+<P>For extract_global() see the src/library.cpp file for the list of
+valid names. New names could easily be added. A double or integer is
+returned. You need to specify the appropriate data type via the type
+argument.
+</P>
+<P>For extract_atom(), a pointer to internal LAMMPS atom-based data is
+returned, which you can use via normal Python subscripting. See the
+extract() method in the src/atom.cpp file for a list of valid names.
+Again, new names could easily be added. A pointer to a vector of
+doubles or integers, or a pointer to an array of doubles (double **)
+or integers (int **) is returned. You need to specify the appropriate
+data type via the type argument.
+</P>
+<P>For extract_compute() and extract_fix(), the global, per-atom, or
+local data calulated by the compute or fix can be accessed. What is
+returned depends on whether the compute or fix calculates a scalar or
+vector or array. For a scalar, a single double value is returned. If
+the compute or fix calculates a vector or array, a pointer to the
+internal LAMMPS data is returned, which you can use via normal Python
+subscripting. The one exception is that for a fix that calculates a
+global vector or array, a single double value from the vector or array
+is returned, indexed by I (vector) or I and J (array). I,J are
+zero-based indices. The I,J arguments can be left out if not needed.
+See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> of the manual for a
+discussion of global, per-atom, and local data, and of scalar, vector,
+and array data types. See the doc pages for individual
+<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
+they calculate and store.
+</P>
+<P>For extract_variable(), an <A HREF = "variable.html">equal-style or atom-style
+variable</A> is evaluated and its result returned.
+</P>
+<P>For equal-style variables a single double value is returned and the
+group argument is ignored. For atom-style variables, a vector of
+doubles is returned, one value per atom, which you can use via normal
+Python subscripting. The values will be zero for atoms not in the
+specified group.
+</P>
+<P>The get_natoms() method returns the total number of atoms in the
+simulation, as an int.
+</P>
+<P>The gather_atoms() method returns a ctypes vector of ints or doubles
+as specified by type, of length count*natoms, for the property of all
+the atoms in the simulation specified by name, ordered by count and
+then by atom ID. The vector can be used via normal Python
+subscripting. If atom IDs are not consecutively ordered within
+LAMMPS, a None is returned as indication of an error.
+</P>
+<P>Note that the data structure gather_atoms("x") returns is different
+from the data structure returned by extract_atom("x") in four ways.
+(1) Gather_atoms() returns a vector which you index as x[i];
+extract_atom() returns an array which you index as x[i][j]. (2)
+Gather_atoms() orders the atoms by atom ID while extract_atom() does
+not. (3) Gathert_atoms() returns a list of all atoms in the
+simulation; extract_atoms() returns just the atoms local to each
+processor. (4) Finally, the gather_atoms() data structure is a copy
+of the atom coords stored internally in LAMMPS, whereas extract_atom()
+returns an array that effectively points directly to the internal
+data. This means you can change values inside LAMMPS from Python by
+assigning a new values to the extract_atom() array. To do this with
+the gather_atoms() vector, you need to change values in the vector,
+then invoke the scatter_atoms() method.
+</P>
+<P>The scatter_atoms() method takes a vector of ints or doubles as
+specified by type, of length count*natoms, for the property of all the
+atoms in the simulation specified by name, ordered by bount and then
+by atom ID. It uses the vector of data to overwrite the corresponding
+properties for each atom inside LAMMPS. This requires LAMMPS to have
+its "map" option enabled; see the <A HREF = "atom_modify.html">atom_modify</A>
+command for details. If it is not, or if atom IDs are not
+consecutively ordered, no coordinates are reset.
+</P>
+<P>The array of coordinates passed to scatter_atoms() must be a ctypes
+vector of ints or doubles, allocated and initialized something like
+this:
+</P>
+<PRE>from ctypes import *
+natoms = lmp.get_natoms()
+n3 = 3*natoms
+x = (n3*c_double)()
+x[0] = x coord of atom with ID 1
+x[1] = y coord of atom with ID 1
+x[2] = z coord of atom with ID 1
+x[3] = x coord of atom with ID 2
+...
+x[n3-1] = z coord of atom with ID natoms
+lmp.scatter_coords("x",1,3,x)
+</PRE>
+<P>Alternatively, you can just change values in the vector returned by
+gather_atoms("x",1,3), since it is a ctypes vector of doubles.
+</P>
+<HR>
+
+<P>As noted above, these Python class methods correspond one-to-one with
+the functions in the LAMMPS library interface in src/library.cpp and
+library.h. This means you can extend the Python wrapper via the
+following steps:
+</P>
+<UL><LI>Add a new interface function to src/library.cpp and
+src/library.h.
+
+<LI>Rebuild LAMMPS as a shared library.
+
+<LI>Add a wrapper method to python/lammps.py for this interface
+function.
+
+<LI>You should now be able to invoke the new interface function from a
+Python script. Isn't ctypes amazing?
+</UL>
+<HR>
+
+<HR>
+
+<A NAME = "py_8"></A><H4>11.8 Example Python scripts that use LAMMPS
+</H4>
+<P>These are the Python scripts included as demos in the python/examples
+directory of the LAMMPS distribution, to illustrate the kinds of
+things that are possible when Python wraps LAMMPS. If you create your
+own scripts, send them to us and we can include them in the LAMMPS
+distribution.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script thru Python</TD></TR>
+<TR><TD >demo.py</TD><TD > invoke various LAMMPS library interface routines</TD></TR>
+<TR><TD >simple.py</TD><TD > mimic operation of couple/simple/simple.cpp in Python</TD></TR>
+<TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
+<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
+<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
+<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz_tool.py and plot.py and gui.py
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<P>For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
+with "gl" or "atomeye" or "pymol" or "vmd", depending on what
+visualization package you have installed.
+</P>
+<P>Note that for GL, you need to be able to run the Pizza.py GL tool,
+which is included in the pizza sub-directory. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
+pages</A> for more info:
+</P>
+
+
+<P>Note that for AtomEye, you need version 3, and there is a line in the
+scripts that specifies the path and name of the executable. See the
+AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
+</P>
+<PRE>http://mt.seas.upenn.edu/Archive/Graphics/A
+http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
+</PRE>
+
+
+
+
+<P>The latter link is to AtomEye 3 which has the scriping
+capability needed by these Python scripts.
+</P>
+<P>Note that for PyMol, you need to have built and installed the
+open-source version of PyMol in your Python, so that you can import it
+from a Python script. See the PyMol WWW pages <A HREF = "http://www.pymol.org">here</A> or
+<A HREF = "http://sourceforge.net/scm/?type=svn&group_id=4546">here</A> for more details:
+</P>
+<PRE>http://www.pymol.org
+http://sourceforge.net/scm/?type=svn&group_id=4546
+</PRE>
+
+
+
+
+<P>The latter link is to the open-source version.
+</P>
+<P>Note that for VMD, you need a fairly current version (1.8.7 works for
+me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
+variables that have to match the VMD installation on your system.
+</P>
+<HR>
+
+<P>See the python/README file for instructions on how to run them and the
+source code for individual scripts for comments about what they do.
+</P>
+<P>Here are screenshots of the vizplotgui_tool.py script in action for
+different visualization package options. Click to see larger images:
+</P>
+<A HREF = "JPG/screenshot_gl.jpg"><IMG SRC = "JPG/screenshot_gl_small.jpg"></A>
+
+<A HREF = "JPG/screenshot_atomeye.jpg"><IMG SRC = "JPG/screenshot_atomeye_small.jpg"></A>
+
+<A HREF = "JPG/screenshot_pymol.jpg"><IMG SRC = "JPG/screenshot_pymol_small.jpg"></A>
+
+<A HREF = "JPG/screenshot_vmd.jpg"><IMG SRC = "JPG/screenshot_vmd_small.jpg"></A>
+
+</HTML>
diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html
new file mode 100644
index 000000000..20769a24b
--- /dev/null
+++ b/doc/doc2/Section_start.html
@@ -0,0 +1,1864 @@
+<HTML>
+<CENTER><A HREF = "Section_intro.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_commands.html">Next Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>2. Getting Started
+</H3>
+<P>This section describes how to build and run LAMMPS, for both new and
+experienced users.
+</P>
+2.1 <A HREF = "#start_1">What's in the LAMMPS distribution</A><BR>
+2.2 <A HREF = "#start_2">Making LAMMPS</A><BR>
+2.3 <A HREF = "#start_3">Making LAMMPS with optional packages</A><BR>
+2.4 <A HREF = "#start_4">Building LAMMPS via the Make.py script</A><BR>
+2.5 <A HREF = "#start_5">Building LAMMPS as a library</A><BR>
+2.6 <A HREF = "#start_6">Running LAMMPS</A><BR>
+2.7 <A HREF = "#start_7">Command-line options</A><BR>
+2.8 <A HREF = "#start_8">Screen output</A><BR>
+2.9 <A HREF = "#start_9">Tips for users of previous versions</A> <BR>
+
+<HR>
+
+<HR>
+
+<H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution
+</H4>
+<P>When you download a LAMMPS tarball you will need to unzip and untar
+the downloaded file with the following commands, after placing the
+tarball in an appropriate directory.
+</P>
+<PRE>gunzip lammps*.tar.gz
+tar xvf lammps*.tar
+</PRE>
+<P>This will create a LAMMPS directory containing two files and several
+sub-directories:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >README</TD><TD > text file</TD></TR>
+<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
+<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
+<TR><TD >doc</TD><TD > documentation</TD></TR>
+<TR><TD >examples</TD><TD > simple test problems</TD></TR>
+<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
+<TR><TD >src</TD><TD > source files</TD></TR>
+<TR><TD >tools</TD><TD > pre- and post-processing tools
+</TD></TR></TABLE></DIV>
+
+<P>Note that the <A HREF = "download">download page</A> also has links to download
+Windows exectubles and installers, as well as pre-built executables
+for a few specific Linux distributions. It also has instructions for
+how to download/install LAMMPS for Macs (via Homebrew), and to
+download and update LAMMPS from SVN and Git repositories, which gives
+you the same files that are in the download tarball.
+</P>
+<P>The Windows and Linux executables for serial or parallel only include
+certain packages and bug-fixes/upgrades listed on <A HREF = "http://lammps.sandia.gov/bug.html">this
+page</A> up to a certain date, as
+stated on the download page. If you want an executable with
+non-included packages or that is more current, then you'll need to
+build LAMMPS yourself, as discussed in the next section.
+</P>
+<P>Skip to the <A HREF = "#start_6">Running LAMMPS</A> sections for info on how to
+launch a LAMMPS Windows executable on a Windows box.
+</P>
+<HR>
+
+<H4><A NAME = "start_2"></A>2.2 Making LAMMPS
+</H4>
+<P>This section has the following sub-sections:
+</P>
+<UL><LI><A HREF = "#start_2_1">Read this first</A>
+<LI><A HREF = "#start_2_2">Steps to build a LAMMPS executable</A>
+<LI><A HREF = "#start_2_3">Common errors that can occur when making LAMMPS</A>
+<LI><A HREF = "#start_2_4">Additional build tips</A>
+<LI><A HREF = "#start_2_5">Building for a Mac</A>
+<LI><A HREF = "#start_2_6">Building for Windows</A>
+</UL>
+<HR>
+
+<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>
+
+<P>If you want to avoid building LAMMPS yourself, read the preceeding
+section about options available for downloading and installing
+executables. Details are discussed on the <A HREF = "download">download</A> page.
+</P>
+<P>Building LAMMPS can be simple or not-so-simple. If all you need are
+the default packages installed in LAMMPS, and MPI is already installed
+on your machine, or you just want to run LAMMPS in serial, then you
+can typically use the Makefile.mpi or Makefile.serial files in
+src/MAKE by typing one of these lines (from the src dir):
+</P>
+<PRE>make mpi
+make serial
+</PRE>
+<P>Note that on a facility supercomputer, there are often "modules"
+loaded in your environment that provide the compilers and MPI you
+should use. In this case, the "mpicxx" compile/link command in
+Makefile.mpi should just work by accessing those modules.
+</P>
+<P>It may be the case that one of the other Makefile.machine files in the
+src/MAKE sub-directories is a better match to your system (type "make"
+to see a list), you can use it as-is by typing (for example):
+</P>
+<PRE>make stampede
+</PRE>
+<P>If any of these builds (with an existing Makefile.machine) works on
+your system, then you're done!
+</P>
+<P>If you want to do one of the following:
+</P>
+<UL><LI>use optional LAMMPS features that require additional libraries
+<LI>use optional packages that require additional libraries
+<LI>use optional accelerator packages that require special compiler/linker settings
+<LI>run on a specialized platform that has its own compilers, settings, or other libs to use
+</UL>
+<P>then building LAMMPS is more complicated. You may need to find where
+auxiliary libraries exist on your machine or install them if they
+don't. You may need to build additional libraries that are part of
+the LAMMPS package, before building LAMMPS. You may need to edit a
+Makefile.machine file to make it compatible with your system.
+</P>
+<P>Note that there is a Make.py tool in the src directory that automates
+several of these steps, but you still have to know what you are doing.
+<A HREF = "#start_4">Section 2.4</A> below describes the tool. It is a convenient
+way to work with installing/un-installing various packages, the
+Makefile.machine changes required by some packages, and the auxiliary
+libraries some of them use.
+</P>
+<P>Please read the following sections carefully. If you are not
+comfortable with makefiles, or building codes on a Unix platform, or
+running an MPI job on your machine, please find a local expert to help
+you. Many compilation, linking, and run problems that users have are
+often not really LAMMPS issues - they are peculiar to the user's
+system, compilers, libraries, etc. Such questions are better answered
+by a local expert.
+</P>
+<P>If you have a build problem that you are convinced is a LAMMPS issue
+(e.g. the compiler complains about a line of LAMMPS source code), then
+please post the issue to the <A HREF = "http://lammps.sandia.gov/mail.html">LAMMPS mail
+list</A>.
+</P>
+<P>If you succeed in building LAMMPS on a new kind of machine, for which
+there isn't a similar machine Makefile included in the
+src/MAKE/MACHINES directory, then send it to the developers and we can
+include it in the LAMMPS distribution.
+</P>
+<HR>
+
+<A NAME = "start_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>
+
+<P><B>Step 0</B>
+</P>
+<P>The src directory contains the C++ source and header files for LAMMPS.
+It also contains a top-level Makefile and a MAKE sub-directory with
+low-level Makefile.* files for many systems and machines. See the
+src/MAKE/README file for a quick overview of what files are available
+and what sub-directories they are in.
+</P>
+<P>The src/MAKE dir has a few files that should work as-is on many
+platforms. The src/MAKE/OPTIONS dir has more that invoke additional
+compiler, MPI, and other setting options commonly used by LAMMPS, to
+illustrate their syntax. The src/MAKE/MACHINES dir has many more that
+have been tweaked or optimized for specific machines. These files are
+all good starting points if you find you need to change them for your
+machine. Put any file you edit into the src/MAKE/MINE directory and
+it will be never be touched by any LAMMPS updates.
+</P>
+<P>>From within the src directory, type "make" or "gmake". You should see
+a list of available choices from src/MAKE and all of its
+sub-directories. If one of those has the options you want or is the
+machine you want, you can type a command like:
+</P>
+<PRE>make mpi
+or
+make serial_icc
+or
+gmake mac
+</PRE>
+<P>Note that the corresponding Makefile.machine can exist in src/MAKE or
+any of its sub-directories. If a file with the same name appears in
+multiple places (not a good idea), the order they are used is as
+follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
+This gives preference to a file you have created/edited and put in
+src/MAKE/MINE.
+</P>
+<P>Note that on a multi-processor or multi-core platform you can launch a
+parallel make, by using the "-j" switch with the make command, which
+will build LAMMPS more quickly.
+</P>
+<P>If you get no errors and an executable like lmp_mpi or lmp_g++_serial
+or lmp_mac is produced, then you're done; it's your lucky day.
+</P>
+<P>Note that by default only a few of LAMMPS optional packages are
+installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
+section</A> below.
+</P>
+<P><B>Step 1</B>
+</P>
+<P>If Step 0 did not work, you will need to create a low-level Makefile
+for your machine, like Makefile.foo. You should make a copy of an
+existing Makefile.* in src/MAKE or one of its sub-directories as a
+starting point. The only portions of the file you need to edit are
+the first line, the "compiler/linker settings" section, and the
+"LAMMPS-specific settings" section. When it works, put the edited
+file in src/MAKE/MINE and it will not be altered by any future LAMMPS
+updates.
+</P>
+<P><B>Step 2</B>
+</P>
+<P>Change the first line of Makefile.foo to list the word "foo" after the
+"#", and whatever other options it will set. This is the line you
+will see if you just type "make".
+</P>
+<P><B>Step 3</B>
+</P>
+<P>The "compiler/linker settings" section lists compiler and linker
+settings for your C++ compiler, including optimization flags. You can
+use g++, the open-source GNU compiler, which is available on all Unix
+systems. You can also use mpicxx which will typically be available if
+MPI is installed on your system, though you should check which actual
+compiler it wraps. Vendor compilers often produce faster code. On
+boxes with Intel CPUs, we suggest using the Intel icc compiler, which
+can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
+</P>
+
+
+<P>If building a C++ code on your machine requires additional libraries,
+then you should list them as part of the LIB variable. You should
+not need to do this if you use mpicxx.
+</P>
+<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
+dependency list for a source file. This speeds re-compilation when
+source (*.cpp) or header (*.h) files are edited. Some compilers do
+not support dependency file creation, or may use a different switch
+than -D. GNU g++ and Intel icc works with -D. If your compiler can't
+create dependency files, then you'll need to create a Makefile.foo
+patterned after Makefile.storm, which uses different rules that do not
+involve dependency files. Note that when you build LAMMPS for the
+first time on a new platform, a long list of *.d files will be printed
+out rapidly. This is not an error; it is the Makefile doing its
+normal creation of dependencies.
+</P>
+<P><B>Step 4</B>
+</P>
+<P>The "system-specific settings" section has several parts. Note that
+if you change any -D setting in this section, you should do a full
+re-compile, after typing "make clean" (which will describe different
+clean options).
+</P>
+<P>The LMP_INC variable is used to include options that turn on ifdefs
+within the LAMMPS code. The options that are currently recogized are:
+</P>
+<UL><LI>-DLAMMPS_GZIP
+<LI>-DLAMMPS_JPEG
+<LI>-DLAMMPS_PNG
+<LI>-DLAMMPS_FFMPEG
+<LI>-DLAMMPS_MEMALIGN
+<LI>-DLAMMPS_XDR
+<LI>-DLAMMPS_SMALLBIG
+<LI>-DLAMMPS_BIGBIG
+<LI>-DLAMMPS_SMALLSMALL
+<LI>-DLAMMPS_LONGLONG_TO_LONG
+<LI>-DPACK_ARRAY
+<LI>-DPACK_POINTER
+<LI>-DPACK_MEMCPY
+</UL>
+<P>The read_data and dump commands will read/write gzipped files if you
+compile with -DLAMMPS_GZIP. It requires that your machine supports
+the "popen" function in the standard runtime library and that a gzip
+executable can be found by LAMMPS during a run.
+</P>
+<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump_image.html">dump image</A> command
+will be able to write out JPEG image files. For JPEG files, you must
+also link LAMMPS with a JPEG library, as described below. If you use
+-DLAMMPS_PNG, the <A HREF = "dump.html">dump image</A> command will be able to write
+out PNG image files. For PNG files, you must also link LAMMPS with a
+PNG library, as described below. If neither of those two defines are
+used, LAMMPS will only be able to write out uncompressed PPM image
+files.
+</P>
+<P>If you use -DLAMMPS_FFMPEG, the <A HREF = "dump_image.html">dump movie</A> command
+will be available to support on-the-fly generation of rendered movies
+the need to store intermediate image files. It requires that your
+machines supports the "popen" function in the standard runtime library
+and that an FFmpeg executable can be found by LAMMPS during the run.
+</P>
+<P>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
+posix_memalign() call instead of malloc() when large chunks or memory
+are allocated by LAMMPS. This can help to make more efficient use of
+vector instructions of modern CPUS, since dynamically allocated memory
+has to be aligned on larger than default byte boundaries (e.g. 16
+bytes instead of 8 bytes on x86 type platforms) for optimal
+performance.
+</P>
+<P>If you use -DLAMMPS_XDR, the build will include XDR compatibility
+files for doing particle dumps in XTC format. This is only necessary
+if your platform does have its own XDR files available. See the
+Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
+</P>
+<P>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
+DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
+settings refer to use of 4-byte (small) vs 8-byte (big) integers
+within LAMMPS, as specified in src/lmptype.h. The only reason to use
+the BIGBIG setting is to enable simulation of huge molecular systems
+(which store bond topology info) with more than 2 billion atoms, or to
+track the image flags of moving atoms that wrap around a periodic box
+more than 512 times. Normally, the only reason to use SMALLSMALL is
+if your machine does not support 64-bit integers, though you can use
+SMALLSMALL setting if you are running in serial or on a desktop
+machine or small cluster where you will never run large systems or for
+long time (more than 2 billion atoms, more than 2 billion timesteps).
+See the <A HREF = "#start_2_4">Additional build tips</A> section below for more
+details on these settings.
+</P>
+<P>Note that two packages, USER-ATC and USER-CUDA are not currently
+compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the
+lib/gpu library to be compiled with the same setting, or the link will
+fail.
+</P>
+<P>The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
+MPI version does not recognize "long long" data types. In this case a
+"long" data type is likely already 64-bits, in which case this setting
+will convert to that data type.
+</P>
+<P>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
+options can make for faster parallel FFTs (in the PPPM solver) on some
+platforms. The -DPACK_ARRAY setting is the default. See the
+<A HREF = "kspace_style.html">kspace_style</A> command for info about PPPM. See
+Step 6 below for info about building LAMMPS with an FFT library.
+</P>
+<P><B>Step 5</B>
+</P>
+<P>The 3 MPI variables are used to specify an MPI library to build LAMMPS
+with. Note that you do not need to set these if you use the MPI
+compiler mpicxx for your CC and LINK setting in the section above.
+The MPI wrapper knows where to find the needed files.
+</P>
+<P>If you want LAMMPS to run in parallel, you must have an MPI library
+installed on your platform. If MPI is installed on your system in the
+usual place (under /usr/local), you also may not need to specify these
+3 variables, assuming /usr/local is in your path. On some large
+parallel machines which use "modules" for their compile/link
+environements, you may simply need to include the correct module in
+your build environment, before building LAMMPS. Or the parallel
+machine may have a vendor-provided MPI which the compiler has no
+trouble finding.
+</P>
+<P>Failing this, these 3 variables can be used to specify where the mpi.h
+file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
+name of the library file (MPI_LIB).
+</P>
+<P>If you are installing MPI yourself, we recommend Argonne's MPICH2
+or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/">Argonne MPI
+site</A>. OpenMPI can
+be downloaded from the <A HREF = "http://www.open-mpi.org">OpenMPI site</A>.
+Other MPI packages should also work. If you are running on a big
+parallel platform, your system people or the vendor should have
+already installed a version of MPI, which is likely to be faster
+than a self-installed MPICH or OpenMPI, so find out how to build
+and link with it. If you use MPICH or OpenMPI, you will have to
+configure and build it for your platform. The MPI configure script
+should have compiler options to enable you to use the same compiler
+you are using for the LAMMPS build, which can avoid problems that can
+arise when linking LAMMPS to the MPI library.
+</P>
+<P>If you just want to run LAMMPS on a single processor, you can use the
+dummy MPI library provided in src/STUBS, since you don't need a true
+MPI library installed on your system. See src/MAKE/Makefile.serial
+for how to specify the 3 MPI variables in this case. You will also
+need to build the STUBS library for your platform before making LAMMPS
+itself. Note that if you are building with src/MAKE/Makefile.serial,
+e.g. by typing "make serial", then the STUBS library is built for you.
+</P>
+<P>To build the STUBS library from the src directory, type "make
+mpi-stubs", or from the src/STUBS dir, type "make". This should
+create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
+build fails, you will need to edit the STUBS/Makefile for your
+platform.
+</P>
+<P>The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
+that calls gettimeofday() . If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+</P>
+<P><B>Step 6</B>
+</P>
+<P>The 3 FFT variables allow you to specify an FFT library which LAMMPS
+uses (for performing 1d FFTs) when running the particle-particle
+particle-mesh (PPPM) option for long-range Coulombics via the
+<A HREF = "kspace_style.html">kspace_style</A> command.
+</P>
+<P>LAMMPS supports various open-source or vendor-supplied FFT libraries
+for this purpose. If you leave these 3 variables blank, LAMMPS will
+use the open-source <A HREF = "http://kissfft.sf.net">KISS FFT library</A>, which is
+included in the LAMMPS distribution. This library is portable to all
+platforms and for typical LAMMPS simulations is almost as fast as FFTW
+or vendor optimized libraries. If you are not including the KSPACE
+package in your build, you can also leave the 3 variables blank.
+</P>
+<P>Otherwise, select which kinds of FFTs to use as part of the FFT_INC
+setting by a switch of the form -DFFT_XXX. Recommended values for XXX
+are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
+ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
+the FFTW2 library. Using -DFFT_NONE will use the KISS library
+described above.
+</P>
+<P>You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
+so the compiler and linker can find the needed FFT header and library
+files. Note that on some large parallel machines which use "modules"
+for their compile/link environements, you may simply need to include
+the correct module in your build environment. Or the parallel machine
+may have a vendor-provided FFT library which the compiler has no
+trouble finding.
+</P>
+<P>FFTW is a fast, portable library that should also work on any
+platform. You can download it from
+<A HREF = "http://www.fftw.org">www.fftw.org</A>. Both the legacy version 2.1.X and
+the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
+Building FFTW for your box should be as simple as ./configure; make.
+Note that on some platforms FFTW2 has been pre-installed, and uses
+renamed files indicating the precision it was compiled with,
+e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
+specify an additional define variable for FFT_INC called -DFFTW_SIZE,
+which will select the correct include file. In this case, for FFT_LIB
+you must also manually specify the correct library, namely -lsfftw or
+-ldfftw.
+</P>
+<P>The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
+use single-precision FFTs with PPPM, which can speed-up long-range
+calulations, particularly in parallel or on GPUs. Fourier transform
+and related PPPM operations are somewhat insensitive to floating point
+truncation errors and thus do not always need to be performed in
+double precision. Using the -DFFT_SINGLE setting trades off a little
+accuracy for reduced memory use and parallel communication costs for
+transposing 3d FFT data. Note that single precision FFTs have only
+been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
+</P>
+<P><B>Step 7</B>
+</P>
+<P>The 3 JPG variables allow you to specify a JPEG and/or PNG library
+which LAMMPS uses when writing out JPEG or PNG files via the <A HREF = "dump_image.html">dump
+image</A> command. These can be left blank if you do not
+use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
+4, since in that case JPEG/PNG output will be disabled.
+</P>
+<P>A standard JPEG library usually goes by the name libjpeg.a or
+libjpeg.so and has an associated header file jpeglib.h. Whichever
+JPEG library you have on your platform, you'll need to set the
+appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
+compiler and linker can find it.
+</P>
+<P>A standard PNG library usually goes by the name libpng.a or libpng.so
+and has an associated header file png.h. Whichever PNG library you
+have on your platform, you'll need to set the appropriate JPG_INC,
+JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
+find it.
+</P>
+<P>As before, if these header and library files are in the usual place on
+your machine, you may not need to set these variables.
+</P>
+<P><B>Step 8</B>
+</P>
+<P>Note that by default only a few of LAMMPS optional packages are
+installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
+section</A> below, before proceeding to Step 9.
+</P>
+<P><B>Step 9</B>
+</P>
+<P>That's it. Once you have a correct Makefile.foo, and you have
+pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
+to do from the src directory is type something like this:
+</P>
+<PRE>make foo
+or
+gmake foo
+</PRE>
+<P>You should get the executable lmp_foo when the build is complete.
+</P>
+<HR>
+
+<A NAME = "start_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
+
+<P>IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
+or linker will state very explicitly what the problem is. The error
+message should give you a hint as to which of the steps above has
+failed, and what you need to do in order to fix it. Building a code
+with a Makefile is a very logical process. The compiler and linker
+need to find the appropriate files and those files need to be
+compatible with LAMMPS source files. When a make fails, there is
+usually a very simple reason, which you or a local expert will need to
+fix.
+</P>
+<P>Here are two non-obvious errors that can occur:
+</P>
+<P>(1) If the make command breaks immediately with errors that indicate
+it can't find files with a "*" in their names, this can be because
+your machine's native make doesn't support wildcard expansion in a
+makefile. Try gmake instead of make. If that doesn't work, try using
+a -f switch with your make command to use a pre-generated
+Makefile.list which explicitly lists all the needed files, e.g.
+</P>
+<PRE>make makelist
+make -f Makefile.list linux
+gmake -f Makefile.list mac
+</PRE>
+<P>The first "make" command will create a current Makefile.list with all
+the file names in your src dir. The 2nd "make" command (make or
+gmake) will use it to build LAMMPS. Note that you should
+include/exclude any desired optional packages before using the "make
+makelist" command.
+</P>
+<P>(2) If you get an error that says something like 'identifier "atoll"
+is undefined', then your machine does not support "long long"
+integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
+above in Step 4.
+</P>
+<HR>
+
+<A NAME = "start_2_4"></A><B><I>Additional build tips:</I></B>
+
+<P>(1) Building LAMMPS for multiple platforms.
+</P>
+<P>You can make LAMMPS for multiple platforms from the same src
+directory. Each target creates its own object sub-directory called
+Obj_target where it stores the system-specific *.o files.
+</P>
+<P>(2) Cleaning up.
+</P>
+<P>Typing "make clean-all" or "make clean-machine" will delete *.o object
+files created when LAMMPS is built, for either all builds or for a
+particular machine.
+</P>
+<P>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
+-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+</P>
+<P>As explained above, any of these 3 settings can be specified on the
+LMP_INC line in your low-level src/MAKE/Makefile.foo.
+</P>
+<P>The default is -DLAMMPS_SMALLBIG which allows for systems with up to
+2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
+atomic systems which do not store bond topology info and thus do not
+require atom IDs. If you use atom IDs for atomic systems (which is
+the default) or if you use a molecular model, which stores bond
+topology info and thus requires atom IDs, the limit is 2^31 atoms
+(about 2 billion). This is because the IDs are stored in 32-bit
+integers.
+</P>
+<P>Likewise, with this setting, the 3 image flags for each atom (see the
+<A HREF = "dump.html">dump</A> doc page for a discussion) are stored in a 32-bit
+integer, which means the atoms can only wrap around a periodic box (in
+each dimension) at most 512 times. If atoms move through the periodic
+box more than this many times, the image flags will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the <A HREF = "compute_msd.html">compute
+msd</A> command, to be faulty.
+</P>
+<P>To allow for larger atomic systems with atom IDs or larger molecular
+systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
+stores atom IDs and image flags in 64-bit integers. This enables
+atomic or molecular systems with atom IDS of up to 2^63 atoms (about
+9e18). And image flags will not "roll over" until they reach 2^20 =
+1048576.
+</P>
+<P>If your system does not support 8-byte integers, you will need to
+compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
+total number of atoms (for atomic or molecular systems) and timesteps
+to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
+</P>
+<P>Note that in src/lmptype.h there are definitions of all these data
+types as well as the MPI data types associated with them. The MPI
+types need to be consistent with the associated C data types, or else
+LAMMPS will generate a run-time error. As far as we know, the
+settings defined in src/lmptype.h are portable and work on every
+current system.
+</P>
+<P>In all cases, the size of problem that can be run on a per-processor
+basis is limited by 4-byte integer storage to 2^31 atoms per processor
+(about 2 billion). This should not normally be a limitation since such
+a problem would have a huge per-processor memory footprint due to
+neighbor lists and would run very slowly in terms of CPU secs/timestep.
+</P>
+<HR>
+
+<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>
+
+<P>OS X is BSD Unix, so it should just work. See the
+src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
+</P>
+<HR>
+
+<A NAME = "start_2_6"></A><B><I>Building for Windows:</I></B>
+
+<P>The LAMMPS download page has an option to download both a serial and
+parallel pre-built Windows executable. See the <A HREF = "#start_6">Running
+LAMMPS</A> section for instructions on running these executables
+on a Windows box.
+</P>
+<P>The pre-built executables hosted on the <A HREF = "http://lammps.sandia.gov/download.html">LAMMPS download
+page</A> are built with a subset
+of the available packages; see the download page for the list. These
+are single executable files. No examples or documentation in
+included. You will need to download the full source code package to
+obtain those.
+</P>
+<P>As an alternative, you can download "daily builds" (and some older
+versions) of the installer packages from
+<A HREF = "http://rpm.lammps.org/windows.html">rpm.lammps.org/windows.html</A>.
+These executables are built with most optional packages and the
+download includes documentation, some tools and most examples.
+</P>
+<P>If you want a Windows version with specific packages included and
+excluded, you can build it yourself.
+</P>
+<P>One way to do this is install and use cygwin to build LAMMPS with a
+standard unix style make program, just as you would on a Linux box;
+see src/MAKE/MACHINES/Makefile.cygwin.
+</P>
+<P>The other way to do this is using Visual Studio and project files.
+See the src/WINDOWS directory and its README.txt file for instructions
+on both a basic build and a customized build with pacakges you select.
+</P>
+<HR>
+
+<H4><A NAME = "start_3"></A>2.3 Making LAMMPS with optional packages
+</H4>
+<P>This section has the following sub-sections:
+</P>
+<UL><LI><A HREF = "#start_3_1">Package basics</A>
+<LI><A HREF = "#start_3_2">Including/excluding packages</A>
+<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
+<LI><A HREF = "#start_3_4">Packages that require Makefile.machine settings</A>
+</UL>
+<P>Note that the following <A HREF = "#start_4">Section 2.4</A> describes the Make.py
+tool which can be used to install/un-install packages and build the
+auxiliary libraries which some of them use. It can also auto-edit a
+Makefile.machine to add settings needed by some packages.
+</P>
+<HR>
+
+<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>
+
+<P>The source code for LAMMPS is structured as a set of core files which
+are always included, plus optional packages. Packages are groups of
+files that enable a specific set of features. For example, force
+fields for molecular systems or granular systems are in packages.
+</P>
+<P>You can see the list of all packages by typing "make package" from
+within the src directory of the LAMMPS distribution. This also lists
+various make commands that can be used to manipulate packages.
+</P>
+<P>If you use a command in a LAMMPS input script that is specific to a
+particular package, you must have built LAMMPS with that package, else
+you will get an error that the style is invalid or the command is
+unknown. Every command's doc page specfies if it is part of a
+package. You can also type
+</P>
+<PRE>lmp_machine -h
+</PRE>
+<P>to run your executable with the optional <A HREF = "#start_7">-h command-line
+switch</A> for "help", which will list the styles and commands
+known to your executable.
+</P>
+<P>There are two kinds of packages in LAMMPS, standard and user packages.
+More information about the contents of standard and user packages is
+given in <A HREF = "Section_packages.html">Section_packages</A> of the manual. The
+difference between standard and user packages is as follows:
+</P>
+<P>Standard packages are supported by the LAMMPS developers and are
+written in a syntax and style consistent with the rest of LAMMPS.
+This means we will answer questions about them, debug and fix them if
+necessary, and keep them compatible with future changes to LAMMPS.
+</P>
+<P>User packages have been contributed by users, and always begin with
+the user prefix. If they are a single command (single file), they are
+typically in the user-misc package. Otherwise, they are a a set of
+files grouped together which add a specific functionality to the code.
+</P>
+<P>User packages don't necessarily meet the requirements of the standard
+packages. If you have problems using a feature provided in a user
+package, you will likely need to contact the contributor directly to
+get help. Information on how to submit additions you make to LAMMPS
+as a user-contributed package is given in <A HREF = "Section_modify.html#mod_15">this
+section</A> of the documentation.
+</P>
+<P>Some packages (both standard and user) require additional libraries.
+See more details below.
+</P>
+<HR>
+
+<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>
+
+<P>To use or not use a package you must include or exclude it before
+building LAMMPS. From the src directory, this is typically as simple
+as:
+</P>
+<PRE>make yes-colloid
+make g++
+</PRE>
+<P>or
+</P>
+<PRE>make no-manybody
+make g++
+</PRE>
+<P>IMPORTANT NOTE: You should NOT include/exclude packages and build
+LAMMPS in a single make command by using multiple targets, e.g. make
+yes-colloid g++. This is because the make procedure creates a list of
+source files that will be out-of-date for the build if the package
+configuration changes during the same command.
+</P>
+<P>Some packages have individual files that depend on other packages
+being included. LAMMPS checks for this and does the right thing.
+I.e. individual files are only included if their dependencies are
+already included. Likewise, if a package is excluded, other files
+dependent on that package are also excluded.
+</P>
+<P>If you will never run simulations that use the features in a
+particular packages, there is no reason to include it in your build.
+For some packages, this will keep you from having to build auxiliary
+libraries (see below), and will also produce a smaller executable
+which may run a bit faster.
+</P>
+<P>When you download a LAMMPS tarball, these packages are pre-installed
+in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
+LAMMPS source files from the SVN or Git repositories, no packages are
+pre-installed.
+</P>
+<P>Packages are included or excluded by typing "make yes-name" or "make
+no-name", where "name" is the name of the package in lower-case, e.g.
+name = kspace for the KSPACE package or name = user-atc for the
+USER-ATC package. You can also type "make yes-standard", "make
+no-standard", "make yes-std", "make no-std", "make yes-user", "make
+no-user", "make yes-all" or "make no-all" to include/exclude various
+sets of packages. Type "make package" to see the all of the
+package-related make options.
+</P>
+<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
+moving files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are seen or not seen when LAMMPS is built. After
+you have included or excluded a package, you must re-build LAMMPS.
+</P>
+<P>Additional package-related make options exist to help manage LAMMPS
+files that exist in both the src directory and in package
+sub-directories. You do not normally need to use these commands
+unless you are editing LAMMPS files or have downloaded a patch from
+the LAMMPS WWW site.
+</P>
+<P>Typing "make package-update" or "make pu" will overwrite src files
+with files from the package sub-directories if the package has been
+included. It should be used after a patch is installed, since patches
+only update the files in the package sub-directory, but not the src
+files. Typing "make package-overwrite" will overwrite files in the
+package sub-directories with src files.
+</P>
+<P>Typing "make package-status" or "make ps" will show which packages are
+currently included. Of those that are included, it will list files
+that are different in the src directory and package sub-directory.
+Typing "make package-diff" lists all differences between these files.
+Again, type "make package" to see all of the package-related make
+options.
+</P>
+<HR>
+
+<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>
+
+<P>A few of the standard and user packages require additional auxiliary
+libraries. Most of them are provided with LAMMPS, in which case they
+must be compiled first, before LAMMPS is built if you wish to include
+that package. If you get a LAMMPS build error about a missing
+library, this is likely the reason. See the
+<A HREF = "Section_packages.html">Section_packages</A> doc page for a list of
+packages that have these kinds of auxiliary libraries.
+</P>
+<P>The lib directory in the distribution has sub-directories with package
+names that correspond to the needed auxiliary libs, e.g. lib/reax.
+Each sub-directory has a README file that gives more details. Code
+for most of the auxiliary libraries is included in that directory.
+Examples are the USER-ATC and MEAM packages.
+</P>
+<P>A few of the lib sub-directories do not include code, but do include
+instructions and sometimes scripts that automate the process of
+downloading the auxiliary library and installing it so LAMMPS can link
+to it. Examples are the KIM and VORONOI and USER-MOLFILE packages.
+</P>
+<P>The lib/python directory (for the PYTHON package) contains only a
+choice of Makefile.lammps.* files. This is because no auxiliary code
+or libraries are needed, only the Python library and other system libs
+that already available on your system. However, the Makefile.lammps
+file is needed to tell the LAMMPS build which libs to use and where to
+find them.
+</P>
+<P>For libraries with provided code, the sub-directory README file
+(e.g. lib/reax/README) has instructions on how to build that library.
+Typically this is done by typing something like:
+</P>
+<PRE>make -f Makefile.g++
+</PRE>
+<P>If one of the provided Makefiles is not appropriate for your system
+you will need to edit or add one. Note that all the Makefiles have a
+setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
+file.
+</P>
+<P>If the library build is successful, it will produce 2 files in the lib
+directory:
+</P>
+<PRE>libpackage.a
+Makefile.lammps
+</PRE>
+<P>The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
+specified in the library Makefile.* you used.
+</P>
+<P>Note that you must insure that the settings in Makefile.lammps are
+appropriate for your system. If they are not, the LAMMPS build will
+fail.
+</P>
+<P>As explained in the lib/package/README files, the settings in
+Makefile.lammps are used to specify additional system libraries and
+their locations so that LAMMPS can build with the auxiliary library.
+For example, if the MEAM or REAX packages are used, the auxiliary
+libraries consist of F90 code, built with a Fortran complier. To link
+that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS
+is built with, typically requires additional Fortran-to-C libraries be
+included in the link. Another example are the BLAS and LAPACK
+libraries needed to use the USER-ATC or USER-AWPMD packages.
+</P>
+<P>For libraries without provided code, the sub-directory README file has
+information on where to download the library and how to build it,
+e.g. lib/voronoi/README. The README files also describe how you must
+either (a) create soft links, via the "ln" command, in those
+directories to point to where you built or installed the packages,
+or (b) check or edit the Makefile.lammps file in the same directory
+to provide that information.
+</P>
+<P>Some of the sub-directories, e.g. lib/voronoi, also have an install.py
+script which can be used to automate the process of
+downloading/building/installing the auxiliary library, and setting the
+needed soft links. Type "python install.py" for further instructions.
+</P>
+<P>As with the sub-directories containing library code, if the soft links
+or settings in the lib/package/Makefile.lammps files are not correct,
+the LAMMPS build will typically fail.
+</P>
+<HR>
+
+<A NAME = "start_3_4"></A><B><I>Packages that require Makefile.machine settings</I></B>
+
+<P>A few packages require specific settings in Makefile.machine, to
+either build or use the package effectively. These are the
+USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
+flags to add or what variables to define are given on the doc pages
+that describe each of these accelerator packages in detail:
+</P>
+<UL><LI><A HREF = "accelerate_intel.html">USER-INTEL package</A>
+<LI><A HREF = "accelerate_kokkos.html">KOKKOS package</A>
+<LI><A HREF = "accelerate_omp.html">USER-OMP package</A>
+<LI><A HREF = "accelerate_opt.html">OPT package</A>
+</UL>
+<P>Here is a brief summary of what Makefile.machine changes are needed.
+Note that the Make.py tool, described in the next <A HREF = "#start_4">Section
+2.4</A> can automatically add the needed info to an existing
+machine Makefile, using simple command-line arguments.
+</P>
+<P>In src/MAKE/OPTIONS see the following Makefiles for examples of the
+changes described below:
+</P>
+<UL><LI>Makefile.intel_cpu
+<LI>Makefile.intel_phi
+<LI>Makefile.kokkos_omp
+<LI>Makefile.kokkos_cuda
+<LI>Makefile.kokkos_phi
+<LI>Makefile.omp
+</UL>
+<P>For the USER-INTEL package, you have 2 choices when building. You can
+build with CPU or Phi support. The latter uses Xeon Phi chips in
+"offload" mode. Each of these modes requires additional settings in
+your Makefile.machine for CCFLAGS and LINKFLAGS.
+</P>
+<P>For CPU mode (if using an Intel compiler):
+</P>
+<UL><LI>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+<LI>LINKFLAGS: add -fopenmp
+</UL>
+<P>For Phi mode add the following in addition to the CPU mode flags:
+</P>
+<UL><LI>CCFLAGS: add -DLMP_INTEL_OFFLOAD and
+<LI>LINKFLAGS: add -offload
+</UL>
+<P>And also add this to CCFLAGS:
+</P>
+<PRE>-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
+</PRE>
+<P>For the KOKKOS package, you have 3 choices when building. You can
+build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
+chips in "native" mode. This can be done by setting the following
+variables in your Makefile.machine:
+</P>
+<UL><LI>for OMP support, set OMP = yes
+<LI>for Cuda support, set OMP = yes and CUDA = yes
+<LI>for Phi support, set OMP = yes and MIC = yes
+</UL>
+<P>These can also be set as additional arguments to the make command, e.g.
+</P>
+<PRE>make g++ OMP=yes MIC=yes
+</PRE>
+<P>Building the KOKKOS package with CUDA support requires a Makefile
+machine that uses the NVIDIA "nvcc" compiler, as well as an
+appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
+software you have on your machine. See
+src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
+Makefile.
+</P>
+<P>For the USER-OMP package, your Makefile.machine needs additional
+settings for CCFLAGS and LINKFLAGS.
+</P>
+<UL><LI>CCFLAGS: add -fopenmp and -restrict
+<LI>LINKFLAGS: add -fopenmp
+</UL>
+<P>For the OPT package, your Makefile.machine needs an additional
+settings for CCFLAGS.
+</P>
+<UL><LI>CCFLAGS: add -restrict
+</UL>
+<HR>
+
+<H4><A NAME = "start_4"></A>2.4 Building LAMMPS via the Make.py script
+</H4>
+<P>The src directory includes a Make.py script, written in Python, which
+can be used to automate various steps of the build process. It is
+particularly useful for working with the accelerator packages, as well
+as other packages which require auxiliary libraries to be built.
+</P>
+<P>The goal of the Make.py tool is to allow any complex multi-step LAMMPS
+build to be performed as a single Make.py command. And you can
+archive the commands, so they can be re-invoked later via the -r
+(redo) switch. If you find some LAMMPS build procedure that can't be
+done in a single Make.py command, let the developers know, and we'll
+see if we can augment the tool.
+</P>
+<P>You can run Make.py from the src directory by typing either:
+</P>
+<PRE>Make.py -h
+python Make.py -h
+</PRE>
+<P>which will give you help info about the tool. For the former to work,
+you may need to edit the first line of Make.py to point to your local
+Python. And you may need to insure the script is executable:
+</P>
+<PRE>chmod +x Make.py
+</PRE>
+<P>Here are examples of build tasks you can perform with Make.py:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >Install/uninstall packages</TD><TD > Make.py -p no-lib kokkos omp intel</TD></TR>
+<TR><TD >Build specific auxiliary libs</TD><TD > Make.py -a lib-atc lib-meam</TD></TR>
+<TR><TD >Build libs for all installed packages</TD><TD > Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all</TD></TR>
+<TR><TD >Create a Makefile from scratch with compiler and MPI settings</TD><TD > Make.py -m none -cc g++ -mpi mpich -a file</TD></TR>
+<TR><TD >Augment Makefile.serial with settings for installed packages</TD><TD > Make.py -p intel -intel cpu -m serial -a file</TD></TR>
+<TR><TD >Add JPG and FFTW support to Makefile.mpi</TD><TD > Make.py -m mpi -jpg -fft fftw -a file</TD></TR>
+<TR><TD >Build LAMMPS with a parallel make using Makefile.mpi</TD><TD > Make.py -j 16 -m mpi -a exe</TD></TR>
+<TR><TD >Build LAMMPS and libs it needs using Makefile.serial with accelerator settings</TD><TD > Make.py -p gpu intel -intel cpu -a lib-all file serial
+</TD></TR></TABLE></DIV>
+
+<P>The bench and examples directories give Make.py commands that can be
+used to build LAMMPS with the various packages and options needed to
+run all the benchmark and example input scripts. See these files for
+more details:
+</P>
+<UL><LI>bench/README
+<LI>bench/FERMI/README
+<LI>bench/KEPLER/README
+<LI>bench/PHI/README
+<LI>examples/README
+<LI>examples/accelerate/README
+<LI>examples/accelerate/make.list
+</UL>
+<P>All of the Make.py options and syntax help can be accessed by using
+the "-h" switch.
+</P>
+<P>E.g. typing "Make.py -h" gives
+</P>
+<PRE>Syntax: Make.py switch args ...
+ switches can be listed in any order
+ help switch:
+ -h prints help and syntax for all other specified switches
+ switch for actions:
+ -a lib-all, lib-dir, clean, file, exe or machine
+ list one or more actions, in any order
+ machine is a Makefile.machine suffix, must be last if used
+ one-letter switches:
+ -d (dir), -j (jmake), -m (makefile), -o (output),
+ -p (packages), -r (redo), -s (settings), -v (verbose)
+ switches for libs:
+ -atc, -awpmd, -colvars, -cuda
+ -gpu, -meam, -poems, -qmmm, -reax
+ switches for build and makefile options:
+ -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
+</PRE>
+<P>Using the "-h" switch with other switches and actions gives additional
+info on all the other specified switches or actions. The "-h" can be
+anywhere in the command-line and the other switches do not need their
+arguments. E.g. type "Make.py -h -d -atc -intel" will print:
+</P>
+<PRE>-d dir
+ dir = LAMMPS home dir
+ if -d not specified, working dir must be lammps/src
+</PRE>
+<PRE>-atc make=suffix lammps=suffix2
+ all args are optional and can be in any order
+ make = use Makefile.suffix (def = g++)
+ lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
+</PRE>
+<PRE>-intel mode
+ mode = cpu or phi (def = cpu)
+ build Intel package for CPU or Xeon Phi
+</PRE>
+<P>Note that Make.py never overwrites an existing Makefile.machine.
+Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
+rename if desired. Likewise it creates an executable named
+src/lmp_auto, which you can rename using the -o switch if desired.
+</P>
+<P>The most recently executed Make.py commmand is saved in
+src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
+the last command, or you can save a sequence of one or more Make.py
+commands to a file and invoke the file of commands using "-r". You
+can also label the commands in the file and invoke one or more of them
+by name.
+</P>
+<P>A typical use of Make.py is to start with a valid Makefile.machine for
+your system, that works for a vanilla LAMMPS build, i.e. when optional
+packages are not installed. You can then use Make.py to add various
+settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
+compiler and MPI options. You can also add additional packages to the
+build, as well as build the needed supporting libraries.
+</P>
+<P>You can also use Make.py to create a new Makefile.machine from
+scratch, using the "-m none" switch, if you also specify what compiler
+and MPI options to use, via the "-cc" and "-mpi" switches.
+</P>
+<HR>
+
+<H4><A NAME = "start_5"></A>2.5 Building LAMMPS as a library
+</H4>
+<P>LAMMPS can be built as either a static or shared library, which can
+then be called from another application or a scripting language. See
+<A HREF = "Section_howto.html#howto_10">this section</A> for more info on coupling
+LAMMPS to other codes. See <A HREF = "Section_python.html">this section</A> for
+more info on wrapping and running LAMMPS from Python.
+</P>
+<H5><B>Static library:</B>
+</H5>
+<P>To build LAMMPS as a static library (*.a file on Linux), type
+</P>
+<PRE>make foo mode=lib
+</PRE>
+<P>where foo is the machine name. This kind of library is typically used
+to statically link a driver application to LAMMPS, so that you can
+insure all dependencies are satisfied at compile time. This will use
+the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
+will create the file liblammps_foo.a which another application can
+link to. It will also create a soft link liblammps.a, which will
+point to the most recently built static library.
+</P>
+<H5><B>Shared library:</B>
+</H5>
+<P>To build LAMMPS as a shared library (*.so file on Linux), which can be
+dynamically loaded, e.g. from Python, type
+</P>
+<PRE>make foo mode=shlib
+</PRE>
+<P>where foo is the machine name. This kind of library is required when
+wrapping LAMMPS with Python; see <A HREF = "Section_python.html">Section_python</A>
+for details. This will use the SHFLAGS and SHLIBFLAGS settings in
+src/MAKE/Makefile.foo and perform the build in the directory
+Obj_shared_foo. This is so that each file can be compiled with the
+-fPIC flag which is required for inclusion in a shared library. The
+build will create the file liblammps_foo.so which another application
+can link to dyamically. It will also create a soft link liblammps.so,
+which will point to the most recently built shared library. This is
+the file the Python wrapper loads by default.
+</P>
+<P>Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries. This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+lib/packages, since they are always built as shared libraries using
+the -fPIC switch. However, if a library like MPI or FFTW does not
+exist as a shared library, the shared library build will generate an
+error. This means you will need to install a shared library version
+of the auxiliary library. The build instructions for the library
+should tell you how to do this.
+</P>
+<P>Here is an example of such errors when the system FFTW or provided
+lib/colvars library have not been built as shared libraries:
+</P>
+<PRE>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
+R_X86_64_32 against `.rodata' can not be used when making a shared
+object; recompile with -fPIC
+/usr/local/lib/libfftw3.a: could not read symbols: Bad value
+</PRE>
+<PRE>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
+relocation R_X86_64_32 against `__pthread_key_create' can not be used
+when making a shared object; recompile with -fPIC
+../../lib/colvars/libcolvars.a: error adding symbols: Bad value
+</PRE>
+<P>As an example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
+library</A>, a popular open-source version of MPI, distributed by
+Argonne National Labs, as a shared library in the default
+/usr/local/lib location:
+</P>
+
+
+<PRE>./configure --enable-shared
+make
+make install
+</PRE>
+<P>You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib. The end result
+should be the file /usr/local/lib/libmpich.so.
+</P>
+<H5><B>Additional requirement for using a shared library:</B>
+</H5>
+<P>The operating system finds shared libraries to load at run-time using
+the environment variable LD_LIBRARY_PATH. So you may wish to copy the
+file src/liblammps.so or src/liblammps_g++.so (for example) to a place
+the system can find it by default, such as /usr/local/lib, or you may
+wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
+current version of the shared library is always available to programs
+that use it.
+</P>
+<P>For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+</P>
+<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
+</PRE>
+<H5><B>Calling the LAMMPS library:</B>
+</H5>
+<P>Either flavor of library (static or shared0 allows one or more LAMMPS
+objects to be instantiated from the calling program.
+</P>
+<P>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+</P>
+<P>When used from a C or Fortran program or a scripting language like
+Python, the library has a simple function-style interface, provided in
+src/library.cpp and src/library.h.
+</P>
+<P>See the sample codes in examples/COUPLE/simple for examples of C++ and
+C and Fortran codes that invoke LAMMPS thru its library interface.
+There are other examples as well in the COUPLE directory which are
+discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
+manual. See <A HREF = "Section_python.html">Section_python</A> of the manual for a
+description of the Python wrapper provided with LAMMPS that operates
+through the LAMMPS library interface.
+</P>
+<P>The files src/library.cpp and library.h define the C-style API for
+using LAMMPS as a library. See <A HREF = "Section_howto.html#howto_19">Section_howto
+19</A> of the manual for a description of the
+interface and how to extend it for your needs.
+</P>
+<HR>
+
+<H4><A NAME = "start_6"></A>2.6 Running LAMMPS
+</H4>
+<P>By default, LAMMPS runs by reading commands from standard input. Thus
+if you run the LAMMPS executable by itself, e.g.
+</P>
+<PRE>lmp_linux
+</PRE>
+<P>it will simply wait, expecting commands from the keyboard. Typically
+you should put commands in an input script and use I/O redirection,
+e.g.
+</P>
+<PRE>lmp_linux < in.file
+</PRE>
+<P>For parallel environments this should also work. If it does not, use
+the '-in' command-line switch, e.g.
+</P>
+<PRE>lmp_linux -in in.file
+</PRE>
+<P><A HREF = "Section_commands.html">This section</A> describes how input scripts are
+structured and what commands they contain.
+</P>
+<P>You can test LAMMPS on any of the sample inputs provided in the
+examples or bench directory. Input scripts are named in.* and sample
+outputs are named log.*.name.P where name is a machine and P is the
+number of processors it was run on.
+</P>
+<P>Here is how you might run a standard Lennard-Jones benchmark on a
+Linux box, using mpirun to launch a parallel job:
+</P>
+<PRE>cd src
+make linux
+cp lmp_linux ../bench
+cd ../bench
+mpirun -np 4 lmp_linux < in.lj
+</PRE>
+<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
+various platforms. Note that some of the example scripts require
+LAMMPS to be built with one or more of its optional packages.
+</P>
+
+
+<HR>
+
+<P>On a Windows box, you can skip making LAMMPS and simply download an
+executable, as described above, though the pre-packaged executables
+include only certain packages.
+</P>
+<P>To run a LAMMPS executable on a Windows machine, first decide whether
+you want to download the non-MPI (serial) or the MPI (parallel)
+version of the executable. Download and save the version you have
+chosen.
+</P>
+<P>For the non-MPI version, follow these steps:
+</P>
+<UL><LI>Get a command prompt by going to Start->Run... ,
+then typing "cmd".
+
+<LI>Move to the directory where you have saved lmp_win_no-mpi.exe
+(e.g. by typing: cd "Documents").
+
+<LI>At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
+with the name of your LAMMPS input script.
+</UL>
+<P>For the MPI version, which allows you to run LAMMPS under Windows on
+multiple processors, follow these steps:
+</P>
+<UL><LI>Download and install
+<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
+for Windows.
+
+<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
+package. Put them in same directory (or path) as the LAMMPS Windows
+executable.
+
+<LI>Get a command prompt by going to Start->Run... ,
+then typing "cmd".
+
+<LI>Move to the directory where you have saved lmp_win_mpi.exe
+(e.g. by typing: cd "Documents").
+
+<LI>Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
+in.lj", replacing in.lj with the name of your LAMMPS input script.
+
+<LI>Note that you may need to provide smpd with a passphrase (it doesn't
+matter what you type).
+
+<LI>In this mode, output may not immediately show up on the screen, so if
+your input script takes a long time to execute, you may need to be
+patient before the output shows up. :l Alternatively, you can still
+use this executable to run on a single processor by typing something
+like: "lmp_win_mpi -in in.lj".
+</UL>
+<HR>
+
+<P>The screen output from LAMMPS is described in the next section. As it
+runs, LAMMPS also writes a log.lammps file with the same information.
+</P>
+<P>Note that this sequence of commands copies the LAMMPS executable
+(lmp_linux) to the directory with the input files. This may not be
+necessary, but some versions of MPI reset the working directory to
+where the executable is, rather than leave it as the directory where
+you launch mpirun from (if you launch lmp_linux on its own and not
+under mpirun). If that happens, LAMMPS will look for additional input
+files and write its output files to the executable directory, rather
+than your working directory, which is probably not what you want.
+</P>
+<P>If LAMMPS encounters errors in the input script or while running a
+simulation it will print an ERROR message and stop or a WARNING
+message and continue. See <A HREF = "Section_errors.html">Section_errors</A> for a
+discussion of the various kinds of errors LAMMPS can or can't detect,
+a list of all ERROR and WARNING messages, and what to do about them.
+</P>
+<P>LAMMPS can run a problem on any number of processors, including a
+single processor. In theory you should get identical answers on any
+number of processors and on any machine. In practice, numerical
+round-off can cause slight differences and eventual divergence of
+molecular dynamics phase space trajectories.
+</P>
+<P>LAMMPS can run as large a problem as will fit in the physical memory
+of one or more processors. If you run out of memory, you must run on
+more processors or setup a smaller problem.
+</P>
+<HR>
+
+<H4><A NAME = "start_7"></A>2.7 Command-line options
+</H4>
+<P>At run time, LAMMPS recognizes several optional command-line switches
+which may be used in any order. Either the full word or a one-or-two
+letter abbreviation can be used:
+</P>
+<UL><LI>-c or -cuda
+<LI>-e or -echo
+<LI>-h or -help
+<LI>-i or -in
+<LI>-k or -kokkos
+<LI>-l or -log
+<LI>-nc or -nocite
+<LI>-pk or -package
+<LI>-p or -partition
+<LI>-pl or -plog
+<LI>-ps or -pscreen
+<LI>-r or -restart
+<LI>-ro or -reorder
+<LI>-sc or -screen
+<LI>-sf or -suffix
+<LI>-v or -var
+</UL>
+<P>For example, lmp_ibm might be launched as follows:
+</P>
+<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy
+mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
+</PRE>
+<P>Here are the details on the options:
+</P>
+<PRE>-cuda on/off
+</PRE>
+<P>Explicitly enable or disable CUDA support, as provided by the
+USER-CUDA package. Even if LAMMPS is built with this package, as
+described above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to
+enable running with the CUDA-enabled styles the package provides. If
+the switch is not set (the default), LAMMPS will operate as if the
+USER-CUDA package were not installed; i.e. you can run standard LAMMPS
+or with the GPU package, for testing or benchmarking purposes.
+</P>
+<PRE>-echo style
+</PRE>
+<P>Set the style of command echoing. The style can be <I>none</I> or <I>screen</I>
+or <I>log</I> or <I>both</I>. Depending on the style, each command read from
+the input script will be echoed to the screen and/or logfile. This
+can be useful to figure out which line of your script is causing an
+input error. The default value is <I>log</I>. The echo style can also be
+set by using the <A HREF = "echo.html">echo</A> command in the input script itself.
+</P>
+<PRE>-help
+</PRE>
+<P>Print a brief help summary and a list of options compiled into this
+executable for each LAMMPS style (atom_style, fix, compute,
+pair_style, bond_style, etc). This can tell you if the command you
+want to use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is
+used.
+</P>
+<PRE>-in file
+</PRE>
+<P>Specify a file to use as an input script. This is an optional switch
+when running LAMMPS in one-partition mode. If it is not specified,
+LAMMPS reads its script from standard input, typically from a script
+via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
+also work in parallel, but if it does not (in the unlikely case that
+an MPI implementation does not support it), then use the -in flag.
+Note that this is a required switch when running LAMMPS in
+multi-partition mode, since multiple processors cannot all read from
+stdin.
+</P>
+<PRE>-kokkos on/off keyword/value ...
+</PRE>
+<P>Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
+package. Even if LAMMPS is built with this package, as described
+above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to enable
+running with the KOKKOS-enabled styles the package provides. If the
+switch is not set (the default), LAMMPS will operate as if the KOKKOS
+package were not installed; i.e. you can run standard LAMMPS or with
+the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking
+purposes.
+</P>
+<P>Additional optional keyword/value pairs can be specified which
+determine how Kokkos will use the underlying hardware on your
+platform. These settings apply to each MPI task you launch via the
+"mpirun" or "mpiexec" command. You may choose to run one or more MPI
+tasks per physical node. Note that if you are running on a desktop
+machine, you typically have one physical node. On a cluster or
+supercomputer there may be dozens or 1000s of physical nodes.
+</P>
+<P>Either the full word or an abbreviation can be used for the keywords.
+Note that the keywords do not use a leading minus sign. I.e. the
+keyword is "t", not "-t". Also note that each of the keywords has a
+default setting. Example of when to use these options and what
+settings to use on different platforms is given in <A HREF = "Section_accelerate.html#acc_8">Section
+5.8</A>.
+</P>
+<UL><LI>d or device
+<LI>g or gpus
+<LI>t or threads
+<LI>n or numa
+</UL>
+<PRE>device Nd
+</PRE>
+<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and if you are running with only one
+MPI task per node. The Nd setting is the ID of the GPU on the node to
+run on. By default Nd = 0. If you have multiple GPUs per node, they
+have consecutive IDs numbered as 0,1,2,etc. This setting allows you
+to launch multiple independent jobs on the node, each with a single
+MPI task per node, and assign each job to run on a different GPU.
+</P>
+<PRE>gpus Ng Ns
+</PRE>
+<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
+have more than one GPU per node, and you are running with multiple MPI
+tasks per node (up to one per GPU). The Ng setting is how many GPUs
+you will use. The Ns setting is optional. If set, it is the ID of a
+GPU to skip when assigning MPI tasks to GPUs. This may be useful if
+your desktop system reserves one GPU to drive the screen and the rest
+are intended for computational work like running LAMMPS. By default
+Ng = 1 and Ns is not set.
+</P>
+<P>Depending on which flavor of MPI you are running, LAMMPS will look for
+one of these 3 environment variables
+</P>
+<PRE>SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
+OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
+</PRE>
+<P>which are initialized by the "srun", "mpirun" or "mpiexec" commands.
+The environment variable setting for each MPI rank is used to assign a
+unique GPU ID to the MPI task.
+</P>
+<PRE>threads Nt
+</PRE>
+<P>This option assigns Nt number of threads to each MPI task for
+performing work when Kokkos is executing in OpenMP or pthreads mode.
+The default is Nt = 1, which essentially runs in MPI-only mode. If
+there are Np MPI tasks per physical node, you generally want Np*Nt =
+the number of physical cores per node, to use your available hardware
+optimally. This also sets the number of threads used by the host when
+LAMMPS is compiled with CUDA=yes.
+</P>
+<PRE>numa Nm
+</PRE>
+<P>This option is only relevant when using pthreads with hwloc support.
+In this case Nm defines the number of NUMA regions (typicaly sockets)
+on a node which will be utilizied by a single MPI rank. By default Nm
+= 1. If this option is used the total number of worker-threads per
+MPI rank is threads*numa. Currently it is always almost better to
+assign at least one MPI rank per NUMA region, and leave numa set to
+its default value of 1. This is because letting a single process span
+multiple NUMA regions induces a significant amount of cross NUMA data
+traffic which is slow.
+</P>
+<PRE>-log file
+</PRE>
+<P>Specify a log file for LAMMPS to write status information to. In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+file log.lammps. If this switch is used, LAMMPS writes to the
+specified file. In multi-partition mode, if the switch is not used, a
+log.lammps file is created with hi-level status information. Each
+partition also writes to a log.lammps.N file where N is the partition
+ID. If the switch is specified in multi-partition mode, the hi-level
+logfile is named "file" and each partition also logs information to a
+file.N. For both one-partition and multi-partition mode, if the
+specified file is "none", then no log files are created. Using a
+<A HREF = "log.html">log</A> command in the input script will override this setting.
+Option -plog will override the name of the partition log files file.N.
+</P>
+<PRE>-nocite
+</PRE>
+<P>Disable writing the log.cite file which is normally written to list
+references for specific cite-able features used during a LAMMPS run.
+See the <A HREF = "http://lammps.sandia.gov/cite.html">citation page</A> for more
+details.
+</P>
+<PRE>-package style args ....
+</PRE>
+<P>Invoke the <A HREF = "package.html">package</A> command with style and args. The
+syntax is the same as if the command appeared at the top of the input
+script. For example "-package gpu 2" or "-pk gpu 2" is the same as
+<A HREF = "package.html">package gpu 2</A> in the input script. The possible styles
+and args are documented on the <A HREF = "package.html">package</A> doc page. This
+switch can be used multiple times, e.g. to set options for the
+USER-INTEL and USER-OMP packages which can be used together.
+</P>
+<P>Along with the "-suffix" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+</P>
+<PRE>-partition 8x2 4 5 ...
+</PRE>
+<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
+processors and this switch is not used, LAMMPS runs in one partition,
+i.e. all P processors run a single simulation. If this switch is
+used, the P processors are split into separate partitions and each
+partition runs its own simulation. The arguments to the switch
+specify the number of processors in each partition. Arguments of the
+form MxN mean M partitions, each with N processors. Arguments of the
+form N mean a single partition with N processors. The sum of
+processors in all partitions must equal P. Thus the command
+"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
+processors.
+</P>
+<P>Running with multiple partitions can e useful for running
+<A HREF = "Section_howto.html#howto_5">multi-replica simulations</A>, where each
+replica runs on on one or a few processors. Note that with MPI
+installed on a machine (e.g. your desktop), you can run on more
+(virtual) processors than you have physical processors.
+</P>
+<P>To run multiple independent simulatoins from one input script, using
+multiple partitions, see <A HREF = "Section_howto.html#howto_4">Section_howto 4</A>
+of the manual. World- and universe-style <A HREF = "variable.html">variables</A>
+are useful in this context.
+</P>
+<PRE>-plog file
+</PRE>
+<P>Specify the base name for the partition log files, so partition N
+writes log information to file.N. If file is none, then no partition
+log files are created. This overrides the filename specified in the
+-log command-line option. This option is useful when working with
+large numbers of partitions, allowing the partition log files to be
+suppressed (-plog none) or placed in a sub-directory (-plog
+replica_files/log.lammps) If this option is not used the log file for
+partition N is log.lammps.N or whatever is specified by the -log
+command-line option.
+</P>
+<PRE>-pscreen file
+</PRE>
+<P>Specify the base name for the partition screen file, so partition N
+writes screen information to file.N. If file is none, then no
+partition screen files are created. This overrides the filename
+specified in the -screen command-line option. This option is useful
+when working with large numbers of partitions, allowing the partition
+screen files to be suppressed (-pscreen none) or placed in a
+sub-directory (-pscreen replica_files/screen). If this option is not
+used the screen file for partition N is screen.N or whatever is
+specified by the -screen command-line option.
+</P>
+<PRE>-restart restartfile <I>remap</I> datafile keyword value ...
+</PRE>
+<P>Convert the restart file into a data file and immediately exit. This
+is the same operation as if the following 2-line input script were
+run:
+</P>
+<PRE>read_restart restartfile <I>remap</I>
+write_data datafile keyword value ...
+</PRE>
+<P>Note that the specified restartfile and datafile can have wild-card
+characters ("*",%") as described by the
+<A HREF = "read_restart.html">read_restart</A> and <A HREF = "write_data.html">write_data</A>
+commands. But a filename such as file.* will need to be enclosed in
+quotes to avoid shell expansion of the "*" character.
+</P>
+<P>Note that following restartfile, the optional flag <I>remap</I> can be
+used. This has the same effect as adding it to the
+<A HREF = "read_restart.html">read_restart</A> command, as explained on its doc
+page. This is only useful if the reading of the restart file triggers
+an error that atoms have been lost. In that case, use of the remap
+flag should allow the data file to still be produced.
+</P>
+<P>Also note that following datafile, the same optional keyword/value
+pairs can be listed as used by the <A HREF = "write_data.html">write_data</A>
+command.
+</P>
+<PRE>-reorder nth N
+-reorder custom filename
+</PRE>
+<P>Reorder the processors in the MPI communicator used to instantiate
+LAMMPS, in one of several ways. The original MPI communicator ranks
+all P processors from 0 to P-1. The mapping of these ranks to
+physical processors is done by MPI before LAMMPS begins. It may be
+useful in some cases to alter the rank order. E.g. to insure that
+cores within each node are ranked in a desired order. Or when using
+the <A HREF = "run_style.html">run_style verlet/split</A> command with 2 partitions
+to insure that a specific Kspace processor (in the 2nd partition) is
+matched up with a specific set of processors in the 1st partition.
+See the <A HREF = "Section_accelerate.html">Section_accelerate</A> doc pages for
+more details.
+</P>
+<P>If the keyword <I>nth</I> is used with a setting <I>N</I>, then it means every
+Nth processor will be moved to the end of the ranking. This is useful
+when using the <A HREF = "run_style.html">run_style verlet/split</A> command with 2
+partitions via the -partition command-line switch. The first set of
+processors will be in the first partition, the 2nd set in the 2nd
+partition. The -reorder command-line switch can alter this so that
+the 1st N procs in the 1st partition and one proc in the 2nd partition
+will be ordered consecutively, e.g. as the cores on one physical node.
+This can boost performance. For example, if you use "-reorder nth 4"
+and "-partition 9 3" and you are running on 12 processors, the
+processors will be reordered from
+</P>
+<PRE>0 1 2 3 4 5 6 7 8 9 10 11
+</PRE>
+<P>to
+</P>
+<PRE>0 1 2 4 5 6 8 9 10 3 7 11
+</PRE>
+<P>so that the processors in each partition will be
+</P>
+<PRE>0 1 2 4 5 6 8 9 10
+3 7 11
+</PRE>
+<P>See the "processors" command for how to insure processors from each
+partition could then be grouped optimally for quad-core nodes.
+</P>
+<P>If the keyword is <I>custom</I>, then a file that specifies a permutation
+of the processor ranks is also specified. The format of the reorder
+file is as follows. Any number of initial blank or comment lines
+(starting with a "#" character) can be present. These should be
+followed by P lines of the form:
+</P>
+<PRE>I J
+</PRE>
+<P>where P is the number of processors LAMMPS was launched with. Note
+that if running in multi-partition mode (see the -partition switch
+above) P is the total number of processors in all partitions. The I
+and J values describe a permutation of the P processors. Every I and
+J should be values from 0 to P-1 inclusive. In the set of P I values,
+every proc ID should appear exactly once. Ditto for the set of P J
+values. A single I,J pairing means that the physical processor with
+rank I in the original MPI communicator will have rank J in the
+reordered communicator.
+</P>
+<P>Note that rank ordering can also be specified by many MPI
+implementations, either by environment variables that specify how to
+order physical processors, or by config files that specify what
+physical processors to assign to each MPI rank. The -reorder switch
+simply gives you a portable way to do this without relying on MPI
+itself. See the <A HREF = "processors">processors out</A> command for how to output
+info on the final assignment of physical processors to the LAMMPS
+simulation domain.
+</P>
+<PRE>-screen file
+</PRE>
+<P>Specify a file for LAMMPS to write its screen information to. In
+one-partition mode, if the switch is not used, LAMMPS writes to the
+screen. If this switch is used, LAMMPS writes to the specified file
+instead and you will see no screen output. In multi-partition mode,
+if the switch is not used, hi-level status information is written to
+the screen. Each partition also writes to a screen.N file where N is
+the partition ID. If the switch is specified in multi-partition mode,
+the hi-level screen dump is named "file" and each partition also
+writes screen information to a file.N. For both one-partition and
+multi-partition mode, if the specified file is "none", then no screen
+output is performed. Option -pscreen will override the name of the
+partition screen files file.N.
+</P>
+<PRE>-suffix style
+</PRE>
+<P>Use variants of various styles if they exist. The specified style can
+be <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I>. These refer to
+optional packages that LAMMPS can be built with, as described above in
+<A HREF = "#start_3">Section 2.3</A>. The "cuda" style corresponds to the USER-CUDA
+package, the "gpu" style to the GPU package, the "intel" style to the
+USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
+style to the OPT package, and the "omp" style to the USER-OMP package.
+</P>
+<P>Along with the "-package" command-line switch, this is a convenient
+mechanism for invoking accelerator packages and their options without
+having to edit an input script.
+</P>
+<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
+lj/cut</A> variant, with style names lj/cut/cuda,
+lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
+variant style can be specified explicitly in your input script,
+e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
+specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
+whenever your input script command creates a new
+<A HREF = "atom_style.html">atom</A>, <A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>,
+<A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style. If the variant
+version does not exist, the standard version is created.
+</P>
+<P>For the GPU package, using this command-line switch also invokes the
+default GPU settings, as if the command "package gpu 1" were used at
+the top of your input script. These settings can be changed by using
+the "-package gpu" command-line switch or the <A HREF = "package.html">package
+gpu</A> command in your script.
+</P>
+<P>For the USER-INTEL package, using this command-line switch also
+invokes the default USER-INTEL settings, as if the command "package
+intel 1" were used at the top of your input script. These settings
+can be changed by using the "-package intel" command-line switch or
+the <A HREF = "package.html">package intel</A> command in your script. If the
+USER-OMP package is also installed, the intel suffix will make the omp
+suffix a second choice, if a requested style is not available in the
+USER-INTEL package. It will also invoke the default USER-OMP
+settings, as if the command "package omp 0" were used at the top of
+your input script. These settings can be changed by using the
+"-package omp" command-line switch or the <A HREF = "package.html">package omp</A>
+command in your script.
+</P>
+<P>For the KOKKOS package, using this command-line switch also invokes
+the default KOKKOS settings, as if the command "package kokkos" were
+used at the top of your input script. These settings can be changed
+by using the "-package kokkos" command-line switch or the <A HREF = "package.html">package
+kokkos</A> command in your script.
+</P>
+<P>For the OMP package, using this command-line switch also invokes the
+default OMP settings, as if the command "package omp 0" were used at
+the top of your input script. These settings can be changed by using
+the "-package omp" command-line switch or the <A HREF = "package.html">package
+omp</A> command in your script.
+</P>
+<P>The <A HREF = "suffix.html">suffix</A> command can also be used within an input
+script to set a suffix, or to turn off or back on any suffix setting
+made via the command line.
+</P>
+<PRE>-var name value1 value2 ...
+</PRE>
+<P>Specify a variable that will be defined for substitution purposes when
+the input script is read. This switch can be used multiple times to
+define multiple variables. "Name" is the variable name which can be a
+single character (referenced as $x in the input script) or a full
+string (referenced as ${abc}). An <A HREF = "variable.html">index-style
+variable</A> will be created and populated with the
+subsequent values, e.g. a set of filenames. Using this command-line
+option is equivalent to putting the line "variable name index value1
+value2 ..." at the beginning of the input script. Defining an index
+variable as a command-line argument overrides any setting for the same
+index variable in the input script, since index variables cannot be
+re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
+defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
+section</A> for more info on using variables
+in input scripts.
+</P>
+<P>NOTE: Currently, the command-line parser looks for arguments that
+start with "-" to indicate new switches. Thus you cannot specify
+multiple variable values if any of they start with a "-", e.g. a
+negative numeric value. It is OK if the first value1 starts with a
+"-", since it is automatically skipped.
+</P>
+<HR>
+
+<H4><A NAME = "start_8"></A>2.8 LAMMPS screen output
+</H4>
+<P>As LAMMPS reads an input script, it prints information to both the
+screen and a log file about significant actions it takes to setup a
+simulation. When the simulation is ready to begin, LAMMPS performs
+various initializations and prints the amount of memory (in MBytes per
+processor) that the simulation requires. It also prints details of
+the initial thermodynamic state of the system. During the run itself,
+thermodynamic information is printed periodically, every few
+timesteps. When the run concludes, LAMMPS prints the final
+thermodynamic state and a total run time for the simulation. It then
+appends statistics about the CPU time and storage requirements for the
+simulation. An example set of statistics is shown here:
+</P>
+<PRE>Loop time of 49.002 on 2 procs for 2004 atoms
+</PRE>
+<PRE>Pair time (%) = 35.0495 (71.5267)
+Bond time (%) = 0.092046 (0.187841)
+Kspce time (%) = 6.42073 (13.103)
+Neigh time (%) = 2.73485 (5.5811)
+Comm time (%) = 1.50291 (3.06703)
+Outpt time (%) = 0.013799 (0.0281601)
+Other time (%) = 2.13669 (4.36041)
+</PRE>
+<PRE>Nlocal: 1002 ave, 1015 max, 989 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 8720 ave, 8724 max, 8716 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 354141 ave, 361422 max, 346860 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+</PRE>
+<PRE>Total # of neighbors = 708282
+Ave neighs/atom = 353.434
+Ave special neighs/atom = 2.34032
+Number of reneighborings = 42
+Dangerous reneighborings = 2
+</PRE>
+<P>The first section gives the breakdown of the CPU run time (in seconds)
+into major categories. The second section lists the number of owned
+atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
+per processor. The max and min values give the spread of these values
+across processors with a 10-bin histogram showing the distribution.
+The total number of histogram counts is equal to the number of
+processors.
+</P>
+<P>The last section gives aggregate statistics for pair-wise neighbors
+and special neighbors that LAMMPS keeps track of (see the
+<A HREF = "special_bonds.html">special_bonds</A> command). The number of times
+neighbor lists were rebuilt during the run is given as well as the
+number of potentially "dangerous" rebuilds. If atom movement
+triggered neighbor list rebuilding (see the
+<A HREF = "neigh_modify.html">neigh_modify</A> command), then dangerous
+reneighborings are those that were triggered on the first timestep
+atom movement was checked for. If this count is non-zero you may wish
+to reduce the delay factor to insure no force interactions are missed
+by atoms moving beyond the neighbor skin distance before a rebuild
+takes place.
+</P>
+<P>If an energy minimization was performed via the
+<A HREF = "minimize.html">minimize</A> command, additional information is printed,
+e.g.
+</P>
+<PRE>Minimization stats:
+ E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
+ Gradient 2-norm init/final= 1920.78 20.9992
+ Gradient inf-norm init/final= 304.283 9.61216
+ Iterations = 36
+ Force evaluations = 177
+</PRE>
+<P>The first line lists the initial and final energy, as well as the
+energy on the next-to-last iteration. The next 2 lines give a measure
+of the gradient of the energy (force on all atoms). The 2-norm is the
+"length" of this force vector; the inf-norm is the largest component.
+The last 2 lines are statistics on how many iterations and
+force-evaluations the minimizer required. Multiple force evaluations
+are typically done at each iteration to perform a 1d line minimization
+in the search direction.
+</P>
+<P>If a <A HREF = "kspace_style.html">kspace_style</A> long-range Coulombics solve was
+performed during the run (PPPM, Ewald), then additional information is
+printed, e.g.
+</P>
+<PRE>FFT time (% of Kspce) = 0.200313 (8.34477)
+FFT Gflps 3d 1d-only = 2.31074 9.19989
+</PRE>
+<P>The first line gives the time spent doing 3d FFTs (4 per timestep) and
+the fraction it represents of the total KSpace time (listed above).
+Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
+(transposes). The total flops performed is 5Nlog_2(N), where N is the
+number of points in the 3d grid. The FFTs are timed with and without
+the communication and a Gflop rate is computed. The 3d rate is with
+communication; the 1d rate is without (just the 1d FFTs). Thus you
+can estimate what fraction of your FFT time was spent in
+communication, roughly 75% in the example above.
+</P>
+<HR>
+
+<H4><A NAME = "start_9"></A>2.9 Tips for users of previous LAMMPS versions
+</H4>
+<P>The current C++ began with a complete rewrite of LAMMPS 2001, which
+was written in F90. Features of earlier versions of LAMMPS are listed
+in <A HREF = "Section_history.html">Section_history</A>. The F90 and F77 versions
+(2001 and 99) are also freely distributed as open-source codes; check
+the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for distribution information if you prefer
+those versions. The 99 and 2001 versions are no longer under active
+development; they do not have all the features of C++ LAMMPS.
+</P>
+<P>If you are a previous user of LAMMPS 2001, these are the most
+significant changes you will notice in C++ LAMMPS:
+</P>
+<P>(1) The names and arguments of many input script commands have
+changed. All commands are now a single word (e.g. read_data instead
+of read data).
+</P>
+<P>(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
+but you may need to specify the relevant commands in different ways.
+</P>
+<P>(3) The format of the data file can be streamlined for some problems.
+See the <A HREF = "read_data.html">read_data</A> command for details. The data file
+section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
+</P>
+<P>(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
+LAMMPS with a <A HREF = "read_restart.html">read_restart</A> command. This is
+because they were output by F90 which writes in a different binary
+format than C or C++ writes or reads. Use the <I>restart2data</I> tool
+provided with LAMMPS 2001 to convert the 2001 restart file to a text
+data file. Then edit the data file as necessary before using the C++
+LAMMPS <A HREF = "read_data.html">read_data</A> command to read it in.
+</P>
+<P>(5) There are numerous small numerical changes in C++ LAMMPS that mean
+you will not get identical answers when comparing to a 2001 run.
+However, your initial thermodynamic energy and MD trajectory should be
+close if you have setup the problem for both codes the same.
+</P>
+</HTML>
diff --git a/doc/doc2/Section_tools.html b/doc/doc2/Section_tools.html
new file mode 100644
index 000000000..a68a6138c
--- /dev/null
+++ b/doc/doc2/Section_tools.html
@@ -0,0 +1,572 @@
+<HTML>
+<CENTER><A HREF = "Section_perf.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS
+Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_modify.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>9. Additional tools
+</H3>
+<P>LAMMPS is designed to be a computational kernel for performing
+molecular dynamics computations. Additional pre- and post-processing
+steps are often necessary to setup and analyze a simulation. A few
+additional tools are provided with the LAMMPS distribution and are
+described in this section.
+</P>
+<P>Our group has also written and released a separate toolkit called
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations. Pizza.py is
+written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
+Pizza.py WWW site</A>.
+</P>
+
+
+
+
+<P>Note that many users write their own setup or analysis tools or use
+other existing codes and convert their output to a LAMMPS input format
+or vice versa. The tools listed here are included in the LAMMPS
+distribution as examples of auxiliary tools. Some of them are not
+actively supported by Sandia, as they were contributed by LAMMPS
+users. If you have problems using them, we can direct you to the
+authors.
+</P>
+<P>The source code for each of these codes is in the tools sub-directory
+of the LAMMPS distribution. There is a Makefile (which you may need
+to edit for your platform) which will build several of the tools which
+reside in that directory. Some of them are larger packages in their
+own sub-directories with their own Makefiles.
+</P>
+<UL><LI><A HREF = "#amber">amber2lmp</A>
+<LI><A HREF = "#binary">binary2txt</A>
+<LI><A HREF = "#charmm">ch2lmp</A>
+<LI><A HREF = "#chain">chain</A>
+<LI><A HREF = "#colvars">colvars</A>
+<LI><A HREF = "#create">createatoms</A>
+<LI><A HREF = "#data">data2xmovie</A>
+<LI><A HREF = "#eamdb">eam database</A>
+<LI><A HREF = "#eamgn">eam generate</A>
+<LI><A HREF = "#eff">eff</A>
+<LI><A HREF = "#emacs">emacs</A>
+<LI><A HREF = "#fep">fep</A>
+<LI><A HREF = "#ipi">i-pi</A>
+<LI><A HREF = "#ipp">ipp</A>
+<LI><A HREF = "#kate">kate</A>
+<LI><A HREF = "#arc">lmp2arc</A>
+<LI><A HREF = "#cfg">lmp2cfg</A>
+<LI><A HREF = "#vmd">lmp2vmd</A>
+<LI><A HREF = "#matlab">matlab</A>
+<LI><A HREF = "#micelle">micelle2d</A>
+<LI><A HREF = "#moltemplate">moltemplate</A>
+<LI><A HREF = "#msi">msi2lmp</A>
+<LI><A HREF = "#phonon">phonon</A>
+<LI><A HREF = "#polybond">polymer bonding</A>
+<LI><A HREF = "#pymol">pymol_asphere</A>
+<LI><A HREF = "#pythontools">python</A>
+<LI><A HREF = "#reax">reax</A>
+<LI><A HREF = "#restart">restart2data</A>
+<LI><A HREF = "#vim">vim</A>
+<LI><A HREF = "#xmgrace">xmgrace</A>
+<LI><A HREF = "#xmovie">xmovie</A>
+</UL>
+<HR>
+
+<H4><A NAME = "amber"></A>amber2lmp tool
+</H4>
+<P>The amber2lmp sub-directory contains two Python scripts for converting
+files back-and-forth between the AMBER MD code and LAMMPS. See the
+README file in amber2lmp for more information.
+</P>
+<P>These tools were written by Keir Novik while he was at Queen Mary
+University of London. Keir is no longer there and cannot support
+these tools which are out-of-date with respect to the current LAMMPS
+version (and maybe with respect to AMBER as well). Since we don't use
+these tools at Sandia, you'll need to experiment with them and make
+necessary modifications yourself.
+</P>
+<HR>
+
+<H4><A NAME = "binary"></A>binary2txt tool
+</H4>
+<P>The file binary2txt.cpp converts one or more binary LAMMPS dump file
+into ASCII text files. The syntax for running the tool is
+</P>
+<PRE>binary2txt file1 file2 ...
+</PRE>
+<P>which creates file1.txt, file2.txt, etc. This tool must be compiled
+on a platform that can read the binary file created by a LAMMPS run,
+since binary files are not compatible across all platforms.
+</P>
+<HR>
+
+<H4><A NAME = "charmm"></A>ch2lmp tool
+</H4>
+<P>The ch2lmp sub-directory contains tools for converting files
+back-and-forth between the CHARMM MD code and LAMMPS.
+</P>
+<P>They are intended to make it easy to use CHARMM as a builder and as a
+post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
+ensemble built in CHARMM into its LAMMPS equivalent. Using
+lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
+</P>
+<P>See the README file in the ch2lmp sub-directory for more information.
+</P>
+<P>These tools were created by Pieter in't Veld (pjintve at sandia.gov)
+and Paul Crozier (pscrozi at sandia.gov) at Sandia.
+</P>
+<HR>
+
+<H4><A NAME = "chain"></A>chain tool
+</H4>
+<P>The file chain.f creates a LAMMPS data file containing bead-spring
+polymer chains and/or monomer solvent atoms. It uses a text file
+containing chain definition parameters as an input. The created
+chains and solvent atoms can strongly overlap, so LAMMPS needs to run
+the system initially with a "soft" pair potential to un-overlap it.
+The syntax for running the tool is
+</P>
+<PRE>chain < def.chain > data.file
+</PRE>
+<P>See the def.chain or def.chain.ab files in the tools directory for
+examples of definition files. This tool was used to create the
+system for the <A HREF = "Section_perf.html">chain benchmark</A>.
+</P>
+<HR>
+
+<H4><A NAME = "colvars"></A>colvars tools
+</H4>
+<P>The colvars directory contains a collection of tools for postprocessing
+data produced by the colvars collective variable library.
+To compile the tools, edit the makefile for your system and run "make".
+</P>
+<P>Please report problems and issues the colvars library and its tools
+at: https://github.com/colvars/colvars/issues
+</P>
+<P>abf_integrate:
+</P>
+<P>MC-based integration of multidimensional free energy gradient
+Version 20110511
+</P>
+<PRE>Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
+</PRE>
+<P>The LAMMPS interface to the colvars collective variable library, as
+well as these tools, were created by Axel Kohlmeyer (akohlmey at
+gmail.com) at ICTP, Italy.
+</P>
+<HR>
+
+<H4><A NAME = "create"></A>createatoms tool
+</H4>
+<P>The tools/createatoms directory contains a Fortran program called
+createAtoms.f which can generate a variety of interesting crystal
+structures and geometries and output the resulting list of atom
+coordinates in LAMMPS or other formats.
+</P>
+<P>See the included Manual.pdf for details.
+</P>
+<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
+</P>
+<HR>
+
+<H4><A NAME = "data"></A>data2xmovie tool
+</H4>
+<P>The file data2xmovie.c converts a LAMMPS data file into a snapshot
+suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it had
+been output with a dump command from LAMMPS itself. The syntax for
+running the tool is
+</P>
+<PRE>data2xmovie [options] < infile > outfile
+</PRE>
+<P>See the top of the data2xmovie.c file for a discussion of the options.
+</P>
+<HR>
+
+<H4><A NAME = "eamdb"></A>eam database tool
+</H4>
+<P>The tools/eam_database directory contains a Fortran program that will
+generate EAM alloy setfl potential files for any combination of 16
+elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
+Zr. The files can then be used with the <A HREF = "pair_eam.html">pair_style
+eam/alloy</A> command.
+</P>
+<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
+and is based on his paper:
+</P>
+<P>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
+144113 (2004).
+</P>
+<HR>
+
+<H4><A NAME = "eamgn"></A>eam generate tool
+</H4>
+<P>The tools/eam_generate directory contains several one-file C programs
+that convert an analytic formula into a tabulated <A HREF = "pair_eam.html">embedded atom
+method (EAM)</A> setfl potential file. The potentials they
+produce are in the potentials directory, and can be used with the
+<A HREF = "pair_eam.html">pair_style eam/alloy</A> command.
+</P>
+<P>The source files and potentials were provided by Gerolf Ziegenhain
+(gerolf at ziegenhain.com).
+</P>
+<HR>
+
+<H4><A NAME = "eff"></A>eff tool
+</H4>
+<P>The tools/eff directory contains various scripts for generating
+structures and post-processing output for simulations using the
+electron force field (eFF).
+</P>
+<P>These tools were provided by Andres Jaramillo-Botero at CalTech
+(ajaramil at wag.caltech.edu).
+</P>
+<HR>
+
+<H4><A NAME = "emacs"></A>emacs tool
+</H4>
+<P>The tools/emacs directory contains a Lips add-on file for Emacs that
+enables a lammps-mode for editing of input scripts when using Emacs,
+with various highlighting options setup.
+</P>
+<P>These tools were provided by Aidan Thompson at Sandia
+(athomps at sandia.gov).
+</P>
+<HR>
+
+<H4><A NAME = "fep"></A>fep tool
+</H4>
+<P>The tools/fep directory contains Python scripts useful for
+post-processing results from performing free-energy perturbation
+simulations using the USER-FEP package.
+</P>
+<P>The scripts were contributed by Agilio Padua (Universite Blaise
+Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
+</P>
+<P>See README file in the tools/fep directory.
+</P>
+<HR>
+
+<H4><A NAME = "ipi"></A>i-pi tool
+</H4>
+<P>The tools/i-pi directory contains a version of the i-PI package, with
+all the LAMMPS-unrelated files removed. It is provided so that it can
+be used with the <A HREF = "fix_ipi.html">fix ipi</A> command to perform
+path-integral molecular dynamics (PIMD).
+</P>
+<P>The i-PI package was created and is maintained by Michele Ceriotti,
+michele.ceriotti at gmail.com, to interface to a variety of molecular
+dynamics codes.
+</P>
+<P>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
+<A HREF = "fix_ipi.html">fix ipi</A> doc page for further details on running PIMD
+calculations with LAMMPS.
+</P>
+<HR>
+
+<H4><A NAME = "ipp"></A>ipp tool
+</H4>
+<P>The tools/ipp directory contains a Perl script ipp which can be used
+to facilitate the creation of a complicated file (say, a lammps input
+script or tools/createatoms input file) using a template file.
+</P>
+<P>ipp was created and is maintained by Reese Jones (Sandia), rjones at
+sandia.gov.
+</P>
+<P>See two examples in the tools/ipp directory. One of them is for the
+tools/createatoms tool's input file.
+</P>
+<HR>
+
+<H4><A NAME = "kate"></A>kate tool
+</H4>
+<P>The file in the tools/kate directory is an add-on to the Kate editor
+in the KDE suite that allow syntax highlighting of LAMMPS input
+scripts. See the README.txt file for details.
+</P>
+<P>The file was provided by Alessandro Luigi Sellerio
+(alessandro.sellerio at ieni.cnr.it).
+</P>
+<HR>
+
+<H4><A NAME = "arc"></A>lmp2arc tool
+</H4>
+<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output
+files to the format for Accelrys' Insight MD code (formerly
+MSI/Biosym and its Discover MD code). See the README file for more
+information.
+</P>
+<P>This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
+(jec at mayo.edu), but still fields questions about the tool.
+</P>
+<P>This tool was updated for the current LAMMPS C++ version by Jeff
+Greathouse at Sandia (jagreat at sandia.gov).
+</P>
+<HR>
+
+<H4><A NAME = "cfg"></A>lmp2cfg tool
+</H4>
+<P>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
+files into a series of *.cfg files which can be read into the
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer. See
+the README file for more information.
+</P>
+<P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
+</P>
+<HR>
+
+<H4><A NAME = "vmd"></A>lmp2vmd tool
+</H4>
+<P>The lmp2vmd sub-directory contains a README.txt file that describes
+details of scripts and plugin support within the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
+package</A> for visualizing LAMMPS
+dump files.
+</P>
+<P>The VMD plugins and other supporting scripts were written by Axel
+Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
+</P>
+<HR>
+
+<H4><A NAME = "matlab"></A>matlab tool
+</H4>
+<P>The matlab sub-directory contains several <A HREF = "http://www.mathworks.com">MATLAB</A> scripts for
+post-processing LAMMPS output. The scripts include readers for log
+and dump files, a reader for EAM potential files, and a converter that
+reads LAMMPS dump files and produces CFG files that can be visualized
+with the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
+visualizer.
+</P>
+<P>See the README.pdf file for more information.
+</P>
+<P>These scripts were written by Arun Subramaniyan at Purdue Univ
+(asubrama at purdue.edu).
+</P>
+
+
+<HR>
+
+<H4><A NAME = "micelle"></A>micelle2d tool
+</H4>
+<P>The file micelle2d.f creates a LAMMPS data file containing short lipid
+chains in a monomer solution. It uses a text file containing lipid
+definition parameters as an input. The created molecules and solvent
+atoms can strongly overlap, so LAMMPS needs to run the system
+initially with a "soft" pair potential to un-overlap it. The syntax
+for running the tool is
+</P>
+<PRE>micelle2d < def.micelle2d > data.file
+</PRE>
+<P>See the def.micelle2d file in the tools directory for an example of a
+definition file. This tool was used to create the system for the
+<A HREF = "Section_example.html">micelle example</A>.
+</P>
+<HR>
+
+<H4><A NAME = "moltemplate"></A>moltemplate tool
+</H4>
+<P>The moltemplate sub-directory contains a Python-based tool for
+building molecular systems based on a text-file description, and
+creating LAMMPS data files that encode their molecular topology as
+lists of bonds, angles, dihedrals, etc. See the README.TXT file for
+more information.
+</P>
+<P>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
+supports it. It has its own WWW page at
+<A HREF = "http://moltemplate.org">http://moltemplate.org</A>.
+</P>
+<HR>
+
+<H4><A NAME = "msi"></A>msi2lmp tool
+</H4>
+<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
+data files from Accelrys' Insight MD code (formerly MSI/Biosym and
+its Discover MD code). See the README file for more information.
+</P>
+<P>This tool was written by John Carpenter (Cray), Michael Peachey
+(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
+(jec at mayo.edu), but still fields questions about the tool.
+</P>
+<P>This tool may be out-of-date with respect to the current LAMMPS and
+Insight versions. Since we don't use it at Sandia, you'll need to
+experiment with it yourself.
+</P>
+<HR>
+
+<H4><A NAME = "phonon"></A>phonon tool
+</H4>
+<P>The phonon sub-directory contains a post-processing tool useful for
+analyzing the output of the <A HREF = "fix_phonon.html">fix phonon</A> command in
+the USER-PHONON package.
+</P>
+<P>See the README file for instruction on building the tool and what
+library it needs. And see the examples/USER/phonon directory
+for example problems that can be post-processed with this tool.
+</P>
+<P>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
+University.
+</P>
+<HR>
+
+<H4><A NAME = "polybond"></A>polymer bonding tool
+</H4>
+<P>The polybond sub-directory contains a Python-based tool useful for
+performing "programmable polymer bonding". The Python file
+lmpsdata.py provides a "Lmpsdata" class with various methods which can
+be invoked by a user-written Python script to create data files with
+complex bonding topologies.
+</P>
+<P>See the Manual.pdf for details and example scripts.
+</P>
+<P>This tool was written by Zachary Kraus at Georgia Tech.
+</P>
+<HR>
+
+<H4><A NAME = "pymol"></A>pymol_asphere tool
+</H4>
+<P>The pymol_asphere sub-directory contains a tool for converting a
+LAMMPS dump file that contains orientation info for ellipsoidal
+particles into an input file for the <A HREF = "http://pymol.sourceforge.net">PyMol visualization
+package</A>.
+</P>
+
+
+<P>Specifically, the tool triangulates the ellipsoids so they can be
+viewed as true ellipsoidal particles within PyMol. See the README and
+examples directory within pymol_asphere for more information.
+</P>
+<P>This tool was written by Mike Brown at Sandia.
+</P>
+<HR>
+
+<H4><A NAME = "pythontools"></A>python tool
+</H4>
+<P>The python sub-directory contains several Python scripts
+that perform common LAMMPS post-processing tasks, such as:
+</P>
+<UL><LI>extract thermodynamic info from a log file as columns of numbers
+<LI>plot two columns of thermodynamic info from a log file using GnuPlot
+<LI>sort the snapshots in a dump file by atom ID
+<LI>convert multiple <A HREF = "neb.html">NEB</A> dump files into one dump file for viz
+<LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages
+</UL>
+<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
+README for more info on Pizza.py and how to use these scripts.
+</P>
+<HR>
+
+<H4><A NAME = "reax"></A>reax tool
+</H4>
+<P>The reax sub-directory contains stand-alond codes that can
+post-process the output of the <A HREF = "fix_reax_bonds.html">fix reax/bonds</A>
+command from a LAMMPS simulation using <A HREF = "pair_reax.html">ReaxFF</A>. See
+the README.txt file for more info.
+</P>
+<P>These tools were written by Aidan Thompson at Sandia.
+</P>
+<HR>
+
+<H4><A NAME = "restart"></A>restart2data tool
+</H4>
+<P>IMPORTANT NOTE: This tool is now obsolete and is not included in the
+current LAMMPS distribution. This is becaues there is now a
+<A HREF = "write_data.html">write_data</A> command, which can create a data file
+from within an input script. Running LAMMPS with the "-r"
+<A HREF = "Section_start.html#start_7">command-line switch</A> as follows:
+</P>
+<P>lmp_g++ -r restartfile datafile
+</P>
+<P>is the same as running a 2-line input script:
+</P>
+<P>read_restart restartfile
+write_data datafile
+</P>
+<P>which will produce the same data file that the restart2data tool used
+to create. The following information is included in case you have an
+older version of LAMMPS which still includes the restart2data tool.
+</P>
+<P>The file restart2data.cpp converts a binary LAMMPS restart file into
+an ASCII data file. The syntax for running the tool is
+</P>
+<PRE>restart2data restart-file data-file (input-file)
+</PRE>
+<P>Input-file is optional and if specified will contain LAMMPS input
+commands for the masses and force field parameters, instead of putting
+those in the data-file. Only a few force field styles currently
+support this option.
+</P>
+<P>This tool must be compiled on a platform that can read the binary file
+created by a LAMMPS run, since binary files are not compatible across
+all platforms.
+</P>
+<P>Note that a text data file has less precision than a binary restart
+file. Hence, continuing a run from a converted data file will
+typically not conform as closely to a previous run as will restarting
+from a binary restart file.
+</P>
+<P>If a "%" appears in the specified restart-file, the tool expects a set
+of multiple files to exist. See the <A HREF = "restart.html">restart</A> and
+<A HREF = "write_restart.html">write_restart</A> commands for info on how such sets
+of files are written by LAMMPS, and how the files are named.
+</P>
+<HR>
+
+<H4><A NAME = "vim"></A>vim tool
+</H4>
+<P>The files in the tools/vim directory are add-ons to the VIM editor
+that allow easier editing of LAMMPS input scripts. See the README.txt
+file for details.
+</P>
+<P>These files were provided by Gerolf Ziegenhain (gerolf at
+ziegenhain.com)
+</P>
+<HR>
+
+<H4><A NAME = "xmgrace"></A>xmgrace tool
+</H4>
+<P>The files in the tools/xmgrace directory can be used to plot the
+thermodynamic data in LAMMPS log files via the xmgrace plotting
+package. There are several tools in the directory that can be used in
+post-processing mode. The lammpsplot.cpp file can be compiled and
+used to create plots from the current state of a running LAMMPS
+simulation.
+</P>
+<P>See the README file for details.
+</P>
+<P>These files were provided by Vikas Varshney (vv0210 at gmail.com)
+</P>
+<HR>
+
+<H4><A NAME = "xmovie"></A>xmovie tool
+</H4>
+<P>The xmovie tool is an X-based visualization package that can read
+LAMMPS dump files and animate them. It is in its own sub-directory
+with the tools directory. You may need to modify its Makefile so that
+it can find the appropriate X libraries to link against.
+</P>
+<P>The syntax for running xmovie is
+</P>
+<PRE>xmovie [options] dump.file1 dump.file2 ...
+</PRE>
+<P>If you just type "xmovie" you will see a list of options. Note that
+by default, LAMMPS dump files are in scaled coordinates, so you
+typically need to use the -scale option with xmovie. When xmovie runs
+it opens a visualization window and a control window. The control
+options are straightforward to use.
+</P>
+<P>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
+spent a summer at Sandia. It displays 2d projections of a 3d domain.
+While simple in design, it is an amazingly fast program that can
+render large numbers of atoms very quickly. It's a useful tool for
+debugging LAMMPS input and output and making sure your simulation is
+doing what you think it should. The animations on the Examples page
+of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A> were created with xmovie.
+</P>
+<P>I've lost contact with Mike, so I hope he's comfortable with us
+distributing his great tool!
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_cuda.html b/doc/doc2/accelerate_cuda.html
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@@ -0,0 +1,228 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.1 USER-CUDA package
+</H4>
+<P>The USER-CUDA package was developed by Christian Trott (Sandia) while
+at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions
+of many pair styles, many fixes, a few computes, and for long-range
+Coulombics via the PPPM command. It has the following general
+features:
+</P>
+<UL><LI>The package is designed to allow an entire LAMMPS calculation, for
+many timesteps, to run entirely on the GPU (except for inter-processor
+MPI communication), so that atom-based data (e.g. coordinates, forces)
+do not have to move back-and-forth between the CPU and GPU.
+
+<LI>The speed-up advantage of this approach is typically better when the
+number of atoms per GPU is large
+
+<LI>Data will stay on the GPU until a timestep where a non-USER-CUDA fix
+or compute is invoked. Whenever a non-GPU operation occurs (fix,
+compute, output), data automatically moves back to the CPU as needed.
+This may incur a performance penalty, but should otherwise work
+transparently.
+
+<LI>Neighbor lists are constructed on the GPU.
+
+<LI>The package only supports use of a single MPI task, running on a
+single CPU (core), assigned to each GPU.
+</UL>
+<P>Here is a quick overview of how to use the USER-CUDA package:
+</P>
+<UL><LI>build the library in lib/cuda for your GPU hardware with desired precision
+<LI>include the USER-CUDA package and build LAMMPS
+<LI>use the mpirun command to specify 1 MPI task per GPU (on each node)
+<LI>enable the USER-CUDA package via the "-c on" command-line switch
+<LI>specify the # of GPUs per node
+<LI>use USER-CUDA styles in your input script
+</UL>
+<P>The latter two steps can be done using the "-pk cuda" and "-sf cuda"
+<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
+the effect of the "-pk" or "-sf" switches can be duplicated by adding
+the <A HREF = "package.html">package cuda</A> or <A HREF = "suffix.html">suffix cuda</A> commands
+respectively to your input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>To use this package, you need to have one or more NVIDIA GPUs and
+install the NVIDIA Cuda software on your system:
+</P>
+<P>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
+help you to find out the Compute Capability of your card:
+</P>
+<P>http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units
+</P>
+<P>Install the Nvidia Cuda Toolkit (version 3.2 or higher) and the
+corresponding GPU drivers. The Nvidia Cuda SDK is not required, but
+we recommend it also be installed. You can then make sure its sample
+projects can be compiled without problems.
+</P>
+<P><B>Building LAMMPS with the USER-CUDA package:</B>
+</P>
+<P>This requires two steps (a,b): build the USER-CUDA library, then build
+LAMMPS with the USER-CUDA package.
+</P>
+<P>You can do both these steps in one line, using the src/Make.py script,
+described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
+Type "Make.py -h" for help. If run from the src directory, this
+command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the
+starting Makefile.machine:
+</P>
+<PRE>Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi
+</PRE>
+<P>Or you can follow these two (a,b) steps:
+</P>
+<P>(a) Build the USER-CUDA library
+</P>
+<P>The USER-CUDA library is in lammps/lib/cuda. If your <I>CUDA</I> toolkit
+is not installed in the default system directoy <I>/usr/local/cuda</I> edit
+the file <I>lib/cuda/Makefile.common</I> accordingly.
+</P>
+<P>To build the library with the settings in lib/cuda/Makefile.default,
+simply type:
+</P>
+<PRE>make
+</PRE>
+<P>To set options when the library is built, type "make OPTIONS", where
+<I>OPTIONS</I> are one or more of the following. The settings will be
+written to the <I>lib/cuda/Makefile.defaults</I> before the build.
+</P>
+<PRE><I>precision=N</I> to set the precision level
+ N = 1 for single precision (default)
+ N = 2 for double precision
+ N = 3 for positions in double precision
+ N = 4 for positions and velocities in double precision
+<I>arch=M</I> to set GPU compute capability
+ M = 35 for Kepler GPUs
+ M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
+ M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
+ M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
+<I>prec_timer=0/1</I> to use hi-precision timers
+ 0 = do not use them (default)
+ 1 = use them
+ this is usually only useful for Mac machines
+<I>dbg=0/1</I> to activate debug mode
+ 0 = no debug mode (default)
+ 1 = yes debug mode
+ this is only useful for developers
+<I>cufft=1</I> for use of the CUDA FFT library
+ 0 = no CUFFT support (default)
+ in the future other CUDA-enabled FFT libraries might be supported
+</PRE>
+<P>If the build is successful, it will produce the files liblammpscuda.a and
+Makefile.lammps.
+</P>
+<P>Note that if you change any of the options (like precision), you need
+to re-build the entire library. Do a "make clean" first, followed by
+"make".
+</P>
+<P>(b) Build LAMMPS with the USER-CUDA package
+</P>
+<PRE>cd lammps/src
+make yes-user-cuda
+make machine
+</PRE>
+<P>No additional compile/link flags are needed in Makefile.machine.
+</P>
+<P>Note that if you change the USER-CUDA library precision (discussed
+above) and rebuild the USER-CUDA library, then you also need to
+re-install the USER-CUDA package and re-build LAMMPS, so that all
+affected files are re-compiled and linked to the new USER-CUDA
+library.
+</P>
+<P><B>Run with the USER-CUDA package from the command line:</B>
+</P>
+<P>The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node. E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
+</P>
+<P>When using the USER-CUDA package, you must use exactly one MPI task
+per physical GPU.
+</P>
+<P>You must use the "-c on" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to enable the USER-CUDA package.
+The "-c on" switch also issues a default <A HREF = "package.html">package cuda 1</A>
+command which sets various USER-CUDA options to default values, as
+discussed on the <A HREF = "package.html">package</A> command doc page.
+</P>
+<P>Use the "-sf cuda" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "cuda" to styles that support it. Use
+the "-pk cuda Ng" <A HREF = "Section_start.html#start_7">command-line switch</A> to
+set Ng = # of GPUs per node to a different value than the default set
+by the "-c on" switch (1 GPU) or change other <A HREF = "package.html">package
+cuda</A> options.
+</P>
+<PRE>lmp_machine -c on -sf cuda -pk cuda 1 -in in.script # 1 MPI task uses 1 GPU
+mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # 2 MPI tasks use 2 GPUs on a single 16-core (or whatever) node
+mpirun -np 24 -ppn 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # ditto on 12 16-core nodes
+</PRE>
+<P>The syntax for the "-pk" switch is the same as same as the "package
+cuda" command. See the <A HREF = "package.html">package</A> command doc page for
+details, including the default values used for all its options if it
+is not specified.
+</P>
+<P>Note that the default for the <A HREF = "package.html">package cuda</A> command is
+to set the Newton flag to "off" for both pairwise and bonded
+interactions. This typically gives fastest performance. If the
+<A HREF = "newton.html">newton</A> command is used in the input script, it can
+override these defaults.
+</P>
+<P><B>Or run with the USER-CUDA package by editing an input script:</B>
+</P>
+<P>The discussion above for the mpirun/mpiexec command and the requirement
+of one MPI task per GPU is the same.
+</P>
+<P>You must still use the "-c on" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to enable the USER-CUDA package.
+</P>
+<P>Use the <A HREF = "suffix.html">suffix cuda</A> command, or you can explicitly add a
+"cuda" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/cuda 2.5
+</PRE>
+<P>You only need to use the <A HREF = "package.html">package cuda</A> command if you
+wish to change any of its option defaults, including the number of
+GPUs/node (default = 1), as set by the "-c on" <A HREF = "Section_start.html#start_7">command-line
+switch</A>.
+</P>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>The performance of a GPU versus a multi-core CPU is a function of your
+hardware, which pair style is used, the number of atoms/GPU, and the
+precision used on the GPU (double, single, mixed).
+</P>
+<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
+LAMMPS web site for performance of the USER-CUDA package on different
+hardware.
+</P>
+<P><B>Guidelines for best performance:</B>
+</P>
+<UL><LI>The USER-CUDA package offers more speed-up relative to CPU performance
+when the number of atoms per GPU is large, e.g. on the order of tens
+or hundreds of 1000s.
+
+<LI>As noted above, this package will continue to run a simulation
+entirely on the GPU(s) (except for inter-processor MPI communication),
+for multiple timesteps, until a CPU calculation is required, either by
+a fix or compute that is non-GPU-ized, or until output is performed
+(thermo or dump snapshot or restart file). The less often this
+occurs, the faster your simulation will run.
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>None.
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_gpu.html b/doc/doc2/accelerate_gpu.html
new file mode 100644
index 000000000..fcf563e17
--- /dev/null
+++ b/doc/doc2/accelerate_gpu.html
@@ -0,0 +1,257 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.2 GPU package
+</H4>
+<P>The GPU package was developed by Mike Brown at ORNL and his
+collaborators, particularly Trung Nguyen (ORNL). It provides GPU
+versions of many pair styles, including the 3-body Stillinger-Weber
+pair style, and for <A HREF = "kspace_style.html">kspace_style pppm</A> for
+long-range Coulombics. It has the following general features:
+</P>
+<UL><LI>It is designed to exploit common GPU hardware configurations where one
+or more GPUs are coupled to many cores of one or more multi-core CPUs,
+e.g. within a node of a parallel machine.
+
+<LI>Atom-based data (e.g. coordinates, forces) moves back-and-forth
+between the CPU(s) and GPU every timestep.
+
+<LI>Neighbor lists can be built on the CPU or on the GPU
+
+<LI>The charge assignement and force interpolation portions of PPPM can be
+run on the GPU. The FFT portion, which requires MPI communication
+between processors, runs on the CPU.
+
+<LI>Asynchronous force computations can be performed simultaneously on the
+CPU(s) and GPU.
+
+<LI>It allows for GPU computations to be performed in single or double
+precision, or in mixed-mode precision, where pairwise forces are
+computed in single precision, but accumulated into double-precision
+force vectors.
+
+<LI>LAMMPS-specific code is in the GPU package. It makes calls to a
+generic GPU library in the lib/gpu directory. This library provides
+NVIDIA support as well as more general OpenCL support, so that the
+same functionality can eventually be supported on a variety of GPU
+hardware.
+</UL>
+<P>Here is a quick overview of how to use the GPU package:
+</P>
+<UL><LI>build the library in lib/gpu for your GPU hardware wity desired precision
+<LI>include the GPU package and build LAMMPS
+<LI>use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU
+<LI>specify the # of GPUs per node
+<LI>use GPU styles in your input script
+</UL>
+<P>The latter two steps can be done using the "-pk gpu" and "-sf gpu"
+<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
+the effect of the "-pk" or "-sf" switches can be duplicated by adding
+the <A HREF = "package.html">package gpu</A> or <A HREF = "suffix.html">suffix gpu</A> commands
+respectively to your input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>To use this package, you currently need to have an NVIDIA GPU and
+install the NVIDIA Cuda software on your system:
+</P>
+<UL><LI>Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
+<LI>Go to http://www.nvidia.com/object/cuda_get.html
+<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
+<LI>Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties
+</UL>
+<P><B>Building LAMMPS with the GPU package:</B>
+</P>
+<P>This requires two steps (a,b): build the GPU library, then build
+LAMMPS with the GPU package.
+</P>
+<P>You can do both these steps in one line, using the src/Make.py script,
+described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
+Type "Make.py -h" for help. If run from the src directory, this
+command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
+starting Makefile.machine:
+</P>
+<PRE>Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi
+</PRE>
+<P>Or you can follow these two (a,b) steps:
+</P>
+<P>(a) Build the GPU library
+</P>
+<P>The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
+lib/gpu) appropriate for your system. You should pay special
+attention to 3 settings in this makefile.
+</P>
+<UL><LI>CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
+<LI>CUDA_ARCH = needs to be appropriate to your GPUs
+<LI>CUDA_PREC = precision (double, mixed, single) you desire
+</UL>
+<P>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
+for different GPU choices, e.g. Fermi vs Kepler. It also lists the
+possible precision settings:
+</P>
+<PRE>CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations
+CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations
+CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double
+</PRE>
+<P>The last setting is the mixed mode referred to above. Note that your
+GPU must support double precision to use either the 2nd or 3rd of
+these settings.
+</P>
+<P>To build the library, type:
+</P>
+<PRE>make -f Makefile.machine
+</PRE>
+<P>If successful, it will produce the files libgpu.a and Makefile.lammps.
+</P>
+<P>The latter file has 3 settings that need to be appropriate for the
+paths and settings for the CUDA system software on your machine.
+Makefile.lammps is a copy of the file specified by the EXTRAMAKE
+setting in Makefile.machine. You can change EXTRAMAKE or create your
+own Makefile.lammps.machine if needed.
+</P>
+<P>Note that to change the precision of the GPU library, you need to
+re-build the entire library. Do a "clean" first, e.g. "make -f
+Makefile.linux clean", followed by the make command above.
+</P>
+<P>(b) Build LAMMPS with the GPU package
+</P>
+<PRE>cd lammps/src
+make yes-gpu
+make machine
+</PRE>
+<P>No additional compile/link flags are needed in Makefile.machine.
+</P>
+<P>Note that if you change the GPU library precision (discussed above)
+and rebuild the GPU library, then you also need to re-install the GPU
+package and re-build LAMMPS, so that all affected files are
+re-compiled and linked to the new GPU library.
+</P>
+<P><B>Run with the GPU package from the command line:</B>
+</P>
+<P>The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node. E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
+</P>
+<P>When using the GPU package, you cannot assign more than one GPU to a
+single MPI task. However multiple MPI tasks can share the same GPU,
+and in many cases it will be more efficient to run this way. Likewise
+it may be more efficient to use less MPI tasks/node than the available
+# of CPU cores. Assignment of multiple MPI tasks to a GPU will happen
+automatically if you create more MPI tasks/node than there are
+GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
+shared by 4 MPI tasks.
+</P>
+<P>Use the "-sf gpu" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "gpu" to styles that support it. Use
+the "-pk gpu Ng" <A HREF = "Section_start.html#start_7">command-line switch</A> to
+set Ng = # of GPUs/node to use.
+</P>
+<PRE>lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
+mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
+mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
+</PRE>
+<P>Note that if the "-sf gpu" switch is used, it also issues a default
+<A HREF = "package.html">package gpu 1</A> command, which sets the number of
+GPUs/node to 1.
+</P>
+<P>Using the "-pk" switch explicitly allows for setting of the number of
+GPUs/node to use and additional options. Its syntax is the same as
+same as the "package gpu" command. See the <A HREF = "package.html">package</A>
+command doc page for details, including the default values used for
+all its options if it is not specified.
+</P>
+<P>Note that the default for the <A HREF = "package.html">package gpu</A> command is to
+set the Newton flag to "off" pairwise interactions. It does not
+affect the setting for bonded interactions (LAMMPS default is "on").
+The "off" setting for pairwise interaction is currently required for
+GPU package pair styles.
+</P>
+<P><B>Or run with the GPU package by editing an input script:</B>
+</P>
+<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+and use of multiple MPI tasks/GPU is the same.
+</P>
+<P>Use the <A HREF = "suffix.html">suffix gpu</A> command, or you can explicitly add an
+"gpu" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/gpu 2.5
+</PRE>
+<P>You must also use the <A HREF = "package.html">package gpu</A> command to enable the
+GPU package, unless the "-sf gpu" or "-pk gpu" <A HREF = "Section_start.html#start_7">command-line
+switches</A> were used. It specifies the
+number of GPUs/node to use, as well as other options.
+</P>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>The performance of a GPU versus a multi-core CPU is a function of your
+hardware, which pair style is used, the number of atoms/GPU, and the
+precision used on the GPU (double, single, mixed).
+</P>
+<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
+LAMMPS web site for performance of the GPU package on various
+hardware, including the Titan HPC platform at ORNL.
+</P>
+<P>You should also experiment with how many MPI tasks per GPU to use to
+give the best performance for your problem and machine. This is also
+a function of the problem size and the pair style being using.
+Likewise, you should experiment with the precision setting for the GPU
+library to see if single or mixed precision will give accurate
+results, since they will typically be faster.
+</P>
+<P><B>Guidelines for best performance:</B>
+</P>
+<UL><LI>Using multiple MPI tasks per GPU will often give the best performance,
+as allowed my most multi-core CPU/GPU configurations.
+
+<LI>If the number of particles per MPI task is small (e.g. 100s of
+particles), it can be more efficient to run with fewer MPI tasks per
+GPU, even if you do not use all the cores on the compute node.
+
+<LI>The <A HREF = "package.html">package gpu</A> command has several options for tuning
+performance. Neighbor lists can be built on the GPU or CPU. Force
+calculations can be dynamically balanced across the CPU cores and
+GPUs. GPU-specific settings can be made which can be optimized
+for different hardware. See the <A HREF = "package.html">packakge</A> command
+doc page for details.
+
+<LI>As described by the <A HREF = "package.html">package gpu</A> command, GPU
+accelerated pair styles can perform computations asynchronously with
+CPU computations. The "Pair" time reported by LAMMPS will be the
+maximum of the time required to complete the CPU pair style
+computations and the time required to complete the GPU pair style
+computations. Any time spent for GPU-enabled pair styles for
+computations that run simultaneously with <A HREF = "bond_style.html">bond</A>,
+<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
+<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
+calculations will not be included in the "Pair" time.
+
+<LI>When the <I>mode</I> setting for the package gpu command is force/neigh,
+the time for neighbor list calculations on the GPU will be added into
+the "Pair" time, not the "Neigh" time. An additional breakdown of the
+times required for various tasks on the GPU (data copy, neighbor
+calculations, force computations, etc) are output only with the LAMMPS
+screen output (not in the log file) at the end of each run. These
+timings represent total time spent on the GPU for each routine,
+regardless of asynchronous CPU calculations.
+
+<LI>The output section "GPU Time Info (average)" reports "Max Mem / Proc".
+This is the maximum memory used at one time on the GPU for data
+storage by a single MPI process.
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>None.
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_intel.html b/doc/doc2/accelerate_intel.html
new file mode 100644
index 000000000..2972e989c
--- /dev/null
+++ b/doc/doc2/accelerate_intel.html
@@ -0,0 +1,352 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.3 USER-INTEL package
+</H4>
+<P>The USER-INTEL package was developed by Mike Brown at Intel
+Corporation. It provides a capability to accelerate simulations by
+offloading neighbor list and non-bonded force calculations to Intel(R)
+Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package).
+Additionally, it supports running simulations in single, mixed, or
+double precision with vectorization, even if a coprocessor is not
+present, i.e. on an Intel(R) CPU. The same C++ code is used for both
+cases. When offloading to a coprocessor, the routine is run twice,
+once with an offload flag.
+</P>
+<P>The USER-INTEL package can be used in tandem with the USER-OMP
+package. This is useful when offloading pair style computations to
+coprocessors, so that other styles not supported by the USER-INTEL
+package, e.g. bond, angle, dihedral, improper, and long-range
+electrostatics, can run simultaneously in threaded mode on the CPU
+cores. Since less MPI tasks than CPU cores will typically be invoked
+when running with coprocessors, this enables the extra CPU cores to be
+used for useful computation.
+</P>
+<P>If LAMMPS is built with both the USER-INTEL and USER-OMP packages
+intsalled, this mode of operation is made easier to use, because the
+"-suffix intel" <A HREF = "Section_start.html#start_7">command-line switch</A> or
+the <A HREF = "suffix.html">suffix intel</A> command will both set a second-choice
+suffix to "omp" so that styles from the USER-OMP package will be used
+if available, after first testing if a style from the USER-INTEL
+package is available.
+</P>
+<P>When using the USER-INTEL package, you must choose at build time
+whether you are building for CPU-only acceleration or for using the
+Xeon Phi in offload mode.
+</P>
+<P>Here is a quick overview of how to use the USER-INTEL package
+for CPU-only acceleration:
+</P>
+<UL><LI>specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost
+<LI>specify -openmp with LINKFLAGS in your Makefile.machine
+<LI>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS
+<LI>specify how many OpenMP threads per MPI task to use
+<LI>use USER-INTEL and (optionally) USER-OMP styles in your input script
+</UL>
+<P>Note that many of these settings can only be used with the Intel
+compiler, as discussed below.
+</P>
+<P>Using the USER-INTEL package to offload work to the Intel(R)
+Xeon Phi(TM) coprocessor is the same except for these additional
+steps:
+</P>
+<UL><LI>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine
+<LI>add the flag -offload to LINKFLAGS in your Makefile.machine
+</UL>
+<P>The latter two steps in the first case and the last step in the
+coprocessor case can be done using the "-pk intel" and "-sf intel"
+<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
+the effect of the "-pk" or "-sf" switches can be duplicated by adding
+the <A HREF = "package.html">package intel</A> or <A HREF = "suffix.html">suffix intel</A>
+commands respectively to your input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>To use the offload option, you must have one or more Intel(R) Xeon
+Phi(TM) coprocessors and use an Intel(R) C++ compiler.
+</P>
+<P>Optimizations for vectorization have only been tested with the
+Intel(R) compiler. Use of other compilers may not result in
+vectorization or give poor performance.
+</P>
+<P>Use of an Intel C++ compiler is recommended, but not required (though
+g++ will not recognize some of the settings, so they cannot be used).
+The compiler must support the OpenMP interface.
+</P>
+<P>The recommended version of the Intel(R) compiler is 14.0.1.106.
+Versions 15.0.1.133 and later are also supported. If using Intel(R)
+MPI, versions 15.0.2.044 and later are recommended.
+</P>
+<P><B>Building LAMMPS with the USER-INTEL package:</B>
+</P>
+<P>You can choose to build with or without support for offload to a
+Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a
+coprocessor, the same binary can be used on nodes with and without
+coprocessors installed. However, if you do not have coprocessors
+on your system, building without offload support will produce a
+smaller binary.
+</P>
+<P>You can do either in one line, using the src/Make.py script, described
+in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type
+"Make.py -h" for help. If run from the src directory, these commands
+will create src/lmp_intel_cpu and lmp_intel_phi using
+src/MAKE/Makefile.mpi as the starting Makefile.machine:
+</P>
+<PRE>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
+Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi
+</PRE>
+<P>Note that this assumes that your MPI and its mpicxx wrapper
+is using the Intel compiler. If it is not, you should
+leave off the "-cc icc" switch.
+</P>
+<P>Or you can follow these steps:
+</P>
+<PRE>cd lammps/src
+make yes-user-intel
+make yes-user-omp (if desired)
+make machine
+</PRE>
+<P>Note that if the USER-OMP package is also installed, you can use
+styles from both packages, as described below.
+</P>
+<P>The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
+both the CCFLAGS and LINKFLAGS variables. You also need to add
+-DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
+</P>
+<P>If you are compiling on the same architecture that will be used for
+the runs, adding the flag <I>-xHost</I> to CCFLAGS will enable
+vectorization with the Intel(R) compiler. Otherwise, you must
+provide the correct compute node architecture to the -x option
+(e.g. -xAVX).
+</P>
+<P>In order to build with support for an Intel(R) Xeon Phi(TM)
+coprocessor, the flag <I>-offload</I> should be added to the LINKFLAGS line
+and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
+</P>
+<P>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
+included in the src/MAKE/OPTIONS directory with settings that perform
+well with the Intel(R) compiler. The latter file has support for
+offload to coprocessors; the former does not.
+</P>
+<P><B>Notes on CPU and core affinity:</B>
+</P>
+<P>Setting core affinity is often used to pin MPI tasks and OpenMP
+threads to a core or group of cores so that memory access can be
+uniform. Unless disabled at build time, affinity for MPI tasks and
+OpenMP threads on the host will be set by default on the host
+when using offload to a coprocessor. In this case, it is unnecessary
+to use other methods to control affinity (e.g. taskset, numactl,
+I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script
+with the <I>no_affinity</I> option to the <A HREF = "package.html">package intel</A>
+command or by disabling the option at build time (by adding
+-DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
+Disabling this option is not recommended, especially when running
+on a machine with hyperthreading disabled.
+</P>
+<P><B>Running with the USER-INTEL package from the command line:</B>
+</P>
+<P>The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node. E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
+</P>
+<P>If you plan to compute (any portion of) pairwise interactions using
+USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU,
+you need to choose how many OpenMP threads per MPI task to use. Note
+that the product of MPI tasks * OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer.
+</P>
+<P>If LAMMPS was built with coprocessor support for the USER-INTEL
+package, you also need to specify the number of coprocessor/node and
+the number of coprocessor threads per MPI task to use. Note that
+coprocessor threads (which run on the coprocessor) are totally
+independent from OpenMP threads (which run on the CPU). The default
+values for the settings that affect coprocessor threads are typically
+fine, as discussed below.
+</P>
+<P>Use the "-sf intel" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "intel" to styles that support it. If
+a style does not support it, an "omp" suffix is tried next. OpenMP
+threads per MPI task can be set via the "-pk intel Nphi omp Nt" or
+"-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switches</A>, which
+set Nt = # of OpenMP threads per MPI task to use. The "-pk omp" form
+is only allowed if LAMMPS was also built with the USER-OMP package.
+</P>
+<P>Use the "-pk intel Nphi" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to set Nphi = # of Xeon Phi(TM)
+coprocessors/node, if LAMMPS was built with coprocessor support. All
+the available coprocessor threads on each Phi will be divided among
+MPI tasks, unless the <I>tptask</I> option of the "-pk intel" <A HREF = "Section_start.html#start_7">command-line
+switch</A> is used to limit the coprocessor
+threads per MPI task. See the <A HREF = "package.html">package intel</A> command
+for details.
+</P>
+<PRE>CPU-only without USER-OMP (but using Intel vectorization on CPU):
+lmp_machine -sf intel -in in.script # 1 MPI task
+mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
+</PRE>
+<PRE>CPU-only with USER-OMP (and Intel vectorization on CPU):
+lmp_machine -sf intel -pk intel 16 0 -in in.script # 1 MPI task on a 16-core node
+mpirun -np 4 lmp_machine -sf intel -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
+mpirun -np 32 lmp_machine -sf intel -pk omp 4 -in in.script # ditto on 8 16-core nodes
+</PRE>
+<PRE>CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
+lmp_machine -sf intel -pk intel 1 omp 16 -in in.script # 1 MPI task, 16 OpenMP threads on CPU, 1 coprocessor, all 240 coprocessor threads
+lmp_machine -sf intel -pk intel 1 omp 16 tptask 32 -in in.script # 1 MPI task, 16 OpenMP threads on CPU, 1 coprocessor, only 32 coprocessor threads
+mpirun -np 4 lmp_machine -sf intel -pk intel 1 omp 4 -in in.script # 4 MPI tasks, 4 OpenMP threads/task, 1 coprocessor, 60 coprocessor threads/task
+mpirun -np 32 -ppn 4 lmp_machine -sf intel -pk intel 1 omp 4 -in in.script # ditto on 8 16-core nodes
+mpirun -np 8 lmp_machine -sf intel -pk intel 4 omp 2 -in in.script # 8 MPI tasks, 2 OpenMP threads/task, 4 coprocessors, 120 coprocessor threads/task
+</PRE>
+<P>Note that if the "-sf intel" switch is used, it also invokes two
+default commands: <A HREF = "package.html">package intel 1</A>, followed by <A HREF = "package.html">package
+omp 0</A>. These both set the number of OpenMP threads per
+MPI task via the OMP_NUM_THREADS environment variable. The first
+command sets the number of Xeon Phi(TM) coprocessors/node to 1 (and
+the precision mode to "mixed", as one of its option defaults). The
+latter command is not invoked if LAMMPS was not built with the
+USER-OMP package. The Nphi = 1 value for the first command is ignored
+if LAMMPS was not built with coprocessor support.
+</P>
+<P>Using the "-pk intel" or "-pk omp" switches explicitly allows for
+direct setting of the number of OpenMP threads per MPI task, and
+additional options for either of the USER-INTEL or USER-OMP packages.
+In particular, the "-pk intel" switch sets the number of
+coprocessors/node and can limit the number of coprocessor threads per
+MPI task. The syntax for these two switches is the same as the
+<A HREF = "package.html">package omp</A> and <A HREF = "package.html">package intel</A> commands.
+See the <A HREF = "package.html">package</A> command doc page for details, including
+the default values used for all its options if these switches are not
+specified, and how to set the number of OpenMP threads via the
+OMP_NUM_THREADS environment variable if desired.
+</P>
+<P><B>Or run with the USER-INTEL package by editing an input script:</B>
+</P>
+<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+OpenMP threads per MPI task, and coprocessor threads per MPI task is
+the same.
+</P>
+<P>Use the <A HREF = "suffix.html">suffix intel</A> command, or you can explicitly add an
+"intel" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/intel 2.5
+</PRE>
+<P>You must also use the <A HREF = "package.html">package intel</A> command, unless the
+"-sf intel" or "-pk intel" <A HREF = "Section_start.html#start_7">command-line
+switches</A> were used. It specifies how many
+coprocessors/node to use, as well as other OpenMP threading and
+coprocessor options. Its doc page explains how to set the number of
+OpenMP threads via an environment variable if desired.
+</P>
+<P>If LAMMPS was also built with the USER-OMP package, you must also use
+the <A HREF = "package.html">package omp</A> command to enable that package, unless
+the "-sf intel" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
+switches</A> were used. It specifies how many
+OpenMP threads per MPI task to use, as well as other options. Its doc
+page explains how to set the number of OpenMP threads via an
+environment variable if desired.
+</P>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>If LAMMPS was not built with coprocessor support when including the
+USER-INTEL package, then acclerated styles will run on the CPU using
+vectorization optimizations and the specified precision. This may
+give a substantial speed-up for a pair style, particularly if mixed or
+single precision is used.
+</P>
+<P>If LAMMPS was built with coproccesor support, the pair styles will run
+on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The
+performance of a Xeon Phi versus a multi-core CPU is a function of
+your hardware, which pair style is used, the number of
+atoms/coprocessor, and the precision used on the coprocessor (double,
+single, mixed).
+</P>
+<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
+LAMMPS web site for performance of the USER-INTEL package on different
+hardware.
+</P>
+<P><B>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
+coprocessor:</B>
+</P>
+<UL><LI>The default for the <A HREF = "package.html">package intel</A> command is to have
+all the MPI tasks on a given compute node use a single Xeon Phi(TM)
+coprocessor. In general, running with a large number of MPI tasks on
+each node will perform best with offload. Each MPI task will
+automatically get affinity to a subset of the hardware threads
+available on the coprocessor. For example, if your card has 61 cores,
+with 60 cores available for offload and 4 hardware threads per core
+(240 total threads), running with 24 MPI tasks per node will cause
+each MPI task to use a subset of 10 threads on the coprocessor. Fine
+tuning of the number of threads to use per MPI task or the number of
+threads to use per core can be accomplished with keyword settings of
+the <A HREF = "package.html">package intel</A> command.
+
+<LI>If desired, only a fraction of the pair style computation can be
+offloaded to the coprocessors. This is accomplished by using the
+<I>balance</I> keyword in the <A HREF = "package.html">package intel</A> command. A
+balance of 0 runs all calculations on the CPU. A balance of 1 runs
+all calculations on the coprocessor. A balance of 0.5 runs half of
+the calculations on the coprocessor. Setting the balance to -1 (the
+default) will enable dynamic load balancing that continously adjusts
+the fraction of offloaded work throughout the simulation. This option
+typically produces results within 5 to 10 percent of the optimal fixed
+balance.
+
+<LI>When using offload with CPU hyperthreading disabled, it may help
+performance to use fewer MPI tasks and OpenMP threads than available
+cores. This is due to the fact that additional threads are generated
+internally to handle the asynchronous offload tasks.
+
+<LI>If running short benchmark runs with dynamic load balancing, adding a
+short warm-up run (10-20 steps) will allow the load-balancer to find a
+near-optimal setting that will carry over to additional runs.
+
+<LI>If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
+coprocessor, a diagnostic line is printed to the screen (not to the
+log file), during the setup phase of a run, indicating that offload
+mode is being used and indicating the number of coprocessor threads
+per MPI task. Additionally, an offload timing summary is printed at
+the end of each run. When offloading, the frequency for <A HREF = "atom_modify.html">atom
+sorting</A> is changed to 1 so that the per-atom data is
+effectively sorted at every rebuild of the neighbor lists.
+
+<LI>For simulations with long-range electrostatics or bond, angle,
+dihedral, improper calculations, computation and data transfer to the
+coprocessor will run concurrently with computations and MPI
+communications for these calculations on the host CPU. The USER-INTEL
+package has two modes for deciding which atoms will be handled by the
+coprocessor. This choice is controlled with the <I>ghost</I> keyword of
+the <A HREF = "package.html">package intel</A> command. When set to 0, ghost atoms
+(atoms at the borders between MPI tasks) are not offloaded to the
+card. This allows for overlap of MPI communication of forces with
+computation on the coprocessor when the <A HREF = "newton.html">newton</A> setting
+is "on". The default is dependent on the style being used, however,
+better performance may be achieved by setting this option
+explictly.
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>When offloading to a coprocessor, <A HREF = "pair_hybrid.html">hybrid</A> styles
+that require skip lists for neighbor builds cannot be offloaded.
+Using <A HREF = "pair_hybrid.html">hybrid/overlay</A> is allowed. Only one intel
+accelerated style may be used with hybrid styles.
+<A HREF = "special_bonds.html">Special_bonds</A> exclusion lists are not currently
+supported with offload, however, the same effect can often be
+accomplished by setting cutoffs for excluded atom types to 0. None of
+the pair styles in the USER-INTEL package currently support the
+"inner", "middle", "outer" options for rRESPA integration via the
+<A HREF = "run_style.html">run_style respa</A> command; only the "pair" option is
+supported.
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_kokkos.html b/doc/doc2/accelerate_kokkos.html
new file mode 100644
index 000000000..885a84b27
--- /dev/null
+++ b/doc/doc2/accelerate_kokkos.html
@@ -0,0 +1,509 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.4 KOKKOS package
+</H4>
+<P>The KOKKOS package was developed primaritly by Christian Trott
+(Sandia) with contributions of various styles by others, including
+Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
+The underlying Kokkos library was written
+primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
+Sandia).
+</P>
+<P>The KOKKOS package contains versions of pair, fix, and atom styles
+that use data structures and macros provided by the Kokkos library,
+which is included with LAMMPS in lib/kokkos.
+</P>
+<P>The Kokkos library is part of
+<A HREF = "http://trilinos.sandia.gov/packages/kokkos">Trilinos</A> and can also
+be downloaded from <A HREF = "https://github.com/kokkos/kokkos">Github</A>. Kokkos is a
+templated C++ library that provides two key abstractions for an
+application like LAMMPS. First, it allows a single implementation of
+an application kernel (e.g. a pair style) to run efficiently on
+different kinds of hardware, such as a GPU, Intel Phi, or many-core
+chip.
+</P>
+<P>The Kokkos library also provides data abstractions to adjust (at
+compile time) the memory layout of basic data structures like 2d and
+3d arrays and allow the transparent utilization of special hardware
+load and store operations. Such data structures are used in LAMMPS to
+store atom coordinates or forces or neighbor lists. The layout is
+chosen to optimize performance on different platforms. Again this
+functionality is hidden from the developer, and does not affect how
+the kernel is coded.
+</P>
+<P>These abstractions are set at build time, when LAMMPS is compiled with
+the KOKKOS package installed. This is done by selecting a "host" and
+"device" to build for, compatible with the compute nodes in your
+machine (one on a desktop machine or 1000s on a supercomputer).
+</P>
+<P>All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos.
+</P>
+<P>Kokkos provides support for two different modes of execution per MPI
+task. This means that computational tasks (pairwise interactions,
+neighbor list builds, time integration, etc) can be parallelized for
+one or the other of the two modes. The first mode is called the
+"host" and is one or more threads running on one or more physical CPUs
+(within the node). Currently, both multi-core CPUs and an Intel Phi
+processor (running in native mode, not offload mode like the
+USER-INTEL package) are supported. The second mode is called the
+"device" and is an accelerator chip of some kind. Currently only an
+NVIDIA GPU is supported via Cuda. If your compute node does not have
+a GPU, then there is only one mode of execution, i.e. the host and
+device are the same.
+</P>
+<P>When using the KOKKOS package, you must choose at build time whether
+you are building for OpenMP, GPU, or for using the Xeon Phi in native
+mode.
+</P>
+<P>Here is a quick overview of how to use the KOKKOS package:
+</P>
+<UL><LI>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
+<LI>include the KOKKOS package and build LAMMPS
+<LI>enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script
+</UL>
+<P>The latter two steps can be done using the "-k on", "-pk kokkos" and
+"-sf kk" <A HREF = "Section_start.html#start_7">command-line switches</A>
+respectively. Or the effect of the "-pk" or "-sf" switches can be
+duplicated by adding the <A HREF = "package.html">package kokkos</A> or <A HREF = "suffix.html">suffix
+kk</A> commands respectively to your input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>The KOKKOS package can be used to build and run LAMMPS on the
+following kinds of hardware:
+</P>
+<UL><LI>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
+<LI>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
+<LI>Phi: on one or more Intel Phi coprocessors (per node)
+<LI>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
+</UL>
+<P>Kokkos support within LAMMPS must be built with a C++11 compatible
+compiler. For example, gcc 4.7.2 or later.
+</P>
+<P>Note that Intel Xeon Phi coprocessors are supported in "native" mode,
+not "offload" mode like the USER-INTEL package supports.
+</P>
+<P>Only NVIDIA GPUs are currently supported.
+</P>
+<P>IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
+you must have Kepler generation GPUs (or later). The Kokkos library
+exploits texture cache options not supported by Telsa generation GPUs
+(or older).
+</P>
+<P>To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
+installed on your system. See the discussion above for the USER-CUDA
+and GPU packages for details of how to check and do this.
+</P>
+<P><B>Building LAMMPS with the KOKKOS package:</B>
+</P>
+<P>You must choose at build time whether to build for OpenMP, Cuda, or
+Phi.
+</P>
+<P>You can do any of these in one line, using the src/Make.py script,
+described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
+Type "Make.py -h" for help. If run from the src directory, these
+commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
+lmp_kokkos_phi. Note that the OMP and PHI options use
+src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
+option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
+</P>
+<PRE>Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
+</PRE>
+<P>Or you can follow these steps:
+</P>
+<P>CPU-only (run all-MPI or with OpenMP threading):
+</P>
+<PRE>cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP
+</PRE>
+<P>Intel Xeon Phi:
+</P>
+<PRE>cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
+</PRE>
+<P>CPUs and GPUs:
+</P>
+<PRE>cd lammps/src
+make yes-kokkos
+make cuda KOKKOS_DEVICES=Cuda
+</PRE>
+<P>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
+make command line which requires a GNU-compatible make command. Try
+"gmake" if your system's standard make complains.
+</P>
+<P>IMPORTANT NOTE: If you build using make line variables and re-build
+LAMMPS twice with different KOKKOS options and the *same* target,
+e.g. g++ in the first two examples above, then you *must* perform a
+"make clean-all" or "make clean-machine" before each build. This is
+to force all the KOKKOS-dependent files to be re-compiled with the new
+options.
+</P>
+<P>You can also hardwire these make variables in the specified machine
+makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
+with a line like:
+</P>
+<PRE>KOKKOS_ARCH = KNC
+</PRE>
+<P>Note that if you build LAMMPS multiple times in this manner, using
+different KOKKOS options (defined in different machine makefiles), you
+do not have to worry about doing a "clean" in between. This is
+because the targets will be different.
+</P>
+<P>IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
+machine makefile, in this case src/MAKE/Makefile.cuda, which is
+included in the LAMMPS distribution. To build the KOKKOS package for
+a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
+have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
+hardware and installed software. Typical values for KOKKOS_ARCH are given
+below, as well
+as other settings that must be included in the machine makefile, if
+you create your own.
+</P>
+<P>IMPORTANT NOTE: Currently, there are no precision options with the
+KOKKOS package. All compilation and computation is performed in
+double precision.
+</P>
+<P>There are other allowed options when building with the KOKKOS package.
+As above, they can be set either as variables on the make command line
+or in Makefile.machine. This is the full list of options, including
+those discussed above, Each takes a value shown below. The
+default value is listed, which is set in the
+lib/kokkos/Makefile.kokkos file.
+</P>
+<P>#Default settings specific options
+#Options: force_uvm,use_ldg,rdc
+</P>
+<UL><LI>KOKKOS_DEVICES, values = <I>OpenMP</I>, <I>Serial</I>, <I>Pthreads</I>, <I>Cuda</I>, default = <I>OpenMP</I>
+<LI>KOKKOS_ARCH, values = <I>KNC</I>, <I>SNB</I>, <I>HSW</I>, <I>Kepler</I>, <I>Kepler30</I>, <I>Kepler32</I>, <I>Kepler35</I>, <I>Kepler37</I>, <I>Maxwell</I>, <I>Maxwell50</I>, <I>Maxwell52</I>, <I>Maxwell53</I>, <I>ARMv8</I>, <I>BGQ</I>, <I>Power7</I>, <I>Power8</I>, default = <I>none</I>
+<LI>KOKKOS_DEBUG, values = <I>yes</I>, <I>no</I>, default = <I>no</I>
+<LI>KOKKOS_USE_TPLS, values = <I>hwloc</I>, <I>librt</I>, default = <I>none</I>
+<LI>KOKKOS_CUDA_OPTIONS, values = <I>force_uvm</I>, <I>use_ldg</I>, <I>rdc</I>
+</UL>
+<P>KOKKOS_DEVICE sets the parallelization method used for Kokkos code
+(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be
+used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
+KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
+</P>
+<P>If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
+directory must use "nvcc" as its compiler, via its CC setting. For
+best performance its CCFLAGS setting should use -O3 and have a
+KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
+hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
+the minimal required compute capability is 2.0, but this will give
+signicantly reduced performance compared to Kepler generation GPUs
+with compute capability 3.x. For the LINK setting, "nvcc" should not
+be used; instead use g++ or another compiler suitable for linking C++
+applications. Often you will want to use your MPI compiler wrapper
+for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
+also have a "Compilation rule" for creating *.o files from *.cu files.
+See src/Makefile.cuda for an example of a lo-level Makefile with all
+of these settings.
+</P>
+<P>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
+migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
+used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
+necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
+provides alternative methods via environment variables for binding
+threads to hardware cores. More info on binding threads to cores is
+given in <A HREF = "Section_accelerate.html#acc_8">this section</A>.
+</P>
+<P>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
+Intel Phi processor.
+</P>
+<P>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
+on most Unix platforms. This library is not available on all
+platforms.
+</P>
+<P>KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
+within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.
+</P>
+<P>KOKKOS_CUDA_OPTIONS are additional options for CUDA.
+</P>
+<P>For more information on Kokkos see the Kokkos programmers' guide here:
+/lib/kokkos/doc/Kokkos_PG.pdf.
+</P>
+<P><B>Run with the KOKKOS package from the command line:</B>
+</P>
+<P>The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node. E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
+</P>
+<P>When using KOKKOS built with host=OMP, you need to choose how many
+OpenMP threads per MPI task will be used (via the "-k" command-line
+switch discussed below). Note that the product of MPI tasks * OpenMP
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+</P>
+<P>When using the KOKKOS package built with device=CUDA, you must use
+exactly one MPI task per physical GPU.
+</P>
+<P>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
+coprocessor support you need to insure there are one or more MPI tasks
+per coprocessor, and choose the number of coprocessor threads to use
+per MPI task (via the "-k" command-line switch discussed below). The
+product of MPI tasks * coprocessor threads/task should not exceed the
+maximum number of threads the coproprocessor is designed to run,
+otherwise performance will suffer. This value is 240 for current
+generation Xeon Phi(TM) chips, which is 60 physical cores * 4
+threads/core. Note that with the KOKKOS package you do not need to
+specify how many Phi coprocessors there are per node; each
+coprocessors is simply treated as running some number of MPI tasks.
+</P>
+<P>You must use the "-k on" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to enable the KOKKOS package. It
+takes additional arguments for hardware settings appropriate to your
+system. Those arguments are <A HREF = "Section_start.html#start_7">documented
+here</A>. The two most commonly used
+options are:
+</P>
+<PRE>-k on t Nt g Ng
+</PRE>
+<P>The "t Nt" option applies to host=OMP (even if device=CUDA) and
+host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
+task to use with a node. For host=MIC, it specifies how many Xeon Phi
+threads per MPI task to use within a node. The default is Nt = 1.
+Note that for host=OMP this is effectively MPI-only mode which may be
+fine. But for host=MIC you will typically end up using far less than
+all the 240 available threads, which could give very poor performance.
+</P>
+<P>The "g Ng" option applies to device=CUDA. It specifies how many GPUs
+per compute node to use. The default is 1, so this only needs to be
+specified is you have 2 or more GPUs per compute node.
+</P>
+<P>The "-k on" switch also issues a "package kokkos" command (with no
+additional arguments) which sets various KOKKOS options to default
+values, as discussed on the <A HREF = "package.html">package</A> command doc page.
+</P>
+<P>Use the "-sf kk" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "kk" to styles that support it. Use
+the "-pk kokkos" <A HREF = "Section_start.html#start_7">command-line switch</A> if
+you wish to change any of the default <A HREF = "package.html">package kokkos</A>
+optionns set by the "-k on" <A HREF = "Section_start.html#start_7">command-line
+switch</A>.
+</P>
+<PRE>host=OMP, dual hex-core nodes (12 threads/node):
+mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
+mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
+mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
+mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
+mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
+</PRE>
+<P>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
+</P>
+<PRE>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
+mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
+</PRE>
+<PRE>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
+mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
+</PRE>
+<P>Note that the default for the <A HREF = "package.html">package kokkos</A> command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. This typically gives fastest
+performance. If the <A HREF = "newton.html">newton</A> command is used in the input
+script, it can override the Newton flag defaults.
+</P>
+<P>However, when running in MPI-only mode with 1 thread per MPI task, it
+will typically be faster to use "half" neighbor lists and set the
+Newton flag to "on", just as is the case for non-accelerated pair
+styles. You can do this with the "-pk" <A HREF = "Section_start.html#start_7">command-line
+switch</A>.
+</P>
+<P><B>Or run with the KOKKOS package by editing an input script:</B>
+</P>
+<P>The discussion above for the mpirun/mpiexec command and setting
+appropriate thread and GPU values for host=OMP or host=MIC or
+device=CUDA are the same.
+</P>
+<P>You must still use the "-k on" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to enable the KOKKOS package, and
+specify its additional arguments for hardware options appopriate to
+your system, as documented above.
+</P>
+<P>Use the <A HREF = "suffix.html">suffix kk</A> command, or you can explicitly add a
+"kk" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/kk 2.5
+</PRE>
+<P>You only need to use the <A HREF = "package.html">package kokkos</A> command if you
+wish to change any of its option defaults, as set by the "-k on"
+<A HREF = "Section_start.html#start_7">command-line switch</A>.
+</P>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>The performance of KOKKOS running in different modes is a function of
+your hardware, which KOKKOS-enable styles are used, and the problem
+size.
+</P>
+<P>Generally speaking, the following rules of thumb apply:
+</P>
+<UL><LI>When running on CPUs only, with a single thread per MPI task,
+performance of a KOKKOS style is somewhere between the standard
+(un-accelerated) styles (MPI-only mode), and those provided by the
+USER-OMP package. However the difference between all 3 is small (less
+than 20%).
+
+<LI>When running on CPUs only, with multiple threads per MPI task,
+performance of a KOKKOS style is a bit slower than the USER-OMP
+package.
+
+<LI>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
+and GPU packages.
+
+<LI>When running on Intel Xeon Phi, KOKKOS is not as fast as
+the USER-INTEL package, which is optimized for that hardware.
+</UL>
+<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
+LAMMPS web site for performance of the KOKKOS package on different
+hardware.
+</P>
+<P><B>Guidelines for best performance:</B>
+</P>
+<P>Here are guidline for using the KOKKOS package on the different
+hardware configurations listed above.
+</P>
+<P>Many of the guidelines use the <A HREF = "package.html">package kokkos</A> command
+See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations.
+</P>
+<P><B>Running on a multi-core CPU:</B>
+</P>
+<P>If N is the number of physical cores/node, then the number of MPI
+tasks/node * number of threads/task should not exceed N, and should
+typically equal N. Note that the default threads/task is 1, as set by
+the "t" keyword of the "-k" <A HREF = "Section_start.html#start_7">command-line
+switch</A>. If you do not change this, no
+additional parallelism (beyond MPI) will be invoked on the host
+CPU(s).
+</P>
+<P>You can compare the performance running in different modes:
+</P>
+<UL><LI>run with 1 MPI task/node and N threads/task
+<LI>run with N MPI tasks/node and 1 thread/task
+<LI>run with settings in between these extremes
+</UL>
+<P>Examples of mpirun commands in these modes are shown above.
+</P>
+<P>When using KOKKOS to perform multi-threading, it is important for
+performance to bind both MPI tasks to physical cores, and threads to
+physical cores, so they do not migrate during a simulation.
+</P>
+<P>If you are not certain MPI tasks are being bound (check the defaults
+for your MPI installation), binding can be forced with these flags:
+</P>
+<PRE>OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
+</PRE>
+<P>For binding threads with the KOKKOS OMP option, use thread affinity
+environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
+later, intel 12 or later) setting the environment variable
+OMP_PROC_BIND=true should be sufficient. For binding threads with the
+KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
+discussed in <A HREF = "Sections_start.html#start_3_4">Section 2.3.4</A> of the
+manual.
+</P>
+<P><B>Running on GPUs:</B>
+</P>
+<P>Insure the -arch setting in the machine makefile you are using,
+e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
+(see <A HREF = "Section_start.html#start_3_4">this section</A> of the manual for
+details).
+</P>
+<P>The -np setting of the mpirun command should set the number of MPI
+tasks/node to be equal to the # of physical GPUs on the node.
+</P>
+<P>Use the "-k" <A HREF = "Section_commands.html#start_7">command-line switch</A> to
+specify the number of GPUs per node, and the number of threads per MPI
+task. As above for multi-core CPUs (and no GPU), if N is the number
+of physical cores/node, then the number of MPI tasks/node * number of
+threads/task should not exceed N. With one GPU (and one MPI task) it
+may be faster to use less than all the available cores, by setting
+threads/task to a smaller value. This is because using all the cores
+on a dual-socket node will incur extra cost to copy memory from the
+2nd socket to the GPU.
+</P>
+<P>Examples of mpirun commands that follow these rules are shown above.
+</P>
+<P>IMPORTANT NOTE: When using a GPU, you will achieve the best
+performance if your input script does not use any fix or compute
+styles which are not yet Kokkos-enabled. This allows data to stay on
+the GPU for multiple timesteps, without being copied back to the host
+CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
+<A HREF = "thermo_style.html">thermo</A> or <A HREF = "dump.html">dump</A> output will cause data
+to be copied back to the CPU.
+</P>
+<P>You cannot yet assign multiple MPI tasks to the same GPU with the
+KOKKOS package. We plan to support this in the future, similar to the
+GPU package in LAMMPS.
+</P>
+<P>You cannot yet use both the host (multi-threaded) and device (GPU)
+together to compute pairwise interactions with the KOKKOS package. We
+hope to support this in the future, similar to the GPU package in
+LAMMPS.
+</P>
+<P><B>Running on an Intel Phi:</B>
+</P>
+<P>Kokkos only uses Intel Phi processors in their "native" mode, i.e.
+not hosted by a CPU.
+</P>
+<P>As illustrated above, build LAMMPS with OMP=yes (the default) and
+MIC=yes. The latter insures code is correctly compiled for the Intel
+Phi. The OMP setting means OpenMP will be used for parallelization on
+the Phi, which is currently the best option within Kokkos. In the
+future, other options may be added.
+</P>
+<P>Current-generation Intel Phi chips have either 61 or 57 cores. One
+core should be excluded for running the OS, leaving 60 or 56 cores.
+Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
+N = 224 (4*56) cores to run on.
+</P>
+<P>The -np setting of the mpirun command sets the number of MPI
+tasks/node. The "-k on t Nt" command-line switch sets the number of
+threads/task as Nt. The product of these 2 values should be N, i.e.
+240 or 224. Also, the number of threads/task should be a multiple of
+4 so that logical threads from more than one MPI task do not run on
+the same physical core.
+</P>
+<P>Examples of mpirun commands that follow these rules are shown above.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>As noted above, if using GPUs, the number of MPI tasks per compute
+node should equal to the number of GPUs per compute node. In the
+future Kokkos will support assigning multiple MPI tasks to a single
+GPU.
+</P>
+<P>Currently Kokkos does not support AMD GPUs due to limits in the
+available backend programming models. Specifically, Kokkos requires
+extensive C++ support from the Kernel language. This is expected to
+change in the future.
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_omp.html b/doc/doc2/accelerate_omp.html
new file mode 100644
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+++ b/doc/doc2/accelerate_omp.html
@@ -0,0 +1,206 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.5 USER-OMP package
+</H4>
+<P>The USER-OMP package was developed by Axel Kohlmeyer at Temple
+University. It provides multi-threaded versions of most pair styles,
+nearly all bonded styles (bond, angle, dihedral, improper), several
+Kspace styles, and a few fix styles. The package currently
+uses the OpenMP interface for multi-threading.
+</P>
+<P>Here is a quick overview of how to use the USER-OMP package:
+</P>
+<UL><LI>use the -fopenmp flag for compiling and linking in your Makefile.machine
+<LI>include the USER-OMP package and build LAMMPS
+<LI>use the mpirun command to set the number of MPI tasks/node
+<LI>specify how many threads per MPI task to use
+<LI>use USER-OMP styles in your input script
+</UL>
+<P>The latter two steps can be done using the "-pk omp" and "-sf omp"
+<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
+the effect of the "-pk" or "-sf" switches can be duplicated by adding
+the <A HREF = "package.html">package omp</A> or <A HREF = "suffix.html">suffix omp</A> commands
+respectively to your input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>Your compiler must support the OpenMP interface. You should have one
+or more multi-core CPUs so that multiple threads can be launched by an
+MPI task running on a CPU.
+</P>
+<P><B>Building LAMMPS with the USER-OMP package:</B>
+</P>
+<P>To do this in one line, use the src/Make.py script, described in
+<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
+-h" for help. If run from the src directory, this command will create
+src/lmp_omp using src/MAKE/Makefile.mpi as the starting
+Makefile.machine:
+</P>
+<PRE>Make.py -p omp -o omp file mpi
+</PRE>
+<P>Or you can follow these steps:
+</P>
+<PRE>cd lammps/src
+make yes-user-omp
+make machine
+</PRE>
+<P>The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
+support. This works for both the GNU and Intel compilers. Without
+this flag the USER-OMP styles will still be compiled and work, but
+will not support multi-threading. For the Intel compilers the CCFLAGS
+setting also needs to include "-restrict".
+</P>
+<P><B>Run with the USER-OMP package from the command line:</B>
+</P>
+<P>The mpirun or mpiexec command sets the total number of MPI tasks used
+by LAMMPS (one or multiple per compute node) and the number of MPI
+tasks used per node. E.g. the mpirun command in MPICH does this via
+its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
+</P>
+<P>You need to choose how many threads per MPI task will be used by the
+USER-OMP package. Note that the product of MPI tasks * threads/task
+should not exceed the physical number of cores (on a node), otherwise
+performance will suffer.
+</P>
+<P>Use the "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "omp" to styles that support it. Use
+the "-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switch</A>, to
+set Nt = # of OpenMP threads per MPI task to use.
+</P>
+<PRE>lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
+mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
+mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes
+</PRE>
+<P>Note that if the "-sf omp" switch is used, it also issues a default
+<A HREF = "package.html">package omp 0</A> command, which sets the number of threads
+per MPI task via the OMP_NUM_THREADS environment variable.
+</P>
+<P>Using the "-pk" switch explicitly allows for direct setting of the
+number of threads and additional options. Its syntax is the same as
+the "package omp" command. See the <A HREF = "package.html">package</A> command doc
+page for details, including the default values used for all its
+options if it is not specified, and how to set the number of threads
+via the OMP_NUM_THREADS environment variable if desired.
+</P>
+<P><B>Or run with the USER-OMP package by editing an input script:</B>
+</P>
+<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+and threads/MPI task is the same.
+</P>
+<P>Use the <A HREF = "suffix.html">suffix omp</A> command, or you can explicitly add an
+"omp" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/omp 2.5
+</PRE>
+<P>You must also use the <A HREF = "package.html">package omp</A> command to enable the
+USER-OMP package, unless the "-sf omp" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
+switches</A> were used. It specifies how many
+threads per MPI task to use, as well as other options. Its doc page
+explains how to set the number of threads via an environment variable
+if desired.
+</P>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>Depending on which styles are accelerated, you should look for a
+reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
+time" values printed at the end of a run.
+</P>
+<P>You may see a small performance advantage (5 to 20%) when running a
+USER-OMP style (in serial or parallel) with a single thread per MPI
+task, versus running standard LAMMPS with its standard
+(un-accelerated) styles (in serial or all-MPI parallelization with 1
+task/core). This is because many of the USER-OMP styles contain
+similar optimizations to those used in the OPT package, as described
+above.
+</P>
+<P>With multiple threads/task, the optimal choice of MPI tasks/node and
+OpenMP threads/task can vary a lot and should always be tested via
+benchmark runs for a specific simulation running on a specific
+machine, paying attention to guidelines discussed in the next
+sub-section.
+</P>
+<P>A description of the multi-threading strategy used in the USER-OMP
+package and some performance examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented
+here</A>
+</P>
+<P><B>Guidelines for best performance:</B>
+</P>
+<P>For many problems on current generation CPUs, running the USER-OMP
+package with a single thread/task is faster than running with multiple
+threads/task. This is because the MPI parallelization in LAMMPS is
+often more efficient than multi-threading as implemented in the
+USER-OMP package. The parallel efficiency (in a threaded sense) also
+varies for different USER-OMP styles.
+</P>
+<P>Using multiple threads/task can be more effective under the following
+circumstances:
+</P>
+<UL><LI>Individual compute nodes have a significant number of CPU cores but
+the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
+(Clovertown) and 54xx (Harpertown) quad core processors. Running one
+MPI task per CPU core will result in significant performance
+degradation, so that running with 4 or even only 2 MPI tasks per node
+is faster. Running in hybrid MPI+OpenMP mode will reduce the
+inter-node communication bandwidth contention in the same way, but
+offers an additional speedup by utilizing the otherwise idle CPU
+cores.
+
+<LI>The interconnect used for MPI communication does not provide
+sufficient bandwidth for a large number of MPI tasks per node. For
+example, this applies to running over gigabit ethernet or on Cray XT4
+or XT5 series supercomputers. As in the aforementioned case, this
+effect worsens when using an increasing number of nodes.
+
+<LI>The system has a spatially inhomogeneous particle density which does
+not map well to the <A HREF = "processors.html">domain decomposition scheme</A> or
+<A HREF = "balance.html">load-balancing</A> options that LAMMPS provides. This is
+because multi-threading achives parallelism over the number of
+particles, not via their distribution in space.
+
+<LI>A machine is being used in "capability mode", i.e. near the point
+where MPI parallelism is maxed out. For example, this can happen when
+using the <A HREF = "kspace_style.html">PPPM solver</A> for long-range
+electrostatics on large numbers of nodes. The scaling of the KSpace
+calculation (see the <A HREF = "kspace_style.html">kspace_style</A> command) becomes
+the performance-limiting factor. Using multi-threading allows less
+MPI tasks to be invoked and can speed-up the long-range solver, while
+increasing overall performance by parallelizing the pairwise and
+bonded calculations via OpenMP. Likewise additional speedup can be
+sometimes be achived by increasing the length of the Coulombic cutoff
+and thus reducing the work done by the long-range solver. Using the
+<A HREF = "run_style.html">run_style verlet/split</A> command, which is compatible
+with the USER-OMP package, is an alternative way to reduce the number
+of MPI tasks assigned to the KSpace calculation.
+</UL>
+<P>Additional performance tips are as follows:
+</P>
+<UL><LI>The best parallel efficiency from <I>omp</I> styles is typically achieved
+when there is at least one MPI task per physical processor,
+i.e. socket or die.
+
+<LI>It is usually most efficient to restrict threading to a single
+socket, i.e. use one or more MPI task per socket.
+
+<LI>Several current MPI implementation by default use a processor affinity
+setting that restricts each MPI task to a single CPU core. Using
+multi-threading in this mode will force the threads to share that core
+and thus is likely to be counterproductive. Instead, binding MPI
+tasks to a (multi-core) socket, should solve this issue.
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>None.
+</P>
+</HTML>
diff --git a/doc/doc2/accelerate_opt.html b/doc/doc2/accelerate_opt.html
new file mode 100644
index 000000000..a539df591
--- /dev/null
+++ b/doc/doc2/accelerate_opt.html
@@ -0,0 +1,87 @@
+<HTML>
+<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
+</P>
+<H4>5.3.6 OPT package
+</H4>
+<P>The OPT package was developed by James Fischer (High Performance
+Technologies), David Richie, and Vincent Natoli (Stone Ridge
+Technologies). It contains a handful of pair styles whose compute()
+methods were rewritten in C++ templated form to reduce the overhead
+due to if tests and other conditional code.
+</P>
+<P>Here is a quick overview of how to use the OPT package:
+</P>
+<UL><LI>include the OPT package and build LAMMPS
+<LI>use OPT pair styles in your input script
+</UL>
+<P>The last step can be done using the "-sf opt" <A HREF = "Section_start.html#start_7">command-line
+switch</A>. Or the effect of the "-sf" switch
+can be duplicated by adding a <A HREF = "suffix.html">suffix opt</A> command to your
+input script.
+</P>
+<P><B>Required hardware/software:</B>
+</P>
+<P>None.
+</P>
+<P><B>Building LAMMPS with the OPT package:</B>
+</P>
+<P>Include the package and build LAMMPS:
+</P>
+<P>To do this in one line, use the src/Make.py script, described in
+<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
+-h" for help. If run from the src directory, this command will create
+src/lmp_opt using src/MAKE/Makefile.mpi as the starting
+Makefile.machine:
+</P>
+<PRE>Make.py -p opt -o opt file mpi
+</PRE>
+<P>Or you can follow these steps:
+</P>
+<PRE>cd lammps/src
+make yes-opt
+make machine
+</PRE>
+<P>If you are using Intel compilers, then the CCFLAGS setting in
+Makefile.machine needs to include "-restrict".
+</P>
+<P><B>Run with the OPT package from the command line:</B>
+</P>
+<P>Use the "-sf opt" <A HREF = "Section_start.html#start_7">command-line switch</A>,
+which will automatically append "opt" to styles that support it.
+</P>
+<PRE>lmp_machine -sf opt -in in.script
+mpirun -np 4 lmp_machine -sf opt -in in.script
+</PRE>
+<P><B>Or run with the OPT package by editing an input script:</B>
+</P>
+<P>Use the <A HREF = "suffix.html">suffix opt</A> command, or you can explicitly add an
+"opt" suffix to individual styles in your input script, e.g.
+</P>
+<PRE>pair_style lj/cut/opt 2.5
+</PRE>
+<P><B>Speed-ups to expect:</B>
+</P>
+<P>You should see a reduction in the "Pair time" value printed at the end
+of a run. On most machines for reasonable problem sizes, it will be a
+5 to 20% savings.
+</P>
+<P><B>Guidelines for best performance:</B>
+</P>
+<P>None. Just try out an OPT pair style to see how it performs.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>None.
+</P>
+</HTML>
diff --git a/doc/doc2/angle_charmm.html b/doc/doc2/angle_charmm.html
new file mode 100644
index 000000000..bfac8e076
--- /dev/null
+++ b/doc/doc2/angle_charmm.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style charmm command
+</H3>
+<H3>angle_style charmm/kk command
+</H3>
+<H3>angle_style charmm/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style charmm
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style charmm
+angle_coeff 1 300.0 107.0 50.0 3.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>charmm</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_charmm.jpg">
+</CENTER>
+<P>with an additional Urey_Bradley term based on the distance <I>r</I> between
+the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
+coefficients defined for each angle type.
+</P>
+<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
+field.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>theta0 (degrees)
+<LI>K_ub (energy/distance^2)
+<LI>r_ub (distance)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "MacKerell"></A>
+
+<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/angle_class2.html b/doc/doc2/angle_class2.html
new file mode 100644
index 000000000..df2f305a9
--- /dev/null
+++ b/doc/doc2/angle_class2.html
@@ -0,0 +1,126 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style class2 command
+</H3>
+<H3>angle_style class2/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style class2
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style class2
+angle_coeff * 75.0
+angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>class2</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_class2.jpg">
+</CENTER>
+<P>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
+bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
+the equilibrium bond lengths.
+</P>
+<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
+</P>
+<P>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
+each angle type via the <A HREF = "angle_coeff.html">angle_coeff</A> command as in
+the example above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>These are the 4 coefficients for the Ea formula:
+</P>
+<UL><LI>theta0 (degrees)
+<LI>K2 (energy/radian^2)
+<LI>K3 (energy/radian^3)
+<LI>K4 (energy/radian^4)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of the various K are in per-radian.
+</P>
+<P>For the Ebb formula, each line in a <A HREF = "angle_coeff.html">angle_coeff</A>
+command in the input script lists 4 coefficients, the first of which
+is "bb" to indicate they are BondBond coefficients. In a data file,
+these coefficients should be listed under a "BondBond Coeffs" heading
+and you must leave out the "bb", i.e. only list 3 coefficients after
+the angle type.
+</P>
+<UL><LI>bb
+<LI>M (energy/distance^2)
+<LI>r1 (distance)
+<LI>r2 (distance)
+</UL>
+<P>For the Eba formula, each line in a <A HREF = "angle_coeff.html">angle_coeff</A>
+command in the input script lists 5 coefficients, the first of which
+is "ba" to indicate they are BondAngle coefficients. In a data file,
+these coefficients should be listed under a "BondAngle Coeffs" heading
+and you must leave out the "ba", i.e. only list 4 coefficients after
+the angle type.
+</P>
+<UL><LI>ba
+<LI>N1 (energy/distance^2)
+<LI>N2 (energy/distance^2)
+<LI>r1 (distance)
+<LI>r2 (distance)
+</UL>
+<P>The theta0 value in the Eba formula is not specified, since it is the
+same value from the Ea formula.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the CLASS2
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/angle_coeff.html b/doc/doc2/angle_coeff.html
new file mode 100644
index 000000000..1ae29b5f2
--- /dev/null
+++ b/doc/doc2/angle_coeff.html
@@ -0,0 +1,104 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_coeff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_coeff N args
+</PRE>
+<UL><LI>N = angle type (see asterisk form below)
+<LI>args = coefficients for one or more angle types
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_coeff 1 300.0 107.0
+angle_coeff * 5.0
+angle_coeff 2*10 5.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Specify the angle force field coefficients for one or more angle types.
+The number and meaning of the coefficients depends on the angle style.
+Angle coefficients can also be set in the data file read by the
+<A HREF = "read_data.html">read_data</A> command or in a restart file.
+</P>
+<P>N can be specified in one of two ways. An explicit numeric value can
+be used, as in the 1st example above. Or a wild-card asterisk can be
+used to set the coefficients for multiple angle types. This takes the
+form "*" or "*n" or "n*" or "m*n". If N = the number of angle types,
+then an asterisk with no numeric values means all types from 1 to N. A
+leading asterisk means all types from 1 to n (inclusive). A trailing
+asterisk means all types from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive).
+</P>
+<P>Note that using an angle_coeff command can override a previous setting
+for the same angle type. For example, these commands set the coeffs
+for all angle types, then overwrite the coeffs for just angle type 2:
+</P>
+<PRE>angle_coeff * 200.0 107.0 1.2
+angle_coeff 2 50.0 107.0
+</PRE>
+<P>A line in a data file that specifies angle coefficients uses the exact
+same format as the arguments of the angle_coeff command in an input
+script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file. For example,
+under the "Angle Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+</P>
+<PRE>1 300.0 107.0
+</PRE>
+<P>The <A HREF = "angle_class2.html">angle_style class2</A> is an exception to this
+rule, in that an additional argument is used in the input script to
+allow specification of the cross-term coefficients. See its
+doc page for details.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command.
+</P>
+<P>Note that there are also additional angle styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
+<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
+</UL>
+<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
+<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
+<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
+<LI><A HREF = "angle_cosine_delta.html">angle_style cosine/delta</A> - difference of cosines angle potential
+<LI><A HREF = "angle_cosine_periodic.html">angle_style cosine/periodic</A> - DREIDING angle
+<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
+<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
+<LI><A HREF = "angle_table.html">angle_style table</A> - tabulated by angle
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>An angle style must be defined before any angle coefficients are
+set, either in the input script or in a data file.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_style.html">angle_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine.html b/doc/doc2/angle_cosine.html
new file mode 100644
index 000000000..709444b5a
--- /dev/null
+++ b/doc/doc2/angle_cosine.html
@@ -0,0 +1,77 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine command
+</H3>
+<H3>angle_style cosine/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine
+angle_coeff * 75.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine.jpg">
+</CENTER>
+<P>where K is defined for each angle type.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine_delta.html b/doc/doc2/angle_cosine_delta.html
new file mode 100644
index 000000000..e7ce77ead
--- /dev/null
+++ b/doc/doc2/angle_cosine_delta.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine/delta command
+</H3>
+<H3>angle_style cosine/delta/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine/delta
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine/delta
+angle_coeff 2*4 75.0 100.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/delta</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine_delta.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium value of the angle, and K is a
+prefactor. Note that the usual 1/2 factor is included in K.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>theta0 (degrees)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_cosine_squared.html">angle_style
+cosine/squared</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine_periodic.html b/doc/doc2/angle_cosine_periodic.html
new file mode 100644
index 000000000..58878bb6a
--- /dev/null
+++ b/doc/doc2/angle_cosine_periodic.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine/periodic command
+</H3>
+<H3>angle_style cosine/periodic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine/periodic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine/periodic
+angle_coeff * 75.0 1 6
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/periodic</I> angle style uses the following potential, which
+is commonly used in the <A HREF = "Section_howto.html#howto_4">DREIDING</A> force
+field, particularly for organometallic systems where <I>n</I> = 4 might be
+used for an octahedral complex and <I>n</I> = 3 might be used for a
+trigonal center:
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine_periodic.jpg">
+</CENTER>
+<P>where C, B and n are coefficients defined for each angle type.
+</P>
+<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>C (energy)
+<LI>B = 1 or -1
+<LI>n = 1, 2, 3, 4, 5 or 6 for periodicity
+</UL>
+<P>Note that the prefactor C is specified and not the overall force
+constant K = C / n^2. When B = 1, it leads to a minimum for the
+linear geometry. When B = -1, it leads to a maximum for the linear
+geometry.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mayo"></A>
+
+<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine_shift.html b/doc/doc2/angle_cosine_shift.html
new file mode 100644
index 000000000..a7ecc30ae
--- /dev/null
+++ b/doc/doc2/angle_cosine_shift.html
@@ -0,0 +1,81 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine/shift command
+</H3>
+<H3>angle_style cosine/shift/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine/shift
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine/shift
+angle_coeff * 10.0 45.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/shift</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine_shift.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium angle. The potential is bounded
+between -Umin and zero. In the neighborhood of the minimum E=- Umin +
+Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>umin (energy)
+<LI>theta (angle)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>,
+<A HREF = "angle_cosineshiftexp.html">angle_cosineshiftexp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine_shift_exp.html b/doc/doc2/angle_cosine_shift_exp.html
new file mode 100644
index 000000000..14b9e71ed
--- /dev/null
+++ b/doc/doc2/angle_cosine_shift_exp.html
@@ -0,0 +1,94 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine/shift/exp command
+</H3>
+<H3>angle_style cosine/shift/exp/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine/shift/exp
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine/shift/exp
+angle_coeff * 10.0 45.0 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/shift/exp</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine_shift_exp.jpg">
+</CENTER>
+<P>where Umin, theta, and a are defined for each angle type.
+</P>
+<P>The potential is bounded between [-Umin:0] and the minimum is
+located at the angle theta0. The a parameter can be both positive or
+negative and is used to control the spring constant at the
+equilibrium.
+</P>
+<P>The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
+For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
+values of the a parameter, the spring constant is essentially zero,
+and anharmonic terms takes over. The potential is furthermore well
+behaved in the limit a -> 0, where it has been implemented to linear
+order in a for a < 0.001. In this limit the potential reduces to the
+cosineshifted potential.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>umin (energy)
+<LI>theta (angle)
+<LI>A (real number)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>,
+<A HREF = "angle_cosineshift.html">angle_cosineshift</A>,
+<A HREF = "dihedral_cosineshift.html">dihedral_cosineshift</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_cosine_squared.html b/doc/doc2/angle_cosine_squared.html
new file mode 100644
index 000000000..7f85d3552
--- /dev/null
+++ b/doc/doc2/angle_cosine_squared.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style cosine/squared command
+</H3>
+<H3>angle_style cosine/squared/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style cosine/squared
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style cosine/squared
+angle_coeff 2*4 75.0 100.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/squared</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_cosine_squared.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium value of the angle, and K is a
+prefactor. Note that the usual 1/2 factor is included in K.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>theta0 (degrees)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_dipole.html b/doc/doc2/angle_dipole.html
new file mode 100644
index 000000000..b9117b3da
--- /dev/null
+++ b/doc/doc2/angle_dipole.html
@@ -0,0 +1,130 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style dipole command
+</H3>
+<H3>angle_style dipole/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style dipole
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style dipole
+angle_coeff 6 2.1 180.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>dipole</I> angle style is used to control the orientation of a dipolar
+atom within a molecule <A HREF = "#Orsi">(Orsi)</A>. Specifically, the <I>dipole</I> angle
+style restrains the orientation of a point dipole mu_j (embedded in atom
+'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
+is another atom of the same molecule (typically, 'i' and 'j' are also
+covalently bonded).
+</P>
+<P>It is convenient to define an angle gamma between the 'free' vector mu_j
+and the reference (bond) vector r_ij:
+</P>
+<CENTER><IMG SRC = "Eqs/angle_dipole_gamma.jpg">
+</CENTER>
+<P>The <I>dipole</I> angle style uses the potential:
+</P>
+<CENTER><IMG SRC = "Eqs/angle_dipole_potential.jpg">
+</CENTER>
+<P>where K is a rigidity constant and gamma0 is an equilibrium (reference)
+angle.
+</P>
+<P>The torque on the dipole can be obtained by differentiating the
+potential using the 'chain rule' as in appendix C.3 of
+<A HREF = "#Allen">(Allen)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/angle_dipole_torque.jpg">
+</CENTER>
+<P>Example: if gamma0 is set to 0 degrees, the torque generated by
+the potential will tend to align the dipole along the reference
+direction defined by the (bond) vector r_ij (in other words, mu_j is
+restrained to point towards atom 'i').
+</P>
+<P>Note that the angle dipole potential does not give rise to any force,
+because it does not depend on the distance between i and j (it only
+depends on the angle between mu_j and r_ij).
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>gamma0 (degrees)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P>IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID
+'j' corresponding to the dipole to restrain must come before the atom
+ID of the reference atom 'i'. A third atom ID 'k' must also be
+provided, although 'k' is just a 'dummy' atom which can be any atom;
+it may be useful to choose a convention (e.g., 'k'='i') and adhere to
+it. For example, if ID=1 for the dipolar atom to restrain, and ID=2
+for the reference atom, the corresponding line in the "Angles" section
+of the data file would read: X X 1 2 2
+</P>
+<P>The "newton" command for intramolecular interactions must be "on"
+(which is the default).
+</P>
+<P>This angle style should not be used with SHAKE.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_hybrid.html">angle_hybrid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Orsi"></A>
+
+<P><B>(Orsi)</B> Orsi & Essex, The ELBA force field for coarse-grain modeling of
+lipid membranes, PloS ONE 6(12): e28637, 2011.
+</P>
+<A NAME = "Allen"></A>
+
+<P><B>(Allen)</B> Allen & Tildesley, Computer Simulation of Liquids,
+Clarendon Press, Oxford, 1987.
+</P>
+</HTML>
diff --git a/doc/doc2/angle_fourier.html b/doc/doc2/angle_fourier.html
new file mode 100644
index 000000000..93d1b083d
--- /dev/null
+++ b/doc/doc2/angle_fourier.html
@@ -0,0 +1,78 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style fourier command
+</H3>
+<H3>angle_style fourier/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style fourier
+</PRE>
+<P><B>Examples:</B>
+</P>
+<P>angle_style fourier
+angle_coeff 75.0 1.0 1.0 1.0
+</P>
+<P><B>Description:</B>
+</P>
+<P>The <I>fourier</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_fourier.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>C0 (real)
+<LI>C1 (real)
+<LI>C2 (real)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_fourier_simple.html b/doc/doc2/angle_fourier_simple.html
new file mode 100644
index 000000000..732ee095c
--- /dev/null
+++ b/doc/doc2/angle_fourier_simple.html
@@ -0,0 +1,77 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style fourier/simple command
+</H3>
+<H3>angle_style fourier/simple/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style fourier/simple
+</PRE>
+<P><B>Examples:</B>
+</P>
+<P>angle_style fourier/simple
+angle_coeff 100.0 -1.0 1.0
+</P>
+<P><B>Description:</B>
+</P>
+<P>The <I>fourier/simple</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_fourier_simple.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>c (real)
+<LI>n (real)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_harmonic.html b/doc/doc2/angle_harmonic.html
new file mode 100644
index 000000000..f5b02202e
--- /dev/null
+++ b/doc/doc2/angle_harmonic.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style harmonic command
+</H3>
+<H3>angle_style harmonic/kk command
+</H3>
+<H3>angle_style harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style harmonic
+angle_coeff 1 300.0 107.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium value of the angle, and K is a
+prefactor. Note that the usual 1/2 factor is included in K.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>theta0 (degrees)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_hybrid.html b/doc/doc2/angle_hybrid.html
new file mode 100644
index 000000000..d5e3412fb
--- /dev/null
+++ b/doc/doc2/angle_hybrid.html
@@ -0,0 +1,96 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style hybrid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style hybrid style1 style2 ...
+</PRE>
+<UL><LI>style1,style2 = list of one or more angle styles
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style hybrid harmonic cosine
+angle_coeff 1 harmonic 80.0 30.0
+angle_coeff 2* cosine 50.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hybrid</I> style enables the use of multiple angle styles in one
+simulation. An angle style is assigned to each angle type. For
+example, angles in a polymer flow (of angle type 1) could be computed
+with a <I>harmonic</I> potential and angles in the wall boundary (of angle
+type 2) could be computed with a <I>cosine</I> potential. The assignment
+of angle type to style is made via the <A HREF = "angle_coeff.html">angle_coeff</A>
+command or in the data file.
+</P>
+<P>In the angle_coeff commands, the name of an angle style must be added
+after the angle type, with the remaining coefficients being those
+appropriate to that style. In the example above, the 2 angle_coeff
+commands set angles of angle type 1 to be computed with a <I>harmonic</I>
+potential with coefficients 80.0, 30.0 for K, theta0. All other angle
+types (2-N) are computed with a <I>cosine</I> potential with coefficient
+50.0 for K.
+</P>
+<P>If angle coefficients are specified in the data file read via the
+<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
+E.g. "harmonic" or "cosine", must be added after the angle type, for each
+line in the "Angle Coeffs" section, e.g.
+</P>
+<PRE>Angle Coeffs
+</PRE>
+<PRE>1 harmonic 80.0 30.0
+2 cosine 50.0
+...
+</PRE>
+<P>If <I>class2</I> is one of the angle hybrid styles, the same rule holds for
+specifying additional BondBond (and BondAngle) coefficients either via
+the input script or in the data file. I.e. <I>class2</I> must be added to
+each line after the angle type. For lines in the BondBond (or
+BondAngle) section of the data file for angle types that are not
+<I>class2</I>, you must use an angle style of <I>skip</I> as a placeholder, e.g.
+</P>
+<PRE>BondBond Coeffs
+</PRE>
+<PRE>1 skip
+2 class2 3.6512 1.0119 1.0119
+...
+</PRE>
+<P>Note that it is not necessary to use the angle style <I>skip</I> in the
+input script, since BondBond (or BondAngle) coefficients need not be
+specified at all for angle types that are not <I>class2</I>.
+</P>
+<P>An angle style of <I>none</I> with no additional coefficients can be used
+in place of an angle style, either in a input script angle_coeff
+command or in the data file, if you desire to turn off interactions
+for specific angle types.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>Unlike other angle styles, the hybrid angle style does not store angle
+coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
+files</A>. Thus when retarting a simulation from a restart
+file, you need to re-specify angle_coeff commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_none.html b/doc/doc2/angle_none.html
new file mode 100644
index 000000000..a589bcc7c
--- /dev/null
+++ b/doc/doc2/angle_none.html
@@ -0,0 +1,34 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style none command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style none
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Using an angle style of none means angle forces are not computed, even
+if triplets of angle atoms were listed in the data file read by the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_quartic.html b/doc/doc2/angle_quartic.html
new file mode 100644
index 000000000..9618b3d7f
--- /dev/null
+++ b/doc/doc2/angle_quartic.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style quartic command
+</H3>
+<H3>angle_style quartic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style quartic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style quartic
+angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>quartic</I> angle style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/angle_quartic.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium value of the angle, and K is a
+prefactor. Note that the usual 1/2 factor is included in K.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>theta0 (degrees)
+<LI>K2 (energy/radian^2)
+<LI>K3 (energy/radian^3)
+<LI>K4 (energy/radian^4)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_sdk.html b/doc/doc2/angle_sdk.html
new file mode 100644
index 000000000..fa1b5f37d
--- /dev/null
+++ b/doc/doc2/angle_sdk.html
@@ -0,0 +1,64 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style sdk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style sdk
+</PRE>
+<PRE>angle_style sdk/omp
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style sdk
+angle_coeff 1 300.0 107.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>sdk</I> angle style is a combination of the harmonic angle potential,
+</P>
+<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
+</CENTER>
+<P>where theta0 is the equilibrium value of the angle and K a prefactor,
+with the <I>repulsive</I> part of the non-bonded <I>lj/sdk</I> pair style
+between the atoms 1 and 3. This angle potential is intended for
+coarse grained MD simulations with the CMM parametrization using the
+<A HREF = "pair_sdk.html">pair_style lj/sdk</A>. Relative to the pair_style
+<I>lj/sdk</I>, however, the energy is shifted by <I>epsilon</I>, to avoid sudden
+jumps. Note that the usual 1/2 factor is included in K.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>theta0 (degrees)
+</UL>
+<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+The also required <I>lj/sdk</I> parameters will be extracted automatically
+from the pair_style.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER-CG-CMM package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_harmonic.html">angle_style
+harmonic</A>, <A HREF = "pair_sdk.html">pair_style lj/sdk</A>,
+<A HREF = "pair_sdk.html">pair_style lj/sdk/coul/long</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/angle_style.html b/doc/doc2/angle_style.html
new file mode 100644
index 000000000..97ea5e7d8
--- /dev/null
+++ b/doc/doc2/angle_style.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style style
+</PRE>
+<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>cosine</I> or <I>cosine/squared</I> or <I>harmonic</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style harmonic
+angle_style charmm
+angle_style hybrid harmonic cosine
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the formula(s) LAMMPS uses to compute angle interactions between
+triplets of atoms, which remain in force for the duration of the
+simulation. The list of angle triplets is read in by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
+from a data or restart file.
+</P>
+<P>Hybrid models where angles are computed using different angle
+potentials can be setup using the <I>hybrid</I> angle style.
+</P>
+<P>The coefficients associated with a angle style can be specified in a
+data or restart file or via the <A HREF = "angle_coeff.html">angle_coeff</A> command.
+</P>
+<P>All angle potentials store their coefficient data in binary restart
+files which means angle_style and <A HREF = "angle_coeff.html">angle_coeff</A>
+commands do not need to be re-specified in an input script that
+restarts a simulation. See the <A HREF = "read_restart.html">read_restart</A>
+command for details on how to do this. The one exception is that
+angle_style <I>hybrid</I> only stores the list of sub-styles in the restart
+file; angle coefficients need to be re-specified.
+</P>
+<P>IMPORTANT NOTE: When both an angle and pair style is defined, the
+<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 3 bonded atoms.
+</P>
+<P>In the formulas listed for each angle style, <I>theta</I> is the angle
+between the 3 atoms in the angle.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command.
+</P>
+<P>Note that there are also additional angle styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
+<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
+</UL>
+<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
+<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
+<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
+<LI><A HREF = "angle_cosine_delta.html">angle_style cosine/delta</A> - difference of cosines angle potential
+<LI><A HREF = "angle_cosine_periodic.html">angle_style cosine/periodic</A> - DREIDING angle
+<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
+<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
+<LI><A HREF = "angle_table.html">angle_style table</A> - tabulated by angle
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Angle styles can only be set for atom_styles that allow angles to be
+defined.
+</P>
+<P>Most angle styles are part of the MOLECULE package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual bond potentials tell if it is part of a
+package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>angle_style none
+</PRE>
+</HTML>
diff --git a/doc/doc2/angle_table.html b/doc/doc2/angle_table.html
new file mode 100644
index 000000000..9f136cd2d
--- /dev/null
+++ b/doc/doc2/angle_table.html
@@ -0,0 +1,163 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>angle_style table command
+</H3>
+<H3>angle_style table/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>angle_style table style N
+</PRE>
+<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
+<LI>N = use N values in table
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>angle_style table linear 1000
+angle_coeff 3 file.table ENTRY1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from angle
+potential and derivative values listed in a file(s) as a function of
+angle The files are read by the <A HREF = "angle_coeff.html">angle_coeff</A>
+command.
+</P>
+<P>The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+<I>N</I> angles. During a simulation, these tables are used to interpolate
+energy and force values on individual atoms as needed. The
+interpolation is done in one of 2 styles: <I>linear</I> or <I>spline</I>.
+</P>
+<P>For the <I>linear</I> style, the angle is used to find 2 surrounding table
+values from which an energy or its derivative is computed by linear
+interpolation.
+</P>
+<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
+stored at each of the <I>N</I> values in the table. The angle is used to
+find the appropriate set of coefficients which are used to evaluate a
+cubic polynomial which computes the energy or derivative.
+</P>
+<P>The following coefficients must be defined for each angle type via the
+<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above.
+</P>
+<UL><LI>filename
+<LI>keyword
+</UL>
+<P>The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file. The
+format of this file is described below.
+</P>
+<HR>
+
+<P>The format of a tabulated file is as follows (without the
+parenthesized comments):
+</P>
+<PRE># Angle potential for harmonic (one or more comment or blank lines)
+</PRE>
+<PRE>HAM (keyword is the first text on line)
+N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
+ (blank line)
+N 181 FP 0 0 (N, FP parameters)
+1 0.0 200.5 2.5 (index, angle, energy, derivative)
+2 1.0 198.0 2.5
+...
+181 180.0 0.0 0.0
+</PRE>
+<P>A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+<A HREF = "angle_coeff.html">angle_coeff</A> command. The next line lists (in any
+order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+</P>
+<P>The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the <I>N</I>
+specified in the <A HREF = "angle_style.html">angle_style table</A> command. Let
+Ntable = <I>N</I> in the angle_style command, and Nfile = "N" in the
+tabulated file. What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points. It
+uses these to interpolate as needed to generate energy and derivative
+values at Ntable different points. The resulting tables of length
+Ntable are then used as described above, when computing energy and
+force for individual angles and their atoms. This means that if you
+want the interpolation tables of length Ntable to match exactly what
+is in the tabulated file (with effectively no preliminary
+interpolation), you should set Ntable = Nfile.
+</P>
+<P>The "FP" parameter is optional. If used, it is followed by two values
+fplo and fphi, which are the 2nd derivatives at the innermost and
+outermost angle settings. These values are needed by the spline
+construction routines. If not specified by the "FP" parameter, they
+are estimated (less accurately) by the first two and last two
+derivative values in the table.
+</P>
+<P>The "EQ" parameter is also optional. If used, it is followed by a the
+equilibrium angle value, which is used, for example, by the <A HREF = "fix_shake.html">fix
+shake</A> command. If not used, the equilibrium angle is
+set to 180.0.
+</P>
+<P>Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value (in degrees), the 3rd value is the energy (in energy
+units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
+term is the energy of the 3-atom configuration for the specified
+angle. The last term is the derivative of the energy with respect to
+the angle (in degrees, not radians). Thus the units of the last term
+are still energy, not force. The angle values must increase from one
+line to the next. The angle values must also begin with 0.0 and end
+with 180.0, i.e. span the full range of possible angles.
+</P>
+<P>Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "angle_coeff.html">angle_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/atom_modify.html b/doc/doc2/atom_modify.html
new file mode 100644
index 000000000..7dc0ab5a7
--- /dev/null
+++ b/doc/doc2/atom_modify.html
@@ -0,0 +1,179 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS
+Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>atom_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>atom_modify keyword values ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>id</I> or <I>map</I> or <I>first</I> or <I>sort</I>
+
+<PRE> <I>id</I> value = <I>yes</I> or <I>no</I>
+ <I>map</I> value = <I>array</I> or <I>hash</I>
+ <I>first</I> value = group-ID = group whose atoms will appear first in internal atom lists
+ <I>sort</I> values = Nfreq binsize
+ Nfreq = sort atoms spatially every this many time steps
+ binsize = bin size for spatial sorting (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>atom_modify map hash
+atom_modify map array sort 10000 2.0
+atom_modify first colloid
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Modify certain attributes of atoms defined and stored within LAMMPS,
+in addition to what is specified by the <A HREF = "atom_style.html">atom_style</A>
+command. The <I>id</I> and <I>map</I> keywords must be specified before a
+simulation box is defined; other keywords can be specified any time.
+</P>
+<P>The <I>id</I> keyword determines whether non-zero atom IDs can be assigned
+to each atom. If the value is <I>yes</I>, which is the default, IDs are
+assigned, whether you use the <A HREF = "create_atoms.html">create atoms</A> or
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands to initialize atoms. If the value is <I>no</I> the IDs for all
+atoms are assumed to be 0.
+</P>
+<P>If atom IDs are used, they must all be positive integers. They should
+also be unique, though LAMMPS does not check for this. Typically they
+should also be consecutively numbered (from 1 to Natoms), though this
+is not required. Molecular <A HREF = "atom_style.html">atom styles</A> are those
+that store bond topology information (styles bond, angle, molecular,
+full). These styles require atom IDs since the IDs are used to encode
+the topology. Some other LAMMPS commands also require the use of atom
+IDs. E.g. some many-body pair styles use them to avoid double
+computation of the I-J interaction between two atoms.
+</P>
+<P>The only reason not to use atom IDs is if you are running an atomic
+simulation so large that IDs cannot be uniquely assigned. For a
+default LAMMPS build this limit is 2^31 or about 2 billion atoms.
+However, even in this case, you can use 64-bit atom IDs, allowing 2^63
+or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
+switch. This is described in <A HREF = "Section_start.html#start_2">Section 2.2</A>
+of the manual. If atom IDs are not used, they must be specified as 0
+for all atoms, e.g. in a data or restart file.
+</P>
+<P>The <I>map</I> keyword determines how atom ID lookup is done for molecular
+atom styles. Lookups are performed by bond (angle, etc) routines in
+LAMMPS to find the local atom index associated with a global atom ID.
+</P>
+<P>When the <I>array</I> value is used, each processor stores a lookup table
+of length N, where N is the largest atom ID in the system. This is a
+fast, simple method for many simulations, but requires too much memory
+for large simulations. The <I>hash</I> value uses a hash table to perform
+the lookups. This can be slightly slower than the <I>array</I> method, but
+its memory cost is proportional to the number of atoms owned by a
+processor, i.e. N/P when N is the total number of atoms in the system
+and P is the number of processors.
+</P>
+<P>When this setting is not specified in your input script, LAMMPS
+creates a map, if one is needed, as an array or hash. See the
+discussion of default values below for how LAMMPS chooses which kind
+of map to build. Note that atomic systems do not normally need to
+create a map. However, even in this case some LAMMPS commands will
+create a map to find atoms (and then destroy it), or require a
+permanent map. An example of the former is the <A HREF = "velocity.html">velocity loop
+all</A> command, which uses a map when looping over all
+atoms and insuring the same velocity values are assigned to an atom
+ID, no matter which processor owns it.
+</P>
+<P>The <I>first</I> keyword allows a <A HREF = "group.html">group</A> to be specified whose
+atoms will be maintained as the first atoms in each processor's list
+of owned atoms. This in only useful when the specified group is a
+small fraction of all the atoms, and there are other operations LAMMPS
+is performing that will be sped-up significantly by being able to loop
+over the smaller set of atoms. Otherwise the reordering required by
+this option will be a net slow-down. The <A HREF = "neigh_modify.html">neigh_modify
+include</A> and <A HREF = "comm_modify.html">comm_modify group</A>
+commands are two examples of commands that require this setting to
+work efficiently. Several <A HREF = "fix.html">fixes</A>, most notably time
+integration fixes like <A HREF = "fix_nve.html">fix nve</A>, also take advantage of
+this setting if the group they operate on is the group specified by
+this command. Note that specifying "all" as the group-ID effectively
+turns off the <I>first</I> option.
+</P>
+<P>It is OK to use the <I>first</I> keyword with a group that has not yet been
+defined, e.g. to use the atom_modify first command at the beginning of
+your input script. LAMMPS does not use the group until a simullation
+is run.
+</P>
+<P>The <I>sort</I> keyword turns on a spatial sorting or reordering of atoms
+within each processor's sub-domain every <I>Nfreq</I> timesteps. If
+<I>Nfreq</I> is set to 0, then sorting is turned off. Sorting can improve
+cache performance and thus speed-up a LAMMPS simulation, as discussed
+in a paper by <A HREF = "#Meloni">(Meloni)</A>. Its efficacy depends on the problem
+size (atoms/processor), how quickly the system becomes disordered, and
+various other factors. As a general rule, sorting is typically more
+effective at speeding up simulations of liquids as opposed to solids.
+In tests we have done, the speed-up can range from zero to 3-4x.
+</P>
+<P>Reordering is peformed every <I>Nfreq</I> timesteps during a dynamics run
+or iterations during a minimization. More precisely, reordering
+occurs at the first reneighboring that occurs after the target
+timestep. The reordering is performed locally by each processor,
+using bins of the specified <I>binsize</I>. If <I>binsize</I> is set to 0.0,
+then a binsize equal to half the <A HREF = "neighbor.html">neighbor</A> cutoff
+distance (force cutoff plus skin distance) is used, which is a
+reasonable value. After the atoms have been binned, they are
+reordered so that atoms in the same bin are adjacent to each other in
+the processor's 1d list of atoms.
+</P>
+<P>The goal of this procedure is for atoms to put atoms close to each
+other in the processor's one-dimensional list of atoms that are also
+near to each other spatially. This can improve cache performance when
+pairwise intereractions and neighbor lists are computed. Note that if
+bins are too small, there will be few atoms/bin. Likewise if bins are
+too large, there will be many atoms/bin. In both cases, the goal of
+cache locality will be undermined.
+</P>
+<P>IMPORTANT NOTE: Running a simulation with sorting on versus off should
+not change the simulation results in a statistical sense. However, a
+different ordering will induce round-off differences, which will lead
+to diverging trajectories over time when comparing two simluations.
+Various commands, particularly those which use random numbers
+(e.g. <A HREF = "velocity.html">velocity create</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>), may generate (statistically identical)
+results which depend on the order in which atoms are processed. The
+order of atoms in a <A HREF = "dump.html">dump</A> file will also typically change
+if sorting is enabled.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>first</I> and <I>sort</I> options cannot be used together. Since sorting
+is on by default, it will be turned off if the <I>first</I> keyword is
+used with a group-ID that is not "all".
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<P>By default, <I>id</I> is yes. By default, atomic systems (no bond topology
+info) do not use a map. For molecular systems (with bond topology
+info), a map is used. The default map style is array if no atom ID is
+larger than 1 million, otherwise the default is hash. By default, a
+"first" group is not defined. By default, sorting is enabled with a
+frequency of 1000 and a binsize of 0.0, which means the neighbor
+cutoff will be used to set the bin size.
+</P>
+<HR>
+
+<A NAME = "Meloni"></A>
+
+<P><B>(Meloni)</B> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/atom_style.html b/doc/doc2/atom_style.html
new file mode 100644
index 000000000..6c690b135
--- /dev/null
+++ b/doc/doc2/atom_style.html
@@ -0,0 +1,268 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>atom_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>atom_style style args
+</PRE>
+<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>template</I> or <I>hybrid</I>
+
+<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
+ <I>body</I> args = bstyle bstyle-args
+ bstyle = style of body particles
+ bstyle-args = additional arguments specific to the bstyle
+ see the <A HREF = "body.html">body</A> doc page for details
+ <I>template</I> args = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+ <I>hybrid</I> args = list of one or more sub-styles, each with their args
+</PRE>
+<LI>accelerated styles (with same args) = <I>angle/cuda</I> or <I>angle/kk</I> or <I>atomic/cuda</I> or <I>atomic/kk</I> or <I>bond/kk</I> or <I>charge/cuda</I> or <I>charge/kk</I> or <I>full/cuda</I> or <I>full/kk</I> or <I>molecular/kk</I>
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>atom_style atomic
+atom_style bond
+atom_style full
+atom_style full/cuda
+atom_style body nparticle 2 10
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle 2 5
+atom_style template myMols
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define what style of atoms to use in a simulation. This determines
+what attributes are associated with the atoms. This command must be
+used before a simulation is setup via a <A HREF = "read_data.html">read_data</A>,
+<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
+command.
+</P>
+<P>Once a style is assigned, it cannot be changed, so use a style general
+enough to encompass all attributes. E.g. with style <I>bond</I>, angular
+terms cannot be used or added later to the model. It is OK to use a
+style more general than needed, though it may be slightly inefficient.
+</P>
+<P>The choice of style affects what quantities are stored by each atom,
+what quantities are communicated between processors to enable forces
+to be computed, and what quantities are listed in the data file read
+by the <A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>These are the additional attributes of each style and the typical
+kinds of physical systems they are used to model. All styles store
+coordinates, velocities, atom IDs and types. See the
+<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
+<A HREF = "set.html">set</A> commands for info on how to set these various
+quantities.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
+<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
+<TR><TD ><I>body</I> </TD><TD > mass, inertia moments, quaternion, angular momentum </TD><TD > arbitrary bodies </TD></TR>
+<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
+<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
+<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
+<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
+<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > aspherical particles </TD></TR>
+<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
+<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
+<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
+<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
+<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
+<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
+<TR><TD ><I>template</I> </TD><TD > template index, template atom </TD><TD > small molecules with fixed topology </TD></TR>
+<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
+<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
+</TD></TR></TABLE></DIV>
+
+<P>IMPORTANT NOTE: It is possible to add some attributes, such as a
+molecule ID, to atom styles that do not have them via the <A HREF = "fix_property_atom.html">fix
+property/atom</A> command. This command also
+allows new custom attributes consisting of extra integer or
+floating-point values to be added to atoms. See the <A HREF = "fix_property_atom.html">fix
+property/atom</A> doc page for examples of cases
+where this is useful and details on how to initialize, access, and
+output the custom values.
+</P>
+<P>All of the above styles define point particles, except the <I>sphere</I>,
+<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, <I>tri</I>, and
+<I>body</I> styles, which define finite-size particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
+14</A> for an overview of using finite-size
+particle models with LAMMPS.
+</P>
+<P>All of the point-particle styles assign mass to particles on a
+per-type basis, using the <A HREF = "mass.html">mass</A> command, The finite-size
+particle styles assign mass to individual particles on a per-particle
+basis.
+</P>
+<P>For the <I>sphere</I> style, the particles are spheres and each stores a
+per-particle diameter and mass. If the diameter > 0.0, the particle
+is a finite-size sphere. If the diameter = 0.0, it is a point
+particle.
+</P>
+<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
+stores a flag which indicates whether it is a finite-size ellipsoid or
+a point particle. If it is an ellipsoid, it also stores a shape
+vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
+with its orientation.
+</P>
+<P>For the <I>electron</I> style, the particles representing electrons are 3d
+Gaussians with a specified position and bandwidth or uncertainty in
+position, which is represented by the eradius = electron size.
+</P>
+<P>For the <I>peri</I> style, the particles are spherical and each stores a
+per-particle mass and volume.
+</P>
+<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
+particles which store a density (rho), energy (e), and heat capacity
+(cv).
+</P>
+<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
+consist of several Gaussian wave packets, summed up with coefficients
+cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
+particle in LAMMPS, wave packets belonging to the same electron must
+have identical <I>etag</I> values.
+</P>
+<P>For the <I>line</I> style, the particles are idealized line segments and
+each stores a per-particle mass and length and orientation (i.e. the
+end points of the line segment).
+</P>
+<P>For the <I>tri</I> style, the particles are planar triangles and each
+stores a per-particle mass and size and orientation (i.e. the corner
+points of the triangle).
+</P>
+<P>The <I>template</I> style allows molecular topolgy (bonds,angles,etc) to be
+defined via a molecule template using the <A HREF = "molecule.txt">molecule</A>
+command. The template stores one or more molecules with a single copy
+of the topology info (bonds,angles,etc) of each. Individual atoms
+only store a template index and template atom to identify which
+molecule and which atom-within-the-molecule they represent. Using the
+<I>template</I> style instead of the <I>bond</I>, <I>angle</I>, <I>molecular</I> styles
+can save memory for systems comprised of a large number of small
+molecules, all of a single type (or small number of types). See the
+paper by Grime and Voth, in <A HREF = "#Grime">(Grime)</A>, for examples of how this
+can be advantageous for large-scale coarse-grained systems.
+</P>
+<P>IMPORTANT NOTE: When using the <I>template</I> style with a <A HREF = "molecule.html">molecule
+template</A> that contains multiple molecules, you should
+insure the atom types, bond types, angle_types, etc in all the
+molecules are consistent. E.g. if one molecule represents H2O and
+another CO2, then you probably do not want each molecule file to
+define 2 atom types and a single bond type, because they will conflict
+with each other when a mixture system of H2O and CO2 molecules is
+defined, e.g. by the <A HREF = "read_data.html">read_data</A> command. Rather the
+H2O molecule should define atom types 1 and 2, and bond type 1. And
+the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
+2 if a single oxygen type is desired), and bond type 2.
+</P>
+<P>For the <I>body</I> style, the particles are arbitrary bodies with internal
+attributes defined by the "style" of the bodies, which is specified by
+the <I>bstyle</I> argument. Body particles can represent complex entities,
+such as surface meshes of discrete points, collections of
+sub-particles, deformable objects, etc.
+</P>
+<P>The <A HREF = "body.html">body</A> doc page descibes the body styles LAMMPS
+currently supports, and provides more details as to the kind of body
+particles they represent. For all styles, each body particle stores
+moments of inertia and a quaternion 4-vector, so that its orientation
+and position can be time integrated due to forces and torques.
+</P>
+<P>Note that there may be additional arguments required along with the
+<I>bstyle</I> specification, in the atom_style body command. These
+arguments are described in the <A HREF = "body.html">body</A> doc page.
+</P>
+<HR>
+
+<P>Typically, simulations require only a single (non-hybrid) atom style.
+If some atoms in the simulation do not have all the properties defined
+by a particular style, use the simplest style that defines all the
+needed properties by any atom. For example, if some atoms in a
+simulation are charged, but others are not, use the <I>charge</I> style.
+If some atoms have bonds, but others do not, use the <I>bond</I> style.
+</P>
+<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
+single style which defines all needed properties of all atoms. For
+example, if you want dipolar particles which will rotate due to
+torque, you would need to use "atom_style hybrid sphere dipole". When
+a hybrid style is used, atoms store and communicate the union of all
+quantities implied by the individual styles.
+</P>
+<P>When using the <I>hybrid</I> style, you cannot combine the <I>template</I> style
+with another molecular style that stores bond,angle,etc info on a
+per-atom basis.
+</P>
+<P>LAMMPS can be extended with new atom styles as well as new body
+styles; see <A HREF = "Section_modify.html">this section</A>.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> or <I>kk</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>Note that other acceleration packages in LAMMPS, specifically the GPU,
+USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
+styles.
+</P>
+<P>The accelerated styles are part of the USER-CUDA and KOKKOS packages
+respectively. They are only enabled if LAMMPS was built with those
+packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, <I>molecular</I>, and <I>template</I> styles are
+part of the MOLECULE package. The <I>line</I> and <I>tri</I> styles are part
+of the ASPHERE pacakge. The <I>body</I> style is part of the BODY package.
+The <I>dipole</I> style is part of the DIPOLE package. The <I>peri</I> style is
+part of the PERI package for Peridynamics. The <I>electron</I> style is
+part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
+fields</A>. The <I>meso</I> style is part of the USER-SPH
+package for smoothed particle hydrodyanmics (SPH). See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
+guide</A> to using SPH in LAMMPS. The
+<I>wavepacket</I> style is part of the USER-AWPMD package for the
+<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>atom_style atomic
+</P>
+<HR>
+
+<A NAME = "Grime"></A>
+
+<P><B>(Grime)</B> Grime and Voth, to appear in J Chem Theory & Computation
+(2014).
+</P>
+</HTML>
diff --git a/doc/doc2/balance.html b/doc/doc2/balance.html
new file mode 100644
index 000000000..39acba35e
--- /dev/null
+++ b/doc/doc2/balance.html
@@ -0,0 +1,360 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>balance command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>balance thresh style args ... keyword value ...
+</PRE>
+<UL><LI>thresh = imbalance threshhold that must be exceeded to perform a re-balance
+
+<LI>one style/arg pair can be used (or multiple for <I>x</I>,<I>y</I>,<I>z</I>)
+
+<LI>style = <I>x</I> or <I>y</I> or <I>z</I> or <I>shift</I> or <I>rcb</I>
+
+<PRE> <I>x</I> args = <I>uniform</I> or Px-1 numbers between 0 and 1
+ <I>uniform</I> = evenly spaced cuts between processors in x dimension
+ numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
+ <I>x</I> can be specified together with <I>y</I> or <I>z</I>
+ <I>y</I> args = <I>uniform</I> or Py-1 numbers between 0 and 1
+ <I>uniform</I> = evenly spaced cuts between processors in y dimension
+ numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
+ <I>y</I> can be specified together with <I>x</I> or <I>z</I>
+ <I>z</I> args = <I>uniform</I> or Pz-1 numbers between 0 and 1
+ <I>uniform</I> = evenly spaced cuts between processors in z dimension
+ numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
+ <I>z</I> can be specified together with <I>x</I> or <I>y</I>
+ <I>shift</I> args = dimstr Niter stopthresh
+ dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+ Niter = # of times to iterate within each dimension of dimstr sequence
+ stopthresh = stop balancing when this imbalance threshhold is reached
+ <I>rcb</I> args = none
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>out</I>
+
+<PRE> <I>out</I> value = filename
+ filename = write each processor's sub-domain to a file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>balance 0.9 x uniform y 0.4 0.5 0.6
+balance 1.2 shift xz 5 1.1
+balance 1.0 shift xz 5 1.1
+balance 1.1 rcb
+balance 1.0 shift x 20 1.0 out tmp.balance
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command adjusts the size and shape of processor sub-domains
+within the simulation box, to attempt to balance the number of
+particles and thus the computational cost (load) evenly across
+processors. The load balancing is "static" in the sense that this
+command performs the balancing once, before or between simulations.
+The processor sub-domains will then remain static during the
+subsequent run. To perform "dynamic" balancing, see the <A HREF = "fix_balance.html">fix
+balance</A> command, which can adjust processor
+sub-domain sizes and shapes on-the-fly during a <A HREF = "run.html">run</A>.
+</P>
+<P>Load-balancing is typically only useful if the particles in the
+simulation box have a spatially-varying density distribution. E.g. a
+model of a vapor/liquid interface, or a solid with an irregular-shaped
+geometry containing void regions. In this case, the LAMMPS default of
+dividing the simulation box volume into a regular-spaced grid of 3d
+bricks, with one equal-volume sub-domain per procesor, may assign very
+different numbers of particles per processor. This can lead to poor
+performance when the simulation is run in parallel.
+</P>
+<P>Note that the <A HREF = "processors.html">processors</A> command allows some control
+over how the box volume is split across processors. Specifically, for
+a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
+Pz, subject to the constraint that Px * Py * Pz = P, the total number
+of processors. This is sufficient to achieve good load-balance for
+some problems on some processor counts. However, all the processor
+sub-domains will still have the same shape and same volume.
+</P>
+<P>The requested load-balancing operation is only performed if the
+current "imbalance factor" in particles owned by each processor
+exceeds the specified <I>thresh</I> parameter. The imbalance factor is
+defined as the maximum number of particles owned by any processor,
+divided by the average number of particles per processor. Thus an
+imbalance factor of 1.0 is perfect balance.
+</P>
+<P>As an example, for 10000 particles running on 10 processors, if the
+most heavily loaded processor has 1200 particles, then the factor is
+1.2, meaning there is a 20% imbalance. Note that a re-balance can be
+forced even if the current balance is perfect (1.0) be specifying a
+<I>thresh</I> < 1.0.
+</P>
+<P>IMPORTANT NOTE: Balancing is performed even if the imbalance factor
+does not exceed the <I>thresh</I> parameter if a "grid" style is specified
+when the current partitioning is "tiled". The meaning of "grid" vs
+"tiled" is explained below. This is to allow forcing of the
+partitioning to "grid" so that the <A HREF = "comm_style.html">comm_style brick</A>
+command can then be used to replace a current <A HREF = "comm_style.html">comm_style
+tiled</A> setting.
+</P>
+<P>When the balance command completes, it prints statistics about the
+result, including the change in the imbalance factor and the change in
+the maximum number of particles on any processor. For "grid" methods
+(defined below) that create a logical 3d grid of processors, the
+positions of all cutting planes in each of the 3 dimensions (as
+fractions of the box length) are also printed.
+</P>
+<P>IMPORTANT NOTE: This command attempts to minimize the imbalance
+factor, as defined above. But depending on the method a perfect
+balance (1.0) may not be achieved. For example, "grid" methods
+(defined below) that create a logical 3d grid cannot achieve perfect
+balance for many irregular distributions of particles. Likewise, if a
+portion of the system is a perfect lattice, e.g. the intiial system is
+generated by the <A HREF = "create_atoms.html">create_atoms</A> command, then "grid"
+methods may be unable to achieve exact balance. This is because
+entire lattice planes will be owned or not owned by a single
+processor.
+</P>
+<P>IMPORTANT NOTE: The imbalance factor is also an estimate of the
+maximum speed-up you can hope to achieve by running a perfectly
+balanced simulation versus an imbalanced one. In the example above,
+the 10000 particle simulation could run up to 20% faster if it were
+perfectly balanced, versus when imbalanced. However, computational
+cost is not strictly proportional to particle count, and changing the
+relative size and shape of processor sub-domains may lead to
+additional computational and communication overheads, e.g. in the PPPM
+solver used via the <A HREF = "kspace_style.html">kspace_style</A> command. Thus
+you should benchmark the run times of a simulation before and after
+balancing.
+</P>
+<HR>
+
+<P>The method used to perform a load balance is specified by one of the
+listed styles (or more in the case of <I>x</I>,<I>y</I>,<I>z</I>), which are
+described in detail below. There are 2 kinds of styles.
+</P>
+<P>The <I>x</I>, <I>y</I>, <I>z</I>, and <I>shift</I> styles are "grid" methods which produce
+a logical 3d grid of processors. They operate by changing the cutting
+planes (or lines) between processors in 3d (or 2d), to adjust the
+volume (area in 2d) assigned to each processor, as in the following 2d
+diagram where processor sub-domains are shown and atoms are colored by
+the processor that owns them. The leftmost diagram is the default
+partitioning of the simulation box across processors (one sub-box for
+each of 16 processors); the middle diagram is after a "grid" method
+has been applied.
+</P>
+<CENTER><A HREF = "JPG/balance_uniform.jpg"><IMG SRC = "JPG/balance_uniform_small.jpg"></A><A HREF = "JPG/balance_nonuniform.jpg"><IMG SRC = "JPG/balance_nonuniform_small.jpg"></A><A HREF = "JPG/balance_rcb.jpg"><IMG SRC = "JPG/balance_rcb_small.jpg"></A>
+</CENTER>
+<P>The <I>rcb</I> style is a "tiling" method which does not produce a logical
+3d grid of processors. Rather it tiles the simulation domain with
+rectangular sub-boxes of varying size and shape in an irregular
+fashion so as to have equal numbers of particles in each sub-box, as
+in the rightmost diagram above.
+</P>
+<P>The "grid" methods can be used with either of the
+<A HREF = "comm_style.html">comm_style</A> command options, <I>brick</I> or <I>tiled</I>. The
+"tiling" methods can only be used with <A HREF = "comm_style.html">comm_style
+tiled</A>. Note that it can be useful to use a "grid"
+method with <A HREF = "comm_style.html">comm_style tiled</A> to return the domain
+partitioning to a logical 3d grid of processors so that "comm_style
+brick" can afterwords be specified for subsequent <A HREF = "run.html">run</A>
+commands.
+</P>
+<P>When a "grid" method is specified, the current domain partitioning can
+be either a logical 3d grid or a tiled partitioning. In the former
+case, the current logical 3d grid is used as a starting point and
+changes are made to improve the imbalance factor. In the latter case,
+the tiled partitioning is discarded and a logical 3d grid is created
+with uniform spacing in all dimensions. This becomes the starting
+point for the balancing operation.
+</P>
+<P>When a "tiling" method is specified, the current domain partitioning
+("grid" or "tiled") is ignored, and a new partitioning is computed
+from scratch.
+</P>
+<HR>
+
+<P>The <I>x</I>, <I>y</I>, and <I>z</I> styles invoke a "grid" method for balancing, as
+described above. Note that any or all of these 3 styles can be
+specified together, one after the other, but they cannot be used with
+any other style. This style adjusts the position of cutting planes
+between processor sub-domains in specific dimensions. Only the
+specified dimensions are altered.
+</P>
+<P>The <I>uniform</I> argument spaces the planes evenly, as in the left
+diagrams above. The <I>numeric</I> argument requires listing Ps-1 numbers
+that specify the position of the cutting planes. This requires
+knowing Ps = Px or Py or Pz = the number of processors assigned by
+LAMMPS to the relevant dimension. This assignment is made (and the
+Px, Py, Pz values printed out) when the simulation box is created by
+the "create_box" or "read_data" or "read_restart" command and is
+influenced by the settings of the <A HREF = "processors.html">processors</A>
+command.
+</P>
+<P>Each of the numeric values must be between 0 and 1, and they must be
+listed in ascending order. They represent the fractional position of
+the cutting place. The left (or lower) edge of the box is 0.0, and
+the right (or upper) edge is 1.0. Neither of these values is
+specified. Only the interior Ps-1 positions are specified. Thus is
+there are 2 procesors in the x dimension, you specify a single value
+such as 0.75, which would make the left processor's sub-domain 3x
+larger than the right processor's sub-domain.
+</P>
+<HR>
+
+<P>The <I>shift</I> style invokes a "grid" method for balancing, as
+described above. It changes the positions of cutting planes between
+processors in an iterative fashion, seeking to reduce the imbalance
+factor, similar to how the <A HREF = "fix_balance.html">fix balance shift</A>
+command operates.
+</P>
+<P>The <I>dimstr</I> argument is a string of characters, each of which must be
+an "x" or "y" or "z". Eacn character can appear zero or one time,
+since there is no advantage to balancing on a dimension more than
+once. You should normally only list dimensions where you expect there
+to be a density variation in the particles.
+</P>
+<P>Balancing proceeds by adjusting the cutting planes in each of the
+dimensions listed in <I>dimstr</I>, one dimension at a time. For a single
+dimension, the balancing operation (described below) is iterated on up
+to <I>Niter</I> times. After each dimension finishes, the imbalance factor
+is re-computed, and the balancing operation halts if the <I>stopthresh</I>
+criterion is met.
+</P>
+<P>A rebalance operation in a single dimension is performed using a
+recursive multisectioning algorithm, where the position of each
+cutting plane (line in 2d) in the dimension is adjusted independently.
+This is similar to a recursive bisectioning for a single value, except
+that the bounds used for each bisectioning take advantage of
+information from neighboring cuts if possible. At each iteration, the
+count of particles on either side of each plane is tallied. If the
+counts do not match the target value for the plane, the position of
+the cut is adjusted to be halfway between a low and high bound. The
+low and high bounds are adjusted on each iteration, using new count
+information, so that they become closer together over time. Thus as
+the recustion progresses, the count of particles on either side of the
+plane gets closer to the target value.
+</P>
+<P>Once the rebalancing is complete and final processor sub-domains
+assigned, particles are migrated to their new owning processor, and
+the balance procedure ends.
+</P>
+<P>IMPORTANT NOTE: At each rebalance operation, the bisectioning for each
+cutting plane (line in 2d) typcially starts with low and high bounds
+separated by the extent of a processor's sub-domain in one dimension.
+The size of this bracketing region shrinks by 1/2 every iteration.
+Thus if <I>Niter</I> is specified as 10, the cutting plane will typically
+be positioned to 1 part in 1000 accuracy (relative to the perfect
+target position). For <I>Niter</I> = 20, it will be accurate to 1 part in
+a million. Thus there is no need ot set <I>Niter</I> to a large value.
+LAMMPS will check if the threshold accuracy is reached (in a
+dimension) is less iterations than <I>Niter</I> and exit early. However,
+<I>Niter</I> should also not be set too small, since it will take roughly
+the same number of iterations to converge even if the cutting plane is
+initially close to the target value.
+</P>
+<HR>
+
+<P>The <I>rcb</I> style invokes a "tiled" method for balancing, as described
+above. It performs a recursive coordinate bisectioning (RCB) of the
+simulation domain. The basic idea is as follows.
+</P>
+<P>The simulation domain is cut into 2 boxes by an axis-aligned cut in
+the longest dimension, leaving one new box on either side of the cut.
+All the processors are also partitioned into 2 groups, half assigned
+to the box on the lower side of the cut, and half to the box on the
+upper side. (If the processor count is odd, one side gets an extra
+processor.) The cut is positioned so that the number of atoms in the
+lower box is exactly the number that the processors assigned to that
+box should own for load balance to be perfect. This also makes load
+balance for the upper box perfect. The positioning is done
+iteratively, by a bisectioning method. Note that counting atoms on
+either side of the cut requires communication between all processors
+at each iteration.
+</P>
+<P>That is the procedure for the first cut. Subsequent cuts are made
+recursively, in exactly the same manner. The subset of processors
+assigned to each box make a new cut in the longest dimension of that
+box, splitting the box, the subset of processsors, and the atoms in
+the box in two. The recursion continues until every processor is
+assigned a sub-box of the entire simulation domain, and owns the atoms
+in that sub-box.
+</P>
+<HR>
+
+<P>The <I>out</I> keyword writes a text file to the specified <I>filename</I> with
+the results of the balancing operation. The file contains the bounds
+of the sub-domain for each processor after the balancing operation
+completes. The format of the file is compatible with the
+<A HREF = "pizza">Pizza.py</A> <I>mdump</I> tool which has support for manipulating and
+visualizing mesh files. An example is shown here for a balancing by 4
+processors for a 2d problem:
+</P>
+<PRE>ITEM: TIMESTEP
+0
+ITEM: NUMBER OF NODES
+16
+ITEM: BOX BOUNDS
+0 10
+0 10
+0 10
+ITEM: NODES
+1 1 0 0 0
+2 1 5 0 0
+3 1 5 5 0
+4 1 0 5 0
+5 1 5 0 0
+6 1 10 0 0
+7 1 10 5 0
+8 1 5 5 0
+9 1 0 5 0
+10 1 5 5 0
+11 1 5 10 0
+12 1 10 5 0
+13 1 5 5 0
+14 1 10 5 0
+15 1 10 10 0
+16 1 5 10 0
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF SQUARES
+4
+ITEM: SQUARES
+1 1 1 2 3 4
+2 1 5 6 7 8
+3 1 9 10 11 12
+4 1 13 14 15 16
+</PRE>
+<P>The coordinates of all the vertices are listed in the NODES section, 5
+per processor. Note that the 4 sub-domains share vertices, so there
+will be duplicate nodes in the list.
+</P>
+<P>The "SQUARES" section lists the node IDs of the 4 vertices in a
+rectangle for each processor (1 to 4).
+</P>
+<P>For a 3d problem, the syntax is similar with 8 vertices listed for
+each processor, instead of 4, and "SQUARES" replaced by "CUBES".
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>For 2d simulations, the <I>z</I> style cannot be used. Nor can a "z"
+appear in <I>dimstr</I> for the <I>shift</I> style.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "processors.html">processors</A>, <A HREF = "fix_balance.html">fix balance</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/body.html b/doc/doc2/body.html
new file mode 100644
index 000000000..3d610764d
--- /dev/null
+++ b/doc/doc2/body.html
@@ -0,0 +1,163 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>Body particles
+</H3>
+<P><B>Overview:</B>
+</P>
+<P>This doc page is not about a LAMMPS input script command, but about
+body particles, which are generalized finite-size particles.
+Individual body particles can represent complex entities, such as
+surface meshes of discrete points, collections of sub-particles,
+deformable objects, etc. Note that other kinds of finite-size
+spherical and aspherical particles are also supported by LAMMPS, such
+as spheres, ellipsoids, line segments, and triangles, but they are
+simpler entities that body particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
+14</A> for a general overview of all these
+particle types.
+</P>
+<P>Body particles are used via the <A HREF = "atom_style.html">atom_style body</A>
+command. It takes a body style as an argument. The current body
+styles supported by LAMMPS are as follows. The name in the first
+column is used as the <I>bstyle</I> argument for the <A HREF = "atom_style.html">atom_style
+body</A> command.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><I>nparticle</I> </TD><TD > rigid body with N sub-particles
+</TD></TR></TABLE></DIV>
+
+<P>The body style determines what attributes are stored for each body and
+thus how they can be used to compute pairwise body/body or
+bond/non-body (point particle) interactions. More details of each
+style are described below.
+</P>
+<P>We hope to add more styles in the future. See <A HREF = "Section_modify.html#mod_12">Section_modify
+12</A> for details on how to add a new body
+style to the code.
+</P>
+<HR>
+
+<P><B>When to use body particles:</B>
+</P>
+<P>You should not use body particles to model a rigid body made of
+simpler particles (e.g. point, sphere, ellipsoid, line segment,
+triangular particles), if the interaction between pairs of rigid
+bodies is just the summation of pairwise interactions between the
+simpler particles. LAMMPS already supports this kind of model via the
+<A HREF = "fix_rigid.html">fix rigid</A> command. Any of the numerous pair styles
+that compute interactions between simpler particles can be used. The
+<A HREF = "fix_rigid.html">fix rigid</A> command time integrates the motion of the
+rigid bodies. All of the standard LAMMPS commands for thermostatting,
+adding constraints, performing output, etc will operate as expected on
+the simple particles.
+</P>
+<P>By contrast, when body particles are used, LAMMPS treats an entire
+body as a single particle for purposes of computing pairwise
+interactions, building neighbor lists, migrating particles between
+processors, outputting particles to a dump file, etc. This means that
+interactions between pairs of bodies or between a body and non-body
+(point) particle need to be encoded in an appropriate pair style. If
+such a pair style were to mimic the <A HREF = "fix_rigid.html">fix rigid</A> model,
+it would need to loop over the entire collection of interactions
+between pairs of simple particles within the two bodies, each time a
+single body/body interaction was computed.
+</P>
+<P>Thus it only makes sense to use body particles and develop such a pair
+style, when particle/particle interactions are more complex than what
+the <A HREF = "fix_rigid.html">fix rigid</A> command can already calculate. For
+example, if particles have one or more of the following attributes:
+</P>
+<UL><LI>represented by a surface mesh
+<LI>represented by a collection of geometric entities (e.g. planes + spheres)
+<LI>deformable
+<LI>internal stress that induces fragmentation
+</UL>
+<P>then the interaction between pairs of particles is likely to be more
+complex than the summation of simple sub-particle interactions. An
+example is contact or frictional forces between particles with planar
+sufaces that inter-penetrate.
+</P>
+<P>These are additional LAMMPS commands that can be used with body
+particles of different styles
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><A HREF = "fix_nve_body.html">fix nve/body</A> </TD><TD > integrate motion of a body particle</TD></TR>
+<TR><TD ><A HREF = "compute_body_local.html">compute body/local</A> </TD><TD > store sub-particle attributes of a body particle</TD></TR>
+<TR><TD ><A HREF = "dump.html">dump local</A> </TD><TD > output sub-particle attributes of a body particle
+</TD></TR></TABLE></DIV>
+
+<P>The pair styles defined for use with specific body styles are listed
+in the sections below.
+</P>
+<HR>
+
+<P><B>Specifics of body style nparticle:</B>
+</P>
+<P>The <I>nparticle</I> body style represents body particles as a rigid body
+with a variable number N of sub-particles. It is provided as a
+vanillia, prototypical example of a body particle, although as
+mentioned above, the <A HREF = "fix_rigid.html">fix rigid</A> command already
+duplicates its functionality.
+</P>
+<P>The atom_style body command for this body style takes two additional
+arguments:
+</P>
+<PRE>atom_style body nparticle Nmin Nmax
+Nmin = minimum # of sub-particles in any body in the system
+Nmax = maximum # of sub-particles in any body in the system
+</PRE>
+<P>The Nmin and Nmax arguments are used to bound the size of data
+structures used internally by each particle.
+</P>
+<P>When the <A HREF = "read_data.html">read_data</A> command reads a data file for this
+body style, the following information must be provided for each entry
+in the <I>Bodies</I> section of the data file:
+</P>
+<PRE>atom-ID 1 M
+N
+ixx iyy izz ixy ixz iyz x1 y1 z1 ...
+...
+... xN yN zN
+</PRE>
+<P>N is the number of sub-particles in the body particle. M = 6 + 3*N.
+The integer line has a single value N. The floating point line(s)
+list 6 moments of inertia followed by the coordinates of the N
+sub-particles (x1 to zN) as 3N values on as many lines as required.
+Note that this in not N lines, but 10 values per line; see the
+<A HREF = "read_data.html">read_data</A> command for details. The 6 moments of
+inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with
+the current orientation of the rigid body around its center of mass.
+The values are with respect to the simulation box XYZ axes, not with
+respect to the prinicpal axes of the rigid body itself. LAMMPS
+performs the latter calculation internally. The coordinates of each
+sub-particle are specified as its x,y,z displacement from the
+center-of-mass of the body particle. The center-of-mass position of
+the particle is specified by the x,y,z values in the <I>Atoms</I> section
+of the data file.
+</P>
+<P>The <A HREF = "pair_body.html">pair_style body</A> command can be used with this
+body style to compute body/body and body/non-body interactions.
+</P>
+<P>For output purposes via the <A HREF = "compute_body_local.html">compute
+body/local</A> and <A HREF = "dump.html">dump local</A>
+commands, this body style produces one datum for each of the N
+sub-particles in a body particle. The datum has 3 values:
+</P>
+<PRE>1 = x position of sub-particle
+2 = y position of sub-particle
+3 = z position of sub-particle
+</PRE>
+<P>These values are the current position of the sub-particle within the
+simulation domain, not a displacement from the center-of-mass (COM) of
+the body particle itself. These values are calculated using the
+current COM and orientiation of the body particle.
+</P>
+</HTML>
diff --git a/doc/doc2/bond_class2.html b/doc/doc2/bond_class2.html
new file mode 100644
index 000000000..2c1611d44
--- /dev/null
+++ b/doc/doc2/bond_class2.html
@@ -0,0 +1,88 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style class2 command
+</H3>
+<H3>bond_style class2/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style class2
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style class2
+bond_coeff 1 1.0 100.0 80.0 80.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>class2</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_class2.jpg">
+</CENTER>
+<P>where r0 is the equilibrium bond distance.
+</P>
+<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>R0 (distance)
+<LI>K2 (energy/distance^2)
+<LI>K3 (energy/distance^3)
+<LI>K4 (energy/distance^4)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the CLASS2
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/bond_coeff.html b/doc/doc2/bond_coeff.html
new file mode 100644
index 000000000..4d6fb4d94
--- /dev/null
+++ b/doc/doc2/bond_coeff.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_coeff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_coeff N args
+</PRE>
+<UL><LI>N = bond type (see asterisk form below)
+<LI>args = coefficients for one or more bond types
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_coeff 5 80.0 1.2
+bond_coeff * 30.0 1.5 1.0 1.0
+bond_coeff 1*4 30.0 1.5 1.0 1.0
+bond_coeff 1 harmonic 200.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Specify the bond force field coefficients for one or more bond types.
+The number and meaning of the coefficients depends on the bond style.
+Bond coefficients can also be set in the data file read by the
+<A HREF = "read_data.html">read_data</A> command or in a restart file.
+</P>
+<P>N can be specified in one of two ways. An explicit numeric value can
+be used, as in the 1st example above. Or a wild-card asterisk can be
+used to set the coefficients for multiple bond types. This takes the
+form "*" or "*n" or "n*" or "m*n". If N = the number of bond types,
+then an asterisk with no numeric values means all types from 1 to N. A
+leading asterisk means all types from 1 to n (inclusive). A trailing
+asterisk means all types from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive).
+</P>
+<P>Note that using a bond_coeff command can override a previous setting
+for the same bond type. For example, these commands set the coeffs
+for all bond types, then overwrite the coeffs for just bond type 2:
+</P>
+<PRE>bond_coeff * 100.0 1.2
+bond_coeff 2 200.0 1.2
+</PRE>
+<P>A line in a data file that specifies bond coefficients uses the exact
+same format as the arguments of the bond_coeff command in an input
+script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file. For example,
+under the "Bond Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+</P>
+<PRE>5 80.0 1.2
+</PRE>
+<HR>
+
+<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command.
+</P>
+<P>Note that here are also additional bond styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
+<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
+</UL>
+<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
+<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
+<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
+<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
+<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
+<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
+<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
+<LI><A HREF = "bond_table.html">bond_style table</A> - tabulated by bond length
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>A bond style must be defined before any bond coefficients are set,
+either in the input script or in a data file.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_style.html">bond_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_fene.html b/doc/doc2/bond_fene.html
new file mode 100644
index 000000000..e75edad89
--- /dev/null
+++ b/doc/doc2/bond_fene.html
@@ -0,0 +1,96 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style fene command
+</H3>
+<H3>bond_style fene/kk command
+</H3>
+<H3>bond_style fene/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style fene
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>fene</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_fene.jpg">
+</CENTER>
+<P>to define a finite extensible nonlinear elastic (FENE) potential
+<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
+term is attractive, the 2nd Lennard-Jones term is repulsive. The
+first term extends to R0, the maximum extent of the bond. The 2nd
+term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/distance^2)
+<LI>R0 (distance)
+<LI>epsilon (energy)
+<LI>sigma (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
+or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
+style. LAMMPS will issue a warning it that's not the case.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Kremer"></A>
+
+<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
+</P>
+</HTML>
diff --git a/doc/doc2/bond_fene_expand.html b/doc/doc2/bond_fene_expand.html
new file mode 100644
index 000000000..db6cc88ae
--- /dev/null
+++ b/doc/doc2/bond_fene_expand.html
@@ -0,0 +1,99 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style fene/expand command
+</H3>
+<H3>bond_style fene/expand/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style fene/expand
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style fene/expand
+bond_coeff 1 30.0 1.5 1.0 1.0 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>fene/expand</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_fene_expand.jpg">
+</CENTER>
+<P>to define a finite extensible nonlinear elastic (FENE) potential
+<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
+term is attractive, the 2nd Lennard-Jones term is repulsive.
+</P>
+<P>The <I>fene/expand</I> bond style is similar to <I>fene</I> except that an extra
+shift factor of delta (positive or negative) is added to <I>r</I> to
+effectively change the bead size of the bonded atoms. The first term
+now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
++ delta.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/distance^2)
+<LI>R0 (distance)
+<LI>epsilon (energy)
+<LI>sigma (distance)
+<LI>delta (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
+or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
+style. LAMMPS will issue a warning it that's not the case.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Kremer"></A>
+
+<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
+</P>
+</HTML>
diff --git a/doc/doc2/bond_harmonic.html b/doc/doc2/bond_harmonic.html
new file mode 100644
index 000000000..f3738011b
--- /dev/null
+++ b/doc/doc2/bond_harmonic.html
@@ -0,0 +1,81 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style harmonic command
+</H3>
+<H3>bond_style harmonic/kk command
+</H3>
+<H3>bond_style harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style harmonic
+bond_coeff 5 80.0 1.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
+</CENTER>
+<P>where r0 is the equilibrium bond distance. Note that the usual 1/2
+factor is included in K.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/distance^2)
+<LI>r0 (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_harmonic_shift.html b/doc/doc2/bond_harmonic_shift.html
new file mode 100644
index 000000000..04b686a1a
--- /dev/null
+++ b/doc/doc2/bond_harmonic_shift.html
@@ -0,0 +1,85 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style harmonic/shift command
+</H3>
+<H3>bond_style harmonic/shift/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style harmonic/shift
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style harmonic/shift
+bond_coeff 5 10.0 0.5 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic/shift</I> bond style is a shifted harmonic bond that uses
+the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic_shift.jpg">
+</CENTER>
+<P>where r0 is the equilibrium bond distance, and rc the critical distance.
+The potential is -Umin at r0 and zero at rc. The spring constant is
+k = Umin / [ 2 (r0-rc)^2].
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>Umin (energy)
+</UL>
+<UL><LI>r0 (distance)
+</UL>
+<UL><LI>rc (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
+<A HREF = "bond_harmonic.html">bond_harmonic</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_harmonic_shift_cut.html b/doc/doc2/bond_harmonic_shift_cut.html
new file mode 100644
index 000000000..9240cd132
--- /dev/null
+++ b/doc/doc2/bond_harmonic_shift_cut.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style harmonic/shift/cut command
+</H3>
+<H3>bond_style harmonic/shift/cut/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style harmonic/shift/cut
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style harmonic/shift/cut
+bond_coeff 5 10.0 0.5 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic/shift/cut</I> bond style is a shifted harmonic bond that
+uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic_shift_cut.jpg">
+</CENTER>
+<P>where r0 is the equilibrium bond distance, and rc the critical distance.
+The bond potential is zero for distances r > rc. The potential is -Umin
+at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2].
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>Umin (energy)
+<LI>r0 (distance)
+<LI>rc (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
+<A HREF = "bond_harmonic.html">bond_harmonic</A>,
+<A HREF = "bond_harmonicshift.html">bond_harmonicshift</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_hybrid.html b/doc/doc2/bond_hybrid.html
new file mode 100644
index 000000000..147776684
--- /dev/null
+++ b/doc/doc2/bond_hybrid.html
@@ -0,0 +1,79 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style hybrid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style hybrid style1 style2 ...
+</PRE>
+<UL><LI>style1,style2 = list of one or more bond styles
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style hybrid harmonic fene
+bond_coeff 1 harmonic 80.0 1.2
+bond_coeff 2* fene 30.0 1.5 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hybrid</I> style enables the use of multiple bond styles in one
+simulation. A bond style is assigned to each bond type. For example,
+bonds in a polymer flow (of bond type 1) could be computed with a
+<I>fene</I> potential and bonds in the wall boundary (of bond type 2) could
+be computed with a <I>harmonic</I> potential. The assignment of bond type
+to style is made via the <A HREF = "bond_coeff.html">bond_coeff</A> command or in
+the data file.
+</P>
+<P>In the bond_coeff commands, the name of a bond style must be added
+after the bond type, with the remaining coefficients being those
+appropriate to that style. In the example above, the 2 bond_coeff
+commands set bonds of bond type 1 to be computed with a <I>harmonic</I>
+potential with coefficients 80.0, 1.2 for K, r0. All other bond types
+(2-N) are computed with a <I>fene</I> potential with coefficients 30.0,
+1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
+</P>
+<P>If bond coefficients are specified in the data file read via the
+<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
+E.g. "harmonic" or "fene" must be added after the bond type, for each
+line in the "Bond Coeffs" section, e.g.
+</P>
+<PRE>Bond Coeffs
+</PRE>
+<PRE>1 harmonic 80.0 1.2
+2 fene 30.0 1.5 1.0 1.0
+...
+</PRE>
+<P>A bond style of <I>none</I> with no additional coefficients can be used in
+place of a bond style, either in a input script bond_coeff command or
+in the data file, if you desire to turn off interactions for specific
+bond types.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>Unlike other bond styles, the hybrid bond style does not store bond
+coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
+files</A>. Thus when retarting a simulation from a restart
+file, you need to re-specify bond_coeff commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_morse.html b/doc/doc2/bond_morse.html
new file mode 100644
index 000000000..38fd43957
--- /dev/null
+++ b/doc/doc2/bond_morse.html
@@ -0,0 +1,80 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style morse command
+</H3>
+<H3>bond_style morse/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style morse
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style morse
+bond_coeff 5 1.0 2.0 1.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>morse</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_morse.jpg">
+</CENTER>
+<P>where r0 is the equilibrium bond distance, alpha is a stiffness
+parameter, and D determines the depth of the potential well.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>D (energy)
+<LI>alpha (inverse distance)
+<LI>r0 (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_none.html b/doc/doc2/bond_none.html
new file mode 100644
index 000000000..ed59eca4c
--- /dev/null
+++ b/doc/doc2/bond_none.html
@@ -0,0 +1,34 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style none command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style none
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Using a bond style of none means bond forces are not computed, even if
+pairs of bonded atoms were listed in the data file read by the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_nonlinear.html b/doc/doc2/bond_nonlinear.html
new file mode 100644
index 000000000..f920a20e0
--- /dev/null
+++ b/doc/doc2/bond_nonlinear.html
@@ -0,0 +1,86 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style nonlinear command
+</H3>
+<H3>bond_style nonlinear/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style nonlinear
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style nonlinear
+bond_coeff 2 100.0 1.1 1.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>nonlinear</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_nonlinear.jpg">
+</CENTER>
+<P>to define an anharmonic spring <A HREF = "#Rector">(Rector)</A> of equilibrium
+length r0 and maximum extension lamda.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>epsilon (energy)
+<LI>r0 (distance)
+<LI>lamda (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Rector"></A>
+
+<P><B>(Rector)</B> Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
+</P>
+</HTML>
diff --git a/doc/doc2/bond_quartic.html b/doc/doc2/bond_quartic.html
new file mode 100644
index 000000000..403af0aa1
--- /dev/null
+++ b/doc/doc2/bond_quartic.html
@@ -0,0 +1,119 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style quartic command
+</H3>
+<H3>bond_style quartic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style quartic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style quartic
+bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>quartic</I> bond style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/bond_quartic.jpg">
+</CENTER>
+<P>to define a bond that can be broken as the simulation proceeds (e.g.
+due to a polymer being stretched). The sigma and epsilon used in the
+LJ portion of the formula are both set equal to 1.0 by LAMMPS.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy/distance^4)
+<LI>B1 (distance)
+<LI>B2 (distance)
+<LI>Rc (distance)
+<LI>U0 (energy)
+</UL>
+<P>This potential was constructed to mimic the FENE bond potential for
+coarse-grained polymer chains. When monomers with sigma = epsilon =
+1.0 are used, the following choice of parameters gives a quartic
+potential that looks nearly like the FENE potential: K = 1200, B1 =
+-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
+can be specified using the <A HREF = "bond_coeff.html">bond_coeff</A> command, but
+you will need to choose them carefully so they form a suitable bond
+potential.
+</P>
+<P>Rc is the cutoff length at which the bond potential goes smoothly to a
+local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
+the bond, which means two things. First, the bond potential is turned
+off by setting its type to 0, and is no longer computed. Second, a
+pairwise interaction between the two atoms is turned on, since they
+are no longer bonded.
+</P>
+<P>LAMMPS does the second task via a computational sleight-of-hand. It
+subtracts the pairwise interaction as part of the bond computation.
+When the bond breaks, the subtraction stops. For this to work, the
+pairwise interaction must always be computed by the
+<A HREF = "pair_style.html">pair_style</A> command, whether the bond is broken or
+not. This means that <A HREF = "special_bonds.html">special_bonds</A> must be set
+to 1,1,1, as indicated as a restriction below.
+</P>
+<P>Note that when bonds are dumped to a file via the <A HREF = "dump.html">dump
+local</A> command, bonds with type 0 are not included. The
+<A HREF = "delete_bonds.html">delete_bonds</A> command can also be used to query the
+status of broken bonds or permanently delete them, e.g.:
+</P>
+<PRE>delete_bonds all stats
+delete_bonds all bond 0 remove
+</PRE>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>The <I>quartic</I> style requires that <A HREF = "special_bonds.html">special_bonds</A>
+parameters be set to 1,1,1. Three- and four-body interactions (angle,
+dihedral, etc) cannot be used with <I>quartic</I> bonds.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_style.html b/doc/doc2/bond_style.html
new file mode 100644
index 000000000..135676886
--- /dev/null
+++ b/doc/doc2/bond_style.html
@@ -0,0 +1,109 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style style args
+</PRE>
+<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>fene</I> or <I>fene/expand</I> or <I>harmonic</I> or <I>morse</I> or <I>nonlinear</I> or <I>quartic</I>
+</UL>
+<PRE> args = none for any style except <I>hybrid</I>
+ <I>hybrid</I> args = list of one or more styles
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style harmonic
+bond_style fene
+bond_style hybrid harmonic fene
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the formula(s) LAMMPS uses to compute bond interactions between
+pairs of atoms. In LAMMPS, a bond differs from a pairwise
+interaction, which are set via the <A HREF = "pair_style.html">pair_style</A>
+command. Bonds are defined between specified pairs of atoms and
+remain in force for the duration of the simulation (unless the bond
+breaks which is possible in some bond potentials). The list of bonded
+atoms is read in by a <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> command from a data or restart file.
+By contrast, pair potentials are typically defined between all pairs
+of atoms within a cutoff distance and the set of active interactions
+changes over time.
+</P>
+<P>Hybrid models where bonds are computed using different bond potentials
+can be setup using the <I>hybrid</I> bond style.
+</P>
+<P>The coefficients associated with a bond style can be specified in a
+data or restart file or via the <A HREF = "bond_coeff.html">bond_coeff</A> command.
+</P>
+<P>All bond potentials store their coefficient data in binary restart
+files which means bond_style and <A HREF = "bond_coeff.html">bond_coeff</A> commands
+do not need to be re-specified in an input script that restarts a
+simulation. See the <A HREF = "read_restart.html">read_restart</A> command for
+details on how to do this. The one exception is that bond_style
+<I>hybrid</I> only stores the list of sub-styles in the restart file; bond
+coefficients need to be re-specified.
+</P>
+<P>IMPORTANT NOTE: When both a bond and pair style is defined, the
+<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 2 bonded atoms.
+</P>
+<P>In the formulas listed for each bond style, <I>r</I> is the distance
+between the 2 atoms in the bond.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command.
+</P>
+<P>Note that there are also additional bond styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
+<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
+</UL>
+<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
+<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
+<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
+<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
+<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
+<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
+<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
+<LI><A HREF = "bond_table.html">bond_style table</A> - tabulated by bond length
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Bond styles can only be set for atom styles that allow bonds to be
+defined.
+</P>
+<P>Most bond styles are part of the MOLECULE package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual bond potentials tell if it is part of a
+package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>bond_style none
+</P>
+</HTML>
diff --git a/doc/doc2/bond_table.html b/doc/doc2/bond_table.html
new file mode 100644
index 000000000..fb92e239f
--- /dev/null
+++ b/doc/doc2/bond_table.html
@@ -0,0 +1,160 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>bond_style table command
+</H3>
+<H3>bond_style table/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>bond_style table style N
+</PRE>
+<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
+<LI>N = use N values in table
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>bond_style table linear 1000
+bond_coeff 1 file.table ENTRY1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from bond
+potential and force values listed in a file(s) as a function of bond
+length. The files are read by the <A HREF = "bond_coeff.html">bond_coeff</A>
+command.
+</P>
+<P>The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and force values at each of <I>N</I>
+distances. During a simulation, these tables are used to interpolate
+energy and force values as needed. The interpolation is done in one
+of 2 styles: <I>linear</I> or <I>spline</I>.
+</P>
+<P>For the <I>linear</I> style, the bond length is used to find 2 surrounding
+table values from which an energy or force is computed by linear
+interpolation.
+</P>
+<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
+stored at each of the <I>N</I> values in the table. The bond length is
+used to find the appropriate set of coefficients which are used to
+evaluate a cubic polynomial which computes the energy or force.
+</P>
+<P>The following coefficients must be defined for each bond type via the
+<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above.
+</P>
+<UL><LI>filename
+<LI>keyword
+</UL>
+<P>The filename specifies a file containing tabulated energy and force
+values. The keyword specifies a section of the file. The format of
+this file is described below.
+</P>
+<HR>
+
+<P>The format of a tabulated file is as follows (without the
+parenthesized comments):
+</P>
+<PRE># Bond potential for harmonic (one or more comment or blank lines)
+</PRE>
+<PRE>HAM (keyword is the first text on line)
+N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
+ (blank line)
+1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
+2 0.01 324.6152 1324.9600
+...
+101 1.00 338.0000 -1352.0000
+</PRE>
+<P>A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+<A HREF = "bond_coeff.html">bond_coeff</A> command. The next line lists (in any
+order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+</P>
+<P>The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the <I>N</I>
+specified in the <A HREF = "bond_style.html">bond_style table</A> command. Let
+Ntable = <I>N</I> in the bond_style command, and Nfile = "N" in the
+tabulated file. What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points. It
+uses these to interpolate as needed to generate energy and force
+values at Ntable different points. The resulting tables of length
+Ntable are then used as described above, when computing energy and
+force for individual bond lengths. This means that if you want the
+interpolation tables of length Ntable to match exactly what is in the
+tabulated file (with effectively no preliminary interpolation), you
+should set Ntable = Nfile.
+</P>
+<P>The "FP" parameter is optional. If used, it is followed by two values
+fplo and fphi, which are the derivatives of the force at the innermost
+and outermost bond lengths. These values are needed by the spline
+construction routines. If not specified by the "FP" parameter, they
+are estimated (less accurately) by the first two and last two force
+values in the table.
+</P>
+<P>The "EQ" parameter is also optional. If used, it is followed by a the
+equilibrium bond length, which is used, for example, by the <A HREF = "fix_shake.html">fix
+shake</A> command. If not used, the equilibrium bond
+length is set to 0.0.
+</P>
+<P>Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+the bond length r (in distance units), the 3rd value is the energy (in
+energy units), and the 4th is the force (in force units). The bond
+lengths must range from a LO value to a HI value, and increase from
+one line to the next. If the actual bond length is ever smaller than
+the LO value or larger than the HI value, then the bond energy and
+force is evaluated as if the bond were the LO or HI length.
+</P>
+<P>Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This bond style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/boundary.html b/doc/doc2/boundary.html
new file mode 100644
index 000000000..a427194ee
--- /dev/null
+++ b/doc/doc2/boundary.html
@@ -0,0 +1,106 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>boundary command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>boundary x y z
+</PRE>
+<UL><LI>x,y,z = <I>p</I> or <I>s</I> or <I>f</I> or <I>m</I>, one or two letters
+
+<PRE> <I>p</I> is periodic
+ <I>f</I> is non-periodic and fixed
+ <I>s</I> is non-periodic and shrink-wrapped
+ <I>m</I> is non-periodic and shrink-wrapped with a minimum value
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>boundary p p f
+boundary p fs p
+boundary s f fm
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the style of boundaries for the global simulation box in each
+dimension. A single letter assigns the same style to both the lower
+and upper face of the box. Two letters assigns the first style to the
+lower face and the second style to the upper face. The initial size
+of the simulation box is set by the <A HREF = "read_data.html">read_data</A>,
+<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
+commands.
+</P>
+<P>The style <I>p</I> means the box is periodic, so that particles interact
+across the boundary, and they can exit one end of the box and re-enter
+the other end. A periodic dimension can change in size due to
+constant pressure boundary conditions or box deformation (see the <A HREF = "fix_nh.html">fix
+npt</A> and <A HREF = "fix_deform.html">fix deform</A> commands). The <I>p</I>
+style must be applied to both faces of a dimension.
+</P>
+<P>The styles <I>f</I>, <I>s</I>, and <I>m</I> mean the box is non-periodic, so that
+particles do not interact across the boundary and do not move from one
+side of the box to the other.
+</P>
+<P>For style <I>f</I>, the position of the face is fixed. If an atom moves
+outside the face it will be deleted on the next timestep that
+reneighboring occurs. This will typically generate an error unless
+you have set the <A HREF = "thermo_modify.html">thermo_modify lost</A> option to
+allow for lost atoms.
+</P>
+<P>For style <I>s</I>, the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move.
+</P>
+<P>For style <I>m</I>, shrink-wrapping occurs, but is bounded by the value
+specified in the data or restart file or set by the
+<A HREF = "create_box.html">create_box</A> command. For example, if the upper z
+face has a value of 50.0 in the data file, the face will always be
+positioned at 50.0 or above, even if the maximum z-extent of all the
+atoms becomes less than 50.0. This can be useful if you start a
+simulation with an empty box or if you wish to leave room on one side
+of the box, e.g. for atoms to evaporate from a surface.
+</P>
+<P>For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
+of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
+enforced with the tilt factor offset. If the 1st dimension is
+shrink-wrapped, then the shrink wrapping is applied to the tilted box
+face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
+and xhi faces of the box are planes tilting in the +y direction as y
+increases. These tilted planes are shrink-wrapped around the atoms to
+determine the x extent of the box.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command or
+<A HREF = "read_restart.html">read_restart</A> command. See the
+<A HREF = "change_box.html">change_box</A> command for how to change the simulation
+box boundaries after it has been defined.
+</P>
+<P>For 2d simulations, the z dimension must be periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P>See the <A HREF = "thermo_modify.html">thermo_modify</A> command for a discussion
+of lost atoms.
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>boundary p p p
+</PRE>
+</HTML>
diff --git a/doc/doc2/box.html b/doc/doc2/box.html
new file mode 100644
index 000000000..162087c7f
--- /dev/null
+++ b/doc/doc2/box.html
@@ -0,0 +1,69 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>box command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>box keyword value ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>tilt</I>
+
+<PRE> <I>tilt</I> value = <I>small</I> or <I>large</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>box tilt large
+box tilt small
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set attributes of the simulation box.
+</P>
+<P>For triclinic (non-orthogonal) simulation boxes, the <I>tilt</I> keyword
+allows simulation domains to be created with arbitrary tilt factors,
+e.g. via the <A HREF = "create_box.html">create_box</A> or
+<A HREF = "read_data.html">read_data</A> commands. Tilt factors determine how
+skewed the triclinic box is; see <A HREF = "Section_howto.html#howto_12">this
+section</A> of the manual for a discussion of
+triclinic boxes in LAMMPS.
+</P>
+<P>LAMMPS normally requires that no tilt factor can skew the box more
+than half the distance of the parallel box length, which is the 1st
+dimension in the tilt factor (x for xz). If <I>tilt</I> is set to
+<I>small</I>, which is the default, then an error will be
+generated if a box is created which exceeds this limit. If <I>tilt</I>
+is set to <I>large</I>, then no limit is enforced. You can create
+a box with any tilt factors you wish.
+</P>
+<P>Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command or
+<A HREF = "read_restart.html">read_restart</A> command.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default value is tilt = small.
+</P>
+</HTML>
diff --git a/doc/doc2/change_box.html b/doc/doc2/change_box.html
new file mode 100644
index 000000000..c40a3f588
--- /dev/null
+++ b/doc/doc2/change_box.html
@@ -0,0 +1,342 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>change_box command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>change_box group-ID parameter args ... keyword args ...
+</PRE>
+<UL><LI>group-ID = ID of group of atoms to (optionally) displace
+
+<LI>one or more parameter/arg pairs may be appended
+
+<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I> or <I>boundary</I> or <I>ortho</I> or <I>triclinic</I> or <I>set</I> or <I>remap</I>
+ <I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
+ style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>volume</I>
+ <I>final</I> values = lo hi
+ lo hi = box boundaries after displacement (distance units)
+ <I>delta</I> values = dlo dhi
+ dlo dhi = change in box boundaries after displacement (distance units)
+ <I>scale</I> values = factor
+ factor = multiplicative factor for change in box length after displacement
+ <I>volume</I> value = none = adjust this dim to preserve volume of system
+ <I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
+ style = <I>final</I> or <I>delta</I>
+ <I>final</I> value = tilt
+ tilt = tilt factor after displacement (distance units)
+ <I>delta</I> value = dtilt
+ dtilt = change in tilt factor after displacement (distance units)
+ <I>boundary</I> args = x y z
+ x,y,z = <I>p</I> or <I>s</I> or <I>f</I> or <I>m</I>, one or two letters
+ <I>p</I> is periodic
+ <I>f</I> is non-periodic and fixed
+ <I>s</I> is non-periodic and shrink-wrapped
+ <I>m</I> is non-periodic and shrink-wrapped with a minimum value
+ <I>ortho</I> args = none = change box to orthogonal
+ <I>triclinic</I> args = none = change box to triclinic
+ <I>set</I> args = none = store state of current box
+ <I>remap</I> args = none = remap atom coords from last saved state to current box
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>units</I>
+
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+ lattice = distances are defined in lattice units
+ box = distances are defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Change the volume and/or shape and/or boundary conditions for the
+simulation box. Orthogonal simulation boxes have 3 adjustable size
+parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
+6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
+them can be adjusted independently by this command. Thus it can be
+used to expand or contract a box, or to apply a shear strain to a
+non-orthogonal box. It can also be used to change the boundary
+conditions for the simulation box, similar to the
+<A HREF = "boundary.html">boundary</A> command.
+</P>
+<P>The size and shape of the initial simulation box are specified by the
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation.
+The size and shape may be altered by subsequent runs, e.g. by use of
+the <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_deform.html">fix deform</A> commands.
+The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
+<A HREF = "read_restart.html">read_restart</A> commands also determine whether the
+simulation box is orthogonal or triclinic and their doc pages explain
+the meaning of the xy,xz,yz tilt factors.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+</P>
+<P>The keywords used in this command are applied sequentially to the
+simulation box and the atoms in it, in the order specified.
+</P>
+<P>Before the sequence of keywords are invoked, the current box
+size/shape is stored, in case a <I>remap</I> keyword is used to map the
+atom coordinates from a previously stored box size/shape to the
+current one.
+</P>
+<P>After all the keywords have been processed, any shrink-wrap boundary
+conditions are invoked (see the <A HREF = "boundary.html">boundary</A> command)
+which may change simulation box boundaries, and atoms are migrated to
+new owning processors.
+</P>
+<P>IMPORTANT_NOTE: This means that you cannot use the change_box command
+to enlarge a shrink-wrapped box, e.g. to make room to insert more
+atoms via the <A HREF = "create_atoms.html">create_atoms</A> command, because the
+simulation box will be re-shrink-wrapped before the change_box command
+completes. Instead you could do something like this, assuming the
+simulation box is non-periodic and atoms extend from 0 to 20 in all
+dimensions:
+</P>
+<PRE>change_box all x final -10 20
+create_atoms 1 single -5 5 5 # this will fail to insert an atom
+</PRE>
+<PRE>change_box all x final -10 20 boundary f s s
+create_atoms 1 single -5 5 5
+change_box boundary s s s # this will work
+</PRE>
+<P>IMPORTANT NOTE: Unlike the earlier "displace_box" version of this
+command, atom remapping is NOT performed by default. This command
+allows remapping to be done in a more general way, exactly when you
+specify it (zero or more times) in the sequence of transformations.
+Thus if you do not use the <I>remap</I> keyword, atom coordinates will not
+be changed even if the box size/shape changes. If a uniformly
+strained state is desired, the <I>remap</I> keyword should be specified.
+</P>
+<P>IMPORTANT NOTE: It is possible to lose atoms with this command.
+E.g. by changing the box without remapping the atoms, and having atoms
+end up outside of non-periodic boundaries. It is also possible to
+alter bonds between atoms straddling a boundary in bad ways. E.g. by
+converting a boundary from periodic to non-periodic. It is also
+possible when remapping atoms to put them (nearly) on top of each
+other. E.g. by converting a boundary from non-periodic to periodic.
+All of these will typically lead to bad dynamics and/or generate error
+messages.
+</P>
+<P>IMPORTANT NOTE: The simulation box size/shape can be changed by
+arbitrarily large amounts by this command. This is not a problem,
+except that the mapping of processors to the simulation box is not
+changed from its initial 3d configuration; see the
+<A HREF = "processors.html">processors</A> command. Thus, if the box size/shape
+changes dramatically, the mapping of processors to the simulation box
+may not end up as optimal as the initial mapping attempted to be.
+</P>
+<P>IMPORTANT NOTE: Because the keywords used in this command are applied
+one at a time to the simulation box and the atoms in it, care must be
+taken with triclinic cells to avoid exceeding the limits on skew after
+each transformation in the sequence. If skew is exceeded before the
+final transformation this can be avoided by changing the order of the
+sequence, or breaking the transformation into two or more smaller
+transformations. For more information on the allowed limits for box
+skew see the discussion on triclinic boxes on <A HREF = "Section_howto.html#howto_12">this
+page</A>.
+</P>
+<HR>
+
+<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
+styles and values.
+</P>
+<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
+are specified. The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+</P>
+<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
+of a dimension are specified. The values can be in lattice or box
+distance units. See the discussion of the units keyword below.
+</P>
+<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
+of a dimension is specified. For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11. A
+factor less than 1.0 means compression.
+</P>
+<P>The <I>volume</I> style changes the specified dimension in such a way that
+the overall box volume remains constant with respect to the operation
+performed by the preceding keyword. The <I>volume</I> style can only be
+used following a keyword that changed the volume, which is any of the
+<I>x</I>, <I>y</I>, <I>z</I> keywords. If the preceding keyword "key" had a <I>volume</I>
+style, then both it and the current keyword apply to the keyword
+preceding "key". I.e. this sequence of keywords is allowed:
+</P>
+<PRE>change_box all x scale 1.1 y volume z volume
+</PRE>
+<P>The <I>volume</I> style changes the associated dimension so that the
+overall box volume is unchanged relative to its value before the
+preceding keyword was invoked.
+</P>
+<P>If the following command is used, then the z box length will shrink by
+the same 1.1 factor the x box length was increased by:
+</P>
+<PRE>change_box all x scale 1.1 z volume
+</PRE>
+<P>If the following command is used, then the y,z box lengths will each
+shrink by sqrt(1.1) to keep the volume constant. In this case, the
+y,z box lengths shrink so as to keep their relative aspect ratio
+constant:
+</P>
+<PRE>change_box all"x scale 1.1 y volume z volume
+</PRE>
+<P>If the following command is used, then the final box will be a factor
+of 10% larger in x and y, and a factor of 21% smaller in z, so as to
+keep the volume constant:
+</P>
+<PRE>change_box all x scale 1.1 z volume y scale 1.1 z volume
+</PRE>
+<P>IMPORTANT NOTE: For solids or liquids, when one dimension of the box
+is expanded, it may be physically undesirable to hold the other 2 box
+lengths constant since that implies a density change. For solids,
+adjusting the other dimensions via the <I>volume</I> style may make
+physical sense (just as for a liquid), but may not be correct for
+materials and potentials whose Poisson ratio is not 0.5.
+</P>
+<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
+compressed around its mid point.
+</P>
+<HR>
+
+<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
+styles and values. Note that changing the tilt factors of a triclinic
+box does not change its volume.
+</P>
+<P>For style <I>final</I>, the final tilt factor is specified. The value
+can be in lattice or box distance units. See the discussion of the
+units keyword below.
+</P>
+<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
+specified. The value can be in lattice or box distance units. See
+the discussion of the units keyword below.
+</P>
+<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
+tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
+than half the distance of the parallel box length. For example, if
+xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
+factor must be between -5 and 5. Similarly, both xz and yz must be
+between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
+limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent. Any tilt factor specified by this command
+must be within these limits.
+</P>
+<HR>
+
+<P>The <I>boundary</I> keyword takes arguments that have exactly the same
+meaning as they do for the <A HREF = "boundary.html">boundary</A> command. In each
+dimension, a single letter assigns the same style to both the lower
+and upper face of the box. Two letters assigns the first style to the
+lower face and the second style to the upper face.
+</P>
+<P>The style <I>p</I> means the box is periodic; the other styles mean
+non-periodic. For style <I>f</I>, the position of the face is fixed. For
+style <I>s</I>, the position of the face is set so as to encompass the
+atoms in that dimension (shrink-wrapping), no matter how far they
+move. For style <I>m</I>, shrink-wrapping occurs, but is bounded by the
+current box edge in that dimension, so that the box will become no
+smaller. See the <A HREF = "boundary.html">boundary</A> command for more
+explanation of these style options.
+</P>
+<P>Note that the "boundary" command itself can only be used before the
+simulation box is defined via a <A HREF = "read_data.html">read_data</A> or
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_restart.html">read_restart</A>
+command. This command allows the boundary conditions to be changed
+later in your input script. Also note that the
+<A HREF = "read_restart.html">read_restart</A> will change boundary conditions to
+match what is stored in the restart file. So if you wish to change
+them, you should use the change_box command after the read_restart
+command.
+</P>
+<HR>
+
+<P>The <I>ortho</I> and <I>triclinic</I> keywords convert the simulation box to be
+orthogonal or triclinic (non-orthongonal). See <A HREF = "Section_howto#howto_13">this
+section</A> for a discussion of how non-orthongal
+boxes are represented in LAMMPS.
+</P>
+<P>The simulation box is defined as either orthogonal or triclinic when
+it is created via the <A HREF = "create_box.html">create_box</A>,
+<A HREF = "read_data.html">read_data</A>, or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>These keywords allow you to toggle the existing simulation box from
+orthogonal to triclinic and vice versa. For example, an initial
+equilibration simulation can be run in an orthogonal box, the box can
+be toggled to triclinic, and then a <A HREF = "Section_howto.html#howto_13">non-equilibrium MD (NEMD)
+simulation</A> can be run with deformation
+via the <A HREF = "fix_deform.html">fix deform</A> command.
+</P>
+<P>If the simulation box is currently triclinic and has non-zero tilt in
+xy, yz, or xz, then it cannot be converted to an orthogonal box.
+</P>
+<HR>
+
+<P>The <I>set</I> keyword saves the current box size/shape. This can be
+useful if you wish to use the <I>remap</I> keyword more than once or if you
+wish it to be applied to an intermediate box size/shape in a sequence
+of keyword operations. Note that the box size/shape is saved before
+any of the keywords are processed, i.e. the box size/shape at the time
+the create_box command is encountered in the input script.
+</P>
+<P>The <I>remap</I> keyword remaps atom coordinates from the last saved box
+size/shape to the current box state. For example, if you stretch the
+box in the x dimension or tilt it in the xy plane via the <I>x</I> and <I>xy</I>
+keywords, then the <I>remap</I> commmand will dilate or tilt the atoms to
+conform to the new box size/shape, as if the atoms moved with the box
+as it deformed.
+</P>
+<P>Note that this operation is performed without regard to periodic
+boundaries. Also, any shrink-wrapping of non-periodic boundaries (see
+the <A HREF = "boundary.html">boundary</A> command) occurs after all keywords,
+including this one, have been processed.
+</P>
+<P>Only atoms in the specified group are remapped.
+</P>
+<HR>
+
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define various arguments. A <I>box</I> value selects standard distance
+units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
+units = real or metal. A <I>lattice</I> value means the distance units are
+in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
+been previously used to define the lattice spacing.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>If you use the <I>ortho</I> or <I>triclinic</I> keywords, then at the point in
+the input script when this command is issued, no <A HREF = "dump.html">dumps</A> can
+be active, nor can a <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_deform.html">fix
+deform</A> be active. This is because these commands
+test whether the simulation box is orthogonal when they are first
+issued. Note that these commands can be used in your script before a
+change_box command is issued, so long as an <A HREF = "undump.html">undump</A> or
+<A HREF = "unfix.html">unfix</A> command is also used to turn them off.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_deform.html">fix deform</A>, <A HREF = "boundary.html">boundary</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/clear.html b/doc/doc2/clear.html
new file mode 100644
index 000000000..ddb7f19a1
--- /dev/null
+++ b/doc/doc2/clear.html
@@ -0,0 +1,43 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>clear command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>clear
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>(commands for 1st simulation)
+clear
+(commands for 2nd simulation)
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command deletes all atoms, restores all settings to their default
+values, and frees all memory allocated by LAMMPS. Once a clear
+command has been executed, it is almost as if LAMMPS were starting
+over, with only the exceptions noted below. This command enables
+multiple jobs to be run sequentially from one input script.
+</P>
+<P>These settings are not affected by a clear command: the working
+directory (<A HREF = "shell.html">shell</A> command), log file status
+(<A HREF = "log.html">log</A> command), echo status (<A HREF = "echo.html">echo</A> command), and
+input script variables (<A HREF = "variable.html">variable</A> command).
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/comm_modify.html b/doc/doc2/comm_modify.html
new file mode 100644
index 000000000..db169c35f
--- /dev/null
+++ b/doc/doc2/comm_modify.html
@@ -0,0 +1,151 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>comm_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>comm_modify keyword value ...
+</PRE>
+<UL><LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>mode</I> or <I>cutoff</I> or <I>group</I> or <I>vel</I>
+
+<PRE> <I>mode</I> value = <I>single</I> or <I>multi</I> = communicate atoms within a single or multiple distances
+ <I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
+ <I>group</I> value = group-ID = only communicate atoms in the group
+ <I>vel</I> value = <I>yes</I> or <I>no</I> = do or do not communicate velocity info with ghost atoms
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>comm_modify mode multi
+comm_modify mode multi group solvent
+comm_modify vel yes
+comm_modify cutoff 5.0 vel yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets parameters that affect the inter-processor
+communication of atom information that occurs each timestep as
+coordinates and other properties are exchanged between neighboring
+processors and stored as properties of ghost atoms.
+</P>
+<P>IMPORTANT NOTE: These options apply to the currently defined comm
+style. When you specify a <A HREF = "comm_style.html">comm_style</A> command, all
+communication settings are restored to their default values, including
+those previously reset by a comm_modify command. Thus if your input
+script specifies a comm_style command, you should use the comm_modify
+command after it.
+</P>
+<P>The <I>mode</I> keyword determines whether a single or multiple cutoff
+distances are used to determine which atoms to communicate.
+</P>
+<P>The default mode is <I>single</I> which means each processor acquires
+information for ghost atoms that are within a single distance from its
+sub-domain. The distance is the maximum of the neighbor cutoff for
+all atom type pairs.
+</P>
+<P>For many systems this is an efficient algorithm, but for systems with
+widely varying cutoffs for different type pairs, the <I>multi</I> mode can
+be faster. In this case, each atom type is assigned its own distance
+cutoff for communication purposes, and fewer atoms will be
+communicated. See the <A HREF = "neighbor.html">neighbor multi</A> command for a
+neighbor list construction option that may also be beneficial for
+simulations of this kind.
+</P>
+<P>The <I>cutoff</I> keyword allows you to set a ghost cutoff distance, which
+is the distance from the borders of a processor's sub-domain at which
+ghost atoms are acquired from other processors. By default the ghost
+cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See
+the <A HREF = "neighbor.html">neighbor</A> command for more information about the
+skin distance. If the specified Rcut is greater than the neighbor
+cutoff, then extra ghost atoms will be acquired. If it is smaller,
+the ghost cutoff is set to the neighbor cutoff.
+</P>
+<P>These are simulation scenarios in which it may be useful or even
+necessary to set a ghost cutoff > neighbor cutoff:
+</P>
+<UL><LI>a single polymer chain with bond interactions, but no pairwise interactions
+<LI>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
+<LI>ghost atoms beyond the pairwise cutoff are needed for some computation
+</UL>
+<P>In the first scenario, a pairwise potential is not defined. Thus the
+pairwise neighbor cutoff will be 0.0. But ghost atoms are still
+needed for computing bond, angle, etc interactions between atoms on
+different processors, or when the interaction straddles a periodic
+boundary.
+</P>
+<P>The appropriate ghost cutoff depends on the <A HREF = "newton.html">newton bond</A>
+setting. For newton bond <I>off</I>, the distance needs to be the furthest
+distance between any two atoms in the bond, angle, etc. E.g. the
+distance between 1-4 atoms in a dihedral. For newton bond <I>on</I>, the
+distance between the central atom in the bond, angle, etc and any
+other atom is sufficient. E.g. the distance between 2-4 atoms in a
+dihedral.
+</P>
+<P>In the second scenario, a pairwise potential is defined, but its
+neighbor cutoff is not sufficiently long enough to enable bond, angle,
+etc terms to be computed. As in the previous scenario, an appropriate
+ghost cutoff should be set.
+</P>
+<P>In the last scenario, a <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> or
+<A HREF = "pair_style.html">pairwise potential</A> needs to calculate with ghost
+atoms beyond the normal pairwise cutoff for some computation it
+performs (e.g. locate neighbors of ghost atoms in a multibody pair
+potential). Setting the ghost cutoff appropriately can insure it will
+find the needed atoms.
+</P>
+<P>IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff
+long enough, and if there is only one processor in a periodic
+dimension (e.g. you are running in serial), then LAMMPS may "find" the
+atom it is looking for (e.g. the partner atom in a bond), that is on
+the far side of the simulation box, across a periodic boundary. This
+will typically lead to bad dynamics (i.e. the bond length is now the
+simulation box length). To detect if this is happening, see the
+<A HREF = "neigh_modify.html">neigh_modify cluster</A> command.
+</P>
+<P>The <I>group</I> keyword will limit communication to atoms in the specified
+group. This can be useful for models where no ghost atoms are needed
+for some kinds of particles. All atoms (not just those in the
+specified group) will still migrate to new processors as they move.
+The group specified with this option must also be specified via the
+<A HREF = "atom_modify.html">atom_modify first</A> command.
+</P>
+<P>The <I>vel</I> keyword enables velocity information to be communicated with
+ghost particles. Depending on the <A HREF = "atom_style.html">atom_style</A>,
+velocity info includes the translational velocity, angular velocity,
+and angular momentum of a particle. If the <I>vel</I> option is set to
+<I>yes</I>, then ghost atoms store these quantities; if <I>no</I> then they do
+not. The <I>yes</I> setting is needed by some pair styles which require
+the velocity state of both the I and J particles to compute a pairwise
+I,J interaction.
+</P>
+<P>Note that if the <A HREF = "fix_deform.html">fix deform</A> command is being used
+with its "remap v" option enabled, then the velocities for ghost atoms
+(in the fix deform group) mirrored across a periodic boundary will
+also include components due to any velocity shift that occurs across
+that boundary (e.g. due to dilation or shear).
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "neighbor.html">neighbor</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defauls are mode = single, group = all, cutoff = 0.0, vel =
+no. The cutoff default of 0.0 means that ghost cutoff = neighbor
+cutoff = pairwise force cutoff + neighbor skin.
+</P>
+</HTML>
diff --git a/doc/doc2/comm_style.html b/doc/doc2/comm_style.html
new file mode 100644
index 000000000..9e4c23a7f
--- /dev/null
+++ b/doc/doc2/comm_style.html
@@ -0,0 +1,68 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>comm_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>comm_style style
+</PRE>
+<UL><LI>style = <I>brick</I> or <I>tiled</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>comm_style brick
+comm_style tiled
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets the style of inter-processor communication of atom
+information that occurs each timestep as coordinates and other
+properties are exchanged between neighboring processors and stored as
+properties of ghost atoms.
+</P>
+<P>For the default <I>brick</I> style, the domain decomposition used by LAMMPS
+to partition the simulation box must be a regular 3d grid of bricks,
+one per processor. Each processor communicates with its 6 Cartesian
+neighbors in the grid to acquire information for nearby atoms.
+</P>
+<P>For the <I>tiled</I> style, a more general domain decomposition can be
+used, as triggered by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
+balance</A> commands. The simulation box can be
+partitioned into non-overlapping rectangular-shaped "tiles" or varying
+sizes and shapes. Again there is one tile per processor. To acquire
+information for nearby atoms, communication must now be done with a
+more complex pattern of neighboring processors.
+</P>
+<P>Note that this command does not actually define a partitoining of the
+simulation box (a domain decomposition), rather it determines what
+kinds of decompositions are allowed and the pattern of communication
+used to enable the decomposition. A decomposition is created when the
+simulation box is first created, via the <A HREF = "create_box.html">create_box</A>
+or <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands. For both the <I>brick</I> and <I>tiled</I> styles, the initial
+decomposition will be the same, as described by
+<A HREF = "create_box.html">create_box</A> and <A HREF = "processors.html">processors</A>
+commands. The decomposition can be changed via the
+<A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix_balance</A> commands.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "comm_modify.html">comm_modify</A>, <A HREF = "processors.html">processors</A>,
+<A HREF = "balance.html">balance</A>, <A HREF = "fix_balance.html">fix balance</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default style is brick.
+</P>
+</HTML>
diff --git a/doc/doc2/compute.html b/doc/doc2/compute.html
new file mode 100644
index 000000000..c6a3030e5
--- /dev/null
+++ b/doc/doc2/compute.html
@@ -0,0 +1,266 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID style args
+</PRE>
+<UL><LI>ID = user-assigned name for the computation
+<LI>group-ID = ID of the group of atoms to perform the computation on
+<LI>style = one of a list of possible style names (see below)
+<LI>args = arguments used by a particular style
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp
+compute newtemp flow temp/partial 1 1 0
+compute 3 all ke/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that will be performed on a group of atoms.
+Quantities calculated by a compute are instantaneous values, meaning
+they are calculated from information about atoms on the current
+timestep or iteration, though a compute may internally store some
+information about a previous state of the system. Defining a compute
+does not perform a computation. Instead computes are invoked by other
+LAMMPS commands as needed, e.g. to calculate a temperature needed for
+a thermostat fix or to generate thermodynamic or dump file output.
+See this <A HREF = "Section_howto.html#howto_15">howto section</A> for a summary of
+various LAMMPS output options, many of which involve computes.
+</P>
+<P>The ID of a compute can only contain alphanumeric characters and
+underscores.
+</P>
+<HR>
+
+<P>Computes calculate one of three styles of quantities: global,
+per-atom, or local. A global quantity is one or more system-wide
+values, e.g. the temperature of the system. A per-atom quantity is
+one or more values per atom, e.g. the kinetic energy of each atom.
+Per-atom values are set to 0.0 for atoms not in the specified compute
+group. Local quantities are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances. Computes that produce per-atom quantities have the
+word "atom" in their style, e.g. <I>ke/atom</I>. Computes that produce
+local quantities have the word "local" in their style,
+e.g. <I>bond/local</I>. Styles with neither "atom" or "local" in their
+style produce global quantities.
+</P>
+<P>Note that a single compute produces either global or per-atom or local
+quantities, but never more than one of these.
+</P>
+<P>Global, per-atom, and local quantities each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values. The
+doc page for each compute describes the style and kind of values it
+produces, e.g. a per-atom vector. Some computes produce more than one
+kind of a single style, e.g. a global scalar and a global vector.
+</P>
+<P>When a compute quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID is the ID of the compute:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
+<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
+<TR><TD >c_ID[I][J] </TD><TD > one element of array
+</TD></TR></TABLE></DIV>
+
+<P>In other words, using one bracket reduces the dimension of the
+quantity once (vector -> scalar, array -> vector). Using two brackets
+reduces the dimension twice (array -> scalar). Thus a command that
+uses scalar compute values as input can also process elements of a
+vector or array.
+</P>
+<P>Note that commands and <A HREF = "variable.html">variables</A> which use compute
+quantities typically do not allow for all kinds, e.g. a command may
+require a vector of values, not a scalar. This means there is no
+ambiguity about referring to a compute quantity as c_ID even if it
+produces, for example, both a scalar and vector. The doc pages for
+various commands explain the details.
+</P>
+<HR>
+
+<P>In LAMMPS, the values generated by a compute can be used in several
+ways:
+</P>
+<UL><LI>The results of computes that calculate a global temperature or
+pressure can be used by fixes that do thermostatting or barostatting
+or when atom velocities are created.
+
+<LI>Global values can be output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
+Or the values can be referenced in a <A HREF = "variable.html">variable equal</A> or
+<A HREF = "variable.html">variable atom</A> command.
+
+<LI>Per-atom values can be output via the <A HREF = "dump.html">dump custom</A> command
+or the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command. Or they can be
+time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command or
+reduced by the <A HREF = "compute_reduce.html">compute reduce</A> command. Or the
+per-atom values can be referenced in an <A HREF = "variable.html">atom-style
+variable</A>.
+
+<LI>Local values can be reduced by the <A HREF = "compute_reduce.html">compute
+reduce</A> command, or histogrammed by the <A HREF = "fix_ave_histo.html">fix
+ave/histo</A> command, or output by the <A HREF = "dump.html">dump
+local</A> command.
+</UL>
+<P>The results of computes that calculate global quantities can be either
+"intensive" or "extensive" values. Intensive means the value is
+independent of the number of atoms in the simulation,
+e.g. temperature. Extensive means the value scales with the number of
+atoms in the simulation, e.g. total rotational kinetic energy.
+<A HREF = "thermo_style.html">Thermodynamic output</A> will normalize extensive
+values by the number of atoms in the system, depending on the
+"thermo_modify norm" setting. It will not normalize intensive values.
+If a compute value is accessed in another way, e.g. by a
+<A HREF = "variable.html">variable</A>, you may want to know whether it is an
+intensive or extensive value. See the doc page for individual
+computes for further info.
+</P>
+<HR>
+
+<P>LAMMPS creates its own computes internally for thermodynamic output.
+Three computes are always created, named "thermo_temp",
+"thermo_press", and "thermo_pe", as if these commands had been invoked
+in the input script:
+</P>
+<PRE>compute thermo_temp all temp
+compute thermo_press all pressure thermo_temp
+compute thermo_pe all pe
+</PRE>
+<P>Additional computes for other quantities are created if the thermo
+style requires it. See the documentation for the
+<A HREF = "thermo_style.html">thermo_style</A> command.
+</P>
+<P>Fixes that calculate temperature or pressure, i.e. for thermostatting
+or barostatting, may also create computes. These are discussed in the
+documentation for specific <A HREF = "fix.html">fix</A> commands.
+</P>
+<P>In all these cases, the default computes LAMMPS creates can be
+replaced by computes defined by the user in the input script, as
+described by the <A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix
+modify</A> commands.
+</P>
+<P>Properties of either a default or user-defined compute can be modified
+via the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>Computes can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
+</P>
+<P>Code for new computes can be added to LAMMPS (see <A HREF = "Section_modify.html">this
+section</A> of the manual) and the results of their
+calculations accessed in the various ways described above.
+</P>
+<HR>
+
+<P>Each compute style has its own doc page which describes its arguments
+and what it does. Here is an alphabetic list of compute styles
+available in LAMMPS. They are also given in more compact form in the
+compute section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<P>There are also additional compute styles (not listed here) submitted
+by users which are included in the LAMMPS distribution. The list of
+these with links to the individual styles are given in the compute
+section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<P>There are also additional accelerated compute styles (note listed
+here) included in the LAMMPS distribution for faster performance on
+CPUs and GPUs. The list of these with links to the individual styles
+are given in the compute section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<UL><LI><A HREF = "compute_bond_local.html">angle/local</A> - theta and energy of each angle
+<LI><A HREF = "compute_body_local.html">body/local</A> - attributes of body sub-particles
+<LI><A HREF = "compute_bond_local.html">bond/local</A> - distance and energy of each bond
+<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
+<LI><A HREF = "compute_cluster_atom.html">cluster/atom</A> - cluster ID for each atom
+<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
+<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
+<LI><A HREF = "compute_com_chunk.html">com/chunk</A> - center-of-mass for each chunk
+<LI><A HREF = "compute_contact_atom.html">contact/atom</A> - contact count for each spherical particle
+<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
+<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
+<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
+<LI><A HREF = "compute_dilatation_atom.html">dilatation/atom</A> - Peridynamic dilatation for each atom
+<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
+<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
+<LI><A HREF = "compute_erotate_rigid.html">erotate/rigid</A> - rotational energy of rigid bodies
+<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
+<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere/atom</A> - rotational energy for each spherical particle
+<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
+<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
+<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
+<LI><A HREF = "compute_gyration_chunk.html">gyration/chunk</A> - radius of gyration for each chunk
+<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
+<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
+<LI><A HREF = "compute_inertia_chunk.html">inertia/chunk</A> - inertia tensor for each chunk
+<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
+<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
+<LI><A HREF = "compute_ke_rigid.html">ke/rigid</A> - translational kinetic energy of rigid bodies
+<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
+<LI><A HREF = "compute_msd_chunk.html">msd/chunk</A> - mean-squared displacement for each chunk
+<LI><A HREF = "compute_msd_nongauss.html">msd/nongauss</A> - MSD and non-Gaussian parameter of group of atoms
+<LI><A HREF = "compute_pair.html">pair</A> - values computed by a pair style
+<LI><A HREF = "compute_pair_local.html">pair/local</A> - distance/energy/force of each pairwise interaction
+<LI><A HREF = "compute_pe.html">pe</A> - potential energy
+<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
+<LI><A HREF = "compute_plasticity_atom.html">plasticity/atom</A> - Peridynamic plasticity for each atom
+<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
+<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
+<LI><A HREF = "compute_property_local.html">property/local</A> - convert local attributes to localvectors/arrays
+<LI><A HREF = "compute_property_chunk.html">property/chunk</A> - extract various per-chunk attributes
+<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
+<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
+<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
+<LI><A HREF = "compute_slice.html">slice</A> - extract values from global vector or array
+<LI><A HREF = "compute_sna.html">sna/atom</A> - calculate bispectrum coefficients for each atom
+<LI><A HREF = "compute_sna.html">snad/atom</A> - derivative of bispectrum coefficients for each atom
+<LI><A HREF = "compute_sna.html">snav/atom</A> - virial contribution from bispectrum coefficients for each atom
+<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
+<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
+<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
+<LI><A HREF = "compute_temp_chunk.html">temp/chunk</A> - temperature of each chunk
+<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
+<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
+<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
+<LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
+<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
+<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
+<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
+<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values
+<LI><A HREF = "compute_torque_chunk.html">torque/chunk</A> - torque applied on each chunk
+<LI><A HREF = "compute_vacf.html">vacf</A> - velocity-autocorrelation function of group of atoms
+<LI><A HREF = "compute_vcm_chunk.html">vcm/chunk</A> - velocity of center-of-mass for each chunk
+<LI><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> - Voronoi volume and neighbors for each atom
+</UL>
+<P>There are also additional compute styles submitted by users which are
+included in the LAMMPS distribution. The list of these with links to
+the individual styles are given in the compute section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<P>There are also additional accelerated compute styles included in the
+LAMMPS distribution for faster performance on CPUs and GPUs. The list
+of these with links to the individual styles are given in the pair
+section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
+ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
+<A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ackland_atom.html b/doc/doc2/compute_ackland_atom.html
new file mode 100644
index 000000000..d3445f2f5
--- /dev/null
+++ b/doc/doc2/compute_ackland_atom.html
@@ -0,0 +1,80 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ackland/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ackland/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ackland/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ackland/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Defines a computation that calculates the local lattice structure
+according to the formulation given in <A HREF = "#Ackland">(Ackland)</A>.
+</P>
+<P>In contrast to the <A HREF = "compute_centro_atom.html">centro-symmetry
+parameter</A> this method is stable against
+temperature boost, because it is based not on the distance between
+particles but the angles. Therefore statistical fluctuations are
+averaged out a little more. A comparison with the Common Neighbor
+Analysis metric is made in the paper.
+</P>
+<P>The result is a number which is mapped to the following different
+lattice structures:
+</P>
+<UL><LI>0 = UNKNOWN
+<LI>1 = BCC
+<LI>2 = FCC
+<LI>3 = HCP
+<LI>4 = ICO
+</UL>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each of
+which computes this quantity.-
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The per-atom vector values will be unitless since they are the
+integers defined above.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ackland"></A>
+
+<P><B>(Ackland)</B> Ackland, Jones, Phys Rev B, 73, 054104 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_angle_local.html b/doc/doc2/compute_angle_local.html
new file mode 100644
index 000000000..60ba03541
--- /dev/null
+++ b/doc/doc2/compute_angle_local.html
@@ -0,0 +1,87 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute angle/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID angle/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>angle/local = style name of this compute command
+
+<LI>one or more keywords may be appended
+
+<LI>keyword = <I>theta</I> or <I>eng</I>
+
+<PRE> <I>theta</I> = tabulate angles
+ <I>eng</I> = tabulate angle energies
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all angle/local theta
+compute 1 all angle/local eng theta
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual angle
+interactions. The number of datums generated, aggregated across all
+processors, equals the number of angles in the system, modified by the
+group parameter as explained below.
+</P>
+<P>The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their angles. An angle will only
+be included if all 3 atoms in the angle are in the specified compute
+group. Any angles that have been broken (see the
+<A HREF = "angle_style.html">angle_style</A> command) by setting their angle type to
+0 are not included. Angles that have been turned off (see the <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> commands) by
+setting their angle type negative are written into the file, but their
+energy will be 0.0.
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, angle output from the <A HREF = "compute_property_local.html">compute
+property/local</A> command can be combined
+with data from this command and output by the <A HREF = "dump.html">dump local</A>
+command in a consistent way.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of angles. If a single keyword is specified, a
+local vector is produced. If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords. The vector or array can be accessed by any command that
+uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The output for <I>theta</I> will be in degrees. The output for <I>eng</I> will
+be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
+property/local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_angmom_chunk.html b/doc/doc2/compute_angmom_chunk.html
new file mode 100644
index 000000000..2017422f1
--- /dev/null
+++ b/doc/doc2/compute_angmom_chunk.html
@@ -0,0 +1,94 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute angmom/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID angmom/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>angmom/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid angmom/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the angular momemtum of multiple
+chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the 3 components of the angular momentum
+vector for each chunk, due to the velocity/momentum of the individual
+atoms in the chunk around the center-of-mass of the chunk. The
+calculation includes all effects due to atoms passing thru periodic
+boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
+angular momentum in "unwrapped" form, by using the image flags
+associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
+for a discussion of "unwrapped" coordinates. See the Atoms section of
+the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute angmom/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all angmom/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+3 for the 3 xyz components of the angular momentum for each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The array values are "intensive". The array values will be in
+mass-velocity-distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable angmom() function</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_basal_atom.html b/doc/doc2/compute_basal_atom.html
new file mode 100644
index 000000000..8427c4e4f
--- /dev/null
+++ b/doc/doc2/compute_basal_atom.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute basal/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID basal/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>basal/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all basal/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Defines a computation that calculates the hexagonal close-packed "c"
+lattice vector for each atom in the group. It does this by
+calculating the normal unit vector to the basal plane for each atom.
+The results enable efficient identification and characterization of
+twins and grains in hexagonal close-packed structures.
+</P>
+<P>The output of the compute is thus the 3 components of a unit vector
+associdate with each atom. The components are set to 0.0 for
+atoms not in the group.
+</P>
+<P>Details of the calculation are given in <A HREF = "#Barrett">(Barrett)</A>.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each of
+which computes this quantity.
+</P>
+<P>An example input script that uses this compute is provided
+in examples/USER/misc/basal.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom array with 3 columns, which can be
+accessed by indices 1-3 by any command that uses per-atom values from
+a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The per-atom vector values are unitless since the 3 columns represent
+components of a unit vector.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The output of this compute will be meaningless unless the atoms are on
+(or near) hcp lattice sites, since the calculation assumes a
+well-defined basal plane.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>, <A HREF = "compute_ackland_atom.html">compute
+ackland/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Barrett"></A>
+
+<P><B>(Barrett)</B> Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_body_local.html b/doc/doc2/compute_body_local.html
new file mode 100644
index 000000000..7b8b74dfe
--- /dev/null
+++ b/doc/doc2/compute_body_local.html
@@ -0,0 +1,99 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute body/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID body/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>body/local = style name of this compute command
+
+<LI>one or more keywords may be appended
+
+<LI>keyword = <I>type</I> or <I>integer</I>
+
+<PRE> <I>type</I> = atom type of the body particle
+ <I>integer</I> = 1,2,3,etc = index of fields defined by body style
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all body/local type 1 2 3
+compute 1 all body/local 3 6
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual body
+sub-particles. The number of datums generated, aggregated across all
+processors, equals the number of body sub-particles plus the number of
+non-body particles in the system, modified by the group parameter as
+explained below. See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
+of the manual and the <A HREF = "body.html">body</A> doc page for more details on
+using body particles.
+</P>
+<P>The local data stored by this command is generated by looping over all
+the atoms. An atom will only be included if it is in the group. If
+the atom is a body particle, then its N sub-particles will be looped
+over, and it will contribute N datums to the count of datums. If it
+is not a body particle, it will contribute 1 datum.
+</P>
+<P>For both body particles and non-body particles, the <I>type</I> keyword
+will store the type of the atom.
+</P>
+<P>The <I>integer</I> keywords mean different things for body and non-body
+particles. If the atom is not a body particle, only its <I>x</I>, <I>y</I>, <I>z</I>
+coordinates can be referenced, using the <I>integer</I> keywords 1,2,3.
+Note that this means that if you want to access more fields than this
+for body particles, then you cannot include non-body particles in the
+group.
+</P>
+<P>For a body particle, the <I>integer</I> keywords refer to fields calculated
+by the body style for each sub-particle. The body style, as specified
+by the <A HREF = "atom_style.html">atom_style body</A>, determines how many fields
+exist and what they are. See the <A HREF = "body.html">body</A> doc page for
+details of the different styles.
+</P>
+<P>Here is an example of how to output body information using the <A HREF = "dump.html">dump
+local</A> command with this compute. If fields 1,2,3 for the
+body sub-particles are x,y,z coordinates, then the dump file will be
+formatted similar to the output of a <A HREF = "dump.html">dump atom or custom</A>
+command.
+</P>
+<PRE>compute 1 all body/local type 1 2 3
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of datums as described above. If a single keyword
+is specified, a local vector is produced. If two or more keywords are
+specified, a local array is produced where the number of columns = the
+number of keywords. The vector or array can be accessed by any
+command that uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The <A HREF = "units.html">units</A> for output values depend on the body style.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_bond_local.html b/doc/doc2/compute_bond_local.html
new file mode 100644
index 000000000..db281b4fa
--- /dev/null
+++ b/doc/doc2/compute_bond_local.html
@@ -0,0 +1,94 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute bond/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID bond/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>bond/local = style name of this compute command
+
+<LI>one or more keywords may be appended
+
+<LI>keyword = <I>dist</I> or <I>eng</I>
+
+<PRE> <I>dist</I> = bond distance
+ <I>eng</I> = bond energy
+ <I>force</I> = bond force
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all bond/local eng
+compute 1 all bond/local dist eng force
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual bond
+interactions. The number of datums generated, aggregated across all
+processors, equals the number of bonds in the system, modified
+by the group parameter as explained below.
+</P>
+<P>The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their bonds. A bond will only be
+included if both atoms in the bond are in the specified compute group.
+Any bonds that have been broken (see the <A HREF = "bond_style.html">bond_style</A>
+command) by setting their bond type to 0 are not included. Bonds that
+have been turned off (see the <A HREF = "fix_shake.html">fix shake</A> or
+<A HREF = "delete_bonds.html">delete_bonds</A> commands) by setting their bond type
+negative are written into the file, but their energy will be 0.0.
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, bond output from the <A HREF = "compute_property_local.html">compute
+property/local</A> command can be combined
+with data from this command and output by the <A HREF = "dump.html">dump local</A>
+command in a consistent way.
+</P>
+<P>Here is an example of how to do this:
+</P>
+<PRE>compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of bonds. If a single keyword is specified, a
+local vector is produced. If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords. The vector or array can be accessed by any command that
+uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The output for <I>dist</I> will be in distance <A HREF = "units.html">units</A>. The
+output for <I>eng</I> will be in energy <A HREF = "units.html">units</A>. The output for
+<I>force</I> will be in force <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
+property/local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_centro_atom.html b/doc/doc2/compute_centro_atom.html
new file mode 100644
index 000000000..6b3c03710
--- /dev/null
+++ b/doc/doc2/compute_centro_atom.html
@@ -0,0 +1,126 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute centro/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID centro/atom lattice
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>centro/atom = style name of this compute command
+<LI>lattice = <I>fcc</I> or <I>bcc</I> or N = # of neighbors per atom to include
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all centro/atom fcc
+</PRE>
+<PRE>compute 1 all centro/atom 8
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the centro-symmetry parameter for
+each atom in the group. In solid-state systems the centro-symmetry
+parameter is a useful measure of the local lattice disorder around an
+atom and can be used to characterize whether the atom is part of a
+perfect lattice, a local defect (e.g. a dislocation or stacking
+fault), or at a surface.
+</P>
+<P>The value of the centro-symmetry parameter will be 0.0 for atoms not
+in the specified compute group.
+</P>
+<P>This parameter is computed using the following formula from
+<A HREF = "#Kelchner">(Kelchner)</A>
+</P>
+<CENTER><IMG SRC = "Eqs/centro_symmetry.jpg">
+</CENTER>
+<P>where the <I>N</I> nearest neighbors or each atom are identified and Ri and
+Ri+N/2 are vectors from the central atom to a particular pair of
+nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that
+can contribute to this formula. The quantity in the sum is computed
+for each, and the N/2 smallest are used. This will typically be for
+pairs of atoms in symmetrically opposite positions with respect to the
+central atom; hence the i+N/2 notation.
+</P>
+<P><I>N</I> is an input parameter, which should be set to correspond to the
+number of nearest neighbors in the underlying lattice of atoms. If
+the keyword <I>fcc</I> or <I>bcc</I> is used, <I>N</I> is set to 12 and 8
+respectively. More generally, <I>N</I> can be set to a positive, even
+integer.
+</P>
+<P>For an atom on a lattice site, surrounded by atoms on a perfect
+lattice, the centro-symmetry parameter will be 0. It will be near 0
+for small thermal perturbations of a perfect lattice. If a point
+defect exists, the symmetry is broken, and the parameter will be a
+larger positive value. An atom at a surface will have a large
+positive parameter. If the atom does not have <I>N</I> neighbors (within
+the potential cutoff), then its centro-symmetry parameter is set to
+0.0.
+</P>
+<P>Only atoms within the cutoff of the pairwise neighbor list are
+considered as possible neighbors. Atoms not in the compute group are
+included in the <I>N</I> neighbors used in this calculation.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+<I>centro/atom</I> style.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitless values >= 0.0. Their
+magnitude depends on the lattice style due to the number of
+contibuting neighbor pairs in the summation in the formula above. And
+it depends on the local defects surrounding the central atom, as
+described above.
+</P>
+<P>Here are typical centro-symmetry values, from a a nanoindentation
+simulation into gold (FCC). These were provided by Jon Zimmerman
+(Sandia):
+</P>
+<PRE>Bulk lattice = 0
+Dislocation core ~ 1.0 (0.5 to 1.25)
+Stacking faults ~ 5.0 (4.0 to 6.0)
+Free surface ~ 23.0
+</PRE>
+<P>These values are *not* normalized by the square of the lattice
+parameter. If they were, normalized values would be:
+</P>
+<PRE>Bulk lattice = 0
+Dislocation core ~ 0.06 (0.03 to 0.075)
+Stacking faults ~ 0.3 (0.24 to 0.36)
+Free surface ~ 1.38
+</PRE>
+<P>For BCC materials, the values for dislocation cores and free surfaces
+would be somewhat different, due to their being only 8 neighbors instead
+of 12.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_cna_atom.html">compute cna/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Kelchner"></A>
+
+<P><B>(Kelchner)</B> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_chunk_atom.html b/doc/doc2/compute_chunk_atom.html
new file mode 100644
index 000000000..24d4598c6
--- /dev/null
+++ b/doc/doc2/compute_chunk_atom.html
@@ -0,0 +1,568 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute chunk/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID chunk/atom style args keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>chunk/atom = style name of this compute command
+
+<PRE>style = <I>bin/1d</I> or <I>bin/2d</I> or <I>bin/3d</I> or <I>type</I> or <I>molecule</I> or <I>compute/fix/variable</I>
+ <I>bin/1d</I> args = dim origin delta
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
+ delta = thickness of spatial bins in dim (distance units)
+ <I>bin/2d</I> args = dim origin delta dim origin delta
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
+ delta = thickness of spatial bins in dim (distance units)
+ <I>bin/3d</I> args = dim origin delta dim origin delta dim origin delta
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
+ delta = thickness of spatial bins in dim (distance units)
+ <I>type</I> args = none
+ <I>molecule</I> args = none
+ <I>compute/fix/variable</I> = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+<LI>zero or more keyword/values pairs may be appended
+
+<LI>keyword = <I>region</I> or <I>nchunk</I> or <I>static</I> or <I>compress</I> or <I>bound</I> or <I>discard</I> or <I>units</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to be part of a chunk
+ <I>nchunk</I> value = <I>once</I> or <I>every</I>
+ once = only compute the number of chunks once
+ every = re-compute the number of chunks whenever invoked
+ <I>limit</I> values = 0 or Nc max or Nc exact
+ 0 = no limit on the number of chunks
+ Nc max = limit number of chunks to be <= Nc
+ Nc exact = set number of chunks to exactly Nc
+ <I>ids</I> value = <I>once</I> or <I>nfreq</I> or <I>every</I>
+ once = assign chunk IDs to atoms only once, they persist thereafter
+ nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> which sets Nfreq)
+ every = assign chunk IDs to atoms whenever invoked
+ <I>compress</I> value = <I>yes</I> or <I>no</I>
+ yes = compress chunk IDs to eliminate IDs with no atoms
+ no = do not compress chunk IDs even if some IDs have no atoms
+ <I>discard</I> value = <I>yes</I> or <I>no</I> or <I>mixed</I>
+ yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
+ no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
+ mixed = keep or discard such atoms according to spatial binning rule
+ <I>bound</I> values = x/y/z lo hi
+ x/y/z = <I>x</I> or <I>y</I> or <I>z</I> to bound sptial bins in this dimension
+ lo = <I>lower</I> or coordinate value (distance units)
+ hi = <I>upper</I> or coordinate value (distance units)
+ <I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all chunk/atom type
+compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
+compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
+compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates an integer chunk ID from 1 to
+Nchunk for each atom in the group. Values of chunk IDs are determined
+by the <I>style</I> of chunk, which can be based on atom type or molecule
+ID or spatial binning or a per-atom property or value calculated by
+another <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">atom-style
+variable</A>. Per-atom chunk IDs can be used by other
+computes with "chunk" in their style name, such as <A HREF = "compute_com_chunk.html">compute
+com/chunk</A> or <A HREF = "compute_msd_chunk.html">compute
+msd/chunk</A>. Or they can be used by the <A HREF = "fix_ave_chunk.html">fix
+ave/chunk</A> command to sum and time average a
+variety of per-atom properties over the atoms in each chunk. Or they
+can simply be accessed by any command that uses per-atom values from a
+compute as input, as discussed in <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A>.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_23">Section_howto 23</A> for an overview of
+how this compute can be used with a variety of other commands to
+tabulate properties of a simulation. The howto section gives several
+examples of input script commands that can be used to calculate
+interesting properties.
+</P>
+<P>Conceptually it is important to realize that this compute does two
+simple things. First, it sets the value of <I>Nchunk</I> = the number of
+chunks, which can be a constant value or change over time. Second, it
+assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1
+to <I>Nchunk</I> inclusive; some chunks may have no atoms assigned to them.
+Atoms that do not belong to any chunk are assigned a value of 0. Note
+that the two operations are not always performed together. For
+example, spatial bins can be setup once (which sets <I>Nchunk</I>), and
+atoms assigned to those bins many times thereafter (setting their
+chunk IDs).
+</P>
+<P>All other commands in LAMMPS that use chunk IDs assume there are
+<I>Nchunk</I> number of chunks, and that every atom is assigned to one of
+those chunks, or not assigned to any chunk.
+</P>
+<P>There are many options for specifying for how and when <I>Nchunk</I> is
+calculated, and how and when chunk IDs are assigned to atoms. The
+details depend on the chunk <I>style</I> and its <I>args</I>, as well as
+optional keyword settings. They can also depend on whether a <A HREF = "fix_ave_chunk.html">fix
+ave/chunk</A> command is using this compute, since
+that command requires <I>Nchunk</I> to remain static across windows of
+timesteps it specifies, while it accumulates per-chunk averages.
+</P>
+<P>The details are described below.
+</P>
+<HR>
+
+<HR>
+
+<P>The different chunk styles operate as follows. For each style, how it
+calculates <I>Nchunk</I> and assigns chunk IDs to atoms is explained. Note
+that using the optional keywords can change both of those actions, as
+described further below where the keywords are discussed.
+</P>
+<HR>
+
+<P>The <I>binning</I> styles perform a spatial binning of atoms, and assign an
+atom the chunk ID corresponding to the bin number it is in. <I>Nchunk</I>
+is set to the number of bins, which can change if the simulation box
+size changes.
+</P>
+<P>The <I>bin/1d</I>, <I>bin/2d</I>, and <I>bin/3d</I> styles define bins as 1d layers
+(slabs), 2d pencils, or 3d boxes. The <I>dim</I>, <I>origin</I>, and <I>delta</I>
+settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is
+no restriction on specifying dim = x before dim = y or z, or dim = y
+before dim = z. Bins in a particular <I>dim</I> have a bin size in that
+dimension given by <I>delta</I>. In each dimension, bins are defined
+relative to a specified <I>origin</I>, which may be the lower/upper edge of
+the simulation box (in that dimension), or its center point, or a
+specified coordinate value. Starting at the origin, sufficient bins
+are created in both directions to completely span the simulation box
+or the bounds specified by the optional <I>bounds</I> keyword.
+</P>
+<P>For orthogonal simulation boxes, the bins are layers, pencils, or
+boxes aligned with the xyz coordinate axes. For triclinic
+(non-orthogonal) simulation boxes, the bin faces are parallel to the
+tilted faces of the simulation box. See <A HREF = "Section_howto.html#howto_12">this
+section</A> of the manual for a discussion of
+the geometry of triclinic boxes in LAMMPS. As described there, a
+tilted simulation box has edge vectors a,b,c. In that nomenclature,
+bins in the x dimension have faces with normals in the "b" cross "c"
+direction. Bins in y have faces normal to the "a" cross "c"
+direction. And bins in z have faces normal to the "a" cross "b"
+direction. Note that in order to define the size and position of
+these bins in an unambiguous fashion, the <I>units</I> option must be set
+to <I>reduced</I> when using a triclinic simulation box, as noted below.
+</P>
+<P>The meaning of <I>origin</I> and <I>delta</I> for triclinic boxes is as follows.
+Consider a triclinic box with bins that are 1d layers or slabs in the
+x dimension. No matter how the box is tilted, an <I>origin</I> of 0.0
+means start layers at the lower "b" cross "c" plane of the simulation
+box and an <I>origin</I> of 1.0 means to start layers at the upper "b"
+cross "c" face of the box. A <I>delta</I> value of 0.1 in <I>reduced</I> units
+means there will be 10 layers from 0.0 to 1.0, regardless of the
+current size or shape of the simulation box.
+</P>
+<P>The created bins (and hence the chunk IDs) are numbered consecutively
+from 1 to the number of bins = <I>Nchunk</I>. For 2d and 3d bins, the
+numbering varies most rapidly in the first dimension (which could be
+x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
+3rd dimension.
+</P>
+<P>Each time this compute is invoked, each atom is mapped to a bin based
+on its current position. Note that between reneighboring timesteps,
+atoms can move outside the current simulation box. If the box is
+periodic (in that dimension) the atom is remapping into the periodic
+box for purposes of binning. If the box in not periodic, the atom may
+have moved outside the bounds of all bins. If an atom is not inside
+any bin, the <I>discard</I> keyword is used to determine how a chunk ID is
+assigned to the atom.
+</P>
+<HR>
+
+<P>The <I>type</I> style uses the atom type as the chunk ID. <I>Nchunk</I> is set
+to the number of atom types defined for the simulation, e.g. via the
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> commands.
+</P>
+<HR>
+
+<P>The <I>molecule</I> style uses the molecule ID of each atom as its chunk
+ID. <I>Nchunk</I> is set to the largest chunk ID. Note that this excludes
+molecule IDs for atoms which are not in the specified group or
+optional region.
+</P>
+<P>There is no requirement that all atoms in a particular molecule are
+assigned the same chunk ID (zero or non-zero), though you probably
+want that to be the case, if you wish to compute a per-molecule
+property. LAMMPS will issue a warning if that is not the case, but
+only the first time that <I>Nchunk</I> is calculated.
+</P>
+<P>Note that atoms with a molecule ID = 0, which may be non-molecular
+solvent atoms, have an out-of-range chunk ID. These atoms are
+discarded (not assigned to any chunk) or assigned to <I>Nchunk</I>,
+depending on the value of the <I>discard</I> keyword.
+</P>
+<HR>
+
+<P>The <I>compute/fix/variable</I> styles set the chunk ID of each atom based
+on a quantity calculated and stored by a compute, fix, or variable.
+In each case, it must be a per-atom quantity. In each case the
+referenced floating point values are converted to an integer chunk ID
+as follows. The floating point value is truncated (rounded down) to
+an integer value. If the integer value is <= 0, then a chunk ID of 0
+is assigned to the atom. If the integer value is > 0, it becomes the
+chunk ID to the atom. <I>Nchunk</I> is set to the largest chunk ID. Note
+that this excludes atoms which are not in the specified group or
+optional region.
+</P>
+<P>If the style begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used. Users can also write code for
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If the style begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used. Note that some fixes only produce
+their values on certain timesteps, which must be compatible with the
+timestep on which this compute accesses the fix, else an error
+results. Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add
+them to LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name for an <I>atom</I> or
+<I>atomfile</I> style <A HREF = "variable.html">variable</A> must follow which has been
+previously defined in the input script. Variables of style <I>atom</I> can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to
+treat as a chunk ID.
+</P>
+<HR>
+
+<HR>
+
+<P>Normally, <I>Nchunk</I> = the number of chunks, is re-calculated every time
+this fix is invoked, though the value may or may not change. As
+explained below, the <I>nchunk</I> keyword can be set to <I>once</I> which means
+<I>Nchunk</I> will never change.
+</P>
+<P>If a <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> command uses this compute, it
+can also turn off the re-calculation of <I>Nchunk</I> for one or more
+windows of timesteps. The extent of the windows, during which Nchunk
+is held constant, are determined by the <I>Nevery</I>, <I>Nrepeat</I>, <I>Nfreq</I>
+values and the <I>ave</I> keyword setting that are used by the <A HREF = "fix_ave_chunk.html">fix
+ave/chunk</A> command.
+</P>
+<P>Specifically, if <I>ave</I> = <I>one</I>, then for each span of <I>Nfreq</I>
+timesteps, <I>Nchunk</I> is held constant between the first timestep when
+averaging is done (within the Nfreq-length window), and the last
+timestep when averaging is done (multiple of Nfreq). If <I>ave</I> =
+<I>running</I> or <I>window</I>, then <I>Nchunk</I> is held constant forever,
+starting on the first timestep when the <A HREF = "fix_ave_chunk.html">fix
+ave/chunk</A> command invokes this compute.
+</P>
+<P>Note that multiple <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> commands can use
+the same compute chunk/atom compute. However, the time windows they
+induce for holding <I>Nchunk</I> constant must be identical, else an error
+will be generated.
+</P>
+<HR>
+
+<HR>
+
+<P>The various optional keywords operate as follows. Note that some of
+them function differently or are ignored by different chunk styles.
+Some of them also have different default values, depending on
+the chunk style, as listed below.
+</P>
+<P>The <I>region</I> keyword applies to all chunk styles. If used, an atom
+must be in both the specified group and the specified geometric
+<A HREF = "region.html">region</A> to be assigned to a chunk.
+</P>
+<HR>
+
+<P>The <I>nchunk</I> keyword applies to all chunk styles. It specifies how
+often <I>Nchunk</I> is recalculated, which in turn can affect the chunk IDs
+assigned to individual atoms.
+</P>
+<P>If <I>nchunk</I> is set to <I>once</I>, then <I>Nchunk</I> is only calculated once,
+the first time this compute is invoked. If <I>nchunk</I> is set to
+<I>every</I>, then <I>Nchunk</I> is re-calculated every time the compute is
+invoked. Note that, as described above, the use of this compute
+by the <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> command can override
+the <I>every</I> setting.
+</P>
+<P>The default values for <I>nchunk</I> are listed below and depend on the
+chunk style and other system and keyword settings. They attempt to
+represent typical use cases for the various chunk styles. The
+<I>nchunk</I> value can always be set explicitly if desired.
+</P>
+<HR>
+
+<P>The <I>limit</I> keyword can be used to limit the calculated value of
+<I>Nchunk</I> = the number of chunks. The limit is applied each time
+<I>Nchunk</I> is calculated, which also limits the chunk IDs assigned to
+any atom. The <I>limit</I> keyword is used by all chunk styles except the
+<I>binning</I> styles, which ignore it. This is because the number of bins
+can be tailored using the <I>bound</I> keyword (described below) which
+effectively limits the size of <I>Nchunk</I>.
+</P>
+<P>If <I>limit</I> is set to <I>Nc</I> = 0, then no limit is imposed on <I>Nchunk</I>,
+though the <I>compress</I> keyword can still be used to reduce <I>Nchunk</I>, as
+described below.
+</P>
+<P>If <I>Nc</I> > 0, then the effect of the <I>limit</I> keyword depends on whether
+the <I>compress</I> keyword is also used with a setting of <I>yes</I>, and
+whether the <I>compress</I> keyword is specified before the <I>limit</I> keyword
+or after.
+</P>
+<P>In all cases, <I>Nchunk</I> is first calculated in the usual way for each
+chunk style, as described above.
+</P>
+<P>First, here is what occurs if <I>compress yes</I> is not set. If <I>limit</I>
+is set to <I>Nc max</I>, then <I>Nchunk</I> is reset to the smaller of <I>Nchunk</I>
+and <I>Nc</I>. If <I>limit</I> is set to <I>Nc exact</I>, then <I>Nchunk</I> is reset to
+<I>Nc</I>, whether the original <I>Nchunk</I> was larger or smaller than <I>Nc</I>.
+If <I>Nchunk</I> shrank due to the <I>limit</I> setting, then atom chunk IDs >
+<I>Nchunk</I> will be reset to 0 or <I>Nchunk</I>, depending on the setting of
+the <I>discard</I> keyword. If <I>Nchunk</I> grew, there will simply be some
+chunks with no atoms assigned to them.
+</P>
+<P>If <I>compress yes</I> is set, and the <I>compress</I> keyword comes before the
+<I>limit</I> keyword, the compression operation is performed first, as
+described below, which resets <I>Nchunk</I>. The <I>limit</I> keyword is then
+applied to the new <I>Nchunk</I> value, exactly as described in the
+preceeding paragraph. Note that in this case, all atoms will end up
+with chunk IDs <= <I>Nc</I>, but their original values (e.g. molecule ID or
+compute/fix/variable value) may have been > <I>Nc</I>, because of the
+compression operation.
+</P>
+<P>If <I>compress yes</I> is set, and the <I>compress</I> keyword comes after the
+<I>limit</I> keyword, then the <I>limit</I> value of <I>Nc</I> is applied first to
+the uncompressed value of <I>Nchunk</I>, but only if <I>Nc</I> < <I>Nchunk</I>
+(whether <I>Nc max</I> or <I>Nc exact</I> is used). This effectively means all
+atoms with chunk IDs > <I>Nc</I> have their chunk IDs reset to 0 or <I>Nc</I>,
+depending on the setting of the <I>discard</I> keyword. The compression
+operation is then performed, which may shrink <I>Nchunk</I> further. If
+the new <I>Nchunk</I> < <I>Nc</I> and <I>limit</I> = <I>Nc exact</I> is specified, then
+<I>Nchunk</I> is reset to <I>Nc</I>, which results in extra chunks with no atoms
+assigned to them. Note that in this case, all atoms will end up with
+chunk IDs <= <I>Nc</I>, and their original values (e.g. molecule ID or
+compute/fix/variable value) will also have been <= <I>Nc</I>.
+</P>
+<HR>
+
+<P>The <I>ids</I> keyword applies to all chunk styles. If the setting is
+<I>once</I> then the chunk IDs assigned to atoms the first time this
+compute is invoked will be permanent, and never be re-computed.
+</P>
+<P>If the setting is <I>nfreq</I> and if a <A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
+command is using this compute, then in each of the <I>Nchunk</I> = constant
+time windows (discussed above), the chunk ID's assigned to atoms on
+the first step of the time window will persist until the end of the
+time window.
+</P>
+<P>If the setting is <I>every</I>, which is the default, then chunk IDs are
+re-calculated on any timestep this compute is invoked.
+</P>
+<P>IMPORTANT NOTE: If you want the persistent chunk-IDs calculated by
+this compute to be continuous when running from a <A HREF = "read_restart.html">restart
+file</A>, then you should use the same ID for this
+compute, as in the original run. This is so that the fix this compute
+creates to store per-atom quantities will also have the same ID, and
+thus be initialized correctly with chunk IDs from the restart file.
+</P>
+<HR>
+
+<P>The <I>compress</I> keyword applies to all chunk styles and affects how
+<I>Nchunk</I> is calculated, which in turn affects the chunk IDs assigned
+to each atom. It is useful for converting a "sparse" set of chunk IDs
+(with many IDs that have no atoms assigned to them), into a "dense"
+set of IDs, where every chunk has one or more atoms assigned to it.
+</P>
+<P>Two possible use cases are as follows. If a large simulation box is
+mostly empty space, then the <I>binning</I> style may produce many bins
+with no atoms. If <I>compress</I> is set to <I>yes</I>, only bins with atoms
+will be contribute to <I>Nchunk</I>. Likewise, the <I>molecule</I> or
+<I>compute/fix/variable</I> styles may produce large <I>Nchunk</I> values. For
+example, the <A HREF = "compute_cluster_atom.html">compute cluster/atom</A> command
+assigns every atom an atom ID for one of the atoms it is clustered
+with. For a million-atom system with 5 clusters, there would only be
+5 unique chunk IDs, but the largest chunk ID might be 1 million,
+resulting in <I>Nchunk</I> = 1 million. If <I>compress</I> is set to <I>yes</I>,
+<I>Nchunk</I> will be reset to 5.
+</P>
+<P>If <I>compress</I> is set to <I>no</I>, which is the default, no compression is
+done. If it is set to <I>yes</I>, all chunk IDs with no atoms are removed
+from the list of chunk IDs, and the list is sorted. The remaining
+chunk IDs are renumbered from 1 to <I>Nchunk</I> where <I>Nchunk</I> is the new
+length of the list. The chunk IDs assigned to each atom reflect
+the new renumbering from 1 to <I>Nchunk</I>.
+</P>
+<P>The original chunk IDs (before renumbering) can be accessed by the
+<A HREF = "compute_property_chunk.html">compute property/chunk</A> command and its
+<I>id</I> keyword, or by the <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> command
+which outputs the original IDs as one of the columns in its global
+output array. For example, using the "compute cluster/atom" command
+discussed above, the original 5 unique chunk IDs might be atom IDs
+(27,4982,58374,857838,1000000). After compresion, these will be
+renumbered to (1,2,3,4,5). The original values (27,...,1000000) can
+be output to a file by the <A HREF = "fix_ave_chunk.html">fix ave/chunk</A> command,
+or by using the <A HREF = "fix_ave_time.html">fix ave/time</A> command in
+conjunction with the <A HREF = "compute_property_chunk.html">compute
+property/chunk</A> command.
+</P>
+<P>IMPORTANT NOTE: The compression operation requires global
+communication across all processors to share their chunk ID values.
+It can require large memory on every processor to store them, even
+after they are compressed, if there are are a large number of unique
+chunk IDs with atoms assigned to them. It uses a STL map to find
+unique chunk IDs and store them in sorted order. Each time an atom is
+assigned a compressed chunk ID, it must access the STL map. All of
+this means that compression can be expensive, both in memory and CPU
+time. The use of the <I>limit</I> keyword in conjunction with the
+<I>compress</I> keyword can affect these costs, depending on which keyword
+is used first. So use this option with care.
+</P>
+<HR>
+
+<P>The <I>discard</I> keyword applies to all chunk styles. It affects what
+chunk IDs are assigned to atoms that do not match one of the valid
+chunk IDs from 1 to <I>Nchunk</I>. Note that it does not apply to atoms
+that are not in the specified group or optionally specified region.
+Those atoms are always assigned a chunk ID = 0.
+</P>
+<P>If the calculated chunk ID for an atom is not within the range 1 to
+<I>Nchunk</I> then it is a "discard" atom. Note that <I>Nchunk</I> may have
+been shrunk by the <I>limit</I> keyword. Or the <I>compress</I> keyword may
+have eliminated chunk IDs that were valid before the compression took
+place, and are now not in the compressed list. Also note that for the
+<I>molecule</I> chunk style, if new molecules are added to the system,
+their chunk IDs may exceed a previously calculated <I>Nchunk</I>.
+Likewise, evaluation of a compute/fix/variable on a later timestep may
+return chunk IDs that are invalid for the previously calculated
+<I>Nchunk</I>.
+</P>
+<P>All the chunk styles except the <I>binning</I> styles, must use <I>discard</I>
+set to either <I>yes</I> or <I>no</I>. If <I>discard</I> is set to <I>yes</I>, which is
+the default, then every "discard" atom has its chunk ID set to 0. If
+<I>discard</I> is set to <I>no</I>, every "discard" atom has its chunk ID set to
+<I>Nchunk</I>. I.e. it becomes part of the last chunk.
+</P>
+<P>The <I>binning</I> styles use the <I>discard</I> keyword to decide whether to
+discard atoms outside the spatial domain covered by bins, or to assign
+them to the bin they are nearest to. Details are as follows.
+</P>
+<P>If <I>discard</I> is set to <I>yes</I>, an out-of-domain atom will have its
+chunk ID set to 0. If <I>discard</I> is set to <I>no</I>, the atom will have
+its chunk ID set to the first or last bin in that dimension. If
+(discard</I> is set to <I>mixed</I>, which is the default, it will only have
+its chunk ID set to the first or last bin if bins extend to the
+simulation box boundary in that dimension. This is the case if the
+<I>bound</I> keyword settings are <I>lower</I> and <I>upper</I>, which is the
+default. If the <I>bound</I> keyword settings are numeric values, then the
+atom will have its chunk ID set to 0 if it is outside the bounds of
+any bin. Note that in this case, it is possible that the first or
+last bin extends beyond the numeric <I>bounds</I> settings, depending on
+the specified <I>origin</I>. If this is the case, the chunk ID of the atom
+is only set to 0 if it is outside the first or last bin, not if it is
+simply outside the numeric <I>bounds</I> setting.
+</P>
+<HR>
+
+<P>The <I>bound</I> keyword only applies to the <I>binning</I> styles; otherwise it
+is ignored. It can be used one or more times to limit the extent of
+bin coverage in a specified dimension, i.e. to only bin a portion of
+the box. If the <I>lo</I> setting is <I>lower</I> or the <I>hi</I> setting is
+<I>upper</I>, the bin extent in that direction extends to the box boundary.
+If a numeric value is used for <I>lo</I> and/or <I>hi</I>, then the bin extent
+in the <I>lo</I> or <I>hi</I> direction extends only to that value, which is
+assumed to be inside (or at least near) the simulation box boundaries,
+though LAMMPS does not check for this. Note that using the <I>bound</I>
+keyword typically reduces the total number of bins and thus the number
+of chunks <I>Nchunk</I>.
+</P>
+<P>The <I>units</I> keyword only applies to the <I>binning</I> styles; otherwise it
+is ignored. It determines the meaning of the distance units used for
+the bin sizes <I>delta</I> and for <I>origin</I> and <I>bounds</I> values if they are
+coordinate values. For orthogonal simulation boxes, any of the 3
+options may be used. For non-orthogonal (triclinic) simulation boxes,
+only the <I>reduced</I> option may be used.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacing. A <I>reduced</I> value means normalized
+unitless values between 0 and 1, which represent the lower and upper
+faces of the simulation box respectively. Thus an <I>origin</I> value of
+0.5 means the center of the box in any dimension. A <I>delta</I> value of
+0.1 means 10 bins span the box in that dimension.
+</P>
+<HR>
+
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitless chunk IDs, ranging from 1 to
+<I>Nchunk</I> (inclusive) for atoms assigned to chunks, and 0 for atoms not
+belonging to a chunk.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Even if the <I>nchunk</I> keyword is set to <I>once</I>, the chunk IDs assigned
+to each atom are not stored in a restart files. This means you cannot
+expect those assignments to persist in a restarted simulation.
+Instead you must re-specify this command and assign atoms to chunks when
+the restarted simulation begins.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are as follows:
+</P>
+<UL><LI>region = none
+<LI>nchunk = every if compress is yes, overriding other defaults listed here
+<LI>nchunk = once for type style
+<LI>nchunk = once for mol style if region is none
+<LI>nchunk = every for mol style if region is set
+<LI>nchunk = once for binning style if the simulation box size is static or units = reduced
+<LI>nchunk = every for binning style if the simulation box size is dynamic and units is lattice or box
+<LI>nchunk = every for compute/fix/variable style
+<LI>limit = 0
+<LI>ids = every
+<LI>compress = no
+<LI>discard = yes for all styles except binning
+<LI>discard = mixed for binning styles
+<LI>bound = lower and upper in all dimensions
+<LI>units = lattice
+</UL>
+</HTML>
diff --git a/doc/doc2/compute_cluster_atom.html b/doc/doc2/compute_cluster_atom.html
new file mode 100644
index 000000000..f972d2fae
--- /dev/null
+++ b/doc/doc2/compute_cluster_atom.html
@@ -0,0 +1,62 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute cluster/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID cluster/atom cutoff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>cluster/atom = style name of this compute command
+<LI>cutoff = distance within which to label atoms as part of same cluster (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all cluster/atom 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that assigns each atom a cluster ID.
+</P>
+<P>A cluster is defined as a set of atoms, each of which is within the
+cutoff distance from one or more other atoms in the cluster. If an
+atom has no neighbors within the cutoff distance, then it is a 1-atom
+cluster. The ID of every atom in the cluster will be the smallest
+atom ID of any atom in the cluster.
+</P>
+<P>Only atoms in the compute group are clustered and assigned cluster
+IDs. Atoms not in the compute group are assigned a cluster ID = 0.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each of a
+<I>clsuter/atom</I> style.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be an ID > 0, as explained above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_cna_atom.html b/doc/doc2/compute_cna_atom.html
new file mode 100644
index 000000000..191b8911c
--- /dev/null
+++ b/doc/doc2/compute_cna_atom.html
@@ -0,0 +1,104 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute cna/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID cna/atom cutoff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>cna/atom = style name of this compute command
+<LI>cutoff = cutoff distance for nearest neighbors (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all cna/atom 3.08
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the CNA (Common Neighbor
+Analysis) pattern for each atom in the group. In solid-state systems
+the CNA pattern is a useful measure of the local crystal structure
+around an atom. The CNA methodology is described in <A HREF = "#Faken">(Faken)</A>
+and <A HREF = "#Tsuzuki">(Tsuzuki)</A>.
+</P>
+<P>Currently, there are five kinds of CNA patterns LAMMPS recognizes:
+</P>
+<UL><LI>fcc = 1
+<LI>hcp = 2
+<LI>bcc = 3
+<LI>icosohedral = 4
+<LI>unknown = 5
+</UL>
+<P>The value of the CNA pattern will be 0 for atoms not in the specified
+compute group. Note that normally a CNA calculation should only be
+performed on mono-component systems.
+</P>
+<P>The CNA calculation can be sensitive to the specified cutoff value.
+You should insure the appropriate nearest neighbors of an atom are
+found within the cutoff distance for the presumed crystal strucure.
+E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+neighbors for perfect BCC crystals. These formulas can be used to
+obtain a good cutoff distance:
+</P>
+<CENTER><IMG SRC = "Eqs/cna_cutoff1.jpg">
+</CENTER>
+<P>where a is the lattice constant for the crystal structure concerned
+and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+for HCP crystals.
+</P>
+<P>Also note that since the CNA calculation in LAMMPS uses the neighbors
+of an owned atom to find the nearest neighbors of a ghost atom, the
+following relation should also be satisfied:
+</P>
+<CENTER><IMG SRC = "Eqs/cna_cutoff2.jpg">
+</CENTER>
+<P>where Rc is the cutoff distance of the potential, Rs is the skin
+distance as specified by the <A HREF = "neighbor.html">neighbor</A> command, and
+cutoff is the argument used with the compute cna/atom command. LAMMPS
+will issue a warning if this is not the case.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+<I>cna/atom</I> style.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be a number from 0 to 5, as explained
+above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Faken"></A>
+
+<P><B>(Faken)</B> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
+</P>
+<A NAME = "Tsuzuki"></A>
+
+<P><B>(Tsuzuki)</B> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_com.html b/doc/doc2/compute_com.html
new file mode 100644
index 000000000..64735c5cf
--- /dev/null
+++ b/doc/doc2/compute_com.html
@@ -0,0 +1,62 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute com command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID com
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>com = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all com
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the center-of-mass of the group
+of atoms, including all effects due to atoms passing thru periodic
+boundaries.
+</P>
+<P>A vector of three quantites is calculated by this compute, which
+are the x,y,z coordinates of the center of mass.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
+center-of-mass in "unwrapped" form, by using the image flags
+associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
+for a discussion of "unwrapped" coordinates. See the Atoms section of
+the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 3, which can be
+accessed by indices 1-3 by any command that uses global vector values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector values are "intensive". The vector values will be in
+distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_com_chunk.html">compute com/chunk</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_com_chunk.html b/doc/doc2/compute_com_chunk.html
new file mode 100644
index 000000000..a2ad970b7
--- /dev/null
+++ b/doc/doc2/compute_com_chunk.html
@@ -0,0 +1,92 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute com/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID com/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>com/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid com/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the center-of-mass for multiple
+chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the x,y,z coordinates of the center-of-mass
+for each chunk, which includes all effects due to atoms passing thru
+periodic boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
+center-of-mass in "unwrapped" form, by using the image flags
+associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
+for a discussion of "unwrapped" coordinates. See the Atoms section of
+the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute com/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+3 for the x,y,z center-of-mass coordinates of each chunk. These
+values can be accessed by any command that uses global array values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The array values are "intensive". The array values will be in
+distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_com.html">compute com</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_contact_atom.html b/doc/doc2/compute_contact_atom.html
new file mode 100644
index 000000000..6c35adf5b
--- /dev/null
+++ b/doc/doc2/compute_contact_atom.html
@@ -0,0 +1,59 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute contact/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID contact/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>contact/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all contact/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the number of contacts
+for each atom in a group.
+</P>
+<P>The contact number is defined for finite-size spherical particles as
+the number of neighbor atoms which overlap the central particle,
+meaning that their distance of separation is less than or equal to the
+sum of the radii of the two particles.
+</P>
+<P>The value of the contact number will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, whose values can be
+accessed by any command that uses per-atom values from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The per-atom vector values will be a number >= 0.0, as explained
+above.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute requires that atoms store a radius as defined by the
+<A HREF = "atom_style.html">atom_style sphere</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_coord_atom.html b/doc/doc2/compute_coord_atom.html
new file mode 100644
index 000000000..98dbe794f
--- /dev/null
+++ b/doc/doc2/compute_coord_atom.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute coord/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID coord/atom cutoff type1 type2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>coord/atom = style name of this compute command
+<LI>cutoff = distance within which to count coordination neighbors (distance units)
+<LI>typeN = atom type for Nth coordination count (see asterisk form below)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all coord/atom 2.0
+compute 1 all coord/atom 6.0 1 2
+compute 1 all coord/atom 6.0 2*4 5*8 *
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates one or more coordination numbers
+for each atom in a group.
+</P>
+<P>A coordination number is defined as the number of neighbor atoms with
+specified atom type(s) that are within the specified cutoff distance
+from the central atom. Atoms not in the group are included in a
+coordination number of atoms in the group.
+</P>
+<P>The <I>typeN</I> keywords allow you to specify which atom types contribute
+to each coordination number. One coordination number is computed for
+each of the <I>typeN</I> keywords listed. If no <I>typeN</I> keywords are
+listed, a single coordination number is calculated, which includes
+atoms of all types (same as the "*" format, see below).
+</P>
+<P>The <I>typeN</I> keywords can be specified in one of two ways. An explicit
+numeric value can be used, as in the 2nd example above. Or a
+wild-card asterisk can be used to specify a range of atom types. This
+takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+</P>
+<P>The value of all coordination numbers will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently.
+</P>
+<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
+<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral. This
+is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
+command, and means those pairwise interactions do not appear in the
+neighbor list. Because this fix uses the neighbor list, it also means
+those pairs will not be included in the coordination count. One way
+to get around this, is to write a dump file, and use the
+<A HREF = "rerun.html">rerun</A> command to compute the coordination for snapshots
+in the dump file. The rerun script can use a
+<A HREF = "special_bonds.html">special_bonds</A> command that includes all pairs in
+the neighbor list.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>If single <I>type1</I> keyword is specified (or if none are specified),
+this compute calculates a per-atom vector. If multiple <I>typeN</I>
+keywords are specified, this compute calculates a per-atom array, with
+N columns. These values can be accessed by any command that uses
+per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The per-atom vector or array values will be a number >= 0.0, as
+explained above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_cluster_atom.html">compute cluster/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_damage_atom.html b/doc/doc2/compute_damage_atom.html
new file mode 100644
index 000000000..d47563130
--- /dev/null
+++ b/doc/doc2/compute_damage_atom.html
@@ -0,0 +1,68 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute damage/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID damage/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>damage/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all damage/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom damage for each atom
+in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>. See <A HREF = "PDF/PDLammps_overview.pdf">this document</A>
+for an overview of LAMMPS commands for Peridynamics modeling.
+</P>
+<P>The "damage" of a Peridymaics particles is based on the bond breakage
+between the particle and its neighbors. If all the bonds are broken
+the particle is considered to be fully damaged.
+</P>
+<P>See the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
+guide</A> for a formal
+definition of "damage" and more details about Peridynamics as it is
+implemented in LAMMPS.
+</P>
+<P>This command can be used with all the Peridynamic pair styles.
+</P>
+<P>The damage value will be 0.0 for atoms not in the specified compute
+group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitlesss numbers (damage) >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_dilatation.html">compute dilatation</A>, <A HREF = "compute_plasticity.html">compute
+plasticity</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_dihedral_local.html b/doc/doc2/compute_dihedral_local.html
new file mode 100644
index 000000000..b8d4bb567
--- /dev/null
+++ b/doc/doc2/compute_dihedral_local.html
@@ -0,0 +1,79 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute dihedral/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID dihedral/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>dihedral/local = style name of this compute command
+
+<LI>one or more keywords may be appended
+
+<LI>keyword = <I>phi</I>
+
+<PRE> <I>phi</I> = tabulate dihedral angles
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all dihedral/local phi
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual dihedral
+interactions. The number of datums generated, aggregated across all
+processors, equals the number of angles in the system, modified by the
+group parameter as explained below.
+</P>
+<P>The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their dihedrals. A dihedral will
+only be included if all 4 atoms in the dihedral are in the specified
+compute group.
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, dihedral output from the <A HREF = "compute_property_local.html">compute
+property/local</A> command can be combined
+with data from this command and output by the <A HREF = "dump.html">dump local</A>
+command in a consistent way.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of dihedrals. If a single keyword is specified, a
+local vector is produced. If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords. The vector or array can be accessed by any command that
+uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The output for <I>phi</I> will be in degrees.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
+property/local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_dilatation_atom.html b/doc/doc2/compute_dilatation_atom.html
new file mode 100644
index 000000000..2f76dee3b
--- /dev/null
+++ b/doc/doc2/compute_dilatation_atom.html
@@ -0,0 +1,71 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute dilatation/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID dilatation/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in compute command
+<LI>dilation/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all dilatation/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom dilatation for each
+atom in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>. See <A HREF = "PDF/PDLammps_overview.pdf">this document</A>
+for an overview of LAMMPS commands for Peridynamics modeling.
+</P>
+<P>For small deformation, dilatation of is the measure of the volumetric
+strain.
+</P>
+<P>The dilatation "theta" for each peridynamic particle I is calculated
+as a sum over its neighbors with unbroken bonds, where the
+contribution of the IJ pair is a function of the change in bond length
+(versus the initial length in the reference state), the volume
+fraction of the particles and an influence function. See the
+<A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
+guide</A> for a formal
+definition of dilatation.
+</P>
+<P>This command can only be used with a subset of the Peridynamic <A HREF = "pair_peri.html">pair
+styles</A>: peri/lps, peri/ves and peri/eps.
+</P>
+<P>The dilatation value will be 0.0 for atoms not in the specified
+compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitlesss numbers (theta) >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_damage.html">compute damage</A>, <A HREF = "compute_plasticity.html">compute
+plasticity</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_displace_atom.html b/doc/doc2/compute_displace_atom.html
new file mode 100644
index 000000000..87370be66
--- /dev/null
+++ b/doc/doc2/compute_displace_atom.html
@@ -0,0 +1,74 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute displace/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID displace/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>displace/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all displace/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the current displacement of each
+atom in the group from its original coordinates, including all effects
+due to atoms passing thru periodic boundaries.
+</P>
+<P>A vector of four quantites per atom is calculated by this compute.
+The first 3 elements of the vector are the dx,dy,dz displacements.
+The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
+dz*dz).
+</P>
+<P>The displacement of an atom is from its original position at the time
+the compute command was issued. The value of the displacement will be
+0.0 for atoms not in the specified compute group.
+</P>
+<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
+using the image flags associated with each atom. See the <A HREF = "dump.html">dump
+custom</A> command for a discussion of "unwrapped" coordinates.
+See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
+discussion of image flags and how they are set for each atom. You can
+reset the image flags (e.g. to 0) before invoking this compute by
+using the <A HREF = "set.html">set image</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
+to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
+then you should use the same ID for this compute, as in the original
+run. This is so that the fix this compute creates to store per-atom
+quantities will also have the same ID, and thus be initialized
+correctly with time=0 atom coordinates from the restart file.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom array with 4 columns, which can be
+accessed by indices 1-4 by any command that uses per-atom values from
+a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_state.html">fix
+store/state</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_erotate_asphere.html b/doc/doc2/compute_erotate_asphere.html
new file mode 100644
index 000000000..8ea9a4e1d
--- /dev/null
+++ b/doc/doc2/compute_erotate_asphere.html
@@ -0,0 +1,75 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute erotate/asphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID erotate/asphere
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>erotate/asphere = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all erotate/asphere
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the rotational kinetic energy of
+a group of aspherical particles. The aspherical particles can be
+ellipsoids, or line segments, or triangles. See the
+<A HREF = "atom_style.html">atom_style</A> and <A HREF = "read_data.html">read_data</A> commands
+for descriptions of these options.
+</P>
+<P>For all 3 types of particles, the rotational kinetic energy is
+computed as 1/2 I w^2, where I is the inertia tensor for the
+aspherical particle and w is its angular velocity, which is computed
+from its angular momentum if needed.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, ellipsoidal particles
+are treated as ellipsoids, not ellipses, meaning their moments of
+inertia will be the same as in 3d.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the KE). This value can be
+used by any command that uses a global scalar value from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute requires that ellipsoidal particles atoms store a shape
+and quaternion orientation and angular momentum as defined by the
+<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
+</P>
+<P>This compute requires that line segment particles atoms store a length
+and orientation and angular velocity as defined by the <A HREF = "atom_style.html">atom_style
+line</A> command.
+</P>
+<P>This compute requires that triangular particles atoms store a size and
+shape and quaternion orientation and angular momentum as defined by
+the <A HREF = "atom_style.html">atom_style tri</A> command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_erotate_rigid.html b/doc/doc2/compute_erotate_rigid.html
new file mode 100644
index 000000000..2e4358e30
--- /dev/null
+++ b/doc/doc2/compute_erotate_rigid.html
@@ -0,0 +1,66 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute erotate/rigid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID erotate/rigid fix-ID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>erotate/rigid = style name of this compute command
+<LI>fix-ID = ID of rigid body fix
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all erotate/rigid myRigid
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the rotational kinetic energy of
+a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
+rigid</A> command variants.
+</P>
+<P>The rotational energy of each rigid body is computed as 1/2 I Wbody^2,
+where I is the inertia tensor for the rigid body, and Wbody is its
+angular velocity vector. Both I and Wbody are in the frame of
+reference of the rigid body, i.e. I is diagonalized.
+</P>
+<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
+commands which defines the rigid bodies. The group specified in the
+compute command is ignored. The rotational energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the summed rotational energy
+of all the rigid bodies). This value can be used by any command that
+uses a global scalar value from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the RIGID package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_ke_rigid.html">compute ke/rigid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_erotate_sphere.html b/doc/doc2/compute_erotate_sphere.html
new file mode 100644
index 000000000..eb6662b13
--- /dev/null
+++ b/doc/doc2/compute_erotate_sphere.html
@@ -0,0 +1,62 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute erotate/sphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID erotate/sphere
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>erotate/sphere = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all erotate/sphere
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the rotational kinetic energy of
+a group of spherical particles.
+</P>
+<P>The rotational energy is computed as 1/2 I w^2, where I is the moment
+of inertia for a sphere and w is the particle's angular velocity.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
+as spheres, not disks, meaning their moment of inertia will be the
+same as in 3d.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the KE). This value can be
+used by any command that uses a global scalar value from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute requires that atoms store a radius and angular velocity
+(omega) as defined by the <A HREF = "atom_style.html">atom_style sphere</A> command.
+</P>
+<P>All particles in the group must be finite-size spheres or point
+particles. They cannot be aspherical. Point particles will not
+contribute to the rotational energy.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_erotate_sphere_atom.html b/doc/doc2/compute_erotate_sphere_atom.html
new file mode 100644
index 000000000..e758b7be4
--- /dev/null
+++ b/doc/doc2/compute_erotate_sphere_atom.html
@@ -0,0 +1,58 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute erotate/sphere/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID erotate/sphere/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>erotate/sphere/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all erotate/sphere/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the rotational kinetic energy for
+each particle in a group.
+</P>
+<P>The rotational energy is computed as 1/2 I w^2, where I is the moment
+of inertia for a sphere and w is the particle's angular velocity.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
+as spheres, not disks, meaning their moment of inertia will be the
+same as in 3d.
+</P>
+<P>The value of the rotational kinetic energy will be 0.0 for atoms not
+in the specified compute group or for point particles with a radius =
+0.0.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_event_displace.html b/doc/doc2/compute_event_displace.html
new file mode 100644
index 000000000..8efff145a
--- /dev/null
+++ b/doc/doc2/compute_event_displace.html
@@ -0,0 +1,67 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute event/displace command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID event/displace threshold
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>event/displace = style name of this compute command
+<LI>threshold = minimum distance anyparticle must move to trigger an event (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all event/displace 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that flags an "event" if any particle in the
+group has moved a distance greater than the specified threshold
+distance when compared to a previously stored reference state
+(i.e. the previous event). This compute is typically used in
+conjunction with the <A HREF = "prd.html">prd</A> and <A HREF = "tad.html">tad</A> commands,
+to detect if a transition
+to a new minimum energy basin has occurred.
+</P>
+<P>This value calculated by the compute is equal to 0 if no particle has
+moved far enough, and equal to 1 if one or more particles have moved
+further than the threshold distance.
+</P>
+<P>NOTE: If the system is undergoing significant center-of-mass motion,
+due to thermal motion, an external force, or an initial net momentum,
+then this compute will not be able to distinguish that motion from
+local atom displacements and may generate "false postives."
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the flag). This value can be
+used by any command that uses a global scalar value from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+scalar value will be a 0 or 1 as explained above.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "prd.html">prd</A>, <A HREF = "tad.html">tad</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_fep.html b/doc/doc2/compute_fep.html
new file mode 100644
index 000000000..6eecc4b02
--- /dev/null
+++ b/doc/doc2/compute_fep.html
@@ -0,0 +1,279 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute fep command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID fep temp attribute args ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in the <A HREF = "compute.html">compute</A> command
+
+<LI>fep = name of this compute command
+
+<LI>temp = external temperature (as specified for constant-temperature run)
+
+<LI>one or more attributes with args may be appended
+
+<LI>attribute = <I>pair</I> or <I>atom</I>
+
+<PRE> <I>pair</I> args = pstyle pparam I J v_delta
+ pstyle = pair style name, e.g. lj/cut
+ pparam = parameter to perturb
+ I,J = type pair(s) to set parameter for
+ v_delta = variable with perturbation to apply (in the units of the parameter)
+ <I>atom</I> args = aparam I v_delta
+ aparam = parameter to perturb
+ I = type to set parameter for
+ v_delta = variable with perturbation to apply (in the units of the parameter)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>tail</I> or <I>volume</I>
+
+<PRE> <I>tail</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = ignore tail correction to pair energies (usually small in fep)
+ <I>yes</I> = include tail correction to pair energies
+ <I>volume</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = ignore volume changes (e.g. in <I>NVE</I> or <I>NVT</I> trajectories)
+ <I>yes</I> = include volume changes (e.g. in <I>NpT</I> trajectories)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
+compute 1 all fep 300 atom charge 2 v_delta
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a perturbation to parameters of the interaction potential and
+recalculate the pair potential energy without changing the atomic
+coordinates from those of the reference, unperturbed system. This
+compute can be used to calculate free energy differences using several
+methods, such as free-energy perturbation (FEP), finite-difference
+thermodynamic integration (FDTI) or Bennet's acceptance ratio method
+(BAR).
+</P>
+<P>The potential energy of the system is decomposed in three terms: a
+background term corresponding to interaction sites whose parameters
+remain constant, a reference term <I>U</I><sub>0</sub> corresponding to the
+initial interactions of the atoms that will undergo perturbation, and
+a term <I>U</I><sub>1</sub> corresponding to the final interactions of
+these atoms:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_u.jpg">
+</CENTER>
+<P>A coupling parameter &lambda; varying from 0 to 1 connects the
+reference and perturbed systems:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_lambda.jpg">
+</CENTER>
+<P>It is possible but not necessary that the coupling parameter (or a
+function thereof) appears as a multiplication factor of the potential
+energy. Therefore, this compute can apply perturbations to interaction
+parameters that are not directly proportional to the potential energy
+(e.g. &sigma; in Lennard-Jones potentials).
+</P>
+<P>This command can be combined with <A HREF = "fix_adapt.html">fix adapt</A> to
+perform multistage free-energy perturbation calculations along
+stepwise alchemical transformations during a simulation run:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_fep.jpg">
+</CENTER>
+<P>This compute is suitable for the finite-difference thermodynamic
+integration (FDTI) method <A HREF = "#Mezei">(Mezei)</A>, which is based on an
+evaluation of the numerical derivative of the free energy by a
+perturbation method using a very small &delta;:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_fdti.jpg">
+</CENTER>
+<P>where <I>w</I><sub>i</sub> are weights of a numerical quadrature. The <A HREF = "fix_adapt.html">fix
+adapt</A> command can be used to define the stages of
+&lambda; at which the derivative is calculated and averaged.
+</P>
+<P>The compute fep calculates the exponential Boltzmann term and also the
+potential energy difference <I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>. By
+choosing a very small perturbation &delta; the thermodynamic
+integration method can be implemented using a numerical evaluation of
+the derivative of the potential energy with respect to &lambda;:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_ti.jpg">
+</CENTER>
+<P>Another technique to calculate free energy differences is the
+acceptance ratio method <A HREF = "#Bennet">(Bennet)</A>, which can be implemented
+by calculating the potential energy differences with &delta; = 1.0 on
+both the forward and reverse routes:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_bar.jpg">
+</CENTER>
+<P>The value of the free energy difference is determined by numerical
+root finding to establish the equality.
+</P>
+<P>Concerning the choice of how the atomic parameters are perturbed in
+order to setup an alchemical transformation route, several strategies
+are available, such as single-topology or double-topology strategies
+<A HREF = "#Pearlman">(Pearlman)</A>. The latter does not require modification of
+bond lengths, angles or other internal coordinates.
+</P>
+<P>IMPORTANT NOTES: This compute command does not take kinetic energy
+into account, therefore the masses of the particles should not be
+modified between the reference and perturbed states, or along the
+alchemical transformation route. This compute command does not change
+bond lengths or other internal coordinates <A HREF = "#BoreschKarplus">(Boresch,
+Karplus)</A>.
+</P>
+<HR>
+
+<P>The <I>pair</I> attribute enables various parameters of potentials defined
+by the <A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
+commands to be changed, if the pair style supports it.
+</P>
+<P>The <I>pstyle</I> argument is the name of the pair style. For example,
+<I>pstyle</I> could be specified as "lj/cut". The <I>pparam</I> argument is the
+name of the parameter to change. This is a (non-exclusive) list of
+pair styles and parameters that can be used with this compute. See
+the doc pages for individual pair styles and their energy formulas for
+the meaning of these parameters:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">coul/long/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft</A></TD><TD > lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft</A></TD><TD > epsilon,sigma,lambda</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_born.html">born</A></TD><TD > a,b,c</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_buck.html">buck</A></TD><TD > a,c </TD><TD > type pairs
+</TD></TR></TABLE></DIV>
+
+<P>Note that it is easy to add new potentials and their parameters to
+this list. All it typically takes is adding an extract() method to
+the pair_*.cpp file associated with the potential.
+</P>
+<P>Similar to the <A HREF = "pair_coeff.html">pair_coeff</A> command, I and J can be
+specified in one of two ways. Explicit numeric values can be used for
+each, as in the 1st example above. I <= J is required. LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same
+values. A wild-card asterisk can be used in place of or in conjunction
+with the I,J arguments to set the coefficients for multiple pairs of
+atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N =
+the number of atom types, then an asterisk with no numeric values
+means all types from 1 to N. A leading asterisk means all types from
+1 to n (inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive). Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+</P>
+<P>If <A HREF = "pair_hybrid.html">pair_style hybrid or hybrid/overlay</A> is being
+used, then the <I>pstyle</I> will be a sub-style name. You must specify
+I,J arguments that correspond to type pair values defined (via the
+<A HREF = "pair_coeff.html">pair_coeff</A> command) for that sub-style.
+</P>
+<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this compute is invoked. It should be specified as v_name, where name
+is the variable name.
+</P>
+<HR>
+
+<P>The <I>atom</I> attribute enables atom properties to be changed. The
+<I>aparam</I> argument is the name of the parameter to change. This is the
+current list of atom parameters that can be used with this compute:
+</P>
+<UL><LI>charge = charge on particle
+</UL>
+<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this compute is invoked. It should be specified as v_name, where name
+is the variable name.
+</P>
+<HR>
+
+<P>The <I>tail</I> keyword controls the calculation of the tail correction to
+"van der Waals" pair energies beyond the cutoff, if this has been
+activated via the <A HREF = "pair_modify.html">pair_modify</A> command. If the
+perturbation is small, the tail contribution to the energy difference
+between the reference and perturbed systems should be negligible.
+</P>
+<P>If the keyword <I>volume</I> = <I>yes</I>, then the Boltzmann term is multiplied
+by the volume so that correct ensemble averaging can be performed over
+trajectories during which the volume fluctuates or changes <A HREF = "#AllenTildesley">(Allen and
+Tildesley)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_fep_vol.jpg">
+</CENTER>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 3 which contains the
+energy difference (<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>) as c_ID[1], the
+Boltzmann factor exp(-(<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>)/<I>kT</I>), or
+<I>V</I>exp(-(<I>U</I><sub>1</sub>-<I>U</I><sub>0</sub>)/<I>kT</I>), as c_ID[2] and the
+volume of the simulation box <I>V</I> as c_ID[3]. <I>U</I><sub>1</sub> is the
+pair potential energy obtained with the perturbed parameters and
+<I>U</I><sub>0</sub> is the pair potential energy obtained with the
+unperturbed parameters. The energies include kspace terms if these
+are used in the simulation.
+</P>
+<P>These output results can be used by any command that uses a global
+scalar or vector from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options. For example, the computed values can be averaged using <A HREF = "fix_ave_time.html">fix
+ave/time</A>.
+</P>
+<P>The values calculated by this compute are "extensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is distributed as the USER-FEP package. It is only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "pair_lj_soft_coul_soft.txt">pair_lj_soft_coul_soft</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are <I>tail</I> = <I>no</I>, <I>volume</I> = <I>no</I>.
+</P>
+<HR>
+
+<A NAME = "Pearlman"></A>
+
+<P><B>(Pearlman)</B> Pearlman, J Chem Phys, 98, 1487 (1994)
+</P>
+<A NAME = "Mezei"></A>
+
+<P><B>(Mezei)</B> Mezei, J Chem Phys, 86, 7084 (1987)
+</P>
+<A NAME = "Bennet"></A>
+
+<P><B>(Bennet)</B> Bennet, J Comput Phys, 22, 245 (1976)
+</P>
+<A NAME = "BoreschKarplus"></A>
+
+<P><B>(BoreschKarplus)</B> Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
+</P>
+<A NAME = "AllenTildesley"></A>
+
+<P><B>(AllenTildesley)</B> Allen and Tildesley, Computer Simulation of
+Liquids, Oxford University Press (1987)
+</P>
+</HTML>
diff --git a/doc/doc2/compute_group_group.html b/doc/doc2/compute_group_group.html
new file mode 100644
index 000000000..268b1f68c
--- /dev/null
+++ b/doc/doc2/compute_group_group.html
@@ -0,0 +1,135 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute group/group command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID group/group group2-ID keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>group/group = style name of this compute command
+
+<LI>group2-ID = group ID of second (or same) group
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>pair</I> or <I>kspace</I> or <I>boundary</I>
+
+<PRE> <I>pair</I> value = <I>yes</I> or <I>no</I>
+ <I>kspace</I> value = <I>yes</I> or <I>no</I>
+ <I>boundary</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 lower group/group upper
+compute 1 lower group/group upper kspace yes
+compute mine fluid group/group wall
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the total energy and force
+interaction between two groups of atoms: the compute group and the
+specified group2. The two groups can be the same.
+</P>
+<P>If the <I>pair</I> keyword is set to <I>yes</I>, which is the default, then the
+the interaction energy will include a pair component which is defined
+as the pairwise energy between all pairs of atoms where one atom in
+the pair is in the first group and the other is in the second group.
+Likewise, the interaction force calculated by this compute will
+include the force on the compute group atoms due to pairwise
+interactions with atoms in the specified group2.
+</P>
+<P>If the <I>kspace</I> keyword is set to <I>yes</I>, which is not the default, and
+if a <A HREF = "kspace_style.html">kspace_style</A> is defined, then the interaction
+energy will include a Kspace component which is the long-range
+Coulombic energy between all the atoms in the first group and all the
+atoms in the 2nd group. Likewise, the interaction force calculated by
+this compute will include the force on the compute group atoms due to
+long-range Coulombic interactions with atoms in the specified group2.
+</P>
+<P>Normally the long-range Coulombic energy converges only when the net
+charge of the unit cell is zero. However, one can assume the net
+charge of the system is neutralized by a uniform background plasma,
+and a correction to the system energy can be applied to reduce
+artifacts. For more information see <A HREF = "#Bogusz">(Bogusz)</A>. If the
+<I>boundary</I> keyword is set to <I>yes</I>, which is the default, and <I>kspace</I>
+contributions are included, then this energy correction term will be
+added to the total group-group energy. This correction term does not
+affect the force calculation and will be zero if one or both of the
+groups are charge neutral. This energy correction term is the same as
+that included in the regular Ewald and PPPM routines.
+</P>
+<P>This compute does not calculate any bond or angle or dihedral or
+improper interactions between atoms in the two groups.
+</P>
+<HR>
+
+<P>The pairwise contributions to the group-group interactions are
+calculated by looping over a neighbor list. The Kspace contribution
+to the group-group interactions require essentially the same amount of
+work (FFTs, Ewald summation) as computing long-range forces for the
+entire system. Thus it can be costly to invoke this compute too
+frequently.
+</P>
+<P>If you desire a breakdown of the interactions into a pairwise and
+Kspace component, simply invoke the compute twice with the appropriate
+yes/no settings for the <I>pair</I> and <I>kspace</I> keywords. This is no more
+costly than using a single compute with both keywords set to <I>yes</I>.
+The individual contributions can be summed in a
+<A HREF = "variable.html">variable</A> if desired.
+</P>
+<P>This <A HREF = "PDF/kspace.pdf">document</A> describes how the long-range
+group-group calculations are performed.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the energy) and a global
+vector of length 3 (force), which can be accessed by indices 1-3.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>Both the scalar and vector values calculated by this compute are
+"extensive". The scalar value will be in energy <A HREF = "units.html">units</A>.
+The vector values will be in force <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Not all pair styles can be evaluated in a pairwise mode as required by
+this compute. For example, 3-body and other many-body potentials,
+such as <A HREF = "pair_tersoff.html">Tersoff</A> and
+<A HREF = "pair_sw.html">Stillinger-Weber</A> cannot be used. <A HREF = "pair_eam.html">EAM</A>
+potentials only include the pair potential portion of the EAM
+interaction when used by this compute, not the embedding term.
+</P>
+<P>Not all Kspace styles support calculation of group/group interactions.
+The <I>ewald</I> and <I>pppm</I> styles do.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are pair = yes, kspace = no, and boundary = yes.
+</P>
+<HR>
+
+<A NAME = "Bogusz"></A>
+
+<P>Bogusz et al, J Chem Phys, 108, 7070 (1998)
+</P>
+</HTML>
diff --git a/doc/doc2/compute_gyration.html b/doc/doc2/compute_gyration.html
new file mode 100644
index 000000000..8d0eed96f
--- /dev/null
+++ b/doc/doc2/compute_gyration.html
@@ -0,0 +1,78 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute gyration command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID gyration
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>gyration = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 molecule gyration
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the radius of gyration Rg of the
+group of atoms, including all effects due to atoms passing thru
+periodic boundaries.
+</P>
+<P>Rg is a measure of the size of the group of atoms, and is computed as
+the square root of the Rg^2 value in this formula
+</P>
+<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
+</CENTER>
+<P>where M is the total mass of the group, Rcm is the center-of-mass
+position of the group, and the sum is over all atoms in the group.
+</P>
+<P>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
+this compute. The formula for the components of the tensor is the
+same as the above formula, except that (Ri - Rcm)^2 is replaced by
+(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
+components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
+that unlike the scalar Rg, each of the 6 values of the tensor is
+effectively a "squared" value, since the cross-terms may be negative
+and taking a sqrt() would be invalid.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
+"unwrapped" form, by using the image flags associated with each atom.
+See the <A HREF = "dump.html">dump custom</A> command for a discussion of
+"unwrapped" coordinates. See the Atoms section of the
+<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
+how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (Rg) and a global vector of
+length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
+values can be used by any command that uses a global scalar value or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar and vector values calculated by this compute are
+"intensive". The scalar and vector values will be in distance and
+distance^2 <A HREF = "units.html">units</A> respectively.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_gyration_chunk.html b/doc/doc2/compute_gyration_chunk.html
new file mode 100644
index 000000000..61f391f8f
--- /dev/null
+++ b/doc/doc2/compute_gyration_chunk.html
@@ -0,0 +1,122 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute gyration/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID gyration/chunk chunkID keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>gyration/chunk = style name of this compute command
+
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>tensor</I>
+
+<PRE> <I>tensor</I> value = none
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 molecule gyration/chunk molchunk
+compute 2 molecule gyration/chunk molchunk tensor
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the radius of gyration Rg for
+multiple chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the radius of gyration Rg for each chunk,
+which includes all effects due to atoms passing thru periodic
+boundaries.
+</P>
+<P>Rg is a measure of the size of a chunk, and is computed by this
+formula
+</P>
+<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
+</CENTER>
+<P>where M is the total mass of the chunk, Rcm is the center-of-mass
+position of the chunk, and the sum is over all atoms in the
+chunk.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>If the <I>tensor</I> keyword is specified, then the scalar Rg value is not
+calculated, but an Rg tensor is instead calculated for each chunk.
+The formula for the components of the tensor is the same as the above
+formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
+Rcmy) for the xy component, etc. The 6 components of the tensor are
+ordered xx, yy, zz, xy, xz, yz.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
+"unwrapped" form, by using the image flags associated with each atom.
+See the <A HREF = "dump.html">dump custom</A> command for a discussion of
+"unwrapped" coordinates. See the Atoms section of the
+<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
+how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute gyration/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all gyration/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector if the <I>tensor</I> keyword is not
+specified and a global array if it is. The length of the vector or
+number of rows in the array = the number of chunks <I>Nchunk</I> as
+calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. If the <I>tensor</I> keyword
+is specified, the global array has 6 columns. The vector or array can
+be accessed by any command that uses global values from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+of LAMMPS output options.
+</P>
+<P>All the vector or array values calculated by this compute are
+"intensive". The vector or array values will be in distance
+<A HREF = "units.html">units</A>, since they are the square root of values
+represented by the formula above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><A HREF = "compute_gyration.html">compute gyration</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_heat_flux.html b/doc/doc2/compute_heat_flux.html
new file mode 100644
index 000000000..8ea72a590
--- /dev/null
+++ b/doc/doc2/compute_heat_flux.html
@@ -0,0 +1,192 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute heat/flux command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID heat/flux ke-ID pe-ID stress-ID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>heat/flux = style name of this compute command
+<LI>ke-ID = ID of a compute that calculates per-atom kinetic energy
+<LI>pe-ID = ID of a compute that calculates per-atom potential energy
+<LI>stress-ID = ID of a compute that calculates per-atom stress
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute myFlux all heat/flux myKE myPE myStress
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the heat flux vector based on
+contributions from atoms in the specified group. This can be used by
+itself to measure the heat flux into or out of a reservoir of atoms,
+or to calculate a thermal conductivity using the Green-Kubo formalism.
+</P>
+<P>See the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
+command for details on how to compute thermal conductivity in an
+alternate way, via the Muller-Plathe method. See the <A HREF = "fix_heat.html">fix
+heat</A> command for a way to control the heat added or
+subtracted to a group of atoms.
+</P>
+<P>The compute takes three arguments which are IDs of other
+<A HREF = "compute.html">computes</A>. One calculates per-atom kinetic energy
+(<I>ke-ID</I>), one calculates per-atom potential energy (<I>pe-ID)</I>, and the
+third calcualtes per-atom stress (<I>stress-ID</I>). These should be
+defined for the same group used by compute heat/flux, though LAMMPS
+does not check for this.
+</P>
+<P>The Green-Kubo formulas relate the ensemble average of the
+auto-correlation of the heat flux J to the thermal conductivity kappa:
+</P>
+<CENTER><IMG SRC = "Eqs/heat_flux_J.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/heat_flux_k.jpg">
+</CENTER>
+<P>Ei in the first term of the equation for J is the per-atom energy
+(potential and kinetic). This is calculated by the computes <I>ke-ID</I>
+and <I>pe-ID</I>. Si in the second term of the equation for J is the
+per-atom stress tensor calculated by the compute <I>stress-ID</I>. The
+tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
+vector. Note that as discussed below, the 1/V scaling factor in the
+equation for J is NOT included in the calculation performed by this
+compute; you need to add it for a volume appropriate to the atoms
+included in the calculation.
+</P>
+<P>IMPORTANT NOTE: The <A HREF = "compute_pe_atom.html">compute pe/atom</A> and
+<A HREF = "compute_stress_atom.html">compute stress/atom</A> commands have options
+for which terms to include in their calculation (pair, bond, etc).
+The heat flux calculation will thus include exactly the same terms.
+Normally you should use <A HREF = "compute_stress_atom.html">compute stress/atom
+virial</A> so as not to include a kinetic energy
+term in the heat flux.
+</P>
+<P>This compute calculates 6 quantities and stores them in a 6-component
+vector. The first 3 components are the x, y, z components of the full
+heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x,
+y, z components of just the convective portion of the flux, i.e. the
+first term in the equation for J above.
+</P>
+<HR>
+
+<P>The heat flux can be output every so many timesteps (e.g. via the
+<A HREF = "thermo_style.html">thermo_style custom</A> command). Then as a
+post-processing operation, an autocorrelation can be performed, its
+integral estimated, and the Green-Kubo formula above evaluated.
+</P>
+<P>The <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command can calclate
+the autocorrelation. The trap() function in the
+<A HREF = "variable.html">variable</A> command can calculate the integral.
+</P>
+<P>An example LAMMPS input script for solid Ar is appended below. The
+result should be: average conductivity ~0.29 in W/mK.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 6 (total heat flux
+vector, followed by convective heat flux vector), which can be
+accessed by indices 1-6. These values can be used by any command that
+uses global vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector values calculated by this compute are "extensive", meaning
+they scale with the number of atoms in the simulation. They can be
+divided by the appropriate volume to get a flux, which would then be
+an "intensive" value, meaning independent of the number of atoms in
+the simulation. Note that if the compute is "all", then the
+appropriate volume to divide by is the simulation box volume.
+However, if a sub-group is used, it should be the volume containing
+those atoms.
+</P>
+<P>The vector values will be in energy*velocity <A HREF = "units.html">units</A>. Once
+divided by a volume the units will be that of flux, namely
+energy/area/time <A HREF = "units.html">units</A>
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>,
+<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
+<A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<PRE># Sample LAMMPS input script for thermal conductivity of solid Ar
+</PRE>
+<PRE>units real
+variable T equal 70
+variable V equal vol
+variable dt equal 4.0
+variable p equal 200 # correlation length
+variable s equal 10 # sample interval
+variable d equal $p*$s # dump interval
+</PRE>
+<PRE># convert from LAMMPS real units to SI
+</PRE>
+<PRE>variable kB equal 1.3806504e-23 # [J/K] Boltzmann
+variable kCal2J equal 4186.0/6.02214e23
+variable A2m equal 1.0e-10
+variable fs2s equal 1.0e-15
+variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
+</PRE>
+<PRE># setup problem
+</PRE>
+<PRE>dimension 3
+boundary p p p
+lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+region box block 0 4 0 4 0 4
+create_box 1 box
+create_atoms 1 box
+mass 1 39.948
+pair_style lj/cut 13.0
+pair_coeff * * 0.2381 3.405
+timestep ${dt}
+thermo $d
+</PRE>
+<PRE># equilibration and thermalization
+</PRE>
+<PRE>velocity all create $T 102486 mom yes rot yes dist gaussian
+fix NVT all nvt temp $T $T 10 drag 0.2
+run 8000
+</PRE>
+<PRE># thermal conductivity calculation, switch to NVE if desired
+</PRE>
+<PRE>#unfix NVT
+#fix NVE all nve
+</PRE>
+<PRE>reset_timestep 0
+compute myKE all ke/atom
+compute myPE all pe/atom
+compute myStress all stress/atom NULL virial
+compute flux all heat/flux myKE myPE myStress
+variable Jx equal c_flux[1]/vol
+variable Jy equal c_flux[2]/vol
+variable Jz equal c_flux[3]/vol
+fix JJ all ave/correlate $s $p $d &
+ c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
+variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
+variable k11 equal trap(f_JJ[3])*${scale}
+variable k22 equal trap(f_JJ[4])*${scale}
+variable k33 equal trap(f_JJ[5])*${scale}
+thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
+run 100000
+variable k equal (v_k11+v_k22+v_k33)/3.0
+variable ndens equal count(all)/vol
+print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
+</PRE>
+</HTML>
diff --git a/doc/doc2/compute_improper_local.html b/doc/doc2/compute_improper_local.html
new file mode 100644
index 000000000..cdf58f1b6
--- /dev/null
+++ b/doc/doc2/compute_improper_local.html
@@ -0,0 +1,79 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute improper/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID improper/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>improper/local = style name of this compute command
+
+<LI>one or more keywords may be appended
+
+<LI>keyword = <I>chi</I>
+
+<PRE> <I>chi</I> = tabulate improper angles
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all improper/local chi
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual improper
+interactions. The number of datums generated, aggregated across all
+processors, equals the number of impropers in the system, modified by
+the group parameter as explained below.
+</P>
+<P>The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their impropers. An improper will
+only be included if all 4 atoms in the improper are in the specified
+compute group.
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, improper output from the <A HREF = "compute_property_local.html">compute
+property/local</A> command can be combined
+with data from this command and output by the <A HREF = "dump.html">dump local</A>
+command in a consistent way.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of impropers. If a single keyword is specified, a
+local vector is produced. If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords. The vector or array can be accessed by any command that
+uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The output for <I>chi</I> will be in degrees.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
+property/local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_inertia_chunk.html b/doc/doc2/compute_inertia_chunk.html
new file mode 100644
index 000000000..9b131c32a
--- /dev/null
+++ b/doc/doc2/compute_inertia_chunk.html
@@ -0,0 +1,93 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute inertia/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID inertia/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>inertia/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid inertia/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the inertia tensor for multiple
+chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the 6 components of the symmetric intertia
+tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
+calculation includes all effects due to atoms passing thru periodic
+boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
+inertia tensor in "unwrapped" form, by using the image flags
+associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
+for a discussion of "unwrapped" coordinates. See the Atoms section of
+the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute inertia/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all inertia/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+6 for the 6 components of the inertia tensor for each chunk, ordered
+as listed above. These values can be accessed by any command that
+uses global array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The array values are "intensive". The array values will be in
+mass*distance^2 <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable inertia() function</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ke.html b/doc/doc2/compute_ke.html
new file mode 100644
index 000000000..90497bec8
--- /dev/null
+++ b/doc/doc2/compute_ke.html
@@ -0,0 +1,64 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ke command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the translational kinetic energy
+of a group of particles.
+</P>
+<P>The kinetic energy of each particle is computed as 1/2 m v^2, where m
+and v are the mass and velocity of the particle.
+</P>
+<P>There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
+keyword used in thermodynamic output, as specified by the
+<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
+energy is "translational" kinetic energy, calculated by the simple
+formula above. For thermodynamic output, the <I>ke</I> keyword infers
+kinetic energy from the temperature of the system with 1/2 Kb T of
+energy for each degree of freedom. For the default temperature
+computation via the <A HREF = "compute_temp.html">compute temp</A> command, these
+are the same. But different computes that calculate temperature can
+subtract out different non-thermal components of velocity and/or
+include different degrees of freedom (translational, rotational, etc).
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the summed KE). This value
+can be used by any command that uses a global scalar value from a
+compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
+for an overview of LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ke_atom.html b/doc/doc2/compute_ke_atom.html
new file mode 100644
index 000000000..fdf97f197
--- /dev/null
+++ b/doc/doc2/compute_ke_atom.html
@@ -0,0 +1,53 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ke/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom translational
+kinetic energy for each atom in a group.
+</P>
+<P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
+the velocity of each atom.
+</P>
+<P>The value of the kinetic energy will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ke_atom_eff.html b/doc/doc2/compute_ke_atom_eff.html
new file mode 100644
index 000000000..d305890bb
--- /dev/null
+++ b/doc/doc2/compute_ke_atom_eff.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ke/atom/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke/atom/eff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke/atom/eff = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke/atom/eff
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom translational
+(nuclei and electrons) and radial kinetic energy (electron only) in a
+group. The particles are assumed to be nuclei and electrons modeled
+with the <A HREF = "pair_eff.html">electronic force field</A>.
+</P>
+<P>The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
+corresponds to the corresponding nuclear mass, and the kinetic energy
+for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
+and v correspond to the mass and translational velocity of each
+electron, and s to its radial velocity, respectively.
+</P>
+<P>There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
+keyword used in thermodynamic output, as specified by the
+<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
+energy is "translational" plus electronic "radial" kinetic energy,
+calculated by the simple formula above. For thermodynamic output, the
+<I>ke</I> keyword infers kinetic energy from the temperature of the system
+with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
+eFF.
+</P>
+<P>IMPORTANT NOTE: The temperature in eFF should be monitored via the
+<A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be printed
+with thermodynamic output by using the
+<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
+example:
+</P>
+<PRE>compute effTemp all temp/eff
+thermo_style custom step etotal pe ke temp press
+thermo_modify temp effTemp
+</PRE>
+<P>The value of the kinetic energy will be 0.0 for atoms (nuclei or
+electrons) not in the specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a scalar quantity for each atom, which can be
+accessed by any command that uses per-atom computes as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ke_eff.html b/doc/doc2/compute_ke_eff.html
new file mode 100644
index 000000000..7c476b9aa
--- /dev/null
+++ b/doc/doc2/compute_ke_eff.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ke/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke/eff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke/eff = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke/eff
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the kinetic energy of motion of a
+group of eFF particles (nuclei and electrons), as modeled with the
+<A HREF = "pair_eff.html">electronic force field</A>.
+</P>
+<P>The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
+kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
+s^2), where m corresponds to the nuclear mass, me to the electron
+mass, v to the translational velocity of each particle, and s to the
+radial velocity of the electron, respectively.
+</P>
+<P>There is a subtle difference between the quantity calculated by this
+compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
+keyword used in thermodynamic output, as specified by the
+<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
+energy is "translational" and "radial" (only for electrons) kinetic
+energy, calculated by the simple formula above. For thermodynamic
+output, the <I>ke</I> keyword infers kinetic energy from the temperature of
+the system with 1/2 Kb T of energy for each degree of freedom. For
+the eFF temperature computation via the <A HREF = "compute_temp_eff.html">compute
+temp_eff</A> command, these are the same. But
+different computes that calculate temperature can subtract out
+different non-thermal components of velocity and/or include other
+degrees of freedom.
+</P>
+<P>IMPRORTANT NOTE: The temperature in eFF models should be monitored via
+the <A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be
+printed with thermodynamic output by using the
+<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
+example:
+</P>
+<PRE>compute effTemp all temp/eff
+thermo_style custom step etotal pe ke temp press
+thermo_modify temp effTemp
+</PRE>
+<P>See <A HREF = "compute_temp_eff.html">compute temp/eff</A>.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the KE). This value can be
+used by any command that uses a global scalar value from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ke_rigid.html b/doc/doc2/compute_ke_rigid.html
new file mode 100644
index 000000000..485cf37fa
--- /dev/null
+++ b/doc/doc2/compute_ke_rigid.html
@@ -0,0 +1,65 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ke/rigid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID ke/rigid fix-ID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>ke = style name of this compute command
+<LI>fix-ID = ID of rigid body fix
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ke/rigid myRigid
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the translational kinetic energy
+of a collection of rigid bodies, as defined by one of the <A HREF = "fix_rigid.html">fix
+rigid</A> command variants.
+</P>
+<P>The kinetic energy of each rigid body is computed as 1/2 M Vcm^2,
+where M is the total mass of the rigid body, and Vcm is its
+center-of-mass velocity.
+</P>
+<P>The <I>fix-ID</I> should be the ID of one of the <A HREF = "fix_rigid.html">fix rigid</A>
+commands which defines the rigid bodies. The group specified in the
+compute command is ignored. The kinetic energy of all the rigid
+bodies defined by the fix rigid command in included in the
+calculation.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the summed KE of all the
+rigid bodies). This value can be used by any command that uses a
+global scalar value from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the RIGID package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_erotate_rigid.html">compute erotate/rigid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_meso_e_atom.html b/doc/doc2/compute_meso_e_atom.html
new file mode 100644
index 000000000..3350eb300
--- /dev/null
+++ b/doc/doc2/compute_meso_e_atom.html
@@ -0,0 +1,61 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute meso_e/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID meso_e/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>meso_e/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all meso_e/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom internal energy
+for each atom in a group.
+</P>
+<P>The internal energy is the energy associated with the internal degrees
+of freedom of a mesoscopic particles, e.g. a Smooth-Particle
+Hydrodynamics particle.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_meso_rho_atom.html b/doc/doc2/compute_meso_rho_atom.html
new file mode 100644
index 000000000..790e2f900
--- /dev/null
+++ b/doc/doc2/compute_meso_rho_atom.html
@@ -0,0 +1,61 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute meso_rho/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID meso_rho/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>meso_rho/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all meso_rho/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom mesoscopic density
+for each atom in a group.
+</P>
+<P>The mesoscopic density is the mass density of a mesoscopic particle,
+calculated by kernel function interpolation using "pair style
+sph/rhosum".
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the mesoscopic density will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in mass/volume <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_meso_t_atom.html b/doc/doc2/compute_meso_t_atom.html
new file mode 100644
index 000000000..39b21ccff
--- /dev/null
+++ b/doc/doc2/compute_meso_t_atom.html
@@ -0,0 +1,63 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute meso_t/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID meso_t/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>meso_t/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all meso_t/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom internal temperature
+for each atom in a group.
+</P>
+<P>The internal temperature is the ratio of internal energy over the heat
+capacity associated with the internal degrees of freedom of a mesoscopic
+particles, e.g. a Smooth-Particle Hydrodynamics particle.
+</P>
+<P>T_<I>int</I> = E_<I>int</I> / C_<I>V, int</I>
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in temperature <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_modify.html b/doc/doc2/compute_modify.html
new file mode 100644
index 000000000..4536ee76b
--- /dev/null
+++ b/doc/doc2/compute_modify.html
@@ -0,0 +1,80 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute_modify compute-ID keyword value ...
+</PRE>
+<UL><LI>compute-ID = ID of the compute to modify
+
+<LI>one or more keyword/value pairs may be listed
+
+<LI>keyword = <I>extra</I> or <I>dynamic</I>
+
+<PRE> <I>extra</I> value = N
+ N = # of extra degrees of freedom to subtract
+ <I>dynamic</I> value = <I>yes</I> or <I>no</I>
+ yes/no = do or do not recompute the number of atoms contributing to the temperature
+ <I>thermo</I> value = <I>yes</I> or <I>no</I>
+ yes/no = do or do not add contributions from fixes to the potential energy
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute_modify myTemp extra 0
+compute_modify newtemp dynamic yes extra 600
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Modify one or more parameters of a previously defined compute. Not
+all compute styles support all parameters.
+</P>
+<P>The <I>extra</I> keyword refers to how many degrees-of-freedom are
+subtracted (typically from 3N) as a normalizing factor in a
+temperature computation. Only computes that compute a temperature use
+this option. The default is 2 or 3 for <A HREF = "dimension.html">2d or 3d
+systems</A> which is a correction factor for an ensemble
+of velocities with zero total linear momentum. You can use a negative
+number for the <I>extra</I> parameter if you need to add
+degrees-of-freedom. See the <A HREF = "compute_temp_asphere.html">compute
+temp/asphere</A> command for an example.
+</P>
+<P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
+compute group is re-computed each time a temperature is computed.
+Only compute styles that compute a temperature use this option. By
+default, N is assumed to be constant. If you are adding atoms to the
+system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
+deposit</A> commands) or expect atoms to be lost
+(e.g. due to evaporation), then this option should be used to insure
+the temperature is correctly normalized.
+</P>
+<P>The <I>thermo</I> keyword determines whether the potential energy
+contribution calculated by some <A HREF = "fix.html">fixes</A> is added to the
+potential energy calculated by the compute. Currently, only the
+compute of style <I>pe</I> uses this option. See the doc pages for
+<A HREF = "fix.html">individual fixes</A> for details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are extra = 2 or 3 for 2d or 3d systems and
+dynamic = no. Thermo is <I>yes</I> if the compute of style <I>pe</I> was
+defined with no extra keywords; otherwise it is <I>no</I>.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_msd.html b/doc/doc2/compute_msd.html
new file mode 100644
index 000000000..137e89cb6
--- /dev/null
+++ b/doc/doc2/compute_msd.html
@@ -0,0 +1,99 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute msd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID msd keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>msd = style name of this compute command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>com</I>
+
+<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all msd
+compute 1 upper msd com yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the mean-squared displacement
+(MSD) of the group of atoms, including all effects due to atoms
+passing thru periodic boundaries. For computation of the non-Gaussian
+parameter of mean-squared displacement, see the <A HREF = "compute_msd_nongauss.html">compute
+msd/nongauss</A> command.
+</P>
+<P>A vector of four quantites is calculated by this compute. The first 3
+elements of the vector are the squared dx,dy,dz displacements, summed
+and averaged over atoms in the group. The 4th element is the total
+squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
+averaged over atoms in the group.
+</P>
+<P>The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing atoms.
+</P>
+<P>The displacement of an atom is from its original position at the time
+the compute command was issued. The value of the displacement will be
+0.0 for atoms not in the specified compute group.
+</P>
+<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
+the center-of-mass of the group of atoms is subtracted out before xhe
+displacment of each atom is calcluated.
+</P>
+<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
+using the image flags associated with each atom. See the <A HREF = "dump.html">dump
+custom</A> command for a discussion of "unwrapped" coordinates.
+See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
+discussion of image flags and how they are set for each atom. You can
+reset the image flags (e.g. to 0) before invoking this compute by
+using the <A HREF = "set.html">set image</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
+to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
+then you should use the same ID for this compute, as in the original
+run. This is so that the fix this compute creates to store per-atom
+quantities will also have the same ID, and thus be initialized
+correctly with time=0 atom coordinates from the restart file.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 4, which can be
+accessed by indices 1-4 by any command that uses global vector values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector values are "intensive". The vector values will be in
+distance^2 <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd_nongauss.html">compute msd/nongauss</A>, <A HREF = "compute_displace_atom.html">compute
+displace_atom</A>, <A HREF = "fix_store_state.html">fix
+store/state</A>, <A HREF = "compute_msd_chunk.html">compute
+msd/chunk</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is com = no.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_msd_chunk.html b/doc/doc2/compute_msd_chunk.html
new file mode 100644
index 000000000..e6ef5bc25
--- /dev/null
+++ b/doc/doc2/compute_msd_chunk.html
@@ -0,0 +1,125 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute msd/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID msd/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>msd/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all msd/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the mean-squared displacement
+(MSD) for multiple chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>Four quantites are calculated by this compute for each chunk. The
+first 3 quantities are the squared dx,dy,dz displacements of the
+center-of-mass. The 4th component is the total squared displacement,
+i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
+calculations include all effects due to atoms passing thru periodic
+boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>The slope of the mean-squared displacement (MSD) versus time is
+proportional to the diffusion coefficient of the diffusing chunks.
+</P>
+<P>The displacement of the center-of-mass of the chunk is from its
+original center-of-mass position, calculated on the timestep this
+compute command was first invoked.
+</P>
+<P>IMPORTANT NOTE: The number of chunks <I>Nchunk</I> calculated by the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command must remain
+constant each time this compute is invoked, so that the displacement
+for each chunk from its original position can be computed
+consistently. If <I>Nchunk</I> does not remain constant, an error will be
+generated. If needed, you can enforce a constant <I>Nchunk</I> by using
+the <I>nchunk once</I> or <I>ids once</I> options when specifying the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command.
+</P>
+<P>IMPORTANT NOTE: This compute stores the original position (of the
+center-of-mass) of each chunk. When a displacement is calculated on a
+later timestep, it is assumed that the same atoms are assigned to the
+same chunk ID. However LAMMPS has no simple way to insure this is the
+case, though you can use the <I>ids once</I> option when specifying the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. Note that if
+this is not the case, the MSD calculation does not have a sensible
+meaning.
+</P>
+<P>IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are
+stored in "unwrapped" form, by using the image flags associated with
+each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion
+of "unwrapped" coordinates. See the Atoms section of the
+<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
+how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> command,
+this compute does not store the initial center-of-mass coorindates of
+its molecules in a restart file. Thus you cannot continue the MSD per
+chunk calculation of this compute when running from a <A HREF = "read_restart.html">restart
+file</A>.
+</P>
+<P>The simplest way to output the results of the compute com/msd
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all com/msd cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+4 for dx,dy,dz and the total displacement. These values can be
+accessed by any command that uses global array values from a compute
+as input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an
+overview of LAMMPS output options.
+</P>
+<P>The array values are "intensive". The array values will be in
+distance^2 <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd.html">compute msd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_msd_nongauss.html b/doc/doc2/compute_msd_nongauss.html
new file mode 100644
index 000000000..e041a3079
--- /dev/null
+++ b/doc/doc2/compute_msd_nongauss.html
@@ -0,0 +1,90 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute msd/nongauss command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID msd/nongauss keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>msd/nongauss = style name of this compute command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>com</I>
+
+<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all msd/nongauss
+compute 1 upper msd/nongauss com yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the mean-squared displacement
+(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
+including all effects due to atoms passing thru periodic boundaries.
+</P>
+<P>A vector of three quantites is calculated by this compute. The first
+element of the vector is the total squared dx,dy,dz displacements
+drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
+fourth power of these displacements drfourth = (dx*dx + dy*dy +
+dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
+group. The 3rd component is the nonGaussian diffusion paramter NGP =
+3*drfourth/(5*drsquared*drsquared), i.e.
+</P>
+<CENTER><IMG SRC = "Eqs/compute_msd_nongauss.jpg">
+</CENTER>
+<P>The NGP is a commonly used quantity in studies of dynamical
+heterogeneity. Its minimum theoretical value (-0.4) occurs when all
+atoms have the same displacement magnitude. NGP=0 for Brownian
+diffusion, while NGP > 0 when some mobile atoms move faster than
+others.
+</P>
+<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
+the center-of-mass of the group of atoms is subtracted out before the
+displacment of each atom is calcluated.
+</P>
+<P>See the <A HREF = "compute_msd.html">compute msd</A> doc page for further IMPORTANT
+NOTES, which also apply to this compute.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 3, which can be
+accessed by indices 1-3 by any command that uses global vector values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector values are "intensive". The first vector value will be in
+distance^2 <A HREF = "units.html">units</A>, the second is in distance^4 units, and
+the 3rd is dimensionless.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd.html">compute msd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is com = no.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_omega_chunk.html b/doc/doc2/compute_omega_chunk.html
new file mode 100644
index 000000000..3c553afbc
--- /dev/null
+++ b/doc/doc2/compute_omega_chunk.html
@@ -0,0 +1,94 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute omega/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID omega/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>omega/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid omega/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the angular velocity (omega) of
+multiple chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the 3 components of the angular velocity
+vector for each chunk, via the formula L = Iw where L is the angular
+momentum vector of the chunk, I is its moment of inertia tensor, and w
+is omega = angular velocity of the chunk. The calculation includes
+all effects due to atoms passing thru periodic boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
+angular velocity in "unwrapped" form, by using the image flags
+associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
+for a discussion of "unwrapped" coordinates. See the Atoms section of
+the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
+and how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute omega/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all omega/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+3 for the 3 xyz components of the angular velocity for each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The array values are "intensive". The array values will be in
+velocity/distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable omega() function</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_pair.html b/doc/doc2/compute_pair.html
new file mode 100644
index 000000000..b456d96ba
--- /dev/null
+++ b/doc/doc2/compute_pair.html
@@ -0,0 +1,86 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pair command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pair pstyle evalue
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>pair = style name of this compute command
+<LI>pstyle = style name of a pair style that calculates additional values
+<LI>evalue = <I>epair</I> or <I>evdwl</I> or <I>ecoul</I> or blank (optional setting)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pair gauss
+compute 1 all pair lj/cut/coul/cut ecoul
+compute 1 all pair reax
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that extracts additional values calculated by a
+pair style, sums them across processors, and makes them accessible for
+output or further processing by other commands. The group specified
+for this command is ignored.
+</P>
+<P>The specified <I>pstyle</I> must be a pair style used in your simulation
+either by itself or as a sub-style in a <A HREF = "pair_hybrid.html">pair_style hybrid or
+hybrid/overlay</A> command.
+</P>
+<P>The <I>evalue</I> setting is optional; it may be left off the command. All
+pair styles tally a potential energy <I>epair</I> which may be broken into
+two parts: <I>evdwl</I> and <I>ecoul</I> such that <I>epair</I> = <I>evdwl</I> + <I>ecoul</I>.
+If the pair style calculates Coulombic interactions, their energy will
+be tallied in <I>ecoul</I>. Everything else (whether it is a Lennard-Jones
+style van der Waals interaction or not) is tallied in <I>evdwl</I>. If
+<I>evalue</I> is specified as <I>epair</I> or left out, then <I>epair</I> is stored
+as a global scalar by this compute. This is useful when using
+<A HREF = "pair_hybrid.html">pair_style hybrid</A> if you want to know the portion
+of the total energy contributed by one sub-style. If <I>evalue</I> is
+specfied as <I>evdwl</I> or <I>ecoul</I>, then just that portion of the energy
+is stored as a global scalar.
+</P>
+<P>Some pair styles tally additional quantities, e.g. a breakdown of
+potential energy into a dozen or so components is tallied by the
+<A HREF = "pair_reax.html">pair_style reax</A> commmand. These values (1 or more)
+are stored as a global vector by this compute. See the doc page for
+<A HREF = "pair_style.html">individual pair styles</A> for info on these values.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar which is <I>epair</I> or <I>evdwl</I> or
+<I>ecoul</I>. If the pair style supports it, it also calculates a global
+vector of length >= 1, as determined by the pair style. These values
+can be used by any command that uses global scalar or vector values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar and vector values calculated by this compute are
+"extensive".
+</P>
+<P>The scalar value will be in energy <A HREF = "units.html">units</A>. The vector
+values will typically also be in energy <A HREF = "units.html">units</A>, but
+see the doc page for the pair style for details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_pe.html">compute pe</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default for <I>evalue</I> is <I>epair</I>.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_pair_local.html b/doc/doc2/compute_pair_local.html
new file mode 100644
index 000000000..d7a17323b
--- /dev/null
+++ b/doc/doc2/compute_pair_local.html
@@ -0,0 +1,127 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pair/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pair/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>pair/local = style name of this compute command
+
+<LI>zero or more keywords may be appended
+
+<LI>keyword = <I>dist</I> or <I>eng</I> or <I>force</I> or <I>fx</I> or <I>fy</I> or <I>fz</I> or <I>pN</I>
+
+<PRE> <I>dist</I> = pairwise distance
+ <I>eng</I> = pairwise energy
+ <I>force</I> = pairwise force
+ <I>fx</I>,<I>fy</I>,<I>fz</I> = components of pairwise force
+ <I>pN</I> = pair style specific quantities for allowed N values
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pair/local eng
+compute 1 all pair/local dist eng force
+compute 1 all pair/local dist eng fx fy fz
+compute 1 all pair/local dist fx fy fz p1 p2 p3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates properties of individual pairwise
+interactions. The number of datums generated, aggregated across all
+processors, equals the number of pairwise interactions in the system.
+</P>
+<P>The local data stored by this command is generated by looping over the
+pairwise neighbor list. Info about an individual pairwise interaction
+will only be included if both atoms in the pair are in the specified
+compute group, and if the current pairwise distance is less than the
+force cutoff distance for that interaction, as defined by the
+<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
+commands.
+</P>
+<P>The output <I>dist</I> is the distance bewteen the pair of atoms.
+</P>
+<P>The output <I>eng</I> is the interaction energy for the pair of atoms.
+</P>
+<P>The output <I>force</I> is the force acting between the pair of atoms,
+which is positive for a repulsive force and negative for an attractive
+force. The outputs <I>fx</I>, <I>fy</I>, and <I>fz</I> are the xyz components of
+<I>force</I> on atom I.
+</P>
+<P>A pair style may define additional pairwise quantities which can be
+accessed as <I>p1</I> to <I>pN</I>, where N is defined by the pair style. Most
+pair styles do not define any additional quantities, so N = 0. An
+example of ones that do are the <A HREF = "pair_gran.html">granular pair styles</A>
+which calculate the tangential force between two particles and return
+its components and magnitude acting on atom I for N = 1,2,3,4. See
+individual pair styles for detils.
+</P>
+<P>The output <I>dist</I> will be in distance <A HREF = "units.html">units</A>. The output
+<I>eng</I> will be in energy <A HREF = "units.html">units</A>. The outputs <I>force</I>,
+<I>fx</I>, <I>fy</I>, and <I>fz</I> will be in force <A HREF = "units.html">units</A>. The output
+<I>pN</I> will be in whatever units the pair style defines.
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, pair output from the <A HREF = "compute_property_local.html">compute
+property/local</A> command can be combined
+with data from this command and output by the <A HREF = "dump.html">dump local</A>
+command in a consistent way.
+</P>
+<P>IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3,
+1-4 interactions within the molecular topology, their pairwise
+interaction may be turned off, and thus they may not appear in the
+neighbor list, and will not be part of the local data created by this
+command. More specifically, this will be true of I,J pairs with a
+weighting factor of 0.0; pairs with a non-zero weighting factor are
+included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
+interactions are set by the <A HREF = "special_bonds.html">special_bonds</A>
+command. An exception is if long-range Coulombics are being computed
+via the <A HREF = "kspace_style.html">kspace_style</A> command, then atom pairs with
+weighting factors of zero are still included in the neighbor list, so
+that a portion of the long-range interaction contribution can be
+computed in the pair style. Hence in that case, those atom pairs will
+be part of the local data created by this command.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of keywords. The length of the vector or number of rows in the
+array is the number of pairs. If a single keyword is specified, a
+local vector is produced. If two or more keywords are specified, a
+local array is produced where the number of columns = the number of
+keywords. The vector or array can be accessed by any command that
+uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The output for <I>dist</I> will be in distance <A HREF = "units.html">units</A>. The
+output for <I>eng</I> will be in energy <A HREF = "units.html">units</A>. The output for
+<I>force</I> will be in force <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
+property/local</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_pe.html b/doc/doc2/compute_pe.html
new file mode 100644
index 000000000..2543ed1da
--- /dev/null
+++ b/doc/doc2/compute_pe.html
@@ -0,0 +1,107 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pe command
+</H3>
+<H3>compute pe/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pe keyword ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>pe = style name of this compute command
+<LI>zero or more keywords may be appended
+<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pe
+compute molPE all pe bond angle dihedral improper
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the potential energy of the
+entire system of atoms. The specified group must be "all". See the
+<A HREF = "compute_pe_atom.html">compute pe/atom</A> command if you want per-atom
+energies. These per-atom values could be summed for a group of atoms
+via the <A HREF = "compute_reduce.html">compute reduce</A> command.
+</P>
+<P>The energy is calculated by the various pair, bond, etc potentials
+defined for the simulation. If no extra keywords are listed, then the
+potential energy is the sum of pair, bond, angle, dihedral, improper,
+and kspace (long-range) energy. If any extra keywords are listed,
+then only those components are summed to compute the potential energy.
+</P>
+<P>The Kspace contribution requires 1 extra FFT each timestep the energy
+is calculated, if using the PPPM solver via the <A HREF = "kspace_style.html">kspace_style
+pppm</A> command. Thus it can increase the cost of the
+PPPM calculation if it is needed on a large fraction of the simulation
+timesteps.
+</P>
+<P>Various fixes can contribute to the total potential energy of the
+system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
+details. The <I>thermo</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command determines whether these
+contributions are added into the computed potential energy. If no
+keywords are specified the default is <I>yes</I>. If any keywords are
+specified, the default is <I>no</I>.
+</P>
+<P>A compute of this style with the ID of "thermo_pe" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_pe all pe
+</PRE>
+<P>See the "thermo_style" command for more details.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the potential energy). This
+value can be used by any command that uses a global scalar value from
+a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "extensive". The
+scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_pe_atom.html">compute pe/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_pe_atom.html b/doc/doc2/compute_pe_atom.html
new file mode 100644
index 000000000..713836983
--- /dev/null
+++ b/doc/doc2/compute_pe_atom.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pe/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pe/atom keyword ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>pe/atom = style name of this compute command
+<LI>zero or more keywords may be appended
+<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pe/atom
+compute 1 all pe/atom pair
+compute 1 all pe/atom pair bond
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that computes the per-atom potential energy for
+each atom in a group. See the <A HREF = "compute_pe.html">compute pe</A> command if
+you want the potential energy of the entire system.
+</P>
+<P>The per-atom energy is calculated by the various pair, bond, etc
+potentials defined for the simulation. If no extra keywords are
+listed, then the potential energy is the sum of pair, bond, angle,
+dihedral,improper, and kspace energy. If any extra keywords are
+listed, then only those components are summed to compute the potential
+energy.
+</P>
+<P>Note that the energy of each atom is due to its interaction with all
+other atoms in the simulation, not just with other atoms in the group.
+</P>
+<P>For an energy contribution produced by a small set of atoms (e.g. 4
+atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
+energy is assigned in equal portions to each atom in the set.
+E.g. 1/4 of the dihedral energy to each of the 4 atoms.
+</P>
+<P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> style calculates
+pairwise interactions between 1-4 atoms. The energy contribution of
+these terms is included in the pair energy, not the dihedral energy.
+</P>
+<P>The KSpace contribution is calculated using the method in
+<A HREF = "#Heyes">(Heyes)</A> for the Ewald method and a related method for PPPM,
+as specified by the <A HREF = "kspace_style.html">kspace_style pppm</A> command.
+For PPPM, the calcluation requires 1 extra FFT each timestep that
+per-atom energy is calculated. Thie <A HREF = "PDF/kspace.pdf">document</A>
+describes how the long-range per-atom energy calculation is performed.
+</P>
+<P>As an example of per-atom potential energy compared to total potential
+energy, these lines in an input script should yield the same result
+in the last 2 columns of thermo output:
+</P>
+<PRE>compute peratom all pe/atom
+compute pe all reduce sum c_peratom
+thermo_style custom step temp etotal press pe c_pe
+</PRE>
+<P>IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
+corrections invoked by the <A HREF = "pair_modify.html">pair_modify tail yes</A>
+command, since those are global contributions to the system energy.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_pe.html">compute pe</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Heyes"></A>
+
+<P><B>(Heyes)</B> Heyes, Phys Rev B 49, 755 (1994),
+</P>
+</HTML>
diff --git a/doc/doc2/compute_plasticity_atom.html b/doc/doc2/compute_plasticity_atom.html
new file mode 100644
index 000000000..ea39315d0
--- /dev/null
+++ b/doc/doc2/compute_plasticity_atom.html
@@ -0,0 +1,73 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute plasticity/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID plasticity/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in compute command
+<LI>plasticity/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all plasticity/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom plasticity for each
+atom in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>. See <A HREF = "PDF/PDLammps_overview.pdf">this document</A>
+for an overview of LAMMPS commands for Peridynamics modeling.
+</P>
+<P>The plasticity for a Peridynamic particle is the so-called consistency
+parameter (lambda). For elastic deformation lambda = 0, otherwise
+lambda > 0 for plastic deformation. For details, see
+<A HREF = "#Mitchell">(Mitchell)</A> and the PDF doc included in the LAMMPS
+distro in <A HREF = "PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</A>.
+</P>
+<P>This command can be invoked for one of the Peridynamic <A HREF = "pair_peri.html">pair
+styles</A>: peri/eps.
+</P>
+<P>The plasticity value will be 0.0 for atoms not in the specified
+compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_damage.html">compute damage</A>, <A HREF = "compute_dilatation.html">compute
+dilatation</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mitchell"></A>
+
+<P><B>(Mitchell)</B> Mitchell, "A non-local, ordinary-state-based
+viscoelasticity model for peridynamics", Sandia National Lab Report,
+8064:1-28 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_pressure.html b/doc/doc2/compute_pressure.html
new file mode 100644
index 000000000..40eb3c0c0
--- /dev/null
+++ b/doc/doc2/compute_pressure.html
@@ -0,0 +1,153 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pressure command
+</H3>
+<H3>compute pressure/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pressure temp-ID keyword ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>pressure = style name of this compute command
+<LI>temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+<LI>zero or more keywords may be appended
+<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pressure thermo_temp
+compute 1 all pressure NULL pair bond
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the pressure of the entire system
+of atoms. The specified group must be "all". See the <A HREF = "compute_stress_atom.html">compute
+stress/atom</A> command if you want per-atom
+pressure (stress). These per-atom values could be summed for a group
+of atoms via the <A HREF = "compute_reduce.html">compute reduce</A> command.
+</P>
+<P>The pressure is computed by the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pressure.jpg">
+</CENTER>
+<P>where N is the number of atoms in the system (see discussion of DOF
+below), Kb is the Boltzmann constant, T is the temperature, d is the
+dimensionality of the system (2 or 3 for 2d/3d), V is the system
+volume (or area in 2d), and the second term is the virial, computed
+within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
+and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
+(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
+virial term.
+</P>
+<P>A symmetric pressure tensor, stored as a 6-element vector, is also
+calculated by this compute. The 6 components of the vector are
+ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
+(where I and J = x,y,z) is similar to the above formula, except that
+the first term uses components of the kinetic energy tensor and the
+second term uses components of the virial tensor:
+</P>
+<CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
+</CENTER>
+<P>If no extra keywords are listed, the entire equations above are
+calculated. This includes a kinetic energy (temperature) term and the
+virial as the sum of pair, bond, angle, dihedral, improper, kspace
+(long-range), and fix contributions to the force on each atom. If any
+extra keywords are listed, then only those components are summed to
+compute temperature or ke and/or the virial. The <I>virial</I> keyword
+means include all terms except the kinetic energy <I>ke</I>.
+</P>
+<P>Details of how LAMMPS computes the virial efficiently for the entire
+system, including the effects of periodic boundary conditions is
+discussed in <A HREF = "#Thompson">(Thompson)</A>.
+</P>
+<P>The temperature and kinetic energy tensor is not calculated by this
+compute, but rather by the temperature compute specified with the
+command. If the kinetic energy is not included in the pressure, than
+the temperature compute is not used and can be specified as NULL.
+Normally the temperature compute used by compute pressure should
+calculate the temperature of all atoms for consistency with the virial
+term, but any compute style that calculates temperature can be used,
+e.g. one that excludes frozen atoms or other degrees of freedom.
+</P>
+<P>Note that if desired the specified temperature compute can be one that
+subtracts off a bias to calculate a temperature using only the thermal
+velocity of the atoms, e.g. by subtracting a background streaming
+velocity. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias.
+</P>
+<P>Also note that the N in the first formula above is really
+degrees-of-freedom divided by d = dimensionality, where the DOF value
+is calcluated by the temperature compute. See the various <A HREF = "compute.html">compute
+temperature</A> styles for details.
+</P>
+<P>A compute of this style with the ID of "thermo_press" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_press all pressure thermo_temp
+</PRE>
+<P>where "thermo_temp" is the ID of a similarly defined compute of style
+"temp". See the "thermo_style" command for more details.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the pressure) and a global
+vector of length 6 (pressure tensor), which can be accessed by indices
+1-6. These values can be used by any command that uses global scalar
+or vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar and vector values calculated by this compute are
+"intensive". The scalar and vector values will be in pressure
+<A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>,
+<A HREF = "thermo_style.html">thermo_style</A>,
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Thompson"></A>
+
+<P><B>(Thompson)</B> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_property_atom.html b/doc/doc2/compute_property_atom.html
new file mode 100644
index 000000000..ca449ada4
--- /dev/null
+++ b/doc/doc2/compute_property_atom.html
@@ -0,0 +1,173 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute property/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID property/atom input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>property/atom = style name of this compute command
+
+<LI>input = one or more atom attributes
+
+<PRE> possible attributes = id, mol, proc, type, mass,
+ x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
+ q, mux, muy, muz, mu,
+ radius, diameter, omegax, omegay, omegaz,
+ angmomx, angmomy, angmomz,
+ shapex,shapey, shapez,
+ quatw, quati, quatj, quatk, tqx, tqy, tqz,
+ end1x, end1y, end1z, end2x, end2y, end2z,
+ corner1x, corner1y, corner1z,
+ corner2x, corner2y, corner2z,
+ corner3x, corner3y, corner3z,
+ nbonds,
+ vfrac, s0,
+ spin, eradius, ervel, erforce,
+ rho, drho, e, de, cv,
+ i_name, d_name
+</PRE>
+<PRE> id = atom ID
+ mol = molecule ID
+ proc = ID of processor that owns atom
+ type = atom type
+ mass = atom mass
+ x,y,z = unscaled atom coordinates
+ xs,ys,zs = scaled atom coordinates
+ xu,yu,zu = unwrapped atom coordinates
+ ix,iy,iz = box image that the atom is in
+ vx,vy,vz = atom velocities
+ fx,fy,fz = forces on atoms
+ q = atom charge
+ mux,muy,muz = orientation of dipole moment of atom
+ mu = magnitude of dipole moment of atom
+ radius,diameter = radius,diameter of spherical particle
+ omegax,omegay,omegaz = angular velocity of spherical particle
+ angmomx,angmomy,angmomz = angular momentum of aspherical particle
+ shapex,shapey,shapez = 3 diameters of aspherical particle
+ quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
+ tqx,tqy,tqz = torque on finite-size particles
+ end12x, end12y, end12z = end points of line segment
+ corner123x, corner123y, corner123z = corner points of triangle
+ nbonds = number of bonds assigned to an atom
+</PRE>
+<PRE> PERI package per-atom properties:
+ vfrac = ???
+ s0 = ???
+</PRE>
+<PRE> USER-EFF and USER-AWPMD package per-atom properties:
+ spin = electron spin
+ eradius = electron radius
+ ervel = electron radial velocity
+ erforce = electron radial force
+</PRE>
+<PRE> USER-SPH package per-atom properties:
+ rho = ???
+ drho = ???
+ e = ???
+ de = ???
+ cv = ???
+</PRE>
+<PRE> <A HREF = "fix_property_atom.html">fix property/atom</A> per-atom properties:
+ i_name = custom integer vector with name
+ d_name = custom integer vector with name
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all property/atom xs vx fx mux
+compute 2 all property/atom type
+compute 1 all property/atom ix iy iz
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that simply stores atom attributes for each atom
+in the group. This is useful so that the values can be used by other
+<A HREF = "Section_howto.html#howto_15">output commands</A> that take computes as
+inputs. See for example, the <A HREF = "compute_reduce.html">compute reduce</A>,
+<A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
+<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, and <A HREF = "variable.html">atom-style
+variable</A> commands.
+</P>
+<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump
+custom</A> command, which describes their meaning, with some
+additional quantities that are only defined for certain <A HREF = "atom_style.html">atom
+styles</A>. Basically, this augmented list gives an
+input script access to any per-atom quantity stored by LAMMPS.
+</P>
+<P>The values are stored in a per-atom vector or array as discussed
+below. Zeroes are stored for atoms not in the specified group or for
+quantities that are not defined for a particular particle in the group
+(e.g. <I>shapex</I> if the particle is not an ellipsoid).
+</P>
+<P>The additional quantities only accessible via this command, and not
+directly via the <A HREF = "dump.html">dump custom</A> command, are as follows.
+</P>
+<P><I>Shapex</I>, <I>shapey</I>, and <I>shapez</I> are defined for ellipsoidal particles
+and define the 3d shape of each particle.
+</P>
+<P><I>Quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> are defined for ellipsoidal
+particles and body particles and store the 4-vector quaternion
+representing the orientation of each particle. See the <A HREF = "set.html">set</A>
+command for an explanation of the quaternion vector.
+</P>
+<P><I>End1x</I>, <I>end1y</I>, <I>end1z</I>, <I>end2x</I>, <I>end2y</I>, <I>end2z</I>, are defined for
+line segment particles and define the end points of each line segment.
+</P>
+<P><I>Corner1x</I>, <I>corner1y</I>, <I>corner1z</I>, <I>corner2x</I>, <I>corner2y</I>,
+<I>corner2z</I>, <I>corner3x</I>, <I>corner3y</I>, <I>corner3z</I>, are defined for
+triangular particles and define the corner points of each triangle.
+</P>
+<P><I>Nbonds</I> is available for all molecular atom styles and refers to the
+number of explicit bonds assigned to an atom. Note that if the
+<A HREF = "newton.html">newton bond</A> command is set to <I>on</I>, which is the
+default, then every bond in the system is assigned to only one of the
+two atoms in the bond. Thus a bond between atoms I,J may be tallied
+for either atom I or atom J. If <A HREF = "newton.html">newton bond off</A> is set,
+it will be tallied with both atom I and atom J.
+</P>
+<P>The <I>i_name</I> and <I>d_name</I> attributes refer to custom integer and
+floating-point properties that have been added to each atom via the
+<A HREF = "fix_property_atom.html">fix property/atom</A> command. When that command
+is used specific names are given to each attribute which are what is
+specified as the "name" portion of <I>i_name</I> or <I>d_name</I>.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector or per-atom array depending
+on the number of input values. If a single input is specified, a
+per-atom vector is produced. If two or more inputs are specified, a
+per-atom array is produced where the number of columns = the number of
+inputs. The vector or array can be accessed by any command that uses
+per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector or array values will be in whatever <A HREF = "units.html">units</A> the
+corresponding attribute is in, e.g. velocity units for vx, charge
+units for q, etc.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>, <A HREF = "compute_reduce.html">compute reduce</A>, <A HREF = "fix_ave_atom.html">fix
+ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
+<A HREF = "fix_property_atom.html">fix property/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_property_chunk.html b/doc/doc2/compute_property_chunk.html
new file mode 100644
index 000000000..cf4cc0301
--- /dev/null
+++ b/doc/doc2/compute_property_chunk.html
@@ -0,0 +1,127 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute property/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID property/chunk chunkID input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>property/chunk = style name of this compute command
+
+<LI>input = one or more attributes
+
+<PRE> attributes = count, id, coord1, coord2, coord3
+ count = # of atoms in chunk
+ id = original chunk IDs before compression by <A HREF = "compute_chunk_atom.html">compute chunk/atom</A>
+ coord123 = coordinates for spatial bins calculated by <A HREF = "compute_chunk_atom.html">compute chunk/atom</A>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all property/chunk count
+compute 1 all property/chunk ID coord1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that stores the specified attributes of chunks of
+atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates and stores the specified attributes of chunks
+as global data so they can be accessed by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> and used in conjunction with
+other commands that generate per-chunk data, such as <A HREF = "compute_com_chunk.html">compute
+com/chunk</A> or <A HREF = "compute_msd_chunk.html">compute
+msd/chunk</A>.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation of the <I>count</I> attribute. The <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command defines its own group;
+atoms will have a chunk ID = 0 if they are not in that group,
+signifying they are not assigned to a chunk, and will thus also not
+contribute to this calculation. You can specify the "all" group for
+this command if you simply want to include atoms with non-zero chunk
+IDs.
+</P>
+<P>The <I>count</I> attribute is the number of atoms in the chunk.
+</P>
+<P>The <I>id</I> attribute stores the original chunk ID for each chunk. It
+can only be used if the <I>compress</I> keyword was set to <I>yes</I> for the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command referenced by
+chunkID. This means that the original chunk IDs (e.g. molecule IDs)
+will have been compressed to remove chunk IDs with no atoms assigned
+to them. Thus a compresed chunk ID of 3 may correspond to an original
+chunk ID (molecule ID in this case) of 415. The <I>id</I> attribute will
+then be 415 for the 3rd chunk.
+</P>
+<P>The <I>coordN</I> attributes can only be used if a <I>binning</I> style was used
+in the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command referenced
+by chunkID. For <I>bin/1d</I>, <I>bin/2d</I>, and <I>bin/3d</I> styles the attribute
+is the center point of the bin in the corresponding dimension. Style
+<I>bin/1d</I> only defines a <I>coord1</I> attribute. Style <I>bin/2d</I> adds a
+<I>coord2</I> attribute. Style <I>bin/3d</I> adds a <I>coord3</I> attribute.
+</P>
+<P>Note that if the value of the <I>units</I> keyword used in the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom command</A> is <I>box</I> or <I>lattice</I>, the
+<I>coordN</I> attributes will be in distance <A HREF = "units.html">units</A>. If the
+value of the <I>units</I> keyword is <I>reduced</I>, the <I>coordN</I> attributes
+will be in unitless reduced units (0-1).
+</P>
+<P>The simplest way to output the results of the compute property/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk1 all property/chunk cc1
+compute myChunk2 all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector or global array depending on
+the number of input values. The length of the vector or number of
+rows in the array is the number of chunks.
+</P>
+<P>This compute calculates a global vector or global array where the
+number of rows = the number of chunks <I>Nchunk</I> as calculated by the
+specified <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. If a
+single input is specified, a global vector is produced. If two or
+more inputs are specified, a global array is produced where the number
+of columns = the number of inputs. The vector or array can be
+accessed by any command that uses global values from a compute as
+input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+of LAMMPS output options.
+</P>
+<P>The vector or array values are "intensive". The values will be
+unitless or in the units discussed above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_property_local.html b/doc/doc2/compute_property_local.html
new file mode 100644
index 000000000..440fa21fe
--- /dev/null
+++ b/doc/doc2/compute_property_local.html
@@ -0,0 +1,151 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute property/local command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID property/local input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>property/local = style name of this compute command
+
+<LI>input = one or more attributes
+
+<PRE> possible attributes = natom1 natom2 ntype1 ntype2
+ patom1 patom2 ptype1 ptype2
+ batom1 batom2 btype
+ aatom1 aatom2 aatom3 atype
+ datom1 datom2 datom3 dtype
+ iatom1 iatom2 iatom3 itype
+</PRE>
+<PRE> natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
+ ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
+ patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
+ ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
+ batom1, batom2 = IDs of 2 atoms in each bond
+ btype = bond type of each bond
+ aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
+ atype = angle type of each angle
+ datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
+ dtype = dihedral type of each dihedral
+ iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
+ itype = improper type of each improper
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all property/local btype batom1 batom2
+compute 1 all property/local atype aatom2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that stores the specified attributes as local
+data so it can be accessed by other <A HREF = "Section_howto.html#howto_15">output
+commands</A>. If the input attributes refer
+to bond information, then the number of datums generated, aggregated
+across all processors, equals the number of bonds in the system.
+Ditto for pairs, angles, etc.
+</P>
+<P>If multiple input attributes are specified then they must all generate
+the same amount of information, so that the resulting local array has
+the same number of rows for each column. This means that only bond
+attributes can be specified together, or angle attributes, etc. Bond
+and angle attributes can not be mixed in the same compute
+property/local command.
+</P>
+<P>If the inputs are pair attributes, the local data is generated by
+looping over the pairwise neighbor list. Info about an individual
+pairwise interaction will only be included if both atoms in the pair
+are in the specified compute group. For <I>natom1</I> and <I>natom2</I>, all
+atom pairs in the neighbor list are considered (out to the neighbor
+cutoff = force cutoff + <A HREF = "neighbor.html">neighbor skin</A>). For <I>patom1</I>
+and <I>patom2</I>, the distance between the atoms must be less than the
+force cutoff distance for that pair to be included, as defined by the
+<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
+commands.
+</P>
+<P>If the inputs are bond, angle, etc attributes, the local data is
+generated by looping over all the atoms owned on a processor and
+extracting bond, angle, etc info. For bonds, info about an individual
+bond will only be included if both atoms in the bond are in the
+specified compute group. Likewise for angles, dihedrals, etc.
+</P>
+<P>For bonds and angles, a bonds/angles that have been broken by setting
+their bond/angle type to 0 will not be included. Bonds/angles that
+have been turned off (see the <A HREF = "fix_shake.html">fix shake</A> or
+<A HREF = "delete_bonds.html">delete_bonds</A> commands) by setting their bond/angle
+type negative are written into the file. This is consistent with the
+<A HREF = "compute_bond_local.html">compute bond/local</A> and <A HREF = "compute_angle_local.html">compute
+angle/local</A> commands
+</P>
+<P>Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next. The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, output from the <A HREF = "compute_bond_local.html">compute
+bond/local</A> command can be combined with bond
+atom indices from this command and output by the <A HREF = "dump.html">dump
+local</A> command in a consistent way.
+</P>
+<P>The <I>natom1</I> and <I>natom2</I>, or <I>patom1</I> and <I>patom2</I> attributes refer
+to the atom IDs of the 2 atoms in each pairwise interaction computed
+by the <A HREF = "pair_style.html">pair_style</A> command. The <I>ntype1</I> and
+<I>ntype2</I>, or <I>ptype1</I> and <I>ptype2</I> attributes refer to the atom types
+of the 2 atoms in each pairwise interaction.
+</P>
+<P>IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3,
+1-4 interactions within the molecular topology, their pairwise
+interaction may be turned off, and thus they may not appear in the
+neighbor list, and will not be part of the local data created by this
+command. More specifically, this may be true of I,J pairs with a
+weighting factor of 0.0; pairs with a non-zero weighting factor are
+included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
+interactions are set by the <A HREF = "special_bonds.html">special_bonds</A>
+command.
+</P>
+<P>The <I>batom1</I> and <I>batom2</I> attributes refer to the atom IDs of the 2
+atoms in each <A HREF = "bond_style.html">bond</A>. The <I>btype</I> attribute refers to
+the type of the bond, from 1 to Nbtypes = # of bond types. The number
+of bond types is defined in the data file read by the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>The attributes that start with "a", "d", "i", refer to similar values
+for <A HREF = "angle_style.html">angles</A>, <A HREF = "dihedral_style.html">dihedrals</A>, and
+<A HREF = "improper_style.html">impropers</A>.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a local vector or local array depending on the
+number of input values. The length of the vector or number of rows in
+the array is the number of bonds, angles, etc. If a single input is
+specified, a local vector is produced. If two or more inputs are
+specified, a local array is produced where the number of columns = the
+number of inputs. The vector or array can be accessed by any command
+that uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector or array values will be integers that correspond to the
+specified attribute.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_reduce.html">compute reduce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_rdf.html b/doc/doc2/compute_rdf.html
new file mode 100644
index 000000000..c2af825cc
--- /dev/null
+++ b/doc/doc2/compute_rdf.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute rdf command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>rdf = style name of this compute command
+<LI>Nbin = number of RDF bins
+<LI>itypeN = central atom type for Nth RDF histogram (see asterisk form below)
+<LI>jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all rdf 100
+compute 1 all rdf 100 1 1
+compute 1 all rdf 100 * 3
+compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
+compute 1 fluid rdf 500 1*3 2 5 *10
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the radial distribution function
+(RDF), also called g(r), and the coordination number for a group of
+particles. Both are calculated in histogram form by binning pairwise
+distances into <I>Nbin</I> bins from 0.0 to the maximum force cutoff
+defined by the <A HREF = "pair_style.html">pair_style</A> command. The bins are of
+uniform size in radial distance. Thus a single bin encompasses a thin
+shell of distances in 3d and a thin ring of distances in 2d.
+</P>
+<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
+<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral. This
+is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
+command, and means those pairwise interactions do not appear in the
+neighbor list. Because this fix uses the neighbor list, it also means
+those pairs will not be included in the RDF. One way to get around
+this, is to write a dump file, and use the <A HREF = "rerun.html">rerun</A> command
+to compute the RDF for snapshots in the dump file. The rerun script
+can use a <A HREF = "special_bonds.html">special_bonds</A> command that includes all
+pairs in the neighbor list.
+</P>
+<P>The <I>itypeN</I> and <I>jtypeN</I> arguments are optional. These arguments
+must come in pairs. If no pairs are listed, then a single histogram
+is computed for g(r) between all atom types. If one or more pairs are
+listed, then a separate histogram is generated for each
+<I>itype</I>,<I>jtype</I> pair.
+</P>
+<P>The <I>itypeN</I> and <I>jtypeN</I> settings can be specified in one of two
+ways. An explicit numeric value can be used, as in the 4th example
+above. Or a wild-card asterisk can be used to specify a range of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+</P>
+<P>If both <I>itypeN</I> and <I>jtypeN</I> are single values, as in the 4th example
+above, this means that a g(r) is computed where atoms of type <I>itypeN</I>
+are the central atom, and atoms of type <I>jtypeN</I> are the distribution
+atom. If either <I>itypeN</I> and <I>jtypeN</I> represent a range of values via
+the wild-card asterisk, as in the 5th example above, this means that a
+g(r) is computed where atoms of any of the range of types represented
+by <I>itypeN</I> are the central atom, and atoms of any of the range of
+types represented by <I>jtypeN</I> are the distribution atom.
+</P>
+<P>Pairwise distances are generated by looping over a pairwise neighbor
+list, just as they would be in a <A HREF = "pair_style.html">pair_style</A>
+computation. The distance between two atoms I and J is included in a
+specific histogram if the following criteria are met:
+</P>
+<UL><LI>atoms I,J are both in the specified compute group
+<LI>the distance between atoms I,J is less than the maximum force cutoff
+<LI>the type of the I atom matches itypeN (one or a range of types)
+<LI>the type of the J atom matches jtypeN (one or a range of types)
+</UL>
+<P>It is OK if a particular pairwise distance is included in more than
+one individual histogram, due to the way the <I>itypeN</I> and <I>jtypeN</I>
+arguments are specified.
+</P>
+<P>The g(r) value for a bin is calculated from the histogram count by
+scaling it by the idealized number of how many counts there would be
+if atoms of type <I>jtypeN</I> were uniformly distributed. Thus it
+involves the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the
+volume of the entire simulation box, and the volume of the bin's thin
+shell in 3d (or the area of the bin's thin ring in 2d).
+</P>
+<P>A coordination number coord(r) is also calculated, which is the number
+of atoms of type <I>jtypeN</I> within the current bin or closer, averaged
+over atoms of type <I>itypeN</I>. This is calculated as the area- or
+volume-weighted sum of g(r) values over all bins up to and including
+the current bin, multiplied by the global average volume density of
+atoms of type jtypeN.
+</P>
+<P>The simplest way to output the results of the compute rdf calculation
+to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A> command, for
+example:
+</P>
+<PRE>compute myRDF all rdf 50
+fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array with the number of rows =
+<I>Nbins</I>, and the number of columns = 1 + 2*Npairs, where Npairs is the
+number of I,J pairings specified. The first column has the bin
+coordinate (center of the bin), Each successive set of 2 columns has
+the g(r) and coord(r) values for a specific set of <I>itypeN</I> versus
+<I>jtypeN</I> interactions, as described above. These values can be used
+by any command that uses a global values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
+LAMMPS output options.
+</P>
+<P>The array values calculated by this compute are all "intensive".
+</P>
+<P>The first column of array values will be in distance
+<A HREF = "units.html">units</A>. The g(r) columns of array values are normalized
+numbers >= 0.0. The coordination number columns of array values are
+also numbers >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The RDF is not computed for distances longer than the force cutoff,
+since processors (in parallel) don't know about atom coordinates for
+atoms further away than that distance. If you want an RDF for larger
+distances, you can use the <A HREF = "rerun.html">rerun</A> command to post-process
+a dump file. The definition of g(r) used by LAMMPS is only appropriate
+for characterizing atoms that are uniformly distributed throughout the
+simulation cell. In such cases, the coordination number is still
+correct and meaningful. As an example, if a large simulation cell
+contains only one atom of type <I>itypeN</I> and one of <I>jtypeN</I>, then g(r)
+will register an arbitrarily large spike at whatever distance they
+happen to be at, and zero everywhere else. coord(r) will show a step
+change from zero to one at the location of the spike in g(r).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_time.html">fix ave/time</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_reduce.html b/doc/doc2/compute_reduce.html
new file mode 100644
index 000000000..ce267fe4e
--- /dev/null
+++ b/doc/doc2/compute_reduce.html
@@ -0,0 +1,200 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute reduce command
+</H3>
+<H3>compute reduce/region command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID style arg mode input1 input2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>style = <I>reduce</I> or <I>reduce/region</I>
+
+<PRE> <I>reduce</I> arg = none
+ <I>reduce/region</I> arg = region-ID
+ region-ID = ID of region to use for choosing atoms
+</PRE>
+<LI>mode = <I>sum</I> or <I>min</I> or <I>max</I> or <I>ave</I> or <I>sumsq</I> or <I>avesq</I>
+
+<LI>one or more inputs can be listed
+
+<LI>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+ c_ID = per-atom or local vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
+ f_ID = per-atom or local vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+<LI>zero or more keyword/args pairs may be appended
+
+<LI>keyword = <I>replace</I>
+
+<PRE> <I>replace</I> args = vec1 vec2
+ vec1 = reduced value from this input vector will be replaced
+ vec2 = replace it with vec1[N] where N is index of max/min value from vec2
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all reduce sum c_force
+compute 1 all reduce/region subbox sum c_force
+compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a calculation that "reduces" one or more vector inputs into
+scalar values, one per listed input. The inputs can be per-atom or
+local quantities; they cannot be global quantities. Atom attributes
+are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>
+may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style
+variables</A> generate per-atom quantities. See the
+<A HREF = "variable">variable</A> command and its special functions which can
+perform the same operations as the compute reduce command on global
+vectors.
+</P>
+<P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I>
+option adds the values in the vector into a global total. The <I>min</I>
+or <I>max</I> options find the minimum or maximum value across all vector
+values. The <I>ave</I> setting adds the vector values into a global total,
+then divides by the number of values in the vector. The <I>sumsq</I>
+option sums the square of the values in the vector into a global
+total. The <I>avesq</I> setting does the same as <I>sumsq</I>, then divdes the
+sum of squares by the number of values. The last two options can be
+useful for calculating the variance of some quantity, e.g. variance =
+sumsq - ave^2.
+</P>
+<P>Each listed input is operated on independently. For per-atom inputs,
+the group specified with this command means only atoms within the
+group contribute to the result. For per-atom inputs, if the compute
+reduce/region command is used, the atoms must also currently be within
+the region. Note that an input that produces per-atom quantities may
+define its own group which affects the quantities it returns. For
+example, if a compute is used as an input which generates a per-atom
+vector, it will generate values of 0.0 for atoms that are not in the
+group specified for that compute.
+</P>
+<P>Each listed input can be an atom attribute (position, velocity, force
+component) or can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an atom-style
+<A HREF = "variable.html">variable</A>.
+</P>
+<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory. Note that other atom attributes can be used as
+inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. Computes can generate
+per-atom or local quantities. See the individual
+<A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer
+is appended, the vector calculated by the compute is used. If a
+bracketed integer is appended, the Ith column of the array calculated
+by the compute is used. Users can also write code for their own
+compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. Fixes can generate per-atom
+or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for
+details. Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute reduce
+references the values, else an error results. If no bracketed integer
+is appended, the vector calculated by the fix is used. If a bracketed
+integer is appended, the Ith column of the array calculated by the fix
+is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add
+them to LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. It must be an
+<A HREF = "variable.html">atom-style variable</A>. Atom-style variables can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to
+reduce.
+</P>
+<HR>
+
+<P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are
+specified, where each index ranges from 1 to the # of input values.
+The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>.
+It works as follows. A min/max is computed as usual on the <I>vec2</I>
+input vector. The index N of that value within <I>vec2</I> is also stored.
+Then, instead of performing a min/max on the <I>vec1</I> input vector, the
+stored index is used to select the Nth element of the <I>vec1</I> vector.
+</P>
+<P>Thus, for example, if you wish to use this compute to find the bond
+with maximum stretch, you can do it as follows:
+</P>
+<PRE>compute 1 all property/local batom1 batom2
+compute 2 all bond/local dist
+compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3[1] c_3[2] c_3[3]
+</PRE>
+<P>The first two input values in the compute reduce command are vectors
+with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute
+property/local</A> command. The last input
+value is bond distance, using the <A HREF = "compute_bond_local.html">compute
+bond/local</A> command. Instead of taking the
+max of the two atom ID vectors, which does not yield useful
+information in this context, the <I>replace</I> keywords will extract the
+atom IDs for the two atoms in the bond of maximum stretch. These atom
+IDs and the bond stretch will be printed with thermodynamic output.
+</P>
+<HR>
+
+<P>If a single input is specified this compute produces a global scalar
+value. If multiple inputs are specified, this compute produces a
+global vector of values, the length of which is equal to the number of
+inputs specified.
+</P>
+<P>As discussed below, for the <I>sum</I> and <I>sumsq</I> modes, the value(s)
+produced by this compute are all "extensive", meaning their value
+scales linearly with the number of atoms involved. If normalized
+values are desired, this compute can be accessed by the <A HREF = "thermo_style.html">thermo_style
+custom</A> command with <A HREF = "thermo_modify.html">thermo_modify norm
+yes</A> set as an option. Or it can be accessed by a
+<A HREF = "variable.html">variable</A> that divides by the appropriate atom count.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar if a single input value is
+specified or a global vector of length N where N is the number of
+inputs, and which can be accessed by indices 1 to N. These values can
+be used by any command that uses global scalar or vector values from a
+compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
+for an overview of LAMMPS output options.
+</P>
+<P>All the scalar or vector values calculated by this compute are
+"intensive", except when the <I>sum</I> or <I>sumsq</I> modes are used on
+per-atom or local vectors, in which case the calculated values are
+"extensive".
+</P>
+<P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the
+quantities being reduced are in.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_saed.html b/doc/doc2/compute_saed.html
new file mode 100644
index 000000000..c99d3ae82
--- /dev/null
+++ b/doc/doc2/compute_saed.html
@@ -0,0 +1,191 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute saed command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>saed = style name of this compute command
+
+<LI>lambda = wavelength of incident radiation (length units)
+
+<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>Kmax</I> or <I>Zone</I> or <I>dR_Ewald</I> or <I>c</I> or <I>manual</I> or <I>echo</I>
+
+<PRE> <I>Kmax</I> value = Maximum distance explored from reciprocal space origin
+ (inverse length units)
+ <I>Zone</I> values = z1 z2 z3
+ z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
+ reciprocal space will be meshed up to <I>Kmax</I>
+ <I>dR_Ewald</I> value = Thickness of Ewald sphere slice intercepting
+ reciprocal space (inverse length units)
+ <I>c</I> values = c1 c2 c3
+ c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+ lattice nodes in the h, k, and l directions respectively
+ <I>manual</I> = flag to use manual spacing of reciprocal lattice points
+ based on the values of the <I>c</I> parameters
+ <I>echo</I> = flag to provide extra output for debugging purposes
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+</PRE>
+<PRE>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates electron diffraction intensity as
+described in <A HREF = "#Coleman">(Coleman)</A> on a mesh of reciprocal lattice nodes
+defined by the entire simulation domain (or manually) using simulated
+radiation of wavelength lambda.
+</P>
+<P>The electron diffraction intensity I at each reciprocal lattice point
+is computed from the structure factor F using the equations:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_saed1.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/compute_saed2.jpg">
+</CENTER>
+<P>Here, K is the location of the reciprocal lattice node, rj is the
+position of each atom, fj are atomic scattering factors.
+</P>
+<P>Diffraction intensities are calculated on a three-dimensional mesh of
+reciprocal lattice nodes. The mesh spacing is defined either (a) by
+the entire simulation domain or (b) manually using selected values as
+shown in the 2D diagram below.
+</P>
+<CENTER><A HREF = "JPG/saed_mesh.jpg"><IMG SRC = "JPG/saed_mesh_small.jpg"></A>
+</CENTER>
+<P>For a mesh defined by the simulation domain, a rectilinear grid is
+constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
+axis. Where A are the vectors corresponding to the edges of the
+simulation cell. If one or two directions has non-periodic boundary
+conditions, then the spacing in these directions is defined from the
+average of the (inversed) box lengths with periodic boundary conditions.
+Meshes defined by the simulation domain must contain at least one periodic
+boundary.
+</P>
+<P>If the <I>manual</I> flag is included, the mesh of reciprocal lattice nodes
+will defined using the <I>c</I> values for the spacing along each reciprocal
+lattice axis. Note that manual mapping of the reciprocal space mesh is
+good for comparing diffraction results from multiple simulations; however
+it can reduce the likelihood that Bragg reflections will be satisfied
+unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
+Meshes with manual spacing do not require a periodic boundary.
+</P>
+<P>The limits of the reciprocal lattice mesh are determined by the use of
+the <I>Kmax</I>, <I>Zone</I>, and <I>dR_Ewald</I> parameters. The rectilinear mesh
+created about the origin of reciprocal space is terminated at the
+boundary of a sphere of radius <I>Kmax</I> centered at the origin. If
+<I>Zone</I> parameters z1=z2=z3=0 are used, diffraction intensities are
+computed throughout the entire spherical volume - note this can greatly
+increase the cost of computation. Otherwise, <I>Zone</I> parameters will
+denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
+intersecting Ewald sphere. Diffraction intensities will only be
+computed at the intersection of the reciprocal lattice mesh and a
+<I>dR_Ewald</I> thick surface of the Ewald sphere. See the example 3D
+intestiety data and the intersection of a [010] zone axis in the below image.
+</P>
+<CENTER><A HREF = "JPG/saed_ewald_intersect.jpg"><IMG SRC = "JPG/saed_ewald_intersect_small.jpg"></A>
+</CENTER>
+<P>The atomic scattering factors, fj, accounts for the reduction in
+diffraction intensity due to Compton scattering. Compute saed uses
+analytical approximations of the atomic scattering factors that vary
+for each atom type (type1 type2 ... typeN) and angle of diffraction.
+The analytic approximation is computed using the formula
+<A HREF = "#Brown">(Brown)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_saed3.jpg">
+</CENTER>
+<P>Coefficients parameterized by <A HREF = "#Fox">(Fox)</A> are assigned for each
+atom type designating the chemical symbol and charge of each atom
+type. Valid chemical symbols for compute saed are:
+</P>
+<P> H: He: Li: Be: B:
+ C: N: O: F: Ne:
+ Na: Mg: Al: Si: P:
+ S: Cl: Ar: K: Ca:
+ Sc: Ti: V: Cr: Mn:
+ Fe: Co: Ni: Cu: Zn:
+ Ga: Ge: As: Se: Br:
+ Kr: Rb: Sr: Y: Zr:
+ Nb: Mo: Tc: Ru: Rh:
+ Pd: Ag: Cd: In: Sn:
+ Sb: Te: I: Xe: Cs:
+ Ba: La: Ce: Pr: Nd:
+ Pm: Sm: Eu: Gd: Tb:
+ Dy: Ho: Er: Tm: Yb:
+ Lu: Hf: Ta: W: Re:
+ Os: Ir: Pt: Au: Hg:
+ Tl: Pb: Bi: Po: At:
+ Rn: Fr: Ra: Ac: Th:
+ Pa: U: Np: Pu: Am:
+ Cm: Bk: Cf:tb(c=5,s=:)
+</P>
+<P>If the <I>echo</I> keyword is specified, compute saed will provide extra
+reporting information to the screen.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector. The length of the vector is
+the number of reciprocal lattice nodes that are explored by the mesh.
+The entries of the global vector are the computed diffraction
+intensities as described above.
+</P>
+<P>The vector can be accessed by any command that uses global values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>All array values calculated by this compute are "intensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The compute_saed command does not work for triclinic cells.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_saed_vtk.html">fix saed_vtk</A>, <A HREF = "compute_xrd.html">compute xrd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
+0.01.
+</P>
+<HR>
+
+<A NAME = "Coleman"></A>
+
+<P><B>(Coleman)</B> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+</P>
+<A NAME = "Brown"></A>
+
+<P><B>(Brown)</B> Brown et al. International Tables for Crystallography
+Volume C: Mathematical and Chemical Tables, 554-95 (2004).
+</P>
+<A NAME = "Fox"></A>
+
+<P><B>(Fox)</B> Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
+(1989).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_slice.html b/doc/doc2/compute_slice.html
new file mode 100644
index 000000000..e4f82a165
--- /dev/null
+++ b/doc/doc2/compute_slice.html
@@ -0,0 +1,124 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute slice command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID slice Nstart Nstop Nskip input1 input2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>slice = style name of this compute command
+
+<LI>Nstart = starting index within input vector(s)
+
+<LI>Nstop = stopping index within input vector(s)
+
+<LI>Nskip = extract every Nskip elements from input vector(s)
+
+<LI>input = c_ID, c_ID[N], f_ID, f_ID[N]
+
+<PRE> c_ID = global vector calculated by a compute with ID
+ c_ID[I] = Ith column of global array calculated by a compute with ID
+ f_ID = global vector calculated by a fix with ID
+ f_ID[I] = Ith column of global array calculated by a fix with ID
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all slice 1 100 10 c_msdmol[4]
+compute 1 all slice 301 400 1 c_msdmol[4]
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a calculation that "slices" one or more vector inputs into
+smaller vectors, one per listed input. The inputs can be global
+quantities; they cannot be per-atom or local quantities.
+<A HREF = "compute.html">Computes</A> and <A HREF = "fix.html">fixes</A> may generate any of the
+three kinds of quantities. <A HREF = "variable.html">Variables</A> do not generate
+global vectors. The group specified with this command is ignored.
+</P>
+<P>The values extracted from the input vector(s) are determined by the
+<I>Nstart</I>, <I>Nstop</I>, and <I>Nskip</I> parameters. The elements of an input
+vector of length N are indexed from 1 to N. Starting at element
+<I>Nstart</I>, every Mth element is extracted, where M = <I>Nskip</I>, until
+element <I>Nstop</I> is reached. The extracted quantities are stored as a
+vector, which is typically shorter than the input vector.
+</P>
+<P>Each listed input is operated on independently to produce one output
+vector. Each listed input must be a global vector or column of a
+global array calculated by another <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A>.
+</P>
+<P>If an input value begins with "c_", a compute ID must follow which has
+been previously defined in the input script and which generates a
+global vector or array. See the individual <A HREF = "compute.html">compute</A> doc
+page for details. If no bracketed integer is appended, the vector
+calculated by the compute is used. If a bracketed integer is
+appended, the Ith column of the array calculated by the compute is
+used. Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add
+them to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script and which generates a global
+vector or array. See the individual <A HREF = "fix.html">fix</A> doc page for
+details. Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute slice references
+the values, else an error results. If no bracketed integer is
+appended, the vector calculated by the fix is used. If a bracketed
+integer is appended, the Ith column of the array calculated by the fix
+is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add
+them to LAMMPS</A>.
+</P>
+<P>If a single input is specified this compute produces a global vector,
+even if the length of the vector is 1. If multiple inputs are
+specified, then a global array of values is produced, with the number
+of columns equal to the number of inputs specified.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector if a single input value is
+specified or a global array with N columns where N is the number of
+inputs. The length of the vector or the number of rows in the array
+is equal to the number of values extracted from each input vector.
+These values can be used by any command that uses global vector or
+array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector or array values calculated by this compute are simply
+copies of values generated by computes or fixes that are input vectors
+to this compute. If there is a single input vector of intensive
+and/or extensive values, then each value in the vector of values
+calculated by this compute will be "intensive" or "extensive",
+depending on the corresponding input value. If there are multiple
+input vectors, and all the values in them are intensive, then the
+array values calculated by this compute are "intensive". If there are
+multiple input vectors, and any value in them is extensive, then the
+array values calculated by this compute are "extensive".
+</P>
+<P>The vector or array values will be in whatever <A HREF = "units.html">units</A> the
+input quantities are in.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, <A HREF = "compute_reduce.html">compute
+reduce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_sna_atom.html b/doc/doc2/compute_sna_atom.html
new file mode 100644
index 000000000..9e9b25d1d
--- /dev/null
+++ b/doc/doc2/compute_sna_atom.html
@@ -0,0 +1,262 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute sna/atom command
+</H3>
+<H3>compute snad/atom command
+</H3>
+<H3>compute snav/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID sna/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snad/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>sna/atom = style name of this compute command
+
+<LI>rcutfac = scale factor applied to all cutoff radii (positive real)
+
+<LI>rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1)
+
+<LI>twojmax = band limit for bispectrum components (non-negative integer)
+
+<LI>R_1, R_2,... = list of cutoff radii, one for each type (distance units)
+
+<LI>w_1, w_2,... = list of neighbor weights, one for each type
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>diagonal</I> or <I>rmin0</I> or <I>switchflag</I>
+
+<PRE> <I>diagonal</I> value = <I>0</I> or <I>1</I> or <I>2</I> or <I>3</I>
+ <I>0</I> = all j1, j2, j <= twojmax, j2 <= j1
+ <I>1</I> = subset satisfying j1 == j2
+ <I>2</I> = subset satisfying j1 == j2 == j3
+ <I>3</I> = subset satisfying j2 <= j1 <= j
+ <I>rmin0</I> value = parameter in distance to angle conversion (distance units)
+ <I>switchflag</I> value = <I>0</I> or <I>1</I>
+ <I>0</I> = do not use switching function
+ <I>1</I> = use switching function
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0
+compute db all sna/atom 1.4 0.95 6 2.0 1.0
+compute vb all sna/atom 1.4 0.95 6 2.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates a set of bispectrum components
+for each atom in a group.
+</P>
+<P>Bispectrum components of an atom are order parameters characterizing
+the radial and angular distribution of neighbor atoms. The detailed
+mathematical definition is given in the paper by Thompson et
+al. <A HREF = "#Thompson2014">(Thompson)</A>
+</P>
+<P>The position of a neighbor atom <I>i'</I> relative to a central atom <I>i</I> is
+a point within the 3D ball of radius <I>R_ii' = rcutfac*(R_i + R_i')</I>
+</P>
+<P>Bartok et al. <A HREF = "#Bartok2010">(Bartok)</A>, proposed mapping this 3D ball
+onto the 3-sphere, the surface of the unit ball in a four-dimensional
+space. The radial distance <I>r</I> within <I>R_ii'</I> is mapped on to a third
+polar angle <I>theta0</I> defined by,
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom1.jpg">
+</CENTER>
+<P>In this way, all possible neighbor positions are mapped on to a subset
+of the 3-sphere. Points south of the latitude <I>theta0max=rfac0*Pi</I>
+are excluded.
+</P>
+<P>The natural basis for functions on the 3-sphere is formed by the 4D
+hyperspherical harmonics <I>U^j_m,m'(theta, phi, theta0).</I> These
+functions are better known as <I>D^j_m,m',</I> the elements of the Wigner
+<I>D</I>-matrices <A HREF = "#Meremianin2006">(Meremianin</A>,
+<A HREF = "#Varshalovich1987">Varshalovich)</A>.
+</P>
+<P>The density of neighbors on the 3-sphere can be written as a sum of
+Dirac-delta functions, one for each neighbor, weighted by species and
+radial distance. Expanding this density function as a generalized
+Fourier series in the basis functions, we can write each Fourier
+coefficient as
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom2.jpg">
+</CENTER>
+<P>The <I>w_i'</I> neighbor weights are dimensionless numbers that are chosen
+to distinguish atoms of different types, while the central atom is
+arbitrarily assigned a unit weight. The function <I>fc(r)</I> ensures that
+the contribution of each neighbor atom goes smoothly to zero at
+<I>R_ii'</I>:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom4.jpg">
+</CENTER>
+<P>The expansion coefficients <I>u^j_m,m'</I> are complex-valued and they are
+not directly useful as descriptors, because they are not invariant
+under rotation of the polar coordinate frame. However, the following
+scalar triple products of expansion coefficients can be shown to be
+real-valued and invariant under rotation <A HREF = "#Bartok2010">(Bartok)</A>.
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom3.jpg">
+</CENTER>
+<P>The constants <I>H^jmm'_j1m1m1'_j2m2m2'</I> are coupling coefficients,
+analogous to Clebsch-Gordan coefficients for rotations on the
+2-sphere. These invariants are the components of the bispectrum and
+these are the quantities calculated by the compute <I>sna/atom</I>. They
+characterize the strength of density correlations at three points on
+the 3-sphere. The j2=0 subset form the power spectrum, which
+characterizes the correlations of two points. The lowest-order
+components describe the coarsest features of the density function,
+while higher-order components reflect finer detail. Note that the
+central atom is included in the expansion, so three point-correlations
+can be either due to three neighbors, or two neighbors and the central
+atom.
+</P>
+<P>Compute <I>snad/atom</I> calculates the derivative of the bispectrum components
+summed separately for each atom type:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom5.jpg">
+</CENTER>
+<P>The sum is over all atoms <I>i'</I> of atom type <I>I</I>. For each atom <I>i</I>,
+this compute evaluates the above expression for each direction, each
+atom type, and each bispectrum component. See section below on output
+for a detailed explanation.
+</P>
+<P>Compute <I>snav/atom</I> calculates the virial contribution due to the
+derivatives:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_sna_atom6.jpg">
+</CENTER>
+<P>Again, the sum is over all atoms <I>i'</I> of atom type <I>I</I>. For each atom
+<I>i</I>, this compute evaluates the above expression for each of the six
+virial components, each atom type, and each bispectrum component. See
+section below on output for a detailed explanation.
+</P>
+<P>The value of all bispectrum components will be zero for atoms not in
+the group. Neighbor atoms not in the group do not contribute to the
+bispectrum of atoms in the group.
+</P>
+<P>The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (i.e. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently.
+</P>
+<P>The argument <I>rcutfac</I> is a scale factor that controls the ratio of
+atomic radius to radial cutoff distance.
+</P>
+<P>The argument <I>rfac0</I> and the optional keyword <I>rmin0</I> define the
+linear mapping from radial distance to polar angle <I>theta0</I> on the
+3-sphere.
+</P>
+<P>The argument <I>twojmax</I> and the keyword <I>diagonal</I> define which
+bispectrum components are generated. See section below on output for a
+detailed explanation of the number of bispectrum components and the
+ordered in which they are listed
+</P>
+<P>The keyword <I>switchflag</I> can be used to turn off the switching
+function.
+</P>
+<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
+<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral. This
+is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
+command, and means those pairwise interactions do not appear in the
+neighbor list. Because this fix uses the neighbor list, it also means
+those pairs will not be included in the calculation. One way to get
+around this, is to write a dump file, and use the <A HREF = "rerun.html">rerun</A>
+command to compute the bispectrum components for snapshots in the dump
+file. The rerun script can use a <A HREF = "special_bonds.html">special_bonds</A>
+command that includes all pairs in the neighbor list.
+</P>
+<P>;line
+</P>
+<P><B>Output info:</B>
+</P>
+<P>Compute <I>sna/atom</I> calculates a per-atom array, each column
+corresponding to a particular bispectrum component. The total number
+of columns and the identities of the bispectrum component contained in
+each column depend on the values of <I>twojmax</I> and <I>diagonal</I>, as
+described by the following piece of python code:
+</P>
+<PRE>for j1 in range(0,twojmax+1):
+ if(diagonal==2):
+ print j1/2,j1/2,j1/2
+ elif(diagonal==1):
+ for j in range(0,min(twojmax,2*j1)+1,2):
+ print j1/2,j1/2,j/2
+ elif(diagonal==0):
+ for j2 in range(0,j1+1):
+ for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+ print j1/2,j2/2,j/2
+ elif(diagonal==3):
+ for j2 in range(0,j1+1):
+ for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+ if (j>=j1): print j1/2,j2/2,j/2
+</PRE>
+<P>Compute <I>snad/atom</I> evaluates a per-atom array. The columns are
+arranged into <I>ntypes</I> blocks, listed in order of atom type <I>I</I>. Each
+block contains three sub-blocks corresponding to the <I>x</I>, <I>y</I>, and <I>z</I>
+components of the atom position. Each of these sub-blocks contains
+one column for each bispectrum component, the same as for compute
+<I>sna/atom</I>
+</P>
+<P>Compute <I>snav/atom</I> evaluates a per-atom array. The columns are
+arranged into <I>ntypes</I> blocks, listed in order of atom type <I>I</I>. Each
+block contains six sub-blocks corresponding to the <I>xx</I>, <I>yy</I>, <I>zz</I>,
+<I>yz</I>, <I>xz</I>, and <I>xy</I> components of the virial tensor in Voigt
+notation. Each of these sub-blocks contains one column for each
+bispectrum component, the same as for compute <I>sna/atom</I>
+</P>
+<P>These values can be accessed by any command that uses per-atom values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These computes are part of the SNAP package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_snap.html">pair_style snap</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The optional keyword defaults are <I>diagonal</I> = 0, <I>rmin0</I> = 0,
+<I>switchflag</I> = 1.
+</P>
+<HR>
+
+<A NAME = "Thompson2014"></A>
+
+<P><B>(Thompson)</B> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
+available at <A HREF = "http://arxiv.org/abs/1409.3880">arXiv:1409.3880</A>
+</P>
+<A NAME = "Bartok2010"></A>
+
+<P><B>(Bartok)</B> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
+</P>
+<A NAME = "Meremianin2006"></A>
+
+<P><B>(Meremianin)</B> Meremianin, J. Phys. A, 39, 3099 (2006).
+</P>
+<A NAME = "Varshalovich1987"></A>
+
+<P><B>(Varshalovich)</B> Varshalovich, Moskalev, Khersonskii, Quantum Theory
+of Angular Momentum, World Scientific, Singapore (1987).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_stress_atom.html b/doc/doc2/compute_stress_atom.html
new file mode 100644
index 000000000..52089c9ae
--- /dev/null
+++ b/doc/doc2/compute_stress_atom.html
@@ -0,0 +1,172 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute stress/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID stress/atom temp-ID keyword ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>stress/atom = style name of this compute command
+<LI>temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+<LI>zero or more keywords may be appended
+<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 mobile stress/atom NULL
+compute 1 mobile stress/atom myRamp
+compute 1 all stress/atom NULL pair bond
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that computes the symmetric per-atom stress
+tensor for each atom in a group. The tensor for each atom has 6
+components and is stored as a 6-element vector in the following order:
+xx, yy, zz, xy, xz, yz. See the <A HREF = "compute_pressure.html">compute
+pressure</A> command if you want the stress tensor
+(pressure) of the entire system.
+</P>
+<P>The stress tensor for atom <I>I</I> is given by the following formula,
+where <I>a</I> and <I>b</I> take on values x,y,z to generate the 6 components of
+the symmetric tensor:
+</P>
+<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
+</CENTER>
+<P>The first term is a kinetic energy contribution for atom <I>I</I>. See
+details below on how the specified <I>temp-ID</I> can affect the velocities
+used in this calculation. The second term is a pairwise energy
+contribution where <I>n</I> loops over the <I>Np</I> neighbors of atom <I>I</I>, <I>r1</I>
+and <I>r2</I> are the positions of the 2 atoms in the pairwise interaction,
+and <I>F1</I> and <I>F2</I> are the forces on the 2 atoms resulting from the
+pairwise interaction. The third term is a bond contribution of
+similar form for the <I>Nb</I> bonds which atom <I>I</I> is part of. There are
+similar terms for the <I>Na</I> angle, <I>Nd</I> dihedral, and <I>Ni</I> improper
+interactions atom <I>I</I> is part of. There is also a term for the KSpace
+contribution from long-range Coulombic interactions, if defined.
+Finally, there is a term for the <I>Nf</I> <A HREF = "fix.html">fixes</A> that apply
+internal constraint forces to atom <I>I</I>. Currently, only the <A HREF = "fix_shake.html">fix
+shake</A> and <A HREF = "fix_rigid.html">fix rigid</A> commands
+contribute to this term.
+</P>
+<P>As the coefficients in the formula imply, a virial contribution
+produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
+atoms in a Tersoff 3-body interaction) is assigned in equal portions
+to each atom in the set. E.g. 1/4 of the dihedral virial to each of
+the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
+to atoms in a a water molecule via the <A HREF = "fix_shake.html">fix shake</A>
+command.
+</P>
+<P>If no extra keywords are listed, all of the terms in this formula are
+included in the per-atom stress tensor. If any extra keywords are
+listed, only those terms are summed to compute the tensor. The
+<I>virial</I> keyword means include all terms except the kinetic energy
+<I>ke</I>.
+</P>
+<P>Note that the stress for each atom is due to its interaction with all
+other atoms in the simulation, not just with other atoms in the group.
+</P>
+<P>Details of how LAMMPS computes the virial for individual atoms for
+either pairwise or manybody potentials, and including the effects of
+periodic boundary conditions is discussed in <A HREF = "#Thompson">(Thompson)</A>.
+The basic idea for manybody potentials is to treat each component of
+the force computation between a small cluster of atoms in the same
+manner as in the formula above for bond, angle, dihedral, etc
+interactions. Namely the quantity R dot F is summed over the atoms in
+the interaction, with the R vectors unwrapped by periodic boundaries
+so that the cluster of atoms is close together. The total
+contribution for the cluster interaction is divided evenly among those
+atoms.
+</P>
+<P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> style calculates
+pairwise interactions between 1-4 atoms. The virial contribution of
+these terms is included in the pair virial, not the dihedral virial.
+</P>
+<P>The KSpace contribution is calculated using the method in
+<A HREF = "#Heyes">(Heyes)</A> for the Ewald method and by the methodology described
+in <A HREF = "#Sirk">(Sirk)</A> for PPPM. The choice of KSpace solver is specified
+by the <A HREF = "kspace_style.html">kspace_style pppm</A> command. Note that for
+PPPM, the calcluation requires 6 extra FFTs each timestep that
+per-atom stress is calculated. Thus it can significantly increase the
+cost of the PPPM calculation if it is needed on a large fraction of
+the simulation timesteps.
+</P>
+<P>The <I>temp-ID</I> argument can be used to affect the per-atom velocities
+used in the kinetic energy contribution to the total stress. If the
+kinetic energy is not included in the stress, than the temperature
+compute is not used and can be specified as NULL. If the kinetic
+energy is included and you wish to use atom velocities as-is, then
+<I>temp-ID</I> can also be specified as NULL. If desired, the specified
+temperature compute can be one that subtracts off a bias to leave each
+atom with only a thermal velocity to use in the formula above, e.g. by
+subtracting a background streaming velocity. See the doc pages for
+individual <A HREF = "compute.html">compute commands</A> to determine which ones
+include a bias.
+</P>
+<HR>
+
+<P>Note that as defined in the formula, per-atom stress is the negative
+of the per-atom pressure tensor. It is also really a stress*volume
+formulation, meaning the computed quantity is in units of
+pressure*volume. It would need to be divided by a per-atom volume to
+have units of stress (pressure), but an individual atom's volume is
+not well defined or easy to compute in a deformed solid or a liquid.
+See the <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A> command for
+one possible way to estimate a per-atom volume.
+</P>
+<P>Thus, if the diagonal components of the per-atom stress tensor are
+summed for all atoms in the system and the sum is divided by dV, where
+d = dimension and V is the volume of the system, the result should be
+-P, where P is the total pressure of the system.
+</P>
+<P>These lines in an input script for a 3d system should yield that
+result. I.e. the last 2 columns of thermo output will be the same:
+</P>
+<PRE>compute peratom all stress/atom NULL
+compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+thermo_style custom step temp etotal press v_press
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom array with 6 columns, which can be
+accessed by indices 1-6 by any command that uses per-atom values from
+a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The per-atom array values will be in pressure*volume
+<A HREF = "units.html">units</A> as discussed above.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_pe.html">compute pe</A>, <A HREF = "compute_pressure.html">compute pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Heyes"></A>
+
+<P><B>(Heyes)</B> Heyes, Phys Rev B 49, 755 (1994),
+</P>
+<A NAME = "Sirk"></A>
+
+<P><B>(Sirk)</B> Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
+</P>
+<A NAME = "Thompson"></A>
+
+<P><B>(Thompson)</B> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp.html b/doc/doc2/compute_temp.html
new file mode 100644
index 000000000..d669eee5e
--- /dev/null
+++ b/doc/doc2/compute_temp.html
@@ -0,0 +1,117 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp command
+</H3>
+<H3>compute temp/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp
+compute myTemp mobile temp
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms. A compute of this style can be used by any command that
+computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>A compute of this style with the ID of "thermo_temp" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_temp all temp
+</PRE>
+<P>See the "thermo_style" command for more details.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
+temp/region</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_asphere.html b/doc/doc2/compute_temp_asphere.html
new file mode 100644
index 000000000..2c6241da9
--- /dev/null
+++ b/doc/doc2/compute_temp_asphere.html
@@ -0,0 +1,163 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/asphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/asphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>temp/asphere = style name of this compute command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>bias</I> or <I>dof</I>
+
+<PRE> <I>bias</I> value = bias-ID
+ bias-ID = ID of a temperature compute that removes a velocity bias
+ <I>dof</I> value = <I>all</I> or <I>rotate</I>
+ all = compute temperature of translational and rotational degrees of freedom
+ rotate = compute temperature of just rotational degrees of freedom
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp/asphere
+compute myTemp mobile temp/asphere bias tempCOM
+compute myTemp mobile temp/asphere dof rotate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+aspherical particles, including a contribution from both their
+translational and rotational kinetic energy. This differs from the
+usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
+particles with only translational kinetic energy.
+</P>
+<P>Only finite-size particles (aspherical or spherical) can be included
+in the group. For 3d finite-size particles, each has 6 degrees of
+freedom (3 translational, 3 rotational). For 2d finite-size
+particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
+</P>
+<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size aspherical or spherical particles in your model will
+freely rotate, sampling all their rotational dof. It is possible to
+use a combination of interaction potentials and fixes that induce no
+torque or otherwise constrain some of all of your particles so that
+this is not the case. Then there are less dof and you should use the
+<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
+accordingly.
+</P>
+<P>For example, an aspherical particle with all three of its shape
+parameters the same is a sphere. If it does not rotate, then it
+should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
+uniaxial aspherical particle has two of its three shape parameters the
+same. If it does not rotate around the axis perpendicular to its
+circular cross section, then it should have 5 dof instead of 6 in 3d.
+The latter is the case for uniaxial ellipsoids in a <A HREF = "pair_gayberne.html">GayBerne
+model</A> since there is no induced torque around the
+optical axis. It will also be the case for biaxial ellipsoids when
+exactly two of the semiaxes have the same length and the corresponding
+relative well depths are equal.
+</P>
+<P>The translational kinetic energy is computed the same as is described
+by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
+kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
+as ellipsoids, not ellipses, meaning their moments of inertia will be
+the same as in 3d.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute. The formula for the components of the
+tensor is the same as the above formula, except that v^2 and w^2 are
+replaced by vx*vy and wx*wy for the xy component, and the appropriate
+elements of the inertia tensor are used. The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
+shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly. If needed, the subtracted degrees-of-freedom can
+be altered using the <I>extra</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom. This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile. Thermostats
+that use this compute will work with this bias term. See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+</P>
+<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
+that includes both translational and rotational degrees of freedom. A
+setting of <I>rotate</I> calculates a temperature that includes only
+rotational degrees of freedom.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the ASPHERE package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This compute requires that atoms store angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_chunk.html b/doc/doc2/compute_temp_chunk.html
new file mode 100644
index 000000000..05947ba73
--- /dev/null
+++ b/doc/doc2/compute_temp_chunk.html
@@ -0,0 +1,251 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>temp/chunk = style name of this compute command
+
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+
+<LI>zero or more values can be listed as value1,value2,etc
+
+<LI>value = <I>temp</I> or <I>kecom</I> or <I>internal</I>
+
+<PRE> temp = temperature of each chunk
+ kecom = kinetic energy of each chunk based on velocity of center of mass
+ internal = internal kinetic energy of each chunk
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>com</I> or <I>bias</I> or <I>adof</I> or <I>cdof</I>
+
+<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
+ yes = subtract center-of-mass velocity from each chunk before calculating temperature
+ no = do not subtract center-of-mass velocity
+ <I>bias</I> value = bias-ID
+ bias-ID = ID of a temperature compute that removes a velocity bias
+ <I>adof</I> value = dof_per_atom
+ dof_per_atom = define this many degrees-of-freedom per atom
+ <I>cdof</I> value = dof_per_chunk
+ dof_per_chunk = define this many degrees-of-freedom per chunk
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid temp/chunk molchunk
+compute 1 fluid temp/chunk molchunk temp internal
+compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms that are also in chunks, after optionally subtracting out the
+center-of-mass velocity of each chunk. By specifying optional values,
+it can also calulate the per-chunk temperature or energies of the
+multiple chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>The temperature is calculated by the formula KE = DOF/2 k T, where KE =
+total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
+v^2), DOF = the total number of degrees of freedom for those atoms, k
+= Boltzmann constant, and T = temperature.
+</P>
+<P>The DOF is calculated as N*adof + Nchunk*cdof, where N = number of
+atoms contributing to the KE, adof = degrees of freedom per atom, and
+cdof = degrees of freedom per chunk. By default adof = 2 or 3 =
+dimensionality of system, as set via the <A HREF = "dimension.html">dimension</A>
+command, and cdof = 0.0. This gives the usual formula for
+temperature.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>Note that the number of atoms contributing to the temperature is
+calculated each time the temperature is evaluated since it is assumed
+the atoms may be dynamically assigned to chunks. Thus there is no
+need to use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command for this compute style.
+</P>
+<P>If any optional values are specified, then per-chunk quantities are
+also calculated and stored in a global array, as described below.
+</P>
+<P>The <I>temp</I> value calculates the temperature for each chunk by the
+formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk
+of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of
+freedom for all atoms in the chunk, k = Boltzmann constant, and T =
+temperature.
+</P>
+<P>The DOF in this case is calculated as N*adof + cdof, where N = number
+of atoms in the chunk, adof = degrees of freedom per atom, and cdof =
+degrees of freedom per chunk. By default adof = 2 or 3 =
+dimensionality of system, as set via the <A HREF = "dimension.html">dimension</A>
+command, and cdof = 0.0. This gives the usual formula for
+temperature.
+</P>
+<P>The <I>kecom</I> value calculates the kinetic energy of each chunk as if
+all its atoms were moving with the velocity of the center-of-mass of
+the chunk.
+</P>
+<P>The <I>internal</I> value calculates the internal kinetic energy of each
+chunk. The interal KE is summed over the atoms in the chunk using an
+internal "thermal" velocity for each atom, which is its velocity minus
+the center-of-mass velocity of the chunk.
+</P>
+<HR>
+
+<P>Note that currently the global and per-chunk temperatures calculated
+by this compute only include translational degrees of freedom for each
+atom. No rotational degrees of freedom are included for finite-size
+particles. Also no degrees of freedom are subtracted for any velocity
+bias or constraints that are applied, such as <A HREF = "compute_temp_partial.html">compute
+temp/partial</A>, or <A HREF = "fix_shake.html">fix shake</A>
+or <A HREF = "fix_rigid.html">fix rigid</A>. This is because those degrees of
+freedom (e.g. a constrained bond) could apply to sets of atoms that
+are both included and excluded from a specific chunk, and hence the
+concept is somewhat ill-defined. In some cases, you can use the
+<I>adof</I> and <I>cdof</I> keywords to adjust the calculated degress of freedom
+appropriately, as explained below.
+</P>
+<P>Note that the per-chunk temperature calulated by this compute and the
+<A HREF = "fix_ave_chunk.html">fix ave/chunk temp</A> command can be different.
+This compute calculates the temperature for each chunk for a single
+snapshot. Fix ave/chunk can do that but can also time average those
+values over many snapshots, or it can compute a temperature as if the
+atoms in the chunk on different timesteps were collected together as
+one set of atoms to calculate their temperature. This compute allows
+the center-of-mass velocity of each chunk to be subtracted before
+calculating the temperature; fix ave/chunk does not.
+</P>
+<P>IMPORTANT NOTE: Only atoms in the specified group contribute to the
+calculations performed by this compute. The <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command defines its own group;
+atoms will have a chunk ID = 0 if they are not in that group,
+signifying they are not assigned to a chunk, and will thus also not
+contribute to this calculation. You can specify the "all" group for
+this command if you simply want to include atoms with non-zero chunk
+IDs.
+</P>
+<P>The simplest way to output the per-chunk results of the compute
+temp/chunk calculation to a file is to use the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all temp/chunk cc1 temp
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>The <I>com</I> keyword can be used with a value of <I>yes</I> to subtract the
+velocity of the center-of-mass for each chunk from the velocity of the
+atoms in that chunk, before calculating either the global or per-chunk
+temperature. This can be useful if the atoms are streaming or
+otherwise moving collectively, and you wish to calculate only the
+thermal temperature.
+</P>
+<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom. This also
+allows calculation of the global or per-chunk temperature using only
+the thermal temperature of atoms in each chunk after the translational
+kinetic energy components have been altered in a prescribed way,
+e.g. to remove a velocity profile. It also applies to the calculation
+of the other per-chunk values, such as <I>kecom</I> or <I>internal</I>, which
+involve the center-of-mass velocity of each chunk, which is calculated
+after the velocity bias is removed from each atom. Note that the
+temperature compute will apply its bias globally to the entire system,
+not on a per-chunk basis.
+</P>
+<P>The <I>adof</I> and <I>cdof</I> keywords define the values used in the degree of
+freedom (DOF) formulas used for the global or per-chunk temperature,
+as described above. They can be used to calculate a more appropriate
+temperature for some kinds of chunks. Here are 3 examples:
+</P>
+<P>If spatially binned chunks contain some number of water molecules and
+<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
+you could calculate a temperature with 6 degrees of freedom (DOF) (3
+translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
+</P>
+<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
+<I>bias</I> keyword to only allow the x component of velocity to contribute
+to the temperature, then <I>adof</I> = 1.0 would be appropriate.
+</P>
+<P>If each chunk consists of a large molecule, with some number of its
+bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
+by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
+set to the remaining degrees of freedom for the entire molecule
+(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
+molecule.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>This compute also optionally calculates a global array, if one or more
+of the optional values are specified. The number of rows in the array
+= the number of chunks <I>Nchunk</I> as calculated by the specified
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. The number of
+columns is the number of specifed values (1 or more). These values
+can be accessed by any command that uses global array values from a
+compute as input. Again, see <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive". The array values are "intensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>. The array values
+will be in temperature <A HREF = "units.html">units</A> for the <I>temp</I> value, and in
+energy <A HREF = "units.html">units</A> for the <I>kecom</I> and <I>internal</I> values.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>com</I> and <I>bias</I> keywords cannot be used together.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "fix_ave_chunk.html">fix ave/chunk
+temp</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are com no, no bias, adof = dimensionality of the
+system (2 or 3), and cdof = 0.0.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_com.html b/doc/doc2/compute_temp_com.html
new file mode 100644
index 000000000..5635c606d
--- /dev/null
+++ b/doc/doc2/compute_temp_com.html
@@ -0,0 +1,98 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/com command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/com
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/com = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp/com
+compute myTemp mobile temp/com
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after subtracting out the center-of-mass velocity of the group.
+This is useful if the group is expected to have a non-zero net
+velocity for some reason. A compute of this style can be used by any
+command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>After the center-of-mass velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of the center-of-mass velocity by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms. If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in. Thermostatting fixes
+that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_cs.html b/doc/doc2/compute_temp_cs.html
new file mode 100644
index 000000000..5d46f1374
--- /dev/null
+++ b/doc/doc2/compute_temp_cs.html
@@ -0,0 +1,117 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/cs command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<P>compute ID group-ID temp/cs group1 group2 pre
+</P>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/cs = style name of this compute command
+<LI>group1 = group-ID of either cores or shells
+<LI>group2 = group-ID of either shells or cores
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute oxygen_c-s all temp/cs O_core O_shell
+compute core_shells all temp/cs cores shells
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a system based
+on the center-of-mass velocity of atom pairs that are bonded to each
+other. This compute is designed to be used with the adiabatic
+core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
+<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
+overview of the model as implemented in LAMMPS. Specifically, this
+compute enables correct temperature calculation and thermostatting of
+core/shell pairs where it is desirable for the internal degrees of
+freedom of the core/shell pairs to not be influenced by a thermostat.
+A compute of this style can be used by any command that computes a
+temperature via <A HREF = "fix_modify.html">fix_modify</A> e.g. <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>For this compute, core and shell particles are specified by two
+respective group IDs, which can be defined using the
+<A HREF = "group.html">group</A> command. The number of atoms in the two groups
+must be the same and there should be one bond defined between a pair
+of atoms in the two groups.
+</P>
+<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature. Note that
+the velocity of each core or shell atom used in the KE calculation is
+the velocity of the center-of-mass (COM) of the core/shell pair the
+atom is part of.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
+COM velocity.
+</P>
+<P>The change this fix makes to core/shell atom velocities is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms. This "bias" is the velocity of the atom
+relative to the COM velocity of the core/shell pair. If this compute
+is used with a fix command that performs thermostatting then this bias
+will be subtracted from each atom, thermostatting of the remaining COM
+velocity will be performed, and the bias will be added back in. This
+means the thermostating will effectively be performed on the
+core/shell pairs, instead of on the individual core and shell atoms.
+Thermostatting fixes that work in this way include <A HREF = "fix_nh.html">fix
+nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>The internal energy of core/shell pairs can be calculated by the
+<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command, if chunks are
+defined as core/shell pairs. See <A HREF = "Section_howto.html#howto_25">Section_howto
+25</A> for more discussion on how to do this.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The number of core/shell pairs contributing to the temperature is
+assumed to be constant for the duration of the run. No fixes should
+be used which generate new molecules or atoms during a simulation.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_chunk.html">compute
+temp/chunk</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "MitchellFinchham"></A>
+
+<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_deform.html b/doc/doc2/compute_temp_deform.html
new file mode 100644
index 000000000..1a2af6128
--- /dev/null
+++ b/doc/doc2/compute_temp_deform.html
@@ -0,0 +1,139 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/deform command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/deform
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/deform = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute myTemp all temp/deform
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after subtracting out a streaming velocity induced by the
+simulation box changing size and/or shape, for example in a
+non-equilibrium MD (NEMD) simulation. The size/shape change is
+induced by use of the <A HREF = "fix_deform.html">fix deform</A> command. A compute
+of this style is created by the <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
+command to compute the thermal temperature of atoms for thermostatting
+purposes. A compute of this style can also be used by any command
+that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>,
+<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>The deformation fix changes the box size and/or shape over time, so
+each atom in the simulation box can be thought of as having a
+"streaming" velocity. For example, if the box is being sheared in x,
+relative to y, then atoms at the bottom of the box (low y) have a
+small x velocity, while atoms at the top of the box (hi y) have a
+large x velocity. This position-dependent streaming velocity is
+subtracted from each atom's actual velocity to yield a thermal
+velocity which is used to compute the temperature.
+</P>
+<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
+remapping either atom coordinates or velocities to the changing
+simulation box. When using this compute in conjunction with a
+deforming box, fix deform should NOT remap atom positions, but rather
+should let atoms respond to the changing box by adjusting their own
+velocities (or let <A HREF = "fix_deform.html">fix deform</A> remap the atom
+velocities, see it's remap option). If fix deform does remap atom
+positions, then they appear to move with the box but their velocity is
+not changed, and thus they do NOT have the streaming velocity assumed
+by this compute. LAMMPS will warn you if fix deform is defined and
+its remap setting is not consistent with this compute.
+</P>
+<P>After the streaming velocity has been subtracted from each atom, the
+temperature is calculated by the formula KE = dim/2 N k T, where KE =
+total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
+or 3 = dimensionality of the simulation, N = number of atoms in the
+group, k = Boltzmann constant, and T = temperature. Note that v in
+the kinetic energy formula is the atom's thermal velocity.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of the box deformation velocity component by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms. If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in. Thermostatting
+fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>IMPORTANT NOTE: The temperature calculated by this compute is only
+accurate if the atoms are indeed moving with a stream velocity profile
+that matches the box deformation. If not, then the compute will
+subtract off an incorrect stream velocity, yielding a bogus thermal
+temperature. You should NOT assume that your atoms are streaming at
+the same rate the box is deforming. Rather, you should monitor their
+velocity profile, e.g. via the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
+command. And you can compare the results of this compute to <A HREF = "compute_temp_profile.html">compute
+temp/profile</A>, which actually calculates the
+stream profile before subtracting it. If the two computes do not give
+roughly the same temperature, then your atoms are not streaming
+consistent with the box deformation. See the <A HREF = "fix_deform.html">fix
+deform</A> command for more details on ways to get atoms
+to stream consistently with the box deformation.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "compute_temp_profile.html">compute
+temp/profile</A>, <A HREF = "fix_deform.html">fix deform</A>,
+<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_deform_eff.html b/doc/doc2/compute_temp_deform_eff.html
new file mode 100644
index 000000000..6331c8e91
--- /dev/null
+++ b/doc/doc2/compute_temp_deform_eff.html
@@ -0,0 +1,78 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/deform/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/deform/eff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/deform/eff = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute myTemp all temp/deform/eff
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
+model, after subtracting out a streaming velocity induced by the
+simulation box changing size and/or shape, for example in a
+non-equilibrium MD (NEMD) simulation. The size/shape change is
+induced by use of the <A HREF = "fix_deform_eff.html">fix deform/eff</A> command. A
+compute of this style is created by the <A HREF = "fix_nvt_sllod_eff.html">fix
+nvt/sllod/eff</A> command to compute the thermal
+temperature of atoms for thermostatting purposes. A compute of this
+style can also be used by any command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_nh.html">fix npt/eff</A>,
+etc.
+</P>
+<P>The calculation performed by this compute is exactly like that
+described by the <A HREF = "compute_temp_deform.html">compute temp/deform</A>
+command, except that the formula for the temperature includes the
+radial electron velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
+temp/eff</A> command. Note that only the
+translational degrees of freedom for each nuclei or electron are
+affected by the streaming velocity adjustment. The radial velocity
+component of the electrons is not affected.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform_eff.html">fix
+deform/eff</A>, <A HREF = "fix_nvt_sllod_eff.html">fix
+nvt/sllod/eff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_drude.html b/doc/doc2/compute_temp_drude.html
new file mode 100644
index 000000000..96d3aac38
--- /dev/null
+++ b/doc/doc2/compute_temp_drude.html
@@ -0,0 +1,87 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/drude command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/drude
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/drude = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute TDRUDE all temp/drude
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperatures of core-Drude
+pairs. This compute is designed to be used with the thermalized Drude
+oscillator model. This compute is designed to be used with the
+<A HREF = "tutorial_drude.html">thermalized Drude oscillator model</A>. Polarizable
+models in LAMMPS are described in <A HREF = "Section_howto.html#howto_25">this
+Section</A>.
+</P>
+<P>Drude oscillators consist of a core particle and a Drude particle
+connected by a harmonic bond, and the relative motion of these Drude
+oscillators is usually maintained cold by a specific thermostat that
+acts on the relative motion of the core-Drude particle
+pairs. Therefore, because LAMMPS considers Drude particles as normal
+atoms in its default temperature compute (<A HREF = "compute_temp.html">compute
+temp</A> command), the reduced temperature of the
+core-Drude particle pairs is not calculated correctly.
+</P>
+<P>By contrast, this compute calculates the temperature of the cores
+using center-of-mass velocities of the core-Drude pairs, and the
+reduced temperature of the Drude particles using the relative
+velocities of the Drude particles with respect to their cores.
+Non-polarizable atoms are considered as cores. Their velocities
+contribute to the temperature of the cores.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6, which can be accessed by indices 1-6, whose components
+are
+</P>
+<OL><LI>temperature of the centers of mass (temperature units)
+<LI>temperature of the dipoles (temperature units)
+<LI>number of degrees of freedom of the centers of mass
+<LI>number of degrees of freedom of the dipoles
+<LI>kinetic energy of the centers of mass (energy units)
+<LI>kinetic energy of the dipoles (energy units)
+</OL>
+<P>These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>Both the scalar value and the first two values of the vector
+calculated by this compute are "intensive". The other 4 vector values
+are "extensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The number of degrees of freedom contributing to the temperature is
+assumed to be constant for the duration of the run unless the
+<I>fix_modify</I> command sets the option <I>dynamic yes</I>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drude.html">fix drude</A>, <A HREF = "fix_langevin_drude.html">fix
+langevin_drude</A>, <A HREF = "fix_drude_transform.html">fix
+drude/transform</A>, <A HREF = "pair_thole.html">pair_style
+thole</A>, <A HREF = "compute_temp.html">compute temp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_eff.html b/doc/doc2/compute_temp_eff.html
new file mode 100644
index 000000000..3cc20e9db
--- /dev/null
+++ b/doc/doc2/compute_temp_eff.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/eff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/eff = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp/eff
+compute myTemp mobile temp/eff
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
+model. A compute of this style can be used by commands that compute a
+temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_npt_eff.html">fix
+npt/eff</A>, etc.
+</P>
+<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
+nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
+includes the radial electron velocity contributions), dim = 2 or 3 =
+dimensionality of the simulation, N = number of atoms (only total
+number of nuclei in the eFF (see the <A HREF = "pair_style.html">pair_eff</A>
+command) in the group, k = Boltzmann constant, and T = temperature.
+This expression is summed over all nuclear and electronic degrees of
+freedom, essentially by setting the kinetic contribution to the heat
+capacity to 3/2k (where only nuclei contribute). This subtlety is
+valid for temperatures well below the Fermi temperature, which for
+densities two to five times the density of liquid H2 ranges from
+86,000 to 170,000 K.
+</P>
+<P>IMPORTANT NOTE: For eFF models, in order to override the default
+temperature reported by LAMMPS in the thermodynamic quantities
+reported via the <A HREF = "thermo.html">thermo</A> command, the user should apply a
+<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
+example:
+</P>
+<PRE>compute effTemp all temp/eff
+thermo_style custom step etotal pe ke temp press
+thermo_modify temp effTemp
+</PRE>
+<P>A 6-component kinetic energy tensor is also calculated by this compute
+for use in the computation of a pressure tensor. The formula for the
+components of the tensor is the same as the above formula, except that
+v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
+again, the radial electronic velocities are also considered.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>The scalar value calculated by this compute is "intensive", meaning it
+is independent of the number of atoms in the simulation. The vector
+values are "extensive", meaning they scale with the number of atoms in
+the simulation.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
+temp/region</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_partial.html b/doc/doc2/compute_temp_partial.html
new file mode 100644
index 000000000..5385c5bfa
--- /dev/null
+++ b/doc/doc2/compute_temp_partial.html
@@ -0,0 +1,125 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/partial command
+</H3>
+<H3>compute temp/partial/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/partial xflag yflag zflag
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/partial = style name of this compute command
+<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute newT flow temp/partial 1 1 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after excluding one or more velocity components. A compute of
+this style can be used by any command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = dimensionality of the simulation, N = number of atoms in the
+group, k = Boltzmann constant, and T = temperature. The calculation
+of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
+0. The dim parameter is adjusted to give the correct number of
+degrees of freedom.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the calculation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of velocity components by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms. If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in. Thermostatting fixes
+that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
+temp/region</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_profile.html b/doc/doc2/compute_temp_profile.html
new file mode 100644
index 000000000..1312ae63e
--- /dev/null
+++ b/doc/doc2/compute_temp_profile.html
@@ -0,0 +1,195 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/profile command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/profile xflag yflag zflag binstyle args
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>temp/profile = style name of this compute command
+
+<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
+
+<LI>binstyle = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>xyz</I>
+
+<PRE> <I>x</I> arg = Nx
+ <I>y</I> arg = Ny
+ <I>z</I> arg = Nz
+ <I>xy</I> args = Nx Ny
+ <I>yz</I> args = Ny Nz
+ <I>xz</I> args = Nx Nz
+ <I>xyz</I> args = Nx Ny Nz
+ Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>out</I>
+
+<PRE> <I>out</I> value = <I>tensor</I> or <I>bin</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute myTemp flow temp/profile 1 1 1 x 10
+compute myTemp flow temp/profile 1 1 1 x 10 out bin
+compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after subtracting out a spatially-averaged center-of-mass
+velocity field, before computing the kinetic energy. This can be
+useful for thermostatting a collection of atoms undergoing a complex
+flow, e.g. via a profile-unbiased thermostat (PUT) as described in
+<A HREF = "#Evans">(Evans)</A>. A compute of this style can be used by any command
+that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>,
+<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>The <I>xflag</I>, <I>yflag</I>, <I>zflag</I> settings determine which components of
+average velocity are subtracted out.
+</P>
+<P>The <I>binstyle</I> setting and its <I>Nx</I>, <I>Ny</I>, <I>Nz</I> arguments determine
+how bins are setup to perform spatial averaging. "Bins" can be 1d
+slabs, 2d pencils, or 3d bricks depending on which <I>binstyle</I> is used.
+The simulation box is partitioned conceptually into <I>Nx</I> by <I>Ny</I> by
+<I>Nz</I> bins. Depending on the <I>binstyle</I>, you may only specify one or
+two of these values; the others are effectively set to 1 (no binning
+in that dimension). For non-orthogonal (triclinic) simulation boxes,
+the bins are "tilted" slabs or pencils or bricks that are parallel to
+the tilted faces of the box. See the <A HREF = "region.html">region prism</A>
+command for a discussion of the geometry of tilted boxes in LAMMPS.
+</P>
+<P>When a temperature is computed, the center-of-mass velocity for the
+set of atoms that are both in the compute group and in the same
+spatial bin is calculated. This bias velocity is then subtracted from
+the velocities of individual atoms in the bin to yield a thermal
+velocity for each atom. Note that if there is only one atom in the
+bin, its thermal velocity will thus be 0.0.
+</P>
+<P>After the spatially-averaged velocity field has been subtracted from
+each atom, the temperature is calculated by the formula KE = (dim/2 N
+- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom
+subtracted to adjust for the removal of the center-of-mass velocity in
+each of Nx*Ny*Nz bins, as discussed in the <A HREF = "#Evans">(Evans)</A> paper.
+</P>
+<P>If the <I>out</I> keyword is used with a <I>tensor</I> value, which is the
+default, a kinetic energy tensor, stored as a 6-element vector, is
+also calculated by this compute for use in the computation of a
+pressure tensor. The formula for the components of the tensor is the
+same as the above formula, except that v^2 is replaced by vx*vy for
+the xy component, etc. The 6 components of the vector are ordered xx,
+yy, zz, xy, xz, yz.
+</P>
+<P>If the <I>out</I> keyword is used with a <I>bin</I> value, the count of atoms
+and computed temperature for each bin are stored for output, as an
+array of values, as described below. The temperature of each bin is
+calculated as described above, where the bias velocity is subtracted
+and only the remaining thermal velocity of atoms in the bin
+contributes to the temperature. See the note below for how the
+temperature is normalized by the degrees-of-freedom of atoms in the
+bin.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of the spatially-averaged velocity field by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms. If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in. Thermostatting
+fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>IMPORTANT NOTE: When using the <I>out</I> keyword with a value of <I>bin</I>,
+the calculated temperature for each bin does not include the
+degrees-of-freedom adjustment described in the preceeding paragraph,
+for fixes that constrain molecular motion. It does include the
+adjustment due to the <I>extra</I> option, which is applied to each bin.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting. Using this compute in conjunction with a
+thermostatting fix, as explained there, will effectively implement a
+profile-unbiased thermostat (PUT), as described in <A HREF = "#Evans">(Evans)</A>.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature). Depending
+on the setting of the <I>out</I> keyword, it also calculates a global
+vector or array. For <I>out</I> = <I>tensor</I>, it calculates a vector of
+length 6 (KE tensor), which can be accessed by indices 1-6. For <I>out</I>
+= <I>bin</I> it calculates a global array which has 2 columns and N rows,
+where N is the number of bins. The first column contains the number
+of atoms in that bin. The second contains the temperature of that
+bin, calculated as described above. The ordering of rows in the array
+is as follows. Bins in x vary fastest, then y, then z. Thus for a
+10x10x10 3d array of bins, there will be 1000 rows. The bin with
+indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
++ ix = 322, where the rows are numbered from 1 to 1000 and the bin
+indices are numbered from 1 to 10 in each dimension.
+</P>
+<P>These values can be used by any command that uses global scalar or
+vector or array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive". The array values are "intensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>. The first column
+of array values are counts; the values in the second column will be in
+temperature <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>You should not use too large a velocity-binning grid, especially in
+3d. In the current implementation, the binned velocity averages are
+summed across all processors, so this will be inefficient if the grid
+is too large, and the operation is performed every timestep, as it
+will be for most thermostats.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_ramp.html">compute
+temp/ramp</A>, <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is out = tensor.
+</P>
+<HR>
+
+<A NAME = "Evans"></A>
+
+<P><B>(Evans)</B> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_ramp.html b/doc/doc2/compute_temp_ramp.html
new file mode 100644
index 000000000..686ad9cd6
--- /dev/null
+++ b/doc/doc2/compute_temp_ramp.html
@@ -0,0 +1,122 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/ramp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/ramp = style name of this compute command
+<LI>vdim = <I>vx</I> or <I>vy</I> or <I>vz</I>
+<LI>vlo,vhi = subtract velocities between vlo and vhi (velocity units)
+<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
+<LI>clo,chi = lower and upper bound of domain to subtract from (distance units)
+<LI>zero or more keyword/value pairs may be appended
+<LI>keyword = <I>units</I>
+</UL>
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after subtracting out an ramped velocity profile before
+computing the kinetic energy. A compute of this style can be used by
+any command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>The meaning of the arguments for this command which define the
+velocity ramp are the same as for the <A HREF = "velocity.html">velocity ramp</A>
+command which was presumably used to impose the velocity.
+</P>
+<P>After the ramp velocity has been subtracted from the specified
+dimension for each atom, the temperature is calculated by the formula
+KE = dim/2 N k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+for coordinates (c1,c2) and velocities (vlo,vhi). A <I>box</I> value
+selects standard distance units as defined by the <A HREF = "units.html">units</A>
+command, e.g. Angstroms for units = real or metal. A <I>lattice</I> value
+means the distance units are in lattice spacings; e.g. velocity =
+lattice spacings / tau. The <A HREF = "lattice.html">lattice</A> command must have
+been previously used to define the lattice spacing.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of the ramped velocity component by this fix is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms. If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in. Thermostatting
+fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_profile.html">compute
+temp/profie</A>, <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_region.html b/doc/doc2/compute_temp_region.html
new file mode 100644
index 000000000..06a525092
--- /dev/null
+++ b/doc/doc2/compute_temp_region.html
@@ -0,0 +1,113 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/region command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/region region-ID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/region = style name of this compute command
+<LI>region-ID = ID of region to use for choosing atoms
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute mine flow temp/region boundary
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms in a geometric region. This can be useful for thermostatting
+one portion of the simulation box. E.g. a McDLT simulation where one
+side is cooled, and the other side is heated. A compute of this style
+can be used by any command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, etc.
+</P>
+<P>Note that a <I>region</I>-style temperature can be used to thermostat with
+<A HREF = "fix_temp_rescale.html">fix temp/rescale</A> or <A HREF = "fix_langevin.html">fix
+langevin</A>, but should probably not be used with
+Nose/Hoover style fixes (<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix
+npt</A>, or <A HREF = "fix_nh.html">fix nph</A>), if the
+degrees-of-freedom included in the computed T varies with time.
+</P>
+<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in both the group and region, k = Boltzmann constant, and T =
+temperature.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is calculated each
+time the temperature is evaluated since it is assumed atoms can
+enter/leave the region. Thus there is no need to use the <I>dynamic</I>
+option of the <A HREF = "compute_modify.html">compute_modify</A> command for this
+compute style.
+</P>
+<P>The removal of atoms outside the region by this fix is essentially
+computing the temperature after a "bias" has been removed, which in
+this case is the velocity of any atoms outside the region. If this
+compute is used with a fix command that performs thermostatting then
+this bias will be subtracted from each atom, thermostatting of the
+remaining thermal velocity will be performed, and the bias will be
+added back in. Thermostatting fixes that work in this way include
+<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>. This means any of the thermostatting
+fixes can operate on a geometric region of atoms, as defined by this
+compute.
+</P>
+<P>Unlike other compute styles that calculate temperature, this compute
+does not subtract out degrees-of-freedom due to fixes that constrain
+motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
+rigid</A>. This is because those degrees of freedom
+(e.g. a constrained bond) could apply to sets of atoms that straddle
+the region boundary, and hence the concept is somewhat ill-defined.
+If needed the number of subtracted degrees-of-freedom can be set
+explicitly using the <I>extra</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_region_eff.html b/doc/doc2/compute_temp_region_eff.html
new file mode 100644
index 000000000..e4e84b9e8
--- /dev/null
+++ b/doc/doc2/compute_temp_region_eff.html
@@ -0,0 +1,69 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/region/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/region/eff region-ID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/region/eff = style name of this compute command
+<LI>region-ID = ID of region to use for choosing atoms
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute mine flow temp/region/eff boundary
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
+model, within a geometric region using the electron force field. A
+compute of this style can be used by commands that compute a
+temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>.
+</P>
+<P>The operation of this compute is exactly like that described by the
+<A HREF = "compute_temp_region.html">compute temp/region</A> command, except that
+the formula for the temperature itself includes the radial electron
+velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
+temp/eff</A> command.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp_region.html">compute temp/region</A>, <A HREF = "compute_temp_eff.html">compute
+temp/eff</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_rotate.html b/doc/doc2/compute_temp_rotate.html
new file mode 100644
index 000000000..cbd3a3104
--- /dev/null
+++ b/doc/doc2/compute_temp_rotate.html
@@ -0,0 +1,101 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/rotate command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/rotate
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>temp/rotate = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute Tbead bead temp/rotate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
+This is useful if the group is expected to have a non-zero net
+velocity and/or global rotation motion for some reason. A compute of this style can be used by any
+command that computes a temperature,
+e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
+</P>
+<P>After the center-of-mass velocity and angular velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
+KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+in the group, k = Boltzmann constant, and T = temperature.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v^2 is replaced by vx*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>The removal of the center-of-mass velocity and angular velocity by this fix is essentially
+computing the temperature after a "bias" has been removed from the
+velocity of the atoms. If this compute is used with a fix command
+that performs thermostatting then this bias will be subtracted from
+each atom, thermostatting of the remaining thermal velocity will be
+performed, and the bias will be added back in. Thermostatting fixes
+that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
+langevin</A>.
+</P>
+<P>This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
+<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
+atoms that include these constraints will be computed correctly. If
+needed, the subtracted degrees-of-freedom can be altered using the
+<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_temp_sphere.html b/doc/doc2/compute_temp_sphere.html
new file mode 100644
index 000000000..dcbfd9a28
--- /dev/null
+++ b/doc/doc2/compute_temp_sphere.html
@@ -0,0 +1,147 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute temp/sphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID temp/sphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>temp/sphere = style name of this compute command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>bias</I> or <I>dof</I>
+
+<PRE> <I>bias</I> value = bias-ID
+ bias-ID = ID of a temperature compute that removes a velocity bias
+ <I>dof</I> value = <I>all</I> or <I>rotate</I>
+ all = compute temperature of translational and rotational degrees of freedom
+ rotate = compute temperature of just rotational degrees of freedom
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all temp/sphere
+compute myTemp mobile temp/sphere bias tempCOM
+compute myTemp mobile temp/sphere dof rotate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the temperature of a group of
+spherical particles, including a contribution from both their
+translational and rotational kinetic energy. This differs from the
+usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
+particles with only translational kinetic energy.
+</P>
+<P>Both point and finite-size particles can be included in the group.
+Point particles do not rotate, so they have only 3 translational
+degrees of freedom. For 3d spherical particles, each has 6 degrees of
+freedom (3 translational, 3 rotational). For 2d spherical particles,
+each has 3 degrees of freedom (2 translational, 1 rotational).
+</P>
+<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size spherical particles in your model will freely rotate,
+sampling all their rotational dof. It is possible to use a
+combination of interaction potentials and fixes that induce no torque
+or otherwise constrain some of all of your particles so that this is
+not the case. Then there are less dof and you should use the
+<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
+accordingly.
+</P>
+<P>The translational kinetic energy is computed the same as is described
+by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
+kinetic energy is computed as 1/2 I w^2, where I is the moment of
+inertia for a sphere and w is the particle's angular velocity.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
+as spheres, not disks, meaning their moment of inertia will be the
+same as in 3d.
+</P>
+<P>A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute. The formula for the components of the
+tensor is the same as the above formulas, except that v^2 and w^2 are
+replaced by vx*vy and wx*wy for the xy component. The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
+</P>
+<P>The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the <I>dynamic</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
+</P>
+<P>This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
+shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly. If needed, the subtracted degrees-of-freedom can
+be altered using the <I>extra</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom. This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile. Thermostats
+that use this compute will work with this bias term. See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+</P>
+<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
+that includes both translational and rotational degrees of freedom. A
+setting of <I>rotate</I> calculates a temperature that includes only
+rotational degrees of freedom.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "intensive". The
+vector values are "extensive".
+</P>
+<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
+vector values will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command.
+</P>
+<P>All particles in the group must be finite-size spheres, or point
+particles with radius = 0.0.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp.html">compute
+temp/asphere</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are no bias and dof = all.
+</P>
+</HTML>
diff --git a/doc/doc2/compute_ti.html b/doc/doc2/compute_ti.html
new file mode 100644
index 000000000..5a7ef6e1e
--- /dev/null
+++ b/doc/doc2/compute_ti.html
@@ -0,0 +1,148 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute ti command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group ti keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>ti = style name of this compute command
+
+<LI>one or more attribute/arg pairs may be appended
+
+<LI>keyword = pair style (lj/cut, gauss, born, etc) or <I>tail</I> or <I>kspace</I>
+
+<PRE> pair style args = atype v_name1 v_name2
+ atype = atom type (see asterisk form below)
+ v_name1 = variable with name1 that is energy scale factor and function of lambda
+ v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+ <I>tail</I> args = atype v_name1 v_name2
+ atype = atom type (see asterisk form below)
+ v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
+ v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+ <I>kspace</I> args = atype v_name1 v_name2
+ atype = atom type (see asterisk form below)
+ v_name1 = variable with name1 that is K-Space scale factor and function of lambda
+ v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
+compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the derivative of the interaction
+potential with respect to <I>lambda</I>, the coupling parameter used in a
+thermodynamic integration. This derivative can be used to infer a
+free energy difference resulting from an alchemical simulation, as
+described in <A HREF = "#Eike">Eike</A>.
+</P>
+<P>Typically this compute will be used in conjunction with the <A HREF = "fix_adapt.html">fix
+adapt</A> command which can perform alchemical
+transformations by adusting the strength of an interaction potential
+as a simulation runs, as defined by one or more
+<A HREF = "pair_style.html">pair_style</A> or <A HREF = "kspace_style.html">kspace_style</A>
+commands. This scaling is done via a prefactor on the energy, forces,
+virial calculated by the pair or K-Space style. The prefactor is
+often a function of a <I>lambda</I> parameter which may be adjusted from 0
+to 1 (or vice versa) over the course of a <A HREF = "run.html">run</A>. The
+time-dependent adjustment is what the <A HREF = "fix_adapt.html">fix adapt</A>
+command does.
+</P>
+<P>Assume that the unscaled energy of a pair_style or kspace_style is
+given by U. Then the scaled energy is
+</P>
+<PRE>Us = f(lambda) U
+</PRE>
+<P>where f() is some function of lambda. What this compute calculates is
+</P>
+<PRE>dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda
+</PRE>
+<P>which is the derivative of the system's scaled potential energy Us
+with respect to <I>lambda</I>.
+</P>
+<P>To perform this calculation, you provide one or more atom types as
+<I>atype</I>. <I>Atype</I> can be specified in one of two ways. An explicit
+numeric values can be used, as in the 1st example above. Or a
+wildcard asterisk can be used in place of or in conjunction with the
+<I>atype</I> argument to select multiple atom types. This takes the form
+"*" or "*n" or "n*" or "m*n". If N = the number of atom types, then
+an asterisk with no numeric values means all types from 1 to N. A
+leading asterisk means all types from 1 to n (inclusive). A trailing
+asterisk means all types from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive).
+</P>
+<P>You also specify two functions, as <A HREF = "variable.html">equal-style
+variables</A>. The first is specified as <I>v_name1</I>, where
+<I>name1</I> is the name of the variable, and is f(lambda) in the notation
+above. The second is specified as <I>v_name2</I>, where <I>name2</I> is the
+name of the variable, and is df(lambda) / dlambda in the notation
+above. I.e. it is the analytic derivative of f() with respect to
+lambda. Note that the <I>name1</I> variable is also typically given as an
+argument to the <A HREF = "fix_adapt.html">fix adapt</A> command.
+</P>
+<P>An alchemical simulation may use several pair potentials together,
+invoked via the <A HREF = "pair_hybrid.html">pair_style hybrid or hybrid/overlay</A>
+command. The total dUs/dlambda for the overall system is calculated
+as the sum of each contributing term as listed by the keywords in the
+compute ti command. Individual pair potentials can be listed, which
+will be sub-styles in the hybrid case. You can also include a K-space
+term via the <I>kspace</I> keyword. You can also include a pairwise
+long-range tail correction to the energy via the <I>tail</I> keyword.
+</P>
+<P>For each term you can specify a different (or the same) scale factor
+by the two variables that you list. Again, these will typically
+correspond toe the scale factors applied to these various potentials
+and the K-Space contribution via the <A HREF = "fix_adapt.html">fix_adapt</A>
+command.
+</P>
+<P>More details about the exact functional forms for the computation of
+du/dl can be found in the paper by <A HREF = "#Eike">Eike</A>.
+</P>
+<HR>
+
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global scalar, namely dUs/dlambda. This
+value can be used by any command that uses a global scalar value from
+a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The scalar value calculated by this compute is "extensive".
+</P>
+<P>The scalar value will be in energy <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_adapt.html">fix adapt</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Eike"></A>
+
+<P><B>(Eike)</B> Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/compute_torque_chunk.html b/doc/doc2/compute_torque_chunk.html
new file mode 100644
index 000000000..593397646
--- /dev/null
+++ b/doc/doc2/compute_torque_chunk.html
@@ -0,0 +1,92 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute torque/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID torque/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>torque/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid torque/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the torque on multiple chunks of
+atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the 3 components of the torque vector for eqch
+chunk, due to the forces on the individual atoms in the chunk around
+the center-of-mass of the chunk. The calculation includes all effects
+due to atoms passing thru periodic boundaries.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
+torque in "unwrapped" form, by using the image flags associated with
+each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion
+of "unwrapped" coordinates. See the Atoms section of the
+<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
+how they are set for each atom. You can reset the image flags
+(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
+image</A> command.
+</P>
+<P>The simplest way to output the results of the compute torque/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all torque/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+3 for the 3 xyz components of the torque for each chunk. These values
+can be accessed by any command that uses global array values from a
+compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
+for an overview of LAMMPS output options.
+</P>
+<P>The array values are "intensive". The array values will be in
+force-distance <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable torque() function</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_vacf.html b/doc/doc2/compute_vacf.html
new file mode 100644
index 000000000..12a3411ee
--- /dev/null
+++ b/doc/doc2/compute_vacf.html
@@ -0,0 +1,76 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute vacf command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID vacf
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>vacf = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all vacf
+compute 1 upper vacf
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the velocity auto-correlation
+function (VACF), averaged over a group of atoms. Each atom's
+contribution to the VACF is its current velocity vector dotted into
+its initial velocity vector at the time the compute was specified.
+</P>
+<P>A vector of four quantites is calculated by this compute. The first 3
+elements of the vector are vx * vx0 (and similarly for the y and z
+components), summed and averaged over atoms in the group. Vx is the
+current x-component of velocity for the atom, vx0 is the initial
+x-component of velocity for the atom. The 4th element of the vector
+is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
+averaged over atoms in the group.
+</P>
+<P>The integral of the VACF versus time is proportional to the diffusion
+coefficient of the diffusing atoms. This can be computed in the
+following manner, using the <A HREF = "variable.html">variable trap()</A> function:
+</P>
+<PRE>compute 2 all vacf
+fix 5 all vector 1 c_2[4]
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff
+</PRE>
+<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
+to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
+then you should use the same ID for this compute, as in the original
+run. This is so that the fix this compute creates to store per-atom
+quantities will also have the same ID, and thus be initialized
+correctly with time=0 atom velocities from the restart file.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global vector of length 4, which can be
+accessed by indices 1-4 by any command that uses global vector values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
+section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The vector values are "intensive". The vector values will be in
+velocity^2 <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd.html">compute msd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_vcm_chunk.html b/doc/doc2/compute_vcm_chunk.html
new file mode 100644
index 000000000..8c23af9a5
--- /dev/null
+++ b/doc/doc2/compute_vcm_chunk.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute vcm/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID vcm/chunk chunkID
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>vcm/chunk = style name of this compute command
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 fluid vcm/chunk molchunk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the center-of-mass velocity for
+multiple chunks of atoms.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>This compute calculates the x,y,z components of the center-of-mass
+velocity for each chunk. This is done by summing mass*velocity for
+each atom in the chunk and dividing the sum by the total mass of the
+chunk.
+</P>
+<P>Note that only atoms in the specified group contribute to the
+calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+defines its own group; atoms will have a chunk ID = 0 if they are not
+in that group, signifying they are not assigned to a chunk, and will
+thus also not contribute to this calculation. You can specify the
+"all" group for this command if you simply want to include atoms with
+non-zero chunk IDs.
+</P>
+<P>The simplest way to output the results of the compute vcm/chunk
+calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command, for example:
+</P>
+<PRE>compute cc1 all chunk/atom molecule
+compute myChunk all vcm/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</PRE>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array where the number of rows = the
+number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The number of columns =
+3 for the x,y,z center-of-mass velocity coordinates of each chunk.
+These values can be accessed by any command that uses global array
+values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The array values are "intensive". The array values will be in
+velocity <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_voronoi_atom.html b/doc/doc2/compute_voronoi_atom.html
new file mode 100644
index 000000000..ea7f0fb50
--- /dev/null
+++ b/doc/doc2/compute_voronoi_atom.html
@@ -0,0 +1,183 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute voronoi/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID voronoi/atom keyword arg ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>voronoi/atom = style name of this compute command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>only_group</I> or <I>surface</I> or <I>radius</I> or <I>edge_histo</I> or <I>edge_threshold</I> or <I>face_threshold</I>
+
+<PRE> <I>only_group</I> = no arg
+ <I>occupation</I> = no arg
+ <I>surface</I> arg = sgroup-ID
+ sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
+ this keyword adds a third column to the compute output
+ <I>radius</I> arg = v_r
+ v_r = radius atom style variable for a poly-disperse Voronoi tessellation
+ <I>edge_histo</I> arg = maxedge
+ maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
+ <I>edge_threshold</I> arg = minlength
+ minlength = minimum length for an edge to be counted
+ <I>face_threshold</I> arg = minarea
+ minarea = minimum area for a face to be counted
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all voronoi/atom
+compute 2 precipitate voronoi/atom surface matrix
+compute 3b precipitate voronoi/atom radius v_r
+compute 4 solute voronoi/atom only_group
+</PRE>
+<PRE>compute 5 defects voronoi/atom occupation
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the Voronoi tessellation of the
+atoms in the simulation box. The tessellation is calculated using all
+atoms in the simulation, but non-zero values are only stored for atoms
+in the group.
+</P>
+<P>By default two quantities per atom are calculated by this compute.
+The first is the volume of the Voronoi cell around each atom. Any
+point in an atom's Voronoi cell is closer to that atom than any other.
+The second is the number of faces of the Voronoi cell, which is also
+the number of nearest neighbors of the atom in the middle of the cell.
+</P>
+<HR>
+
+<P>If the <I>only_group</I> keyword is specified the tessellation is performed
+only with respect to the atoms contained in the compute group. This is
+equivalent to deleting all atoms not contained in the group prior to
+evaluating the tessellation.
+</P>
+<P>If the <I>surface</I> keyword is specified a third quantity per atom is
+computed: the Voronoi cell surface of the given atom. <I>surface</I> takes
+a group ID as an argument. If a group other than <I>all</I> is specified,
+only the Voronoi cell facets facing a neighbor atom from the specified
+group are counted towards the surface area.
+</P>
+<P>In the example above, a precipitate embedded in a matrix, only atoms
+at the surface of the precipitate will have non-zero surface area, and
+only the outward facing facets of the Voronoi cells are counted (the
+hull of the precipitate). The total surface area of the precipitate
+can be obtained by running a "reduce sum" compute on c_2[3]
+</P>
+<P>If the <I>radius</I> keyword is specified with an atom style variable as
+the argument, a poly-disperse Voronoi tessellation is
+performed. Examples for radius variables are
+</P>
+<PRE>variable r1 atom (type==1)*0.1+(type==2)*0.4
+compute radius all property/atom radius
+variable r2 atom c_radius
+</PRE>
+<P>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
+and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
+present in atom_style sphere for granular models.
+</P>
+<P>The <I>edge_histo</I> keyword activates the compilation of a histogram of
+number of edges on the faces of the Voronoi cells in the compute
+group. The argument maxedge of the this keyword is the largest number
+of edges on a single Voronoi cell face expected to occur in the
+sample. This keyword adds the generation of a global vector with
+maxedge+1 entries. The last entry in the vector contains the number of
+faces with with more than maxedge edges. Since the polygon with the
+smallest amount of edges is a triangle, entries 1 and 2 of the vector
+will always be zero.
+</P>
+<P>The <I>edge_threshold</I> and <I>face_threshold</I> keywords allow the
+suppression of edges below a given minimum length and faces below a
+given minimum area. Ultra short edges and ultra small faces can occur
+as artifacts of the Voronoi tessellation. These keywords will affect
+the neighbor count and edge histogram outputs.
+</P>
+<P>If the <I>occupation</I> keyword is specified the tessellation is only
+performed for the first invocation of the compute and then stored.
+For all following invocations of the compute the number of atoms in
+each Voronoi cell in the stored tessellation is counted. In this mode
+the compute returns a per-atom array with 2 columns. The first column
+is the number of atoms currently in the Voronoi volume defined by this
+atom at the time of the first invocation of the compute (note that the
+atom may have moved significantly). The second column contains the
+total number of atoms sharing the Voronoi cell of the stored
+tessellation at the location of the current atom. Numbers in column
+one can be any positive integer including zero, while column two
+values will always be greater than zero. Column one data can be used
+to locate vacancies (the coordinates are given by the atom coordinates
+at the time step when the compute was first invoked), while column two
+data can be used to identify interstitial atoms.
+</P>
+<HR>
+
+<P>The Voronoi calculation is performed by the freely available <A HREF = "http://math.lbl.gov/voro++">Voro++
+package</A>, written by Chris Rycroft at UC Berkeley and LBL,
+which must be installed on your system when building LAMMPS for use
+with this compute. See instructions on obtaining and installing the
+Voro++ software in the src/VORONOI/README file.
+</P>
+
+
+<P>IMPORTANT NOTE: The calculation of Voronoi volumes is performed by
+each processor for the atoms it owns, and includes the effect of ghost
+atoms stored by the processor. This assumes that the Voronoi cells of
+owned atoms are not affected by atoms beyond the ghost atom cut-off
+distance. This is usually a good assumption for liquid and solid
+systems, but may lead to underestimation of Voronoi volumes in low
+density systems. By default, the set of ghost atoms stored by each
+processor is determined by the cutoff used for
+<A HREF = "pair_style.html">pair_style</A> interactions. The cutoff can be set
+explicitly via the <A HREF = "comm_modify.html">comm_modify cutoff</A> command.
+</P>
+<P>IMPORTANT NOTE: The Voro++ package performs its calculation in 3d.
+This should still work for a 2d LAMMPS simulation, to effectively
+compute Voronoi "areas", so long as the z-dimension of the box is
+roughly the same (or smaller) compared to the separation of the atoms.
+Typical values for the z box dimensions in a 2d LAMMPS model are -0.5
+to 0.5, which satisfies the criterion for most <A HREF = "units.html">units</A>
+systems. Note that you define the z extent of the simulation box for
+2d simulations when using the <A HREF = "create_box.html">create_box</A> or
+<A HREF = "read_data.html">read_data</A> commands.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom array with 2 columns. In regular
+dynamic tessellation mode the first column is the Voronoi volume, the
+second is the neighbor count, as described above (read above for the
+output data in case the <I>occupation</I> keyword is specified).
+These values can be accessed by any command that
+uses per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
+</P>
+<P>The Voronoi cell volume will be in distance <A HREF = "units.html">units</A> cubed.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the VORONOI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/compute_xrd.html b/doc/doc2/compute_xrd.html
new file mode 100644
index 000000000..e69612ac1
--- /dev/null
+++ b/doc/doc2/compute_xrd.html
@@ -0,0 +1,214 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute xrd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+
+<LI>xrd = style name of this compute command
+
+<LI>lambda = wavelength of incident radiation (length units)
+
+<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>2Theta</I> or <I>c</I> or <I>LP</I> or <I>manual</I> or <I>echo</I>
+
+<PRE> <I>2Theta</I> values = Min2Theta Max2Theta
+ Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
+ (radians or degrees)
+ <I>c</I> values = c1 c2 c3
+ c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+ lattice nodes in the h, k, and l directions respectively
+ <I>LP</I> value = switch to apply Lorentz-polarization factor
+ 0/1 = off/on
+ <I>manual</I> = flag to use manual spacing of reciprocal lattice points
+ based on the values of the <I>c</I> parameters
+ <I>echo</I> = flag to provide extra output for debugging purposes
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
+compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
+</PRE>
+<PRE>fix 1 all ave/histo/weights 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+</PRE>
+<PRE>
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates x-ray diffraction intensity as described
+in <A HREF = "#Coleman">(Coleman)</A> on a mesh of reciprocal lattice nodes defined
+by the entire simulation domain (or manually) using a simulated radiation
+of wavelength lambda.
+</P>
+<P>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
+is computed from the structure factor, F, using the equations:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_xrd1.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/compute_xrd2.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/compute_xrd3.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/compute_xrd4.jpg">
+</CENTER>
+<P>Here, K is the location of the reciprocal lattice node, rj is the
+position of each atom, fj are atomic scattering factors, LP is the
+Lorentz-polarization factor, and theta is the scattering angle of
+diffraction. The Lorentz-polarization factor can be turned off using
+the optional <I>LP</I> keyword.
+</P>
+<P>Diffraction intensities are calculated on a three-dimensional mesh of
+reciprocal lattice nodes. The mesh spacing is defined either (a)
+by the entire simulation domain or (b) manually using selected values as
+shown in the 2D diagram below.
+</P>
+<CENTER><A HREF = "JPG/xrd_mesh.jpg"><IMG SRC = "JPG/xrd_mesh_small.jpg"></A>
+</CENTER>
+<P>For a mesh defined by the simulation domain, a rectilinear grid is
+constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
+axis. Where A are the vectors corresponding to the edges of the
+simulation cell. If one or two directions has non-periodic boundary
+conditions, then the spacing in these directions is defined from the
+average of the (inversed) box lengths with periodic boundary conditions.
+Meshes defined by the simulation domain must contain at least one periodic
+boundary.
+</P>
+<P>If the <I>manual</I> flag is included, the mesh of reciprocal lattice nodes
+will defined using the <I>c</I> values for the spacing along each
+reciprocal lattice axis. Note that manual mapping of the reciprocal
+space mesh is good for comparing diffraction results from multiple
+simulations; however it can reduce the likelihood that Bragg
+reflections will be satisfied unless small spacing parameters (< 0.05
+Angstrom^(-1)) are implemented. Meshes with manual spacing do not
+require a periodic boundary.
+</P>
+<P>The limits of the reciprocal lattice mesh are determined by range of
+scattering angles explored. The <I>2Theta</I> parameters allows the user
+to reduce the scattering angle range to only the region of interest
+which reduces the cost of the computation.
+</P>
+<P>The atomic scattering factors, fj, accounts for the reduction in
+diffraction intensity due to Compton scattering. Compute xrd uses
+analytical approximations of the atomic scattering factors that vary
+for each atom type (type1 type2 ... typeN) and angle of diffraction.
+The analytic approximation is computed using the formula
+<A HREF = "#Colliex">(Colliex)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/compute_xrd5.jpg">
+</CENTER>
+<P>Coefficients parameterized by <A HREF = "#Peng">(Peng)</A> are assigned for each
+atom type designating the chemical symbol and charge of each atom
+type. Valid chemical symbols for compute xrd are:
+</P>
+<P> H: He1-: He: Li: Li1+:
+ Be: Be2+: B: C: Cval:
+ N: O: O1-: F: F1-:
+ Ne: Na: Na1+: Mg: Mg2+:
+ Al: Al3+: Si: Sival: Si4+:
+ P: S: Cl: Cl1-: Ar:
+ K: Ca: Ca2+: Sc: Sc3+:
+ Ti: Ti2+: Ti3+: Ti4+: V:
+ V2+: V3+: V5+: Cr: Cr2+:
+ Cr3+: Mn: Mn2+: Mn3+: Mn4+:
+ Fe: Fe2+: Fe3+: Co: Co2+:
+ Co: Ni: Ni2+: Ni3+: Cu:
+ Cu1+: Cu2+: Zn: Zn2+: Ga:
+ Ga3+: Ge: Ge4+: As: Se:
+ Br: Br1-: Kr: Rb: Rb1+:
+ Sr: Sr2+: Y: Y3+: Zr:
+ Zr4+: Nb: Nb3+: Nb5+: Mo:
+ Mo3+: Mo5+: Mo6+: Tc: Ru:
+ Ru3+: Ru4+: Rh: Rh3+: Rh4+:
+ Pd: Pd2+: Pd4+: Ag: Ag1+:
+ Ag2+: Cd: Cd2+: In: In3+:
+ Sn: Sn2+: Sn4+: Sb: Sb3+:
+ Sb5+: Te: I: I1-: Xe:
+ Cs: Cs1+: Ba: Ba2+: La:
+ La3+: Ce: Ce3+: Ce4+: Pr:
+ Pr3+: Pr4+: Nd: Nd3+: Pm:
+ Pm3+: Sm: Sm3+: Eu: Eu2+:
+ Eu3+: Gd: Gd3+: Tb: Tb3+:
+ Dy: Dy3+: Ho: Ho3+: Er:
+ Er3+: Tm: Tm3+: Yb: Yb2+:
+ Yb3+: Lu: Lu3+: Hf: Hf4+:
+ Ta: Ta5+: W: W6+: Re:
+ Os: Os4+: Ir: Ir3+: Ir4+:
+ Pt: Pt2+: Pt4+: Au: Au1+:
+ Au3+: Hg: Hg1+: Hg2+: Tl:
+ Tl1+: Tl3+: Pb: Pb2+: Pb4+:
+ Bi: Bi3+: Bi5+: Po: At:
+ Rn: Fr: Ra: Ra2+: Ac:
+ Ac3+: Th: Th4+: Pa: U:
+ U3+: U4+: U6+: Np: Np3+:
+ Np4+: Np6+: Pu: Pu3+: Pu4+:
+ Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)
+</P>
+<P>If the <I>echo</I> keyword is specified, compute xrd will provide extra
+reporting information to the screen.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a global array. The number of rows in the
+array is the number of reciprocal lattice nodes that are explored
+which by the mesh. The global array has 2 columns.
+</P>
+<P>The first column contains the diffraction angle in the units (radians
+or degrees) provided with the <I>2Theta</I> values. The second column contains
+the computed diffraction intensities as described above.
+</P>
+<P>The array can be accessed by any command that uses global values
+from a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS output
+options.
+</P>
+<P>All array values calculated by this compute are "intensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The compute_xrd command does not work for triclinic cells.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_histo.html">fix ave/histo</A>,
+<A HREF = "compute_saed.html">compute saed</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
+no manual flag, no echo flag.
+</P>
+<HR>
+
+<A NAME = "Coleman"></A>
+
+<P><B>(Coleman)</B> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+</P>
+<A NAME = "Colliex"></A>
+
+<P><B>(Colliex)</B> Colliex et al. International Tables for Crystallography
+Volume C: Mathematical and Chemical Tables, 249-429 (2004).
+</P>
+<A NAME = "Peng"></A>
+
+<P><B>(Peng)</B> Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
+(1996).
+</P>
+</HTML>
diff --git a/doc/doc2/create_atoms.html b/doc/doc2/create_atoms.html
new file mode 100644
index 000000000..dff7b6c97
--- /dev/null
+++ b/doc/doc2/create_atoms.html
@@ -0,0 +1,329 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>create_atoms command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>create_atoms type style args keyword values ...
+</PRE>
+<UL><LI>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
+
+<LI>style = <I>box</I> or <I>region</I> or <I>single</I> or <I>random</I>
+
+<PRE> <I>box</I> args = none
+ <I>region</I> args = region-ID
+ region-ID = particles will only be created if contained in the region
+ <I>single</I> args = x y z
+ x,y,z = coordinates of a single particle (distance units)
+ <I>random</I> args = N seed region-ID
+ N = number of particles to create
+ seed = random # seed (positive integer)
+ region-ID = create atoms within this region, use NULL for entire simulation box
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>mol</I> or <I>basis</I> or <I>remap</I> or <I>var</I> or <I>set</I> or <I>units</I>
+
+<PRE> <I>mol</I> value = template-ID seed
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+ seed = random # seed (positive integer)
+ <I>basis</I> values = M itype
+ M = which basis atom
+ itype = atom type (1-N) to assign to this basis atom
+ <I>remap</I> value = <I>yes</I> or <I>no</I>
+ <I>var</I> value = name = variable name to evaluate for test of atom creation
+ <I>set</I> values = dim vname
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ name = name of variable to set with x,y,z atom position
+ <I>rotate</I> values = Rx Ry Rz theta
+ Rx,Ry,Rz = rotation vector for single molecule
+ theta = rotation angle for single molecule (degrees)
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the geometry is defined in lattice units
+ <I>box</I> = the geometry is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>create_atoms 1 box
+create_atoms 3 region regsphere basis 2 3
+create_atoms 3 single 0 0 5
+create_atoms 1 box var v set x xpos set y ypos
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command creates atoms (or molecules) on a lattice, or a single
+atom (or molecule), or a random collection of atoms (or molecules), as
+an alternative to reading in their coordinates explicitly via a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+command. A simulation box must already exist, which is typically
+created via the <A HREF = "create_box.html">create_box</A> command. Before using
+this command, a lattice must also be defined using the
+<A HREF = "lattice.html">lattice</A> command, unless you specify the <I>single</I> style
+with units = box or the <I>random</I> style. For the remainder of this doc
+page, a created atom or molecule is referred to as a "particle".
+</P>
+<P>If created particles are individual atoms, they are assigned the
+specified atom <I>type</I>, though this can be altered via the <I>basis</I>
+keyword as discussed below. If molecules are being created, the type
+of each atom in the created molecule is specified in the file read by
+the <A HREF = "molecule.html">molecule</A> command, and those values are added to
+the specified atom <I>type</I>. E.g. if <I>type</I> = 2, and the file specifies
+atom types 1,2,3, then each created molecule will have atom types
+3,4,5.
+</P>
+<P>For the <I>box</I> style, the create_atoms command fills the entire
+simulation box with particles on the lattice. If your simulation box
+is periodic, you should insure its size is a multiple of the lattice
+spacings, to avoid unwanted atom overlaps at the box boundaries. If
+your box is periodic and a multiple of the lattice spacing in a
+particular dimension, LAMMPS is careful to put exactly one particle at
+the boundary (on either side of the box), not zero or two.
+</P>
+<P>For the <I>region</I> style, a geometric volume is filled with particles on
+the lattice. This volume what is inside the simulation box and is
+also consistent with the region volume. See the <A HREF = "region.html">region</A>
+command for details. Note that a region can be specified so that its
+"volume" is either inside or outside a geometric boundary. Also note
+that if your region is the same size as a periodic simulation box (in
+some dimension), LAMMPS does not implement the same logic described
+above as for the <I>box</I> style, to insure exactly one particle at
+periodic boundaries. if this is what you desire, you should either
+use the <I>box</I> style, or tweak the region size to get precisely the
+particles you want.
+</P>
+<P>For the <I>single</I> style, a single particle is added to the system at
+the specified coordinates. This can be useful for debugging purposes
+or to create a tiny system with a handful of particles at specified
+positions.
+</P>
+<P>For the <I>random</I> style, N particles are added to the system at
+randomly generated coordinates, which can be useful for generating an
+amorphous system. The particles are created one by one using the
+speficied random number <I>seed</I>, resulting in the same set of particles
+coordinates, independent of how many processors are being used in the
+simulation. If the <I>region-ID</I> argument is specified as NULL, then
+the created particles will be anywhere in the simulation box. If a
+<I>region-ID</I> is specified, a geometric volume is filled which is both
+inside the simulation box and is also consistent with the region
+volume. See the <A HREF = "region.html">region</A> command for details. Note that
+a region can be specified so that its "volume" is either inside or
+outside a geometric boundary.
+</P>
+<P>IMPORTANT NOTE: Particles generated by the <I>random</I> style will
+typically be highly overlapped which will cause many interatomic
+potentials to compute large energies and forces. Thus you should
+either perform an <A HREF = "minimize.html">energy minimization</A> or run dynamics
+with <A HREF = "fix_nve_limit.html">fix nve/limit</A> to equilibrate such a system,
+before running normal dynamics.
+</P>
+<P>Note that this command adds particles to those that already exist.
+This means it can be used to add particles to a system previously read
+in from a data or restart file. Or the create_atoms command can be
+used multiple times, to add multiple sets of particles to the
+simulation. For example, grain boundaries can be created, by
+interleaving create_atoms with <A HREF = "lattice.html">lattice</A> commands
+specifying different orientations. By using the create_atoms command
+in conjunction with the <A HREF = "delete_atoms.html">delete_atoms</A> command,
+reasonably complex geometries can be created, or a protein can be
+solvated with a surrounding box of water molecules.
+</P>
+<P>In all these cases, care should be taken to insure that new atoms do
+not overlap existing atoms inappropriately, especially if molecules
+are being added. The <A HREF = "delete_atoms.html">delete_atoms</A> command can be
+used to remove overlapping atoms or molecules.
+</P>
+<HR>
+
+<P>Individual atoms are inserted by this command, unless the <I>mol</I>
+keyword is used. It specifies a <I>template-ID</I> previously defined
+using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
+defines the molecule. The coordinates, atom types, charges, etc, as
+well as any bond/angle/etc and special neighbor information for the
+molecule can be specified in the molecule file. See the
+<A HREF = "molecule.html">molecule</A> command for details. The only settings
+required to be in this file are the coordinates and types of atoms in
+the molecule.
+</P>
+<P>Using a lattice to add molecules, e.g. via the <I>box</I> or <I>region</I> or
+<I>single</I> styles, is exactly the same as adding atoms on lattice
+points, except that entire molecules are added at each point, i.e. on
+the point defined by each basis atom in the unit cell as it tiles the
+simulation box or region. This is done by placing the geometric
+center of the molecule at the lattice point, and giving the molecule a
+random orientation about the point. The random <I>seed</I> specified with
+the <I>mol</I> keyword is used for this operation, and the random numbers
+generated by each processor are different. This means the coordinates
+of individual atoms (in the molecules) will be different when running
+on different numbers of processors, unlike when atoms are being
+created in parallel.
+</P>
+<P>Also note that because of the random rotations, it may be important to
+use a lattice with a large enough spacing that adjacent molecules will
+not overlap, regardless of their relative orientations.
+</P>
+<P>IMPORTANT NOTE: If the <A HREF = "create_box.html">create_box</A> command is used to
+create the simulation box, followed by the create_atoms command with
+its <I>mol</I> option for adding molecules, then you typically need to use
+the optional keywords allowed by the <A HREF = "create_box.html">create_box</A>
+command for extra bonds (angles,etc) or extra special neighbors. This
+is because by default, the <A HREF = "create_box.html">create_box</A> command sets
+up a non-molecular system which doesn't allow molecules to be added.
+</P>
+<HR>
+
+<P>This is the meaning of the other allowed keywords.
+</P>
+<P>The <I>basis</I> keyword is only used when atoms (not molecules) are being
+created. It specifies an atom type that will be assigned to specific
+basis atoms as they are created. See the <A HREF = "lattice.html">lattice</A>
+command for specifics on how basis atoms are defined for the unit cell
+of the lattice. By default, all created atoms are assigned the
+argument <I>type</I> as their atom type.
+</P>
+<P>The <I>remap</I> keyword only applies to the <I>single</I> style. If it is set
+to <I>yes</I>, then if the specified position is outside the simulation
+box, it will mapped back into the box, assuming the relevant
+dimensions are periodic. If it is set to <I>no</I>, no remapping is done
+and no particle is created if its position is outside the box.
+</P>
+<P>The <I>var</I> and <I>set</I> keywords can be used to provide a criterion for
+accepting or rejecting the addition of an individual atom, based on
+its coordinates. The <I>vname</I> specified for the <I>var</I> keyword is the
+name of an <A HREF = "variable.html">equal-style variable</A> which should evaluate
+to a zero or non-zero value based on one or two or three variables
+which will store the x, y, or z coordinates of an atom (one variable
+per coordinate). These other variables must be <A HREF = "variable.html">equal-style
+variables</A> defined in the input script, but their
+formula can by anything. The <I>set</I> keyword is used to identify the
+names of these other variables, one variable for the x-coordinate of a
+created atom, one for y, and one for z.
+</P>
+<P>When an atom is created, its x, y, or z coordinates override the
+formula for any <I>set</I> variable that is defined. The <I>var</I> variable is
+then evaluated. If the returned value is 0.0, the atom is not
+created. If it is non-zero, the atom is created. After all atoms are
+created, the formulas defined for all of the <I>set</I> variables are
+restored to their original strings.
+</P>
+<P>As an example, these commands can be used in a 2d simulation, to
+create a sinusoidal surface. Note that the surface is "rough" due to
+individual lattice points being "above" or "below" the mathematical
+expression for the sinusoidal curve. If a finer lattice were used,
+the sinusoid would appear to be "smoother". Also note the use of the
+"xlat" and "ylat" <A HREF = "thermo_style.html">thermo_style</A> keywords which
+converts lattice spacings to distance. Click on the image for a
+larger version.
+</P>
+<PRE>variable x equal 100
+variable y equal 25
+lattice hex 0.8442
+region box block 0 $x 0 $y -0.5 0.5
+create_box 1 box
+</PRE>
+<PRE>variable xx equal 0.0
+variable yy equal 0.0
+variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
+create_atoms 1 box var v set x xx set y yy
+</PRE>
+<CENTER><A HREF = "JPG/sinusoid.jpg"><IMG SRC = "JPG/sinusoid_small.jpg"></A>
+</CENTER>
+<P>The <I>rotate</I> keyword can be used with the <I>single</I> style, when adding
+a single molecule to specify the orientation at which the molecule is
+inserted. The axis of rotation is determined by the rotation vector
+(Rx,Ry,Rz) that goes through the insertion point. The specified
+<I>theta</I> determines the angle of rotation around that axis. Note that
+the direction of rotation for the atoms around the rotation axis is
+consistent with the right-hand rule: if your right-hand's thumb points
+along <I>R</I>, then your fingers wrap around the axis in the direction of
+rotation.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to specify the coordinates of the one particle created by the <I>single</I>
+style. A <I>box</I> value selects standard distance units as defined by
+the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
+metal. A <I>lattice</I> value means the distance units are in lattice
+spacings.
+</P>
+<HR>
+
+<P>Atom IDs are assigned to created atoms in the following way. The
+collection of created atoms are assigned consecutive IDs that start
+immediately following the largest atom ID existing before the
+create_atoms command was invoked. When a simulation is performed on
+different numbers of processors, there is no guarantee a particular
+created atom will be assigned the same ID. If molecules are being
+created, molecule IDs are assigned to created molecules in a similar
+fashion.
+</P>
+<P>Aside from their ID, atom type, and xyz position, other properties of
+created atoms are set to default values, depending on which quantities
+are defined by the chosen <A HREF = "atom_style.html">atom style</A>. See the <A HREF = "atom_style.html">atom
+style</A> command for more details. See the
+<A HREF = "set.html">set</A> and <A HREF = "velocity.html">velocity</A> commands for info on how
+to change these values.
+</P>
+<UL><LI>charge = 0.0
+<LI>dipole moment magnitude = 0.0
+<LI>diameter = 1.0
+<LI>shape = 0.0 0.0 0.0
+<LI>density = 1.0
+<LI>volume = 1.0
+<LI>velocity = 0.0 0.0 0.0
+<LI>angular velocity = 0.0 0.0 0.0
+<LI>angular momentum = 0.0 0.0 0.0
+<LI>quaternion = (1,0,0,0)
+<LI>bonds, angles, dihedrals, impropers = none
+</UL>
+<P>If molecules are being created, these defaults can be overridden by
+values specified in the file read by the <A HREF = "molecule.html">molecule</A>
+command. E.g. the file typically defines bonds (angles,etc) between
+atoms in the molecule, and can optionally define charges on each atom.
+</P>
+<P>Note that the <I>sphere</I> atom style sets the default particle diameter
+to 1.0 as well as the density. This means the mass for the particle
+is not 1.0, but is PI/6 * diameter^3 = 0.5236.
+</P>
+<P>Note that the <I>ellipsoid</I> atom style sets the default particle shape
+to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
+particle, not an ellipsoid, and has a mass of 1.0.
+</P>
+<P>Note that the <I>peri</I> style sets the default volume and density to 1.0
+and thus also set the mass for the particle to 1.0.
+</P>
+<P>The <A HREF = "set.html">set</A> command can be used to override many of these
+default settings.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>An <A HREF = "atom_style.html">atom_style</A> must be previously defined to use this
+command.
+</P>
+<P>A rotation vector specified for a single molecule must be in
+the z-direction for a 2d model.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "lattice.html">lattice</A>, <A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default for the <I>basis</I> keyword is that all created atoms are
+assigned the argument <I>type</I> as their atom type (when single atoms are
+being created). The other defaults are <I>remap</I> = no, <I>rotate</I> =
+random, and <I>units</I> = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/create_bonds.html b/doc/doc2/create_bonds.html
new file mode 100644
index 000000000..13267df97
--- /dev/null
+++ b/doc/doc2/create_bonds.html
@@ -0,0 +1,114 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>create_bonds command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>create_bonds group-ID group2-ID btype rmin rmax
+</PRE>
+<UL><LI>group-ID = ID of first group
+<LI>group2-ID = ID of second group, bonds will be between atoms in the 2 groups
+<LI>btype = bond type of created bonds
+<LI>rmin = minimum distance between pair of atoms to bond together
+<LI>rmax = minimum distance between pair of atoms to bond together
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>create_bonds all all 1 1.0 1.2
+create_bonds surf solvent 3 2.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Create bonds between pairs of atoms that meet specified distance
+criteria. The bond interactions can then be computed during a
+simulation by the bond potential defined by the
+<A HREF = "bond_style.html">bond_style</A> and <A HREF = "bond_coeff.html">bond_coeff</A>
+commands. This command is useful for adding bonds to a system,
+e.g. between nearest neighbors in a lattice of atoms, without having
+to enumerate all the bonds in the data file read by the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Note that the flexibility of this command is limited. It can be used
+several times to create different types of bond at different
+distances. But it cannot typically create all the bonds that would
+normally be defined in a complex system of molecules. Also note that
+this command does not add any 3-body or 4-body interactions which,
+depending on your model, may be induced by added bonds,
+e.g. <A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>, or
+<A HREF = "improper_style.html">improper</A> interactions.
+</P>
+<P>All created bonds will be between pairs of atoms I,J where I is in one
+of the two specified groups, and J is in the other. The two groups
+can be the same, e.g. group "all". The created bonds will be of bond
+type <I>btype</I>, where <I>btype</I> must be a value between 1 and the number
+of bond types defined. This maximum value is set by the "bond types"
+field in the header of the data file read by the
+<A HREF = "read_data.html">read_data</A> command, or via the optional "bond/types"
+argument of the <A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>For a bond to be created, an I,J pair of atoms must be a distance D
+apart such that <I>rmin</I> <= D <= <I>rmax</I>.
+</P>
+<P>The following settings must have been made in an input
+script before this command is used:
+</P>
+<UL><LI>special_bonds weight for 1-2 interactions must be 0.0
+<LI>a <A HREF = "pair_style.html">pair_style</A> must be defined
+<LI>no <A HREF = "kspace_style.html">kspace_style</A> defined
+<LI>minimum <A HREF = "pair_style.html">pair_style</A> cutoff + <A HREF = "neighbor.html">neighbor</A> skin >= <I>rmax</I>
+</UL>
+<P>These settings are required so that a neighbor list can be created to
+search for nearby atoms. Pairs of atoms that are already bonded
+cannot appear in the neighbor list, to avoid creation of duplicate
+bonds. The neighbor list for all atom type pairs must also extend to
+a distance that encompasses the <I>rmax</I> for new bonds to create.
+</P>
+<P>An additional requirement is that your system must be ready to perform
+a simulation. This means, for example, that all
+<A HREF = "pair_style.html">pair_style</A> coefficients be set via the
+<A HREF = "pair_coeff.html">pair_coeff</A> command. A <A HREF = "bond_style.html">bond_style</A>
+command and all bond coefficients must also be set, even if no bonds
+exist before this command is invoked. This is because the building of
+neighbor list requires initialization and setup of a simulation,
+similar to what a <A HREF = "run.html">run</A> command would require.
+</P>
+<P>Note that you can change any of these settings after this command
+executes, e.g. if you wish to use long-range Coulombic interactions
+via the <A HREF = "kspace_style.html">kspace_style</A> command for your subsequent
+simulation.
+</P>
+<P>IMPORTANT NOTE: If the system has no bonds to begin with, or if more
+bonds per atom are being added than currently exist, then you must
+insure that the number of bond types and the maximum number of bonds
+per atom are set to large enough values. Otherwise an error may occur
+when too many bonds are added to an atom. If the
+<A HREF = "read_data.html">read_data</A> command is used to define the system, these
+2 parameters can be set via the "bond types" and "extra bond per atom"
+fields in the header section of the data file. If the
+<A HREF = "create_box.html">create_box</A> command is used to define the system,
+these 2 parameters can be set via its optional "bond/types" and
+"extra/bond/per/atom" arguments. See the doc pages for the 2 commands
+for details.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used with molecular systems defined using
+molecule template files via the <A HREF = "molecule.html">molecule</A> and
+<A HREF = "atom_style.html">atom_style template</A> commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/create_box.html b/doc/doc2/create_box.html
new file mode 100644
index 000000000..85be5f5f6
--- /dev/null
+++ b/doc/doc2/create_box.html
@@ -0,0 +1,162 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>create_box command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>create_box N region-ID keyword value ...
+</PRE>
+<UL><LI>N = # of atom types to use in this simulation
+
+<LI>region-ID = ID of region to use as simulation domain
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>bond/types</I> or <I>angle/types</I> or <I>dihedral/types</I> or <I>improper/types</I> or <I>extra/bond/per/atom</I> or <I>extra/angle/per/atom</I> or <I>extra/dihedral/per/atom</I> or <I>extra/improper/per/atom</I>
+
+<PRE> <I>bond/types</I> value = # of bond types
+ <I>angle/types</I> value = # of angle types
+ <I>dihedral/types</I> value = # of dihedral types
+ <I>improper/types</I> value = # of improper types
+ <I>extra/bond/per/atom</I> value = # of bonds per atom
+ <I>extra/angle/per/atom</I> value = # of angles per atom
+ <I>extra/dihedral/per/atom</I> value = # of dihedrals per atom
+ <I>extra/improper/per/atom</I> value = # of impropers per atom
+ <I>extra/special/per/atom</I> value = # of special neighbors per atom
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>create_box 2 mybox
+create_box 2 mybox bond/types 2 extra/bond/per/atom 1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command creates a simulation box based on the specified region.
+Thus a <A HREF = "region.html">region</A> command must first be used to define a
+geometric domain. It also partitions the simulation box into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors being used and the settings of the
+<A HREF = "processors.html">processors</A> command. The partitioning can later be
+changed by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
+balance</A> commands.
+</P>
+<P>The argument N is the number of atom types that will be used in the
+simulation.
+</P>
+<P>If the region is not of style <I>prism</I>, then LAMMPS encloses the region
+(block, sphere, etc) with an axis-aligned orthogonal bounding box
+which becomes the simulation domain.
+</P>
+<P>If the region is of style <I>prism</I>, LAMMPS creates a non-orthogonal
+simulation domain shaped as a parallelepiped with triclinic symmetry.
+As defined by the <A HREF = "region.html">region prism</A> command, the
+parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3
+edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
+(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or
+positive or negative values and are called "tilt factors" because they
+are the amount of displacement applied to faces of an originally
+orthogonal box to transform it into the parallelipiped.
+</P>
+<P>By default, a <I>prism</I> region used with the create_box command must
+have tilt factors (xy,xz,yz) that do not skew the box more than half
+the distance of the parallel box length. For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
+between -5 and 5. Similarly, both xz and yz must be between
+-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
+since if the maximum tilt factor is 5 (as in this example), then
+configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
+geometrically equivalent. If you wish to define a box with tilt
+factors that exceed these limits, you can use the <A HREF = "box.html">box tilt</A>
+command, with a setting of <I>large</I>; a setting of <I>small</I> is the
+default.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+</P>
+<P>When a prism region is used, the simulation domain should normally be
+periodic in the dimension that the tilt is applied to, which is given
+by the second dimension of the tilt factor (e.g. y for xy tilt). This
+is so that pairs of atoms interacting across that boundary will have
+one of them shifted by the tilt factor. Periodicity is set by the
+<A HREF = "boundary.html">boundary</A> command. For example, if the xy tilt factor
+is non-zero, then the y dimension should be periodic. Similarly, the
+z dimension should be periodic if xz or yz is non-zero. LAMMPS does
+not require this periodicity, but you may lose atoms if this is not
+the case.
+</P>
+<P>Also note that if your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
+deform</A> command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0. You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the <A HREF = "change_box.html">change box</A> command with its <I>ortho</I> and
+<I>triclinic</I> options.
+</P>
+<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
+you should not make the lo/hi box dimensions (as defined in your
+<A HREF = "region.html">region</A> command) radically smaller/larger than the extent
+of the atoms you eventually plan to create, e.g. via the
+<A HREF = "create_atoms.html">create_atoms</A> command. For example, if your atoms
+extend from 0 to 50, you should not specify the box bounds as -10000
+and 10000. This is because as described above, LAMMPS uses the
+specified box size to layout the 3d grid of processors. A huge
+(mostly empty) box will be sub-optimal for performance when using
+"fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
+command). When using "shrink-wrap" boundary conditions (see the
+<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
+a parallel simulation to lose atoms the first time that LAMMPS
+shrink-wraps the box around the atoms.
+</P>
+<HR>
+
+<P>The optional keywords can be used to create a system that allows for
+bond (angle, dihedral, improper) interactions, or for molecules with
+special 1-2,1-3,1-4 neighbors to be added later. These optional
+keywords serve the same purpose as the analogous keywords that can be
+used in a data file which are recognized by the
+<A HREF = "read_data.html">read_data</A> command when it sets up a system.
+</P>
+<P>Note that if these keywords are not used, then the create_box command
+creates an atomic (non-molecular) simulation that does not allow bonds
+between pairs of atoms to be defined, or a <A HREF = "bond_style.html">bond
+potential</A> to be specified, or for molecules with
+special neighbors to be added to the system by commands such as
+<A HREF = "create_atoms.html">create_atoms mol</A>, <A HREF = "fix_deposit.html">fix deposit</A>
+or <A HREF = "fix_pour.html">fix pour</A>.
+</P>
+<P>As an example, see the examples/deposit/in.deposit.molecule script,
+which deposits molecules onto a substrate. Initially there are no
+molecules in the system, but they are added later by the <A HREF = "fix_deposit.html">fix
+deposit</A> command. The create_box command in the
+script uses the bond/types and extra/bond/per/atom keywords to allow
+this. If the added molecule contained more than 1 special bond
+(allowed by default), an extra/special/per/atom keyword would also
+need to be specified.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have
+been previously defined to use this command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>,
+<A HREF = "region.html">region</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/delete_atoms.html b/doc/doc2/delete_atoms.html
new file mode 100644
index 000000000..c0dc0590d
--- /dev/null
+++ b/doc/doc2/delete_atoms.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>delete_atoms command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>delete_atoms style args keyword value ...
+</PRE>
+<UL><LI>style = <I>group</I> or <I>region</I> or <I>overlap</I> or <I>porosity</I>
+
+<PRE> <I>group</I> args = group-ID
+ <I>region</I> args = region-ID
+ <I>overlap</I> args = cutoff group1-ID group2-ID
+ cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
+ group1-ID = one atom in pair must be in this group
+ group2-ID = other atom in pair must be in this group
+ <I>porosity</I> args = region-ID fraction seed
+ region-ID = region within which to perform deletions
+ fraction = delete this fraction of atoms
+ seed = random number seed (positive integer)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>compress</I> or <I>bond</I> or <I>mol</I>
+
+<PRE> <I>compress</I> value = <I>no</I> or <I>yes</I>
+ <I>bond</I> value = <I>no</I> or <I>yes</I>
+ <I>mol</I> value = <I>no</I> or <I>yes</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>delete_atoms group edge
+delete_atoms region sphere compress no
+delete_atoms overlap 0.3 all all
+delete_atoms overlap 0.5 solvent colloid
+delete_atoms porosity cube 0.1 482793 bond yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Delete the specified atoms. This command can be used to carve out
+voids from a block of material or to delete created atoms that are too
+close to each other (e.g. at a grain boundary).
+</P>
+<P>For style <I>group</I>, all atoms belonging to the group are deleted.
+</P>
+<P>For style <I>region</I>, all atoms in the region volume are deleted.
+Additional atoms can be deleted if they are in a molecule for which
+one or more atoms were deleted within the region; see the <I>mol</I>
+keyword discussion below.
+</P>
+<P>For style <I>overlap</I> pairs of atoms whose distance of separation is
+within the specified cutoff distance are searched for, and one of the
+2 atoms is deleted. Only pairs where one of the two atoms is in the
+first group specified and the other atom is in the second group are
+considered. The atom that is in the first group is the one that is
+deleted.
+</P>
+<P>Note that it is OK for the two group IDs to be the same (e.g. group
+<I>all</I>), or for some atoms to be members of both groups. In these
+cases, either atom in the pair may be deleted. Also note that if
+there are atoms which are members of both groups, the only guarantee
+is that at the end of the deletion operation, enough deletions will
+have occurred that no atom pairs within the cutoff will remain
+(subject to the group restriction). There is no guarantee that the
+minimum number of atoms will be deleted, or that the same atoms will
+be deleted when running on different numbers of processors.
+</P>
+<P>For style <I>porosity</I> a specified <I>fraction</I> of atoms are deleted
+within the specified region. For example, if fraction is 0.1, then
+10% of the atoms will be deleted. The atoms to delete are chosen
+randomly. There is no guarantee that the exact fraction of atoms will
+be deleted, or that the same atoms will be deleted when running on
+different numbers of processors.
+</P>
+<P>If the <I>compress</I> keyword is set to <I>yes</I>, then after atoms are
+deleted, then atom IDs are re-assigned so that they run from 1 to the
+number of atoms in the system. Note that this is not done for
+molecular systems (see the <A HREF = "atom_style.html">atom_style</A> command),
+regardless of the <I>compress</I> setting, since it would foul up the bond
+connectivity that has already been assigned.
+</P>
+<P>A molecular system with fixed bonds, angles, dihedrals, or improper
+interactions, is one where the topology of the interactions is
+typically defined in the data file read by the
+<A HREF = "read_data.html">read_data</A> command, and where the interactions
+themselves are defined with the <A HREF = "bond_style.html">bond_style</A>,
+<A HREF = "angle_style.html">angle_style</A>, etc commands. If you delete atoms
+from such a system, you must be careful not to end up with bonded
+interactions that are stored by remaining atoms but which include
+deleted atoms. This will cause LAMMPS to generate a "missing atoms"
+error when the bonded interaction is computed. The <I>bond</I> and <I>mol</I>
+keywords offer two ways to do that.
+</P>
+<P>It the <I>bond</I> keyword is set to <I>yes</I> then any bond or angle or
+dihedral or improper interaction that includes a deleted atom is also
+removed from the lists of such interactions stored by non-deleted
+atoms. Note that simply deleting interactions due to dangling bonds
+(e.g. at a surface) may result in a inaccurate or invalid model for
+the remaining atoms.
+</P>
+<P>It the <I>mol</I> keyword is set to <I>yes</I>, then for every atom that is
+deleted, all other atoms in the same molecule (with the same molecule
+ID) will also be deleted. This is not done for atoms with molecule ID
+= 0, since such an ID is assumed to flag isolated atoms that are not
+part of molecules.
+</P>
+<P>IMPORTANT NOTE: The molecule deletion operation in invoked after all
+individual atoms have been deleted using the rules described above for
+each style. This means additional atoms may be deleted that are not
+in the group or region, that are not required by the overlap cutoff
+criterion, or that will create a higher fraction of porosity than was
+requested.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>overlap</I> styles requires inter-processor communication to acquire
+ghost atoms and build a neighbor list. This means that your system
+must be ready to perform a simulation before using this command (force
+fields setup, atom masses set, etc). Since a neighbor list is used to
+find overlapping atom pairs, it also means that you must define a
+<A HREF = "pair_style.html">pair style</A> with the minimum force cutoff distance
+between any pair of atoms types (plus the <A HREF = "neighbor.html">neighbor</A>
+skin) >= the specified overlap cutoff.
+</P>
+<P>If the <A HREF = "special_bonds.html">special_bonds</A> command is used with a
+setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
+appear in the neighbor list, and thus will not be considered for
+deletion by the <I>overlap</I> styles. You probably don't want to be
+deleting one atom in a bonded pair anyway.
+</P>
+<P>The <I>bond yes</I> option cannot be used with molecular systems defined
+using molecule template files via the <A HREF = "molecular.html">molecule</A> and
+<A HREF = "atom_style.html">atom_style template</A> commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "create_atoms.html">create_atoms</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are compress = yes, bond = no, mol = no.
+</P>
+</HTML>
diff --git a/doc/doc2/delete_bonds.html b/doc/doc2/delete_bonds.html
new file mode 100644
index 000000000..ccd35f452
--- /dev/null
+++ b/doc/doc2/delete_bonds.html
@@ -0,0 +1,159 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>delete_bonds command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>delete_bonds group-ID style arg keyword ...
+</PRE>
+<UL><LI>group-ID = group ID
+
+<LI>style = <I>multi</I> or <I>atom</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or
+ <I>improper</I> or <I>stats</I>
+
+<PRE> <I>multi</I> arg = none
+ <I>atom</I> arg = an atom type or range of types (see below)
+ <I>bond</I> arg = a bond type or range of types (see below)
+ <I>angle</I> arg = an angle type or range of types (see below)
+ <I>dihedral</I> arg = a dihedral type or range of types (see below)
+ <I>improper</I> arg = an improper type or range of types (see below)
+ <I>stats</I> arg = none
+</PRE>
+<LI>zero or more keywords may be appended
+
+<LI>keyword = <I>any</I> or <I>undo</I> or <I>remove</I> or <I>special</I>
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>delete_bonds frozen multi remove
+delete_bonds all atom 4 special
+delete_bonds all bond 0*3 special
+delete_bonds all stats
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Turn off (or on) molecular topology interactions, i.e. bonds, angles,
+dihedrals, impropers. This command is useful for deleting
+interactions that have been previously turned off by bond-breaking
+potentials. It is also useful for turning off topology interactions
+between frozen or rigid atoms. Pairwise interactions can be turned
+off via the <A HREF = "neigh_modify.html">neigh_modify exclude</A> command. The
+<A HREF = "fix_shake.html">fix shake</A> command also effectively turns off certain
+bond and angle interactions.
+</P>
+<P>For all styles, by default, an interaction is only turned off (or on)
+if all the atoms involved are in the specified group. See the <I>any</I>
+keyword to change the behavior.
+</P>
+<P>Several of the styles (<I>atom</I>, <I>bond</I>, <I>angle</I>, <I>dihedral</I>,
+<I>improper</I>) take a <I>type</I> as an argument. The specified <I>type</I> should
+be an integer from 0 to N, where N is the number of relevant types
+(atom types, bond types, etc). A value of 0 is only relevant for
+style <I>bond</I>; see details below. In all cases, a wildcard asterisk
+can be used in place of or in conjunction with the <I>type</I> argument to
+specify a range of types. This takes the form "*" or "*n" or "n*" or
+"m*n". If N = the number of types, then an asterisk with no numeric
+values means all types from 0 to N. A leading asterisk means all
+types from 0 to n (inclusive). A trailing asterisk means all types
+from n to N (inclusive). A middle asterisk means all types from m to
+n (inclusive). Note that it is fine to include a type of 0 for
+non-bond styles; it will simply be ignored.
+</P>
+<P>For style <I>multi</I> all bond, angle, dihedral, and improper interactions
+of any type, involving atoms in the group, are turned off.
+</P>
+<P>Style <I>atom</I> is the same as style <I>multi</I> except that in addition, one
+or more of the atoms involved in the bond, angle, dihedral, or
+improper interaction must also be of the specified atom type.
+</P>
+<P>For style <I>bond</I>, only bonds are candidates for turn-off, and the bond
+must also be of the specified type. Styles <I>angle</I>, <I>dihedral</I>, and
+<I>improper</I> are treated similarly.
+</P>
+<P>For style <I>bond</I>, you can set the type to 0 to delete bonds that have
+been previously broken by a bond-breaking potential (which sets the
+bond type to 0 when a bond is broken); e.g. see the <A HREF = "bond_style.html">bond_style
+quartic</A> command.
+</P>
+<P>For style <I>stats</I> no interactions are turned off (or on); the status
+of all interactions in the specified group is simply reported. This
+is useful for diagnostic purposes if bonds have been turned off by a
+bond-breaking potential during a previous run.
+</P>
+<P>The default behavior of the delete_bonds command is to turn off
+interactions by toggling their type to a negative value, but not to
+permanently remove the interaction. E.g. a bond_type of 2 is set to
+-2. The neighbor list creation routines will not include such an
+interaction in their interaction lists. The default is also to not
+alter the list of 1-2, 1-3, 1-4 neighbors computed by the
+<A HREF = "special_bonds.html">special_bonds</A> command and used to weight pairwise
+force and energy calculations. This means that pairwise computations
+will proceed as if the bond (or angle, etc) were still turned on.
+</P>
+<P>Several keywords can be appended to the argument list to alter the
+default behaviors.
+</P>
+<P>The <I>any</I> keyword changes the requirement that all atoms in the bond
+(angle, etc) must be in the specified group in order to turn-off the
+interaction. Instead, if any of the atoms in the interaction are in
+the specified group, it will be turned off (or on if the <I>undo</I>
+keyword is used).
+</P>
+<P>The <I>undo</I> keyword inverts the delete_bonds command so that the
+specified bonds, angles, etc are turned on if they are currently
+turned off. This means a negative value is toggled to positive. For
+example, for style <I>angle</I>, if <I>type</I> is specified as 2, then all
+angles with current type = -2, are reset to type = 2. Note that the
+<A HREF = "fix_shake.html">fix shake</A> command also sets bond and angle types
+negative, so this option should not be used on those interactions.
+</P>
+<P>The <I>remove</I> keyword is invoked at the end of the delete_bonds
+operation. It causes turned-off bonds (angles, etc) to be removed
+from each atom's data structure and then adjusts the global bond
+(angle, etc) counts accordingly. Removal is a permanent change;
+removed bonds cannot be turned back on via the <I>undo</I> keyword.
+Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.
+</P>
+<P>The <I>special</I> keyword is invoked at the end of the delete_bonds
+operation, after (optional) removal. It re-computes the pairwise 1-2,
+1-3, 1-4 weighting list. The weighting list computation treats
+turned-off bonds the same as turned-on. Thus, turned-off bonds must
+be removed if you wish to change the weighting list.
+</P>
+<P>Note that the choice of <I>remove</I> and <I>special</I> options affects how
+1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
+have been modified by the delete_bonds command.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command requires inter-processor communication to coordinate the
+deleting of bonds. This means that your system must be ready to
+perform a simulation before using this command (force fields setup,
+atom masses set, etc).
+</P>
+<P>If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
+weighting list is not recomputed, this can cause a later <A HREF = "fix_shake.html">fix
+shake</A> command to fail due to an atom's bonds being
+inconsistent with the weighting list. This should only happen if the
+group used in the fix command includes both atoms in the bond, in
+which case you probably should be recomputing the weighting list.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "neigh_modify.html">neigh_modify</A> exclude,
+<A HREF = "special_bonds.html">special_bonds</A>, <A HREF = "fix_shake.html">fix shake</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dielectric.html b/doc/doc2/dielectric.html
new file mode 100644
index 000000000..9ba1459bc
--- /dev/null
+++ b/doc/doc2/dielectric.html
@@ -0,0 +1,44 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dielectric command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dielectric value
+</PRE>
+<UL><LI>value = dielectric constant
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dielectric 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the dielectric constant for Coulombic interactions (pairwise and
+long-range) to this value. The constant is unitless, since it is used
+to reduce the strength of the interactions. The value is used in the
+denominator of the formulas for Coulombic interactions - e.g. a value
+of 4.0 reduces the Coulombic interactions to 25% of their default
+strength. See the <A HREF = "pair_style.html">pair_style</A> command for more
+details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_style.html">pair_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>dielectric 1.0
+</PRE>
+</HTML>
diff --git a/doc/doc2/dihedral_charmm.html b/doc/doc2/dihedral_charmm.html
new file mode 100644
index 000000000..10a1588f6
--- /dev/null
+++ b/doc/doc2/dihedral_charmm.html
@@ -0,0 +1,123 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style charmm command
+</H3>
+<H3>dihedral_style charmm/kk command
+</H3>
+<H3>dihedral_style charmm/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style charmm
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style charmm
+dihedral_coeff 1 120.0 1 60 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>charmm</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
+</CENTER>
+<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
+field. This dihedral style can also be used for the AMBER force field
+(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
+for a description of the AMBER force field.
+</P>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>n (integer >= 0)
+<LI>d (integer value of degrees)
+<LI>weighting factor (0.0 to 1.0)
+</UL>
+<P>The weighting factor is applied to pairwise interaction between the
+1st and 4th atoms in the dihedral, which are computed by a CHARMM
+<A HREF = "pair_charmm.html">pair_style</A> with epsilon and sigma values specified
+with a <A HREF = "pair_charmm.html">pair_coeff</A> command. Note that this
+weighting factor is unrelated to the weighting factor specified by the
+<A HREF = "special_bonds.html">special bonds</A> command which applies to all 1-4
+interactions in the system.
+</P>
+<P>For CHARMM force fields, the special_bonds 1-4 weighting factor should
+be set to 0.0. This is because the pair styles that contain "charmm"
+(e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A>) define extra
+1-4 interaction coefficients that are used by this dihedral style to
+compute those interactions explicitly. This means that if any of the
+weighting factors defined as dihedral coefficients (4th coeff above)
+are non-zero, then you must use a charmm pair style. Note that if you
+do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
+default) then 1-4 interactions in dihedrals will be computed twice,
+once by the pair routine and once by the dihedral routine, which is
+probably not what you want.
+</P>
+<P>For AMBER force fields, the special_bonds 1-4 weighting factor should
+be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
+weighting factors (4th coeff above) should be set to 0.0. In this
+case, you can use any pair style you wish, since the dihedral does not
+need any 1-4 information.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Cornell"></A>
+
+<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+</P>
+<A NAME = "MacKerell"></A>
+
+<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_class2.html b/doc/doc2/dihedral_class2.html
new file mode 100644
index 000000000..1dc4af3f4
--- /dev/null
+++ b/doc/doc2/dihedral_class2.html
@@ -0,0 +1,185 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style class2 command
+</H3>
+<H3>dihedral_style class2/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style class2
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style class2
+dihedral_coeff 1 100 75 100 70 80 60
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
+dihedral_coeff * aat -13.5271 110.2453 105.1270
+dihedral_coeff * bb13 0.0 1.0119 1.1010
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>class2</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_class2.jpg">
+</CENTER>
+<P>where Ed is the dihedral term, Embt is a middle-bond-torsion term,
+Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
+is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
+</P>
+<P>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
+bond lengths.
+</P>
+<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
+</P>
+<P>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
+must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>These are the 6 coefficients for the Ed formula:
+</P>
+<UL><LI>K1 (energy)
+<LI>phi1 (degrees)
+<LI>K2 (energy)
+<LI>phi2 (degrees)
+<LI>K3 (energy)
+<LI>phi3 (degrees)
+</UL>
+<P>For the Embt formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+5 coefficients, the first of which is "mbt" to indicate they are
+MiddleBondTorsion coefficients. In a data file, these coefficients
+should be listed under a "MiddleBondTorsion Coeffs" heading and you
+must leave out the "mbt", i.e. only list 4 coefficients after the
+dihedral type.
+</P>
+<UL><LI>mbt
+<LI>A1 (energy/distance)
+<LI>A2 (energy/distance)
+<LI>A3 (energy/distance)
+<LI>r2 (distance)
+</UL>
+<P>For the Eebt formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+9 coefficients, the first of which is "ebt" to indicate they are
+EndBondTorsion coefficients. In a data file, these coefficients
+should be listed under a "EndBondTorsion Coeffs" heading and you must
+leave out the "ebt", i.e. only list 8 coefficients after the dihedral
+type.
+</P>
+<UL><LI>ebt
+<LI>B1 (energy/distance)
+<LI>B2 (energy/distance)
+<LI>B3 (energy/distance)
+<LI>C1 (energy/distance)
+<LI>C2 (energy/distance)
+<LI>C3 (energy/distance)
+<LI>r1 (distance)
+<LI>r3 (distance)
+</UL>
+<P>For the Eat formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+9 coefficients, the first of which is "at" to indicate they are
+AngleTorsion coefficients. In a data file, these coefficients should
+be listed under a "AngleTorsion Coeffs" heading and you must leave out
+the "at", i.e. only list 8 coefficients after the dihedral type.
+</P>
+<UL><LI>at
+<LI>D1 (energy/radian)
+<LI>D2 (energy/radian)
+<LI>D3 (energy/radian)
+<LI>E1 (energy/radian)
+<LI>E2 (energy/radian)
+<LI>E3 (energy/radian)
+<LI>theta1 (degrees)
+<LI>theta2 (degrees)
+</UL>
+<P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
+to radians internally; hence the units of D and E are in
+energy/radian.
+</P>
+<P>For the Eaat formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+4 coefficients, the first of which is "aat" to indicate they are
+AngleAngleTorsion coefficients. In a data file, these coefficients
+should be listed under a "AngleAngleTorsion Coeffs" heading and you
+must leave out the "aat", i.e. only list 3 coefficients after the
+dihedral type.
+</P>
+<UL><LI>aat
+<LI>M (energy/radian^2)
+<LI>theta1 (degrees)
+<LI>theta2 (degrees)
+</UL>
+<P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
+to radians internally; hence the units of M are in energy/radian^2.
+</P>
+<P>For the Ebb13 formula, each line in a
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
+4 coefficients, the first of which is "bb13" to indicate they are
+BondBond13 coefficients. In a data file, these coefficients should be
+listed under a "BondBond13 Coeffs" heading and you must leave out the
+"bb13", i.e. only list 3 coefficients after the dihedral type.
+</P>
+<UL><LI>bb13
+<LI>N (energy/distance^2)
+<LI>r1 (distance)
+<LI>r3 (distance)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+CLASS2 package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_coeff.html b/doc/doc2/dihedral_coeff.html
new file mode 100644
index 000000000..5461b7e70
--- /dev/null
+++ b/doc/doc2/dihedral_coeff.html
@@ -0,0 +1,113 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_coeff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_coeff N args
+</PRE>
+<UL><LI>N = dihedral type (see asterisk form below)
+<LI>args = coefficients for one or more dihedral types
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_coeff 1 80.0 1 3
+dihedral_coeff * 80.0 1 3 0.5
+dihedral_coeff 2* 80.0 1 3 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<HR>
+
+<P>Specify the dihedral force field coefficients for one or more dihedral types.
+The number and meaning of the coefficients depends on the dihedral style.
+Dihedral coefficients can also be set in the data file read by the
+<A HREF = "read_data.html">read_data</A> command or in a restart file.
+</P>
+<P>N can be specified in one of two ways. An explicit numeric value can
+be used, as in the 1st example above. Or a wild-card asterisk can be
+used to set the coefficients for multiple dihedral types. This takes the
+form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral types,
+then an asterisk with no numeric values means all types from 1 to N. A
+leading asterisk means all types from 1 to n (inclusive). A trailing
+asterisk means all types from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive).
+</P>
+<P>Note that using a dihedral_coeff command can override a previous setting
+for the same dihedral type. For example, these commands set the coeffs
+for all dihedral types, then overwrite the coeffs for just dihedral type 2:
+</P>
+<PRE>dihedral_coeff * 80.0 1 3
+dihedral_coeff 2 200.0 1 3
+</PRE>
+<P>A line in a data file that specifies dihedral coefficients uses the exact
+same format as the arguments of the dihedral_coeff command in an input
+script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file. For example,
+under the "Dihedral Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+</P>
+<PRE>1 80.0 1 3
+</PRE>
+<P>The <A HREF = "dihedral_class2.html">dihedral_style class2</A> is an exception to
+this rule, in that an additional argument is used in the input script
+to allow specification of the cross-term coefficients. See its doc
+page for details.
+</P>
+<P>IMPORTANT NOTE: When comparing the formulas and coefficients for
+various LAMMPS dihedral styles with dihedral equations defined by
+other force fields, note that some force field implementations
+divide/multiply the energy prefactor <I>K</I> by the multiple number of
+torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
+not do this, i.e. the listed dihedral equation applies to each
+individual dihedral. Thus you need to define <I>K</I> appropriately to
+account for this difference if necessary.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command.
+</P>
+<P>Note that there are also additional dihedral styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the dihedral section of
+<A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
+<LI><A HREF = "dihedral_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
+</UL>
+<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
+<LI><A HREF = "dihedral_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
+<LI><A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
+<LI><A HREF = "dihedral_helix.html">dihedral_style helix</A> - helix dihedral
+<LI><A HREF = "dihedral_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
+<LI><A HREF = "dihedral_opls.html">dihedral_style opls</A> - OPLS dihedral
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>A dihedral style must be defined before any dihedral coefficients are
+set, either in the input script or in a data file.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_style.html">dihedral_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_cosine_shift_exp.html b/doc/doc2/dihedral_cosine_shift_exp.html
new file mode 100644
index 000000000..b6712072e
--- /dev/null
+++ b/doc/doc2/dihedral_cosine_shift_exp.html
@@ -0,0 +1,92 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style cosine/shift/exp command
+</H3>
+<H3>dihedral_style cosine/shift/exp/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style cosine/shift/exp
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style cosine/shift/exp
+dihedral_coeff 1 10.0 45.0 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cosine/shift/exp</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_cosine_shift_exp.jpg">
+</CENTER>
+<P>where Umin, theta, and a are defined for each dihedral type.
+</P>
+<P>The potential is bounded between [-Umin:0] and the minimum is located
+at the angle theta0. The a parameter can be both positive or negative
+and is used to control the spring constant at the equilibrium.
+</P>
+<P>The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)].
+For a>3 k/Umin = a/2 to better than 5% relative error. For negative
+values of the a parameter, the spring constant is essentially zero,
+and anharmonic terms takes over. The potential is furthermore well
+behaved in the limit a->0, where it has been implemented to linear
+order in a for a < 0.001.
+</P>
+<P>The following coefficients must be defined for each dihedral type via
+the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>umin (energy)
+<LI>theta (angle)
+<LI>A (real number)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
+<A HREF = "angle_cosineshiftexp.html">angle_cosineshiftexp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_fourier.html b/doc/doc2/dihedral_fourier.html
new file mode 100644
index 000000000..f1b85a169
--- /dev/null
+++ b/doc/doc2/dihedral_fourier.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style fourier command
+</H3>
+<H3>dihedral_style fourier/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style fourier
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style fourier
+dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>fourier</I> dihedral style uses the potential:
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_fourier.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>m (integer >=1)
+<LI>K1 (energy)
+<LI>n1 (integer >= 0)
+<LI>d1 (degrees)
+<LI>....
+<LI>Km (energy)
+<LI>nm (integer >= 0)
+<LI>dm (degrees)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_harmonic.html b/doc/doc2/dihedral_harmonic.html
new file mode 100644
index 000000000..b4bc70655
--- /dev/null
+++ b/doc/doc2/dihedral_harmonic.html
@@ -0,0 +1,90 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style harmonic command
+</H3>
+<H3>dihedral_style harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style harmonic
+dihedral_coeff 1 80.0 1 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_harmonic.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K (energy)
+<LI>d (+1 or -1)
+<LI>n (integer >= 0)
+</UL>
+<P>IMPORTANT NOTE: Here are important points to take note of when
+defining LAMMPS dihedral coefficients for the harmonic style, so that
+they are compatible with how harmonic dihedrals are defined by other
+force fields:
+</P>
+<UL><LI>The LAMMPS convention is that the trans position = 180 degrees, while
+in some force fields trans = 0 degrees.
+
+<LI>Some force fields reverse the sign convention on <I>d</I>.
+
+<LI>Some force fields let <I>n</I> be positive or negative which corresponds to
+<I>d</I> = 1 or -1 for the harmonic style.
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_helix.html b/doc/doc2/dihedral_helix.html
new file mode 100644
index 000000000..461cbb399
--- /dev/null
+++ b/doc/doc2/dihedral_helix.html
@@ -0,0 +1,91 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style helix command
+</H3>
+<H3>dihedral_style helix/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style helix
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style helix
+dihedral_coeff 1 80.0 100.0 40.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>helix</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_helix.jpg">
+</CENTER>
+<P>This coarse-grain dihedral potential is described in <A HREF = "#Guo">(Guo)</A>.
+For dihedral angles in the helical region, the energy function is
+represented by a standard potential consisting of three minima, one
+corresponding to the trans (t) state and the other to gauche states
+(g+ and g-). The paper describes how the A,B,C parameters are chosen
+so as to balance secondary (largely driven by local interactions) and
+tertiary structure (driven by long-range interactions).
+</P>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>A (energy)
+<LI>B (energy)
+<LI>C (energy)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Guo"></A>
+
+<P><B>(Guo)</B> Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_hybrid.html b/doc/doc2/dihedral_hybrid.html
new file mode 100644
index 000000000..23960e40c
--- /dev/null
+++ b/doc/doc2/dihedral_hybrid.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style hybrid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style hybrid style1 style2 ...
+</PRE>
+<UL><LI>style1,style2 = list of one or more dihedral styles
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style hybrid harmonic helix
+dihedral_coeff 1 harmonic 6.0 1 3
+dihedral_coeff 2* helix 10 10 10
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hybrid</I> style enables the use of multiple dihedral styles in one
+simulation. An dihedral style is assigned to each dihedral type. For
+example, dihedrals in a polymer flow (of dihedral type 1) could be
+computed with a <I>harmonic</I> potential and dihedrals in the wall
+boundary (of dihedral type 2) could be computed with a <I>helix</I>
+potential. The assignment of dihedral type to style is made via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command or in the data file.
+</P>
+<P>In the dihedral_coeff commands, the name of a dihedral style must be
+added after the dihedral type, with the remaining coefficients being
+those appropriate to that style. In the example above, the 2
+dihedral_coeff commands set dihedrals of dihedral type 1 to be
+computed with a <I>harmonic</I> potential with coefficients 6.0, 1, 3 for
+K, d, n. All other dihedral types (2-N) are computed with a <I>helix</I>
+potential with coefficients 10, 10, 10 for A, B, C.
+</P>
+<P>If dihedral coefficients are specified in the data file read via the
+<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
+E.g. "harmonic" or "helix", must be added after the dihedral type, for
+each line in the "Dihedral Coeffs" section, e.g.
+</P>
+<PRE>Dihedral Coeffs
+</PRE>
+<PRE>1 harmonic 6.0 1 3
+2 helix 10 10 10
+...
+</PRE>
+<P>If <I>class2</I> is one of the dihedral hybrid styles, the same rule holds
+for specifying additional AngleTorsion (and EndBondTorsion, etc)
+coefficients either via the input script or in the data file.
+I.e. <I>class2</I> must be added to each line after the dihedral type. For
+lines in the AngleTorsion (or EndBondTorsion, etc) section of the data
+file for dihedral types that are not <I>class2</I>, you must use an
+dihedral style of <I>skip</I> as a placeholder, e.g.
+</P>
+<PRE>AngleTorsion Coeffs
+</PRE>
+<PRE>1 skip
+2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
+...
+</PRE>
+<P>Note that it is not necessary to use the dihedral style <I>skip</I> in the
+input script, since AngleTorsion (or EndBondTorsion, etc) coefficients
+need not be specified at all for dihedral types that are not <I>class2</I>.
+</P>
+<P>A dihedral style of <I>none</I> with no additional coefficients can be used
+in place of a dihedral style, either in a input script dihedral_coeff
+command or in the data file, if you desire to turn off interactions
+for specific dihedral types.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>Unlike other dihedral styles, the hybrid dihedral style does not store
+dihedral coefficient info for individual sub-styles in a <A HREF = "restart.html">binary
+restart files</A>. Thus when retarting a simulation from a
+restart file, you need to re-specify dihedral_coeff commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_multi_harmonic.html b/doc/doc2/dihedral_multi_harmonic.html
new file mode 100644
index 000000000..5557b772b
--- /dev/null
+++ b/doc/doc2/dihedral_multi_harmonic.html
@@ -0,0 +1,79 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style multi/harmonic command
+</H3>
+<H3>dihedral_style multi/harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style multi/harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style multi/harmonic
+dihedral_coeff 1 20 20 20 20 20
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>multi/harmonic</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_multi_harmonic.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>A1 (energy)
+<LI>A2 (energy)
+<LI>A3 (energy)
+<LI>A4 (energy)
+<LI>A5 (energy)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_nharmonic.html b/doc/doc2/dihedral_nharmonic.html
new file mode 100644
index 000000000..256ea0651
--- /dev/null
+++ b/doc/doc2/dihedral_nharmonic.html
@@ -0,0 +1,79 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style nharmonic command
+</H3>
+<H3>dihedral_style nharmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style nharmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style nharmonic
+dihedral_coeff 3 10.0 20.0 30.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>nharmonic</I> dihedral style uses the potential:
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_nharmonic.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>n (integer >=1)
+<LI>A1 (energy)
+<LI>A2 (energy)
+<LI>...
+<LI>An (energy)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_none.html b/doc/doc2/dihedral_none.html
new file mode 100644
index 000000000..439ab7703
--- /dev/null
+++ b/doc/doc2/dihedral_none.html
@@ -0,0 +1,34 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style none command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style none
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Using an dihedral style of none means dihedral forces are not
+computed, even if quadruplets of dihedral atoms were listed in the
+data file read by the <A HREF = "read_data.html">read_data</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_opls.html b/doc/doc2/dihedral_opls.html
new file mode 100644
index 000000000..133841c79
--- /dev/null
+++ b/doc/doc2/dihedral_opls.html
@@ -0,0 +1,93 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style opls command
+</H3>
+<H3>dihedral_style opls/kk command
+</H3>
+<H3>dihedral_style opls/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style opls
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style opls
+dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
+dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
+dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>opls</I> dihedral style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_opls.jpg">
+</CENTER>
+<P>Note that the usual 1/2 factor is not included in the K values.
+</P>
+<P>This dihedral potential is used in the OPLS force field and is
+described in <A HREF = "#Watkins">(Watkins)</A>.
+</P>
+<P>The following coefficients must be defined for each dihedral type via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI>K1 (energy)
+<LI>K2 (energy)
+<LI>K3 (energy)
+<LI>K4 (energy)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Watkins"></A>
+
+<P><B>(Watkins)</B> Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_quadratic.html b/doc/doc2/dihedral_quadratic.html
new file mode 100644
index 000000000..2d6ffa43f
--- /dev/null
+++ b/doc/doc2/dihedral_quadratic.html
@@ -0,0 +1,80 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style quadratic command
+</H3>
+<H3>dihedral_style quadratic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style quadratic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style quadratic
+dihedral_coeff 100.0 80.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>quadratic</I> dihedral style uses the potential:
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_quadratic.jpg">
+</CENTER>
+<P>This dihedral potential can be used to keep a dihedral in a predefined
+value (cis=zero, right-hand convention is used).
+</P>
+<P>The following coefficients must be defined for each dihedral type via
+the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>phi0 (degrees)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_style.html b/doc/doc2/dihedral_style.html
new file mode 100644
index 000000000..0eb962ead
--- /dev/null
+++ b/doc/doc2/dihedral_style.html
@@ -0,0 +1,121 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style style
+</PRE>
+<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>harmonic</I> or <I>helix</I> or <I>multi/harmonic</I> or <I>opls</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style harmonic
+dihedral_style multi/harmonic
+dihedral_style hybrid harmonic charmm
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the formula(s) LAMMPS uses to compute dihedral interactions
+between quadruplets of atoms, which remain in force for the duration
+of the simulation. The list of dihedral quadruplets is read in by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
+from a data or restart file.
+</P>
+<P>Hybrid models where dihedrals are computed using different dihedral
+potentials can be setup using the <I>hybrid</I> dihedral style.
+</P>
+<P>The coefficients associated with a dihedral style can be specified in
+a data or restart file or via the <A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+command.
+</P>
+<P>All dihedral potentials store their coefficient data in binary restart
+files which means dihedral_style and
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands do not need to be
+re-specified in an input script that restarts a simulation. See the
+<A HREF = "read_restart.html">read_restart</A> command for details on how to do
+this. The one exception is that dihedral_style <I>hybrid</I> only stores
+the list of sub-styles in the restart file; dihedral coefficients need
+to be re-specified.
+</P>
+<P>IMPORTANT NOTE: When both a dihedral and pair style is defined, the
+<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 4 bonded atoms.
+</P>
+<P>In the formulas listed for each dihedral style, <I>phi</I> is the torsional
+angle defined by the quadruplet of atoms. This angle has a sign
+convention as shown in this diagram:
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_sign.jpg">
+</CENTER>
+<P>where the I,J,K,L ordering of the 4 atoms that define the dihedral
+is from left to right.
+</P>
+<P>This sign convention effects several of the dihedral styles listed
+below (e.g. charmm, helix) in the sense that the energy formula
+depends on the sign of phi, which may be reflected in the value of the
+coefficients you specify.
+</P>
+<P>IMPORTANT NOTE: When comparing the formulas and coefficients for
+various LAMMPS dihedral styles with dihedral equations defined by
+other force fields, note that some force field implementations
+divide/multiply the energy prefactor <I>K</I> by the multiple number of
+torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
+not do this, i.e. the listed dihedral equation applies to each
+individual dihedral. Thus you need to define <I>K</I> appropriately via
+the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command to account for this
+difference if necessary.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command.
+</P>
+<P>Note that there are also additional dihedral styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the dihedral section of
+<A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
+<LI><A HREF = "dihedral_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
+</UL>
+<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
+<LI><A HREF = "dihedral_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
+<LI><A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
+<LI><A HREF = "dihedral_helix.html">dihedral_style helix</A> - helix dihedral
+<LI><A HREF = "dihedral_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
+<LI><A HREF = "dihedral_opls.html">dihedral_style opls</A> - OPLS dihedral
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Dihedral styles can only be set for atom styles that allow dihedrals
+to be defined.
+</P>
+<P>Most dihedral styles are part of the MOLECULE package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual dihedral potentials tell if it is part of
+a package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>dihedral_style none
+</P>
+</HTML>
diff --git a/doc/doc2/dihedral_table.html b/doc/doc2/dihedral_table.html
new file mode 100644
index 000000000..754bac683
--- /dev/null
+++ b/doc/doc2/dihedral_table.html
@@ -0,0 +1,211 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dihedral_style table command
+</H3>
+<H3>dihedral_style table/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dihedral_style table style Ntable
+</PRE>
+<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
+<LI>Ntable = size of the internal lookup table
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dihedral_style table spline 400
+dihedral_style table linear 1000
+dihedral_coeff 1 file.table DIH_TABLE1
+dihedral_coeff 2 file.table DIH_TABLE2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>table</I> dihedral style creates interpolation tables of length
+<I>Ntable</I> from dihedral potential and derivative values listed in a
+file(s) as a function of the dihedral angle "phi". The files are read
+by the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command.
+</P>
+<P>The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+<I>Ntable</I> dihedral angles. During a simulation, these tables are used
+to interpolate energy and force values on individual atoms as
+needed. The interpolation is done in one of 2 styles: <I>linear</I> or
+<I>spline</I>.
+</P>
+<P>For the <I>linear</I> style, the dihedral angle (phi) is used to find 2
+surrounding table values from which an energy or its derivative is
+computed by linear interpolation.
+</P>
+<P>For the <I>spline</I> style, cubic spline coefficients are computed and
+stored at each of the <I>Ntable</I> evenly-spaced values in the
+interpolated table. For a given dihedral angle (phi), the appropriate
+coefficients are chosen from this list, and a cubic polynomial is used
+to compute the energy and the derivative at this angle.
+</P>
+<P>The following coefficients must be defined for each dihedral type via
+the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example
+above.
+</P>
+<UL><LI>filename
+<LI>keyword
+</UL>
+<P>The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file. The
+format of this file is described below.
+</P>
+<HR>
+
+<P>The format of a tabulated file is as follows (without the
+parenthesized comments). It can begin with one or more comment
+or blank lines.
+</P>
+<PRE># Table of the potential and its negative derivative
+</PRE>
+<PRE>DIH_TABLE1 (keyword is the first text on line)
+N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
+ (blank line)
+1 -168.0 -1.40351172223 -0.0423346818422
+2 -156.0 -1.70447981034 -0.00811786522531
+3 -144.0 -1.62956100432 0.0184129719987
+...
+30 180.0 -0.707106781187 -0.0719306095245
+</PRE>
+<PRE># Example 2: table of the potential. Forces omitted
+</PRE>
+<PRE>DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat
+</PRE>
+<PRE>1 -168.0 -1.40351172223
+2 -156.0 -1.70447981034
+3 -144.0 -1.62956100432
+...
+30 180.0 -0.707106781187
+</PRE>
+<P>A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command. The next line lists (in
+any order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+</P>
+<P>Following a blank line, the next N lines list the tabulated values. On
+each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value, the 3rd value is the energy (in energy units), and
+the 4th is -dE/d(phi) also in energy units). The 3rd term is the
+energy of the 4-atom configuration for the specified angle. The 4th
+term (when present) is the negative derivative of the energy with
+respect to the angle (in degrees, or radians depending on whether the
+user selected DEGREES or RADIANS). Thus the units of the last term
+are still energy, not force. The dihedral angle values must increase
+from one line to the next.
+</P>
+<P>Dihedral table splines are cyclic. There is no discontinuity at 180
+degrees (or at any other angle). Although in the examples above, the
+angles range from -180 to 180 degrees, in general, the first angle in
+the list can have any value (positive, zero, or negative). However
+the <I>range</I> of angles represented in the table must be <I>strictly</I> less
+than 360 degrees (2pi radians) to avoid angle overlap. (You may not
+supply entries in the table for both 180 and -180, for example.) If
+the user's table covers only a narrow range of dihedral angles,
+strange numerical behavior can occur in the large remaining gap.
+</P>
+<P><B>Parameters:</B>
+</P>
+<P>The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the N
+specified in the <A HREF = "dihedral_style.html">dihedral_style table</A> command.
+Let <I>Ntable</I> is the number of table entries requested dihedral_style
+command, and let <I>Nfile</I> be the parameter following "N" in the
+tabulated file ("30" in the sparse example above). What LAMMPS does
+is a preliminary interpolation by creating splines using the <I>Nfile</I>
+tabulated values as nodal points. It uses these to interpolate as
+needed to generate energy and derivative values at <I>Ntable</I> different
+points (which are evenly spaced over a 360 degree range, even if the
+angles in the file are not). The resulting tables of length <I>Ntable</I>
+are then used as described above, when computing energy and force for
+individual dihedral angles and their atoms. This means that if you
+want the interpolation tables of length <I>Ntable</I> to match exactly what
+is in the tabulated file (with effectively nopreliminary
+interpolation), you should set <I>Ntable</I> = <I>Nfile</I>. To insure the
+nodal points in the user's file are aligned with the interpolated
+table entries, the angles in the table should be integer multiples of
+360/<I>Ntable</I> degrees, or 2*PI/<I>Ntable</I> radians (depending on your
+choice of angle units).
+</P>
+<P>The optional "NOF" keyword allows the user to omit the forces
+(negative energy derivatives) from the table file (normally located in
+the 4th column). In their place, forces will be calculated
+automatically by differentiating the potential energy function
+indicated by the 3rd column of the table (using either linear or
+spline interpolation).
+</P>
+<P>The optional "DEGREES" keyword allows the user to specify angles in
+degrees instead of radians (default).
+</P>
+<P>The optional "RADIANS" keyword allows the user to specify angles in
+radians instead of degrees. (Note: This changes the way the forces
+are scaled in the 4th column of the data file.)
+</P>
+<P>The optional "CHECKU" keyword is followed by a filename. This allows
+the user to save all of the the <I>Ntable</I> different entries in the
+interpolated energy table to a file to make sure that the interpolated
+function agrees with the user's expectations. (Note: You can
+temporarily increase the <I>Ntable</I> parameter to a high value for this
+purpose. "<I>Ntable</I>" is explained above.)
+</P>
+<P>The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
+It is followed by a filename, and it allows the user to check the
+interpolated force table. This option is available even if the user
+selected the "NOF" option.
+</P>
+<P>Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds one
+that matches the specified keyword.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/dimension.html b/doc/doc2/dimension.html
new file mode 100644
index 000000000..65099ab25
--- /dev/null
+++ b/doc/doc2/dimension.html
@@ -0,0 +1,53 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dimension command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dimension N
+</PRE>
+<UL><LI>N = 2 or 3
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dimension 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the dimensionality of the simulation. By default LAMMPS runs 3d
+simulations. To run a 2d simulation, this command should be used
+prior to setting up a simulation box via the
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> commands.
+Restart files also store this setting.
+</P>
+<P>See the discussion in <A HREF = "Section_howto.html">Section_howto</A> for
+additional instructions on how to run 2d simulations.
+</P>
+<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
+spheres or ellipsoids, as opposed to point particles. In 2d, the
+particles will still be spheres or ellipsoids, not circular disks or
+ellipses, meaning their moment of inertia will be the same as in 3d.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command must be used before the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_enforce2d.html">fix enforce2d</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>dimension 3
+</PRE>
+</HTML>
diff --git a/doc/doc2/displace_atoms.html b/doc/doc2/displace_atoms.html
new file mode 100644
index 000000000..4906a78c5
--- /dev/null
+++ b/doc/doc2/displace_atoms.html
@@ -0,0 +1,125 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>displace_atoms command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>displace_atoms group-ID style args keyword value ...
+</PRE>
+<UL><LI>group-ID = ID of group of atoms to displace
+
+<LI>style = <I>move</I> or <I>ramp</I> or <I>random</I> or <I>rotate</I>
+
+<PRE> <I>move</I> args = delx dely delz
+ delx,dely,delz = distance to displace in each dimension (distance units)
+ <I>ramp</I> args = ddim dlo dhi dim clo chi
+ ddim = <I>x</I> or <I>y</I> or <I>z</I>
+ dlo,dhi = displacement distance between dlo and dhi (distance units)
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ clo,chi = lower and upper bound of domain to displace (distance units)
+ <I>random</I> args = dx dy dz seed
+ dx,dy,dz = random displacement magnitude in each dimension (distance units)
+ seed = random # seed (positive integer)
+ <I>rotate</I> args = Px Py Pz Rx Ry Rz theta
+ Px,Py,Pz = origin point of axis of rotation (distance units)
+ Rx,Ry,Rz = axis of rotation vector
+ theta = angle of rotation (degrees)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE> keyword = <I>units</I>
+ value = <I>box</I> or <I>lattice</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>displace_atoms top move 0 -5 0 units box
+displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Displace a group of atoms. This can be used to move atoms a large
+distance before beginning a simulation or to randomize atoms initially
+on a lattice. For example, in a shear simulation, an initial strain
+can be imposed on the system. Or two groups of atoms can be brought
+into closer proximity.
+</P>
+<P>The <I>move</I> style displaces the group of atoms by the specified 3d
+distance.
+</P>
+<P>The <I>ramp</I> style displaces atoms a variable amount in one dimension
+depending on the atom's coordinate in a (possibly) different
+dimension. For example, the second example command displaces atoms in
+the x-direction an amount between 0.0 and 5.0 distance units. Each
+atom's displacement depends on the fractional distance its y
+coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
+those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
+</P>
+<P>The <I>random</I> style independently moves each atom in the group by a
+random displacement, uniformly sampled from a value between -dx and
++dx in the x dimension, and similarly for y and z. Random numbers are
+used in such a way that the displacement of a particular atom is the
+same, regardless of how many processors are being used.
+</P>
+<P>The <I>rotate</I> style rotates each atom in the group by the angle <I>theta</I>
+around a rotation axis <I>R</I> = (Rx,Ry,Rz) that goes thru a point <I>P</I> =
+(Px,Py,Pz). The direction of rotation for the atoms around the
+rotation axis is consistent with the right-hand rule: if your
+right-hand's thumb points along <I>R</I>, then your fingers wrap around the
+axis in the direction of positive theta.
+</P>
+<P>Distance units for displacements and the origin point of the <I>rotate</I>
+style are determined by the setting of <I>box</I> or <I>lattice</I> for the
+<I>units</I> keyword. <I>Box</I> means distance units as defined by the
+<A HREF = "units.html">units</A> command - e.g. Angstroms for <I>real</I> units.
+<I>Lattice</I> means distance units are in lattice spacings. The
+<A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacing.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: Care should be taken not to move atoms on top of other
+atoms. After the move, atoms are remapped into the periodic
+simulation box if needed, and any shrink-wrap boundary conditions (see
+the <A HREF = "boundary.html">boundary</A> command) are enforced which may change
+the box size. Other than this effect, this command does not change
+the size or shape of the simulation box. See the
+<A HREF = "change_box.html">change_box</A> command if that effect is desired.
+</P>
+<P>IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
+command. If the simulation box is non-periodic and shrink-wrapped
+(see the <A HREF = "boundary.html">boundary</A> command), this can change its size
+or shape. This is not a problem, except that the mapping of
+processors to the simulation box is not changed by this command from
+its initial 3d configuration; see the <A HREF = "processors.html">processors</A>
+command. Thus, if the box size/shape changes dramatically, the
+mapping of processors to the simulation box may not end up as optimal
+as the initial mapping attempted to be.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>You cannot rotate around any rotation vector except the z-axis for a
+2d simulation.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "lattice.html">lattice</A>, <A HREF = "change_box.html">change_box</A>,
+<A HREF = "fix_move.html">fix_move</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/dump.html b/doc/doc2/dump.html
new file mode 100644
index 000000000..05256568a
--- /dev/null
+++ b/doc/doc2/dump.html
@@ -0,0 +1,622 @@
+<HTML>
+<CENTER> <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dump command
+</H3>
+<H3><A HREF = "dump_image.html">dump image</A> command
+</H3>
+<H3><A HREF = "dump_image.html">dump movie</A> command
+</H3>
+<H3><A HREF = "dump_molfile.html">dump molfile</A> command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dump ID group-ID style N file args
+</PRE>
+<UL><LI>ID = user-assigned name for the dump
+
+<LI>group-ID = ID of the group of atoms to be dumped
+
+<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>cfg/mpiio</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
+
+<LI>N = dump every this many timesteps
+
+<LI>file = name of file to write dump info to
+
+<LI>args = list of arguments for a particular style
+
+<PRE> <I>atom</I> args = none
+ <I>atom/mpiio</I> args = none
+ <I>cfg</I> args = same as <I>custom</I> args, see below
+ <I>cfg/mpiio</I> args = same as <I>custom</I> args, see below
+ <I>dcd</I> args = none
+ <I>xtc</I> args = none
+ <I>xyz</I> args = none
+</PRE>
+<PRE> <I>xyz/mpiio</I> args = none
+</PRE>
+<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
+</PRE>
+<PRE> <I>movie</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
+</PRE>
+<PRE> <I>molfile</I> args = discussed on <A HREF = "dump_molfile.html">dump molfile</A> doc page
+</PRE>
+<PRE> <I>local</I> args = list of local attributes
+ possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
+ index = enumeration of local values
+ c_ID = local vector calculated by a compute with ID
+ c_ID[N] = Nth column of local array calculated by a compute with ID
+ f_ID = local vector calculated by a fix with ID
+ f_ID[N] = Nth column of local array calculated by a fix with ID
+</PRE>
+<PRE> <I>custom</I> or <I>custom/mpiio</I> args = list of atom attributes
+ possible attributes = id, mol, proc, procp1, type, element, mass,
+ x, y, z, xs, ys, zs, xu, yu, zu,
+ xsu, ysu, zsu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
+ q, mux, muy, muz, mu,
+ radius, diameter, omegax, omegay, omegaz,
+ angmomx, angmomy, angmomz, tqx, tqy, tqz,
+ c_ID, c_ID[N], f_ID, f_ID[N], v_name
+</PRE>
+<PRE> id = atom ID
+ mol = molecule ID
+ proc = ID of processor that owns atom
+ procp1 = ID+1 of processor that owns atom
+ type = atom type
+ element = name of atom element, as defined by <A HREF = "dump_modify.html">dump_modify</A> command
+ mass = atom mass
+ x,y,z = unscaled atom coordinates
+ xs,ys,zs = scaled atom coordinates
+ xu,yu,zu = unwrapped atom coordinates
+ xsu,ysu,zsu = scaled unwrapped atom coordinates
+ ix,iy,iz = box image that the atom is in
+ vx,vy,vz = atom velocities
+ fx,fy,fz = forces on atoms
+ q = atom charge
+ mux,muy,muz = orientation of dipole moment of atom
+ mu = magnitude of dipole moment of atom
+ radius,diameter = radius,diameter of spherical particle
+ omegax,omegay,omegaz = angular velocity of spherical particle
+ angmomx,angmomy,angmomz = angular momentum of aspherical particle
+ tqx,tqy,tqz = torque on finite-size particles
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[N] = Nth column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[N] = Nth column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+ d_name = per-atom floating point vector with name, managed by fix property/atom
+ i_name = per-atom integer vector with name, managed by fix property/atom
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dump myDump all atom 100 dump.atom
+dump myDump all atom/mpiio 100 dump.atom.mpiio
+dump 2 subgroup atom 50 dump.run.bin
+dump 2 subgroup atom 50 dump.run.mpiio.bin
+dump 4a all custom 100 dump.myforce.* id type x y vx fx
+dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
+dump 1 all xtc 1000 file.xtc
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Dump a snapshot of atom quantities to one or more files every N
+timesteps in one of several styles. The <I>image</I> and <I>movie</I> styles are
+the exception: the <I>image</I> style renders a JPG, PNG, or PPM image file
+of the atom configuration every N timesteps while the <I>movie</I> style
+combines and compresses them into a movie file; both are discussed in
+detail on the <A HREF = "dump_image.html">dump image</A> doc page. The timesteps on
+which dump output is written can also be controlled by a variable.
+See the <A HREF = "dump_modify.html">dump_modify every</A> command.
+</P>
+<P>Only information for atoms in the specified group is dumped. The
+<A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also
+alter what atoms are included. Not all styles support all these
+options; see details below.
+</P>
+<P>As described below, the filename determines the kind of output (text
+or binary or gzipped, one big file or one per timestep, one big file
+or multiple smaller files).
+</P>
+<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+</P>
+<P>IMPORTANT NOTE: Unless the <A HREF = "dump_modify.html">dump_modify sort</A> option
+is invoked, the lines of atom information written to dump files
+(typically one line per atom) will be in an indeterminate order for
+each snapshot. This is even true when running on a single processor,
+if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it is
+by default. In this case atoms are re-ordered periodically during a
+simulation, due to spatial sorting. It is also true when running in
+parallel, because data for a single snapshot is collected from
+multiple processors, each of which owns a subset of the atoms.
+</P>
+<P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
+default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles, sorting by
+atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
+page for details.
+</P>
+<P>As explained below, the <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and
+<I>xyz/mpiio</I> styles are identical in command syntax and in the format
+of the dump files they create, to the corresponding styles without
+"mpiio", except the single dump file they produce is written in
+parallel via the MPI-IO library. For the remainder of this doc page,
+you should thus consider the <I>atom</I> and <I>atom/mpiio</I> styles (etc) to
+be inter-changeable. The one exception is how the filename is
+specified for the MPI-IO styles, as explained below.
+</P>
+<HR>
+
+<P>The <I>style</I> keyword determines what atom quantities are written to the
+file and in what format. Settings made via the
+<A HREF = "dump_modify.html">dump_modify</A> command can also alter the format of
+individual values and the file itself.
+</P>
+<P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
+format that is self-explanatory when viewing a dump file. Many of the
+LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with this
+format, as does the <A HREF = "rerun.html">rerun</A> command.
+</P>
+<P>For post-processing purposes the <I>atom</I>, <I>local</I>, and <I>custom</I> text
+files are self-describing in the following sense.
+</P>
+<P>The dimensions of the simulation box are included in each snapshot.
+For an orthogonal simulation box this information is is formatted as:
+</P>
+<PRE>ITEM: BOX BOUNDS xx yy zz
+xlo xhi
+ylo yhi
+zlo zhi
+</PRE>
+<P>where xlo,xhi are the maximum extents of the simulation box in the
+x-dimension, and similarly for y and z. The "xx yy zz" represent 6
+characters that encode the style of boundary for each of the 6
+simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
+the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
+or m = shrink wrapped with a minimum value. See the
+<A HREF = "boundary.html">boundary</A> command for details.
+</P>
+<P>For triclinic simulation boxes (non-orthogonal), an orthogonal
+bounding box which encloses the triclinic simulation box is output,
+along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
+formatted as follows:
+</P>
+<PRE>ITEM: BOX BOUNDS xy xz yz xx yy zz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+</PRE>
+<P>The presence of the text "xy xz yz" in the ITEM line indicates that
+the 3 tilt factors will be included on each of the 3 following lines.
+This bounding box is convenient for many visualization programs. The
+meaning of the 6 character flags for "xx yy zz" is the same as above.
+</P>
+<P>Note that the first two numbers on each line are now xlo_bound instead
+of xlo, etc, since they repesent a bounding box. See <A HREF = "Section_howto.html#howto_12">this
+section</A> of the doc pages for a geometric
+description of triclinic boxes, as defined by LAMMPS, simple formulas
+for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
+calculated from the triclinic parameters, and how to transform those
+parameters to and from other commonly used triclinic representations.
+</P>
+<P>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
+the per-atom lines that follow. For example, the descriptors would be
+"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
+attributes you specify in the dump command for the <I>custom</I> style.
+</P>
+<P>For style <I>atom</I>, atom coordinates are written to the file, along with
+the atom ID and atom type. By default, atom coords are written in a
+scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
+is at a location 1/4 of the distance from xlo to xhi of the box
+boundaries. The format can be changed to unscaled coords via the
+<A HREF = "dump_modify.html">dump_modify</A> settings. Image flags can also be
+added for each atom via dump_modify.
+</P>
+<P>Style <I>custom</I> allows you to specify a list of atom attributes to be
+written to the dump file for each atom. Possible attributes are
+listed above and will appear in the order specified. You cannot
+specify a quantity that is not defined for a particular simulation -
+such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
+assign charges. Dumps occur at the very end of a timestep, so atom
+attributes will include effects due to fixes that are applied during
+the timestep. An explanation of the possible dump custom attributes
+is given below.
+</P>
+<P>For style <I>local</I>, local output generated by <A HREF = "compute.html">computes</A>
+and <A HREF = "fix.html">fixes</A> is used to generate lines of output that is
+written to the dump file. This local data is typically calculated by
+each processor based on the atoms it owns, but there may be zero or
+more entities per atom, e.g. a list of bond distances. An explanation
+of the possible dump local attributes is given below. Note that by
+using input from the <A HREF = "compute_property_local.html">compute
+property/local</A> command with dump local,
+it is possible to generate information on bonds, angles, etc that can
+be cut and pasted directly into a data file read by the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
+extended CFG format files, as used by the
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization
+package. Since the extended CFG format uses a single snapshot of the
+system per file, a wildcard "*" must be included in the filename, as
+discussed below. The list of atom attributes for style <I>cfg</I> must
+begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
+since these quantities are needed to write the CFG files in the
+appropriate format (though the "mass" and "type" fields do not appear
+explicitly in the file). Any remaining attributes will be stored as
+"auxiliary properties" in the CFG files. Note that you will typically
+want to use the <A HREF = "dump_modify.html">dump_modify element</A> command with
+CFG-formatted files, to associate element names with atom types, so
+that AtomEye can render atoms appropriately. When unwrapped
+coordinates <I>xsu</I>, <I>ysu</I>, and <I>zsu</I> are requested, the nominal AtomEye
+periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
+10.0, which ensures atoms that are displayed correctly for up to
+UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond
+this, AtomEye will rewrap the unwrapped coordinates. The expansion
+causes the atoms to be drawn farther away from the viewer, but it is
+easy to zoom the atoms closer, and the interatomic distances are
+unaffected.
+</P>
+<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
+used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
+files are binary and thus may not be portable to different machines.
+The number of atoms per snapshot cannot change with the <I>dcd</I> style.
+The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command
+allows DCD coordinates to be written "unwrapped" by the image flags
+for each atom. Unwrapped means that if the atom has passed through
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box. Note that these coordinates may thus be far outside
+the box size stored with the snapshot.
+</P>
+<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
+by the GROMACS molecular dynamics package, and described
+<A HREF = "http://manual.gromacs.org/current/online/xtc.html">here</A>.
+The precision used in XTC files can be adjusted via the
+<A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
+means that coordinates are stored to 1/1000 nanometer accuracy. XTC
+files are portable binary files written in the NFS XDR data format,
+so that any machine which supports XDR should be able to read them.
+The number of atoms per snapshot cannot change with the <I>xtc</I> style.
+The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
+XTC coordinates to be written "unwrapped" by the image flags for each
+atom. Unwrapped means that if the atom has passed thru a periodic
+boundary one or more times, the value is printed for what the
+coordinate would be if it had not been wrapped back into the periodic
+box. Note that these coordinates may thus be far outside the box size
+stored with the snapshot.
+</P>
+<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
+coordinate format that many codes can read. Specifically it has
+a line with the number of atoms, then a comment line that is
+usually ignored followed by one line per atom with the atom type
+and the x-, y-, and z-coordinate of that atom. You can use the
+<A HREF = "dump_modify.html">dump_modify element</A> option to change the output
+from using the (numerical) atom type to an element name (or some
+other label). This will help many visualization programs to guess
+bonds and colors.
+</P>
+<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files
+can be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>, a
+popular molecular viewing program. See <A HREF = "Section_tools.html#vmd">Section
+tools</A> of the manual and the
+tools/lmp2vmd/README.txt file for more information about support in
+VMD for reading and visualizing LAMMPS dump files.
+</P>
+<HR>
+
+<P>Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges. Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N. This behavior can be
+changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep. N can be changed between runs by
+using the <A HREF = "dump_modify.html">dump_modify every</A> command (not allowed
+for <I>dcd</I> style). The <A HREF = "dump_modify.html">dump_modify every</A> command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written. In this mode a dump on the
+first timestep of a run will also not be written unless the
+<A HREF = "dump_modify.html">dump_modify first</A> command is used.
+</P>
+<P>The specified filename determines how the dump file(s) is written.
+The default is to write one large text file, which is opened when the
+dump command is invoked and closed when an <A HREF = "undump.html">undump</A>
+command is used or when LAMMPS exits. For the <I>dcd</I> and <I>xtc</I> styles,
+this is a single large binary file.
+</P>
+<P>Dump filenames can contain two wildcard characters. If a "*"
+character appears in the filename, then one file per snapshot is
+written and the "*" character is replaced with the timestep value.
+For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
+tmp.dump.20000, etc. This option is not available for the <I>dcd</I> and
+<I>xtc</I> styles. Note that the <A HREF = "dump_modify.html">dump_modify pad</A>
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+</P>
+<P>If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1. For example, tmp.dump.% becomes
+tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
+files and can be a fast mode of output on parallel machines that
+support parallel I/O for output. This option is not available for the
+<I>dcd</I>, <I>xtc</I>, and <I>xyz</I> styles.
+</P>
+<P>By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the <I>nfile</I> or
+<I>fileper</I> keywords of the <A HREF = "dump_modify.html">dump_modify</A> command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+</P>
+<P>Note that using the "*" and "%" characters together can produce a
+large number of small dump files!
+</P>
+<P>For the <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I>
+styles, a single dump file is written in parallel via the MPI-IO
+library, which is part of the MPI standard for versions 2.0 and above.
+Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
+package installed, e.g.
+</P>
+<PRE>make yes-mpiio # installs the MPIIO package
+make g++ # build LAMMPS for your platform
+</PRE>
+<P>Second, use a dump filename which contains ".mpiio". Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO restart files, which must be both written and read using
+MPI-IO, the dump files produced by these MPI-IO styles are identical
+in format to the files produced by their non-MPI-IO style
+counterparts. This means you can write a dump file using MPI-IO and
+use the <A HREF = "read_dump.html">read_dump</A> command or perform other
+post-processing, just as if the dump file was not written using
+MPI-IO.
+</P>
+<P>Note that MPI-IO dump files are one large file which all processors
+write to. You thus cannot use the "%" wildcard character described
+above in the filename since that specifies generation of multiple
+files. You can use the ".bin" suffix described below in an MPI-IO
+dump file; again this file will be written in parallel and have the
+same binary format as if it were written without MPI-IO.
+</P>
+<P>If the filename ends with ".bin", the dump file (or files, if "*" or
+"%" is also used) is written in binary format. A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster. Of course, when post-processing, you will need
+to convert it back to text format (see the <A HREF = "Section_tools.html#binary">binary2txt
+tool</A>) or write your own code to read the
+binary file. The format of the binary file can be understood by
+looking at the tools/binary2txt.cpp file. This option is only
+available for the <I>atom</I> and <I>custom</I> styles.
+</P>
+<P>If the filename ends with ".gz", the dump file (or files, if "*" or "%"
+is also used) is written in gzipped format. A gzipped dump file will
+be about 3x smaller than the text version, but will also take longer
+to write. This option is not available for the <I>dcd</I> and <I>xtc</I>
+styles.
+</P>
+<HR>
+
+<P>This section explains the local attributes that can be specified as
+part of the <I>local</I> style.
+</P>
+<P>The <I>index</I> attribute can be used to generate an index number from 1
+to N for each line written into the dump file, where N is the total
+number of local datums from all processors, or lines of output that
+will appear in the snapshot. Note that because data from different
+processors depend on what atoms they currently own, and atoms migrate
+between processor, there is no guarantee that the same index will be
+used for the same info (e.g. a particular bond) in successive
+snapshots.
+</P>
+<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow local vectors or arrays
+calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script. See the
+<A HREF = "compute.html">compute</A> command for details. There are computes for
+calculating local information such as indices, types, and energies for
+bonds and angles.
+</P>
+<P>Note that computes which calculate global or per-atom quantities, as
+opposed to local quantities, cannot be output in a dump local command.
+Instead, global quantities can be output by the <A HREF = "thermo_style.html">thermo_style
+custom</A> command, and per-atom quantities can be
+output by the dump custom command.
+</P>
+<P>If <I>c_ID</I> is used as a attribute, then the local vector calculated by
+the compute is printed. If <I>c_ID[N]</I> is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length local
+array calculated by the compute.
+</P>
+<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow local vectors or arrays
+calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the attribute
+should be replaced by the actual ID of the fix that has been defined
+previously in the input script.
+</P>
+<P>If <I>f_ID</I> is used as a attribute, then the local vector calculated by
+the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length local
+array calculated by the fix.
+</P>
+<P>Here is an example of how to dump bond info for a system,
+including the distance and energy of each bond:
+</P>
+<PRE>compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+</PRE>
+<HR>
+
+<P>This section explains the atom attributes that can be specified as
+part of the <I>custom</I> and <I>cfg</I> styles.
+</P>
+<P>The <I>id</I>, <I>mol</I>, <I>proc</I>, <I>procp1</I>, <I>type</I>, <I>element</I>, <I>mass</I>, <I>vx</I>,
+<I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, <I>q</I> attributes are self-explanatory.
+</P>
+<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
+file for molecular systems. <I>Proc</I> is the ID of the processor (0 to
+Nprocs-1) that currently owns the atom. <I>Procp1</I> is the proc ID+1,
+which can be convenient in place of a <I>type</I> attribute (1 to Ntypes)
+for coloring atoms in a visualization program. <I>Type</I> is the atom
+type (1 to Ntypes). <I>Element</I> is typically the chemical name of an
+element, which you must assign to each type via the <A HREF = "dump_modify.html">dump_modify
+element</A> command. More generally, it can be any
+string you wish to associated with an atom type. <I>Mass</I> is the atom
+mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, and <I>q</I> are components of
+atom velocity and force and atomic charge.
+</P>
+<P>There are several options for outputting atom coordinates. The <I>x</I>,
+<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
+appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use
+<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
+so that each value is 0.0 to 1.0. If the simulation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0. Use
+<I>xu</I>, <I>yu</I>, <I>zu</I> if you want the coordinates "unwrapped" by the image
+flags for each atom. Unwrapped means that if the atom has passed thru
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
+coordinate values may be far outside the box bounds printed with the
+snapshot. Using <I>xsu</I>, <I>ysu</I>, <I>zsu</I> is similar to using <I>xu</I>, <I>yu</I>, <I>zu</I>,
+except that the unwrapped coordinates are scaled by the box size. Atoms
+that have passed through a periodic boundary will have the corresponding
+cooordinate increased or decreased by 1.0.
+</P>
+<P>The image flags can be printed directly using the <I>ix</I>, <I>iy</I>, <I>iz</I>
+attributes. For periodic dimensions, they specify which image of the
+simulation box the atom is considered to be in. An image of 0 means
+it is inside the box as defined. A value of 2 means add 2 box lengths
+to get the true value. A value of -1 means subtract 1 box length to
+get the true value. LAMMPS updates these flags as atoms cross
+periodic boundaries during the simulation.
+</P>
+<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
+defined with an atom style of <I>dipole</I>. They give the orientation of
+the atom's point dipole moment. The <I>mu</I> attribute gives the
+magnitude of the atom's dipole moment.
+</P>
+<P>The <I>radius</I> and <I>diameter</I> attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of <I>sphere</I>.
+</P>
+<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
+finite-size spherical particles that have an angular velocity. Only
+certain atom styles, such as <I>sphere</I> define this quantity.
+</P>
+<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
+finite-size aspherical particles that have an angular momentum. Only
+the <I>ellipsoid</I> atom style defines this quantity.
+</P>
+<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
+</P>
+<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
+calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script. See the
+<A HREF = "compute.html">compute</A> command for details. There are computes for
+calculating the per-atom energy, stress, centro-symmetry parameter,
+and coordination number of individual atoms.
+</P>
+<P>Note that computes which calculate global or local quantities, as
+opposed to per-atom quantities, cannot be output in a dump custom
+command. Instead, global quantities can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command, and local quantities
+can be output by the dump local command.
+</P>
+<P>If <I>c_ID</I> is used as a attribute, then the per-atom vector calculated
+by the compute is printed. If <I>c_ID[N]</I> is used, then N must be in
+the range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the compute.
+</P>
+<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow vector or array per-atom
+quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
+attribute should be replaced by the actual ID of the fix that has been
+defined previously in the input script. The <A HREF = "fix_ave_atom.html">fix
+ave/atom</A> command is one that calculates per-atom
+quantities. Since it can time-average per-atom quantities produced by
+any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-style
+<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
+be written to a dump file.
+</P>
+<P>If <I>f_ID</I> is used as a attribute, then the per-atom vector calculated
+by the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the fix.
+</P>
+<P>The <I>v_name</I> attribute allows per-atom vectors calculated by a
+<A HREF = "variable.html">variable</A> to be output. The name in the attribute
+should be replaced by the actual name of the variable that has been
+defined previously in the input script. Only an atom-style variable
+can be referenced, since it is the only style that generates per-atom
+values. Variables of style <I>atom</I> can reference individual atom
+attributes, per-atom atom attributes, thermodynamic keywords, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of creating quantities to output to a
+dump file.
+</P>
+<P>The <I>d_name</I> and <I>i_name</I> attributes allow to output custom per atom
+floating point or integer properties that are managed by
+<A HREF = "fix_property_atom.html">fix property/atom</A>.
+</P>
+<P>See <A HREF = "Section_modify.html">Section_modify</A> of the manual for information
+on how to add new compute and fix styles to LAMMPS to calculate
+per-atom quantities which could then be output into dump files.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To write gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
+LAMMPS</A> section of the documentation.
+</P>
+<P>The <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles
+are part of the MPIIO package. They are only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The <I>xtc</I> style is part of the XTC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. This is
+because some machines may not support the low-level XDR data format
+that XTC files are written with, which will result in a compile-time
+error when a low-level include file is not found. Putting this style
+in a package makes it easy to exclude from a LAMMPS build for those
+machines. However, the XTC package also includes two compatibility
+header files and associated functions, which should be a suitable
+substitute on machines that do not have the appropriate native header
+files. This option can be invoked at build time by adding
+-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
+Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
+been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
+machines and should also work on IBM BG/P, and Windows XP/Vista/7
+machines.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump_image.html">dump image</A>, <A HREF = "dump_modify.html">dump_modify</A>,
+<A HREF = "undump.html">undump</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The defaults for the <I>image</I> and <I>movie</I> styles are listed on the
+<A HREF = "dump_image.html">dump image</A> doc page.
+</P>
+</HTML>
diff --git a/doc/doc2/dump_image.html b/doc/doc2/dump_image.html
new file mode 100644
index 000000000..c2babe4f6
--- /dev/null
+++ b/doc/doc2/dump_image.html
@@ -0,0 +1,566 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dump image command
+</H3>
+<H3>dump movie command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dump ID group-ID style N file color diameter keyword value ...
+</PRE>
+<UL><LI>ID = user-assigned name for the dump
+
+<LI>group-ID = ID of the group of atoms to be imaged
+
+<LI>style = <I>image</I> or <I>movie</I> = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
+
+<LI>N = dump every this many timesteps
+
+<LI>file = name of file to write image to
+
+<LI>color = atom attribute that determines color of each atom
+
+<LI>diameter = atom attribute that determines size of each atom
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>adiam</I> or <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>subbox</I> or <I>shiny</I> or <I>ssao</I>
+
+<PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
+ <I>atom</I> = yes/no = do or do not draw atoms
+ <I>bond</I> values = color width = color and width of bonds
+ color = <I>atom</I> or <I>type</I> or <I>none</I>
+ width = number or <I>atom</I> or <I>type</I> or <I>none</I>
+ number = numeric value for bond width (distance units)
+ <I>size</I> values = width height = size of images
+ width = width of image in # of pixels
+ height = height of image in # of pixels
+ <I>view</I> values = theta phi = view of simulation box
+ theta = view angle from +z axis (degrees)
+ phi = azimuthal view angle (degrees)
+ theta or phi can be a variable (see below)
+ <I>center</I> values = flag Cx Cy Cz = center point of image
+ flag = "s" for static, "d" for dynamic
+ Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
+ Cx,Cy,Cz can be variables (see below)
+ <I>up</I> values = Ux Uy Uz = direction that is "up" in image
+ Ux,Uy,Uz = components of up vector
+ Ux,Uy,Uz can be variables (see below)
+ <I>zoom</I> value = zfactor = size that simulation box appears in image
+ zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
+ zfactor can be a variable (see below)
+ <I>persp</I> value = pfactor = amount of "perspective" in image
+ pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
+ pfactor can be a variable (see below)
+ <I>box</I> values = yes/no diam = draw outline of simulation box
+ yes/no = do or do not draw simulation box lines
+ diam = diameter of box lines as fraction of shortest box length
+ <I>axes</I> values = yes/no length diam = draw xyz axes
+ yes/no = do or do not draw xyz axes lines next to simulation box
+ length = length of axes lines as fraction of respective box lengths
+ diam = diameter of axes lines as fraction of shortest box length
+ <I>subbox</I> values = yes/no diam = draw outline of processor sub-domains
+ yes/no = do or do not draw sub-domain lines
+ diam = diameter of sub-domain lines as fraction of shortest box length
+ <I>shiny</I> value = sfactor = shinyness of spheres and cylinders
+ sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
+ <I>ssao</I> value = yes/no seed dfactor = SSAO depth shading
+ yes/no = turn depth shading on/off
+ seed = random # seed (positive integer)
+ dfactor = strength of shading from 0.0 to 1.0
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dump d0 all image 100 dump.*.jpg type type
+dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
+dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
+dump m0 all movie 1000 movie.mpg type type size 640 480
+dump m1 all movie 1000 movie.avi type type size 640 480
+dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Dump a high-quality rendered image of the atom configuration every N
+timesteps and save the images either as a sequence of JPEG or PNG or
+PPM files, or as a single movie file. The options for this command as
+well as the <A HREF = "dump_modify.html">dump_modify</A> command control what is
+included in the image or movie and how it appears. A series of such
+images can easily be manually converted into an animated movie of your
+simulation or the process can be automated without writing the
+intermediate files using the dump movie style; see further details
+below. Other dump styles store snapshots of numerical data asociated
+with atoms in various formats, as discussed on the <A HREF = "dump.html">dump</A>
+doc page.
+</P>
+<P>Note that a set of images or a movie can be made after a simulation
+has been run, using the <A HREF = "rerun.html">rerun</A> command to read snapshots
+from an existing dump file, and using these dump commands in the rerun
+script to generate the images/movie.
+</P>
+<P>Here are two sample images, rendered as 1024x1024 JPEG files. Click
+to see the full-size images:
+</P>
+<DIV ALIGN=center>
+
+<A HREF = "JPG/dump1.jpg"><IMG SRC = "JPG/dump1_small.jpg"></A>
+
+<A HREF = "JPG/dump2.jpg"><IMG SRC = "JPG/dump2_small.jpg"></A>
+
+</DIV>
+
+<P>Only atoms in the specified group are rendered in the image. The
+<A HREF = "dump_modify.html">dump_modify region and thresh</A> commands can also
+alter what atoms are included in the image.</P>
+<P>The filename suffix determines whether a JPEG, PNG, or PPM file is
+created with the <I>image</I> dump style. If the suffix is ".jpg" or
+".jpeg", then a JPEG format file is created, if the suffix is ".png",
+then a PNG format is created, else a PPM (aka NETPBM) format file is
+created. The JPEG and PNG files are binary; PPM has a text mode
+header followed by binary data. JPEG images have lossy compression;
+PNG has lossless compression; and PPM files are uncompressed but can
+be compressed with gzip, if LAMMPS has been compiled with
+-DLAMMPS_GZIP and a ".gz" suffix is used.
+</P>
+<P>Similarly, the format of the resulting movie is chosen with the
+<I>movie</I> dump style. This is handled by the underlying FFmpeg converter
+and thus details have to be looked up in the FFmpeg documentation.
+Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
+Additional settings of the movie compression like bitrate and
+framerate can be set using the <A HREF = "dump_modify.html">dump_modify</A> command.
+</P>
+<P>To write out JPEG and PNG format files, you must build LAMMPS with
+support for the corresponding JPEG or PNG library. To convert images
+into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
+flag. See <A HREF = "Section_start.html#start_2_4">this section</A> of the manual
+for instructions on how to do this.
+</P>
+<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom in the image may be slightly outside the simulation box.
+</P>
+<HR>
+
+<P>Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges. Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N. This behavior can be
+changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
+can be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep. N can be changed between runs by
+using the <A HREF = "dump_modify.html">dump_modify every</A> command.
+</P>
+<P>Dump <I>image</I> filenames must contain a wildcard character "*", so that
+one image file per snapshot is written. The "*" character is replaced
+with the timestep value. For example, tmp.dump.*.jpg becomes
+tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
+that the <A HREF = "dump_modify.html">dump_modify pad</A> command can be used to
+insure all timestep numbers are the same length (e.g. 00010), which
+can make it easier to convert a series of images into a movie in the
+correct ordering.
+</P>
+<P>Dump <I>movie</I> filenames on the other hand, must not have any wildcard
+character since only one file combining all images into a single
+movie will be written by the movie encoder.
+</P>
+<HR>
+
+<P>The <I>color</I> and <I>diameter</I> settings determine the color and size of
+atoms rendered in the image. They can be any atom attribute defined
+for the <A HREF = "dump.html">dump custom</A> command, including <I>type</I> and
+<I>element</I>. This includes per-atom quantities calculated by a
+<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>,
+which are prefixed by "c_", "f_", or "v_" respectively. Note that the
+<I>diameter</I> setting can be overridden with a numeric value by the
+optional <I>adiam</I> keyword, in which case you can specify the <I>diameter</I>
+setting with any valid atom attribute.
+</P>
+<P>If <I>type</I> is specified for the <I>color</I> setting, then the color of each
+atom is determined by its atom type. By default the mapping of types
+to colors is as follows:
+</P>
+<UL><LI>type 1 = red
+<LI>type 2 = green
+<LI>type 3 = blue
+<LI>type 4 = yellow
+<LI>type 5 = aqua
+<LI>type 6 = cyan
+</UL>
+<P>and repeats itself for types > 6. This mapping can be changed by the
+<A HREF = "dump_modify.html">dump_modify acolor</A> command.
+</P>
+<P>If <I>type</I> is specified for the <I>diameter</I> setting then the diameter of
+each atom is determined by its atom type. By default all types have
+diameter 1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
+adiam</A> command.
+</P>
+<P>If <I>element</I> is specified for the <I>color</I> and/or <I>diameter</I> setting,
+then the color and/or diameter of each atom is determined by which
+element it is, which in turn is specified by the element-to-type
+mapping specified by the "dump_modify element" command. By default
+every atom type is C (carbon). Every element has a color and diameter
+associated with it, which is the same as the colors and sizes used by
+the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
+</P>
+
+
+<P>If other atom attributes are used for the <I>color</I> or <I>diameter</I>
+settings, they are interpreted in the following way.
+</P>
+<P>If "vx", for example, is used as the <I>color</I> setting, then the color
+of the atom will depend on the x-component of its velocity. The
+association of a per-atom value with a specific color is determined by
+a "color map", which can be specified via the
+<A HREF = "dump_modify.html">dump_modify</A> command. The basic idea is that the
+atom-attribute will be within a range of values, and every value
+within the range is mapped to a specific color. Depending on how the
+color map is defined, that mapping can take place via interpolation so
+that a value of -3.2 is halfway between "red" and "blue", or
+discretely so that the value of -3.2 is "orange".
+</P>
+<P>If "vx", for example, is used as the <I>diameter</I> setting, then the atom
+will be rendered using the x-component of its velocity as the
+diameter. If the per-atom value <= 0.0, them the atom will not be
+drawn. Note that finite-size spherical particles, as defined by
+<A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius or
+diameter, which can be used as the <I>diameter</I> setting.
+</P>
+<HR>
+
+<P>The various kewords listed above control how the image is rendered.
+As listed below, all of the keywords have defaults, most of which you
+will likely not need to change. The <A HREF = "dump_modify.html">dump modify</A>
+also has options specific to the dump image style, particularly for
+assigning colors to atoms, bonds, and other image features.
+</P>
+<HR>
+
+<P>The <I>adiam</I> keyword allows you to override the <I>diameter</I> setting to a
+per-atom attribute with a specified numeric value. All atoms will be
+drawn with that diameter, e.g. 1.5, which is in whatever distance
+<A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
+</P>
+<P>The <I>atom</I> keyword allow you to turn off the drawing of all atoms,
+if the specified value is <I>no</I>.
+</P>
+<P>The <I>bond</I> keyword allows to you to alter how bonds are drawn. A bond
+is only drawn if both atoms in the bond are being drawn due to being
+in the specified group and due to other selection criteria
+(e.g. region, threshhold settings of the
+<A HREF = "dump_modify.html">dump_modify</A> command). By default, bonds are drawn
+if they are defined in the input data file as read by the
+<A HREF = "read_data.html">read_data</A> command. Using <I>none</I> for both the bond
+<I>color</I> and <I>width</I> value will turn off the drawing of all bonds.
+</P>
+<P>If <I>atom</I> is specified for the bond <I>color</I> value, then each bond is
+drawn in 2 halves, with the color of each half being the color of the
+atom at that end of the bond.
+</P>
+<P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
+bond is determined by its bond type. By default the mapping of bond
+types to colors is as follows:
+</P>
+<UL><LI>type 1 = red
+<LI>type 2 = green
+<LI>type 3 = blue
+<LI>type 4 = yellow
+<LI>type 5 = aqua
+<LI>type 6 = cyan
+</UL>
+<P>and repeats itself for bond types > 6. This mapping can be changed by
+the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
+</P>
+<P>The bond <I>width</I> value can be a numeric value or <I>atom</I> or <I>type</I> (or
+<I>none</I> as indicated above).
+</P>
+<P>If a numeric value is specified, then all bonds will be drawn as
+cylinders with that diameter, e.g. 1.0, which is in whatever distance
+<A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
+</P>
+<P>If <I>atom</I> is specified for the <I>width</I> value, then each bond
+will be drawn with a width corresponding to the minimum diameter
+of the 2 atoms in the bond.
+</P>
+<P>If <I>type</I> is specified for the <I>width</I> value then the diameter of each
+bond is determined by its bond type. By default all types have
+diameter 0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
+bdiam</A> command.
+</P>
+<HR>
+
+<P>The <I>size</I> keyword sets the width and height of the created images,
+i.e. the number of pixels in each direction.
+</P>
+<HR>
+
+<P>The <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values determine how
+3d simulation space is mapped to the 2d plane of the image. Basically
+they control how the simulation box appears in the image.
+</P>
+<P>All of the <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values can be
+specified as numeric quantities, whose meaning is explained below.
+Any of them can also be specified as an <A HREF = "variable.html">equal-style
+variable</A>, by using v_name as the value, where "name" is
+the variable name. In this case the variable will be evaluated on the
+timestep each image is created to create a new value. If the
+equal-style variable is time-dependent, this is a means of changing
+the way the simulation box appears from image to image, effectively
+doing a pan or fly-by view of your simulation.
+</P>
+<P>The <I>view</I> keyword determines the viewpoint from which the simulation
+box is viewed, looking towards the <I>center</I> point. The <I>theta</I> value
+is the vertical angle from the +z axis, and must be an angle from 0 to
+180 degrees. The <I>phi</I> value is an azimuthal angle around the z axis
+and can be positive or negative. A value of 0.0 is a view along the
++x axis, towards the <I>center</I> point. If <I>theta</I> or <I>phi</I> are
+specified via variables, then the variable values should be in
+degrees.
+</P>
+<P>The <I>center</I> keyword determines the point in simulation space that
+will be at the center of the image. <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are
+speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
+the center of the simulation box. These values do not have to be
+between 0.0 and 1.0, if you want the simulation box to be offset from
+the center of the image. Note, however, that if you choose strange
+values for <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally,
+<I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space.
+If <I>flag</I> is set to "s" for static, then this conversion is done once,
+at the time the dump command is issued. If <I>flag</I> is set to "d" for
+dynamic then the conversion is performed every time a new image is
+created. If the box size or shape is changing, this will adjust the
+center point in simulation space.
+</P>
+<P>The <I>up</I> keyword determines what direction in simulation space will be
+"up" in the image. Internally it is stored as a vector that is in the
+plane perpendicular to the view vector implied by the <I>theta</I> and
+<I>pni</I> values, and which is also in the plane defined by the view
+vector and user-specified up vector. Thus this internal vector is
+computed from the user-specified <I>up</I> vector as
+</P>
+<PRE>up_internal = view cross (up cross view)
+</PRE>
+<P>This means the only restriction on the specified <I>up</I> vector is that
+it cannot be parallel to the <I>view</I> vector, implied by the <I>theta</I> and
+<I>phi</I> values.
+</P>
+<P>The <I>zoom</I> keyword scales the size of the simulation box as it appears
+in the image. The default <I>zfactor</I> value of 1 should display an
+image mostly filled by the atoms in the simulation box. A <I>zfactor</I> >
+1 will make the simulation box larger; a <I>zfactor</I> < 1 will make it
+smaller. <I>Zfactor</I> must be a value > 0.0.
+</P>
+<P>The <I>persp</I> keyword determines how much depth perspective is present
+in the image. Depth perspective makes lines that are parallel in
+simulation space appear non-parallel in the image. A <I>pfactor</I> value
+of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
+which is an orthographic rendering with no persepctive. A <I>pfactor</I>
+value between 0.0 and 1.0 will introduce more perspective. A <I>pfactor</I>
+value > 1 will create a highly skewed image with a large amount of
+perspective.
+</P>
+<P>IMPORTANT NOTE: The <I>persp</I> keyword is not yet supported as an option.
+</P>
+<HR>
+
+<P>The <I>box</I> keyword determines if and how the simulation box boundaries
+are rendered as thin cylinders in the image. If <I>no</I> is set, then the
+box boundaries are not drawn and the <I>diam</I> setting is ignored. If
+<I>yes</I> is set, the 12 edges of the box are drawn, with a diameter that
+is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
+2d). The color of the box boundaries can be set with the <A HREF = "dump_modify.html">dump_modify
+boxcolor</A> command.
+</P>
+<P>The <I>axes</I> keyword determines if and how the coordinate axes are
+rendered as thin cylinders in the image. If <I>no</I> is set, then the
+axes are not drawn and the <I>length</I> and <I>diam</I> settings are ignored.
+If <I>yes</I> is set, 3 thin cylinders are drawn to represent the x,y,z
+axes in colors red,green,blue. The origin of these cylinders will be
+offset from the lower left corner of the box by 10%. The <I>length</I>
+setting determines how long the cylinders will be as a fraction of the
+respective box lengths. The <I>diam</I> setting determines their thickness
+as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
+2d).
+</P>
+<P>The <I>subbox</I> keyword determines if and how processor sub-domain
+boundaries are rendered as thin cylinders in the image. If <I>no</I> is
+set (default), then the sub-domain boundaries are not drawn and the
+<I>diam</I> setting is ignored. If <I>yes</I> is set, the 12 edges of each
+processor sub-domain are drawn, with a diameter that is a fraction of
+the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
+of the sub-domain boundaries can be set with the <A HREF = "dump_modify.html">dump_modify
+boxcolor</A> command.
+</P>
+<HR>
+
+<P>The <I>shiny</I> keyword determines how shiny the objects rendered in the
+image will appear. The <I>sfactor</I> value must be a value 0.0 <=
+<I>sfactor</I> <= 1.0, where <I>sfactor</I> = 1 is a highly reflective surface
+and <I>sfactor</I> = 0 is a rough non-shiny surface.
+</P>
+<P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion
+(SSAO) model for depth shading. If <I>yes</I> is set, then atoms further
+away from the viewer are darkened via a randomized process, which is
+perceived as depth. The calculation of this effect can increase the
+cost of computing the image by roughly 2x. The strength of the effect
+can be scaled by the <I>dfactor</I> parameter. If <I>no</I> is set, no depth
+shading is performed.
+</P>
+<HR>
+
+<P>A series of JPEG, PNG, or PPM images can be converted into a movie
+file and then played as a movie using commonly available tools. Using
+dump style <I>movie</I> automates this step and avoids the intermediate
+step of writing (many) image snapshot file. But LAMMPS has to be
+compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be
+installed.
+</P>
+<P>To manually convert JPEG, PNG or PPM files into an animated GIF or
+MPEG or other movie file you can use:
+</P>
+<UL><LI>a) Use the ImageMagick convert program.
+
+<PRE>% convert *.jpg foo.gif
+% convert -loop 1 *.ppm foo.mpg
+</PRE>
+<P>Animated GIF files from ImageMagick are unoptimized. You can use a
+program like gifsicle to optimize and massively shrink them.
+MPEG files created by ImageMagick are in MPEG-1 format with rather
+inefficient compression and low quality.
+</P>
+<LI>b) Use QuickTime.
+
+<P>Select "Open Image Sequence" under the File menu Load the images into
+QuickTime to animate them Select "Export" under the File menu Save the
+movie as a QuickTime movie (*.mov) or in another format. QuickTime
+can generate very high quality and efficiently compressed movie
+files. Some of the supported formats require to buy a license and some
+are not readable on all platforms until specific runtime libraries are
+installed.
+</P>
+<LI>c) Use FFmpeg
+
+<P>FFmpeg is a command line tool that is available on many platforms and
+allows extremely flexible encoding and decoding of movies.
+</P>
+<PRE>cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
+</PRE>
+<P>Frontends for FFmpeg exist for multiple platforms. For more
+information see the <A HREF = "http://www.ffmpeg.org/">FFmpeg homepage</A>
+</P>
+
+</UL>
+<HR>
+
+<P>Play the movie:
+</P>
+<UL><LI>a) Use your browser to view an animated GIF movie.
+
+<P>Select "Open File" under the File menu
+Load the animated GIF file
+</P>
+<LI>b) Use the freely available mplayer or ffplay tool to view a
+movie. Both are available for multiple OSes and support a large
+variety of file formats and decoders.
+
+<PRE>% mplayer foo.mpg
+% ffplay bar.avi
+</PRE>
+<LI>c) Use the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</A>,
+which works directly on a series of image files.
+
+<PRE>a = animate("foo*.jpg")
+</PRE>
+<LI>d) QuickTime and other Windows- or MacOS-based media players can
+obviously play movie files directly. Similarly for corresponding tools
+bundled with Linux desktop environments. However, due to licensing
+issues with some file formats, the formats may require installing
+additional libraries, purchasing a license, or may not be
+supported.
+</UL>
+<HR>
+
+<P>See <A HREF = "Section_modify.html">Section_modify</A> of the manual for information
+on how to add new compute and fix styles to LAMMPS to calculate
+per-atom quantities which could then be output into dump files.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To write JPEG images, you must use the -DLAMMPS_JPEG switch when
+building LAMMPS and link with a JPEG library. To write PNG images, you
+must use the -DLAMMPS_PNG switch when building LAMMPS and link with a
+PNG library.
+</P>
+<P>To write <I>movie</I> dumps, you must use the -DLAMMPS_FFMPEG switch when
+building LAMMPS and have the FFmpeg executable available on the
+machine where LAMMPS is being run. Typically it's name is lowercase,
+i.e. ffmpeg.
+</P>
+<P>See the <A HREF = "Section_start.html#start_2_4">Making LAMMPS</A> section of the
+documentation for details on how to compile with optional switches.
+</P>
+<P>Note that since FFmpeg is run as an external program via a pipe,
+LAMMPS has limited control over its execution and no knowledge about
+errors and warnings printed by it. Those warnings and error messages
+will be printed to the screen only. Due to the way image data is
+communicated to FFmpeg, it will often print the message
+</P>
+<PRE>pipe:: Input/output error
+</PRE>
+<P>which can be safely ignored. Other warnings
+and errors have to be addressed according to the FFmpeg documentation.
+One known issue is that certain movie file formats (e.g. MPEG level 1
+and 2 format streams) have video bandwith limits that can be crossed
+when rendering too large of image sizes. Typical warnings look like
+this:
+</P>
+<PRE>[mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it
+[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
+[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
+</PRE>
+<P>In this case it is recommended to either reduce the size of the image
+or encode in a different format that is also supported by your copy of
+FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
+mp4).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The defaults for the keywords are as follows:
+</P>
+<UL><LI>adiam = not specified (use diameter setting)
+<LI>atom = yes
+<LI>bond = none none (if no bonds in system)
+<LI>bond = atom 0.5 (if bonds in system)
+<LI>size = 512 512
+<LI>view = 60 30 (for 3d)
+<LI>view = 0 0 (for 2d)
+<LI>center = s 0.5 0.5 0.5
+<LI>up = 0 0 1 (for 3d)
+<LI>up = 0 1 0 (for 2d)
+<LI>zoom = 1.0
+<LI>persp = 0.0
+<LI>box = yes 0.02
+<LI>axes = no 0.0 0.0
+<LI>subbox no 0.0
+<LI>shiny = 1.0
+<LI>ssao = no
+</UL>
+</HTML>
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+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dump_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dump_modify dump-ID keyword values ...
+</PRE>
+<UL><LI>dump-ID = ID of dump to modify
+
+<LI>one or more keyword/value pairs may be appended
+
+<LI>these keywords apply to various dump styles
+
+<LI>keyword = <I>append</I> or <I>buffer</I> or <I>element</I> or <I>every</I> or <I>fileper</I> or <I>first</I> or <I>flush</I> or <I>format</I> or <I>image</I> or <I>label</I> or <I>nfile</I> or <I>pad</I> or <I>precision</I> or <I>region</I> or <I>scale</I> or <I>sort</I> or <I>thresh</I> or <I>unwrap</I>
+
+<PRE> <I>append</I> arg = <I>yes</I> or <I>no</I>
+ <I>buffer</I> arg = <I>yes</I> or <I>no</I>
+ <I>element</I> args = E1 E2 ... EN, where N = # of atom types
+ E1,...,EN = element name, e.g. C or Fe or Ga
+ <I>every</I> arg = N
+ N = dump every this many timesteps
+ N can be a variable (see below)
+ <I>fileper</I> arg = Np
+ Np = write one file for every this many processors
+ <I>first</I> arg = <I>yes</I> or <I>no</I>
+ <I>format</I> arg = C-style format string for one line of output
+ <I>flush</I> arg = <I>yes</I> or <I>no</I>
+ <I>image</I> arg = <I>yes</I> or <I>no</I>
+ <I>label</I> arg = string
+ string = character string (e.g. BONDS) to use in header of dump local file
+ <I>nfile</I> arg = Nf
+ Nf = write this many files, one from each of Nf processors
+ <I>pad</I> arg = Nchar = # of characters to convert timestep to
+ <I>precision</I> arg = power-of-10 value from 10 to 1000000
+ <I>region</I> arg = region-ID or "none"
+ <I>scale</I> arg = <I>yes</I> or <I>no</I>
+ <I>sfactor</I> arg = coordinate scaling factor (> 0.0)
+ <I>tfactor</I> arg = time scaling factor (> 0.0)
+ <I>sort</I> arg = <I>off</I> or <I>id</I> or N or -N
+ off = no sorting of per-atom lines within a snapshot
+ id = sort per-atom lines by atom ID
+ N = sort per-atom lines in ascending order by the Nth column
+ -N = sort per-atom lines in descending order by the Nth column
+ <I>thresh</I> args = attribute operation value
+ attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
+ operation = "<" or "<=" or ">" or ">=" or "==" or "!="
+ value = numeric value to compare to
+ these 3 args can be replaced by the word "none" to turn off thresholding
+ <I>unwrap</I> arg = <I>yes</I> or <I>no</I>
+</PRE>
+<LI>these keywords apply only to the <I>image</I> and <I>movie</I> <A HREF = "dump_image.html">styles</A>
+
+<LI>keyword = <I>acolor</I> or <I>adiam</I> or <I>amap</I> or <I>backcolor</I> or <I>bcolor</I> or <I>bdiam</I> or <I>boxcolor</I> or <I>color</I> or <I>bitrate</I> or <I>framerate</I>
+
+<PRE> <I>acolor</I> args = type color
+ type = atom type or range of types (see below)
+ color = name of color or color1/color2/...
+ <I>adiam</I> args = type diam
+ type = atom type or range of types (see below)
+ diam = diameter of atoms of that type (distance units)
+ <I>amap</I> args = lo hi style delta N entry1 entry2 ... entryN
+ lo = number or <I>min</I> = lower bound of range of color map
+ hi = number or <I>max</I> = upper bound of range of color map
+ style = 2 letters = "c" or "d" or "s" plus "a" or "f"
+ "c" for continuous
+ "d" for discrete
+ "s" for sequential
+ "a" for absolute
+ "f" for fractional
+ delta = binsize (only used for style "s", otherwise ignored)
+ binsize = range is divided into bins of this width
+ N = # of subsequent entries
+ entry = value color (for continuous style)
+ value = number or <I>min</I> or <I>max</I> = single value within range
+ color = name of color used for that value
+ entry = lo hi color (for discrete style)
+ lo/hi = number or <I>min</I> or <I>max</I> = lower/upper bound of subset of range
+ color = name of color used for that subset of values
+ entry = color (for sequential style)
+ color = name of color used for a bin of values
+ <I>backcolor</I> arg = color
+ color = name of color for background
+ <I>bcolor</I> args = type color
+ type = bond type or range of types (see below)
+ color = name of color or color1/color2/...
+ <I>bdiam</I> args = type diam
+ type = bond type or range of types (see below)
+ diam = diameter of bonds of that type (distance units)
+ <I>boxcolor</I> arg = color
+ color = name of color for simulation box lines and processor sub-domain lines
+ <I>color</I> args = name R G B
+ name = name of color
+ R,G,B = red/green/blue numeric values from 0.0 to 1.0
+ <I>bitrate</I> arg = rate
+ rate = target bitrate for movie in kbps
+ <I>framerate</I> arg = fps
+ fps = frames per second for movie
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
+dump_modify myDump image yes scale no flush yes
+dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+dump_modify xtcdump precision 10000 sfactor 0.1
+dump_modify 1 every 1000 nfile 20
+dump_modify 1 every v_myVar
+dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Modify the parameters of a previously defined dump command. Not all
+parameters are relevant to all dump styles.
+</P>
+<P>As explained on the <A HREF = "dump.html">dump</A> doc page, the <I>atom/mpiio</I>,
+<I>custom/mpiio</I>, and <I>xyz/mpiio</I> dump styles are identical in command
+syntax and in the format of the dump files they create, to the
+corresponding styles without "mpiio", except the single dump file they
+produce is written in parallel via the MPI-IO library. Thus if a
+dump_modify option below is valid for the <I>atom</I> style, it is also
+valid for the <I>atom/mpiio</I> style, and similarly for the other styles
+which allow for use of MPI-IO.
+</P>
+<HR>
+
+<HR>
+
+<P>These keywords apply to various dump styles, including the <A HREF = "dump_image.html">dump
+image</A> and <A HREF = "dump_image.html">dump movie</A> styles. The
+description gives details.
+</P>
+<HR>
+
+<P>The <I>append</I> keyword applies to all dump styles except <I>cfg</I> and <I>xtc</I>
+and <I>dcd</I>. It also applies only to text output files, not to binary
+or gzipped or image/movie files. If specified as <I>yes</I>, then dump
+snapshots are appended to the end of an existing dump file. If
+specified as <I>no</I>, then a new dump file will be created which will
+overwrite an existing file with the same name. This keyword can only
+take effect if the dump_modify command is used after the
+<A HREF = "dump.html">dump</A> command, but before the first command that causes
+dump snapshots to be output, e.g. a <A HREF = "run.html">run</A> or
+<A HREF = "minimize.html">minimize</A> command. Once the dump file has been opened,
+this keyword has no further effect.
+</P>
+<HR>
+
+<P>The <I>buffer</I> keyword applies only to dump styles <I>atom</I>, <I>cfg</I>,
+<I>custom</I>, <I>local</I>, and <I>xyz</I>. It also applies only to text output
+files, not to binary or gzipped files. If specified as <I>yes</I>, which
+is the default, then each processor writes its output into an internal
+text buffer, which is then sent to the processor(s) which perform file
+writes, and written by those processors(s) as one large chunk of text.
+If specified as <I>no</I>, each processor sends its per-atom data in binary
+format to the processor(s) which perform file wirtes, and those
+processor(s) format and write it line by line into the output file.
+</P>
+<P>The buffering mode is typically faster since each processor does the
+relatively expensive task of formatting the output for its own atoms.
+However it requires about twice the memory (per processor) for the
+extra buffering.
+</P>
+<HR>
+
+<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I>, <I>xyz</I>, and
+<I>image</I> styles. It associates element names (e.g. H, C, Fe) with
+LAMMPS atom types. See the list of element names at the bottom of
+this page.
+</P>
+<P>In the case of dump <I>cfg</I>, this allows the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
+visualization package to read the dump file and render atoms with the
+appropriate size and color.
+</P>
+<P>In the case of dump <I>image</I>, the output images will follow the same
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> convention. An element name is specified for each
+atom type (1 to Ntype) in the simulation. The same element name can
+be given to multiple atom types.
+</P>
+<P>In the case of <I>xyz</I> format dumps, there are no restrictions to what
+label can be used as an element name. Any whitespace separated text
+will be accepted.
+</P>
+
+
+<HR>
+
+<P>The <I>every</I> keyword changes the dump frequency originally specified by
+the <A HREF = "dump.html">dump</A> command to a new value. The every keyword can be
+specified in one of two ways. It can be a numeric value in which case
+it must be > 0. Or it can be an <A HREF = "variable.html">equal-style variable</A>,
+which should be specified as v_name, where name is the variable name.
+</P>
+<P>In this case, the variable is evaluated at the beginning of a run to
+determine the next timestep at which a dump snapshot will be written
+out. On that timestep the variable will be evaluated again to
+determine the next timestep, etc. Thus the variable should return
+timestep values. See the stagger() and logfreq() and stride() math
+functions for <A HREF = "variable.html">equal-style variables</A>, as examples of
+useful functions to use in this context. Other similar math functions
+could easily be added as options for <A HREF = "variable.html">equal-style
+variables</A>. Also see the next() function, which allows
+use of a file-style variable which reads successive values from a
+file, each time the variable is evaluated. Used with the <I>every</I>
+keyword, if the file contains a list of ascending timesteps, you can
+output snapshots whenever you wish.
+</P>
+<P>Note that when using the variable option with the <I>every</I> keyword, you
+need to use the <I>first</I> option if you want an initial snapshot written
+to the dump file. The <I>every</I> keyword cannot be used with the dump
+<I>dcd</I> style.
+</P>
+<P>For example, the following commands will
+write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+</P>
+<PRE>variable s equal logfreq(10,3,10)
+dump 1 all atom 100 tmp.dump
+dump_modify 1 every v_s first yes
+</PRE>
+<P>The following commands would write snapshots at the timesteps listed
+in file tmp.times:
+</P>
+<PRE>variable f file tmp.times
+variable s equal next(f)
+dump 1 all atom 100 tmp.dump
+dump_modify 1 every v_s
+</PRE>
+<P>IMPORTANT NOTE: When using a file-style variable with the <I>every</I>
+keyword, the file of timesteps must list a first timestep that is
+beyond the current timestep (e.g. it cannot be 0). And it must list
+one or more timesteps beyond the length of the run you perform. This
+is because the dump command will generate an error if the next
+timestep it reads from the file is not a value greater than the
+current timestep. Thus if you wanted output on steps 0,15,100 of a
+100-timestep run, the file should contain the values 15,100,101 and
+you should also use the dump_modify first command. Any final value >
+100 could be used in place of 101.
+</P>
+<HR>
+
+<P>The <I>first</I> keyword determines whether a dump snapshot is written on
+the very first timestep after the dump command is invoked. This will
+always occur if the current timestep is a multiple of N, the frequency
+specified in the <A HREF = "dump.html">dump</A> command, including timestep 0. But
+if this is not the case, a dump snapshot will only be written if the
+setting of this keyword is <I>yes</I>. If it is <I>no</I>, which is the
+default, then it will not be written.
+</P>
+<HR>
+
+<P>The <I>flush</I> keyword determines whether a flush operation is invoked
+after a dump snapshot is written to the dump file. A flush insures
+the output in that file is current (no buffering by the OS), even if
+LAMMPS halts before the simulation completes. Flushes cannot be
+performed with dump style <I>xtc</I>.
+</P>
+<HR>
+
+<P>The text-based dump styles have a default C-style format string which
+simply specifies %d for integers and %g for floating-point values.
+The <I>format</I> keyword can be used to override the default with a new
+C-style format string. Do not include a trailing "\n" newline
+character in the format string. This option has no effect on the
+<I>dcd</I> and <I>xtc</I> dump styles since they write binary files. Note that
+for the <I>cfg</I> style, the first two fields (atom id and type) are not
+actually written into the CFG file, though you must include formats
+for them in the format string.
+</P>
+<P>IMPORTANT NOTE: Any value written to a text-based dump file that is a
+per-atom quantity calculated by a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> is stored internally as a floating-point value. If the
+value is actually an integer and you wish it to appear in the text
+dump file as a (large) integer, then you need to use an appropriate
+format. For example, these commands:
+</P>
+<PRE>compute 1 all property/local batom1 batom2
+dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
+dump_modify 1 format "%d %0.0f %0.0f"
+</PRE>
+<P>will output the two atom IDs for atoms in each bond as integers. If
+the dump_modify command were omitted, they would appear as
+floating-point values, assuming they were large integers (more than 6
+digits). The "index" keyword should use the "%d" format since it is
+not generated by a compute or fix, and is stored internally as an
+integer.
+</P>
+<HR>
+
+<P>The <I>fileper</I> keyword is documented below with the <I>nfile</I> keyword.
+</P>
+<HR>
+
+<P>The <I>image</I> keyword applies only to the dump <I>atom</I> style. If the
+image value is <I>yes</I>, 3 flags are appended to each atom's coords which
+are the absolute box image of the atom in each dimension. For
+example, an x image flag of -2 with a normalized coord of 0.5 means
+the atom is in the center of the box, but has passed thru the box
+boundary 2 times and is really 2 box lengths to the left of its
+current coordinate. Note that for dump style <I>custom</I> these various
+values can be printed in the dump file by using the appropriate atom
+attributes in the dump command itself.
+</P>
+<HR>
+
+<P>The <I>label</I> keyword applies only to the dump <I>local</I> style. When
+it writes local information, such as bond or angle topology
+to a dump file, it will use the specified <I>label</I> to format
+the header. By default this includes 2 lines:
+</P>
+<PRE>ITEM: NUMBER OF ENTRIES
+ITEM: ENTRIES ...
+</PRE>
+<P>The word "ENTRIES" will be replaced with the string specified,
+e.g. BONDS or ANGLES.
+</P>
+<HR>
+
+<P>The <I>nfile</I> or <I>fileper</I> keywords can be used in conjunction with the
+"%" wildcard character in the specified dump file name, for all dump
+styles except the <I>dcd</I>, <I>image</I>, <I>movie</I>, <I>xtc</I>, and <I>xyz</I> styles
+(for which "%" is not allowed). As explained on the <A HREF = "dump.html">dump</A>
+command doc page, the "%" character causes the dump file to be written
+in pieces, one piece for each of P processors. By default P = the
+number of processors the simulation is running on. The <I>nfile</I> or
+<I>fileper</I> keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+</P>
+<P>The <I>nfile</I> keyword sets P to the specified Nf value. For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75. Each will collect information
+from itself and the next 24 processors and write it to a dump file.
+</P>
+<P>For the <I>fileper</I> keyword, the specified value of Np means write one
+file for every Np processors. For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a dump file.
+</P>
+<HR>
+
+<P>The <I>pad</I> keyword only applies when the dump filename is specified
+with a wildcard "*" character which becomes the timestep. If <I>pad</I> is
+0, which is the default, the timestep is converted into a string of
+unpadded length, e.g. 100 or 12000 or 2000000. When <I>pad</I> is
+specified with <I>Nchar</I> > 0, the string is padded with leading zeroes
+so they are all the same length = <I>Nchar</I>. For example, pad 7 would
+yield 0000100, 0012000, 2000000. This can be useful so that
+post-processing programs can easily read the files in ascending
+timestep order.
+</P>
+<HR>
+
+<P>The <I>precision</I> keyword only applies to the dump <I>xtc</I> style. A
+specified value of N means that coordinates are stored to 1/N
+nanometer accuracy, e.g. for N = 1000, the coordinates are written to
+1/1000 nanometer accuracy.
+</P>
+<HR>
+
+<P>The <I>sfactor</I> and <I>tfactor</I> keywords only apply to the dump <I>xtc</I>
+style. They allow customization of the unit conversion factors used
+when writing to XTC files. By default they are initialized for
+whatever <A HREF = "units.html">units</A> style is being used, to write out
+coordinates in nanometers and time in picoseconds. I.e. for <I>real</I>
+units, LAMMPS defines <I>sfactor</I> = 0.1 and <I>tfactor</I> = 0.001, since the
+Angstroms and fmsec used by <I>real</I> units are 0.1 nm and 0.001 psec
+respectively. If you are using a units system with distance and time
+units far from nm and psec, you may wish to write XTC files with
+different units, since the compression algorithm used in XTC files is
+most effective when the typical magnitude of position data is between
+10.0 and 0.1.
+</P>
+<HR>
+
+<P>The <I>region</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
+<I>image</I>, and <I>movie</I> styles. If specified, only atoms in the region
+will be written to the dump file or included in the image/movie. Only
+one region can be applied as a filter (the last one specified). See
+the <A HREF = "region.html">region</A> command for more details. Note that a region
+can be defined as the "inside" or "outside" of a geometric shape, and
+it can be the "union" or "intersection" of a series of simpler
+regions.
+</P>
+<HR>
+
+<P>The <I>scale</I> keyword applies only to the dump <I>atom</I> style. A scale
+value of <I>yes</I> means atom coords are written in normalized units from
+0.0 to 1.0 in each box dimension. If the simluation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0. A
+value of <I>no</I> means they are written in absolute distance units
+(e.g. Angstroms or sigma).
+</P>
+<HR>
+
+<P>The <I>sort</I> keyword determines whether lines of per-atom output in a
+snapshot are sorted or not. A sort value of <I>off</I> means they will
+typically be written in indeterminate order, either in serial or
+parallel. This is the case even in serial if the <A HREF = "atom_modify.html">atom_modify
+sort</A> option is turned on, which it is by default, to
+improve performance. A sort value of <I>id</I> means sort the output by
+atom ID. A sort value of N or -N means sort the output by the value
+in the Nth column of per-atom info in either ascending or descending
+order.
+</P>
+<P>The dump <I>local</I> style cannot be sorted by atom ID, since there are
+typically multiple lines of output per atom. Some dump styles, such
+as <I>dcd</I> and <I>xtc</I>, require sorting by atom ID to format the output
+file correctly. If multiple processors are writing the dump file, via
+the "%" wildcard in the dump filename, then sorting cannot be
+performed.
+</P>
+<P>IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
+file output requires extra overhead in terms of CPU and communication
+cost, as well as memory, versus unsorted output.
+</P>
+<HR>
+
+<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
+<I>image</I>, and <I>movie</I> styles. Multiple thresholds can be specified.
+Specifying "none" turns off all threshold criteria. If thresholds are
+specified, only atoms whose attributes meet all the threshold criteria
+are written to the dump file or included in the image. The possible
+attributes that can be tested for are the same as those that can be
+specified in the <A HREF = "dump.html">dump custom</A> command, with the exception
+of the <I>element</I> attribute, since it is not a numeric value. Note
+that different attributes can be output by the dump custom command
+than are used as threshold criteria by the dump_modify command.
+E.g. you can output the coordinates and stress of atoms whose energy
+is above some threshold.
+</P>
+<HR>
+
+<P>The <I>unwrap</I> keyword only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
+If set to <I>yes</I>, coordinates will be written "unwrapped" by the image
+flags for each atom. Unwrapped means that if the atom has passed thru
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box. Note that these coordinates may thus be far outside the
+box size stored with the snapshot.
+</P>
+<HR>
+
+<HR>
+
+<P>These keywords apply only to the <A HREF = "dump_image.html">dump image</A> and
+<A HREF = "dump_image.html">dump movie</A> styles. Any keyword that affects an
+image, also affects a movie, since the movie is simply a collection of
+images. Some of the keywords only affect the <A HREF = "dump_image.html">dump
+movie</A> style. The descriptions give details.
+</P>
+<HR>
+
+<P>The <I>acolor</I> keyword can be used with the <A HREF = "dump_image.html">dump image</A>
+command, when its atom color setting is <I>type</I>, to set the color that
+atoms of each type will be drawn in the image.
+</P>
+<P>The specified <I>type</I> should be an integer from 1 to Ntypes = the
+number of atom types. A wildcard asterisk can be used in place of or
+in conjunction with the <I>type</I> argument to specify a range of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+</P>
+<P>The specified <I>color</I> can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option. Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue. In the former case, that
+color is assigned to all the specified atom types. In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified atom types.
+</P>
+<HR>
+
+<P>The <I>adiam</I> keyword can be used with the <A HREF = "dump_image.html">dump image</A>
+command, when its atom diameter setting is <I>type</I>, to set the size
+that atoms of each type will be drawn in the image. The specified
+<I>type</I> should be an integer from 1 to Ntypes. As with the <I>acolor</I>
+keyword, a wildcard asterisk can be used as part of the <I>type</I>
+argument to specify a range of atomt types. The specified <I>diam</I> is
+the size in whatever distance <A HREF = "units.html">units</A> the input script is
+using, e.g. Angstroms.
+</P>
+<HR>
+
+<P>The <I>amap</I> keyword can be used with the <A HREF = "dump_image.html">dump image</A>
+command, with its <I>atom</I> keyword, when its atom setting is an
+atom-attribute, to setup a color map. The color map is used to assign
+a specific RGB (red/green/blue) color value to an individual atom when
+it is drawn, based on the atom's attribute, which is a numeric value,
+e.g. its x-component of velocity if the atom-attribute "vx" was
+specified.
+</P>
+<P>The basic idea of a color map is that the atom-attribute will be
+within a range of values, and that range is associated with a a series
+of colors (e.g. red, blue, green). An atom's specific value (vx =
+-3.2) can then mapped to the series of colors (e.g. halfway between
+red and blue), and a specific color is determined via an interpolation
+procedure.
+</P>
+<P>There are many possible options for the color map, enabled by the
+<I>amap</I> keyword. Here are the details.
+</P>
+<P>The <I>lo</I> and <I>hi</I> settings determine the range of values allowed for
+the atom attribute. If numeric values are used for <I>lo</I> and/or <I>hi</I>,
+then values that are lower/higher than that value are set to the
+value. I.e. the range is static. If <I>lo</I> is specified as <I>min</I> or
+<I>hi</I> as <I>max</I> then the range is dynamic, and the lower and/or
+upper bound will be calculated each time an image is drawn, based
+on the set of atoms being visualized.
+</P>
+<P>The <I>style</I> setting is two letters, such as "ca". The first letter is
+either "c" for continuous, "d" for discrete, or "s" for sequential.
+The second letter is either "a" for absolute, or "f" for fractional.
+</P>
+<P>A continuous color map is one in which the color changes continuously
+from value to value within the range. A discrete color map is one in
+which discrete colors are assigned to sub-ranges of values within the
+range. A sequential color map is one in which discrete colors are
+assigned to a sequence of sub-ranges of values covering the entire
+range.
+</P>
+<P>An absolute color map is one in which the values to which colors are
+assigned are specified explicitly as values within the range. A
+fractional color map is one in which the values to which colors are
+assigned are specified as a fractional portion of the range. For
+example if the range is from -10.0 to 10.0, and the color red is to be
+assigned to atoms with a value of 5.0, then for an absolute color map
+the number 5.0 would be used. But for a fractional map, the number
+0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
+</P>
+<P>The <I>delta</I> setting must be specified for all styles, but is only used
+for the sequential style; otherwise the value is ignored. It
+specifies the bin size to use within the range for assigning
+consecutive colors to. For example, if the range is from -10.0 to
+10.0 and a <I>delta</I> of 1.0 is used, then 20 colors will be assigned to
+the range. The first will be from -10.0 <= color1 < -9.0, then 2nd
+from -9.0 <= color2 < -8.0, etc.
+</P>
+<P>The <I>N</I> setting is how many entries follow. The format of the entries
+depends on whether the color map style is continuous, discrete or
+sequential. In all cases the <I>color</I> setting can be any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+</P>
+<P>For continuous color maps, each entry has a <I>value</I> and a <I>color</I>.
+The <I>value</I> is either a number within the range of values or <I>min</I> or
+<I>max</I>. The <I>value</I> of the first entry must be <I>min</I> and the <I>value</I>
+of the last entry must be <I>max</I>. Any entries in between must have
+increasing values. Note that numeric values can be specified either
+as absolute numbers or as fractions (0.0 to 1.0) of the range,
+depending on the "a" or "f" in the style setting for the color map.
+</P>
+<P>Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute. X will fall
+between 2 of the entry values. The color of the atom is linearly
+interpolated (in each of the RGB values) between the 2 colors
+associated with those entries. For example, if X = -5.0 and the 2
+surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+atom's color will be halfway between "red" and "blue", which happens
+to be "purple".
+</P>
+<P>For discrete color maps, each entry has a <I>lo</I> and <I>hi</I> value and a
+<I>color</I>. The <I>lo</I> and <I>hi</I> settings are either numbers within the
+range of values or <I>lo</I> can be <I>min</I> or <I>hi</I> can be <I>max</I>. The <I>lo</I>
+and <I>hi</I> settings of the last entry must be <I>min</I> and <I>max</I>. Other
+entries can have any <I>lo</I> and <I>hi</I> values and the sub-ranges of
+different values can overlap. Note that numeric <I>lo</I> and <I>hi</I> values
+can be specified either as absolute numbers or as fractions (0.0 to
+1.0) of the range, depending on the "a" or "f" in the style setting
+for the color map.
+</P>
+<P>Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute. The entries
+are scanned from first to last. The first time that <I>lo</I> <= X <=
+<I>hi</I>, X is assigned the color associated with that entry. You can
+think of the last entry as assigning a default color (since it will
+always be matched by X), and the earlier entries as colors that
+override the default. Also note that no interpolation of a color RGB
+is done. All atoms will be drawn with one of the colors in the list
+of entries.
+</P>
+<P>For sequential color maps, each entry has only a <I>color</I>. Here is how
+the entries are used to determine the color of an individual atom,
+given the value X of its atom attribute. The range is partitioned
+into N bins of width <I>binsize</I>. Thus X will fall in a specific bin
+from 1 to N, say the Mth bin. If it falls on a boundary between 2
+bins, it is considered to be in the higher of the 2 bins. Each bin is
+assigned a color from the E entries. If E < N, then the colors are
+repeated. For example if 2 entries with colors red and green are
+specified, then the odd numbered bins will be red and the even bins
+green. The color of the atom is the color of its bin. Note that the
+sequential color map is really a shorthand way of defining a discrete
+color map without having to specify where all the bin boundaries are.
+</P>
+<P>Here is an example of using a sequential color map to color all the
+atoms in individual molecules with a different color. See the
+examples/pour/in.pour.2d.molecule input script for an example of how
+this is used.
+</P>
+<PRE>variable colors string &
+ "red green blue yellow white &
+ purple pink orange lime gray"
+variable mol atom mol%10
+dump 1 all image 250 image.*.jpg v_mol type &
+ zoom 1.6 adiam 1.5
+dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
+</PRE>
+<P>In this case, 10 colors are defined, and molecule IDs are
+mapped to one of the colors, even if there are 1000s of molecules.
+</P>
+<HR>
+
+<P>The <I>backcolor</I> sets the background color of the images. The color
+name can be any of the 140 pre-defined colors (see below) or a color
+name defined by the dump_modify color option.
+</P>
+<HR>
+
+<P>The <I>bcolor</I> keyword can be used with the <A HREF = "dump_image.html">dump image</A>
+command, with its <I>bond</I> keyword, when its color setting is <I>type</I>, to
+set the color that bonds of each type will be drawn in the image.
+</P>
+<P>The specified <I>type</I> should be an integer from 1 to Nbondtypes = the
+number of bond types. A wildcard asterisk can be used in place of or
+in conjunction with the <I>type</I> argument to specify a range of bond
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of bond types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+</P>
+<P>The specified <I>color</I> can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option. Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue. In the former case, that
+color is assigned to all the specified bond types. In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified bond types.
+</P>
+<HR>
+
+<P>The <I>bdiam</I> keyword can be used with the <A HREF = "dump_image.html">dump image</A>
+command, with its <I>bond</I> keyword, when its diam setting is <I>type</I>, to
+set the diameter that bonds of each type will be drawn in the image.
+The specified <I>type</I> should be an integer from 1 to Nbondtypes. As
+with the <I>bcolor</I> keyword, a wildcard asterisk can be used as part of
+the <I>type</I> argument to specify a range of bond types. The specified
+<I>diam</I> is the size in whatever distance <A HREF = "units.html">units</A> you are
+using, e.g. Angstroms.
+</P>
+<HR>
+
+<P>The <I>bitrate</I> keyword can be used with the <A HREF = "dump_image.html">dump
+movie</A> command to define the size of the resulting
+movie file and its quality via setting how many kbits per second are
+to be used for the movie file. Higher bitrates require less
+compression and will result in higher quality movies. The quality is
+also determined by the compression format and encoder. The default
+setting is 2000 kbit/s, which will result in average quality with
+older compression formats.
+</P>
+<P>IMPORTANT NOTE: Not all movie file formats supported by dump movie
+allow the bitrate to be set. If not, the setting is silently ignored.
+</P>
+<HR>
+
+<P>The <I>boxcolor</I> keyword sets the color of the simulation box drawn
+around the atoms in each image as well as the color of processor
+sub-domain boundaries. See the "dump image box" command for how to
+specify that a box be drawn via the <I>box</I> keyword, and the sub-domain
+boundaries via the <I>subbox</I> keyword. The color name can be any of the
+140 pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+</P>
+<HR>
+
+<P>The <I>color</I> keyword allows definition of a new color name, in addition
+to the 140-predefined colors (see below), and associates 3
+red/green/blue RGB values with that color name. The color name can
+then be used with any other dump_modify keyword that takes a color
+name as a value. The RGB values should each be floating point values
+between 0.0 and 1.0 inclusive.
+</P>
+<P>When a color name is converted to RGB values, the user-defined color
+names are searched first, then the 140 pre-defined color names. This
+means you can also use the <I>color</I> keyword to overwrite one of the
+pre-defined color names with new RBG values.
+</P>
+<HR>
+
+<P>The <I>framerate</I> keyword can be used with the <A HREF = "dump_image.html">dump
+movie</A> command to define the duration of the resulting
+movie file. Movie files written by the dump <I>movie</I> command have a
+default frame rate of 24 frames per second and the images generated
+will be converted at that rate. Thus a sequence of 1000 dump images
+will result in a movie of about 42 seconds. To make a movie run
+longer you can either generate images more frequently or lower the
+frame rate. To speed a movie up, you can do the inverse. Using a
+frame rate higher than 24 is not recommended, as it will result in
+simply dropping the rendered images. It is more efficient to dump
+images less frequently.
+</P>
+<HR>
+
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>, <A HREF = "undump.html">undump</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are
+</P>
+<UL><LI>append = no
+<LI>buffer = yes for dump styles <I>atom</I>, <I>custom</I>, <I>loca</I>, and <I>xyz</I>
+<LI>element = "C" for every atom type
+<LI>every = whatever it was set to via the <A HREF = "dump.html">dump</A> command
+<LI>fileper = # of processors
+<LI>first = no
+<LI>flush = yes
+<LI>format = %d and %g for each integer or floating point value
+<LI>image = no
+<LI>label = ENTRIES
+<LI>nfile = 1
+<LI>pad = 0
+<LI>precision = 1000
+<LI>region = none
+<LI>scale = yes
+<LI>sort = off for dump styles <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I>
+<LI>sort = id for dump styles <I>dcd</I>, <I>xtc</I>, and <I>xyz</I>
+<LI>thresh = none
+<LI>unwrap = no
+</UL>
+<UL><LI>acolor = * red/green/blue/yellow/aqua/cyan
+<LI>adiam = * 1.0
+<LI>amap = min max cf 0.0 2 min blue max red
+<LI>backcolor = black
+<LI>bcolor = * red/green/blue/yellow/aqua/cyan
+<LI>bdiam = * 0.5
+<LI>bitrate = 2000
+<LI>boxcolor = yellow
+<LI>color = 140 color names are pre-defined as listed below
+<LI>framerate = 24
+</UL>
+<HR>
+
+<P>These are the standard 109 element names that LAMMPS pre-defines for
+use with the <A HREF = "dump_image.html">dump image</A> and dump_modify commands.
+</P>
+<UL><LI>1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
+<LI>11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
+<LI>21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
+<LI>31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
+<LI>41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
+<LI>51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
+<LI>61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
+<LI>71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
+<LI>81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
+<LI>91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
+<LI>101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
+</UL>
+<HR>
+
+<P>These are the 140 colors that LAMMPS pre-defines for use with the
+<A HREF = "dump_image.html">dump image</A> and dump_modify commands. Additional
+colors can be defined with the dump_modify color command. The 3
+numbers listed for each name are the RGB (red/green/blue) values.
+Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >aliceblue = 240, 248, 255 </TD><TD >antiquewhite = 250, 235, 215 </TD><TD >aqua = 0, 255, 255 </TD><TD >aquamarine = 127, 255, 212 </TD><TD >azure = 240, 255, 255 </TD></TR>
+<TR><TD >beige = 245, 245, 220 </TD><TD >bisque = 255, 228, 196 </TD><TD >black = 0, 0, 0 </TD><TD >blanchedalmond = 255, 255, 205 </TD><TD >blue = 0, 0, 255 </TD></TR>
+<TR><TD >blueviolet = 138, 43, 226 </TD><TD >brown = 165, 42, 42 </TD><TD >burlywood = 222, 184, 135 </TD><TD >cadetblue = 95, 158, 160 </TD><TD >chartreuse = 127, 255, 0 </TD></TR>
+<TR><TD >chocolate = 210, 105, 30 </TD><TD >coral = 255, 127, 80 </TD><TD >cornflowerblue = 100, 149, 237 </TD><TD >cornsilk = 255, 248, 220 </TD><TD >crimson = 220, 20, 60 </TD></TR>
+<TR><TD >cyan = 0, 255, 255 </TD><TD >darkblue = 0, 0, 139 </TD><TD >darkcyan = 0, 139, 139 </TD><TD >darkgoldenrod = 184, 134, 11 </TD><TD >darkgray = 169, 169, 169 </TD></TR>
+<TR><TD >darkgreen = 0, 100, 0 </TD><TD >darkkhaki = 189, 183, 107 </TD><TD >darkmagenta = 139, 0, 139 </TD><TD >darkolivegreen = 85, 107, 47 </TD><TD >darkorange = 255, 140, 0 </TD></TR>
+<TR><TD >darkorchid = 153, 50, 204 </TD><TD >darkred = 139, 0, 0 </TD><TD >darksalmon = 233, 150, 122 </TD><TD >darkseagreen = 143, 188, 143 </TD><TD >darkslateblue = 72, 61, 139 </TD></TR>
+<TR><TD >darkslategray = 47, 79, 79 </TD><TD >darkturquoise = 0, 206, 209 </TD><TD >darkviolet = 148, 0, 211 </TD><TD >deeppink = 255, 20, 147 </TD><TD >deepskyblue = 0, 191, 255 </TD></TR>
+<TR><TD >dimgray = 105, 105, 105 </TD><TD >dodgerblue = 30, 144, 255 </TD><TD >firebrick = 178, 34, 34 </TD><TD >floralwhite = 255, 250, 240 </TD><TD >forestgreen = 34, 139, 34 </TD></TR>
+<TR><TD >fuchsia = 255, 0, 255 </TD><TD >gainsboro = 220, 220, 220 </TD><TD >ghostwhite = 248, 248, 255 </TD><TD >gold = 255, 215, 0 </TD><TD >goldenrod = 218, 165, 32 </TD></TR>
+<TR><TD >gray = 128, 128, 128 </TD><TD >green = 0, 128, 0 </TD><TD >greenyellow = 173, 255, 47 </TD><TD >honeydew = 240, 255, 240 </TD><TD >hotpink = 255, 105, 180 </TD></TR>
+<TR><TD >indianred = 205, 92, 92 </TD><TD >indigo = 75, 0, 130 </TD><TD >ivory = 255, 240, 240 </TD><TD >khaki = 240, 230, 140 </TD><TD >lavender = 230, 230, 250 </TD></TR>
+<TR><TD >lavenderblush = 255, 240, 245 </TD><TD >lawngreen = 124, 252, 0 </TD><TD >lemonchiffon = 255, 250, 205 </TD><TD >lightblue = 173, 216, 230 </TD><TD >lightcoral = 240, 128, 128 </TD></TR>
+<TR><TD >lightcyan = 224, 255, 255 </TD><TD >lightgoldenrodyellow = 250, 250, 210 </TD><TD >lightgreen = 144, 238, 144 </TD><TD >lightgrey = 211, 211, 211 </TD><TD >lightpink = 255, 182, 193 </TD></TR>
+<TR><TD >lightsalmon = 255, 160, 122 </TD><TD >lightseagreen = 32, 178, 170 </TD><TD >lightskyblue = 135, 206, 250 </TD><TD >lightslategray = 119, 136, 153 </TD><TD >lightsteelblue = 176, 196, 222 </TD></TR>
+<TR><TD >lightyellow = 255, 255, 224 </TD><TD >lime = 0, 255, 0 </TD><TD >limegreen = 50, 205, 50 </TD><TD >linen = 250, 240, 230 </TD><TD >magenta = 255, 0, 255 </TD></TR>
+<TR><TD >maroon = 128, 0, 0 </TD><TD >mediumaquamarine = 102, 205, 170 </TD><TD >mediumblue = 0, 0, 205 </TD><TD >mediumorchid = 186, 85, 211 </TD><TD >mediumpurple = 147, 112, 219 </TD></TR>
+<TR><TD >mediumseagreen = 60, 179, 113 </TD><TD >mediumslateblue = 123, 104, 238 </TD><TD >mediumspringgreen = 0, 250, 154 </TD><TD >mediumturquoise = 72, 209, 204 </TD><TD >mediumvioletred = 199, 21, 133 </TD></TR>
+<TR><TD >midnightblue = 25, 25, 112 </TD><TD >mintcream = 245, 255, 250 </TD><TD >mistyrose = 255, 228, 225 </TD><TD >moccasin = 255, 228, 181 </TD><TD >navajowhite = 255, 222, 173 </TD></TR>
+<TR><TD >navy = 0, 0, 128 </TD><TD >oldlace = 253, 245, 230 </TD><TD >olive = 128, 128, 0 </TD><TD >olivedrab = 107, 142, 35 </TD><TD >orange = 255, 165, 0 </TD></TR>
+<TR><TD >orangered = 255, 69, 0 </TD><TD >orchid = 218, 112, 214 </TD><TD >palegoldenrod = 238, 232, 170 </TD><TD >palegreen = 152, 251, 152 </TD><TD >paleturquoise = 175, 238, 238 </TD></TR>
+<TR><TD >palevioletred = 219, 112, 147 </TD><TD >papayawhip = 255, 239, 213 </TD><TD >peachpuff = 255, 239, 213 </TD><TD >peru = 205, 133, 63 </TD><TD >pink = 255, 192, 203 </TD></TR>
+<TR><TD >plum = 221, 160, 221 </TD><TD >powderblue = 176, 224, 230 </TD><TD >purple = 128, 0, 128 </TD><TD >red = 255, 0, 0 </TD><TD >rosybrown = 188, 143, 143 </TD></TR>
+<TR><TD >royalblue = 65, 105, 225 </TD><TD >saddlebrown = 139, 69, 19 </TD><TD >salmon = 250, 128, 114 </TD><TD >sandybrown = 244, 164, 96 </TD><TD >seagreen = 46, 139, 87 </TD></TR>
+<TR><TD >seashell = 255, 245, 238 </TD><TD >sienna = 160, 82, 45 </TD><TD >silver = 192, 192, 192 </TD><TD >skyblue = 135, 206, 235 </TD><TD >slateblue = 106, 90, 205 </TD></TR>
+<TR><TD >slategray = 112, 128, 144 </TD><TD >snow = 255, 250, 250 </TD><TD >springgreen = 0, 255, 127 </TD><TD >steelblue = 70, 130, 180 </TD><TD >tan = 210, 180, 140 </TD></TR>
+<TR><TD >teal = 0, 128, 128 </TD><TD >thistle = 216, 191, 216 </TD><TD >tomato = 253, 99, 71 </TD><TD >turquoise = 64, 224, 208 </TD><TD >violet = 238, 130, 238 </TD></TR>
+<TR><TD >wheat = 245, 222, 179 </TD><TD >white = 255, 255, 255 </TD><TD >whitesmoke = 245, 245, 245 </TD><TD >yellow = 255, 255, 0 </TD><TD >yellowgreen = 154, 205, 50
+</TD></TR></TABLE></DIV>
+
+</HTML>
diff --git a/doc/doc2/dump_molfile.html b/doc/doc2/dump_molfile.html
new file mode 100644
index 000000000..07c3b9f88
--- /dev/null
+++ b/doc/doc2/dump_molfile.html
@@ -0,0 +1,138 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>dump molfile command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>dump ID group-ID molfile N file format path
+</PRE>
+<UL><LI>ID = user-assigned name for the dump
+
+<LI>group-ID = ID of the group of atoms to be imaged
+
+<LI>molfile = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
+
+<LI>N = dump every this many timesteps
+
+<LI>file = name of file to write to
+
+<LI>format = file format to be used
+
+<LI>path = file path with plugins (optional)
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>dump mf1 all molfile 10 melt1.xml hoomd
+dump mf2 all molfile 10 melt2-*.pdb pdb .
+dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Dump a snapshot of atom coordinates and selected additional quantities
+to one or more files every N timesteps in one of several formats.
+Only information for atoms in the specified group is dumped. This
+specific dump style uses molfile plugins that are bundled with the
+<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and
+analysis program. See <A HREF = "Section_tools.html#vmd">Section tools</A> of the
+manual and the tools/lmp2vmd/README.txt file for more information
+about support in VMD for reading and visualizing native LAMMPS dump
+files.
+</P>
+<P>Unless the filename contains a * character, the output will be written
+to one single file with the specified format. Otherwise there will be
+one file per snapshot and the * will be replaced by the time step number
+when the snapshot is written.
+</P>
+<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+</P>
+<P>The molfile plugin API has a few restrictions that have to be honored
+by this dump style: the number of atoms must not change, the atoms
+must be sorted, outside of the coordinates no change in atom properties
+(like type, mass, charge) will be recorded.
+</P>
+<HR>
+
+<P>The <I>format</I> keyword determines what format is used to write out the
+dump. For this to work, LAMMPS must be able to find and load a
+compatible molfile plugin that supports this format. Settings made via
+the <A HREF = "dump_modify.html">dump_modify</A> command can alter per atom properties
+like element names.
+</P>
+<P>The <I>path</I> keyword determines which in directories. This is a "path"
+like other search paths, i.e. it can contain multiple directories
+separated by a colon (or semi-colon on windows). This keyword is
+optional and default to ".", the current directory.
+</P>
+<P>The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
+coordinates to be written "unwrapped" by the image flags for each atom.
+Unwrapped means that if the atom has passed through a periodic boundary
+one or more times, the value is printed for what the coordinate would be
+if it had not been wrapped back into the periodic box. Note that these
+coordinates may thus be far outside the box size stored with the
+snapshot.
+</P>
+<HR>
+
+<P>Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges. Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N. This behavior can be
+changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which can
+be useful if the dump command is invoked after a minimization ended on
+an arbitrary timestep. N can be changed between runs by using the
+<A HREF = "dump_modify.html">dump_modify every</A> command. The <A HREF = "dump_modify.html">dump_modify
+every</A> command also allows a variable to be used to
+determine the sequence of timesteps on which dump files are written.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>molfile</I> dump style is part of the USER-MOLFILE package. It is
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Molfile plugins provide a consistent programming interface to read and
+write file formats commonly used in molecular simulations. The
+USER-MOLFILE package only provides the interface code, not the plugins.
+These can be obtained from a VMD installation which has to match the
+platform that you are using to compile LAMMPS for. By adding plugins
+to VMD, support for new file formats can be added to LAMMPS (or VMD
+or other programs that use them) without having to recompile the
+application itself. The plugins are installed in the directory:
+<VMDHOME>/plugins/<VMDARCH>/molfile
+</P>
+<P>NOTE: while the programming interface (API) to the plugins is backward
+compatible, the binary interface (ABI) has been changing over time, so
+it is necessary to compile this package with the plugin header files
+from VMD that match the binary plugins. These header files in the
+directory: <VMDHOME>/plugins/include For convenience, the package ships
+with a set of header files that are compatible with VMD 1.9 and 1.9.1
+(June 2012)
+</P>
+<HR>
+
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default path is ".". All other properties have to be specified.
+</P>
+</HTML>
diff --git a/doc/doc2/echo.html b/doc/doc2/echo.html
new file mode 100644
index 000000000..15ca28365
--- /dev/null
+++ b/doc/doc2/echo.html
@@ -0,0 +1,43 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>echo command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>echo style
+</PRE>
+<UL><LI>style = <I>none</I> or <I>screen</I> or <I>log</I> or <I>both</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>echo both
+echo log
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command determines whether LAMMPS echoes each input script
+command to the screen and/or log file as it is read and processed. If
+an input script has errors, it can be useful to look at echoed output
+to see the last command processed.
+</P>
+<P>The <A HREF = "Section_start.html#start_5">command-line switch</A> -echo can be used
+in place of this command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>echo log
+</PRE>
+</HTML>
diff --git a/doc/doc2/fix.html b/doc/doc2/fix.html
new file mode 100644
index 000000000..ad6b904b3
--- /dev/null
+++ b/doc/doc2/fix.html
@@ -0,0 +1,285 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style args
+</PRE>
+<UL><LI>ID = user-assigned name for the fix
+<LI>group-ID = ID of the group of atoms to apply the fix to
+<LI>style = one of a long list of possible style names (see below)
+<LI>args = arguments used by a particular style
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve
+fix 3 all nvt temp 300.0 300.0 0.01
+fix mine top setforce 0.0 NULL 0.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set a fix that will be applied to a group of atoms. In LAMMPS, a
+"fix" is any operation that is applied to the system during
+timestepping or minimization. Examples include updating of atom
+positions and velocities due to time integration, controlling
+temperature, applying constraint forces to atoms, enforcing boundary
+conditions, computing diagnostics, etc. There are dozens of fixes
+defined in LAMMPS and new ones can be added; see <A HREF = "Section_modify.html">this
+section</A> for a discussion.
+</P>
+<P>Fixes perform their operations at different stages of the timestep.
+If 2 or more fixes operate at the same stage of the timestep, they are
+invoked in the order they were specified in the input script.
+</P>
+<P>The ID of a fix can only contain alphanumeric characters and
+underscores.
+</P>
+<P>Fixes can be deleted with the <A HREF = "unfix.html">unfix</A> command.
+</P>
+<P>IMPORTANT NOTE: The <A HREF = "unfix.html">unfix</A> command is the only way to turn
+off a fix; simply specifying a new fix with a similar style will not
+turn off the first one. This is especially important to realize for
+integration fixes. For example, using a <A HREF = "fix_nve.html">fix nve</A>
+command for a second run after using a <A HREF = "fix_nh.html">fix nvt</A> command
+for the first run, will not cancel out the NVT time integration
+invoked by the "fix nvt" command. Thus two time integrators would be
+in place!
+</P>
+<P>If you specify a new fix with the same ID and style as an existing
+fix, the old fix is deleted and the new one is created (presumably
+with new settings). This is the same as if an "unfix" command were
+first performed on the old fix, except that the new fix is kept in the
+same order relative to the existing fixes as the old one originally
+was. Note that this operation also wipes out any additional changes
+made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
+</P>
+<P>The <A HREF = "fix_modify.html">fix modify</A> command allows settings for some
+fixes to be reset. See the doc page for individual fixes for details.
+</P>
+<P>Some fixes store an internal "state" which is written to binary
+restart files via the <A HREF = "restart.html">restart</A> or
+<A HREF = "write_restart.html">write_restart</A> commands. This allows the fix to
+continue on with its calculations in a restarted simulation. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file. See the doc pages
+for individual fixes for info on which ones can be restarted.
+</P>
+<HR>
+
+<P>Some fixes calculate one of three styles of quantities: global,
+per-atom, or local, which can be used by other commands or output as
+described below. A global quantity is one or more system-wide values,
+e.g. the energy of a wall interacting with particles. A per-atom
+quantity is one or more values per atom, e.g. the displacement vector
+for each atom since time 0. Per-atom values are set to 0.0 for atoms
+not in the specified fix group. Local quantities are calculated by
+each processor based on the atoms it owns, but there may be zero or
+more per atoms.
+</P>
+<P>Note that a single fix may produces either global or per-atom or local
+quantities (or none at all), but never more than one of these.
+</P>
+<P>Global, per-atom, and local quantities each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values. The
+doc page for each fix describes the style and kind of values it
+produces, e.g. a per-atom vector. Some fixes produce more than one
+kind of a single style, e.g. a global scalar and a global vector.
+</P>
+<P>When a fix quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID is the ID of the fix:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >f_ID </TD><TD > entire scalar, vector, or array</TD></TR>
+<TR><TD >f_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
+<TR><TD >f_ID[I][J] </TD><TD > one element of array
+</TD></TR></TABLE></DIV>
+
+<P>In other words, using one bracket reduces the dimension of the
+quantity once (vector -> scalar, array -> vector). Using two brackets
+reduces the dimension twice (array -> scalar). Thus a command that
+uses scalar fix values as input can also process elements of a vector
+or array.
+</P>
+<P>Note that commands and <A HREF = "variable.html">variables</A> which use fix
+quantities typically do not allow for all kinds, e.g. a command may
+require a vector of values, not a scalar. This means there is no
+ambiguity about referring to a fix quantity as f_ID even if it
+produces, for example, both a scalar and vector. The doc pages for
+various commands explain the details.
+</P>
+<HR>
+
+<P>In LAMMPS, the values generated by a fix can be used in several ways:
+</P>
+<UL><LI>Global values can be output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
+Or the values can be referenced in a <A HREF = "variable.html">variable equal</A> or
+<A HREF = "variable.html">variable atom</A> command.
+
+<LI>Per-atom values can be output via the <A HREF = "dump.html">dump custom</A> command
+or the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command. Or they can be
+time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command or
+reduced by the <A HREF = "compute_reduce.html">compute reduce</A> command. Or the
+per-atom values can be referenced in an <A HREF = "variable.html">atom-style
+variable</A>.
+
+<LI>Local values can be reduced by the <A HREF = "compute_reduce.html">compute
+reduce</A> command, or histogrammed by the <A HREF = "fix_ave_histo.html">fix
+ave/histo</A> command.
+</UL>
+<P>See this <A HREF = "Section_howto.html#howto_15">howto section</A> for a summary of
+various LAMMPS output options, many of which involve fixes.
+</P>
+<P>The results of fixes that calculate global quantities can be either
+"intensive" or "extensive" values. Intensive means the value is
+independent of the number of atoms in the simulation,
+e.g. temperature. Extensive means the value scales with the number of
+atoms in the simulation, e.g. total rotational kinetic energy.
+<A HREF = "thermo_style.html">Thermodynamic output</A> will normalize extensive
+values by the number of atoms in the system, depending on the
+"thermo_modify norm" setting. It will not normalize intensive values.
+If a fix value is accessed in another way, e.g. by a
+<A HREF = "variable.html">variable</A>, you may want to know whether it is an
+intensive or extensive value. See the doc page for individual fixes
+for further info.
+</P>
+<HR>
+
+<P>Each fix style has its own documentation page which describes its
+arguments and what it does, as listed below. Here is an alphabetic
+list of fix styles available in LAMMPS. They are also given in more
+compact form in the fix section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<P>There are also additional fix styles (not listed here) submitted by
+users which are included in the LAMMPS distribution. The list of
+these with links to the individual styles are given in the fix section
+of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<P>There are also additional accelerated fix styles (not listed here)
+included in the LAMMPS distribution for faster performance on CPUs and
+GPUs. The list of these with links to the individual styles are given
+in the fix section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "fix_adapt.html">adapt</A> - change a simulation parameter over time
+<LI><A HREF = "fix_addforce.html">addforce</A> - add a force to each atom
+<LI><A HREF = "fix_append_atoms.html">append/atoms</A> - append atoms to a running simulation
+<LI><A HREF = "fix_aveforce.html">aveforce</A> - add an averaged force to each atom
+<LI><A HREF = "fix_ave_atom.html">ave/atom</A> - compute per-atom time-averaged quantities
+<LI><A HREF = "fix_ave_correlate.html">ave/correlate</A> - compute/output time correlations
+<LI><A HREF = "fix_ave_histo.html">ave/histo</A> - compute/output time-averaged histograms
+<LI><A HREF = "fix_ave_spatial.html">ave/spatial</A> - compute/output time-averaged per-atom quantities by layer
+<LI><A HREF = "fix_ave_time.html">ave/time</A> - compute/output global time-averaged quantities
+<LI><A HREF = "fix_balance.html">balance</A> - perform dynamic load-balancing
+<LI><A HREF = "fix_bond_break.html">bond/break</A> - break bonds on the fly
+<LI><A HREF = "fix_bond_create.html">bond/create</A> - create bonds on the fly
+<LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping
+<LI><A HREF = "fix_box_relax.html">box/relax</A> - relax box size during energy minimization
+<LI><A HREF = "fix_deform.html">deform</A> - change the simulation box size/shape
+<LI><A HREF = "fix_deposit.html">deposit</A> - add new atoms above a surface
+<LI><A HREF = "fix_drag.html">drag</A> - drag atoms towards a defined coordinate
+<LI><A HREF = "fix_dt_reset.html">dt/reset</A> - reset the timestep based on velocity, forces
+<LI><A HREF = "fix_efield.html">efield</A> - impose electric field on system
+<LI><A HREF = "fix_enforce2d.html">enforce2d</A> - zero out z-dimension velocity and force
+<LI><A HREF = "fix_evaporate.html">evaporate</A> - remove atoms from simulation periodically
+<LI><A HREF = "fix_external.html">external</A> - callback to an external driver program
+<LI><A HREF = "fix_freeze.html">freeze</A> - freeze atoms in a granular simulation
+<LI><A HREF = "fix_gcmc.html">gcmc</A> - grand canonical insertions/deletions
+<LI><A HREF = "fix_gcmc.html">gld</A> - generalized Langevin dynamics integrator
+<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
+<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
+<LI><A HREF = "fix_indent.html">indent</A> - impose force due to an indenter
+<LI><A HREF = "fix_langevin.html">langevin</A> - Langevin temperature control
+<LI><A HREF = "fix_lineforce.html">lineforce</A> - constrain atoms to move in a line
+<LI><A HREF = "fix_momentum.html">momentum</A> - zero the linear and/or angular momentum of a group of atoms
+<LI><A HREF = "fix_move.html">move</A> - move atoms in a prescribed fashion
+<LI><A HREF = "fix_msst.html">msst</A> - multi-scale shock technique (MSST) integration
+<LI><A HREF = "fix_neb.html">neb</A> - nudged elastic band (NEB) spring forces
+<LI><A HREF = "fix_nh.html">nph</A> - constant NPH time integration via Nose/Hoover
+<LI><A HREF = "fix_nphug.html">nphug</A> - constant-stress Hugoniostat integration
+<LI><A HREF = "fix_nph_asphere.html">nph/asphere</A> - NPH for aspherical particles
+<LI><A HREF = "fix_nph_sphere.html">nph/sphere</A> - NPH for spherical particles
+<LI><A HREF = "fix_nh.html">npt</A> - constant NPT time integration via Nose/Hoover
+<LI><A HREF = "fix_npt_asphere.html">npt/asphere</A> - NPT for aspherical particles
+<LI><A HREF = "fix_npt_sphere.html">npt/sphere</A> - NPT for spherical particles
+<LI><A HREF = "fix_nve.html">nve</A> - constant NVE time integration
+<LI><A HREF = "fix_nve_asphere.html">nve/asphere</A> - NVE for aspherical particles
+<LI><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A> - NVE for aspherical particles without forces"
+<LI><A HREF = "fix_nve_body.html">nve/body</A> - NVE for body particles
+<LI><A HREF = "fix_nve_limit.html">nve/limit</A> - NVE with limited step length
+<LI><A HREF = "fix_nve_line.html">nve/line</A> - NVE for line segments
+<LI><A HREF = "fix_nve_noforce.html">nve/noforce</A> - NVE without forces (v only)
+<LI><A HREF = "fix_nve_sphere.html">nve/sphere</A> - NVE for spherical particles
+<LI><A HREF = "fix_nve_tri.html">nve/tri</A> - NVE for triangles
+<LI><A HREF = "fix_nh.html">nvt</A> - constant NVT time integration via Nose/Hoover
+<LI><A HREF = "fix_nvt_asphere.html">nvt/asphere</A> - NVT for aspherical particles
+<LI><A HREF = "fix_nvt_sllod.html">nvt/sllod</A> - NVT for NEMD with SLLOD equations
+<LI><A HREF = "fix_nvt_sphere.html">nvt/sphere</A> - NVT for spherical particles
+<LI><A HREF = "fix_orient_fcc.html">orient/fcc</A> - add grain boundary migration force
+<LI><A HREF = "fix_planeforce.html">planeforce</A> - constrain atoms to move in a plane
+<LI><A HREF = "fix_poems.html">poems</A> - constrain clusters of atoms to move as coupled rigid bodies
+<LI><A HREF = "fix_pour.html">pour</A> - pour new atoms/molecules into a granular simulation domain
+<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
+<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
+<LI><A HREF = "fix_property_atom.html">property/atom</A> - add customized per-atom values
+<LI><A HREF = "fix_qeq_comb.html">qeq/comb</A> - charge equilibration for COMB potential <A HREF = "fix_qeq.html">qeq/dynamic</A> - charge equilibration via dynamic method <A HREF = "fix_qeq.html">qeq/point</A> - charge equilibration via point method <A HREF = "fix_qeq.html">qeq/shielded</A> - charge equilibration via shielded method <A HREF = "fix_qeq.html">qeq/slater</A> - charge equilibration via Slater method <A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
+<LI><A HREF = "fix_restrain.html">restrain</A> - constrain a bond, angle, dihedral
+<LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to move as a rigid body with NVE integration
+<LI><A HREF = "fix_rigid.html">rigid/nph</A> - constrain one or more clusters of atoms to move as a rigid body with NPH integration
+<LI><A HREF = "fix_rigid.html">rigid/npt</A> - constrain one or more clusters of atoms to move as a rigid body with NPT integration
+<LI><A HREF = "fix_rigid.html">rigid/nve</A> - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
+<LI><A HREF = "fix_rigid.html">rigid/nvt</A> - constrain one or more clusters of atoms to move as a rigid body with NVT integration
+<LI><A HREF = "fix_rigid.html">rigid/small</A> - constrain many small clusters of atoms to move as a rigid body with NVE integration
+<LI><A HREF = "fix_setforce.html">setforce</A> - set the force on each atom
+<LI><A HREF = "fix_shake.html">shake</A> - SHAKE constraints on bonds and/or angles
+<LI><A HREF = "fix_spring.html">spring</A> - apply harmonic spring force to group of atoms
+<LI><A HREF = "fix_spring_rg.html">spring/rg</A> - spring on radius of gyration of group of atoms
+<LI><A HREF = "fix_spring_self.html">spring/self</A> - spring from each atom to its origin
+<LI><A HREF = "fix_srd.html">srd</A> - stochastic rotation dynamics (SRD)
+<LI><A HREF = "fix_store_force.html">store/force</A> - store force on each atom
+<LI><A HREF = "fix_store_state.html">store/state</A> - store attributes for each atom
+<LI><A HREF = "fix_temp_berendsen.html">temp/berendsen</A> - temperature control by Berendsen thermostat
+<LI><A HREF = "fix_temp_rescale.html">temp/rescale</A> - temperature control by velocity rescaling
+<LI><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A> - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
+<LI><A HREF = "fix_tmd.html">tmd</A> - guide a group of atoms to a new configuration
+<LI><A HREF = "fix_ttm.html">ttm</A> - two-temperature model for electronic/atomic coupling
+<LI><A HREF = "fix_tune_kspace.html">tune/kspace</A> - auto-tune KSpace parameters
+<LI><A HREF = "fix_vector.html">vector</A> - accumulate a global vector every N timesteps
+<LI><A HREF = "fix_viscosity.html">viscosity</A> - Muller-Plathe momentum exchange for viscosity calculation
+<LI><A HREF = "fix_viscous.html">viscous</A> - viscous damping for granular simulations
+<LI><A HREF = "fix_wall.html">wall/colloid</A> - Lennard-Jones wall interacting with finite-size particles
+<LI><A HREF = "fix_wall_gran.html">wall/gran</A> - frictional wall(s) for granular simulations
+<LI><A HREF = "fix_wall.html">wall/harmonic</A> - harmonic spring wall
+<LI><A HREF = "fix_wall.html">wall/lj1043</A> - Lennard-Jones 10-4-3 wall
+<LI><A HREF = "fix_wall.html">wall/lj126</A> - Lennard-Jones 12-6 wall
+<LI><A HREF = "fix_wall.html">wall/lj93</A> - Lennard-Jones 9-3 wall
+<LI><A HREF = "fix_wall_piston.html">wall/piston</A> - moving reflective piston wall
+<LI><A HREF = "fix_wall_reflect.html">wall/reflect</A> - reflecting wall(s)
+<LI><A HREF = "fix_wall_region.html">wall/region</A> - use region surface as wall
+<LI><A HREF = "fix_wall_srd.html">wall/srd</A> - slip/no-slip wall for SRD particles
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>Some fix styles are part of specific packages. They are only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual fixes tell if it is part of a package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "unfix.html">unfix</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_adapt.html b/doc/doc2/fix_adapt.html
new file mode 100644
index 000000000..51ad3ce48
--- /dev/null
+++ b/doc/doc2/fix_adapt.html
@@ -0,0 +1,263 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix adapt command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID adapt N attribute args ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>adapt = style name of this fix command
+
+<LI>N = adapt simulation settings every this many timesteps
+
+<LI>one or more attribute/arg pairs may be appended
+
+<LI>attribute = <I>pair</I> or <I>kspace</I> or <I>atom</I>
+
+<PRE> <I>pair</I> args = pstyle pparam I J v_name
+ pstyle = pair style name, e.g. lj/cut
+ pparam = parameter to adapt over time
+ I,J = type pair(s) to set parameter for
+ v_name = variable with name that calculates value of pparam
+ <I>kspace</I> arg = v_name
+ v_name = variable with name that calculates scale factor on K-space terms
+ <I>atom</I> args = aparam v_name
+ aparam = parameter to adapt over time
+ v_name = variable with name that calculates value of aparam
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>scale</I> or <I>reset</I>
+
+<PRE> <I>scale</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = the variable value is the new setting
+ <I>yes</I> = the variable value multiplies the original setting
+ <I>reset</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = values will remain altered at the end of a run
+ <I>yes</I> = reset altered values to their original values at the end of a run
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all adapt 1 pair soft a 1 1 v_prefactor
+fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
+fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+fix 1 all adapt 10 atom diameter v_size
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Change or adapt one or more specific simulation attributes or settings
+over time as a simulation runs. Pair potential and K-space and atom
+attributes which can be varied by this fix are discussed below. Many
+other fixes can also be used to time-vary simulation parameters,
+e.g. the "fix deform" command will change the simulation box
+size/shape and the "fix move" command will change atom positions and
+velocities in a prescribed manner. Also note that many commands allow
+variables as arguments for specific parameters, if described in that
+manner on their doc pages. An equal-style variable can calculate a
+time-dependent quantity, so this is another way to vary a simulation
+parameter over time.
+</P>
+<P>If <I>N</I> is specified as 0, the specified attributes are only changed
+once, before the simulation begins. This is all that is needed if the
+associated variables are not time-dependent. If <I>N</I> > 0, then changes
+are made every <I>N</I> steps during the simulation, presumably with a
+variable that is time-dependent.
+</P>
+<P>Depending on the value of the <I>reset</I> keyword, attributes changed by
+this fix will or will not be reset back to their original values at
+the end of a simulation. Even if <I>reset</I> is specified as <I>yes</I>, a
+restart file written during a simulation will contain the modified
+settings.
+</P>
+<P>If the <I>scale</I> keyword is set to <I>no</I>, then the value the parameter is
+set to will be whatever the variable generates. If the <I>scale</I>
+keyword is set to <I>yes</I>, then the value of the altered parameter will
+be the initial value of that parameter multiplied by whatever the
+variable generates. I.e. the variable is now a "scale factor" applied
+in (presumably) a time-varying fashion to the parameter.
+</P>
+<P>Note that whether scale is <I>no</I> or <I>yes</I>, internally, the parameters
+themselves are actually altered by this fix. Make sure you use the
+<I>reset yes</I> option if you want the parameters to be restored to their
+initial values after the run.
+</P>
+<HR>
+
+<P>The <I>pair</I> keyword enables various parameters of potentials defined by
+the <A HREF = "pair_style.html">pair_style</A> command to be changed, if the pair
+style supports it. Note that the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands must be used in the usual manner
+to specify these parameters initially; the fix adapt command simply
+overrides the parameters.
+</P>
+<P>The <I>pstyle</I> argument is the name of the pair style. If <A HREF = "pair_hybrid.html">pair_style
+hybrid or hybrid/overlay</A> is used, <I>pstyle</I> should be
+a sub-style name. For example, <I>pstyle</I> could be specified as "soft"
+or "lubricate". The <I>pparam</I> argument is the name of the parameter to
+change. This is the current list of pair styles and parameters that
+can be varied by this fix. See the doc pages for individual pair
+styles and their energy formulas for the meaning of these parameters:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><A HREF = "pair_born.html">born</A></TD><TD > a,b,c</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_buck.html">buck</A></TD><TD > a,c</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD > epsilon,sigma,delta</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD > mu</TD><TD > global</TD></TR>
+<TR><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD > a</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_morse.html">morse</A></TD><TD > d0,r0,alpha</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_soft.html">soft</A></TD><TD > a</TD><TD > type pairs
+</TD></TR></TABLE></DIV>
+
+<P>IMPORTANT NOTE: It is easy to add new potentials and their parameters
+to this list. All it typically takes is adding an extract() method to
+the pair_*.cpp file associated with the potential.
+</P>
+<P>Some parameters are global settings for the pair style, e.g. the
+viscosity setting "mu" for <A HREF = "pair_lubricate.html">pair_style lubricate</A>.
+Other parameters apply to atom type pairs within the pair style,
+e.g. the prefactor "a" for <A HREF = "pair_soft.html">pair_style soft</A>.
+</P>
+<P>Note that for many of the potentials, the parameter that can be varied
+is effectively a prefactor on the entire energy expression for the
+potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
+are exactly that, since the energy expression for the
+<A HREF = "pair_coul.html">coul/cut</A> potential (for example) has no labeled
+prefactor in its formula. To apply an effective prefactor to some
+potentials, multiple parameters need to be altered. For example, the
+<A HREF = "pair_buck.html">Buckingham potential</A> needs both the A and C terms
+altered together. To scale the Buckingham potential, you should thus
+list the pair style twice, once for A and once for C.
+</P>
+<P>If a type pair parameter is specified, the <I>I</I> and <I>J</I> settings should
+be specified to indicate which type pairs to apply it to. If a global
+parameter is specified, the <I>I</I> and <I>J</I> settings still need to be
+specified, but are ignored.
+</P>
+<P>Similar to the <A HREF = "pair_coeff.html">pair_coeff command</A>, I and J can be
+specified in one of two ways. Explicit numeric values can be used for
+each, as in the 1st example above. I <= J is required. LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same values.
+</P>
+<P>A wild-card asterisk can be used in place of or in conjunction with
+the I,J arguments to set the coefficients for multiple pairs of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive). Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+</P>
+<P>IMPROTANT NOTE: If <A HREF = "pair_hybrid.html">pair_style hybrid or
+hybrid/overlay</A> is being used, then the <I>pstyle</I> will
+be a sub-style name. You must specify I,J arguments that correspond
+to type pair values defined (via the <A HREF = "pair_coeff.html">pair_coeff</A>
+command) for that sub-style.
+</P>
+<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this fix is invoked to set the parameter to a new value. It should be
+specified as v_name, where name is the variable name. Equal-style
+variables can specify formulas with various mathematical functions,
+and include <A HREF = "thermo_style.html">thermo_style</A> command keywords for the
+simulation box parameters and timestep and elapsed time. Thus it is
+easy to specify parameters that change as a function of time or span
+consecutive runs in a continuous fashion. For the latter, see the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command and the
+<I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style custom</A> for
+details.
+</P>
+<P>For example, these commands would change the prefactor coefficient of
+the <A HREF = "pair_soft.html">pair_style soft</A> potential from 10.0 to 30.0 in a
+linear fashion over the course of a simulation:
+</P>
+<PRE>variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</PRE>
+<HR>
+
+<P>The <I>kspace</I> keyword used the specified variable as a scale factor on
+the energy, forces, virial calculated by whatever K-Space solver is
+defined by the <A HREF = "kspace_style.html">kspace_style</A> command. If the
+variable has a value of 1.0, then the solver is unaltered.
+</P>
+<P>The <I>kspace</I> keyword works this way whether the <I>scale</I> keyword
+is set to <I>no</I> or <I>yes</I>.
+</P>
+<HR>
+
+<P>The <I>atom</I> keyword enables various atom properties to be changed. The
+<I>aparam</I> argument is the name of the parameter to change. This is the
+current list of atom parameters that can be varied by this fix:
+</P>
+<UL><LI>charge = charge on particle
+<LI>diameter = diameter of particle
+</UL>
+<P>The <I>v_name</I> argument of the <I>atom</I> keyword is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this fix is invoked to set the parameter to a new value. It should be
+specified as v_name, where name is the variable name. See the
+discussion above describing the formulas associated with equal-style
+variables. The new value is assigned to the corresponding attribute
+for all atoms in the fix group.
+</P>
+<P>IMPORTANT NOTE: The <I>atom</I> keyword works this way whether the <I>scale</I>
+keyword is set to <I>no</I> or <I>yes</I>. I.e. the use of scale yes is not yet
+supported by the <I>atom</I> keyword.
+</P>
+<P>If the atom parameter is <I>diameter</I> and per-atom density and per-atom
+mass are defined for particles (e.g. <A HREF = "atom_style.html">atom_style
+granular</A>), then the mass of each particle is also
+changed when the diameter changes (density is assumed to stay
+constant).
+</P>
+<P>For example, these commands would shrink the diameter of all granular
+particles in the "center" group from 1.0 to 0.1 in a linear fashion
+over the course of a 1000-step simulation:
+</P>
+<PRE>variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter v_size
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix changes
+parameters on the outermost rRESPA level.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_ti.html">compute ti</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are scale = no, reset = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_adapt_fep.html b/doc/doc2/fix_adapt_fep.html
new file mode 100644
index 000000000..a1e3009c1
--- /dev/null
+++ b/doc/doc2/fix_adapt_fep.html
@@ -0,0 +1,275 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix adapt/fep command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID adapt/fep N attribute args ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>adapt/fep = style name of this fix command
+
+<LI>N = adapt simulation settings every this many timesteps
+
+<LI>one or more attribute/arg pairs may be appended
+
+<LI>attribute = <I>pair</I> or <I>kspace</I> or <I>atom</I>
+
+<PRE> <I>pair</I> args = pstyle pparam I J v_name
+ pstyle = pair style name, e.g. lj/cut
+ pparam = parameter to adapt over time
+ I,J = type pair(s) to set parameter for
+ v_name = variable with name that calculates value of pparam
+ <I>kspace</I> arg = v_name
+ v_name = variable with name that calculates scale factor on K-space terms
+ <I>atom</I> args = aparam v_name
+ aparam = parameter to adapt over time
+ I = type(s) to set parameter for
+ v_name = variable with name that calculates value of aparam
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>scale</I> or <I>reset</I> or <I>after</I>
+
+<PRE> <I>scale</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = the variable value is the new setting
+ <I>yes</I> = the variable value multiplies the original setting
+ <I>reset</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = values will remain altered at the end of a run
+ <I>yes</I> = reset altered values to their original values at the end
+ of a run
+ <I>after</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = parameters are adapted at timestep N
+ <I>yes</I> = parameters are adapted one timestep after N
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
+fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
+fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+fix 1 all adapt/fep 10 atom diameter 1 v_size
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Change or adapt one or more specific simulation attributes or settings
+over time as a simulation runs.
+</P>
+<P>This is an enhanced version of the <A HREF = "fix_adapt.html">fix_adapt</A> command
+with two differences,
+</P>
+<UL><LI>It is possible to modify the charges of chosen atom types only,
+instead of scaling all the charges in the system.
+
+<LI>There is a new option <I>after</I> for better compatibility with "fix
+ave/time".
+</UL>
+<P>This version is suited for free energy calculations using
+<A HREF = "compute_ti.html">compute_ti</A> or <A HREF = "compute_fep.html">compute_fep</A>.
+</P>
+<P>If <I>N</I> is specified as 0, the specified attributes are only changed
+once, before the simulation begins. This is all that is needed if the
+associated variables are not time-dependent. If <I>N</I> > 0, then changes
+are made every <I>N</I> steps during the simulation, presumably with a
+variable that is time-dependent.
+</P>
+<P>Depending on the value of the <I>reset</I> keyword, attributes changed by
+this fix will or will not be reset back to their original values at
+the end of a simulation. Even if <I>reset</I> is specified as <I>yes</I>, a
+restart file written during a simulation will contain the modified
+settings.
+</P>
+<P>If the <I>scale</I> keyword is set to <I>no</I>, then the value the parameter is
+set to will be whatever the variable generates. If the <I>scale</I>
+keyword is set to <I>yes</I>, then the value of the altered parameter will
+be the initial value of that parameter multiplied by whatever the
+variable generates. I.e. the variable is now a "scale factor" applied
+in (presumably) a time-varying fashion to the parameter. Internally,
+the parameters themselves are actually altered; make sure you use the
+<I>reset yes</I> option if you want the parameters to be restored to their
+initial values after the run.
+</P>
+<P>If the <I>after</I> keyword is set to <I>yes</I>, then the parameters are
+changed one timestep after the multiple of N. In this manner, if a fix
+such as "fix ave/time" is used to calculate averages at every N
+timesteps, all the contributions to the average will be obtained with
+the same values of the parameters.
+</P>
+<HR>
+
+<P>The <I>pair</I> keyword enables various parameters of potentials defined by
+the <A HREF = "pair_style.html">pair_style</A> command to be changed, if the pair
+style supports it. Note that the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands must be used in the usual manner
+to specify these parameters initially; the fix adapt command simply
+overrides the parameters.
+</P>
+<P>The <I>pstyle</I> argument is the name of the pair style. If <A HREF = "pair_hybrid.html">pair_style
+hybrid or hybrid/overlay</A> is used, <I>pstyle</I> should be
+a sub-style name. For example, <I>pstyle</I> could be specified as "soft"
+or "lubricate". The <I>pparam</I> argument is the name of the parameter to
+change. This is the current list of pair styles and parameters that
+can be varied by this fix. See the doc pages for individual pair
+styles and their energy formulas for the meaning of these parameters:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD ><A HREF = "pair_born.html">born</A></TD><TD > a,b,c</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_buck.html">buck</A></TD><TD > a,c</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD > epsilon,sigma,delta</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD > mu</TD><TD > global</TD></TR>
+<TR><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD > a</TD><TD > type pairs</TD></TR>
+<TR><TD ><A HREF = "pair_soft.html">soft</A></TD><TD > a</TD><TD > type pairs
+</TD></TR></TABLE></DIV>
+
+<P>IMPORTANT NOTE: It is easy to add new potentials and their parameters
+to this list. All it typically takes is adding an extract() method to
+the pair_*.cpp file associated with the potential.
+</P>
+<P>Some parameters are global settings for the pair style, e.g. the
+viscosity setting "mu" for <A HREF = "pair_lubricate.html">pair_style lubricate</A>.
+Other parameters apply to atom type pairs within the pair style,
+e.g. the prefactor "a" for <A HREF = "pair_soft.html">pair_style soft</A>.
+</P>
+<P>Note that for many of the potentials, the parameter that can be varied
+is effectively a prefactor on the entire energy expression for the
+potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
+are exactly that, since the energy expression for the
+<A HREF = "pair_coul.html">coul/cut</A> potential (for example) has no labeled
+prefactor in its formula. To apply an effective prefactor to some
+potentials, multiple parameters need to be altered. For example, the
+<A HREF = "pair_buck.html">Buckingham potential</A> needs both the A and C terms
+altered together. To scale the Buckingham potential, you should thus
+list the pair style twice, once for A and once for C.
+</P>
+<P>If a type pair parameter is specified, the <I>I</I> and <I>J</I> settings should
+be specified to indicate which type pairs to apply it to. If a global
+parameter is specified, the <I>I</I> and <I>J</I> settings still need to be
+specified, but are ignored.
+</P>
+<P>Similar to the <A HREF = "pair_coeff.html">pair_coeff command</A>, I and J can be
+specified in one of two ways. Explicit numeric values can be used for
+each, as in the 1st example above. I <= J is required. LAMMPS sets
+the coefficients for the symmetric J,I interaction to the same values.
+</P>
+<P>A wild-card asterisk can be used in place of or in conjunction with
+the I,J arguments to set the coefficients for multiple pairs of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive). Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+</P>
+<P>IMPROTANT NOTE: If <A HREF = "pair_hybrid.html">pair_style hybrid or
+hybrid/overlay</A> is being used, then the <I>pstyle</I> will
+be a sub-style name. You must specify I,J arguments that correspond
+to type pair values defined (via the <A HREF = "pair_coeff.html">pair_coeff</A>
+command) for that sub-style.
+</P>
+<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this fix is invoked to set the parameter to a new value. It should be
+specified as v_name, where name is the variable name. Equal-style
+variables can specify formulas with various mathematical functions,
+and include <A HREF = "thermo_style.html">thermo_style</A> command keywords for the
+simulation box parameters and timestep and elapsed time. Thus it is
+easy to specify parameters that change as a function of time or span
+consecutive runs in a continuous fashion. For the latter, see the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command and the
+<I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style custom</A> for
+details.
+</P>
+<P>For example, these commands would change the prefactor coefficient of
+the <A HREF = "pair_soft.html">pair_style soft</A> potential from 10.0 to 30.0 in a
+linear fashion over the course of a simulation:
+</P>
+<PRE>variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</PRE>
+<HR>
+
+<P>The <I>kspace</I> keyword used the specified variable as a scale factor on
+the energy, forces, virial calculated by whatever K-Space solver is
+defined by the <A HREF = "kspace_style.html">kspace_style</A> command. If the
+variable has a value of 1.0, then the solver is unaltered.
+</P>
+<P>The <I>kspace</I> keyword works this way whether the <I>scale</I> keyword
+is set to <I>no</I> or <I>yes</I>.
+</P>
+<HR>
+
+<P>The <I>atom</I> keyword enables various atom properties to be changed. The
+<I>aparam</I> argument is the name of the parameter to change. This is the
+current list of atom parameters that can be varied by this fix:
+</P>
+<UL><LI>charge = charge on particle
+<LI>diameter = diameter of particle
+</UL>
+<P>The <I>I</I> argument indicates which atom types are affected. A wild-card
+asterisk can be used in place of or in conjunction with the I argument
+to set the coefficients for multiple atom types.
+</P>
+<P>The <I>v_name</I> argument of the <I>atom</I> keyword is the name of an
+<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
+this fix is invoked to set the parameter to a new value. It should be
+specified as v_name, where name is the variable name. See the
+discussion above describing the formulas associated with equal-style
+variables. The new value is assigned to the corresponding attribute
+for all atoms in the fix group.
+</P>
+<P>If the atom parameter is <I>diameter</I> and per-atom density and per-atom
+mass are defined for particles (e.g. <A HREF = "atom_style.html">atom_style
+granular</A>), then the mass of each particle is also
+changed when the diameter changes (density is assumed to stay
+constant).
+</P>
+<P>For example, these commands would shrink the diameter of all granular
+particles in the "center" group from 1.0 to 0.1 in a linear fashion
+over the course of a 1000-step simulation:
+</P>
+<PRE>variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter * v_size
+</PRE>
+<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix changes
+parameters on the outermost rRESPA level.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_fep.html">compute fep</A>, <A HREF = "fix_adapt.html">fix_adapt</A>, <A HREF = "compute_ti.html">compute
+ti</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are scale = no, reset = no, after = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_addforce.html b/doc/doc2/fix_addforce.html
new file mode 100644
index 000000000..e6ba94273
--- /dev/null
+++ b/doc/doc2/fix_addforce.html
@@ -0,0 +1,184 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix addforce command
+</H3>
+<H3>fix addforce/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID addforce fx fy fz keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>addforce = style name of this fix command
+
+<LI>fx,fy,fz = force component values (force units)
+
+<PRE> any of fx,fy,fz can be a variable (see below)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>every</I> or <I>region</I> or <I>energy</I>
+
+<PRE> <I>every</I> value = Nevery
+ Nevery = add force every this many timesteps
+ <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to have added force
+ <I>energy</I> value = v_name
+ v_name = variable with name that calculates the potential energy of each atom in the added force field
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix kick flow addforce 1.0 0.0 0.0
+fix kick flow addforce 1.0 0.0 v_oscillate
+fix ff boundary addforce 0.0 0.0 v_push energy v_espace
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add fx,fy,fz to the corresponding component of force for each atom in
+the group. This command can be used to give an additional push to
+atoms in a simulation, such as for a simulation of Poiseuille flow in
+a channel.
+</P>
+<P>Any of the 3 quantities defining the force components can be specified
+as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
+<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value(s) used to determine
+the force component.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent force field.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent force
+field with optional time-dependence as well.
+</P>
+<P>If the <I>every</I> keyword is used, the <I>Nevery</I> setting determines how
+often the forces are applied. The default value is 1, for every
+timestep.
+</P>
+<P>If the <I>region</I> keyword is used, the atom must also be in the
+specified geometric <A HREF = "region.html">region</A> in order to have force added
+to it.
+</P>
+<HR>
+
+<P>Adding a force to atoms implies a change in their potential energy as
+they move due to the applied force field. For dynamics via the "run"
+command, this energy can be optionally added to the system's potential
+energy for thermodynamic output (see below). For energy minimization
+via the "minimize" command, this energy must be added to the system's
+potential energy to formulate a self-consistent minimization problem
+(see below).
+</P>
+<P>The <I>energy</I> keyword is not allowed if the added force is a constant
+vector F = (fx,fy,fz), with all components defined as numeric
+constants and not as variables. This is because LAMMPS can compute
+the energy for each atom directly as E = -x dot F = -(x*fx + y*fy +
+z*fz), so that -Grad(E) = F.
+</P>
+<P>The <I>energy</I> keyword is optional if the added force is defined with
+one or more variables, and if you are performing dynamics via the
+<A HREF = "run.html">run</A> command. If the keyword is not used, LAMMPS will set
+the energy to 0.0, which is typically fine for dynamics.
+</P>
+<P>The <I>energy</I> keyword is required if the added force is defined with
+one or more variables, and you are performing energy minimization via
+the "minimize" command. The keyword specifies the name of an
+atom-style <A HREF = "variable.html">variable</A> which is used to compute the
+energy of each atom as function of its position. Like variables used
+for <I>fx</I>, <I>fy</I>, <I>fz</I>, the energy variable is specified as v_name,
+where name is the variable name.
+</P>
+<P>Note that when the <I>energy</I> keyword is used during an energy
+minimization, you must insure that the formula defined for the
+atom-style <A HREF = "variable.html">variable</A> is consistent with the force
+variable formulas, i.e. that -Grad(E) = F. For example, if the force
+were a spring-like F = kx, then the energy formula should be E =
+-0.5kx^2. If you don't do this correctly, the minimization will not
+converge properly.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential "energy" inferred by the added force to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. This is a fictitious quantity but is
+needed so that the <A HREF = "minimize.html">minimize</A> command can include the
+forces added by this fix in a consistent manner. I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added force.
+</P>
+<P>This fix computes a global scalar and a global 3-vector of forces,
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar is the potential
+energy discussed above. The vector is the total force on the group of
+atoms before the forces on individual atoms are changed by the fix.
+The scalar and vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+</P>
+<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
+with the added forces to be included in the total potential energy of
+the system (the quantity being minimized), you MUST enable the
+<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_setforce.html">fix setforce</A>, <A HREF = "fix_aveforce.html">fix aveforce</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default for the every keyword is every = 1.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_addtorque.html b/doc/doc2/fix_addtorque.html
new file mode 100644
index 000000000..a9a521e3b
--- /dev/null
+++ b/doc/doc2/fix_addtorque.html
@@ -0,0 +1,102 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix addtorque command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID addtorque Tx Ty Tz
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>addtorque = style name of this fix command
+
+<LI>Tx,Ty,Tz = torque component values (torque units)
+
+<LI>any of Tx,Ty,Tz can be a variable (see below)
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix kick bead addtorque 2.0 3.0 5.0
+fix kick bead addtorque 0.0 0.0 v_oscillate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add a set of forces to each atom in
+the group such that:
+</P>
+<UL><LI>the components of the total torque applied on the group (around its
+center of mass) are Tx,Ty,Tz
+
+<LI>the group would move as a rigid body in the absence of other
+forces.
+</UL>
+<P>This command can be used to drive a group of atoms into rotation.
+</P>
+<P>Any of the 3 quantities defining the torque components can be specified
+as an equal-style <A HREF = "variable.html">variable</A>, namely <I>Tx</I>,
+<I>Ty</I>, <I>Tz</I>. If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+torque component.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent torque.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential "energy" inferred by the added forces to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. This is a fictitious quantity but is
+needed so that the <A HREF = "minimize.html">minimize</A> command can include the
+forces added by this fix in a consistent manner. I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added forces.
+</P>
+<P>This fix computes a global scalar and a global 3-vector, which can be
+accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+The scalar is the potential energy discussed above. The vector is the
+total torque on the group of atoms before the forces on individual
+atoms are changed by the fix. The scalar and vector values calculated
+by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_addforce.html">fix addforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_append_atoms.html b/doc/doc2/fix_append_atoms.html
new file mode 100644
index 000000000..f2df05674
--- /dev/null
+++ b/doc/doc2/fix_append_atoms.html
@@ -0,0 +1,123 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix append/atoms command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID append/atoms face ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>append/atoms = style name of this fix command
+
+<LI>face = <I>zhi</I>
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>basis</I> or <I>size</I> or <I>freq</I> or <I>temp</I> or <I>random</I> or <I>units</I>
+
+<PRE> <I>basis</I> values = M itype
+ M = which basis atom
+ itype = atom type (1-N) to assign to this basis atom
+ <I>size</I> args = Lz
+ Lz = z size of lattice region appended in a single event(distance units)
+ <I>freq</I> args = freq
+ freq = the number of timesteps between append events
+ <I>temp</I> args = target damp seed extent
+ target = target temperature for the region between zhi-extent and zhi (temperature units)
+ damp = damping parameter (time units)
+ seed = random number seed for langevin kicks
+ extent = extent of thermostated region (distance units)
+ <I>random</I> args = xmax ymax zmax seed
+ <I>xmax</I>, <I>ymax</I>, <I>zmax</I> = maximum displacement in particular direction (distance units)
+ <I>seed</I> = random number seed for random displacement
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the wall position is defined in lattice units
+ <I>box</I> = the wall position is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all append/atoms zhi size 5.0 freq 295 units lattice
+fix 4 all append/atoms zhi size 15.0 freq 5 units box
+fix A all append/atoms zhi size 1.0 freq 1000 units lattice
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix creates atoms on a lattice, appended on the zhi edge of the
+system box. This can be useful when a shock or wave is propagating
+from zlo. This allows the system to grow with time to accommodate an
+expanding wave. A simulation box must already exist, which is
+typically created via the <A HREF = "create_box.html">create_box</A> command.
+Before using this command, a lattice must also be defined using the
+<A HREF = "lattice.html">lattice</A> command.
+</P>
+<P>This fix will automatically freeze atoms on the zhi edge of the
+system, so that overlaps are avoided when new atoms are appended.
+</P>
+<P>The <I>basis</I> keyword specifies an atom type that will be assigned to
+specific basis atoms as they are created. See the
+<A HREF = "lattice.html">lattice</A> command for specifics on how basis atoms are
+defined for the unit cell of the lattice. By default, all created
+atoms are assigned type = 1 unless this keyword specifies differently.
+</P>
+<P>The <I>size</I> keyword defines the size in z of the chunk of material to
+be added.
+</P>
+<P>The <I>random</I> keyword will give the atoms random displacements around
+their lattice points to simulate some initial temperature.
+</P>
+<P>The <I>temp</I> keyword will cause a region to be thermostated with a
+Langevin thermostat on the zhi boundary. The size of the region is
+measured from zhi and is set with the <I>extent</I> argument.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the SHOCK package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The boundary on which atoms are added with append/atoms must be
+shrink/minimum. The opposite boundary may be any boundary type other
+than periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall_piston.html">fix wall/piston</A> command
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are size = 0.0, freq = 0, units = lattice. All
+added atoms are of type 1 unless the basis keyword is used.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_atc.html b/doc/doc2/fix_atc.html
new file mode 100644
index 000000000..86db40087
--- /dev/null
+++ b/doc/doc2/fix_atc.html
@@ -0,0 +1,258 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix atc command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix <fixID> <group> atc <type> <parameter_file>
+</PRE>
+<LI>fixID = name of fix
+
+<LI>group = name of group fix is to be applied
+
+<LI>type = <I>thermal</I> or <I>two_temperature</I> or <I>hardy</I> or <I>field</I>
+
+<PRE> <I>thermal</I> = thermal coupling with fields: temperature
+ <I>two_temperature</I> = electron-phonon coupling with field: temperature and electron_temperature
+ <I>hardy</I> = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
+ <I>field</I> = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
+</PRE>
+<LI>parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix AtC internal atc thermal Ar_thermal.dat
+fix AtC internal atc two_temperature Ar_ttm.mat
+fix AtC internal atc hardy
+fix AtC internal atc field
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+</P>
+<CENTER><IMG SRC = "JPG/atc_nanotube.jpg">
+</CENTER>
+<PRE>The following coupling example is typical, but non-exhaustive:
+ # ... commands to create and initialize the MD system
+</PRE>
+<PRE> # initial fix to designate coupling type and group to apply it to
+ # tag group physics material_file
+ fix AtC internal atc thermal Ar_thermal.mat
+</PRE>
+<PRE> # create a uniform 12 x 2 x 2 mesh that covers region contain the group
+ # nx ny nz region periodicity
+ fix_modify AtC mesh create 12 2 2 mdRegion f p p
+</PRE>
+<PRE> # specify the control method for the type of coupling
+ # physics control_type
+ fix_modify AtC thermal control flux
+</PRE>
+<PRE> # specify the initial values for the empirical field "temperature"
+ # field node_group value
+ fix_modify AtC initial temperature all 30
+</PRE>
+<PRE> # create an output stream for nodal fields
+ # filename output_frequency
+ fix_modify AtC output atc_fe_output 100
+</PRE>
+<PRE> run 1000
+</PRE>
+<P>likewise for this post-processing example:
+</P>
+<PRE> # ... commands to create and initialize the MD system
+</PRE>
+<PRE> # initial fix to designate post-processing and the group to apply it to
+ # no material file is allowed nor required
+ fix AtC internal atc hardy
+</PRE>
+<PRE> # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
+ fix AtC kernel quartic_sphere 10.0
+</PRE>
+<PRE> # create a uniform 1 x 1 x 1 mesh that covers region contain the group
+ # with periodicity this effectively creats a system average
+ fix_modify AtC mesh create 1 1 1 box p p p
+</PRE>
+<PRE> # change from default lagrangian map to eulerian
+ # refreshed every 100 steps
+ fix_modify AtC atom_element_map eulerian 100
+</PRE>
+<PRE> # start with no field defined
+ # add mass density, potential energy density, stress and temperature
+ fix_modify AtC fields add density energy stress temperature
+</PRE>
+<PRE> # create an output stream for nodal fields
+ # filename output_frequency
+ fix_modify AtC output nvtFE 100 text
+</PRE>
+<PRE> run 1000
+</PRE>
+<P>the mesh's linear interpolation functions can be used as the localization function
+ by using the field option:
+</P>
+<P> fix AtC internal atc field
+</P>
+<P> fix_modify AtC mesh create 1 1 1 box p p p
+</P>
+<P> ...
+</P>
+<P>Note coupling and post-processing can be combined in the same simulations using separate fixes.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart files</A>. The <A HREF = "fix_modify.html">fix_modify</A> options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No parameter of this fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
+</P>
+<UL><LI>Currently,
+<LI>- the coupling is restricted to thermal physics
+<LI>- the FE computations are done in serial on each processor.
+</UL>
+<P><B>Related commands:</B>
+</P>
+<P>After specifying this fix in your input script, several other <A HREF = "fix_modify.html">fix_modify</A> commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+</P>
+<P>fix_modify commands for setup:
+</P>
+<UL><LI><A HREF = "USER/atc/man_mesh_create.html">fix_modify AtC mesh create</A>
+<LI><A HREF = "USER/atc/man_mesh_quadrature.html">fix_modify AtC mesh quadrature</A>
+<LI><A HREF = "USER/atc/man_mesh_read.html">fix_modify AtC mesh read</A>
+<LI><A HREF = "USER/atc/man_mesh_write.html">fix_modify AtC mesh write</A>
+<LI><A HREF = "USER/atc/man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</A>
+<LI><A HREF = "USER/atc/man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</A>
+<LI><A HREF = "USER/atc/man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</A>
+<LI><A HREF = "USER/atc/man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</A>
+<LI><A HREF = "USER/atc/man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</A>
+<LI><A HREF = "USER/atc/man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</A>
+<LI><A HREF = "USER/atc/man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</A>
+<LI><A HREF = "USER/atc/man_boundary.html">fix_modify AtC boundary</A>
+<LI><A HREF = "USER/atc/man_internal_quadrature.html">fix_modify AtC internal_quadrature</A>
+<LI><A HREF = "USER/atc/man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</A>
+<LI><A HREF = "USER/atc/man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</A>
+<LI><A HREF = "USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</A>
+<LI><A HREF = "USER/atc/man_internal_element_set.html">fix_modify AtC internal_element_set</A>
+<LI><A HREF = "USER/atc/man_decomposition.html">fix_modify AtC decomposition</A>
+</UL>
+<P>fix_modify commands for boundary and initial conditions:
+</P>
+<UL><LI><A HREF = "USER/atc/man_initial.html">fix_modify AtC initial</A>
+<LI><A HREF = "USER/atc/man_fix_nodes.html">fix_modify AtC fix</A>
+<LI><A HREF = "USER/atc/man_unfix_nodes.html">fix_modify AtC unfix</A>
+<LI><A HREF = "USER/atc/man_fix_flux.html">fix_modify AtC fix_flux</A>
+<LI><A HREF = "USER/atc/man_unfix_flux.html">fix_modify AtC unfix_flux</A>
+<LI><A HREF = "USER/atc/man_source.html">fix_modify AtC source</A>
+<LI><A HREF = "USER/atc/man_remove_source.html">fix_modify AtC remove_source</A>
+</UL>
+<P>fix_modify commands for control and filtering:
+</P>
+<UL><LI><A HREF = "USER/atc/man_control.html">fix_modify AtC control</A>
+<LI><A HREF = "USER/atc/man_control_thermal.html">fix_modify AtC control thermal</A>
+<LI><A HREF = "USER/atc/man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</A>
+<LI><A HREF = "USER/atc/man_control_momentum.html">fix_modify AtC control momentum</A>
+<LI><A HREF = "USER/atc/man_localized_lambda.html">fix_modify AtC control localized_lambda</A>
+<LI><A HREF = "USER/atc/man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</A>
+<LI><A HREF = "USER/atc/man_mask_direction.html">fix_modify AtC control mask_direction</A> control
+<LI><A HREF = "USER/atc/man_time_filter.html">fix_modify AtC filter</A>
+<LI><A HREF = "USER/atc/man_filter_scale.html">fix_modify AtC filter scale</A>
+<LI><A HREF = "USER/atc/man_filter_type.html">fix_modify AtC filter type</A>
+<LI><A HREF = "USER/atc/man_equilibrium_start.html">fix_modify AtC equilibrium_start</A>
+<LI><A HREF = "USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</A>
+<LI><A HREF = "USER/atc/man_poisson_solver.html">fix_modify AtC poisson_solver</A>
+</UL>
+<P>fix_modify commands for output:
+</P>
+<UL><LI><A HREF = "USER/atc/man_output.html">fix_modify AtC output</A>
+<LI><A HREF = "USER/atc/man_output_nodeset.html">fix_modify AtC output nodeset</A>
+<LI><A HREF = "USER/atc/man_output_elementset.html">fix_modify AtC output elementset</A>
+<LI><A HREF = "USER/atc/man_boundary_integral.html">fix_modify AtC output boundary_integral</A>
+<LI><A HREF = "USER/atc/man_contour_integral.html">fix_modify AtC output contour_integral</A>
+<LI><A HREF = "USER/atc/man_mesh_output.html">fix_modify AtC mesh output</A>
+<LI><A HREF = "USER/atc/man_write_restart.html">fix_modify AtC write_restart</A>
+<LI><A HREF = "USER/atc/man_read_restart.html">fix_modify AtC read_restart</A>
+</UL>
+<P>fix_modify commands for post-processing:
+</P>
+<UL><LI><A HREF = "USER/atc/man_hardy_kernel.html">fix_modify AtC kernel</A>
+<LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC fields</A>
+<LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC grdients</A>
+<LI><A HREF = "USER/atc/man_hardy_rates.html">fix_modify AtC rates</A>
+<LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC computes</A>
+<LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</A>
+<LI><A HREF = "USER/atc/man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</A>
+<LI><A HREF = "USER/atc/man_sample_frequency.html">fix_modify AtC sample_frequency</A>
+<LI><A HREF = "USER/atc/man_set.html">fix_modify AtC set</A>
+</UL>
+<P>miscellaneous fix_modify commands:
+</P>
+<UL><LI><A HREF = "USER/atc/man_atom_element_map.html">fix_modify AtC atom_element_map</A>
+<LI><A HREF = "USER/atc/man_atom_weight.html">fix_modify AtC atom_weight</A>
+<LI><A HREF = "USER/atc/man_write_atom_weights.html">fix_modify AtC write_atom_weights</A>
+<LI><A HREF = "USER/atc/man_reset_time.html">fix_modify AtC reset_time</A>
+<LI><A HREF = "USER/atc/man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</A>
+<LI><A HREF = "USER/atc/man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</A>
+<LI><A HREF = "USER/atc/man_boundary_faceset.html">fix_modify AtC boundary_faceset</A>
+<LI><A HREF = "USER/atc/man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</A>
+<LI><A HREF = "USER/atc/man_mass_matrix.html">fix_modify AtC mass_matrix</A>
+<LI><A HREF = "USER/atc/man_material.html">fix_modify AtC material</A>
+<LI><A HREF = "USER/atc/man_atomic_charge.html">fix_modify AtC atomic_charge</A>
+<LI><A HREF = "USER/atc/man_source_integration.html">fix_modify AtC source_integration</A>
+<LI><A HREF = "USER/atc/man_temperature_definition.html">fix_modify AtC temperature_definition</A>
+<LI><A HREF = "USER/atc/man_track_displacement.html">fix_modify AtC track_displacement</A>
+<LI><A HREF = "USER/atc/man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</A>
+<LI><A HREF = "USER/atc/man_add_species.html">fix_modify AtC add_species</A>
+<LI><A HREF = "USER/atc/man_add_molecule.html">fix_modify AtC add_molecule</A>
+<LI><A HREF = "USER/atc/man_remove_species.html">fix_modify AtC remove_species</A>
+<LI><A HREF = "USER/atc/man_remove_molecule.html">fix_modify AtC remove_molecule</A>
+</UL>
+<P>Note: a set of example input files with the attendant material files are included with this package
+</P>
+<P><B>Default:</B>
+None
+</P>
+<HR>
+
+<P>For detailed exposition of the theory and algorithms please see:
+</P>
+<A NAME = "Wagner"></A>
+
+<P><B>(Wagner)</B> Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
+</P>
+<A NAME = "Zimmeman2004"></A>
+
+<P><B>(Zimmerman2004)</B> Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
+</P>
+<A NAME = "Zimmerman2010"></A>
+
+<P><B>(Zimmerman2010)</B> Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
+</P>
+<A NAME = "Templeton2010"></A>
+
+<P><B>(Templeton2010)</B> Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
+</P>
+<A NAME = "Jones"></A>
+
+<P><B>(Jones)</B> Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
+</P>
+<A NAME = "Templeton2011"></A>
+
+<P><B>(Templeton2011)</B> Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
+</P>
+<A NAME = "Mandadapu"></A>
+
+<P><B>(Mandadapu)</B> Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
+</P>
+<P>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_atom_swap.html b/doc/doc2/fix_atom_swap.html
new file mode 100644
index 000000000..739845a39
--- /dev/null
+++ b/doc/doc2/fix_atom_swap.html
@@ -0,0 +1,199 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix atom/swap command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID atom/swap N X seed T keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>atom/swap = style name of this fix command
+
+<LI>N = invoke this fix every N steps
+
+<LI>X = number of swaps to attempt every N steps
+
+<LI>seed = random # seed (positive integer)
+
+<LI>T = scaling temperature of the MC swaps (temperature units)
+
+<LI>one or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>types</I> or <I>delta_mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
+
+<PRE> <I>types</I> values = two or more atom types
+ <I>delta_mu</I> values = number_of_types-1 relative chemical potentials (energy units)
+ <I>ke</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = no conservation of kinetic energy after atom swaps
+ <I>yes</I> = kinetic energy is conserved after atom swaps
+ <I>semi-grand</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = particle type counts and fractions conserved
+ <I>yes</I> = semi-grand canonical ensemble, particle fractions not conserved
+ <I>region</I> value = region-ID
+ region-ID = ID of region to use as an exchange/move volume
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
+fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
+fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix performs Monte Carlo swaps of atoms of one given atom type
+with atoms of the other given atom types. The specified T is used in
+the Metropolis criterion dictating swap probabilities.
+</P>
+<P>Perform X swaps of atoms of one type with atoms of another type
+according to a Monte Carlo probability. Swap candidates must be in the
+fix group, must be in the region (if specified), and must be of one of
+the listed types. Swaps are attempted between candidates that are
+chosen randomly with equal probability among the candidate
+atoms. Swaps are not attempted between atoms of the same type since
+nothing would happen.
+</P>
+<P>All atoms in the simulation domain can be moved using regular time
+integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
+in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
+be needed when running such a hybrid simulation, especially if the
+swapped atoms are not well equilibrated.
+</P>
+<P>The <I>types</I> keyword is required. At least two atom types must be
+specified.
+</P>
+<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
+conservation for swaps. The default is <I>yes</I>, which means that swapped
+atoms have their velocities scaled by the ratio of the masses of the
+swapped atom types. This ensures that the kinetic energy of each atom
+is the same after the swap as it was before the swap, even though the
+atom masses have changed.
+</P>
+<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
+semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
+means that the total number of each particle type does not need to be
+conserved. The default is <I>no</I>, which means that the only kind of swap
+allowed exchanges an atom of one type with an atom of a different
+given type. In other words, the relative mole fractions of the swapped
+atoms remains constant. Whereas in the semi-grand canonical ensemble,
+the composition of the system can change. Note that when using
+<I>semi-grand</I>, all atoms in the fix group are eligible for attempted
+conversion to one of the given types, even if its current type is not
+one of the given types. An attempt is made to switch the selected atom
+to one of the listed <I>types</I> with equal probability. Acceptance of
+each attempt depends upon the Metropolis criterion.
+</P>
+<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical
+potentials for each of the atom types. All chemical potentials are
+relative to the first atom type, so no value is given for the first
+atom type. These parameters are useful for semi-grand canonical
+ensemble simulations where it may be desirable to actively control the
+composition of the system. When given, there must be ntypes-1 values
+given, where ntypes is the number of atom types in the simulated
+system. Note that a value for delta_mu is required for all atom types
+when using <I>semi-grand</I>, even for atom types not listed following the
+<I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
+possible that any of the atom types in the system could be part of the
+fix group and therefore are eligible for swapping to one of the listed
+atom types.
+</P>
+<P>This command may optionally use the <I>region</I> keyword to define swap
+volume. The specified region must have been previously defined with a
+<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
+Swap attempts occur only between atoms that are both within the
+specified region. Swaps are not otherwise attempted.
+</P>
+<P>You should ensure you do not swap atoms belonging to a molecule, or
+LAMMPS will soon generate an error when it tries to find those atoms.
+LAMMPS will warn you if any of the atoms eligible for swapping have a
+non-zero molecule ID, but does not check for this at the time of
+swapping.
+</P>
+<P>This fix checks to ensure all atoms of the given types have the same
+atomic charge. LAMMPS doesn't enforce this in general, but it is
+needed for this fix to simplify the swapping procedure. Successful
+swaps will swap the atom type and charge of the swapped atoms.
+</P>
+<P>Since this fix computes total potential energies before and after
+proposed swaps, so even complicated potential energy calculations are
+OK, including the following:
+</P>
+<UL><LI> long-range electrostatics (kspace)
+<LI> many body pair styles
+<LI> hybrid pair styles
+<LI> eam pair styles
+<LI> triclinic systems
+<LI> need to include potential energy contributions from other fixes
+</UL>
+<P>Some fixes have an associated potential energy. Examples of such fixes
+include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
+<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
+<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
+<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC moves),
+you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
+that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
+specify if this should be done.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
+files</A>. This includes information about the random
+number generator seed, the next timestep for MC exchanges, etc. See
+the <A HREF = "read_restart.html">read_restart</A> command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>This fix computes a global vector of length 2, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
+values are the following global cumulative quantities:
+</P>
+<UL><LI>1 = swap attempts
+<LI>2 = swap successes
+</UL>
+<P>The vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
+<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
+<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "fix_gcmc.html">fix_gcmc</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are ke = yes, semi-grand = no, delta_mu = 0.0 for
+all atom types.
+</P>
+<HR>
+
+<A NAME = "Sadigh"></A>
+
+<P><B>(Sadigh)</B> B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
+L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_atom.html b/doc/doc2/fix_ave_atom.html
new file mode 100644
index 000000000..f80025c8f
--- /dev/null
+++ b/doc/doc2/fix_ave_atom.html
@@ -0,0 +1,165 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/atom = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+one or more input values can be listed
+
+<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
+
+<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/atom 1 100 100 vx vy vz
+fix 1 all ave/atom 10 20 1000 c_my_stress[1]
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more per-atom vectors as inputs every few timesteps, and
+average them atom by atom over longer timescales. The resulting
+per-atom averages can be used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> such as the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> or <A HREF = "dump.html">dump custom</A> commands.
+</P>
+<P>The group specified with the command means only atoms within the group
+have their averages computed. Results are set to 0.0 for atoms not in
+the group.
+</P>
+<P>Each input value can be an atom attribute (position, velocity, force
+component) or can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an atom-style
+<A HREF = "variable.html">variable</A>. In the latter cases, the compute, fix, or
+variable must produce a per-atom vector, not a global quantity or
+local quantity. If you wish to time-average global quantities from a
+compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce per-atom vectors or arrays are
+those which have the word <I>atom</I> in their style name. See the doc
+pages for individual <A HREF = "fix.html">fixes</A> to determine which ones produce
+per-atom vectors or arrays. <A HREF = "variable.html">Variables</A> of style <I>atom</I>
+are the only ones that can be used with this fix since they produce
+per-atom vectors.
+</P>
+<P>Each per-atom value of each input vector is averaged independently.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average. The final averaged quantities are generated on timesteps
+that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.
+</P>
+<HR>
+
+<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory. Note that other atom attributes can be used as
+inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>IMPORTANT NOTE: The x,y,z attributes are values that are re-wrapped
+inside the periodic box whenever an atom crosses a periodic boundary.
+Thus if you time average an atom that spends half its time on either
+side of the periodic box, you will get a value in the middle of the
+box. If this is not what you want, consider averaging unwrapped
+coordinates, which can be provided by the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command via its xu,yu,zu
+attributes.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the per-atom vector calculated by the compute is used. If a
+bracketed term containing an index I is appended, the Ith column of
+the per-atom array calculated by the compute is used. Users can also
+write code for their own compute styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the per-atom vector calculated by the fix is used. If a
+bracketed term containing an index I is appended, the Ith column of
+the per-atom array calculated by the fix is used. Note that some
+fixes only produce their values on certain timesteps, which must be
+compatible with <I>Nevery</I>, else an error will result. Users can also
+write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script as an <A HREF = "variable.html">atom-style
+variable</A> Variables of style <I>atom</I> can reference
+thermodynamic keywords, or invoke other computes, fixes, or variables
+when they are evaluated, so this is a very general means of generating
+per-atom quantities to time average.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global scalar or vector quantities are
+stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>.
+</P>
+<P>This fix produces a per-atom vector or array which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. A vector is
+produced if only a single quantity is averaged by this fix. If two or
+more quantities are averaged, then an array of values is produced.
+The per-atom values can only be accessed on timesteps that are
+multiples of <I>Nfreq</I> since that is when averaging is performed.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "variable.html">variable</A>,
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_chunk.html b/doc/doc2/fix_ave_chunk.html
new file mode 100644
index 000000000..a1c1a9dc2
--- /dev/null
+++ b/doc/doc2/fix_ave_chunk.html
@@ -0,0 +1,457 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/chunk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/chunk = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+
+<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
+
+<LI>one or more input values can be listed
+
+<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+
+<PRE> vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+ density/number, density/mass = number or mass density
+ temp = temperature
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>norm</I> or <I>ave</I> or <I>bias</I> or <I>adof</I> or <I>cdof</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>norm</I> arg = <I>all</I> or <I>sample</I> or <I>none</I> = how output on <I>Nfreq</I> steps is normalized
+ all = output is sum of atoms across all <I>Nrepeat</I> samples, divided by atom count
+ sample = output is sum of <I>Nrepeat</I> sample averages, divided by <I>Nrepeat</I>
+ none = output is sum of <I>Nrepeat</I> sums, divided by <I>Nrepeat</I>
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+ one = output new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>bias</I> arg = bias-ID
+ bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
+ <I>adof</I> value = dof_per_atom
+ dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
+ <I>cdof</I> value = dof_per_chunk
+ dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
+ <I>file</I> arg = filename
+ filename = file to write results to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
+fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+</PRE>
+<P><B>IMPORTANT NOTE:</B>
+</P>
+<P>If you are trying to replace an older fix ave/spatial command with the
+newer, more flexible fix ave/chunk and <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> commands, you simply need to split
+the fix ave/spatial arguments across the two new commands. For
+example, this command:
+</P>
+<PRE>fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
+</PRE>
+<P>could be replaced by:
+</P>
+<PRE>compute cc1 flow chunk/atom bin/1d y 0.0 1.0
+fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more per-atom vectors as inputs every few timesteps, sum
+the values over the atoms in each chunk at each timestep, then average
+the per-chunk values over longer timescales. The resulting chunk
+averages can be used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> such as <A HREF = "thermo_style.html">thermo_style
+custom</A>, and can also be written to a file.
+</P>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
+23</A> for details of how chunks can be
+defined and examples of how they can be used to measure properties of
+a system.
+</P>
+<P>Note that only atoms in the specified group contribute to the summing
+and averaging calculations. The <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command defines its own group as
+well as an optional region. Atoms will have a chunk ID = 0, meaning
+they belong to no chunk, if they are not in that group or region.
+Thus you can specify the "all" group for this command if you simply
+want to use the chunk definitions provided by chunkID.
+</P>
+<P>Each specified per-atom value can be an atom attribute (position,
+velocity, force component), a mass or number density, or the result of
+a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
+atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
+compute, fix, or variable must produce a per-atom quantity, not a
+global quantity. Note that the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command provides access to
+any attribute defined and stored by atoms. If you wish to
+time-average global quantities from a compute, fix, or variable, then
+see the <A HREF = "fix_ave_time.html">fix ave/time</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
+which have the word <I>atom</I> in their style name. See the doc pages for
+individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
+quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
+ones that can be used with this fix since all other styles of variable
+produce global quantities.
+</P>
+<P>The per-atom values of each input vector are summed and averaged
+independently of the per-atom values in other input vectors.
+</P>
+<P>IMPORTANT NOTE: This fix works by creating an array of size <I>Nchunk</I>
+by Nvalues on each processor. <I>Nchunk</I> is the number of chunks which
+is defined by the <A HREF = "doc/compute_chunk_atom.html">compute chunk/atom</A>
+command. Nvalues is the number of input values specified. Each
+processor loops over its atoms, tallying its values to the appropriate
+chunk. Then the entire array is summed across all processors. This
+means that using a large number of chunks will incur an overhead in
+memory and computational cost (summing across processors), so be
+careful to define a reasonable number of chunks.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be accessed and contribute to the
+average. The final averaged quantities are generated on timesteps
+that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+</P>
+<P>Each input value can also be averaged over the atoms in each chunk.
+The way the averaging is done across the <I>Nrepeat</I> timesteps to
+produce output on the <I>Nfreq</I> timesteps, and across multiple <I>Nfreq</I>
+outputs, is determined by the <I>norm</I> and <I>ave</I> keyword settings, as
+discussed below.
+</P>
+<P>IMPORTANT NOTE: To perform per-chunk averaging within a <I>Nfreq</I> time
+window, the number of chunks <I>Nchunk</I> defined by the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command must remain constant. If
+the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then <I>Nchunk</I> must
+remain constant for the duration of the simulation. This fix forces
+the chunk/atom compute specified by chunkID to hold <I>Nchunk</I> constant
+for the appropriate time windows, by not allowing it to re-calcualte
+<I>Nchunk</I>, which can also affect how it assigns chunk IDs to atoms.
+More details are given on the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> doc page.
+</P>
+<HR>
+
+<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
+As noted above, any other atom attributes can be used as input values
+to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>The <I>density/number</I> value means the number density is computed for
+each chunk, i.e. number/volume. The <I>density/mass</I> value means the
+mass density is computed for each chunk, i.e. total-mass/volume. The
+output values are in units of 1/volume or density (mass/volume). See
+the <A HREF = "units.html">units</A> command doc page for the definition of density
+for each choice of units, e.g. gram/cm^3. If the chunks defined by
+the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command are spatial
+bins, the volume is the bin volume. Otherwise it is the volume of the
+entire simulation box.
+</P>
+<P>The <I>temp</I> value means the temperature is computed for each chunk, by
+the formula KE = DOF/2 k T, where KE = total kinetic energy of the
+chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees
+of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
+temperature.
+</P>
+<P>The DOF is calculated as N*adof + cdof, where N = number of atoms in
+the chunk, adof = degrees of freedom per atom, and cdof = degrees of
+freedom per chunk. By default adof = 2 or 3 = dimensionality of
+system, as set via the <A HREF = "dimension.html">dimension</A> command, and cdof =
+0.0. This gives the usual formula for temperature.
+</P>
+<P>Note that currently this temperature only includes translational
+degrees of freedom for each atom. No rotational degrees of freedom
+are included for finite-size particles. Also no degrees of freedom
+are subtracted for any velocity bias or constraints that are applied,
+such as <A HREF = "compute_temp_partial.html">compute temp/partial</A>, or <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
+those degrees of freedom (e.g. a constrained bond) could apply to sets
+of atoms that are both included and excluded from a specific chunk,
+and hence the concept is somewhat ill-defined. In some cases, you can
+use the <I>adof</I> and <I>cdof</I> keywords to adjust the calculated degress of
+freedom appropriately, as explained below.
+</P>
+<P>Also note that a bias can be subtracted from atom velocities before
+they are used in the above formula for KE, by using the <I>bias</I>
+keyword. This allows, for example, a thermal temperature to be
+computed after removal of a flow velocity profile.
+</P>
+<P>Note that the per-chunk temperature calculated by this fix and the
+<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command can be different.
+The compute calculates the temperature for each chunk for a single
+snapshot. This fix can do that but can also time average those values
+over many snapshots, or it can compute a temperature as if the atoms
+in the chunk on different timesteps were collected together as one set
+of atoms to calculate their temperature. The compute allows the
+center-of-mass velocity of each chunk to be subtracted before
+calculating the temperature; this fix does not.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used. Users can also write code for
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used. Note that some fixes only produce
+their values on certain timesteps, which must be compatible with
+<I>Nevery</I>, else an error results. Users can also write code for their
+own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Variables of style
+<I>atom</I> can reference thermodynamic keywords and various per-atom
+attributes, or invoke other computes, fixes, or variables when they
+are evaluated, so this is a very general means of generating per-atom
+quantities to average within chunks.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix
+and its outputs.
+</P>
+<P>The <I>norm</I> keyword affects how averaging is done for the per-chunk
+values that are output every <I>Nfreq</I> timesteps.
+</P>
+<P>It the <I>norm</I> setting is <I>all</I>, which is the default, a chunk value is
+summed over all atoms in all <I>Nrepeat</I> samples, as is the count of
+atoms in the chunk. The averaged output value for the chunk on the
+<I>Nfreq</I> timesteps is Total-sum / Total-count. In other words it is an
+average over atoms across the entire <I>Nfreq</I> timescale.
+</P>
+<P>If the <I>norm</I> setting is <I>sample</I>, the chunk value is summed over atoms
+for each sample, as is the count, and an "average sample value" is
+computed for each sample, i.e. Sample-sum / Sample-count. The outuput
+value for the chunk on the <I>Nfreq</I> timesteps is the average of the
+<I>Nrepeat</I> "average sample values", i.e. the sum of <I>Nrepeat</I> "average
+sample values" divided by <I>Nrepeat</I>. In other words it is an average
+of an average.
+</P>
+<P>If the <I>norm</I> setting is <I>none</I>, a similar computation as for the
+<I>sample</I> seting is done, except the individual "average sample values"
+are "summed sample values". A summed sample value is simply the chunk
+value summed over atoms in the sample, without dividing by the number
+of atoms in the sample. The outuput value for the chunk on the
+<I>Nfreq</I> timesteps is the average of the <I>Nrepeat</I> "summed sample
+values", i.e. the sum of <I>Nrepeat</I> "summed sample values" divided by
+<I>Nrepeat</I>.
+</P>
+<P>The <I>ave</I> keyword determines how the per-chunk values produced every
+<I>Nfreq</I> steps are averaged with values produced on previous steps that
+were multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, which is the default, then the chunk
+values produced on timesteps that are multiples of <I>Nfreq</I> are
+independent of each other; they are output as-is without further
+averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the chunk values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cumulative sense before being output. Each output chunk value is thus
+the average of the chunk value produced on that timestep with all
+preceding values for the same chunk. This running average begins when
+the fix is defined; it can only be restarted by deleting the fix via
+the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
+re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the chunk values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values for the same
+chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
+then the output on step 10000 will be the average of the individual
+chunk values on steps 8000,9000,10000. Outputs on early steps will
+average over less than M values if they are not available.
+</P>
+<P>The <I>bias</I> keyword specifies the ID of a temperature compute that
+removes a "bias" velocity from each atom, specified as <I>bias-ID</I>. It
+is only used when the <I>temp</I> value is calculated, to compute the
+thermal temperature of each chunk after the translational kinetic
+energy components have been altered in a prescribed way, e.g. to
+remove a flow velocity profile. See the doc pages for individual
+computes that calculate a temperature to see which ones implement a
+bias.
+</P>
+<P>The <I>adof</I> and <I>cdof</I> keywords define the values used in the degree of
+freedom (DOF) formula described above for for temperature calculation
+for each chunk. They are only used when the <I>temp</I> value is
+calculated. They can be used to calculate a more appropriate
+temperature for some kinds of chunks. Here are 3 examples:
+</P>
+<P>If spatially binned chunks contain some number of water molecules and
+<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
+you could calculate a temperature with 6 degrees of freedom (DOF) (3
+translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
+</P>
+<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
+<I>bias</I> keyword to only allow the x component of velocity to contribute
+to the temperature, then <I>adof</I> = 1.0 would be appropriate.
+</P>
+<P>If each chunk consists of a large molecule, with some number of its
+bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
+by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
+set to the remaining degrees of freedom for the entire molecule
+(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
+molecule.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+timesteps, a section of chunk info will be written to a text file in
+the following format. A line with the timestep and number of chunks
+is written. Then one line per chunk is written, containing the chunk
+ID (1-Nchunk), an optional original ID value, optional coordinate
+values for chunks that represent spatial bins, the number of atoms in
+the chunk, and one or more calculated values. More explanation of the
+optional values is given below. The number of values in each line
+corresponds to the number of values specified in the fix ave/chunk
+command. The number of atoms and the value(s) are summed or average
+quantities, as explained above.
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the <I>file</I> keyword was used. LAMMPS uses default
+values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows:
+</P>
+<PRE># Chunk-averaged data for fix ID and group name
+# Timestep Number-of-chunks
+# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ...
+</PRE>
+<P>In the first line, ID and name are replaced with the fix-ID and group
+name. The second line describes the two values that are printed at
+the first of each section of output. In the third line the values are
+replaced with the appropriate value names, e.g. fx or c_myCompute<B>2</B>.
+</P>
+<P>The words in parenthesis only appear with corresponding columns if the
+chunk style specified for the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command supports them. The OrigID
+column is only used if the <I>compress</I> keyword was set to <I>yes</I> for the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. This means that
+the original chunk IDs (e.g. molecule IDs) will have been compressed
+to remove chunk IDs with no atoms assigned to them. Thus a compresed
+chunk ID of 3 may correspond to an original chunk ID or molecule ID of
+415. The OrigID column will list 415 for the 3rd chunk.
+</P>
+<P>The CoordN columns only appear if a <I>binning</I> style was used in the
+<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. For <I>bin/1d</I>,
+<I>bin/2d</I>, and <I>bin/3d</I> styles the column values are the center point
+of the bin in the corresponding dimension. Just Coord1 is used for
+<I>bin/1d</I>, Coord2 is added for <I>bin/2d</I>, Coord3 is added for <I>bin/3d</I>.
+</P>
+<P>Note that if the value of the <I>units</I> keyword used in the <A HREF = "compute_chunk_atom.html">compute
+chunk/atom command</A> is <I>box</I> or <I>lattice</I>, the
+coordinate values will be in distance <A HREF = "units.html">units</A>. If the
+value of the <I>units</I> keyword is <I>reduced</I>, the coordinate values will
+be in unitless reduced units (0-1).
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global array of values which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
+only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
+is when averaging is performed. The global array has # of rows =
+the number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command. The # of columns =
+M+1+Nvalues, where M = 1 to 4, depending on whether the optional
+columns for OrigID and CoordN are used, as explained above.
+Following the optional columns, the next column contains the count of
+atoms in the chunk, and the remaining columns are the Nvalue
+quantities. When the array is accessed with a row I that exceeds the
+current number of chunks, than a 0.0 is returned by the fix instead of
+an error, since the number of chunks can vary as a simulation runs
+depending on how that value is computed by the compute chunk/atom
+command.
+</P>
+<P>The array values calculated by this fix are treated as "intensive",
+since they are typically already normalized by the count of atoms in
+each chunk.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
+ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are norm = all, ave = one, bias = none, no file output, and
+title 1,2,3 = strings as described above.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_correlate.html b/doc/doc2/fix_ave_correlate.html
new file mode 100644
index 000000000..eda6a0785
--- /dev/null
+++ b/doc/doc2/fix_ave_correlate.html
@@ -0,0 +1,349 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/correlate command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/correlate = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of correlation time windows to accumulate
+
+<LI>Nfreq = calculate tine window averages every this many timesteps
+
+<LI>one or more input values can be listed
+
+<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> c_ID = global scalar calculated by a compute with ID
+ c_ID[I] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID[I] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>type</I> or <I>ave</I> or <I>start</I> or <I>prefactor</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>type</I> arg = <I>auto</I> or <I>upper</I> or <I>lower</I> or <I>auto/upper</I> or <I>auto/lower</I> or <I>full</I>
+ auto = correlate each value with itself
+ upper = correlate each value with each succeeding value
+ lower = correlate each value with each preceding value
+ auto/upper = auto + upper
+ auto/lower = auto + lower
+ full = correlate each value with every other value, including itself = auto + upper + lower
+ <I>ave</I> args = <I>one</I> or <I>running</I>
+ one = zero the correlation accumulation every Nfreq steps
+ running = accumulate correlations continuously
+ <I>start</I> args = Nstart
+ Nstart = start accumulating correlations on this timestep
+ <I>prefactor</I> args = value
+ value = prefactor to scale all the correlation data by
+ <I>file</I> arg = filename
+ filename = name of file to output correlation data to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate 1 50 10000 &
+ c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+ type upper ave running title1 "My correlation data"
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more global scalar values as inputs every few timesteps,
+calculate time correlations bewteen them at varying time intervals,
+and average the correlation data over longer timescales. The
+resulting correlation values can be time integrated by
+<A HREF = "variable.html">variables</A> or used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> such as <A HREF = "thermo_style.html">thermo_style
+custom</A>, and can also be written to a file.
+</P>
+<P>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+</P>
+<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
+<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity. If
+you wish to spatial- or time-average or histogram per-atom quantities
+from a compute, fix, or variable, then see the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>,
+or <A HREF = "fix_ave_histo.html">fix ave/histo</A> commands. If you wish to sum a
+per-atom quantity into a single global quantity, see the <A HREF = "compute_reduce.html">compute
+reduce</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
+do not have the word <I>atom</I> in their style name. Only a few
+<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
+individual fixes for info on which ones produce such values.
+<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
+be used with this fix. Variables of style <I>atom</I> cannot be used,
+since they produce per-atom values.
+</P>
+<P>The input values must either be all scalars. What kinds of
+correlations between input values are calculated is determined by the
+<I>type</I> keyword as discussed below.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used to calculate correlation data.
+The input values are sampled every <I>Nevery</I> timesteps. The
+correlation data for the preceding samples is computed on timesteps
+that are a multiple of <I>Nfreq</I>. Consider a set of samples from some
+initial time up to an output timestep. The initial time could be the
+beginning of the simulation or the last output time; see the <I>ave</I>
+keyword for options. For the set of samples, the correlation value
+Cij is calculated as:
+</P>
+<PRE>Cij(delta) = ave(Vi(t)*Vj(t+delta))
+</PRE>
+<P>which is the correlation value between input values Vi and Vj,
+separated by time delta. Note that the second value Vj in the pair is
+always the one sampled at the later time. The ave() represents an
+average over every pair of samples in the set that are separated by
+time delta. The maximum delta used is of size (<I>Nrepeat</I>-1)*<I>Nevery</I>.
+Thus the correlation between a pair of input values yields <I>Nrepeat</I>
+correlation datums:
+</P>
+<PRE>Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
+</PRE>
+<P>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
+timesteps 0,5,10,15,...,100 will be used to compute the final averages
+on timestep 100. Six averages will be computed: Cij(0), Cij(5),
+Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
+be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
+Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
+</P>
+<P><I>Nfreq</I> must be a multiple of <I>Nevery</I>; <I>Nevery</I> and <I>Nrepeat</I> must be
+non-zero. Also, if the <I>ave</I> keyword is set to <I>one</I> which is the
+default, then <I>Nfreq</I> >= (<I>Nrepeat</I>-1)*<I>Nevery</I> is required.
+</P>
+<HR>
+
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the compute is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.
+</P>
+<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/correlate. Or it can be a compute
+defined not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
+output</A> or other fixes such as <A HREF = "fix_nh.html">fix nvt</A>
+or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See the doc pages for
+these commands which give the IDs of these computes. Users can also
+write code for their own compute styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the fix is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.
+</P>
+<P>Note that some fixes only produce their values on certain timesteps,
+which must be compatible with <I>Nevery</I>, else an error will result.
+Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Only equal-style
+variables can be referenced. See the <A HREF = "variable.html">variable</A> command
+for details. Note that variables of style <I>equal</I> define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to time correlate.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+</P>
+<P>The <I>type</I> keyword determines which pairs of input values are
+correlated with each other. For N input values Vi, for i = 1 to N,
+let the number of pairs = Npair. Note that the second value in the
+pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.
+</P>
+<UL><LI>If <I>type</I> is set to <I>auto</I> then each input value is correlated with
+itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N.
+
+<LI>If <I>type</I> is set
+to <I>upper</I> then each input value is correlated with every succeeding
+value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2.
+
+<LI>If <I>type</I> is set
+to <I>lower</I> then each input value is correlated with every preceeding
+value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2.
+
+<LI>If <I>type</I> is set to <I>auto/upper</I> then each input value is correlated
+with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
+so Npair = N*(N+1)/2.
+
+<LI>If <I>type</I> is set to <I>auto/lower</I> then each input value is correlated
+with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
+so Npair = N*(N+1)/2.
+
+<LI>If <I>type</I> is set to <I>full</I> then each input value is correlated with
+itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
+Npair = N^2.
+</UL>
+<P>The <I>ave</I> keyword determines what happens to the accumulation of
+correlation samples every <I>Nfreq</I> timesteps. If the <I>ave</I> setting is
+<I>one</I>, then the accumulation is restarted or zeroed every <I>Nfreq</I>
+timesteps. Thus the outputs on successive <I>Nfreq</I> timesteps are
+essentially independent of each other. The exception is that the
+Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
+<I>Nfreq</I>, contributes to the correlation output both at time T and at
+time T+Nfreq.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the accumulation is never
+zeroed. Thus the output of correlation data at any timestep is the
+average over samples accumulated every <I>Nevery</I> steps since the fix
+was defined. it can only be restarted by deleting the fix via the
+<A HREF = "unfix.html">unfix</A> command, or by re-defining the fix by re-specifying
+it.
+</P>
+<P>The <I>start</I> keyword specifies what timestep the accumulation of
+correlation samples will begin on. The default is step 0. Setting it
+to a larger value can avoid adding non-equilibrated data to the
+correlation averages.
+</P>
+<P>The <I>prefactor</I> keyword specifies a constant which will be used as a
+multiplier on the correlation data after it is averaged. It is
+effectively a scale factor on Vi*Vj, which can be used to account for
+the size of the time window or other unit conversions.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+steps, an array of correlation data is written to the file. The
+number of rows is <I>Nrepeat</I>, as described above. The number of
+columns is the Npair+2, also as described above. Thus the file ends
+up to be a series of these array sections.
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the <I>file</I> keyword was used. LAMMPS uses default
+values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows:
+</P>
+<PRE># Time-correlated data for fix ID
+# TimeStep Number-of-time-windows
+# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
+</PRE>
+<P>In the first line, ID is replaced with the fix-ID. The second line
+describes the two values that are printed at the first of each section
+of output. In the third line the value pairs are replaced with the
+appropriate fields from the fix ave/correlate command.
+</P>
+<HR>
+
+<P>Let Sij = a set of time correlation data for input values I and J,
+namely the <I>Nrepeat</I> values:
+</P>
+<PRE>Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
+</PRE>
+<P>As explained below, these datums are output as one column of a global
+array, which is effectively the correlation matrix.
+</P>
+<P>The <I>trap</I> function defined for <A HREF = "variable.html">equal-style variables</A>
+can be used to perform a time integration of this vector of datums,
+using a trapezoidal rule. This is useful for calculating various
+quantities which can be derived from time correlation data. If a
+normalization factor is needed for the time integration, it can be
+included in the variable formula or via the <I>prefactor</I> keyword.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global array of values which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
+only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
+is when averaging is performed. The global array has # of rows =
+<I>Nrepeat</I> and # of columns = Npair+2. The first column has the time
+delta (in timesteps) between the pairs of input values used to
+calculate the correlation, as described above. The 2nd column has the
+number of samples contributing to the correlation average, as
+described above. The remaining Npair columns are for I,J pairs of the
+N input values, as determined by the <I>type</I> keyword, as described
+above.
+</P>
+<UL><LI>For <I>type</I> = <I>auto</I>, the Npair = N columns are ordered: C11, C22, ...,
+CNN.
+
+<LI>For <I>type</I> = <I>upper</I>, the Npair = N*(N-1)/2 columns are ordered: C12,
+C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
+
+<LI>For <I>type</I> = <I>lower</I>, the Npair = N*(N-1)/2 columns are ordered: C21,
+C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
+
+<LI>For <I>type</I> = <I>auto/upper</I>, the Npair = N*(N+1)/2 columns are ordered:
+C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
+CNN.
+
+<LI>For <I>type</I> = <I>auto/lower</I>, the Npair = N*(N+1)/2 columns are ordered:
+C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
+CNN.
+
+<LI>For <I>type</I> = <I>full</I>, the Npair = N^2 columns are ordered: C11, C12,
+..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
+CNN.
+</UL>
+<P>The array values calculated by this fix are treated as "intensive".
+If you need to divide them by the number of atoms, you must do this in
+a later processing step, e.g. when using them in a
+<A HREF = "variable.html">variable</A>.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
+ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
+<A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<P>The option defaults are ave = one, type = auto, start = 0, no file
+output, title 1,2,3 = strings as described above, and prefactor = 1.0.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_histo.html b/doc/doc2/fix_ave_histo.html
new file mode 100644
index 000000000..96e16bd57
--- /dev/null
+++ b/doc/doc2/fix_ave_histo.html
@@ -0,0 +1,351 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/histo command
+</H3>
+<H3>fix ave/histo/weight command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style = <I>ave/histo</I> or <I>ave/histo/weight</I> = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating histogram
+
+<LI>Nfreq = calculate histogram every this many timesteps
+
+<LI>lo,hi = lo/hi bounds within which to histogram
+
+<LI>Nbin = # of histogram bins
+
+<LI>one or more input values can be listed
+
+<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+ c_ID = scalar or vector calculated by a compute with ID
+ c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
+ f_ID = scalar or vector calculated by a fix with ID
+ f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
+ v_name = value(s) calculated by an equal-style or atom-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>mode</I> or <I>file</I> or <I>ave</I> or <I>start</I> or <I>beyond</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
+ scalar = all input values are scalars
+ vector = all input values are vectors
+ <I>file</I> arg = filename
+ filename = name of file to output histogram(s) to
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window</I>
+ one = output a new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>start</I> args = Nstart
+ Nstart = start averaging on this timestep
+ <I>beyond</I> arg = <I>ignore</I> or <I>end</I> or <I>extra</I>
+ ignore = ignore values outside histogram lo/hi bounds
+ end = count values outside histogram lo/hi bounds in end bins
+ extra = create 2 extra bins for value outside histogram lo/hi bounds
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file, only for vector mode
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
+fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
+fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more values as inputs every few timesteps, histogram them,
+and average the histogram over longer timescales. The resulting
+histogram can be used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A>, and can also be written to a
+file. The fix ave/histo/weight command has identical syntax to fix
+ave/histo, except that exactly two values must be specified. See
+details below.
+</P>
+<P>The group specified with this command is ignored for global and local
+input values. For per-atom input values, only atoms in the group
+contribute to the histogram. Note that regardless of the specified
+group, specified values may represent calculations performed by
+computes and fixes which store their own "group" definition.
+</P>
+<P>A histogram is simply a count of the number of values that fall within
+a histogram bin. <I>Nbins</I> are defined, with even spacing between <I>lo</I>
+and <I>hi</I>. Values that fall outside the lo/hi bounds can be treated in
+different ways; see the discussion of the <I>beyond</I> keyword below.
+</P>
+<P>Each input value can be an atom attribute (position, velocity, force
+component) or can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an equal-style or atom-style
+<A HREF = "variable.html">variable</A>. The set of input values can be either all
+global, all per-atom, or all local quantities. Inputs of different
+kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are
+per-atom vector values. See the doc page for individual "compute" and
+"fix" commands to see what kinds of quantities they generate.
+</P>
+<P>The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the <I>mode</I> keyword.
+</P>
+<P>Note that the output of this command is a single histogram for all
+input values combined together, not one histogram per input value.
+See below for details on the format of the output of this fix.
+</P>
+<P>If <I>mode</I> = vector, then the input values may either be vectors or
+arrays. If a global array is listed, then it is the same as if the
+individual columns of the array had been listed one by one.
+E.g. these 2 fix ave/histo commands are equivalent, since the <A HREF = "compute_com_chunk.html">compute
+com/chunk</A> command creates a global array
+with 3 columns:
+</P>
+<PRE>compute myCOM all com/chunk
+fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+</PRE>
+<P>If the fix ave/histo/weight command is used, exactly two values must
+be specified. If the values are vectors, they must be the same
+length. The first value (a scalar or vector) is what is histogrammed
+into bins, in the same manner the fix ave/histo command operates. The
+second value (a scalar or vector) is used as a "weight". This means
+that instead of each value tallying a "1" to its bin, the
+corresponding weight is tallied. E.g. the Nth entry in the first
+vector tallies the Nth entry (weight) in the second vector.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used in order to contribute to the
+histogram. The final histogram is generated on timesteps that are
+multiple of <I>Nfreq</I>. It is averaged over <I>Nrepeat</I> histograms,
+computed in the preceding portion of the simulation every <I>Nevery</I>
+timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must
+be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps contributing
+to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
+required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
+on timesteps 90,92,94,96,98,100 will be used to compute the final
+histogram on timestep 100. Similarly for timesteps
+190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq
+= 100, then no time averaging of the histogram is done; a histogram is
+simply generated on timesteps 100,200,etc.
+</P>
+<HR>
+
+<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+self-explanatory. Note that other atom attributes can be used as
+inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If <I>mode</I> = scalar, then if
+no bracketed term is appended, the global scalar calculated by the
+compute is used. If a bracketed term is appended, the Ith element of
+the global vector calculated by the compute is used. If <I>mode</I> =
+vector, then if no bracketed term is appended, the global or per-atom
+or local vector calculated by the compute is used. Or if the compute
+calculates an array, all of the columns of the array are used as if
+they had been specified as individual vectors (see description above).
+If a bracketed term is appended, the Ith column of the global or
+per-atom or local array calculated by the compute is used.
+</P>
+<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/histo. Or it can be a compute defined
+not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
+output</A> or other fixes such as <A HREF = "fix_nh.html">fix
+nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See
+the doc pages for these commands which give the IDs of these computes.
+Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them
+to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If <I>mode</I> = scalar, then if
+no bracketed term is appended, the global scalar calculated by the fix
+is used. If a bracketed term is appended, the Ith element of the
+global vector calculated by the fix is used. If <I>mode</I> = vector, then
+if no bracketed term is appended, the global or per-atom or local
+vector calculated by the fix is used. Or if the fix calculates an
+array, all of the columns of the array are used as if they had been
+specified as individual vectors (see description above). If a
+bracketed term is appended, the Ith column of the global or per-atom
+or local array calculated by the fix is used.
+</P>
+<P>Note that some fixes only produce their values on certain timesteps,
+which must be compatible with <I>Nevery</I>, else an error will result.
+Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. If <I>mode</I> = scalar, then
+only equal-style variables can be used, which produce a global value.
+If <I>mode</I> = vector, then only atom-style variables can be used, which
+produce a per-atom vector. See the <A HREF = "variable.html">variable</A> command
+for details. Note that variables of style <I>equal</I> and <I>atom</I> define a
+formula which can reference individual atom properties or
+thermodynamic keywords, or they can invoke other computes, fixes, or
+variables when they are evaluated, so this is a very general means of
+specifying quantities to histogram.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+</P>
+<P>If the <I>mode</I> keyword is set to <I>scalar</I>, then all input values must
+be global scalars, or elements of global vectors. If the <I>mode</I>
+keyword is set to <I>vector</I>, then all input values must be global or
+per-atom or local vectors, or columns of global or per-atom or local
+arrays.
+</P>
+<P>The <I>beyond</I> keyword determines how input values that fall outside the
+<I>lo</I> to <I>hi</I> bounds are treated. Values such that <I>lo</I> <= value <=
+<I>hi</I> are assigned to one bin. Values on a bin boundary are assigned
+to the lower of the 2 bins. If <I>beyond</I> is set to <I>ignore</I> then
+values < <I>lo</I> and values > <I>hi</I> are ignored, i.e. they are not binned.
+If <I>beyond</I> is set to <I>end</I> then values < <I>lo</I> are counted in the
+first bin and values > <I>hi</I> are counted in the last bin. If <I>beyond</I>
+is set to <I>extend</I> then two extra bins are created, so that there are
+Nbins+2 total bins. Values < <I>lo</I> are counted in the first bin and
+values > <I>hi</I> are counted in the last bin (Nbins+1). Values between
+<I>lo</I> and <I>hi</I> (inclusive) are counted in bins 2 thru Nbins+1. The
+"coordinate" stored and printed for these two extra bins is <I>lo</I> and
+<I>hi</I>.
+</P>
+<P>The <I>ave</I> keyword determines how the histogram produced every <I>Nfreq</I>
+steps are averaged with histograms produced on previous steps that
+were multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the histograms produced on
+timesteps that are multiples of <I>Nfreq</I> are independent of each other;
+they are output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the histograms produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cumulative sense before being output. Each bin value in the histogram
+is thus the average of the bin value produced on that timestep with
+all preceding values for the same bin. This running average begins
+when the fix is defined; it can only be restarted by deleting the fix
+via the <A HREF = "unfix.html">unfix</A> command, or by re-defining the fix by
+re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the histograms produced on
+timesteps that are multiples of <I>Nfreq</I> are summed within a moving
+"window" of time, so that the last M histograms are used to produce
+the output. E.g. if M = 3 and Nfreq = 1000, then the output on step
+10000 will be the combined histogram of the individual histograms on
+steps 8000,9000,10000. Outputs on early steps will be sums over less
+than M histograms if they are not available.
+</P>
+<P>The <I>start</I> keyword specifies what timestep histogramming will begin
+on. The default is step 0. Often input values can be 0.0 at time 0,
+so setting <I>start</I> to a larger value can avoid including a 0.0 in
+a running or windowed histogram.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+steps, one histogram is written to the file. This includes a leading
+line that contains the timestep, number of bins, the total count of
+values contributing to the histogram, the count of values that were
+not histogrammed (see the <I>beyond</I> keyword), the minimum value
+encountered, and the maximum value encountered. The min/max values
+include values that were not histogrammed. Following the leading
+line, one line per bin is written into the file. Each line contains
+the bin #, the coordinate for the center of the bin (between <I>lo</I> and
+<I>hi</I>), the count of values in the bin, and the normalized count. The
+normalized count is the bin count divided by the total count (not
+including values not histogrammed), so that the normalized values sum
+to 1.0 across all bins.
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the <I>file</I> keyword was used. LAMMPS uses default
+values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows:
+</P>
+<PRE># Histogram for fix ID
+# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
+# Bin Coord Count Count/Total
+</PRE>
+<P>In the first line, ID is replaced with the fix-ID. The second line
+describes the six values that are printed at the first of each section
+of output. The third describes the 4 values printed for each bin in
+the histogram.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a global vector and global array which can be
+accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+The values can only be accessed on timesteps that are multiples of
+<I>Nfreq</I> since that is when a histogram is generated. The global
+vector has 4 values:
+</P>
+<UL><LI>1 = total counts in the histogram
+<LI>2 = values that were not histogrammed (see <I>beyond</I> keyword)
+<LI>3 = min value of all input values, including ones not histogrammed
+<LI>4 = max value of all input values, including ones not histogrammed
+</UL>
+<P>The global array has # of rows = Nbins and # of columns = 3. The
+first column has the bin coordinate, the 2nd column has the count of
+values in that histogram bin, and the 3rd column has the bin count
+divided by the total count (not including missing counts), so that the
+values in the 3rd column sum to 1.0.
+</P>
+<P>The vector and array values calculated by this fix are all treated as
+"intensive". If this is not the case, e.g. due to histogramming
+per-atom input values, then you will need to account for that when
+interpreting the values produced by this fix.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
+</P>
+<P><B>Default:</B> none
+</P>
+<P>The option defaults are mode = scalar, ave = one, start = 0, no file
+output, beyond = ignore, and title 1,2,3 = strings as described above.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_spatial.html b/doc/doc2/fix_ave_spatial.html
new file mode 100644
index 000000000..9d41f243a
--- /dev/null
+++ b/doc/doc2/fix_ave_spatial.html
@@ -0,0 +1,435 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/spatial command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/spatial = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+
+<LI>dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins
+
+<PRE> dim = <I>x</I> or <I>y</I> or <I>z</I>
+ origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
+ delta = thickness of spatial bins in dim (distance units)
+</PRE>
+<LI>one or more input values can be listed
+
+<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+
+<PRE> vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+ density/number, density/mass = number or mass density
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>region</I> or <I>bound</I> or <I>discard</I> or <I>norm</I> or <I>ave</I> or <I>units</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>region</I> arg = region-ID
+ <I>bound</I> args = x/y/z lo hi
+ x/y/z = <I>x</I> or <I>y</I> or <I>z</I> to bound bins in this dimension
+ lo = <I>lower</I> or coordinate value (distance units)
+ hi = <I>upper</I> or coordinate value (distance units)
+ <I>discard</I> arg = <I>mixed</I> or <I>no</I> or <I>yes</I>
+ mixed = discard atoms outside bins only if bin bounds are explicitly set
+ no = always keep out-of-bounds atoms
+ yes = always discard out-of-bounds atoms
+ <I>norm</I> arg = <I>all</I> or <I>sample</I>
+ region-ID = ID of region atoms must be in to contribute to spatial averaging
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+ one = output new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
+ <I>file</I> arg = filename
+ filename = file to write results to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
+ title1 "My output values"
+fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
+fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
+fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running
+</PRE>
+<P><B>IMPORTANT NOTE:</B>
+</P>
+<P> The fix ave/spatial command has been replaced by the more flexible
+<A HREF = "fix_ave_chunk.html">fix ave/chunk</A> and <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> commands. The fix ave/spatial
+command will be removed from LAMMPS sometime in the summer of 2015.
+</P>
+<P>Any fix ave/spatial command can be replaced by the two new commands.
+You simply need to split the fix ave/spatial arguments across the two
+new commands. For example, this command:
+</P>
+<PRE>fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
+</PRE>
+<P>could be replaced by:
+</P>
+<PRE>compute cc1 flow chunk/atom bin/1d y 0.0 1.0
+fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more per-atom vectors as inputs every few timesteps, bin
+their values spatially into 1d, 2d, or 3d bins based on current atom
+coordinates, and average the bin values over longer timescales. The
+resulting bin averages can be used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> such as <A HREF = "thermo_style.html">thermo_style
+custom</A>, and can also be written to a file.
+</P>
+<P>The group specified with the command means only atoms within the group
+contribute to bin averages. If the <I>region</I> keyword is used, the atom
+must be in both the specified group and the specified geometric
+<A HREF = "region.html">region</A> in order to contribute to bin averages.
+</P>
+<P>Each listed value can be an atom attribute (position, velocity, force
+component), a mass or number density, or the result of a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
+atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
+compute, fix, or variable must produce a per-atom quantity, not a
+global quantity. If you wish to time-average global quantities from a
+compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
+which have the word <I>atom</I> in their style name. See the doc pages for
+individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
+quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
+ones that can be used with this fix since all other styles of variable
+produce global quantities.
+</P>
+<P>The per-atom values of each input vector are binned and averaged
+independently of the per-atom values in other input vectors.
+</P>
+<P>The size and dimensionality of the bins (1d = layers or slabs, 2d =
+pencils, 3d = boxes) are determined by the <I>dim</I>, <I>origin</I>, and
+<I>delta</I> settings and how many times they are specified (1, 2, or 3).
+See details below.
+</P>
+<P>IMPORTANT NOTE: This fix works by creating an array of size Nbins by
+Nvalues on each processor. Nbins is the total number of bins; Nvalues
+is the number of input values specified. Each processor loops over
+its atoms, tallying its values to the appropriate bin. Then the
+entire array is summed across all processors. This means that using a
+large number of bins (easy to do for 2d or 3d bins) will incur an
+overhead in memory and computational cost (summing across processors),
+so be careful to use reasonable numbers of bins.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used to bin them and contribute to
+the average. The final averaged quantities are generated on timesteps
+that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+</P>
+<HR>
+
+<P>Each per-atom property is also averaged over atoms in each bin. The
+way the averaging is one across the <I>Nrepeat</I> timesteps to produce
+output on the <I>Nfreq</I> timesteps, and across multiple <I>Nfreq</I> outputs,
+is determined by the <I>norm</I> and <I>av</I> keyword settings, as discussed
+below.
+</P>
+<P>Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends
+on how many times (1, 2, or 3) the <I>dim</I>, <I>origin</I>, and <I>delta</I>
+settings are specified in the fix ave/spatial command. For 2d or 3d
+bins, there is no restriction on specifying dim = x before dim = y, or
+dim = y before dim = z. Bins in a particular <I>dim</I> have a bin size in
+that dimension given by <I>delta</I>. Every Nfreq steps, when averaging is
+being performed and the per-atom property is calculated for the first
+time, the number of bins and the bin sizes and boundaries are
+computed. Thus if the simulation box changes size during a
+simulation, the number of bins and their boundaries may also change.
+In each dimension, bins are defined relative to a specified <I>origin</I>,
+which may be the lower/upper edge of the simulation box in that
+dimension, or its center point, or a specified coordinate value.
+Starting at the origin, sufficient bins are created in both directions
+to completely span the bin extent in that dimension. By default the
+bin extent is the entire simulation box.
+</P>
+<P>The <I>bound</I> keyword can be used one or more times to limit the extent
+of bin coverage in specified dimensions, i.e. to only bin a portion of
+the box. If the <I>lo</I> setting is <I>lower</I> or the <I>hi</I> setting is
+<I>upper</I>, the bin extent in that direction extends to the box boundary.
+If a numeric value is used for <I>lo</I> and/or <I>hi</I>, then the bin extent
+in the <I>lo</I> or <I>hi</I> direction extends only to that value, which is
+assumed to be inside (or at least near) the simulation box boundaries,
+though LAMMPS does not check for this.
+</P>
+<P>On each sampling timestep, each atom is mapped to the bin it currently
+belongs to, based on its current position. Note that the group-ID and
+region keyword can exclude specific atoms from this operation, as
+discussed above. Note that between reneighboring timesteps, atoms can
+move outside the current simulation box. If the box is periodic (in
+that dimension) the atom is remapping into the periodic box for
+purposes of binning. If the box in not periodic, the atom may have
+moved outside the bounds of any bin.
+</P>
+<P>The <I>discard</I> keyword determines what is done with any atom which is
+outside the bounds of any bin. If <I>discard</I> is set to <I>yes</I>, the atom
+will be ignored and not contribute to any bin averages. If <I>discard</I>
+is set to <I>no</I>, the atom will be counted as if it were in the first or
+last bin in that dimension. If (discard</I> is set to <I>mixed</I>, which is
+the default, it will only be counted in the first or last bin if bins
+extend to the box boundary in that dimension. This is the case if the
+<I>bound</I> keyword settings are <I>lower</I> and <I>upper</I>, which is the
+default. If the <I>bound</I> keyword settings are numeric values, then the
+atom will be ignored if it is outside the bounds of any bin. Note
+that in this case, it is possible that the first or last bin extends
+beyond the numeric <I>bounds</I> settings, depending on the specified
+<I>origin</I>. If this is the case, the atom is only ignored if it is
+outside the first or last bin, not if it is simply outside the numeric
+<I>bounds</I> setting.
+</P>
+<P>For orthogonal simulation boxes, the bins are also layers, pencils, or
+boxes aligned with the xyz coordinate axes. For triclinic
+(non-orthogonal) simulation boxes, the bins are so that they are
+parallel to the tilted faces of the simulation box. See <A HREF = "Section_howto.html#howto_12">this
+section</A> of the manual for a discussion of
+the geometry of triclinic boxes in LAMMPS. As described there, a
+tilted simulation box has edge vectors a,b,c. In that nomenclature,
+bins in the x dimension have faces with normals in the "b" cross "c"
+direction. Bins in y have faces normal to the "a" cross "c"
+direction. And bins in z have faces normal to the "a" cross "b"
+direction. Note that in order to define the size and position of
+these bins in an unambiguous fashion, the <I>units</I> option must be set
+to <I>reduced</I> when using a triclinic simulation box, as noted below.
+</P>
+<HR>
+
+<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
+Note that other atom attributes (including atom postitions x,y,z) can
+be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>The <I>density/number</I> value means the number density is computed in
+each bin, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
+value means the mass density is computed in each bind, i.e. each atom
+is weighted by its mass. The resulting density is normalized by the
+volume of the bin so that units of number/volume or density are
+output. See the <A HREF = "units.html">units</A> command doc page for the
+definition of density for each choice of units, e.g. gram/cm^3.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used. Users can also write code for
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used. Note that some fixes only produce
+their values on certain timesteps, which must be compatible with
+<I>Nevery</I>, else an error results. Users can also write code for their
+own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Variables of style
+<I>atom</I> can reference thermodynamic keywords and various per-atom
+attributes, or invoke other computes, fixes, or variables when they
+are evaluated, so this is a very general means of generating per-atom
+quantities to spatially average.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+The <I>region</I>, <I>bound</I>, and <I>discard</I> keywords were discussed above.
+</P>
+<P>The <I>norm</I> keyword affects how averaging is done for the output
+produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a bin
+quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
+count of atoms in the bin. The printed value for the bin is
+Total-quantity / Total-count. In other words it is an average over
+the entire <I>Nfreq</I> timescale.
+</P>
+<P>For a <I>sample</I> setting, the bin quantity is summed over atoms for only
+a single sample, as is the count, and a "average sample value" is
+computed, i.e. Sample-quantity / Sample-count. The printed value for
+the bin is the average of the <I>Nrepeat</I> "average sample values", In
+other words it is an average of an average.
+</P>
+<P>The <I>ave</I> keyword determines how the bin values produced every <I>Nfreq</I>
+steps are averaged with bin values produced on previous steps that
+were multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are independent of each other;
+they are output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cumulative sense before being output. Each output bin value is thus
+the average of the bin value produced on that timestep with all
+preceding values for the same bin. This running average begins when
+the fix is defined; it can only be restarted by deleting the fix via
+the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
+re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values for the same bin
+are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
+the output on step 10000 will be the average of the individual bin
+values on steps 8000,9000,10000. Outputs on early steps will average
+over less than M values if they are not available.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+for the bin size <I>delta</I> and for <I>origin</I> and <I>bounds</I> values if they
+are coordinate value. For orthogonal simulation boxes, any of the 3
+options may be used. For non-orthogonal (triclinic) simulation boxes,
+only the <I>reduced</I> option may be used.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacing. A <I>reduced</I> value means normalized
+unitless values between 0 and 1, which represent the lower and upper
+faces of the simulation box respectively. Thus an <I>origin</I> value of
+0.5 means the center of the box in any dimension. A <I>delta</I> value of
+0.1 means 10 bins span the box in that dimension.
+</P>
+<P>Consider a non-orthogonal box, with bins that are 1d layers or slabs
+in the x dimension. No matter how the box is tilted, an <I>origin</I> of
+0.0 means start layers at the lower "b" cross "c" plane of the
+simulation box and an <I>origin</I> of 1.0 means to start layers at the
+upper "b" cross "c" face of the box. A <I>delta</I> value of 0.1 means
+there will be 10 layers from 0.0 to 1.0, regardless of the current
+size or shape of the simulation box.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+timesteps, a section of bin info will be written to a text file in the
+following format. A line with the timestep and number of bin is
+written. Then one line per bin is written, containing the bin ID
+(1-N), the coordinate of the center of the bin, the number of atoms
+in the bin, and one or more calculated values. The number of values
+in each line corresponds to the number of values specified in the fix
+ave/spatial command. The number of atoms and the value(s) are average
+quantities. If the value of the <I>units</I> keyword is <I>box</I> or
+<I>lattice</I>, the "coord" is printed in box units. If the value of the
+<I>units</I> keyword is <I>reduced</I>, the "coord" is printed in reduced units
+(0-1).
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the <I>file</I> keyword was used. LAMMPS uses default
+values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows:
+</P>
+<PRE># Spatial-averaged data for fix ID and group name
+# Timestep Number-of-bins
+# Bin Coord1 Coord2 Coord3 Count value1 value2 ...
+</PRE>
+<P>In the first line, ID and name are replaced with the fix-ID and group
+name. The second line describes the two values that are printed at
+the first of each section of output. In the third line the values are
+replaced with the appropriate fields from the fix ave/spatial command.
+The Coord2 and Coord3 entries in the third line only appear for 2d and
+3d bins respectively. For 1d bins, the word Coord1 is replaced by
+just Coord.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global array of values which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
+only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
+is when averaging is performed. The global array has # of rows =
+Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
+1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
+(center of the bin) in the appropriate dimensions, the next column has
+the count of atoms in that bin, and the remaining columns are the
+Nvalue quantities. When the array is accessed with an I that exceeds
+the current number of bins, than a 0.0 is returned by the fix instead
+of an error, since the number of bins can vary as a simulation runs,
+depending on the simulation box size. 2d or 3d bins are ordered so
+that the last dimension(s) vary fastest. The array values calculated
+by this fix are "intensive", since they are already normalized by the
+count of atoms in each bin.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
+of bins must remain the same during the simulation, so that the
+appropriate averaging can be done. This will be the case if the
+simulation box size doesn't change or if the <I>units</I> keyword is set to
+<I>reduced</I>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
+ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
+<A HREF = "fix_ave_spatial_sphere.html">fix ave/spatial/sphere</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are bound = lower and upper in all dimensions,
+discard = mixed, norm = all, ave = one, units = lattice, no file
+output, and title 1,2,3 = strings as described above.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_spatial_sphere.html b/doc/doc2/fix_ave_spatial_sphere.html
new file mode 100644
index 000000000..d7d55d725
--- /dev/null
+++ b/doc/doc2/fix_ave_spatial_sphere.html
@@ -0,0 +1,342 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/spatial/sphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/spatial = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+
+<LI>origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below)
+
+<LI>r_min = radial distance at which binning begins
+
+<LI>r_max = radial distance at which binning ends
+
+<LI>nbins = number of spherical shells to create between r_min and r_max
+
+<LI>one or more input values can be listed
+
+<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+
+<PRE> vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+ density/number, density/mass = number or mass density
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>region</I> or <I>norm</I> or <I>units</I> or <I>ave</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>region</I> arg = region-ID
+ region-ID = ID of region atoms must be in to contribute to spatial averaging
+ <I>norm</I> arg = <I>all</I> or <I>sample</I>
+ <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+ one = output new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>file</I> arg = filename
+ filename = file to write results to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values"
+fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more per-atom vectors as inputs every few timesteps, bin
+their values spatially into spherical shells based on current atom
+coordinates, and average the bin values over longer timescales. The
+resulting bin averages can be used by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> such as <A HREF = "thermo_style.html">thermo_style
+custom</A>, and can also be written to a file.
+</P>
+<P>The group specified with the command means only atoms within the group
+contribute to bin averages. If the <I>region</I> keyword is used, the atom
+must be in both the group and the specified geometric
+<A HREF = "region.html">region</A> in order to contribute to bin averages.
+</P>
+<P>Each listed value can be an atom attribute (position, velocity, force
+component), a mass or number density, or the result of a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
+atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
+compute, fix, or variable must produce a per-atom quantity, not a
+global quantity. If you wish to time-average global quantities from a
+compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
+which have the word <I>atom</I> in their style name. See the doc pages for
+individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
+quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
+ones that can be used with this fix since all other styles of variable
+produce global quantities.
+</P>
+<P>The per-atom values of each input vector are binned and averaged
+independently of the per-atom values in other input vectors.
+</P>
+<P><I>Nbins</I> specifies the number of spherical shells which will be created
+between r_min and r_max centered at (origin_x, origin_y, origin_z).
+</P>
+<P>IMPORTANT NOTE: This fix works by creating an array of size Nbins by
+Nvalues on each processor. Nbins is the total number of bins; Nvalues
+is the number of input values specified. Each processor loops over
+its atoms, tallying its values to the appropriate bin. Then the
+entire array is summed across all processors. This means that using a
+large number of bins will incur an overhead in memory and computational
+cost (summing across processors), so be careful to use reasonable numbers
+of bins.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used to bin them and contribute to
+the average. The final averaged quantities are generated on timesteps
+that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+</P>
+<HR>
+
+<P>The <I>origin_x</I>, <I>origin_y</I>, and <I>origin_z</I> parameters may be specified
+by either a compute or a variable. This allows, for example, the
+center of the spherical bins to be attached to the center of mass of a
+group of atoms. If a variable origin is used and periodic boundary
+conditions are in effect, then the origin will be wrapped across
+periodic boundaries whenever it changes so that it is always inside
+the simulation box.
+</P>
+<HR>
+
+<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
+Note that other atom attributes (including atom postitions x,y,z) can
+be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+an input value from that compute.
+</P>
+<P>The <I>density/number</I> value means the number density is computed in
+each bin, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
+value means the mass density is computed in each bin, i.e. each atom
+is weighted by its mass. The resulting density is normalized by the
+volume of the bin so that units of number/volume or density are
+output. See the <A HREF = "units.html">units</A> command doc page for the
+definition of density for each choice of units, e.g. gram/cm^3.
+The bin volume will always be calculated in box units, independent
+of the use of the <I>units</I> keyword in this command.
+</P>
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the compute is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the compute is used. Users can also write code for
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed integer is
+appended, the per-atom vector calculated by the fix is used. If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used. Note that some fixes only produce
+their values on certain timesteps, which must be compatible with
+<I>Nevery</I>, else an error results. Users can also write code for their
+own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Variables of style
+<I>atom</I> can reference thermodynamic keywords and various per-atom
+attributes, or invoke other computes, fixes, or variables when they
+are evaluated, so this is a very general means of generating per-atom
+quantities to spatially average.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+The <I>region</I> keyword was discussed above.
+</P>
+<P>The <I>norm</I> keyword affects how averaging is done for the output
+produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a bin
+quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
+count of atoms in the bin. The printed value for the bin is
+Total-quantity / Total-count. In other words it is an average over
+the entire <I>Nfreq</I> timescale.
+</P>
+<P>For a <I>sample</I> setting, the bin quantity is summed over atoms for only
+a single sample, as is the count, and a "average sample value" is
+computed, i.e. Sample-quantity / Sample-count. The printed value for
+the bin is the average of the <I>Nrepeat</I> "average sample values", In
+other words it is an average of an average.
+</P>
+<P>The <I>ave</I> keyword determines how the bin values produced every <I>Nfreq</I>
+steps are averaged with bin values produced on previous steps that
+were multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are independent of each other;
+they are output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cumulative sense before being output. Each output bin value is thus
+the average of the bin value produced on that timestep with all
+preceding values for the same bin. This running average begins when
+the fix is defined; it can only be restarted by deleting the fix via
+the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
+re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the bin values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values for the same bin
+are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
+the output on step 10000 will be the average of the individual bin
+values on steps 8000,9000,10000. Outputs on early steps will average
+over less than M values if they are not available.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+for the sphere origin and the two radial lengths. For orthogonal
+simulation boxes, any of the 3 options may be used. For
+non-orthogonal (triclinic) simulation boxes, only the <I>reduced</I> option
+may be used.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacing.
+</P>
+<P>IMPORTANT NOTE: The <I>lattice</I> style may only be used if the lattice
+spacing is the same in each direction.
+</P>
+<P>A <I>reduced</I> value means normalized unitless values between 0 and 1,
+which represent the lower and upper faces of the simulation box
+respectively. Thus an <I>origin</I> value of 0.5 means the center of the
+box in any dimension.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+timesteps, a section of bin info will be written to a text file in the
+following format. A line with the timestep and number of bin is
+written. Then one line per bin is written, containing the bin ID
+(1-N), the coordinate of the center of the bin, the number of atoms in
+the bin, and one or more calculated values. The number of values in
+each line corresponds to the number of values specified in the fix
+ave/spatial command. The number of atoms and the value(s) are average
+quantities. If the value of the <I>units</I> keyword is <I>box</I> or
+<I>lattice</I>, the "coord" is printed in box units. If the value of the
+<I>units</I> keyword is <I>reduced</I>, the "coord" is printed in reduced units
+(0-1).
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 3 lines of the output
+file, assuming the <I>file</I> keyword was used. LAMMPS uses default
+values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows:
+</P>
+<PRE># Spatial-averaged data for fix ID and group name
+# Timestep Number-of-bins
+# Bin r Count value1 value2 ...
+</PRE>
+<P>In the first line, ID and name are replaced with the fix-ID and group
+name. The second line describes the two values that are printed at
+the first of each section of output. In the third line the values are
+replaced with the appropriate fields from the fix ave/spatial command.
+The Coord2 and Coord3 entries in the third line only appear for 2d and
+3d bins respectively. For 1d bins, the word Coord1 is replaced by
+just Coord.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global array of values which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
+only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
+is when averaging is performed. The global array has # of rows =
+Nbins and # of columns = 2+Nvalues. The first column contains the
+radius at the center of the shell. For units <I>reduced</I>, this is in
+reduced units, while for units <I>box</I> and <I>lattice</I> this is in box
+units. The next column has the count of atoms in that bin, and the
+remaining columns are the Nvalue quantities. When the array is
+accessed with an I that exceeds the current number of bins, than a 0.0
+is returned by the fix instead of an error. The array values
+calculated by this fix are "intensive", since they are already
+normalized by the count of atoms in each bin.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
+of bins must remain the same during the simulation, so that the
+appropriate averaging can be done. This will be the case if the
+simulation box size doesn't change or if the <I>units</I> keyword is set to
+<I>reduced</I>.
+</P>
+<P>This style is part of the USER-MISC package. It is only enabled if
+LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
+ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
+<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
+<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are norm = all, ave = one, units = lattice, no
+file output, and title 1,2,3 = strings as described above.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ave_time.html b/doc/doc2/fix_ave_time.html
new file mode 100644
index 000000000..77c0fd34d
--- /dev/null
+++ b/doc/doc2/fix_ave_time.html
@@ -0,0 +1,334 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/time command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/time = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+
+<LI>one or more input values can be listed
+
+<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> c_ID = global scalar, vector, or array calculated by a compute with ID
+ c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
+ f_ID = global scalar, vector, or array calculated by a fix with ID
+ f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>mode</I> or <I>file</I> or <I>ave</I> or <I>start</I> or <I>off</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
+
+<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
+ scalar = all input values are global scalars
+ vector = all input values are global vectors or global arrays
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+ one = output a new average value every Nfreq steps
+ running = output cummulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>start</I> args = Nstart
+ Nstart = start averaging on this timestep
+ <I>off</I> arg = M = do not average this value
+ M = value # from 1 to Nvalues
+ <I>file</I> arg = filename
+ filename = name of file to output time averages to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>title3</I> arg = string
+ string = text to print as 3rd line of output file, only for vector mode
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
+fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
+ title1 "My output values"
+fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more global values as inputs every few timesteps, and
+average them over longer timescales. The resulting averages can be
+used by other <A HREF = "Section_howto.html#howto_15">output commands</A> such as
+<A HREF = "thermo_style.html">thermo_style custom</A>, and can also be written to a
+file. Note that if no time averaging is done, this command can be
+used as a convenient way to simply output one or more global values to
+a file.
+</P>
+<P>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+</P>
+<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
+<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity. If
+you wish to spatial- or time-average or histogram per-atom quantities
+from a compute, fix, or variable, then see the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>,
+or <A HREF = "fix_ave_histo.html">fix ave/histo</A> commands. If you wish to sum a
+per-atom quantity into a single global quantity, see the <A HREF = "compute_reduce.html">compute
+reduce</A> command.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
+do not have the word <I>atom</I> in their style name. Only a few
+<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
+individual fixes for info on which ones produce such values.
+<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
+be used with this fix. Variables of style <I>atom</I> cannot be used,
+since they produce per-atom values.
+</P>
+<P>The input values must either be all scalars or all vectors (or
+arrays), depending on the setting of the <I>mode</I> keyword. In both
+cases, the averaging is performed independently on each input value.
+I.e. each input scalar is averaged independently and each element of
+each input vector (or array) is averaged independently.
+</P>
+<P>If <I>mode</I> = vector, then the input values may either be vectors or
+arrays and all must be the same "length", which is the length of the
+vector or number of rows in the array. If a global array is listed,
+then it is the same as if the individual columns of the array had been
+listed one by one. E.g. these 2 fix ave/time commands are equivalent,
+since the <A HREF = "compute_rdf.html">compute rdf</A> command creates, in this
+case, a global array with 3 columns, each of length 50:
+</P>
+<PRE>compute myRDF all rdf 50 1 2
+fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
+fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
+</PRE>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average. The final averaged quantities are generated on timesteps
+that are a mlutiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+</P>
+<HR>
+
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If <I>mode</I> = scalar, then if
+no bracketed term is appended, the global scalar calculated by the
+compute is used. If a bracketed term is appended, the Ith element of
+the global vector calculated by the compute is used. If <I>mode</I> =
+vector, then if no bracketed term is appended, the global vector
+calculated by the compute is used. Or if the compute calculates an
+array, all of the columns of the global array are used as if they had
+been specified as individual vectors (see description above). If a
+bracketed term is appended, the Ith column of the global array
+calculated by the compute is used.
+</P>
+<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix ave/time. Or it can be a compute defined
+not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
+output</A> or other fixes such as <A HREF = "fix_nh.html">fix
+nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See
+the doc pages for these commands which give the IDs of these computes.
+Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them
+to LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If <I>mode</I> = scalar, then if
+no bracketed term is appended, the global scalar calculated by the fix
+is used. If a bracketed term is appended, the Ith element of the
+global vector calculated by the fix is used. If <I>mode</I> = vector, then
+if no bracketed term is appended, the global vector calculated by the
+fix is used. Or if the fix calculates an array, all of the columns of
+the global array are used as if they had been specified as individual
+vectors (see description above). If a bracketed term is appended, the
+Ith column of the global array calculated by the fix is used.
+</P>
+<P>Note that some fixes only produce their values on certain timesteps,
+which must be compatible with <I>Nevery</I>, else an error will result.
+Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Variables can only be
+used as input for <I>mode</I> = scalar. Only equal-style variables can be
+referenced. See the <A HREF = "variable.html">variable</A> command for details.
+Note that variables of style <I>equal</I> define a formula which can
+reference individual atom properties or thermodynamic keywords, or
+they can invoke other computes, fixes, or variables when they are
+evaluated, so this is a very general means of specifying quantities to
+time average.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+</P>
+<P>If the <I>mode</I> keyword is set to <I>scalar</I>, then all input values must
+be global scalars, or elements of global vectors. If the <I>mode</I>
+keyword is set to <I>vector</I>, then all input values must be global
+vectors, or columns of global arrays. They can also be global arrays,
+which are converted into a series of global vectors (one per column),
+as explained above.
+</P>
+<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
+steps are averaged with values produced on previous steps that were
+multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
+that are multiples of <I>Nfreq</I> are independent of each other; they are
+output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cummulative sense before being output. Each output value is thus the
+average of the value produced on that timestep with all preceding
+values. This running average begins when the fix is defined; it can
+only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
+command, or by re-defining the fix by re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000. Outputs on early steps will average over less than M
+values if they are not available.
+</P>
+<P>The <I>start</I> keyword specifies what timestep averaging will begin on.
+The default is step 0. Often input values can be 0.0 at time 0, so
+setting <I>start</I> to a larger value can avoid including a 0.0 in a
+running or windowed average.
+</P>
+<P>The <I>off</I> keyword can be used to flag any of the input values. If a
+value is flagged, it will not be time averaged. Instead the most
+recent input value will always be stored and output. This is useful
+if one of more of the inputs produced by a compute or fix or variable
+are effectively constant or are simply current values. E.g. they are
+being written to a file with other time-averaged values for purposes
+of creating well-formatted output.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+steps, one quantity or vector of quantities is written to the file for
+each input value specified in the fix ave/time command. For <I>mode</I> =
+scalar, this means a single line is written each time output is
+performed. Thus the file ends up to be a series of lines, i.e. one
+column of numbers for each input value. For <I>mode</I> = vector, an array
+of numbers is written each time output is performed. The number of
+rows is the length of the input vectors, and the number of columns is
+the number of values. Thus the file ends up to be a series of these
+array sections.
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
+the strings that will be printed as the first 2 or 3 lines of the
+output file, assuming the <I>file</I> keyword was used. LAMMPS uses
+default values for each of these, so they do not need to be specified.
+</P>
+<P>By default, these header lines are as follows for <I>mode</I> = scalar:
+</P>
+<PRE># Time-averaged data for fix ID
+# TimeStep value1 value2 ...
+</PRE>
+<P>In the first line, ID is replaced with the fix-ID. In the second line
+the values are replaced with the appropriate fields from the fix
+ave/time command. There is no third line in the header of the file,
+so the <I>title3</I> setting is ignored when <I>mode</I> = scalar.
+</P>
+<P>By default, these header lines are as follows for <I>mode</I> = vector:
+</P>
+<PRE># Time-averaged data for fix ID
+# TimeStep Number-of-rows
+# Row value1 value2 ...
+</PRE>
+<P>In the first line, ID is replaced with the fix-ID. The second line
+describes the two values that are printed at the first of each section
+of output. In the third line the values are replaced with the
+appropriate fields from the fix ave/time command.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a global scalar or global vector or global array
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The values can only be
+accessed on timesteps that are multiples of <I>Nfreq</I> since that is when
+averaging is performed.
+</P>
+<P>A scalar is produced if only a single input value is averaged and
+<I>mode</I> = scalar. A vector is produced if multiple input values are
+averaged for <I>mode</I> = scalar, or a single input value for <I>mode</I> =
+vector. In the first case, the length of the vector is the number of
+inputs. In the second case, the length of the vector is the same as
+the length of the input vector. An array is produced if multiple
+input values are averaged and <I>mode</I> = vector. The global array has #
+of rows = length of the input vectors and # of columns = number of
+inputs.
+</P>
+<P>If the fix prouduces a scalar or vector, then the scalar and each
+element of the vector can be either "intensive" or "extensive",
+depending on whether the values contributing to the scalar or vector
+element are "intensive" or "extensive". If the fix produces an array,
+then all elements in the array must be the same, either "intensive" or
+"extensive". If a compute or fix provides the value being time
+averaged, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
+<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are mode = scalar, ave = one, start = 0, no file
+output, title 1,2,3 = strings as described above, and no off settings
+for any input values.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_aveforce.html b/doc/doc2/fix_aveforce.html
new file mode 100644
index 000000000..d7c1011ce
--- /dev/null
+++ b/doc/doc2/fix_aveforce.html
@@ -0,0 +1,128 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix aveforce command
+</H3>
+<H3>fix aveforce/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID aveforce fx fy fz keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>aveforce = style name of this fix command
+
+<LI>fx,fy,fz = force component values (force units)
+
+<PRE> any of fx,fy,fz can be a variable (see below)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to have added force
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix pressdown topwall aveforce 0.0 -1.0 0.0
+fix 2 bottomwall aveforce NULL -1.0 0.0 region top
+fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply an additional external force to a group of atoms in such a way
+that every atom experiences the same force. This is useful for
+pushing on wall or boundary atoms so that the structure of the wall
+does not change over time.
+</P>
+<P>The existing force is averaged for the group of atoms, component by
+component. The actual force on each atom is then set to the average
+value plus the component specified in this command. This means each
+atom in the group receives the same force.
+</P>
+<P>Any of the fx,fy,fz values can be specified as NULL which means the
+force in that dimension is not changed. Note that this is not the
+same as specifying a 0.0 value, since that sets all forces to the same
+average value without adding in any additional force.
+</P>
+<P>Any of the 3 quantities defining the force components can be specified
+as an equal-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.
+If the value is a variable, it should be specified as v_name, where
+name is the variable name. In this case, the variable will be
+evaluated each timestep, and its value used to determine the average
+force.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent average force.
+</P>
+<P>If the <I>region</I> keyword is used, the atom must also be in the
+specified geometric <A HREF = "region.html">region</A> in order to have force added
+to it.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global 3-vector of forces, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix. The vector values calculated by this
+fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_setforce.html">fix setforce</A>, <A HREF = "fix_addforce.html">fix addforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_balance.html b/doc/doc2/fix_balance.html
new file mode 100644
index 000000000..5634916d2
--- /dev/null
+++ b/doc/doc2/fix_balance.html
@@ -0,0 +1,361 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix balance command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID balance Nfreq thresh style args keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>balance = style name of this fix command
+
+<LI>Nfreq = perform dynamic load balancing every this many steps
+
+<LI>thresh = imbalance threshhold that must be exceeded to perform a re-balance
+
+<LI>style = <I>shift</I> or <I>rcb</I>
+
+<PRE> shift args = dimstr Niter stopthresh
+ dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+ Niter = # of times to iterate within each dimension of dimstr sequence
+ stopthresh = stop balancing when this imbalance threshhold is reached
+ rcb args = none
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>out</I>
+
+<PRE> <I>out</I> value = filename
+ filename = write each processor's sub-domain to a file, at each re-balancing
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 all balance 1000 1.05 shift x 10 1.05
+fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance
+fix 2 all balance 1000 1.1 rcb
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command adjusts the size and shape of processor sub-domains
+within the simulation box, to attempt to balance the number of
+particles and thus the computational cost (load) evenly across
+processors. The load balancing is "dynamic" in the sense that
+rebalancing is performed periodically during the simulation. To
+perform "static" balancing, before or between runs, see the
+<A HREF = "balance.html">balance</A> command.
+</P>
+<P>Load-balancing is typically only useful if the particles in the
+simulation box have a spatially-varying density distribution. E.g. a
+model of a vapor/liquid interface, or a solid with an irregular-shaped
+geometry containing void regions. In this case, the LAMMPS default of
+dividing the simulation box volume into a regular-spaced grid of 3d
+bricks, with one equal-volume sub-domain per processor, may assign
+very different numbers of particles per processor. This can lead to
+poor performance when the simulation is run in parallel.
+</P>
+<P>Note that the <A HREF = "processors.html">processors</A> command allows some control
+over how the box volume is split across processors. Specifically, for
+a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
+Pz, subject to the constraint that Px * Py * Pz = P, the total number
+of processors. This is sufficient to achieve good load-balance for
+some problems on some processor counts. However, all the processor
+sub-domains will still have the same shape and same volume.
+</P>
+<P>On a particular timestep, a load-balancing operation is only performed
+if the current "imbalance factor" in particles owned by each processor
+exceeds the specified <I>thresh</I> parameter. The imbalance factor is
+defined as the maximum number of particles owned by any processor,
+divided by the average number of particles per processor. Thus an
+imbalance factor of 1.0 is perfect balance.
+</P>
+<P>As an example, for 10000 particles running on 10 processors, if the
+most heavily loaded processor has 1200 particles, then the factor is
+1.2, meaning there is a 20% imbalance. Note that re-balances can be
+forced even if the current balance is perfect (1.0) be specifying a
+<I>thresh</I> < 1.0.
+</P>
+<P>IMPORTANT NOTE: This command attempts to minimize the imbalance
+factor, as defined above. But depending on the method a perfect
+balance (1.0) may not be achieved. For example, "grid" methods
+(defined below) that create a logical 3d grid cannot achieve perfect
+balance for many irregular distributions of particles. Likewise, if a
+portion of the system is a perfect lattice, e.g. the initial system is
+generated by the <A HREF = "create_atoms.html">create_atoms</A> command, then "grid"
+methods may be unable to achieve exact balance. This is because
+entire lattice planes will be owned or not owned by a single
+processor.
+</P>
+<P>IMPORTANT NOTE: The imbalance factor is also an estimate of the
+maximum speed-up you can hope to achieve by running a perfectly
+balanced simulation versus an imbalanced one. In the example above,
+the 10000 particle simulation could run up to 20% faster if it were
+perfectly balanced, versus when imbalanced. However, computational
+cost is not strictly proportional to particle count, and changing the
+relative size and shape of processor sub-domains may lead to
+additional computational and communication overheads, e.g. in the PPPM
+solver used via the <A HREF = "kspace_style.html">kspace_style</A> command. Thus
+you should benchmark the run times of a simulation before and after
+balancing.
+</P>
+<HR>
+
+<P>The method used to perform a load balance is specified by one of the
+listed styles, which are described in detail below. There are 2 kinds
+of styles.
+</P>
+<P>The <I>shift</I> style is a "grid" method which produces a logical 3d grid
+of processors. It operates by changing the cutting planes (or lines)
+between processors in 3d (or 2d), to adjust the volume (area in 2d)
+assigned to each processor, as in the following 2d diagram where
+processor sub-domains are shown and atoms are colored by the processor
+that owns them. The leftmost diagram is the default partitioning of
+the simulation box across processors (one sub-box for each of 16
+processors); the middle diagram is after a "grid" method has been
+applied.
+</P>
+<CENTER><A HREF = "JPG/balance_uniform.jpg"><IMG SRC = "JPG/balance_uniform_small.jpg"></A><A HREF = "JPG/balance_nonuniform.jpg"><IMG SRC = "JPG/balance_nonuniform_small.jpg"></A><A HREF = "JPG/balance_rcb.jpg"><IMG SRC = "JPG/balance_rcb_small.jpg"></A>
+</CENTER>
+<P>The <I>rcb</I> style is a "tiling" method which does not produce a logical
+3d grid of processors. Rather it tiles the simulation domain with
+rectangular sub-boxes of varying size and shape in an irregular
+fashion so as to have equal numbers of particles in each sub-box, as
+in the rightmost diagram above.
+</P>
+<P>The "grid" methods can be used with either of the
+<A HREF = "comm_style.html">comm_style</A> command options, <I>brick</I> or <I>tiled</I>. The
+"tiling" methods can only be used with <A HREF = "comm_style.html">comm_style
+tiled</A>.
+</P>
+<P>When a "grid" method is specified, the current domain partitioning can
+be either a logical 3d grid or a tiled partitioning. In the former
+case, the current logical 3d grid is used as a starting point and
+changes are made to improve the imbalance factor. In the latter case,
+the tiled partitioning is discarded and a logical 3d grid is created
+with uniform spacing in all dimensions. This is the starting point
+for the balancing operation.
+</P>
+<P>When a "tiling" method is specified, the current domain partitioning
+("grid" or "tiled") is ignored, and a new partitioning is computed
+from scratch.
+</P>
+<HR>
+
+<P>The <I>group-ID</I> is currently ignored. In the future it may be used to
+determine what particles are considered for balancing. Normally it
+would only makes sense to use the <I>all</I> group. But in some cases it
+may be useful to balance on a subset of the particles, e.g. when
+modeling large nanoparticles in a background of small solvent
+particles.
+</P>
+<P>The <I>Nfreq</I> setting determines how often a rebalance is performed. If
+<I>Nfreq</I> > 0, then rebalancing will occur every <I>Nfreq</I> steps. Each
+time a rebalance occurs, a reneighboring is triggered, so <I>Nfreq</I>
+should not be too small. If <I>Nfreq</I> = 0, then rebalancing will be
+done every time reneighboring normally occurs, as determined by the
+the <A HREF = "neighbor.html">neighbor</A> and <A HREF = "neigh_modify.html">neigh_modify</A>
+command settings.
+</P>
+<P>On rebalance steps, rebalancing will only be attempted if the current
+imbalance factor, as defined above, exceeds the <I>thresh</I> setting.
+</P>
+<HR>
+
+<P>The <I>shift</I> style invokes a "grid" method for balancing, as described
+above. It changes the positions of cutting planes between processors
+in an iterative fashion, seeking to reduce the imbalance factor.
+</P>
+<P>The <I>dimstr</I> argument is a string of characters, each of which must be
+an "x" or "y" or "z". Eacn character can appear zero or one time,
+since there is no advantage to balancing on a dimension more than
+once. You should normally only list dimensions where you expect there
+to be a density variation in the particles.
+</P>
+<P>Balancing proceeds by adjusting the cutting planes in each of the
+dimensions listed in <I>dimstr</I>, one dimension at a time. For a single
+dimension, the balancing operation (described below) is iterated on up
+to <I>Niter</I> times. After each dimension finishes, the imbalance factor
+is re-computed, and the balancing operation halts if the <I>stopthresh</I>
+criterion is met.
+</P>
+<P>A rebalance operation in a single dimension is performed using a
+density-dependent recursive multisectioning algorithm, where the
+position of each cutting plane (line in 2d) in the dimension is
+adjusted independently. This is similar to a recursive bisectioning
+for a single value, except that the bounds used for each bisectioning
+take advantage of information from neighboring cuts if possible, as
+well as counts of particles at the bounds on either side of each cuts,
+which themselves were cuts in previous iterations. The latter is used
+to infer a density of pariticles near each of the current cuts. At
+each iteration, the count of particles on either side of each plane is
+tallied. If the counts do not match the target value for the plane,
+the position of the cut is adjusted based on the local density. The
+low and high bounds are adjusted on each iteration, using new count
+information, so that they become closer together over time. Thus as
+the recursion progresses, the count of particles on either side of the
+plane gets closer to the target value.
+</P>
+<P>The density-dependent part of this algorithm is often an advantage
+when you rebalance a system that is already nearly balanced. It
+typically converges more quickly than the geometric bisectioning
+algorithm used by the <A HREF = "balance.html">balance</A> command. However, if can
+be a disadvantage if you attempt to rebalance a system that is far
+from balanced, and converge more slowly. In this case you probably
+want to use the <A HREF = "balance.html">balance</A> command before starting a run,
+so that you begin the run with a balanced system.
+</P>
+<P>Once the rebalancing is complete and final processor sub-domains
+assigned, particles migrate to their new owning processor as part of
+the normal reneighboring procedure.
+</P>
+<P>IMPORTANT NOTE: At each rebalance operation, the bisectioning for each
+cutting plane (line in 2d) typcially starts with low and high bounds
+separated by the extent of a processor's sub-domain in one dimension.
+The size of this bracketing region shrinks based on the local density,
+as described above, which should typically be 1/2 or more every
+iteration. Thus if <I>Niter</I> is specified as 10, the cutting plane will
+typically be positioned to better than 1 part in 1000 accuracy
+(relative to the perfect target position). For <I>Niter</I> = 20, it will
+be accurate to better than 1 part in a million. Thus there is no need
+to set <I>Niter</I> to a large value. This is especially true if you are
+rebalancing often enough that each time you expect only an incremental
+adjustement in the cutting planes is necessary. LAMMPS will check if
+the threshold accuracy is reached (in a dimension) is less iterations
+than <I>Niter</I> and exit early.
+</P>
+<HR>
+
+<P>The <I>rcb</I> style invokes a "tiled" method for balancing, as described
+above. It performs a recursive coordinate bisectioning (RCB) of the
+simulation domain. The basic idea is as follows.
+</P>
+<P>The simulation domain is cut into 2 boxes by an axis-aligned cut in
+the longest dimension, leaving one new box on either side of the cut.
+All the processors are also partitioned into 2 groups, half assigned
+to the box on the lower side of the cut, and half to the box on the
+upper side. (If the processor count is odd, one side gets an extra
+processor.) The cut is positioned so that the number of atoms in the
+lower box is exactly the number that the processors assigned to that
+box should own for load balance to be perfect. This also makes load
+balance for the upper box perfect. The positioning is done
+iteratively, by a bisectioning method. Note that counting atoms on
+either side of the cut requires communication between all processors
+at each iteration.
+</P>
+<P>That is the procedure for the first cut. Subsequent cuts are made
+recursively, in exactly the same manner. The subset of processors
+assigned to each box make a new cut in the longest dimension of that
+box, splitting the box, the subset of processsors, and the atoms in
+the box in two. The recursion continues until every processor is
+assigned a sub-box of the entire simulation domain, and owns the atoms
+in that sub-box.
+</P>
+<HR>
+
+<P>The <I>out</I> keyword writes a text file to the specified <I>filename</I> with
+the results of each rebalancing operation. The file contains the
+bounds of the sub-domain for each processor after the balancing
+operation completes. The format of the file is compatible with the
+<A HREF = "pizza">Pizza.py</A> <I>mdump</I> tool which has support for manipulating and
+visualizing mesh files. An example is shown here for a balancing by 4
+processors for a 2d problem:
+</P>
+<PRE>ITEM: TIMESTEP
+0
+ITEM: NUMBER OF NODES
+16
+ITEM: BOX BOUNDS
+0 10
+0 10
+0 10
+ITEM: NODES
+1 1 0 0 0
+2 1 5 0 0
+3 1 5 5 0
+4 1 0 5 0
+5 1 5 0 0
+6 1 10 0 0
+7 1 10 5 0
+8 1 5 5 0
+9 1 0 5 0
+10 1 5 5 0
+11 1 5 10 0
+12 1 10 5 0
+13 1 5 5 0
+14 1 10 5 0
+15 1 10 10 0
+16 1 5 10 0
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF SQUARES
+4
+ITEM: SQUARES
+1 1 1 2 3 4
+2 1 5 6 7 8
+3 1 9 10 11 12
+4 1 13 14 15 16
+</PRE>
+<P>The coordinates of all the vertices are listed in the NODES section, 5
+per processor. Note that the 4 sub-domains share vertices, so there
+will be duplicate nodes in the list.
+</P>
+<P>The "SQUARES" section lists the node IDs of the 4 vertices in a
+rectangle for each processor (1 to 4).
+</P>
+<P>For a 3d problem, the syntax is similar with 8 vertices listed for
+each processor, instead of 4, and "SQUARES" replaced by "CUBES".
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which is the imbalance factor
+after the most recent rebalance and a global vector of length 3 with
+additional information about the most recent rebalancing. The 3
+values in the vector are as follows:
+</P>
+<UL><LI>1 = max # of particles per processor
+<LI>2 = total # iterations performed in last rebalance
+<LI>3 = imbalance factor right before the last rebalance was performed
+</UL>
+<P>As explained above, the imbalance factor is the ratio of the maximum
+number of particles on any processor to the average number of
+particles per processor.
+</P>
+<P>These quantities can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar and vector values
+calculated by this fix are "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>For 2d simulations, a "z" cannot appear in <I>dimstr</I> for the <I>shift</I>
+style.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "processors.html">processors</A>, <A HREF = "balance.html">balance</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_bond_break.html b/doc/doc2/fix_bond_break.html
new file mode 100644
index 000000000..2bb8d5e66
--- /dev/null
+++ b/doc/doc2/fix_bond_break.html
@@ -0,0 +1,158 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix bond/break command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>bond/break = style name of this fix command
+
+<LI>Nevery = attempt bond breaking every this many steps
+
+<LI>bondtype = type of bonds to break
+
+<LI>Rmax = bond longer than Rmax can break (distance units)
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>prob</I>
+
+<PRE> <I>prob</I> values = fraction seed
+ fraction = break a bond with this probability if otherwise eligible
+ seed = random number seed (positive integer)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 5 all bond/break 10 2 1.2
+fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Break bonds between pairs of atoms as a simulation runs according to
+specified criteria. This can be used to model the dissolution of a
+polymer network due to stretching of the simulation box or other
+deformations. In this context, a bond means an interaction between a
+pair of atoms computed by the <A HREF = "bond_style.html">bond_style</A> command.
+Once the bond is broken it will be permanently deleted, as will all
+angle, dihedral, and improper interactions that bond is part of.
+</P>
+<P>This is different than a <A HREF = "pair_style.html">pairwise</A> bond-order
+potential such as Tersoff or AIREBO which infers bonds and many-body
+interactions based on the current geometry of a small cluster of atoms
+and effectively creates and destroys bonds and higher-order many-body
+interactions from timestep to timestep as atoms move.
+</P>
+<P>A check for possible bond breakage is performed every <I>Nevery</I>
+timesteps. If two bonded atoms I,J are further than a distance <I>Rmax</I>
+of each other, if the bond is of type <I>bondtype</I>, and if both I and J
+are in the specified fix group, then I,J is labeled as a "possible"
+bond to break.
+</P>
+<P>If several bonds involving an atom are stretched, it may have multiple
+possible bonds to break. Every atom checks its list of possible bonds
+to break and labels the longest such bond as its "sole" bond to break.
+After this is done, if atom I is bonded to atom J in its sole bond,
+and atom J is bonded to atom I in its sole bond, then the I,J bond is
+"eligible" to be broken.
+</P>
+<P>Note that these rules mean an atom will only be part of at most one
+broken bond on a given timestep. It also means that if atom I chooses
+atom J as its sole partner, but atom J chooses atom K is its sole
+partner (due to Rjk > Rij), then this means atom I will not be part of
+a broken bond on this timestep, even if it has other possible bond
+partners.
+</P>
+<P>The <I>prob</I> keyword can effect whether an eligible bond is actually
+broken. The <I>fraction</I> setting must be a value between 0.0 and 1.0.
+A uniform random number between 0.0 and 1.0 is generated and the
+eligible bond is only broken if the random number < fraction.
+</P>
+<P>When a bond is broken, data structures within LAMMPS that store bond
+topology are updated to reflect the breakage. Likewise, if the bond
+is part of a 3-body (angle) or 4-body (dihedral, improper)
+interaction, that interaction is removed as well. These changes
+typically affect pairwise interactions between atoms that used to be
+part of bonds, angles, etc.
+</P>
+<P>IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom. Even though
+one molecule becomes two moleclues due to the broken bond, all atoms
+in both new moleclues retain their original molecule IDs.
+</P>
+<P>Computationally, each timestep this fix operates, it loops over all
+the bonds in the system and computes distances between pairs of bonded
+atoms. It also communicates between neighboring processors to
+coordinate which bonds are broken. Moreover, if any bonds are broken,
+neighbor lists must be immediately updated on the same timestep. This
+is to insure that any pairwise interactions that should be turned "on"
+due to a bond breaking, because they are no longer excluded by the
+presence of the bond and the settings of the
+<A HREF = "special_bonds.html">special_bonds</A> command, will be immediately
+recognized. All of these operations increase the cost of a timestep.
+Thus you should be cautious about invoking this fix too frequently.
+</P>
+<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
+local</A> command.
+</P>
+<P>IMPORTANT NOTE: Breaking a bond typically alters the energy of a
+system. You should be careful not to choose bond breaking criteria
+that induce a dramatic change in energy. For example, if you define a
+very stiff harmonic bond and break it when 2 atoms are separated by a
+distance far from the equilibribum bond length, then the 2 atoms will
+be dramatically released when the bond is broken. More generally, you
+may need to thermostat your system to compensate for energy changes
+resulting from broken bonds (and angles, dihedrals, impropers).
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes two statistics which it stores in a global vector of
+length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The vector values calculated
+by this fix are "intensive".
+</P>
+<P>These are the 2 quantities:
+</P>
+<UL><LI>(1) # of bonds broken on the most recent breakage timestep
+<LI>(2) cummulative # of bonds broken
+</UL>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_bond_create.html">fix bond/create</A>, <A HREF = "fix_bond_swap.html">fix
+bond/swap</A>, <A HREF = "dump.html">dump local</A>,
+<A HREF = "special_bonds.html">special_bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are prob = 1.0.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_bond_create.html b/doc/doc2/fix_bond_create.html
new file mode 100644
index 000000000..f0cd61dba
--- /dev/null
+++ b/doc/doc2/fix_bond_create.html
@@ -0,0 +1,256 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix bond/create command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>bond/create = style name of this fix command
+
+<LI>Nevery = attempt bond creation every this many steps
+
+<LI>itype,jtype = atoms of itype can bond to atoms of jtype
+
+<LI>Rmin = 2 atoms separated by less than Rmin can bond (distance units)
+
+<LI>bondtype = type of created bonds
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I> or <I>atype</I> or <I>dtype</I> or <I>itype</I>
+
+<PRE> <I>iparam</I> values = maxbond, newtype
+ maxbond = max # of bonds of bondtype the itype atom can have
+ newtype = change the itype atom to this type when maxbonds exist
+ <I>jparam</I> values = maxbond, newtype
+ maxbond = max # of bonds of bondtype the jtype atom can have
+ newtype = change the jtype atom to this type when maxbonds exist
+ <I>prob</I> values = fraction seed
+ fraction = create a bond with this probability if otherwise eligible
+ seed = random number seed (positive integer)
+ <I>atype</I> value = angletype
+ angletype = type of created angles
+ <I>dtype</I> value = dihedraltype
+ dihedraltype = type of created dihedrals
+ <I>itype</I> value = impropertype
+ impropertype = type of created impropers
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 5 all bond/create 10 1 2 0.8 1
+fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
+fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Create bonds between pairs of atoms as a simulation runs according to
+specified criteria. This can be used to model cross-linking of
+polymers, the formation of a percolation network, etc. In this
+context, a bond means an interaction between a pair of atoms computed
+by the <A HREF = "bond_style.html">bond_style</A> command. Once the bond is created
+it will be permanently in place. Optionally, the creation of a bond
+can also create angle, dihedral, and improper interactions that bond
+is part of. See the discussion of the <I>atype</I>, <I>dtype</I>, and <I>itype</I>
+keywords below.
+</P>
+<P>This is different than a <A HREF = "pair_style.html">pairwise</A> bond-order
+potential such as Tersoff or AIREBO which infers bonds and many-body
+interactions based on the current geometry of a small cluster of atoms
+and effectively creates and destroys bonds and higher-order many-body
+interactions from timestep to timestep as atoms move.
+</P>
+<P>A check for possible new bonds is performed every <I>Nevery</I> timesteps.
+If two atoms I,J are within a distance <I>Rmin</I> of each other, if I is
+of atom type <I>itype</I>, if J is of atom type <I>jtype</I>, if both I and J
+are in the specified fix group, if a bond does not already exist
+between I and J, and if both I and J meet their respective <I>maxbond</I>
+requirement (explained below), then I,J is labeled as a "possible"
+bond pair.
+</P>
+<P>If several atoms are close to an atom, it may have multiple possible
+bond partners. Every atom checks its list of possible bond partners
+and labels the closest such partner as its "sole" bond partner. After
+this is done, if atom I has atom J as its sole partner, and atom J has
+atom I as its sole partner, then the I,J bond is "eligible" to be
+formed.
+</P>
+<P>Note that these rules mean an atom will only be part of at most one
+created bond on a given timestep. It also means that if atom I
+chooses atom J as its sole partner, but atom J chooses atom K is its
+sole partner (due to Rjk < Rij), then this means atom I will not form
+a bond on this timestep, even if it has other possible bond partners.
+</P>
+<P>It is permissible to have <I>itype</I> = <I>jtype</I>. <I>Rmin</I> must be <= the
+pairwise cutoff distance between <I>itype</I> and <I>jtype</I> atoms, as defined
+by the <A HREF = "pair_style.html">pair_style</A> command.
+</P>
+<P>The <I>iparam</I> and <I>jparam</I> keywords can be used to limit the bonding
+functionality of the participating atoms. Each atom keeps track of
+how many bonds of <I>bondtype</I> it already has. If atom I of
+itype already has <I>maxbond</I> bonds (as set by the <I>iparam</I>
+keyword), then it will not form any more. Likewise for atom J. If
+<I>maxbond</I> is set to 0, then there is no limit on the number of bonds
+that can be formed with that atom.
+</P>
+<P>The <I>newtype</I> value for <I>iparam</I> and <I>jparam</I> can be used to change
+the atom type of atom I or J when it reaches <I>maxbond</I> number of bonds
+of type <I>bondtype</I>. This means it can now interact in a pairwise
+fashion with other atoms in a different way by specifying different
+<A HREF = "pair_coeff.html">pair_coeff</A> coefficients. If you do not wish the
+atom type to change, simply specify <I>newtype</I> as <I>itype</I> or <I>jtype</I>.
+</P>
+<P>The <I>prob</I> keyword can also effect whether an eligible bond is
+actually created. The <I>fraction</I> setting must be a value between 0.0
+and 1.0. A uniform random number between 0.0 and 1.0 is generated and
+the eligible bond is only created if the random number < fraction.
+</P>
+<P>Any bond that is created is assigned a bond type of <I>bondtype</I>
+</P>
+<P>When a bond is created, data structures within LAMMPS that store bond
+topology are updated to reflect the creation. If the bond is part of
+new 3-body (angle) or 4-body (dihedral, improper) interactions, you
+can choose to create new angles, dihedrals, impropers as well, using
+the <I>atype</I>, <I>dtype</I>, and <I>itype</I> keywords. All of these changes
+typically affect pairwise interactions between atoms that are now part
+of new bonds, angles, etc.
+</P>
+<P>IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom. Even though two
+molecules become one moleclue due to the created bond, all atoms in
+the new moleclue retain their original molecule IDs.
+</P>
+<P>If the <I>atype</I> keyword is used and if an angle potential is defined
+via the <A HREF = "angle.html">angle_style</A> command, then any new 3-body
+interactions inferred by the creation of a bond will create new angles
+of type <I>angletype</I>, with parameters assigned by the corresponding
+<A HREF = "angle_coeff.html">angle_coeff</A> command. Likewise, the <I>dtype</I> and
+<I>itype</I> keywords will create new dihedrals and impropers of type
+<I>dihedraltype</I> and <I>impropertype</I>.
+</P>
+<P>IMPORTANT NOTE: To create a new bond, the internal LAMMPS data
+structures that store this information must have space for it. When
+LAMMPS is initialized from a data file, the list of bonds is scanned
+and the maximum number of bonds per atom is tallied. If some atom
+will acquire more bonds than this limit as this fix operates, then the
+"extra bond per atom" parameter must be set to allow for it. Ditto
+for "extra angle per atom", "extra dihedral per atom", and "extra
+improper per atom" if angles, dihedrals, or impropers are being added
+when bonds are created. See the <A HREF = "read_data.html">read_data</A> or
+<A HREF = "create_box.html">create_box</A> command for more details. Note that a
+data file with no atoms can be used if you wish to add unbonded atoms
+via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a
+percolation simulation.
+</P>
+<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
+topology of the system) for use in weighting pairwise interactions for
+bonded atoms. Note that adding a single bond always adds a new 1st
+neighbor but may also induce *many* new 2nd and 3rd neighbors,
+depending on the molecular topology of your system. The "extra
+special per atom" parameter must typically be set to allow for the new
+maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
+There are 3 ways to do this. See the <A HREF = "read_data.html">read_data</A> or
+<A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
+details.
+</P>
+<P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or
+<I>itype</I> keywords, the list of topological neighbors is updated for
+atoms affected by the new bond. This in turn affects which neighbors
+are considered for pairwise interactions, using the weighting rules
+set by the <A HREF = "special_bonds.html">special_bonds</A> command. Consider a new
+bond created between atoms I,J. If J has a bonded neighbor K, then K
+becomes a 2nd neighbor of I. Even if the <I>atype</I> keyword is not used
+to create angle I-J-K, the pairwise interaction between I and K will
+be potentially turned off or weighted by the 1-3 weighting specified
+by the <A HREF = "special_bonds.html">special_bonds</A> command. This is the case
+even if the "angle yes" option was used with that command. The same
+is true for 3rd neighbors (1-4 interactions), the <I>dtype</I> keyword, and
+the "dihedral yes" option used with the
+<A HREF = "special_bonds.html">special_bonds</A> command.
+</P>
+<P>Note that even if your simulation starts with no bonds, you must
+define a <A HREF = "bond_style.html">bond_style</A> and use the
+<A HREF = "bond_coeff.html">bond_coeff</A> command to specify coefficients for the
+<I>bondtype</I>. Similarly, if new atom types are specified by the
+<I>iparam</I> or <I>jparam</I> keywords, they must be within the range of atom
+types allowed by the simulation and pairwise coefficients must be
+specified for the new types.
+</P>
+<P>Computationally, each timestep this fix operates, it loops over
+neighbor lists and computes distances between pairs of atoms in the
+list. It also communicates between neighboring processors to
+coordinate which bonds are created. Moreover, if any bonds are
+created, neighbor lists must be immediately updated on the same
+timestep. This is to insure that any pairwise interactions that
+should be turned "off" due to a bond creation, because they are now
+excluded by the presence of the bond and the settings of the
+<A HREF = "special_bonds.html">special_bonds</A> command, will be immediately
+recognized. All of these operations increase the cost of a timestep.
+Thus you should be cautious about invoking this fix too frequently.
+</P>
+<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
+local</A> command.
+</P>
+<P>IMPORTANT NOTE: Creating a bond typically alters the energy of a
+system. You should be careful not to choose bond creation criteria
+that induce a dramatic change in energy. For example, if you define a
+very stiff harmonic bond and create it when 2 atoms are separated by a
+distance far from the equilibribum bond length, then the 2 atoms will
+oscillate dramatically when the bond is formed. More generally, you
+may need to thermostat your system to compensate for energy changes
+resulting from created bonds (and angles, dihedrals, impropers).
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes two statistics which it stores in a global vector of
+length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The vector values calculated
+by this fix are "intensive".
+</P>
+<P>These are the 2 quantities:
+</P>
+<UL><LI>(1) # of bonds created on the most recent creation timestep
+<LI>(2) cummulative # of bonds created
+</UL>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_bond_break.html">fix bond/break</A>, <A HREF = "fix_bond_swap.html">fix
+bond/swap</A>, <A HREF = "dump.html">dump local</A>,
+<A HREF = "special_bonds.html">special_bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are iparam = (0,itype), jparam = (0,jtype), and
+prob = 1.0.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_bond_swap.html b/doc/doc2/fix_bond_swap.html
new file mode 100644
index 000000000..fbf228861
--- /dev/null
+++ b/doc/doc2/fix_bond_swap.html
@@ -0,0 +1,199 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix bond/swap command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID bond/swap Nevery fraction cutoff seed
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>bond/swap = style name of this fix command
+<LI>Nevery = attempt bond swapping every this many steps
+<LI>fraction = fraction of group atoms to consider for swapping
+<LI>cutoff = distance at which swapping will be considered (distance units)
+<LI>seed = random # seed (positive integer)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all bond/swap 50 0.5 1.3 598934
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>In a simulation of polymer chains, this command attempts to swap bonds
+between two different chains, effectively grafting the end of one
+chain onto another chain and vice versa. This is done via Monte Carlo
+rules using the Boltzmann acceptance criterion. The purpose is to
+equilibrate the polymer chain conformations more rapidly than dynamics
+alone would do it, by enabling instantaneous large conformational
+changes in a dense polymer melt. The polymer chains should thus more
+rapidly converge to the proper end-to-end distances and radii of
+gyration. It is designed for use with systems of
+<A HREF = "bond_fene.html">FENE</A> or <A HREF = "bond_harmonic.html">harmonic</A> bead-spring
+polymer chains where each polymer is a linear chain of monomers, but
+LAMMPS does not enforce this requirement, i.e. any
+<A HREF = "bond_style.html">bond_style</A> can be used.
+</P>
+<P>A schematic of the kinds of bond swaps that can occur is shown here:
+</P>
+<CENTER><IMG SRC = "JPG/bondswap.jpg">
+</CENTER>
+<P>On the left, the red and blue chains have two monomers A1 and B1 close
+to each other, which are currently bonded to monomers A2 and B2
+respectively within their own chains. The bond swap operation will
+attempt to delete the A1-A2 and B1-B2 bonds and replace them with
+A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
+two chains on the right are the result and each polymer chain has
+undergone a dramatic conformational change. This reference,
+<A HREF = "#Sides">(Sides)</A> provides more details on how the algorithm works and
+its application:
+</P>
+<P>The bond swapping operation is invoked every <I>Nevery</I> timesteps. If
+any bond is swapped, a re-build of the neighbor lists is triggered,
+since a swap alters the list of which neighbors are considered for
+pairwise interaction. At each invocation, each processor considers a
+random specified <I>fraction</I> of its atoms as potential swapping
+monomers for this timestep. Choosing a small <I>fraction</I> value can
+reduce the likelihood of a reverse swap occurring soon after an
+initial swap.
+</P>
+<P>For each monomer A1, its neighbors are examined to find a possible B1
+monomer. Both A1 and B1 must be in the fix group, their separation
+must be less than the specified <I>cutoff</I>, and the molecule IDs of A1
+and B1 must be the same (see below). If a suitable partner is found,
+the energy change due to swapping the 2 bonds is computed. This
+includes changes in pairwise, bond, and angle energies due to the
+altered connectivity of the 2 chains. Dihedral and improper
+interactions are not allowed to be defined when this fix is used.
+</P>
+<P>If the energy decreases due to the swap operation, the bond swap is
+accepted. If the energy increases it is accepted with probability
+exp(-delta/kT) where delta is the increase in energy, k is the
+Boltzmann constant, and T is the current temperature of the system.
+Whether the swap is accepted or rejected, no other swaps are attempted
+by this processor on this timestep.
+</P>
+<P>The criterion for matching molecule IDs is how bond swaps performed by
+this fix conserve chain length. To use this features you must setup
+the molecule IDs for your polymer chains in a certain way, typically
+in the data file, read by the <A HREF = "read_data.html">read_data</A> comand.
+Consider a system of 6-mer chains. You have 2 choices. If the
+molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
+swaps will conserve chain length. For a particular momoner there will
+be only one other monomer on another chain which is a potential swap
+partner. If the molecule IDs for monomers on each chain are set to
+1,2,3,3,2,1 then swaps will conserve chain length but swaps will be
+able to occur at either end of a chain. Thus for a particular monomer
+there will be 2 possible swap partners on another chain. In this
+scenario, swaps can also occur within a single chain, i.e. the two
+ends of a chain swap with each other.
+</P>
+<P>IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
+where all monomers on a single chain are assigned the same ID
+(different for each chain), then swaps will only occur within the same
+chain. If you assign the same molecule ID to all monomers in all
+chains then inter-chain swaps will occur, but they will not conserve
+chain length. Neither of these scenarios is probably what you want
+for this fix.
+</P>
+<P>IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in
+the new polymer chains can become inconsistent. See the
+<A HREF = "dump.html">dump</A> command for a discussion of image flags. This is not
+an issue for running dynamics, but can affect calculation of some
+diagnostic quantities or the printing of unwrapped coordinates to a
+dump file.
+</P>
+<HR>
+
+<P>This fix computes a temperature each time it is invoked for use by the
+Boltzmann criterion. To do this, the fix creates its own compute of
+style <I>temp</I>, as if this command had been issued:
+</P>
+<PRE>compute fix-ID_temp all temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
+that the ID of the new compute is the fix-ID with underscore + "temp"
+appended and the group for the new compute is "all", so that the
+temperature of the entire system is used.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place. However, in a statistical sense, a
+restarted simulation should produce the same behavior. Also note that
+each processor generates possible swaps independently of other
+processors. Thus if you repeat the same simulation on a different number
+of processors, the specific swaps performed will be different.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used to compute the temperature for
+the Boltzmann criterion.
+</P>
+<P>This fix computes two statistical quantities as a global 2-vector of
+output, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The first component of the
+vector is the cummulative number of swaps performed by all processors.
+The second component of the vector is the cummulative number of swaps
+attempted (whether accepted or rejected). Note that a swap "attempt"
+only occurs when swap partners meeting the criteria described above
+are found on a particular timestep. The vector values calculated by
+this fix are "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The setings of the "special_bond" command must be 0,1,1 in order to
+use this fix, which is typical of bead-spring chains with FENE or
+harmonic bonds. This means that pairwise interactions between bonded
+atoms are turned off, but are turned on between atoms two or three
+hops away along the chain backbone.
+</P>
+<P>Currently, energy changes in dihedral and improper interactions due to
+a bond swap are not considered. Thus a simulation that uses this fix
+cannot use a dihedral or improper potential.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_atom_swap.html">fix atom/swap</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sides"></A>
+
+<P><B>(Sides)</B> Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
+199-208 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_box_relax.html b/doc/doc2/fix_box_relax.html
new file mode 100644
index 000000000..13af69fe3
--- /dev/null
+++ b/doc/doc2/fix_box_relax.html
@@ -0,0 +1,369 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix box/relax command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID box/relax keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>box/relax = style name of this fix command
+
+<PRE>one or more keyword value pairs may be appended
+keyword = <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>nreset</I> or <I>vmax</I> or <I>dilate</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</I> or <I>fixedpoint</I>
+ <I>iso</I> or <I>aniso</I> or <I>tri</I> value = Ptarget = desired pressure (pressure units)
+ <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> value = Ptarget = desired pressure (pressure units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>nreset</I> value = reset reference cell every this many minimizer iterations
+ <I>vmax</I> value = fraction = max allowed volume change in one iteration
+ <I>dilate</I> value = <I>all</I> or <I>partial</I>
+ <I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
+ <I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
+ <I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
+ <I>fixedpoint</I> values = x y z
+ x,y,z = perform relaxation dilation/contraction around this point (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all box/relax iso 0.0 vmax 0.001
+fix 2 water box/relax aniso 0.0 dilate partial
+fix 2 ice box/relax tri 0.0 couple xy nreset 100
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply an external pressure or stress tensor to the simulation box
+during an <A HREF = "minimize.html">energy minimization</A>. This allows the box
+size and shape to vary during the iterations of the minimizer so that
+the final configuration will be both an energy minimum for the
+potential energy of the atoms, and the system pressure tensor will be
+close to the specified external tensor. Conceptually, specifying a
+positive pressure is like squeezing on the simulation box; a negative
+pressure typically allows the box to expand.
+</P>
+<HR>
+
+<P>The external pressure tensor is specified using one or more of the
+<I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>, and <I>couple</I>
+keywords. These keywords give you the ability to specify all 6
+components of an external stress tensor, and to couple various of
+these components together so that the dimensions they represent are
+varied together during the mimimization.
+</P>
+<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
+Triclinic (non-orthogonal) simulation boxes have 6 adjustable
+dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
+data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
+</P>
+<P>The target pressures <I>Ptarget</I> for each of the 6 components of the
+stress tensor can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>,
+<I>xy</I>, <I>xz</I>, <I>yz</I> keywords, which correspond to the 6 simulation box
+dimensions. For example, if the <I>y</I> keyword is used, the y-box length
+will change during the minimization. If the <I>xy</I> keyword is used, the
+xy tilt factor will change. A box dimension will not change if that
+component is not specified.
+</P>
+<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
+simulation box must be triclinic, even if its initial tilt factors are
+0.0.
+</P>
+<P>When the size of the simulation box changes, all atoms are re-scaled
+to new positions, unless the keyword <I>dilate</I> is specified with a
+value of <I>partial</I>, in which case only the atoms in the fix group are
+re-scaled. This can be useful for leaving the coordinates of atoms in
+a solid substrate unchanged and controlling the pressure of a
+surrounding fluid.
+</P>
+<P>The <I>scaleyz</I>, <I>scalexz</I>, and <I>scalexy</I> keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when relaxing triclinic periodic cells. The default
+values <I>yes</I> will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape. Choosing
+<I>no</I> ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to <I>no</I>.
+</P>
+<P>The <I>fixedpoint</I> keyword specifies the fixed point for cell relaxation.
+By default, it is the center of the box. Whatever point is
+chosen will not move during the simulation. For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to <I>fixedpoint</I>, then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle positions at each iteration are
+unaffected by the chosen value, except that all particles are
+displaced by the same amount, different on each iteration.
+</P>
+<P>IMPORTANT NOTE: Appling an external pressure to tilt dimensions <I>xy</I>,
+<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
+tilt factors, i.e. a dramatically deformed simulation box. This
+typically indicates that there is something badly wrong with how the
+simulation was constructed. The two most common sources of this error
+are applying a shear stress to a liquid system or specifying an
+external shear stress tensor that exceeds the yield stress of the
+solid. In either case the minimization may converge to a bogus
+conformation or not converge at all. Also note that if the box shape
+tilts to an extreme shape, LAMMPS will run less efficiently, due to
+the large volume of communication needed to acquire ghost atoms around
+a processor's irregular-shaped sub-domain. For extreme values of
+tilt, LAMMPS may also lose atoms and generate an error.
+</P>
+<P>IMPORTANT NOTE: Performing a minimization with this fix is not a
+mathematically well-defined minimization problem. This is because the
+objective function being minimized changes if the box size/shape
+changes. In practice this means the minimizer can get "stuck" before
+you have reached the desired tolerance. The solution to this is to
+restart the minmizer from the new adjusted box size/shape, since that
+creates a new objective function valid for the new box size/shape.
+Repeat as necessary until the box size/shape has reached its new
+equilibrium.
+</P>
+<HR>
+
+<HR>
+
+<HR>
+
+<P>The <I>couple</I> keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together. The value specified
+with the keyword determines which are coupled. For example, <I>xz</I>
+means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
+<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep. The
+<I>Ptarget</I> values for any coupled dimensions must be identical.
+<I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I> dimension is
+simply ignored.
+</P>
+<HR>
+
+<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+</P>
+<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together. Using "iso Ptarget" is the same as specifying
+these 4 keywords:
+</P>
+<PRE>x Ptarget
+y Ptarget
+z Ptarget
+couple xyz
+</PRE>
+<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
+independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure. Using "aniso Ptarget" is the same as specifying these 4
+keywords:
+</P>
+<PRE>x Ptarget
+y Ptarget
+z Ptarget
+couple none
+</PRE>
+<P>The keyword <I>tri</I> means <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, and <I>yz</I> dimensions
+are controlled independently using their individual stress components
+as the driving forces, and the specified scalar pressure as the
+external normal stress. Using "tri Ptarget" is the same as specifying
+these 7 keywords:
+</P>
+<PRE>x Ptarget
+y Ptarget
+z Ptarget
+xy 0.0
+yz 0.0
+xz 0.0
+couple none
+</PRE>
+<HR>
+
+<P>The <I>vmax</I> keyword can be used to limit the fractional change in the
+volume of the simulation box that can occur in one iteration of the
+minimizer. If the pressure is not settling down during the
+minimization this can be because the volume is fluctuating too much.
+The specified fraction must be greater than 0.0 and should be << 1.0.
+A value of 0.001 means the volume cannot change by more than 1/10 of a
+percent in one iteration when <I>couple xyz</I> has been specified. For
+any other case it means no linear dimension of the simulation box can
+change by more than 1/10 of a percent.
+</P>
+<HR>
+
+<P>With this fix, the potential energy used by the minimizer is augmented
+by an additional energy provided by the fix. The overall objective
+function then is:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_box_relax1.jpg">
+</CENTER>
+<P>where <I>U</I> is the system potential energy, <I>P</I>_t is the desired
+hydrostatic pressure, <I>V</I> and <I>V</I>_0 are the system and reference
+volumes, respectively. <I>E</I>_<I>strain</I> is the strain energy expression
+proposed by Parrinello and Rahman <A HREF = "#Parrinello1981">(Parrinello1981)</A>.
+Taking derivatives of <I>E</I> w.r.t. the box dimensions, and setting these
+to zero, we find that at the minimum of the objective function, the
+global system stress tensor <B>P</B> will satisfy the relation:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_box_relax2.jpg">
+</CENTER>
+<P>where <B>I</B> is the identity matrix, <B>h</B>_0 is the box dimension tensor of
+the reference cell, and <B>h</B>_0<I>d</I> is the diagonal part of
+<B>h</B>_0. <B>S</B>_<I>t</I> is a symmetric stress tensor that is chosen by LAMMPS
+so that the upper-triangular components of <B>P</B> equal the stress tensor
+specified by the user.
+</P>
+<P>This equation only applies when the box dimensions are equal to those
+of the reference dimensions. If this is not the case, then the
+converged stress tensor will not equal that specified by the user. We
+can resolve this problem by periodically resetting the reference
+dimensions. The keyword <I>nreset_ref</I> controls how often this is done.
+If this keyword is not used, or is given a value of zero, then the
+reference dimensions are set to those of the initial simulation domain
+and are never changed. A value of <I>nstep</I> means that every <I>nstep</I>
+minimization steps, the reference dimensions are set to those of the
+current simulation domain. Note that resetting the reference
+dimensions changes the objective function and gradients, which
+sometimes causes the minimization to fail. This can be resolved by
+changing the value of <I>nreset</I>, or simply continuing the minimization
+from a restart file.
+</P>
+<P>IMPORTANT NOTE: As normally computed, pressure includes a kinetic-
+energy or temperature-dependent component; see the <A HREF = "compute_pressure.html">compute
+pressure</A> command. However, atom velocities are
+ignored during a minimization, and the applied pressure(s) specified
+with this command are assumed to only be the virial component of the
+pressure (the non-kinetic portion). Thus if atoms have a non-zero
+temperature and you print the usual thermodynamic pressure, it may not
+appear the system is converging to your specified pressure. The
+solution for this is to either (a) zero the velocities of all atoms
+before performing the minimization, or (b) make sure you are
+monitoring the pressure without its kinetic component. The latter can
+be done by outputting the pressure from the fix this command creates
+(see below) or a pressure fix you define yourself.
+</P>
+<P>IMPORTANT NOTE: Because pressure is often a very sensitive function of
+volume, it can be difficult for the minimizer to equilibrate the
+system the desired pressure with high precision, particularly for
+solids. Some techniques that seem to help are (a) use the
+"min_modify line quadratic" option when minimizing with box
+relaxations, (b) minimize several times in succession if need be,
+to drive the pressure closer to the target pressure, (c) relax
+the atom positions before relaxing the box, and (d) relax the box
+to the target hydrostatic pressure before relaxing to a target
+shear stress state. Also note that
+some systems (e.g. liquids) will not sustain a non-hydrostatic applied
+pressure, which means the minimizer will not converge.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. The
+temperature is used to compute the kinetic contribution to the
+pressure, even though this is subsequently ignored by default. To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp virial
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is the same
+as the fix group. Also note that the pressure compute does not
+include a kinetic component.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its temperature and pressure calculation, as described above. Note
+that as described above, if you assign a pressure compute to this fix
+that includes a kinetic energy component it will affect the
+minimization, most likely in an undesirable way.
+</P>
+<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
+single thermo_modify command (or in two separate commands), then the
+order in which the keywords are specified is important. Note that a
+<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
+compute as an argument when it is specified. The <I>temp</I> keyword will
+override this (for the pressure compute being used by fix npt), but
+only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
+<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
+compute specified by the <I>press</I> keyword will be unaffected by the
+<I>temp</I> setting.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+pressure-volume energy, plus the strain energy, if it exists.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>This fix is invoked during <A HREF = "minimize.html">energy minimization</A>, but
+not for the purpose of adding a contribution to the energy or forces
+being minimized. Instead it alters the simulation box geometry as
+described above.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Only dimensions that are available can be adjusted by this fix.
+Non-periodic dimensions are not available. <I>z</I>, <I>xz</I>, and <I>yz</I>, are
+not available for 2D simulations. <I>xy</I>, <I>xz</I>, and <I>yz</I> are only
+available if the simulation domain is non-orthogonal. The
+<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
+<A HREF = "read_restart.html">read_restart</A> commands specify whether the
+simulation box is orthogonal or non-orthogonal (triclinic) and explain
+the meaning of the xy,xz,yz tilt factors.
+</P>
+<P>The <I>scaleyz yes</I> and <I>scalexz yes</I> keyword/value pairs can not be used
+for 2D simulations. <I>scaleyz yes</I>, <I>scalexz yes</I>, and <I>scalexy yes</I> options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+<I>tri</I>, <I>yz</I>, <I>xz</I>, and <I>xy</I>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "minimize.html">minimize</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0.
+</P>
+<HR>
+
+<A NAME = "Parrinello1981"></A>
+
+<P><B>(Parrinello1981)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_colvars.html b/doc/doc2/fix_colvars.html
new file mode 100644
index 000000000..5aa30bb70
--- /dev/null
+++ b/doc/doc2/fix_colvars.html
@@ -0,0 +1,147 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix colvars command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID colvars configfile keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>colvars = style name of this fix command
+
+<LI>configfile = the configuration file for the colvars module
+
+<LI>keyword = <I>input</I> or <I>output</I> or <I>seed</I> or <I>tstat</I>
+
+<PRE> <I>input</I> arg = colvars.state file name or prefix or NULL (default: NULL)
+ <I>output</I> arg = output filename prefix (default: out)
+ <I>seed</I> arg = seed for random number generator (default: 1966)
+ <I>unwrap</I> arg = <I>yes</I> or <I>no</I>
+ use unwrapped coordinates in collective variables (default: yes)
+ <I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
+fix abf all colvars colvars.inp tstat 1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix interfaces LAMMPS to a "collective variables" or "colvars"
+module library which allows to calculate potentials of mean force
+(PMFs) for any set of colvars, using different sampling methods:
+currently implemented are the Adaptive Biasing Force (ABF) method,
+metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
+(US) via a flexible harmonic restraint bias. The colvars library is
+hosted at <A HREF = "http://colvars.github.io/">http://colvars.github.io/</A>
+</P>
+<P>This documentation describes only the fix colvars command itself and
+LAMMPS specific parts of the code. The full documentation of the
+colvars library is available as <A HREF = "PDF/colvars-refman-lammps.pdf">this supplementary PDF document</A>
+</P>
+<P>A detailed discussion of the implementation of the portable collective
+variable library is in <A HREF = "#Fiorin">(Fiorin)</A>. Additional information can
+be found in <A HREF = "#Henin">(Henin)</A>.
+</P>
+<P>There are some example scripts for using this package with LAMMPS in the
+examples/USER/colvars directory.
+</P>
+<HR>
+
+<P>The only mandatory argument to the fix is the filename to the colvars
+input file that contains the input that is independent from the MD
+program in which the colvars library has been integrated.
+</P>
+<P>The <I>group-ID</I> entry is ignored. The collective variable module will
+always apply to the entire system and there can only be one instance
+of the colvars fix at a time. The colvars fix will only communicate
+the minimum information necessary and the colvars library supports
+multiple, completely independent collective variables, so there is
+no restriction to functionaliry by limiting the number of colvars fixes.
+</P>
+<P>The <I>input</I> keyword allows to specify a state file that would contain
+the restart information required in order to continue a calculation from
+a prerecorded state. Fix colvars records it state in <A HREF = "restart.html">binary restart</A>
+files, so when using the <A HREF = "read_restart.html">read_restart</A> command,
+this is usually not needed.
+</P>
+<P>The <I>output</I> keyword allows to specify the output prefix. All output
+files generated will use this prefix followed by the ".colvars." and
+a word like "state" or "traj".
+</P>
+<P>The <I>seed</I> keyword contains the seed for the random number generator
+that will be used in the colvars module.
+</P>
+<P>The <I>unwrap</I> keyword controls whether wrapped or unwrapped coordinates
+are passed to the colvars library for calculation of the collective
+variables and the resulting forces. The default is <I>yes</I>, i.e. to use
+the image flags to reconstruct the absolute atom positions.
+Setting this to <I>no</I> will use the current local coordinates that are
+wrapped back into the simulation cell at each re-neighboring instead.
+</P>
+<P>The <I>tstat</I> keyword can be either NULL or the label of a thermostating
+fix that thermostats all atoms in the fix colvars group. This will be
+used to provide the colvars module with the current thermostat target
+temperature.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the current status of the colvars module into
+<A HREF = "restart.html">binary restart files</A>. This is in addition to the text
+mode status file that is written by the colvars module itself and the
+kind of information in both files is identical.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change from the biasing force added by the fix
+to the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-COLVARS package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>There can only be one colvars fix active at a time. Since the interface
+communicates only the minimum amount of information and colvars module
+itself can handle an arbitrary number of collective variables, this is
+not a limitation of functionality.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_smd.html">fix smd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default options are input = NULL, output = out, seed = 1966, unwrap yes,
+and tstat = NULL.
+</P>
+<HR>
+
+<A NAME = "Fiorin"></A>
+
+<P><B>(Fiorin)</B> Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
+</P>
+<A NAME = "Henin"></A>
+
+<P><B>(Henin)</B> Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
+35-47 (2010)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_deform.html b/doc/doc2/fix_deform.html
new file mode 100644
index 000000000..f9a7526b5
--- /dev/null
+++ b/doc/doc2/fix_deform.html
@@ -0,0 +1,582 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix deform command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID deform N parameter args ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>deform = style name of this fix command
+
+<LI>N = perform box deformation every this many timesteps
+
+<LI>one or more parameter/arg pairs may be appended
+
+<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I>
+ <I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
+ style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>vel</I> or <I>erate</I> or <I>trate</I> or <I>volume</I> or <I>wiggle</I> or <I>variable</I>
+ <I>final</I> values = lo hi
+ lo hi = box boundaries at end of run (distance units)
+ <I>delta</I> values = dlo dhi
+ dlo dhi = change in box boundaries at end of run (distance units)
+ <I>scale</I> values = factor
+ factor = multiplicative factor for change in box length at end of run
+ <I>vel</I> value = V
+ V = change box length at this velocity (distance/time units),
+ effectively an engineering strain rate
+ <I>erate</I> value = R
+ R = engineering strain rate (1/time units)
+ <I>trate</I> value = R
+ R = true strain rate (1/time units)
+ <I>volume</I> value = none = adjust this dim to preserve volume of system
+ <I>wiggle</I> values = A Tp
+ A = amplitude of oscillation (distance units)
+ Tp = period of oscillation (time units)
+ <I>variable</I> values = v_name1 v_name2
+ v_name1 = variable with name1 for box length change as function of time
+ v_name2 = variable with name2 for change rate as function of time
+ <I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
+ style = <I>final</I> or <I>delta</I> or <I>vel</I> or <I>erate</I> or <I>trate</I> or <I>wiggle</I>
+ <I>final</I> value = tilt
+ tilt = tilt factor at end of run (distance units)
+ <I>delta</I> value = dtilt
+ dtilt = change in tilt factor at end of run (distance units)
+ <I>vel</I> value = V
+ V = change tilt factor at this velocity (distance/time units),
+ effectively an engineering shear strain rate
+ <I>erate</I> value = R
+ R = engineering shear strain rate (1/time units)
+ <I>trate</I> value = R
+ R = true shear strain rate (1/time units)
+ <I>wiggle</I> values = A Tp
+ A = amplitude of oscillation (distance units)
+ Tp = period of oscillation (time units)
+ <I>variable</I> values = v_name1 v_name2
+ v_name1 = variable with name1 for tilt change as function of time
+ v_name2 = variable with name2 for change rate as function of time
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>remap</I> or <I>flip</I> or <I>units</I>
+
+<PRE> <I>remap</I> value = <I>x</I> or <I>v</I> or <I>none</I>
+ x = remap coords of atoms in group into deforming box
+ v = remap velocities of all atoms when they cross periodic boundaries
+ none = no remapping of x or v
+ <I>flip</I> value = <I>yes</I> or <I>no</I>
+ allow or disallow box flips when it becomes highly skewed
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ lattice = distances are defined in lattice units
+ box = distances are defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box
+fix 1 all deform 1 x trate 0.1 y volume z volume
+fix 1 all deform 1 xy erate 0.001 remap v
+fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Change the volume and/or shape of the simulation box during a dynamics
+run. Orthogonal simulation boxes have 3 adjustable parameters
+(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
+adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
+adjusted independently and simultaneously by this command. This fix
+can be used to perform non-equilibrium MD (NEMD) simulations of a
+continuously strained system. See the <A HREF = "fix_nvt_sllod.html">fix
+nvt/sllod</A> and <A HREF = "compute_temp_deform.html">compute
+temp/deform</A> commands for more details.
+</P>
+<P>For the <I>x</I>, <I>y</I>, <I>z</I> parameters, the associated dimension cannot be
+shrink-wrapped. For the <I>xy</I>, <I>yz</I>, <I>xz</I> parameters, the associated
+2nd dimension cannot be shrink-wrapped. Dimensions not varied by this
+command can be periodic or non-periodic. Dimensions corresponding to
+unspecified parameters can also be controlled by a <A HREF = "fix_nh.html">fix
+npt</A> or <A HREF = "fix_nh.html">fix nph</A> command.
+</P>
+<P>The size and shape of the simulation box at the beginning of the
+simulation run were either specified by the
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation
+initially if it is the first run, or they are the values from the end
+of the previous run. The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
+data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If
+fix deform changes the xy,xz,yz tilt factors, then the simulation box
+must be triclinic, even if its initial tilt factors are 0.0.
+</P>
+<P>As described below, the desired simulation box size and shape at the
+end of the run are determined by the parameters of the fix deform
+command. Every Nth timestep during the run, the simulation box is
+expanded, contracted, or tilted to ramped values between the initial
+and final values.
+</P>
+<HR>
+
+<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
+styles and values.
+</P>
+<P>The <I>final</I>, <I>delta</I>, <I>scale</I>, <I>vel</I>, and <I>erate</I> styles all change
+the specified dimension of the box via "constant displacement" which
+is effectively a "constant engineering strain rate". This means the
+box dimension changes linearly with time from its initial to final
+value.
+</P>
+<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
+are specified. The values can be in lattice or box distance units.
+See the discussion of the units keyword below.
+</P>
+<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
+of a dimension are specified. The values can be in lattice or box
+distance units. See the discussion of the units keyword below.
+</P>
+<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
+of a dimension is specified. For example, if the initial box length
+is 10, and the factor is 1.1, then the final box length will be 11. A
+factor less than 1.0 means compression.
+</P>
+<P>For style <I>vel</I>, a velocity at which the box length changes is
+specified in units of distance/time. This is effectively a "constant
+engineering strain rate", where rate = V/L0 and L0 is the initial box
+length. The distance can be in lattice or box distance units. See
+the discussion of the units keyword below. For example, if the
+initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
+after 10 psec, the box length will have doubled. After 20 psec, it
+will have tripled.
+</P>
+<P>The <I>erate</I> style changes a dimension of the the box at a "constant
+engineering strain rate". The units of the specified strain rate are
+1/time. See the <A HREF = "units.html">units</A> command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units). Tensile strain is unitless and
+is defined as delta/L0, where L0 is the original box length and delta
+is the change relative to the original length. The box length L as a
+function of time will change as
+</P>
+<PRE>L(t) = L0 (1 + erate*dt)
+</PRE>
+<P>where dt is the elapsed time (in time units). Thus if <I>erate</I> R is
+specified as 0.1 and time units are picoseconds, this means the box
+length will increase by 10% of its original length every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. R =
+-0.01 means the box length will shrink by 1% of its original length
+every picosecond. Note that for an "engineering" rate the change is
+based on the original box length, so running with R = 1 for 10
+picoseconds expands the box length by a factor of 11 (strain of 10),
+which is different that what the <I>trate</I> style would induce.
+</P>
+<P>The <I>trate</I> style changes a dimension of the box at a "constant true
+strain rate". Note that this is not an "engineering strain rate", as
+the other styles are. Rather, for a "true" rate, the rate of change
+is constant, which means the box dimension changes non-linearly with
+time from its initial to final value. The units of the specified
+strain rate are 1/time. See the <A HREF = "units.html">units</A> command for the
+time units associated with different choices of simulation units,
+e.g. picoseconds for "metal" units). Tensile strain is unitless and
+is defined as delta/L0, where L0 is the original box length and delta
+is the change relative to the original length.
+</P>
+<P>The box length L as a function of time will change as
+</P>
+<PRE>L(t) = L0 exp(trate*dt)
+</PRE>
+<P>where dt is the elapsed time (in time units). Thus if <I>trate</I> R is
+specified as ln(1.1) and time units are picoseconds, this means the
+box length will increase by 10% of its current (not original) length
+every picosecond. I.e. strain after 1 psec = 0.1, strain after 2 psec
+= 0.21, etc. R = ln(2) or ln(3) means the box length will double or
+triple every picosecond. R = ln(0.99) means the box length will
+shrink by 1% of its current length every picosecond. Note that for a
+"true" rate the change is continuous and based on the current length,
+so running with R = ln(2) for 10 picoseconds does not expand the box
+length by a factor of 11 as it would with <I>erate</I>, but by a factor of
+1024 since the box length will double every picosecond.
+</P>
+<P>Note that to change the volume (or cross-sectional area) of the
+simulation box at a constant rate, you can change multiple dimensions
+via <I>erate</I> or <I>trate</I>. E.g. to double the box volume in a picosecond
+picosecond, you could set "x erate M", "y erate M", "z erate M", with
+M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%,
+the box volume doubles. Or you could set "x trate M", "y trate M", "z
+trate M", with M = ln(1.26) = 0.231, and the box volume would double
+every picosecond.
+</P>
+<P>The <I>volume</I> style changes the specified dimension in such a way that
+the box volume remains constant while other box dimensions are changed
+explicitly via the styles discussed above. For example, "x scale 1.1
+y scale 1.1 z volume" will shrink the z box length as the x,y box
+lengths increase, to keep the volume constant (product of x,y,z
+lengths). If "x scale 1.1 z volume" is specified and parameter <I>y</I> is
+unspecified, then the z box length will shrink as x increases to keep
+the product of x,z lengths constant. If "x scale 1.1 y volume z
+volume" is specified, then both the y,z box lengths will shrink as x
+increases to keep the volume constant (product of x,y,z lengths). In
+this case, the y,z box lengths shrink so as to keep their relative
+aspect ratio constant.
+</P>
+<P>For solids or liquids, note that when one dimension of the box is
+expanded via fix deform (i.e. tensile strain), it may be physically
+undesirable to hold the other 2 box lengths constant (unspecified by
+fix deform) since that implies a density change. Using the <I>volume</I>
+style for those 2 dimensions to keep the box volume constant may make
+more physical sense, but may also not be correct for materials and
+potentials whose Poisson ratio is not 0.5. An alternative is to use
+<A HREF = "fix_nh.html">fix npt aniso</A> with zero applied pressure on those 2
+dimensions, so that they respond to the tensile strain dynamically.
+</P>
+<P>The <I>wiggle</I> style oscillates the specified box length dimension
+sinusoidally with the specified amplitude and period. I.e. the box
+length L as a function of time is given by
+</P>
+<PRE>L(t) = L0 + A sin(2*pi t/Tp)
+</PRE>
+<P>where L0 is its initial length. If the amplitude A is a positive
+number the box initially expands, then contracts, etc. If A is
+negative then the box initially contracts, then expands, etc. The
+amplitude can be in lattice or box distance units. See the discussion
+of the units keyword below.
+</P>
+<P>The <I>variable</I> style changes the specified box length dimension by
+evaluating a variable, which presumably is a function of time. The
+variable with <I>name1</I> must be an <A HREF = "variable.html">equal-style variable</A>
+and should calculate a change in box length in units of distance.
+Note that this distance is in box units, not lattice units; see the
+discussion of the <I>units</I> keyword below. The formula associated with
+variable <I>name1</I> can reference the current timestep. Note that it
+should return the "change" in box length, not the absolute box length.
+This means it should evaluate to 0.0 when invoked on the initial
+timestep of the run following the definition of fix deform. It should
+evaluate to a value > 0.0 to dilate the box at future times, or a
+value < 0.0 to compress the box.
+</P>
+<P>The variable <I>name2</I> must also be an <A HREF = "variable.html">equal-style
+variable</A> and should calculate the rate of box length
+change, in units of distance/time, i.e. the time-derivative of the
+<I>name1</I> variable. This quantity is used internally by LAMMPS to reset
+atom velocities when they cross periodic boundaries. It is computed
+internally for the other styles, but you must provide it when using an
+arbitrary variable.
+</P>
+<P>Here is an example of using the <I>variable</I> style to perform the same
+box deformation as the <I>wiggle</I> style formula listed above, where we
+assume that the current timestep = 0.
+</P>
+<PRE>variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 x variable v_displace v_rate remap v
+</PRE>
+<P>For the <I>scale</I>, <I>vel</I>, <I>erate</I>, <I>trate</I>, <I>volume</I>, <I>wiggle</I>, and
+<I>variable</I> styles, the box length is expanded or compressed around its
+mid point.
+</P>
+<HR>
+
+<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
+styles and values. Note that changing the tilt factors of a triclinic
+box does not change its volume.
+</P>
+<P>The <I>final</I>, <I>delta</I>, <I>vel</I>, and <I>erate</I> styles all change the shear
+strain at a "constant engineering shear strain rate". This means the
+tilt factor changes linearly with time from its initial to final
+value.
+</P>
+<P>For style <I>final</I>, the final tilt factor is specified. The value
+can be in lattice or box distance units. See the discussion of the
+units keyword below.
+</P>
+<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
+specified. The value can be in lattice or box distance units. See
+the discussion of the units keyword below.
+</P>
+<P>For style <I>vel</I>, a velocity at which the tilt factor changes is
+specified in units of distance/time. This is effectively an
+"engineering shear strain rate", where rate = V/L0 and L0 is the
+initial box length perpendicular to the direction of shear. The
+distance can be in lattice or box distance units. See the discussion
+of the units keyword below. For example, if the initial tilt factor
+is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
+tilt factor will be 15 Angstroms. After 2 psec, it will be 25
+Angstroms.
+</P>
+<P>The <I>erate</I> style changes a tilt factor at a "constant engineering
+shear strain rate". The units of the specified shear strain rate are
+1/time. See the <A HREF = "units.html">units</A> command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units). Shear strain is unitless and is
+defined as offset/length, where length is the box length perpendicular
+to the shear direction (e.g. y box length for xy deformation) and
+offset is the displacement distance in the shear direction (e.g. x
+direction for xy deformation) from the unstrained orientation.
+</P>
+<P>The tilt factor T as a function of time will change as
+</P>
+<PRE>T(t) = T0 + L0*erate*dt
+</PRE>
+<P>where T0 is the initial tilt factor, L0 is the original length of the
+box perpendicular to the shear direction (e.g. y box length for xy
+deformation), and dt is the elapsed time (in time units). Thus if
+<I>erate</I> R is specified as 0.1 and time units are picoseconds, this
+means the shear strain will increase by 0.1 every picosecond. I.e. if
+the xy shear strain was initially 0.0, then strain after 1 psec = 0.1,
+strain after 2 psec = 0.2, etc. Thus the tilt factor would be 0.0 at
+time 0, 0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the
+original y box length. R = 1 or 2 means the tilt factor will increase
+by 1 or 2 every picosecond. R = -0.01 means a decrease in shear
+strain by 0.01 every picosecond.
+</P>
+<P>The <I>trate</I> style changes a tilt factor at a "constant true shear
+strain rate". Note that this is not an "engineering shear strain
+rate", as the other styles are. Rather, for a "true" rate, the rate
+of change is constant, which means the tilt factor changes
+non-linearly with time from its initial to final value. The units of
+the specified shear strain rate are 1/time. See the
+<A HREF = "units.html">units</A> command for the time units associated with
+different choices of simulation units, e.g. picoseconds for "metal"
+units). Shear strain is unitless and is defined as offset/length,
+where length is the box length perpendicular to the shear direction
+(e.g. y box length for xy deformation) and offset is the displacement
+distance in the shear direction (e.g. x direction for xy deformation)
+from the unstrained orientation.
+</P>
+<P>The tilt factor T as a function of time will change as
+</P>
+<PRE>T(t) = T0 exp(trate*dt)
+</PRE>
+<P>where T0 is the initial tilt factor and dt is the elapsed time (in
+time units). Thus if <I>trate</I> R is specified as ln(1.1) and time units
+are picoseconds, this means the shear strain or tilt factor will
+increase by 10% every picosecond. I.e. if the xy shear strain was
+initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
+0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or
+triple every picosecond. R = ln(0.99) means the tilt factor will
+shrink by 1% every picosecond. Note that the change is continuous, so
+running with R = ln(2) for 10 picoseconds does not change the tilt
+factor by a factor of 10, but by a factor of 1024 since it doubles
+every picosecond. Note that the initial tilt factor must be non-zero
+to use the <I>trate</I> option.
+</P>
+<P>Note that shear strain is defined as the tilt factor divided by the
+perpendicular box length. The <I>erate</I> and <I>trate</I> styles control the
+tilt factor, but assume the perpendicular box length remains constant.
+If this is not the case (e.g. it changes due to another fix deform
+parameter), then this effect on the shear strain is ignored.
+</P>
+<P>The <I>wiggle</I> style oscillates the specified tilt factor sinusoidally
+with the specified amplitude and period. I.e. the tilt factor T as a
+function of time is given by
+</P>
+<PRE>T(t) = T0 + A sin(2*pi t/Tp)
+</PRE>
+<P>where T0 is its initial value. If the amplitude A is a positive
+number the tilt factor initially becomes more positive, then more
+negative, etc. If A is negative then the tilt factor initially
+becomes more negative, then more positive, etc. The amplitude can be
+in lattice or box distance units. See the discussion of the units
+keyword below.
+</P>
+<P>The <I>variable</I> style changes the specified tilt factor by evaluating a
+variable, which presumably is a function of time. The variable with
+<I>name1</I> must be an <A HREF = "variable.html">equal-style variable</A> and should
+calculate a change in tilt in units of distance. Note that this
+distance is in box units, not lattice units; see the discussion of the
+<I>units</I> keyword below. The formula associated with variable <I>name1</I>
+can reference the current timestep. Note that it should return the
+"change" in tilt factor, not the absolute tilt factor. This means it
+should evaluate to 0.0 when invoked on the initial timestep of the run
+following the definition of fix deform.
+</P>
+<P>The variable <I>name2</I> must also be an <A HREF = "variable.html">equal-style
+variable</A> and should calculate the rate of tilt change,
+in units of distance/time, i.e. the time-derivative of the <I>name1</I>
+variable. This quantity is used internally by LAMMPS to reset atom
+velocities when they cross periodic boundaries. It is computed
+internally for the other styles, but you must provide it when using an
+arbitrary variable.
+</P>
+<P>Here is an example of using the <I>variable</I> style to perform the same
+box deformation as the <I>wiggle</I> style formula listed above, where we
+assume that the current timestep = 0.
+</P>
+<PRE>variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 xy variable v_displace v_rate remap v
+</PRE>
+<HR>
+
+<P>All of the tilt styles change the xy, xz, yz tilt factors during a
+simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
+are normally bounded by half the distance of the parallel box length.
+See the discussion of the <I>flip</I> keyword below, to allow this bound to
+be exceeded, if desired.
+</P>
+<P>For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5. Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all equivalent.
+</P>
+<P>To obey this constraint and allow for large shear deformations to be
+applied via the <I>xy</I>, <I>xz</I>, or <I>yz</I> parameters, the following
+algorithm is used. If <I>prd</I> is the associated parallel box length (10
+in the example above), then if the tilt factor exceeds the accepted
+range of -5 to 5 during the simulation, then the box is flipped to the
+other limit (an equivalent box) and the simulation continues. Thus
+for this example, if the initial xy tilt factor was 0.0 and "xy final
+100.0" was specified, then during the simulation the xy tilt factor
+would increase from 0.0 to 5.0, the box would be flipped so that the
+tilt factor becomes -5.0, the tilt factor would increase from -5.0 to
+5.0, the box would be flipped again, etc. The flip occurs 10 times
+and the final tilt factor at the end of the simulation would be 0.0.
+During each flip event, atoms are remapped into the new box in the
+appropriate manner.
+</P>
+<P>The one exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic. In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity. In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient due to the highly skewed simulation box.
+</P>
+<HR>
+
+<P>Each time the box size or shape is changed, the <I>remap</I> keyword
+determines whether atom positions are remapped to the new box. If
+<I>remap</I> is set to <I>x</I> (the default), atoms in the fix group are
+remapped; otherwise they are not. Note that their velocities are not
+changed, just their positions are altered. If <I>remap</I> is set to <I>v</I>,
+then any atom in the fix group that crosses a periodic boundary will
+have a delta added to its velocity equal to the difference in
+velocities between the lo and hi boundaries. Note that this velocity
+difference can include tilt components, e.g. a delta in the x velocity
+when an atom crosses the y periodic boundary. If <I>remap</I> is set to
+<I>none</I>, then neither of these remappings take place.
+</P>
+<P>Conceptually, setting <I>remap</I> to <I>x</I> forces the atoms to deform via an
+affine transformation that exactly matches the box deformation. This
+setting is typically appropriate for solids. Note that though the
+atoms are effectively "moving" with the box over time, it is not due
+to their having a velocity that tracks the box change, but only due to
+the remapping. By contrast, setting <I>remap</I> to <I>v</I> is typically
+appropriate for fluids, where you want the atoms to respond to the
+change in box size/shape on their own and acquire a velocity that
+matches the box change, so that their motion will naturally track the
+box without explicit remapping of their coordinates.
+</P>
+<P>IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
+performed using this fix, the option "remap v" should normally be
+used. This is because <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> adjusts the
+atom positions and velocities to induce a velocity profile that
+matches the changing box size/shape. Thus atom coordinates should NOT
+be remapped by fix deform, but velocities SHOULD be when atoms cross
+periodic boundaries, since that is consistent with maintaining the
+velocity profile already created by fix nvt/sllod. LAMMPS will warn
+you if the <I>remap</I> setting is not consistent with fix nvt/sllod.
+</P>
+<P>IMPORTANT NOTE: For non-equilibrium MD (NEMD) simulations using "remap
+v" it is usually desirable that the fluid (or flowing material,
+e.g. granular particles) stream with a velocity profile consistent
+with the deforming box. As mentioned above, using a thermostat such
+as <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> or <A HREF = "doc/fix_langevin.html">fix
+lavgevin</A> (with a bias provided by <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>), will typically accomplish
+that. If you do not use a thermostat, then there is no driving force
+pushing the atoms to flow in a manner consistent with the deforming
+box. E.g. for a shearing system the box deformation velocity may vary
+from 0 at the bottom to 10 at the top of the box. But the stream
+velocity profile of the atoms may vary from -5 at the bottom to +5 at
+the top. You can monitor these effects using the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>, and <A HREF = "compute_temp_profile.html">compute
+temp/profile</A> commands. One way to induce
+atoms to stream consistent with the box deformation is to give them an
+initial velocity profile, via the <A HREF = "velocity.html">velocity ramp</A>
+command, that matches the box deformation rate. This also typically
+helps the system come to equilibrium more quickly, even if a
+thermostat is used.
+</P>
+<P>IMPORTANT NOTE: If a <A HREF = "fix_rigid.html">fix rigid</A> is defined for rigid
+bodies, and <I>remap</I> is set to <I>x</I>, then the center-of-mass coordinates
+of rigid bodies will be remapped to the changing simulation box. This
+will be done regardless of whether atoms in the rigid bodies are in
+the fix deform group or not. The velocity of the centers of mass are
+not remapped even if <I>remap</I> is set to <I>v</I>, since <A HREF = "fix_nvt_sllod.html">fix
+nvt/sllod</A> does not currently do anything special
+for rigid particles. If you wish to perform a NEMD simulation of
+rigid particles, you can either thermostat them independently or
+include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod.html">fix
+nvt/sllod</A>.
+</P>
+<P>The <I>flip</I> keyword allows the tilt factors for a triclinic box to
+exceed half the distance of the parallel box length, as discussed
+above. If the <I>flip</I> value is set to <I>yes</I>, the bound is enforced by
+flipping the box when it is exceeded. If the <I>flip</I> value is set to
+<I>no</I>, the tilt will continue to change without flipping. Note that if
+you apply large deformations, this means the box shape can tilt
+dramatically LAMMPS will run less efficiently, due to the large volume
+of communication needed to acquire ghost atoms around a processor's
+irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may
+also lose atoms and generate an error.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define various arguments. A <I>box</I> value selects standard distance
+units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
+units = real or metal. A <I>lattice</I> value means the distance units are
+in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
+been previously used to define the lattice spacing. Note that the
+units choice also affects the <I>vel</I> style parameters since it is
+defined in terms of distance/time. Also note that the units keyword
+does not affect the <I>variable</I> style. You should use the <I>xlat</I>,
+<I>ylat</I>, <I>zlat</I> keywords of the <A HREF = "thermo_style.html">thermo_style</A>
+command if you want to include lattice spacings in a variable formula.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>.
+</P>
+<P>This fix can perform deformation over multiple runs, using the <I>start</I>
+and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>You cannot apply x, y, or z deformations to a dimension that is
+shrink-wrapped via the <A HREF = "boundary.html">boundary</A> comamnd.
+</P>
+<P>You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
+xy) that is shrink-wrapped via the <A HREF = "boundary.html">boundary</A> comamnd.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "change_box.html">change_box</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are remap = x, flip = yes, and units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_deposit.html b/doc/doc2/fix_deposit.html
new file mode 100644
index 000000000..93a498194
--- /dev/null
+++ b/doc/doc2/fix_deposit.html
@@ -0,0 +1,292 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix deposit command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID deposit N type M seed keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>deposit = style name of this fix command
+
+<LI>N = # of atoms or molecules to insert
+
+<LI>type = atom type to assign to inserted atoms (offset for moleclue insertion)
+
+<LI>M = insert a single atom or molecule every M steps
+
+<LI>seed = random # seed (positive integer)
+
+<LI>one or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I> or <I>id</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>mol</I> or <I>rigid</I> or <I>shake</I> or <I>units</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region to use as insertion volume
+ <I>id</I> value = <I>max</I> or <I>next</I>
+ max = atom ID for new atom(s) is max ID of all current atoms plus one
+ next = atom ID for new atom(s) increments by one for every deposition
+ <I>global</I> values = lo hi
+ lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
+ <I>local</I> values = lo hi delta
+ lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
+ delta = lateral distance within which a neighbor is considered "nearby" (distance units)
+ <I>near</I> value = R
+ R = only insert atom/molecule if further than R from existing particles (distance units)
+ <I>attempt</I> value = Q
+ Q = attempt a single insertion up to Q times
+ <I>rate</I> value = V
+ V = z velocity (y in 2d) at which insertion volume moves (velocity units)
+ <I>vx</I> values = vxlo vxhi
+ vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
+ <I>vy</I> values = vylo vyhi
+ vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
+ <I>vz</I> values = vzlo vzhi
+ vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
+ <I>target</I> values = tx ty tz
+ tx,ty,tz = location of target point (distance units)
+ <I>mol</I> value = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+ <I>molfrac</I> values = f1 f2 ... fN
+ f1 to fN = relative probability of creating each of N molecules in template-ID
+ <I>rigid</I> value = fix-ID
+ fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
+ <I>shake</I> value = fix-ID
+ fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ lattice = the geometry is defined in lattice units
+ box = the geometry is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
+fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
+fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Insert a single atom or molecule into the simulation domain every M
+timesteps until N atoms or molecules have been inserted. This is
+useful for simulating deposition onto a surface. For the remainder of
+this doc page, a single inserted atom or molecule is referred to as a
+"particle".
+</P>
+<P>If inserted particles are individual atoms, they are assigned the
+specified atom type. If they are molecules, the type of each atom in
+the inserted molecule is specified in the file read by the
+<A HREF = "molecule.html">molecule</A> command, and those values are added to the
+specified atom type. E.g. if the file specifies atom types 1,2,3, and
+those are the atom types you want for inserted molecules, then specify
+<I>type</I> = 0. If you specify <I>type</I> = 2, the in the inserted molecule
+will have atom types 3,4,5.
+</P>
+<P>All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix deposit command
+(which can also be "all").
+</P>
+<P>If you are computing temperature values which include inserted
+particles, you will want to use the
+<A HREF = "compute_modify.html">compute_modify</A> dynamic option, which insures the
+current number of atoms is used as a normalizing factor each time the
+temperature is computed.
+</P>
+<P>Care must be taken that inserted particles are not too near existing
+atoms, using the options described below. When inserting particles
+above a surface in a non-periodic box (see the
+<A HREF = "boundary.html">boundary</A> command), the possibility of a particle
+escaping the surface and flying upward should be considered, since the
+particle may be lost or the box size may grow infinitely large. A
+<A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command can be used to
+prevent this behavior. Note that if a shrink-wrap boundary is used,
+it is OK to insert the new particle outside the box, however the box
+will immediately be expanded to include the new particle. When
+simulating a sputtering experiment it is probably more realistic to
+ignore those atoms using the <A HREF = "thermo_modify.html">thermo_modify</A>
+command with the <I>lost ignore</I> option and a fixed
+<A HREF = "boundary.html">boundary</A>.
+</P>
+<P>The fix deposit command must use the <I>region</I> keyword to define an
+insertion volume. The specified region must have been previously
+defined with a <A HREF = "region.html">region</A> command. It must be defined with
+side = <I>in</I>.
+</P>
+<P>IMPORTANT NOTE: LAMMPS checks that the specified region is wholly
+inside the simulation box. It can do this correctly for orthonormal
+simulation boxes. However for <A HREF = "Section_howto.html#howto_12">triclinic
+boxes</A>, it only tests against the larger
+orthonormal box that bounds the tilted simulation box. If the
+specified region includes volume outside the tilted box, then an
+insertion will likely fail, leading to a "lost atoms" error. Thus for
+triclinic boxes you should insure the specified region is wholly
+inside the simulation box.
+</P>
+<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
+specifies a <I>template-ID</I> previously defined using the
+<A HREF = "molecule.html">molecule</A> command, which reads files that define one or
+more molecules. The coordinates, atom types, charges, etc, as well as
+any bond/angle/etc and special neighbor information for the molecule
+can be specified in the molecule file. See the
+<A HREF = "molecule.html">molecule</A> command for details. The only settings
+required to be in each file are the coordinates and types of atoms in
+the molecule.
+</P>
+<P>If the molecule template contains more than one molecule, the relative
+probability of depositing each molecule can be specified by the
+<I>molfrac</I> keyword. N relative probablities, each from 0.0 to 1.0, are
+specified, where N is the number of molecules in the template. Each
+time a molecule is deposited, a random number is used to sample from
+the list of relative probabilities. The N values must sum to 1.0.
+</P>
+<P>If you wish to insert molecules via the <I>mol</I> keyword, that will be
+treated as rigid bodies, use the <I>rigid</I> keyword, specifying as its
+value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A>
+command which also appears in your input script.
+</P>
+<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
+their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
+specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
+shake</A> command which also appears in your input script.
+</P>
+<P>Each timestep a particle is inserted, the coordinates for its atoms
+are chosen as follows. For insertion of individual atoms, the
+"position" referred to in the following description is the coordinate
+of the atom. For insertion of molecule, the "position" is the
+geometric center of the molecule; see the <A HREF = "molecule.html">molecule</A> doc
+page for details. A random rotation of the molecule around its center
+point is performed, which determines the coordinates all the
+individual atoms.
+</P>
+<P>A random position within the region insertion volume is generated. If
+neither the <I>global</I> or <I>local</I> keyword is used, the random position
+is the trial position. If the <I>global</I> keyword is used, the random
+x,y values are used, but the z position of the new particle is set
+above the highest current atom in the simulation by a distance
+randomly chosen between lo/hi. (For a 2d simulation, this is done for
+the y position.) If the <I>local</I> keyword is used, the z position is
+set a distance between lo/hi above the highest current atom in the
+simulation that is "nearby" the chosen x,y position. In this context,
+"nearby" means the lateral distance (in x,y) between the new and old
+particles is less than the <I>delta</I> setting.
+</P>
+<P>Once a trial x,y,z position has been selected, the insertion is only
+performed if no current atom in the simulation is within a distance R
+of any atom in the new particle, including the effect of periodic
+boundary conditions if applicable. R is defined by the <I>near</I>
+keyword. Note that the default value for R is 0.0, which will allow
+atoms to strongly overlap if you are inserting where other atoms are
+present. This distance test is performed independently for each atom
+in an inserted molecule, based on the randomly rotated configuration
+of the molecule. If this test fails, a new random position within the
+insertion volume is chosen and another trial is made. Up to Q
+attempts are made. If the particle is not successfully inserted,
+LAMMPS prints a warning message.
+</P>
+<P>IMPORTANT NOTE: If you are inserting finite size particles or a
+molecule or rigid body consisting of finite-size particles, then you
+should typically set R larger than the distance at which any inserted
+particle may overlap with either a previouly inserted particle or an
+existing particle. LAMMPS will issue a warning if R is smaller than
+this value, based on the radii of existing and inserted particles.
+</P>
+<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
+or y direction (2d). This enables particles to be inserted from a
+successively higher height over time. Note that this parameter is
+ignored if the <I>global</I> or <I>local</I> keywords are used, since those
+options choose a z-coordinate for insertion independently.
+</P>
+<P>The vx, vy, and vz components of velocity for the inserted particle
+are set using the values specified for the <I>vx</I>, <I>vy</I>, and <I>vz</I>
+keywords. Note that normally, new particles should be a assigned a
+negative vertical velocity so that they move towards the surface. For
+molecules, the same velocity is given to every particle (no rotation
+or bond vibration).
+</P>
+<P>If the <I>target</I> option is used, the velocity vector of the inserted
+particle is changed so that it points from the insertion position
+towards the specified target point. The magnitude of the velocity is
+unchanged. This can be useful, for example, for simulating a
+sputtering process. E.g. the target point can be far away, so that
+all incident particles strike the surface as if they are in an
+incident beam of particles at a prescribed angle.
+</P>
+<P>The <I>id</I> keyword determines how atom IDs and molecule IDs are assigned
+to newly deposited particles. Molecule IDs are only assigned if
+molecules are being inserted. For the <I>max</I> setting, the atom and
+molecule IDs of all current atoms are checked. Atoms in the new
+particle are assigned IDs starting with the current maximum plus one.
+If a molecule is inserted it is assigned an ID = current maximum plus
+one. This means that if particles leave the system, the new IDs may
+replace the lost ones. For the <I>next</I> setting, the maximum ID of any
+atom and molecule is stored at the time the fix is defined. Each time
+a new particle is added, this value is incremented to assign IDs to
+the new atom(s) or molecule. Thus atom and molecule IDs for deposited
+particles will be consecutive even if particles leave the system over
+time.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+for the other deposition parameters. A <I>box</I> value selects standard
+distance units as defined by the <A HREF = "units.html">units</A> command,
+e.g. Angstroms for units = real or metal. A <I>lattice</I> value means the
+distance units are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
+command must have been previously used to define the lattice spacing.
+Note that the units choice affects all the keyword values that have
+units of distance or velocity.
+</P>
+<P>IMPORTANT NOTE: If you are monitoring the temperature of a system
+where the atom count is changing due to adding particles, you
+typically should use the <A HREF = "compute_modify.html">compute_modify dynamic
+yes</A> command for the temperature compute you are
+using.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
+files</A>. This includes information about how many
+particles have been depositied, the random number generator seed, the
+next timestep for deposition, etc. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The specified insertion region cannot be a "dynamic" region, as
+defined by the <A HREF = "region.html">region</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_pour.html">fix_pour</A>, <A HREF = "region.html">region</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>Insertions are performed for individual atoms, i.e. no <I>mol</I> setting
+is defined. If the <I>mol</I> keyword is used, the default for <I>molfrac</I>
+is an equal probabilities for all molecules in the template.
+Additional option defaults are id = max, delta = 0.0, near = 0.0,
+attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
+and units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_drag.html b/doc/doc2/fix_drag.html
new file mode 100644
index 000000000..adef7e657
--- /dev/null
+++ b/doc/doc2/fix_drag.html
@@ -0,0 +1,66 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix drag command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID drag x y z fmag delta
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>drag = style name of this fix command
+<LI>x,y,z = coord to drag atoms towards
+<LI>fmag = magnitude of force to apply to each atom (force units)
+<LI>delta = cutoff distance inside of which force is not applied (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a force to each atom in a group to drag it towards the point
+(x,y,z). The magnitude of the force is specified by fmag. If an atom
+is closer than a distance delta to the point, then the force is not
+applied.
+</P>
+<P>Any of the x,y,z values can be specified as NULL which means do not
+include that dimension in the distance calculation or force
+application.
+</P>
+<P>This command can be used to steer one or more atoms to a new location
+in the simulation.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global 3-vector of forces, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
+total force on the group of atoms by the drag force. The vector
+values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_spring.html">fix spring</A>, <A HREF = "fix_spring_self.html">fix spring/self</A>,
+<A HREF = "fix_spring_rg.html">fix spring/rg</A>, <A HREF = "fix_smd.html">fix smd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_drude.html b/doc/doc2/fix_drude.html
new file mode 100644
index 000000000..398abd701
--- /dev/null
+++ b/doc/doc2/fix_drude.html
@@ -0,0 +1,60 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix drude command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID drude flag1 flag2 ... flagN
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>drude = style name of this fix command
+<LI>tag = Drude flag for each atom type (1 to N) in the system
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all drude 1 1 0 1 0 2 2 2
+fix 1 all drude C C N C N D D D
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Assign each atom type in the system to be one of 3 kinds of atoms
+within the Drude polarization model. This compute is designed to be
+used with the <A HREF = "tutorial_drude.html">thermalized Drude oscillator
+model</A>. Polarizable models in LAMMPS
+are described in <A HREF = "Section_howto.html#howto_25">this Section</A>.
+</P>
+<P>The three possible types can be designated with an integer (0,1,2)
+or capital letter (N,C,D):
+</P>
+<UL><LI>0 or N = non-polarizable atom (not part of Drude model)
+<LI>1 or C = Drude core
+<LI>2 or D = Drude electron
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix should be invoked before any other commands that implement
+the Drude oscillator model, such as <A HREF = "fix_langevin_drude.html">fix
+langevin_drude</A>, <A HREF = "fix_drude_transform.html">fix
+drude/transform</A>, <A HREF = "compute_temp_drude.html">compute
+temp/drude</A>, <A HREF = "pair_thole.html">pair_style
+thole</A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin_drude.html">fix langevin_drude</A>, <A HREF = "fix_drude_transform.html">fix
+drude/transform</A>, <A HREF = "compute_temp_drude.html">compute
+temp/drude</A>, <A HREF = "pair_thole.html">pair_style
+thole</A>
+</P>
+<P><B>Default:</B> None
+</P>
+</HTML>
diff --git a/doc/doc2/fix_drude_transform.html b/doc/doc2/fix_drude_transform.html
new file mode 100644
index 000000000..f19e5df09
--- /dev/null
+++ b/doc/doc2/fix_drude_transform.html
@@ -0,0 +1,171 @@
+<HTML>
+<script type="text/javascript"
+ src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix drude/transform/direct command
+</H3>
+<H3>fix drude/transform/inverse command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>style = <I>drude/transform/direct</I> or <I>drude/transform/inverse</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 all drude/transform/direct
+fix 1 all drude/transform/inverse
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Transform the coordinates of Drude oscillators from real to reduced
+and back for thermalizing the Drude oscillators as described in
+<A HREF = "#Lamoureux">(Lamoureux)</A> using a Nose-Hoover thermostat. This fix is
+designed to be used with the <A HREF = "tutorial_drude.html">thermalized Drude oscillator
+model</A>. Polarizable models in LAMMPS are
+described in <A HREF = "Section_howto.html#howto_25">this Section</A>.
+</P>
+<P>Drude oscillators are a pair of atoms representing a single
+polarizable atom. Ideally, the mass of Drude particles would vanish
+and their positions would be determined self-consistently by iterative
+minimization of the energy, the cores' positions being fixed. It is
+however more efficient and it yields comparable results, if the Drude
+oscillators (the motion of the Drude particle relative to the core)
+are thermalized at a low temperature. In that case, the Drude
+particles need a small mass.
+</P>
+<P>The thermostats act on the reduced degrees of freedom, which are
+defined by the following equations. Note that in these equations
+upper case denotes atomic or center of mass values and lower case
+denotes Drude particle or dipole values. Primes denote the transformed
+(reduced) values, while bare letters denote the original values.
+</P>
+<P>Masses: \begin{equation} M' = M + m \end{equation}
+\begin{equation} m' = \frac {M\, m } {M'} \end{equation}
+Positions: \begin{equation} X' = \frac {M\, X + m\, x} {M'}
+\end{equation} \begin{equation} x' = x - X \end{equation}
+Velocities: \begin{equation} V' = \frac {M\, V + m\, v} {M'}
+\end{equation} \begin{equation} v' = v - V \end{equation}
+Forces: \begin{equation} F' = F + f \end{equation}
+\begin{equation} f' = \frac { M\, f - m\, F} {M'}
+\end{equation}
+</P>
+<P>This transform conserves the total kinetic energy
+\begin{equation} \frac 1 2 \, (M\, V^2\ + m\, v^2)
+= \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end{equation}
+and the virial defined with absolute positions
+\begin{equation} X\, F + x\, f = X'\, F' + x'\, f' \end{equation}
+</P>
+<HR>
+
+<P>This fix requires each atom know whether it is a Drude particle or
+not. You must therefore use the <A HREF = "fix_drude.html">fix drude</A> command to
+specify the Drude status of each atom type.
+</P>
+<P>IMPORTANT NOTE: only the Drude core atoms need to be in the group
+specified for this fix. A Drude electron will be transformed together
+with its cores even if it is not itself in the group. It is safe to
+include Drude electrons or non-polarizable atoms in the group. The
+non-polarizable atoms will simply not be transformed.
+</P>
+<HR>
+
+<P>This fix does NOT perform time integration. It only transform masses,
+coordinates, velocities and forces. Thus you must use separate time
+integration fixes, like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix
+npt</A> to actually update the velocities and positions of
+atoms. In order to thermalize the reduced degrees of freedom at
+different temperatures, two Nose-Hoover thermostats must be defined,
+acting on two distinct groups.
+</P>
+<P>IMPORTANT NOTE: The <I>fix drude/transform/direct</I> command must appear
+before any Nose-Hoover thermostating fixes. The <I>fix
+drude/transform/inverse</I> command must appear after any Nose-Hoover
+thermostating fixes.
+</P>
+<P>Example:
+</P>
+<PRE>fix fDIRECT all drude/transform/direct
+fix fNVT gCORES nvt temp 300.0 300.0 100.0
+fix fNVT gDRUDES nvt temp 1.0 1.0 100.0
+fix fINVERSE all drude/transform/inverse
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+</PRE>
+<P>In this example, <I>gCORES</I> is the group of the atom cores and <I>gDRUDES</I>
+is the group of the Drude particles (electrons). The centers of mass
+of the Drude oscillators will be thermostated at 300.0 and the
+internal degrees of freedom will be thermostated at 1.0. The
+temperatures of cores and Drude particles, in center-of-mass and
+relatice coordinates, are calculated using <A HREF = "compute_temp_drude.html">compute
+temp/drude</A>
+</P>
+<P>In addition, if you want to use a barostat to simulate a system at
+constant pressure, only one of the Nose-Hoover fixes must be <I>npt</I>,
+the other one should be <I>nvt</I>. You must add a <I>compute temp/com</I> and a
+<I>fix_modify</I> command so that the temperature of the <I>npt</I> fix be just
+that of its group but the pressure be the overall pressure
+<I>thermo_press</I>.
+</P>
+<P>Example:
+</P>
+<PRE>compute cTEMP_CORE gCORES temp/com
+fix fDIRECT all drude/transform/direct
+fix fNPT gCORES npt temp 298.0 298.0 100.0 iso 1.0 1.0 500.0
+fix_modify fNPT temp cTEMP_CORE press thermo_press
+fix fNVT gDRUDES nvt temp 5.0 5.0 100.0
+fix fINVERSE all drude/transform/inverse
+</PRE>
+<P>In this example, <I>gCORES</I> is the group of the atom cores and <I>gDRUDES</I>
+is the group of the Drude particles. The centers of mass of the Drude
+oscillators will be thermostated at 298.0 and the internal degrees of
+freedom will be thermostated at 5.0. The whole system will be
+barostated at 1.0.
+</P>
+<P>In order to avoid the flying ice cube problem (irreversible transfer
+of linear momentum to the center of mass of the system), you may need
+to add a <I>fix momentum</I> command like such as
+</P>
+<PRE>fix fMOMENTUM all momentum 100 linear 1 1 1
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drude.html">fix drude</A>,
+<A HREF = "fix_langevin_drude.html">fix langevin/drude</A>,
+<A HREF = "compute_temp_drude.html">compute temp/drude</A>,
+<A HREF = "pair_thole.html">pair_style thole</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Lamoureux"></A>
+
+<P><B>(Lamoureux)</B> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_dt_reset.html b/doc/doc2/fix_dt_reset.html
new file mode 100644
index 000000000..039327b17
--- /dev/null
+++ b/doc/doc2/fix_dt_reset.html
@@ -0,0 +1,96 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix dt/reset command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>dt/reset = style name of this fix command
+<LI>N = recompute dt every N timesteps
+<LI>Tmin = minimum dt allowed which can be NULL (time units)
+<LI>Tmax = maximum dt allowed which can be NULL (time units)
+<LI>Xmax = maximum distance for an atom to move in one timestep (distance units)
+<LI>zero or more keyword/value pairs may be appended
+<LI>keyword = <I>units</I>
+</UL>
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+ lattice = Xmax is defined in lattice units
+ box = Xmax is defined in simulation box units
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 5 all dt/reset 10 1.0e-5 0.01 0.1
+fix 5 all dt/reset 10 0.01 2.0 0.2 units box
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the timestep size every N steps during a run, so that no atom
+moves further than Xmax, based on current atom velocities and forces.
+This can be useful when starting from a configuration with overlapping
+atoms, where forces will be large. Or it can be useful when running
+an impact simulation where one or more high-energy atoms collide with
+a solid, causing a damage cascade.
+</P>
+<P>This fix overrides the timestep size setting made by the
+<A HREF = "timestep.html">timestep</A> command. The new timestep size <I>dt</I> is
+computed in the following manner.
+</P>
+<P>For each atom, the timestep is computed that would cause it to
+displace <I>Xmax</I> on the next integration step, as a function of its
+current velocity and force. Since performing this calculation exactly
+would require the solution to a quartic equation, a cheaper estimate
+is generated. The estimate is conservative in that the atom's
+displacement is guaranteed not to exceed <I>Xmax</I>, though it may be
+smaller.
+</P>
+<P>Given this putative timestep for each atom, the minimum timestep value
+across all atoms is computed. Then the <I>Tmin</I> and <I>Tmax</I> bounds are
+applied, if specified. If one (or both) is specified as NULL, it is
+not applied.
+</P>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix resets the
+outer loop (largest) timestep, which is the same timestep that the
+<A HREF = "timestep.html">timestep</A> command sets.
+</P>
+<P>Note that the cumulative simulation time (in time units), which
+accounts for changes in the timestep size as a simulation proceeds,
+can be accessed by the <A HREF = "thermo_style.html">thermo_style time</A> keyword.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar stores
+the last timestep on which the timestep was reset to a new value.
+</P>
+<P>The scalar value calculated by this fix is "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "timestep.html">timestep</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults is units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_efield.html b/doc/doc2/fix_efield.html
new file mode 100644
index 000000000..339e4db52
--- /dev/null
+++ b/doc/doc2/fix_efield.html
@@ -0,0 +1,170 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix efield command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID efield ex ey ez keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>efield = style name of this fix command
+
+<LI>ex,ey,ez = E-field component values (electric field units)
+
+<LI>any of ex,ey,ez can be a variable (see below)
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I> or <I>energy</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to have added force
+ <I>energy</I> value = v_name
+ v_name = variable with name that calculates the potential energy of each atom in the added E-field
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix kick external-field efield 1.0 0.0 0.0
+fix kick external-field efield 0.0 0.0 v_oscillate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add a force F = qE to each charged atom in the group due to an
+external electric field being applied to the system. If the system
+contains point-dipoles, also add a torque on the dipoles due to the
+external electric field.
+</P>
+<P>For charges, any of the 3 quantities defining the E-field components
+can be specified as an equal-style or atom-style
+<A HREF = "variable.html">variable</A>, namely <I>ex</I>, <I>ey</I>, <I>ez</I>. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value used to determine the E-field component.
+</P>
+<P>For point-dipoles, equal-style variables can be used, but atom-style
+variables are not currently supported, since they imply a spatial
+gradient in the electric field which means additional terms with
+gradients of the field are required for the force and torque on
+dipoles.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent E-field.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent E-field
+with optional time-dependence as well.
+</P>
+<P>If the <I>region</I> keyword is used, the atom must also be in the
+specified geometric <A HREF = "region.html">region</A> in order to have force added
+to it.
+</P>
+<HR>
+
+<P>Adding a force or torque to atoms implies a change in their potential
+energy as they move or rotate due to the applied E-field.
+</P>
+<P>For dynamics via the "run" command, this energy can be optionally
+added to the system's potential energy for thermodynamic output (see
+below). For energy minimization via the "minimize" command, this
+energy must be added to the system's potential energy to formulate a
+self-consistent minimization problem (see below).
+</P>
+<P>The <I>energy</I> keyword is not allowed if the added field is a constant
+vector (ex,ey,ez), with all components defined as numeric constants
+and not as variables. This is because LAMMPS can compute the energy
+for each charged particle directly as E = -x dot qE = -q (x*ex + y*ey
++ z*ez), so that -Grad(E) = F. Similarly for point-dipole particles
+the energy can be computed as E = -mu dot E = -(mux*ex + muy*ey +
+muz*ez).
+</P>
+<P>The <I>energy</I> keyword is optional if the added force is defined with
+one or more variables, and if you are performing dynamics via the
+<A HREF = "run.html">run</A> command. If the keyword is not used, LAMMPS will set
+the energy to 0.0, which is typically fine for dynamics.
+</P>
+<P>The <I>energy</I> keyword is required if the added force is defined with
+one or more variables, and you are performing energy minimization via
+the "minimize" command for charged particles. It is not required for
+point-dipoles, but a warning is issued since the minimizer in LAMMPS
+does not rotate dipoles, so you should not expect to be able to
+minimize the orientation of dipoles in an applied electric field.
+</P>
+<P>The <I>energy</I> keyword specifies the name of an atom-style
+<A HREF = "variable.html">variable</A> which is used to compute the energy of each
+atom as function of its position. Like variables used for <I>ex</I>, <I>ey</I>,
+<I>ez</I>, the energy variable is specified as v_name, where name is the
+variable name.
+</P>
+<P>Note that when the <I>energy</I> keyword is used during an energy
+minimization, you must insure that the formula defined for the
+atom-style <A HREF = "variable.html">variable</A> is consistent with the force
+variable formulas, i.e. that -Grad(E) = F. For example, if the force
+due to the electric field were a spring-like F = kx, then the energy
+formula should be E = -0.5kx^2. If you don't do this correctly, the
+minimization will not converge properly.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential "energy" inferred by the added force due to
+the electric field to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>. This is a fictitious
+quantity but is needed so that the <A HREF = "minimize.html">minimize</A> command
+can include the forces added by this fix in a consistent manner.
+I.e. there is a decrease in potential energy when atoms move in the
+direction of the added force due to the electric field.
+</P>
+<P>This fix computes a global scalar and a global 3-vector of forces,
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar is the potential
+energy discussed above. The vector is the total force added to the
+group of atoms. The scalar and vector values calculated by this fix
+are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
+specify force components with a variable that has time-dependence for
+use with a minimizer, since the minimizer increments the timestep as
+the iteration count during the minimization.
+</P>
+<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
+with the added forces to be included in the total potential energy of
+the system (the quantity being minimized), you MUST enable the
+<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_addforce.html">fix addforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_enforce2d.html b/doc/doc2/fix_enforce2d.html
new file mode 100644
index 000000000..87b0546b4
--- /dev/null
+++ b/doc/doc2/fix_enforce2d.html
@@ -0,0 +1,74 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix enforce2d command
+</H3>
+<H3>fix enforce2d/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID enforce2d
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>enforce2d = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 5 all enforce2d
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Zero out the z-dimension velocity and force on each atom in the group.
+This is useful when running a 2d simulation to insure that atoms do
+not move from their initial z coordinate.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_evaporate.html b/doc/doc2/fix_evaporate.html
new file mode 100644
index 000000000..5918faffc
--- /dev/null
+++ b/doc/doc2/fix_evaporate.html
@@ -0,0 +1,109 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix evaporate command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID evaporate N M region-ID seed
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>evaporate = style name of this fix command
+
+<LI>N = delete atoms every this many timesteps
+
+<LI>M = number of atoms to delete each time
+
+<LI>region-ID = ID of region within which to perform deletions
+
+<LI>seed = random number seed to use for choosing atoms to delete
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>molecule</I>
+ <I>molecule</I> value = <I>no</I> or <I>yes</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 solvent evaporate 1000 10 surface 49892
+fix 1 solvent evaporate 1000 10 surface 38277 molecule yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Remove M atoms from the simulation every N steps. This can be used,
+for example, to model evaporation of solvent particles or moleclues
+(i.e. drying) of a system. Every N steps, the number of atoms in the
+fix group and within the specifed region are counted. M of these are
+chosen at random and deleted. If there are less than M eligible
+particles, then all of them are deleted.
+</P>
+<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
+atoms are deleted. In this case, you should insure you do not delete
+only a portion of a molecule (only some of its atoms), or LAMMPS will
+soon generate an error when it tries to find those atoms. LAMMPS will
+warn you if any of the atoms eligible for deletion have a non-zero
+molecule ID, but does not check for this at the time of deletion.
+</P>
+<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, then when an atom
+is chosen for deletion, the entire molecule it is part of is deleted.
+The count of deleted atoms is incremented by the number of atoms in
+the molecule, which may make it exceed <I>M</I>. If the molecule ID of the
+chosen atom is 0, then it is assumed to not be part of a molecule, and
+just the single atom is deleted.
+</P>
+<P>As an example, if you wish to delete 10 water molecules every <I>N</I>
+steps, you should set <I>M</I> to 30. If only the water's oxygen atoms
+were in the fix group, then two hydrogen atoms would be deleted when
+an oxygen atom is selected for deletion, whether the hydrogens are
+inside the evaporation region or not.
+</P>
+<P>Note that neighbor lists are re-built on timesteps that atoms are
+removed. Thus you should not remove atoms too frequently or you will
+incur overhead due to the cost of building neighbor lists.
+</P>
+<P>IMPORTANT NOTE: If you are monitoring the temperature of a system
+where the atom count is changing due to evaporation, you typically
+should use the <A HREF = "compute_modify.html">compute_modify dynamic yes</A>
+command for the temperature compute you are using.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar, which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative number of deleted atoms. The scalar value calculated by
+this fix is "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_deposit.html">fix deposit</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are molecule = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_external.html b/doc/doc2/fix_external.html
new file mode 100644
index 000000000..717bc456e
--- /dev/null
+++ b/doc/doc2/fix_external.html
@@ -0,0 +1,163 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix external command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID external mode args
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>external = style name of this fix command
+
+<LI>mode = <I>pf/callback</I> or <I>pf/array</I>
+
+<PRE> <I>pf/callback</I> args = Ncall Napply
+ Ncall = make callback every Ncall steps
+ Napply = apply callback forces every Napply steps
+ <I>pf/array</I> args = Napply
+ Napply = apply array forces every Napply steps
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all external pf/callback 1 1
+fix 1 all external pf/callback 100 1
+fix 1 all external pf/array 10
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix allows external programs that are running LAMMPS through its
+<A HREF = "Section_howto.html#howto_19">library interface</A> to modify certain
+LAMMPS properties on specific timesteps, similar to the way other
+fixes do. The external driver can be a <A HREF = "Section_howto.html#howto_19">C/C++ or Fortran
+program</A> or a <A HREF = "Section_python.html">Python
+script</A>.
+</P>
+<HR>
+
+<P>If mode is <I>pf/callback</I> then the fix will make a callback every
+<I>Ncall</I> timesteps or minimization iterations to the external program.
+The external program computes forces on atoms by setting values in an
+array owned by the fix. The fix then adds these forces to each atom
+in the group, once every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
+addforce</A> command works. Note that if <I>Ncall</I> >
+<I>Napply</I>, the force values produced by one callback will persist, and
+be used multiple times to update atom forces.
+</P>
+<P>The callback function "foo" is invoked by the fix as:
+</P>
+<PRE>foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
+</PRE>
+<P>The arguments are as follows:
+</P>
+<UL><LI>ptr = pointer provided by and simply passed back to external driver
+<LI>timestep = current LAMMPS timestep
+<LI>nlocal = # of atoms on this processor
+<LI>ids = list of atom IDs on this processor
+<LI>x = coordinates of atoms on this processor
+<LI>fexternal = forces to add to atoms on this processor
+</UL>
+<P>Note that timestep is a "bigint" which is defined in src/lmptype.h,
+typically as a 64-bit integer.
+</P>
+<P>Fexternal are the forces returned by the driver program.
+</P>
+<P>The fix has a set_callback() method which the external driver can call
+to pass a pointer to its foo() function. See the
+couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an
+example of how this is done. This sample application performs
+classical MD using quantum forces computed by a density functional
+code <A HREF = "http://dft.sandia.gov/Quest">Quest</A>.
+</P>
+
+
+<HR>
+
+<P>If mode is <I>pf/array</I> then the fix simply stores force values in an
+array. The fix adds these forces to each atom in the group, once
+every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
+addforce</A> command works.
+</P>
+<P>The name of the public force array provided by the FixExternal
+class is
+</P>
+<PRE>double **fexternal;
+</PRE>
+<P>It is allocated by the FixExternal class as an (N,3) array where N is
+the number of atoms owned by a processor. The 3 corresponds to the
+fx, fy, fz components of force.
+</P>
+<P>It is up to the external program to set the values in this array to
+the desired quantities, as often as desired. For example, the driver
+program might perform an MD run in stages of 1000 timesteps each. In
+between calls to the LAMMPS <A HREF = "run.html">run</A> command, it could retrieve
+atom coordinates from LAMMPS, compute forces, set values in fexternal,
+etc.
+</P>
+<HR>
+
+<P>To use this fix during energy minimization, the energy corresponding
+to the added forces must also be set so as to be consistent with the
+added forces. Otherwise the minimization will not converge correctly.
+</P>
+<P>This can be done from the external driver by calling this public
+method of the FixExternal class:
+</P>
+<PRE>void set_energy(double eng);
+</PRE>
+<P>where eng is the potential energy. Eng is an extensive quantity,
+meaning it should be the sum over per-atom energies of all affected
+atoms. It should also be provided in <A HREF = "units.html">energy units</A>
+consistent with the simulation. See the details below for how to
+insure this energy setting is used appropriately in a minimization.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential "energy" set by the external driver to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. This is a fictitious quantity but is
+needed so that the <A HREF = "minimize.html">minimize</A> command can include the
+forces added by this fix in a consistent manner. I.e. there is a
+decrease in potential energy when atoms move in the direction of the
+added force.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+potential energy discussed above. The scalar stored by this fix
+is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
+with the added forces to be included in the total potential energy of
+the system (the quantity being minimized), you MUST enable the
+<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_freeze.html b/doc/doc2/fix_freeze.html
new file mode 100644
index 000000000..ec829e410
--- /dev/null
+++ b/doc/doc2/fix_freeze.html
@@ -0,0 +1,93 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix freeze command
+</H3>
+<H3>fix freeze/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID freeze
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>freeze = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 bottom freeze
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Zero out the force and torque on a granular particle. This is useful
+for preventing certain particles from moving in a simulation. The
+<A HREF = "pair_gran.html">granular pair styles</A> also detect if this fix has been
+defined and compute interactions between frozen and non-frozen
+particles appropriately, as if the frozen particle has infinite mass.
+A similar functionality for normal (point) particles can be obtained
+using <A HREF = "fix_setforce.html">fix setforce</A>.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global 3-vector of forces, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix. The vector values calculated by this
+fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the GRANULAR package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>There can only be a single freeze fix defined. This is because other
+the <A HREF = "pair_gran.html">granular pair styles</A> treat frozen particles
+differently and need to be able to reference a single group to which
+this fix is applied.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "atom_style.html">atom_style sphere</A>, <A HREF = "fix_setforce.html">fix setforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_gcmc.html b/doc/doc2/fix_gcmc.html
new file mode 100644
index 000000000..576e6d6b4
--- /dev/null
+++ b/doc/doc2/fix_gcmc.html
@@ -0,0 +1,354 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix gcmc command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>gcmc = style name of this fix command
+
+<LI>N = invoke this fix every N steps
+
+<LI>X = average number of GCMC exchanges to attempt every N steps
+
+<LI>M = average number of MC moves to attempt every N steps
+
+<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
+
+<LI>seed = random # seed (positive integer)
+
+<LI>T = temperature of the ideal gas reservoir (temperature units)
+
+<LI>mu = chemical potential of the ideal gas reservoir (energy units)
+
+<LI>translate = maximum Monte Carlo translation distance (length units)
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, or <I>intra_energy</I>
+ <I>mol</I> value = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+ <I>shake</I> value = fix-ID
+ fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
+ <I>region</I> value = region-ID
+ region-ID = ID of region where MC moves are allowed
+ <I>maxangle</I> value = maximum molecular rotation angle (degrees)
+ <I>pressure</I> value = pressure of the gas reservoir (pressure units)
+ <I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
+ <I>full_energy</I> = compute the entire system energy when performing MC moves
+ <I>charge</I> value = charge of inserted atoms (charge units)
+ <I>group</I> value = group-ID
+ group-ID = group-ID for inserted atoms (string)
+ <I>grouptype</I> values = type group-ID
+ type = atom type (int)
+ group-ID = group-ID for inserted atoms (string)
+ <I>intra_energy</I> value = intramolecular energy (energy units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
+fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
+atoms or molecules of the given type with an imaginary ideal gas reservoir at
+the specified T and chemical potential (mu) as discussed in
+<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
+simulations in the grand canonical ensemble (muVT, constant chemical
+potential, constant volume, and constant temperature) can be
+performed. Specific uses include computing isotherms in microporous
+materials, or computing vapor-liquid coexistence curves.
+</P>
+<P>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
+or deletions) of gas atoms or molecules of
+the given type between the simulation cell and the imaginary
+reservoir. It also attempts a number of Monte Carlo
+moves (translations and molecule rotations) of gas of the given type
+within the simulation cell or region. The average number of
+attempted GCMC exchanges is X. The average number of attempted MC moves is M.
+M should typically be chosen to be
+approximately equal to the expected number of gas atoms or molecules
+of the given type within the simulation cell or region,
+which will result in roughly one
+MC translation per atom or molecule per MC cycle.
+</P>
+<P>For MC moves of molecular gasses, rotations and translations are each
+attempted with 50% probability. For MC moves of atomic gasses,
+translations are attempted 100% of the time. For MC exchanges of
+either molecular or atomic gasses, deletions and insertions are each
+attempted with 50% probability.
+</P>
+<P>All inserted particles are always assigned to two groups: the default group
+"all" and the group specified in the fix gcmc command (which can also
+be "all"). In addition, particles are also added to any groups specified
+by the <I>group</I> and <I>grouptype</I> keywords.
+If inserted particles are individual atoms, they are
+assigned the specified atom type. If they are molecules, the type of
+each atom in the inserted molecule is specified in the file read by
+the <A HREF = "molecule.html">molecule</A> command, and those values are added to
+the specified atom type. E.g. if <I>type</I> = 2, and the file specifies
+atom types 1,2,3, then the inserted molecule will have atom types
+3,4,5.
+</P>
+<P>This fix cannot be used to perform MC insertions of gas atoms or
+molecules other than the exchanged type, but MC deletions,
+translations, and rotations can be performed on any atom/molecule in
+the fix group. All atoms in the simulation cell can be moved using
+regular time integration translations, e.g. via
+<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation. A
+smaller-than-usual timestep size may be needed when running such a
+hybrid simulation, especially if the inserted molecules are not well
+equilibrated.
+</P>
+<P>This command may optionally use the <I>region</I> keyword to define an
+exchange and move volume. The specified region must have been
+previously defined with a <A HREF = "region.html">region</A> command. It must be
+defined with side = <I>in</I>. Insertion attempts occur only within the
+specified region. For non-rectangular regions, random trial
+points are generated within the rectangular bounding box until a point is found
+that lies inside the region. If no valid point is generated after 1000 trials,
+no insertion is performed, but it is counted as an attempted insertion.
+Move and deletion attempt candidates are selected
+from gas atoms or molecules within the region. If there are no candidates,
+no move or deletion is performed, but it is counted as an attempt move
+or deletion. If an attempted move places the atom or molecule center-of-mass outside
+the specified region, a new attempted move is generated. This process is repeated
+until the atom or molecule center-of-mass is inside the specified region.
+</P>
+<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
+reservoir, T, should be set to be equivalent to the target temperature
+used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
+will not be in thermal equilibrium with the simulation cell.
+</P>
+<P>Note that neighbor lists are re-built every timestep that this fix is
+invoked, so you should not set N to be too small. However, periodic
+rebuilds are necessary in order to avoid dangerous rebuilds and missed
+interactions. Specifically, avoid performing so many MC translations
+per timestep that atoms can move beyond the neighbor list skin
+distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
+</P>
+<P>When an atom or molecule is to be inserted, its
+coordinates are chosen at a random position within the current
+simulation cell or region, and new atom velocities are randomly chosen from
+the specified temperature distribution given by T. Relative
+coordinates for atoms in a molecule are taken from the template
+molecule provided by the user, with the origin of the relative
+coordinates coinciding with the chosen insertion point. This means
+that if the origin of the template molecule coordinate system
+lies far from the center of the template molecule,
+the inserted molecule will lie far from the insertion point.
+A random initial rotation is used in
+the case of molecule insertions.
+</P>
+<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
+specifies a <I>template-ID</I> previously defined using the
+<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
+molecule. The coordinates, atom types, charges, etc, as well as any
+bond/angle/etc and special neighbor information for the molecule can
+be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
+command for details. The only settings required to be in this file
+are the coordinates and types of atoms in the molecule.
+</P>
+<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
+atoms that are bonded to other atoms, or LAMMPS will
+soon generate an error when it tries to find bonded neighbors. LAMMPS will
+warn you if any of the atoms eligible for deletion have a non-zero
+molecule ID, but does not check for this at the time of deletion.
+</P>
+<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
+their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
+specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
+shake</A> command which also appears in your input script.
+</P>
+<P>Optionally, users may specify the maximum rotation angle for
+molecular rotations using the <I>maxangle</I> keyword and specifying
+the angle in degrees. Rotations are performed by generating a random
+point on the unit sphere and a random rotation angle on the
+range [0,maxangle). The molecule is then rotated by that angle about an
+axis passing through the molecule center of mass. The axis is parallel
+to the unit vector defined by the point on the unit sphere. The
+same procedure is used for randomly rotating molecules when they
+are inserted, except that the rotation axis passes through whatever
+origin is used for the molecule template, and the maximum angle is
+360 degrees.
+</P>
+<P>Note that fix GCMC does not use configurational bias
+MC or any other kind of sampling of intramolecular degrees of freedom.
+Inserted molecules can have different orientations, but they will all
+have the same intramolecular configuration,
+which was specified in the molecule command input.
+</P>
+<P>For atomic gasses, inserted atoms have the specified atom type, but
+deleted atoms are any atoms that have been inserted or that belong
+to the user-specified fix group. For molecular gasses, exchanged
+molecules use the same atom types as in the template molecule
+supplied by the user. In both cases, exchanged
+atoms/molecules are assigned to two groups: the default group "all"
+and the group specified in the fix gcmc command (which can also be
+"all").
+</P>
+<P>The gas reservoir pressure can be specified using the <I>pressure</I>
+keyword, in which case the user-specified chemical potential is
+ignored. For non-ideal gas reservoirs, the user may also specify the
+fugacity coefficient using the <I>fugacity_coeff</I> keyword.
+</P>
+<P>The <I>full_energy</I> option means that fix GCMC will compute the total
+potential energy of the entire simulated system. The total system
+energy before and after the proposed GCMC move is then used in the
+Metropolis criterion to determine whether or not to accept the
+proposed GCMC move. By default, this option is off, in which case
+only partial energies are computed to determine the difference in
+energy that would be caused by the proposed GCMC move.
+</P>
+<P>The <I>full_energy</I> option is needed for systems with complicated
+potential energy calculations, including the following:
+</P>
+<UL><LI> long-range electrostatics (kspace)
+<LI> many-body pair styles
+<LI> hybrid pair styles
+<LI> eam pair styles
+<LI> triclinic systems
+<LI> need to include potential energy contributions from other fixes
+</UL>
+<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
+keyword and issue a warning message.
+</P>
+<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
+the intramolecular energy of inserted and deleted molecules. If this
+is not desired, the <I>intra_energy</I> keyword can be used to define an
+amount of energy that is subtracted from the final energy when a molecule
+is inserted, and added to the initial energy when a molecule is
+deleted. For molecules that have a non-zero intramolecular energy, this
+will ensure roughly the same behavior whether or not the <I>full_energy</I>
+option is used.
+</P>
+<P>Some fixes have an associated potential energy. Examples of such fixes
+include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
+<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
+<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
+<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC moves),
+you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
+that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
+specify if this should be done.
+</P>
+<P>Use the <I>charge</I> option to insert atoms with a user-specified point
+charge. Note that doing so will cause the system to become non-neutral.
+LAMMPS issues a warning when using long-range electrostatics (kspace)
+with non-neutral systems. See the
+<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
+details about simulating non-neutral systems with kspace on.
+</P>
+<P>Use of this fix typically will cause the number of atoms to fluctuate,
+therefore, you will want to use the
+<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
+current number of atoms is used as a normalizing factor each time
+temperature is computed. Here is the necessary command:
+</P>
+<PRE>compute_modify thermo_temp dynamic yes
+</PRE>
+<P>If LJ units are used, note that a value of 0.18292026 is used by this
+fix as the reduced value for Planck's constant. This value was
+derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
+epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
+mass = 39.948 amu.
+</P>
+<P>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
+of the group-ID value. The <I>grouptype</I> keyword assigns all
+inserted atoms of the specified type to the <A HREF = "group.html">group</A>
+of the group-ID value.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
+files</A>. This includes information about the random
+number generator seed, the next timestep for MC exchanges, etc. See
+the <A HREF = "read_restart.html">read_restart</A> command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>This fix computes a global vector of length 8, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
+values are the following global cumulative quantities:
+</P>
+<UL><LI>1 = translation attempts
+<LI>2 = translation successes
+<LI>3 = insertion attempts
+<LI>4 = insertion successes
+<LI>5 = deletion attempts
+<LI>6 = deletion successes
+<LI>7 = rotation attempts
+<LI>8 = rotation successes
+</UL>
+<P>The vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Do not set "neigh_modify once yes" or else this fix will never be
+called. Reneighboring is required.
+</P>
+<P>Can be run in parallel, but aspects of the GCMC part will not scale
+well in parallel. Only usable for 3D simulations.
+</P>
+<P>Note that very lengthy simulations involving insertions/deletions of
+billions of gas molecules may run out of atom or molecule IDs and
+trigger an error, so it is better to run multiple shorter-duration
+simulations. Likewise, very large molecules have not been tested
+and may turn out to be problematic.
+</P>
+<P>Use of multiple fix gcmc commands in the same input script can be
+problematic if using a template molecule. The issue is that the
+user-referenced template molecule in the second fix gcmc command
+may no longer exist since it might have been deleted by the first
+fix gcmc command. An existing template molecule will need to be
+referenced by the user for each subsequent fix gcmc command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_atom_swap.html">fix_atom_swap</A>,
+<A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
+<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
+<A HREF = "delete_atoms.html">delete_atoms</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are mol = no, maxangle = 10, full_energy = no,
+except for the situations where full_energy is required, as
+listed above.
+</P>
+<HR>
+
+<A NAME = "Frenkel"></A>
+
+<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
+Academic Press, London, 2002.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_gld.html b/doc/doc2/fix_gld.html
new file mode 100644
index 000000000..840a47265
--- /dev/null
+++ b/doc/doc2/fix_gld.html
@@ -0,0 +1,171 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix gld command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>gld = style name of this fix command
+
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+
+<LI>N_k = number of terms in the Prony series representation of the memory kernel
+
+<LI>seed = random number seed to use for white noise (positive integer)
+
+<LI>series = <I>pprony</I> is presently the only available option
+
+<LI>c_k = the weight of the kth term in the Prony series (mass per time units)
+
+<LI>tau_k = the time constant of the kth term in the Prony series (time units)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>frozen</I> or <I>zero</I>
+ <I>frozen</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = initialize extended variables using values drawn from equilibrium distribution at Tstart
+ <I>yes</I> = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
+ <I>zero</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not set total random force to zero
+ <I>yes</I> = set total random force to zero
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes
+fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Applies Generalized Langevin Dynamics to a group of atoms, as
+described in <A HREF = "#Baczewski">(Baczewski)</A>. This is intended to model the
+effect of an implicit solvent with a temporally non-local dissipative
+force and a colored Gaussian random force, consistent with the
+Fluctuation-Dissipation Theorem. The functional form of the memory
+kernel associated with the temporally non-local force is constrained
+to be a Prony series.
+</P>
+<P>IMPORTANT NOTE: While this fix bears many similarities to <A HREF = "fix_langevin.html">fix
+langevin</A>, it has one significant
+difference. Namely, <A HREF = "fix_gld.html">fix gld</A> performs time integration,
+whereas <A HREF = "fix_langevin.html">fix langevin</A> does NOT. To this end, the
+specification of another fix to perform time integration, such as <A HREF = "fix_nve.html">fix
+nve</A>, is NOT necessary.
+</P>
+<P>With this fix active, the force on the <I>j</I>th atom is given as
+</P>
+<CENTER><IMG SRC = "Eqs/fix_gld1.jpg">
+</CENTER>
+<P>Here, the first term is representative of all conservative (pairwise,
+bonded, etc) forces external to this fix, the second is the temporally
+non-local dissipative force given as a Prony series, and the third is
+the colored Gaussian random force.
+</P>
+<P>The Prony series form of the memory kernel is chosen to enable an
+extended variable formalism, with a number of exemplary mathematical
+features discussed in <A HREF = "#Baczewski">(Baczewski)</A>. In particular, 3N_k
+extended variables are added to each atom, which effect the action of
+the memory kernel without having to explicitly evaluate the integral
+over time in the second term of the force. This also has the benefit
+of requiring the generation of uncorrelated random forces, rather than
+correlated random forces as specified in the third term of the force.
+</P>
+<P>Presently, the Prony series coefficients are limited to being greater
+than or equal to zero, and the time constants are limited to being
+greater than zero. To this end, the value of series MUST be set to
+<I>pprony</I>, for now. Future updates will allow for negative coefficients
+and other representations of the memory kernel. It is with these
+updates in mind that the series option was included.
+</P>
+<P>The units of the Prony series coefficients are chosen to be mass per
+time to ensure that the numerical integration scheme stably approaches
+the Newtonian and Langevin limits. Details of these limits, and the
+associated numerical concerns are discussed in
+<A HREF = "#Baczewski">(Baczewski)</A>.
+</P>
+<P>The desired temperature at each timestep is ramped from <I>Tstart</I> to
+<I>Tstop</I> over the course of the next run.
+</P>
+<P>The random # <I>seed</I> must be a positive integer. A Marsaglia random
+number generator is used. Each processor uses the input seed to
+generate its own unique seed and its own stream of random
+numbers. Thus the dynamics of the system will not be identical on two
+runs on different numbers of processors.
+</P>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>The keyword <I>frozen</I> can be used to specify how the extended variables
+associated with the GLD memory kernel are initialized. Specifying no
+(the default), the initial values are drawn at random from an
+equilibrium distribution at <I>Tstart</I>, consistent with the
+Fluctuation-Dissipation Theorem. Specifying yes, initializes the
+extended variables to zero.
+</P>
+<P>The keyword <I>zero</I> can be used to eliminate drift due to the
+thermostat. Because the random forces on different atoms are
+independent, they do not sum exactly to zero. As a result, this fix
+applies a small random force to the entire system, and the
+center-of-mass of the system undergoes a slow random walk. If the
+keyword <I>zero</I> is set to <I>yes</I>, the total random force is set exactly
+to zero by subtracting off an equal part of it from each atom in the
+group. As a result, the center-of-mass of a system with zero initial
+momentum will not drift over time.
+</P>
+<HR>
+
+<P><B>Restart, run start/stop, minimize info:</B>
+</P>
+<P>The instantaneous values of the extended variables are written to
+<A HREF = "restart.html">binary restart files</A>. Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>,
+<A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are frozen = no, zero = no.
+</P>
+<HR>
+
+<A NAME = "Baczewski"></A>
+
+<P><B>(Baczewski)</B> A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_gle.html b/doc/doc2/fix_gle.html
new file mode 100644
index 000000000..ec749d513
--- /dev/null
+++ b/doc/doc2/fix_gle.html
@@ -0,0 +1,170 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix gle command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride]
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>gle = style name of this fix command
+
+<LI>Ns = number of additional fictitious momenta
+
+<LI>Tstart, Tstop = temperature ramp during the run
+
+<LI>Amatrix = file to read the drift matrix A from
+
+<LI>seed = random number seed to use for generating noise (positive integer)
+
+<LI>zero or more keyword/value pairs may be appended
+
+keyword = <I>noneq</I> and/or <I>every</I>
+ <I>noneq</I> Cmatrix = file to read the non-equilibrium covariance matrix from
+ <I>every</I> stride = apply the GLE once every time steps. Reduces the accuracy
+ of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
+ sampling. It might change sampling properties when used together with <I>noneq</I>.
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>fix 3 boundary gle 6 300 300 31415 smart.A
+fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C
+</P>
+<P><B>Description:</B>
+</P>
+<P>Apply a Generalized Langevin Equation (GLE) thermostat as described
+in <A HREF = "#Ceriotti">(Ceriotti)</A>. The formalism allows one to obtain a number
+of different effects ranging from efficient sampling of all
+vibrational modes in the system to inexpensive (approximate)
+modelling of nuclear quantum effects. Contrary to
+<A HREF = "fix_langevin.html">fix langevin</A>, this fix performs both
+thermostatting and evolution of the Hamiltonian equations of motion, so it
+should not be used together with <A HREF = "fix_nve.html">fix nve</A> -- at least not
+on the same atom groups.
+</P>
+<P>Each degree of freedom in the thermostatted group is supplemented
+with Ns additional degrees of freedom s, and the equations of motion
+become
+</P>
+<P>dq/dt=p/m
+d(p,s)/dt=(F,0) - A(p,s) + B dW/dt
+</P>
+<P>where F is the physical force, A is the drift matrix (that generalizes
+the friction in Langevin dynamics), B is the diffusion term and dW/dt
+un-correlated Gaussian random forces. The A matrix couples the physical
+(q,p) dynamics with that of the additional degrees of freedom,
+and makes it possible to obtain effectively a history-dependent
+noise and friction kernel.
+</P>
+<P>The drift matrix should be given as an external file <I>Afile</I>,
+as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
+optimal for a given application and the system of choice can be
+obtained from <A HREF = "#GLE4MD">(GLE4MD)</A>.
+</P>
+<P>Equilibrium sampling a temperature T is obtained by specifiying the
+target value as the <I>Tstart</I> and <I>Tstop</I> arguments, so that the diffusion
+matrix that gives canonical sampling for a given A is computed automatically.
+However, the GLE framework also allow for non-equilibrium sampling, that
+can be used for instance to model inexpensively zero-point energy
+effects <A HREF = "#Ceriotti2">(Ceriotti2)</A>. This is achieved specifying the
+<I>noneq</I> keyword followed by the name of the file that contains the
+static covariance matrix for the non-equilibrium dynamics.
+</P>
+<P>Since integrating GLE dynamics can be costly when used together with
+simple potentials, one can use the <I>every</I> optional keyword to
+apply the Langevin terms only once every several MD steps, in a
+multiple time-step fashion. This should be used with care when doing
+non-equilibrium sampling, but should have no effect on equilibrium
+averages when using canonical sampling.
+</P>
+<P>The random number <I>seed</I> must be a positive integer. A Marsaglia random
+number generator is used. Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+</P>
+<P>Note also that the Generalized Langevin Dynamics scheme that is
+implemented by the <A HREF = "fix_gld.html">fix gld</A> scheme is closely related
+to the present one. In fact, it should be always possible to cast the
+Prony series form of the memory kernel used by GLD into an appropriate
+input matrix for <A HREF = "fix_gle.html">fix_gle</A>. While the GLE scheme is more
+general, the form used by <A HREF = "fix_gld.html">fix gld</A> can be more directly
+related to the representation of an implicit solvent environment.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>The instantaneous values of the extended variables are written to
+<A HREF = "restart.html">binary restart files</A>. Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+Note however that you should use a different seed each time you
+restart, otherwise the same sequence of random numbers will be used
+each time, which might lead to stochastic synchronization and
+subtle artefacts in the sampling.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The GLE thermostat in its current implementation should not be used
+with rigid bodies, SHAKE or RATTLE. It is expected that all the
+thermostatted degrees of freedom are fully flexible, and the sampled
+ensemble will not be correct otherwise.
+</P>
+<P>In order to perform constant-pressure simulations please use
+<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>, rather than
+<A HREF = "fix_npt.html">fix_npt</A>, to avoid duplicate integration of the
+equations of motion.
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
+viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "pair_dpd.html">pair_style
+dpd/tstat</A>, <A HREF = "fix_gld.html">fix_gld</A>
+</P>
+<HR>
+
+<A NAME = "Ceriotti"></A>
+
+<P><B>(Ceriotti)</B> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
+1170-80 (2010)
+</P>
+<A NAME = "GLE4MD"></A>
+
+<P><B>(GLE4MD)</B> <A HREF = "http://epfl-cosmo.github.io/gle4md/">http://epfl-cosmo.github.io/gle4md/</A>
+</P>
+<A NAME = "Ceriotti2"></A>
+
+<P><B>(Ceriotti2)</B> Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
+030603 (2009)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_gravity.html b/doc/doc2/fix_gravity.html
new file mode 100644
index 000000000..cde892dc2
--- /dev/null
+++ b/doc/doc2/fix_gravity.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix gravity command
+</H3>
+<H3>fix gravity/cuda command
+</H3>
+<H3>fix gravity/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group gravity magnitude style args
+</PRE>
+<UL><LI>ID, group are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>gravity = style name of this fix command
+
+<LI>magnitude = size of acceleration (force/mass units)
+
+<LI>magnitude can be a variable (see below)
+
+<LI>style = <I>chute</I> or <I>spherical</I> or <I>gradient</I> or <I>vector</I>
+
+<PRE> <I>chute</I> args = angle
+ angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
+ angle can be a variable (see below)
+ <I>spherical</I> args = phi theta
+ phi = azimuthal angle from +x axis (in degrees)
+ theta = angle from +z or +y axis in 3d/2d (in degrees)
+ phi or theta can be a variable (see below)
+ <I>vector</I> args = x y z
+ x y z = vector direction to apply the acceleration
+ x or y or z can be a variable (see below)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all gravity 1.0 chute 24.0
+fix 1 all gravity v_increase chute 24.0
+fix 1 all gravity 1.0 spherical 0.0 -180.0
+fix 1 all gravity 10.0 spherical v_phi v_theta
+fix 1 all gravity 100.0 vector 1 1 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Impose an additional acceleration on each particle in the group. This
+fix is typically used with granular systems to include a "gravity"
+term acting on the macroscopic particles. More generally, it can
+represent any kind of driving field, e.g. a pressure gradient inducing
+a Poiseuille flow in a fluid. Note that this fix operates differently
+than the <A HREF = "fix_addforce.html">fix addforce</A> command. The addforce fix
+adds the same force to each atom, independent of its mass. This
+command imparts the same acceleration to each atom (force/mass).
+</P>
+<P>The <I>magnitude</I> of the acceleration is specified in force/mass units.
+For granular systems (LJ units) this is typically 1.0. See the
+<A HREF = "units.html">units</A> command for details.
+</P>
+<P>Style <I>chute</I> is typically used for simulations of chute flow where
+the specified <I>angle</I> is the chute angle, with flow occurring in the +x
+direction. For 3d systems, the tilt is away from the z axis; for 2d
+systems, the tilt is away from the y axis.
+</P>
+<P>Style <I>spherical</I> allows an arbitrary 3d direction to be specified for
+the acceleration vector. <I>Phi</I> and <I>theta</I> are defined in the usual
+spherical coordinates. Thus for acceleration acting in the -z
+direction, <I>theta</I> would be 180.0 (or -180.0). <I>Theta</I> = 90.0 and
+<I>phi</I> = -90.0 would mean acceleration acts in the -y direction. For
+2d systems, <I>phi</I> is ignored and <I>theta</I> is an angle in the xy plane
+where <I>theta</I> = 0.0 is the y-axis.
+</P>
+<P>Style <I>vector</I> imposes an acceleration in the vector direction given
+by (x,y,z). Only the direction of the vector is important; it's
+length is ignored. For 2d systems, the <I>z</I> component is ignored.
+</P>
+<P>Any of the quantities <I>magnitude</I>, <I>angle</I>, <I>phi</I>, <I>theta</I>, <I>x</I>, <I>y</I>,
+<I>z</I> which define the gravitational magnitude and direction, can be
+specified as an equal-style <A HREF = "variable.html">variable</A>. If the value is
+a variable, it should be specified as v_name, where name is the
+variable name. In this case, the variable will be evaluated each
+timestep, and its value used to determine the quantity. You should
+insure that the variable calculates a result in the approriate units,
+e.g. force/mass or degrees.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent gravitational
+field.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the gravitational potential energy of the system to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. This scalar is the
+gravitational potential energy of the particles in the defined field,
+namely mass * (g dot x) for each particles, where x and mass are the
+particles position and mass, and g is the gravitational field. The
+scalar value calculated by this fix is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "atom_style.html">atom_style sphere</A>, <A HREF = "fix_addforce.html">fix addforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_heat.html b/doc/doc2/fix_heat.html
new file mode 100644
index 000000000..b519acab6
--- /dev/null
+++ b/doc/doc2/fix_heat.html
@@ -0,0 +1,137 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix heat command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID heat N eflux
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>heat = style name of this fix command
+
+<LI>N = add/subtract heat every this many timesteps
+
+<LI>eflux = rate of heat addition or subtraction (energy/time units)
+
+<LI>eflux can be a variable (see below)
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to have added force
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 qin heat 1 1.0
+fix 3 qin heat 10 v_flux
+fix 4 qout heat 1 -1.0 region top
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add non-translational kinetic energy (heat) to a group of atoms in a
+manner that conserves their aggregate momentum. Two of these fixes
+can be used to establish a temperature gradient across a simulation
+domain by adding heat (energy) to one group of atoms (hot reservoir)
+and subtracting heat from another (cold reservoir). E.g. a simulation
+sampling from the McDLT ensemble.
+</P>
+<P>If the <I>region</I> keyword is used, the atom must be in both the group
+and the specified geometric <A HREF = "region.html">region</A> in order to have
+energy added or subtracted to it. If not specified, then the atoms in
+the group are affected wherever they may move to.
+</P>
+<P>Heat addition/subtraction is performed every N timesteps. The <I>eflux</I>
+parameter can be specified as a numeric constant or as a variable (see
+below). If it is a numeric constant or equal-style variable which
+evaluates to a scalar value, then the <I>eflux</I> determines the change in
+aggregate energy of the entire group of atoms per unit time, e.g. in
+eV/psec for <A HREF = "units.html">metal units</A>. In this case it is an
+"extensive" quantity, meaning its magnitude should be scaled with the
+number of atoms in the group. Note that since <I>eflux</I> has per-time
+units (i.e. it is a flux), this means that a larger value of N will
+add/subtract a larger amount of energy each time the fix is invoked.
+</P>
+<P>If <I>eflux</I> is specified as an atom-style variable (see below), then
+the variable computes one value per atom. In this case, each value is
+the energy flux for a single atom, again in units of energy per unit
+time. In this case, each value is an "intensive" quantity, which need
+not be scaled with the number of atoms in the group.
+</P>
+<P>As mentioned above, the <I>eflux</I> parameter can be specified as an
+equal-style or atom_style <A HREF = "variable.html">variable</A>. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value(s) used to determine the flux.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent flux.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent flux
+with optional time-dependence as well.
+</P>
+<P>IMPORTANT NOTE: If heat is subtracted from the system too aggressively
+so that the group's kinetic energy would go to zero, or any individual
+atom's kinetic energy would go to zero for the case where <I>eflux</I> is
+an atom-style variable, then LAMMPS will halt with an error message.
+</P>
+<P>Fix heat is different from a thermostat such as <A HREF = "fix_nh.html">fix nvt</A>
+or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> in that energy is
+added/subtracted continually. Thus if there isn't another mechanism
+in place to counterbalance this effect, the entire system will heat or
+cool continuously. You can use multiple heat fixes so that the net
+energy change is 0.0 or use <A HREF = "fix_viscous.html">fix viscous</A> to drain
+energy from the system.
+</P>
+<P>This fix does not change the coordinates of its atoms; it only scales
+their velocities. Thus you must still use an integration fix
+(e.g. <A HREF = "fix_nve.html">fix nve</A>) on the affected atoms. This fix should
+not normally be used on atoms that have their temperature controlled
+by another fix - e.g. <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
+langevin</A> fix.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. This scalar is the
+most recent value by which velocites were scaled. The scalar value
+calculated by this fix is "intensive". If <I>eflux</I> is specified as
+an atom-style variable, this fix computes the average value by which
+the velocities were scaled for all of the atoms that had their
+velocities scaled.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
+temp/region</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_imd.html b/doc/doc2/fix_imd.html
new file mode 100644
index 000000000..1d8914887
--- /dev/null
+++ b/doc/doc2/fix_imd.html
@@ -0,0 +1,172 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix imd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID imd trate port keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>imd = style name of this fix command
+
+<LI>port = port number on which the fix listens for an IMD client
+
+<LI>keyword = <I>unwrap</I> or <I>fscale</I> or <I>trate</I>
+
+<PRE> <I>unwrap</I> arg = <I>on</I> or <I>off</I>
+ off = coordinates are wrapped back into the principal unit cell (default)
+ on = "unwrapped" coordinates using the image flags used
+ <I>fscale</I> arg = factor
+ factor = floating point number to scale IMD forces (default: 1.0)
+ <I>trate</I> arg = transmission rate of coordinate data sets (default: 1)
+ <I>nowait</I> arg = <I>on</I> or <I>off</I>
+ off = LAMMPS waits to be connected to an IMD client before continuing (default)
+ on = LAMMPS listens for an IMD client, but continues with the run
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix vmd all imd 5678
+fix comm all imd 8888 trate 5 unwrap on fscale 10.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix implements the "Interactive MD" (IMD) protocol which allows
+realtime visualization and manipulation of MD simulations through the
+IMD protocol, as initially implemented in VMD and NAMD. Specifically
+it allows LAMMPS to connect an IMD client, for example the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
+visualization program</A>, so that it can monitor the progress of the
+simulation and interactively apply forces to selected atoms.
+</P>
+<P>If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD
+then fix imd will use POSIX threads to spawn a IMD communication
+thread on MPI rank 0 in order to offload data reading and writing
+from the main execution thread and potentially lower the inferred
+latencies for slow communication links. This feature has only been
+tested under linux.
+</P>
+<P>There are example scripts for using this package with LAMMPS in
+examples/USER/imd. Additional examples and a driver for use with the
+Novint Falcon game controller as haptic device can be found at:
+http://sites.google.com/site/akohlmey/software/vrpn-icms.
+</P>
+<P>The source code for this fix includes code developed by the
+Theoretical and Computational Biophysics Group in the Beckman
+Institute for Advanced Science and Technology at the University of
+Illinois at Urbana-Champaign. We thank them for providing a software
+interface that allows codes like LAMMPS to hook to <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
+</P>
+<P>Upon initialization of the fix, it will open a communication port on
+the node with MPI task 0 and wait for an incoming connection. As soon
+as an IMD client is connected, the simulation will continue and the
+fix will send the current coordinates of the fix's group to the IMD
+client at every trate MD step. When using r-RESPA, trate applies to
+the steps of the outmost RESPA level. During a run with an active IMD
+connection also the IMD client can request to apply forces to selected
+atoms of the fix group.
+</P>
+<P>The port number selected must be an available network port number. On
+many machines, port numbers < 1024 are reserved for accounts with
+system manager privilege and specific applications. If multiple imd
+fixes would be active at the same time, each needs to use a different
+port number.
+</P>
+<P>The <I>nowait</I> keyword controls the behavior of the fix when no IMD
+client is connected. With the default setting of <I>off</I>, LAMMPS will
+wait until a connection is made before continuing with the
+execution. Setting <I>nowait</I> to <I>on</I> will have the LAMMPS code be ready
+to connect to a client, but continue with the simulation. This can for
+example be used to monitor the progress of an ongoing calculation
+without the need to be permanently connected or having to download a
+trajectory file.
+</P>
+<P>The <I>trate</I> keyword allows to select how often the coordinate data is
+sent to the IMD client. It can also be changed on request of the IMD
+client through an IMD protocol message. The <I>unwrap</I> keyword allows
+to send "unwrapped" coordinates to the IMD client that undo the
+wrapping back of coordinates into the principle unit cell, as done by
+default in LAMMPS. The <I>fscale</I> keyword allows to apply a scaling
+factor to forces transmitted by the IMD client. The IMD protocols
+stipulates that forces are transferred in kcal/mol/angstrom under the
+assumption that coordinates are given in angstrom. For LAMMPS runs
+with different units or as a measure to tweak the forces generated by
+the manipulation of the IMD client, this option allows to make
+adjustments.
+</P>
+<P>To connect VMD to a listening LAMMPS simulation on the same machine
+with fix imd enabled, one needs to start VMD and load a coordinate or
+topology file that matches the fix group. When the VMD command
+prompts appears, one types the command line:
+</P>
+<PRE>imd connect localhost 5678
+</PRE>
+<P>This assumes that <I>fix imd</I> was started with 5678 as a port
+number for the IMD protocol.
+</P>
+<P>The steps to do interactive manipulation of a running simulation in
+VMD are the following:
+</P>
+<P>In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
+Atom". You may alternately select "Residue", or "Fragment" to apply
+forces to whole residues or fragments. Your mouse can now be used to
+apply forces to your simulation. Click on an atom, residue, or
+fragment and drag to apply a force. Click quickly without moving the
+mouse to turn the force off. You can also use a variety of 3D position
+trackers to apply forces to your simulation. Game controllers or haptic
+devices with force-feedback such as the Novint Falcon or Sensable
+PHANTOM allow you to feel the resistance due to inertia or interactions
+with neighbors that the atoms experience you are trying to move, as if
+they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> and the
+<A HREF = "http://sites.google.com/site/akohlmey/software/vrpn-icms">VRPN-ICMS Homepage</A> for more details.
+</P>
+<P>If IMD control messages are received, a line of text describing the
+message and its effect will be printed to the LAMMPS output screen, if
+screen output is active.
+</P>
+
+
+
+
+
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global scalar or vector or per-atom
+quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>When used in combination with VMD, a topology or coordinate file has
+to be loaded, which matches (in number and ordering of atoms) the
+group the fix is applied to. The fix internally sorts atom IDs by
+ascending integer value; in VMD (and thus the IMD protocol) those will
+be assigned 0-based consecutive index numbers.
+</P>
+<P>When using multiple active IMD connections at the same time, each
+needs to use a different port number.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_indent.html b/doc/doc2/fix_indent.html
new file mode 100644
index 000000000..4e77d2e94
--- /dev/null
+++ b/doc/doc2/fix_indent.html
@@ -0,0 +1,211 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix indent command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID indent K keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>indent = style name of this fix command
+
+<LI>K = force constant for indenter surface (force/distance^2 units)
+
+<LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>sphere</I> or <I>cylinder</I> or <I>plane</I> or <I>side</I> or <I>units</I>
+
+<PRE> <I>sphere</I> args = x y z R
+ x,y,z = initial position of center of indenter (distance units)
+ R = sphere radius of indenter (distance units)
+ any of x,y,z,R can be a variable (see below)
+ <I>cylinder</I> args = dim c1 c2 R
+ dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
+ c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+ R = cylinder radius of indenter (distance units)
+ any of c1,c2,R can be a variable (see below)
+ <I>plane</I> args = dim pos side
+ dim = <I>x</I> or <I>y</I> or <I>z</I> = plane perpendicular to this dimension
+ pos = position of plane in dimension x, y, or z (distance units)
+ pos can be a variable (see below)
+ side = <I>lo</I> or <I>hi</I>
+ <I>side</I> value = <I>in</I> or <I>out</I>
+ <I>in</I> = the indenter acts on particles inside the sphere or cylinder
+ <I>out</I> = the indenter acts on particles outside the sphere or cylinder
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ lattice = the geometry is defined in lattice units
+ box = the geometry is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
+fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
+fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Insert an indenter within a simulation box. The indenter repels all
+atoms that touch it, so it can be used to push into a material or as
+an obstacle in a flow. Or it can be used as a constraining wall
+around a simulation; see the discussion of the <I>side</I> keyword below.
+</P>
+<P>The indenter can either be spherical or cylindrical or planar. You
+must set one of those 3 keywords.
+</P>
+<P>A spherical indenter exerts a force of magnitude
+</P>
+<PRE>F(r) = - K (r - R)^2
+</PRE>
+<P>on each atom where <I>K</I> is the specified force constant, <I>r</I> is the
+distance from the atom to the center of the indenter, and <I>R</I> is the
+radius of the indenter. The force is repulsive and F(r) = 0 for <I>r</I> >
+<I>R</I>.
+</P>
+<P>A cylindrical indenter exerts the same force, except that <I>r</I> is the
+distance from the atom to the center axis of the cylinder. The
+cylinder extends infinitely along its axis.
+</P>
+<P>Spherical and cylindrical indenters account for periodic boundaries in
+two ways. First, the center point of a spherical indenter (x,y,z) or
+axis of a cylindrical indenter (c1,c2) is remapped back into the
+simulation box, if the box is periodic in a particular dimension.
+This occurs every timestep if the indenter geometry is specified with
+a variable (see below), e.g. it is moving over time. Second, the
+calculation of distance to the indenter center or axis accounts for
+periodic boundaries. Both of these mean that an indenter can
+effectively move through and straddle one or more periodic boundaries.
+</P>
+<P>A planar indenter is really an axis-aligned infinite-extent wall
+exerting the same force on atoms in the system, where <I>R</I> is the
+position of the plane and <I>r-R</I> is the distance from the plane. If
+the <I>side</I> parameter of the plane is specified as <I>lo</I> then it will
+indent from the lo end of the simulation box, meaning that atoms with
+a coordinate less than the plane's current position will be pushed
+towards the hi end of the box and atoms with a coordinate higher than
+the plane's current position will feel no force. Vice versa if <I>side</I>
+is specified as <I>hi</I>.
+</P>
+<P>Any of the 4 quantities defining a spherical indenter's geometry can
+be specified as an equal-style <A HREF = "variable.html">variable</A>, namely <I>x</I>,
+<I>y</I>, <I>z</I>, or <I>R</I>. Similarly, for a cylindrical indenter, any of <I>c1</I>,
+<I>c2</I>, or <I>R</I>, can be a variable. For a planar indenter, <I>pos</I> can be
+a variable. If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value used to define the
+indenter geometry.
+</P>
+<P>Note that equal-style variables can specify formulas with various
+mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>
+command keywords for the simulation box parameters and timestep and
+elapsed time. Thus it is easy to specify indenter properties that
+change as a function of time or span consecutive runs in a continuous
+fashion. For the latter, see the <I>start</I> and <I>stop</I> keywords of the
+<A HREF = "run.html">run</A> command and the <I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style
+custom</A> for details.
+</P>
+<P>For example, if a spherical indenter's x-position is specfied as v_x,
+then this variable definition will keep it's center at a relative
+position in the simulation box, 1/4 of the way from the left edge to
+the right edge, even if the box size changes:
+</P>
+<PRE>variable x equal "xlo + 0.25*lx"
+</PRE>
+<P>Similarly, either of these variable definitions will move the indenter
+from an initial position at 2.5 at a constant velocity of 5:
+</P>
+<PRE>variable x equal "2.5 + 5*elaplong*dt"
+variable x equal vdisplace(2.5,5)
+</PRE>
+<P>If a spherical indenter's radius is specified as v_r, then these
+variable definitions will grow the size of the indenter at a specfied
+rate.
+</P>
+<PRE>variable r0 equal 0.0
+variable rate equal 1.0
+variable r equal "v_r0 + step*dt*v_rate"
+</PRE>
+<P>If the <I>side</I> keyword is specified as <I>out</I>, which is the default,
+then particles outside the indenter are pushded away from its outer
+surface, as described above. This only applies to spherical or
+cylindrical indenters. If the <I>side</I> keyword is specified as <I>in</I>,
+the action of the indenter is reversed. Particles inside the indenter
+are pushed away from its inner surface. In other words, the indenter
+is now a containing wall that traps the particles inside it. If the
+radius shrinks over time, it will squeeze the particles.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define the indenter geometry. A <I>box</I> value selects standard
+distance units as defined by the <A HREF = "units.html">units</A> command,
+e.g. Angstroms for units = real or metal. A <I>lattice</I> value means the
+distance units are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
+command must have been previously used to define the lattice spacing.
+The (x,y,z) coords of the indenter position are scaled by the x,y,z
+lattice spacings respectively. The radius of a spherical or
+cylindrical indenter is scaled by the x lattice spacing.
+</P>
+<P>Note that the units keyword only affects indenter geometry parameters
+specified directly with numbers, not those specified as variables. In
+the latter case, you should use the <I>xlat</I>, <I>ylat</I>, <I>zlat</I> keywords of
+the <A HREF = "thermo_style.html">thermo_style</A> command if you want to include
+lattice spacings in a variable formula.
+</P>
+<P>The force constant <I>K</I> is not affected by the <I>units</I> keyword. It is
+always in force/distance^2 units where force and distance are defined
+by the <A HREF = "units.html">units</A> command. If you wish K to be scaled by the
+lattice spacing, you can define K with a variable whose formula
+contains <I>xlat</I>, <I>ylat</I>, <I>zlat</I> keywords of the
+<A HREF = "thermo_style.html">thermo_style</A> command, e.g.
+</P>
+<PRE>variable k equal 100.0/xlat/xlat
+fix 1 all indent $k sphere ...
+</PRE>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and the indenter to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. The energy of each particle interacting
+with the indenter is K/3 (r - R)^3.
+</P>
+<P>This fix computes a global scalar energy and a global 3-vector of
+forces (on the indenter), which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar and vector values
+calculated by this fix are "extensive".
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. Note that if you
+define the indenter geometry with a variable using a time-dependent
+formula, LAMMPS uses the iteration count in the minimizer as the
+timestep. But it is almost certainly a bad idea to have the indenter
+change its position or size during a minimization. LAMMPS does not
+check if you have done this.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you must enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are side = out and units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ipi.html b/doc/doc2/fix_ipi.html
new file mode 100644
index 000000000..1c76f7af2
--- /dev/null
+++ b/doc/doc2/fix_ipi.html
@@ -0,0 +1,98 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ipi command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ipi address port [unix]
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>ipi = style name of this fix command
+<LI>address = internet address (FQDN or IP), or UNIX socket name
+<LI>port = port number (ignored for UNIX sockets)
+<LI>optional keyword = <I>unix</I>, if present uses a unix socket
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>fix 1 all ipi my.server.com 12345
+fix 1 all ipi mysocket 666 unix
+</P>
+<P><B>Description:</B>
+</P>
+<P>This fix enables LAMMPS to be run as a client for the i-PI Python
+wrapper <A HREF = "#IPI">(IPI)</A> for performing a path integral molecular dynamics
+(PIMD) simulation. The philosophy behind i-PI is described in the
+following publication <A HREF = "#IPICPC">(IPI-CPC)</A>.
+</P>
+<P>A version of the i-PI package, containing only files needed for use
+with LAMMPS, is provided in the tools/i-pi directory. See the
+tools/i-pi/manual.pdf for an introduction to i-PI. The
+examples/USER/i-pi directory contains example scripts for using i-PI
+with LAMMPS.
+</P>
+<P>In brief, the path integral molecular dynamics is performed by the
+Python wrapper, while the client (LAMMPS in this case) simply computes
+forces and energy for each configuration. The communication between
+the two components takes place using sockets, and is reduced to the
+bare minimum. All the parameters of the dynamics are specified in the
+input of i-PI, and all the parameters of the force field must be
+specified as LAMMPS inputs, preceding the <I>fix ipi</I> command.
+</P>
+<P>The server address must be specified by the <I>address</I> argument, and
+can be either the IP address, the fully-qualified name of the server,
+or the name of a UNIX socket for local, faster communication. In the
+case of internet sockets, the <I>port</I> argument specifies the port
+number on which i-PI is listening, while the <I>unix</I> optional switch
+specifies that the socket is a UNIX socket.
+</P>
+<P>Note that there is no check of data integrity, or that the atomic
+configurations make sense. It is assumed that the species in the i-PI
+input are listed in the same order as in the data file of LAMMPS. The
+initial configuration is ignored, as it will be substituted with the
+coordinates received from i-PI before forces are ever evaluated.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>There is no restart information associated with this fix, since all
+the dynamical parameters are dealt with by i-PI.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Using this fix on anything other than all atoms requires particular
+care, since i-PI will know nothing on atoms that are not those whose
+coordinates are transferred. However, one could use this strategy to
+define an external potential acting on the atoms that are moved by
+i-PI.
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. Because of
+the use of UNIX domain sockets, this fix will only work in a UNIX
+environment.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>
+</P>
+<HR>
+
+<A NAME = "IPICPC"></A>
+
+<P><B>(IPI-CPC)</B> Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
+1019-1026 (2014).
+</P>
+<A NAME = "IPI"></A>
+
+<P><B>(IPI)</B>
+<A HREF = "http://epfl-cosmo.github.io/gle4md/index.html?page=ipi">http://epfl-cosmo.github.io/gle4md/index.html?page=ipi</A>
+</P>
+</HTML>
diff --git a/doc/doc2/fix_langevin.html b/doc/doc2/fix_langevin.html
new file mode 100644
index 000000000..78687927d
--- /dev/null
+++ b/doc/doc2/fix_langevin.html
@@ -0,0 +1,362 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix langevin command
+</H3>
+<H3>fix langevin/kk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>langevin = style name of this fix command
+
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+
+<LI>Tstart can be a variable (see below)
+
+<LI>damp = damping parameter (time units)
+
+<LI>seed = random number seed to use for white noise (positive integer)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>angmom</I> or <I>omega</I> or <I>scale</I> or <I>tally</I> or <I>zero</I>
+
+<PRE> <I>angmom</I> value = <I>no</I> or scale
+ <I>no</I> = do not thermostat rotational degrees of freedom via the angular momentum
+ factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
+ <I>gjf</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = use standard formulation
+ <I>yes</I> = use Gronbech-Jensen/Farago formulation
+ <I>omega</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not thermostat rotational degrees of freedom via the angular velocity
+ <I>yes</I> = do thermostat rotational degrees of freedom via the angular velocity
+ <I>scale</I> values = type ratio
+ type = atom type (1-N)
+ ratio = factor by which to scale the damping coefficient
+ <I>tally</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not tally the energy added/subtracted to atoms
+ <I>yes</I> = do tally the energy added/subtracted to atoms
+ <I>zero</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not set total random force to zero
+ <I>yes</I> = set total random force to zero
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 boundary langevin 1.0 1.0 1000.0 699483
+fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
+fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
+to a group of atoms which models an interaction with a background
+implicit solvent. Used with <A HREF = "fix_nve.html">fix nve</A>, this command
+performs Brownian dynamics (BD), since the total force on each atom
+will have the form:
+</P>
+<PRE>F = Fc + Ff + Fr
+Ff = - (m / damp) v
+Fr is proportional to sqrt(Kb T m / (dt damp))
+</PRE>
+<P>Fc is the conservative force computed via the usual inter-particle
+interactions (<A HREF = "pair_style.html">pair_style</A>,
+<A HREF = "bond_style.html">bond_style</A>, etc).
+</P>
+<P>The Ff and Fr terms are added by this fix on a per-particle basis.
+See the <A HREF = "pair_dpd.html">pair_style dpd/tstat</A> command for a
+thermostatting option that adds similar terms on a pairwise basis to
+pairs of interacting particles.
+</P>
+<P>Ff is a frictional drag or viscous damping term proportional to the
+particle's velocity. The proportionality constant for each atom is
+computed as m/damp, where m is the mass of the particle and damp is
+the damping factor specified by the user.
+</P>
+<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
+into the particle. As derived from the fluctuation/dissipation
+theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
+dt damp), where Kb is the Boltzmann constant, T is the desired
+temperature, m is the mass of the particle, dt is the timestep size,
+and damp is the damping factor. Random numbers are used to randomize
+the direction and magnitude of this force as described in
+<A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used (instead of
+a Gaussian random number) for speed.
+</P>
+<P>Note that unless you use the <I>omega</I> or <I>angmom</I> keywords, the
+thermostat effect of this fix is applied to only the translational
+degrees of freedom for the particles, which is an important
+consideration for finite-size particles, which have rotational degrees
+of freedom, are being thermostatted. The translational degrees of
+freedom can also have a bias velocity removed from them before
+thermostatting takes place; see the description below.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration. It only modifies forces to effect
+thermostatting. Thus you must use a separate time integration fix,
+like <A HREF = "fix_nve.html">fix nve</A> to actually update the velocities and
+positions of atoms using the modified forces. Likewise, this fix
+should not normally be used on atoms that also have their temperature
+controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P>The desired temperature at each timestep is a ramped value during the
+run from <I>Tstart</I> to <I>Tstop</I>.
+</P>
+<P><I>Tstart</I> can be specified as an equal-style or atom-style
+<A HREF = "variable.html">variable</A>. In this case, the <I>Tstop</I> setting is
+ignored. If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+target temperature.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent temperature.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent
+temperature with optional time-dependence as well.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that remove a "bias" from the
+atom velocities. E.g. removing the center-of-mass velocity from a
+group of atoms or removing the x-component of velocity from the
+calculation. This is not done by default, but only if the
+<A HREF = "fix_modify.html">fix_modify</A> command is used to assign a temperature
+compute to this fix that includes such a bias term. See the doc pages
+for individual <A HREF = "compute.html">compute commands</A> to determine which ones
+include a bias. In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostatting is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in.
+</P>
+<P>The <I>damp</I> parameter is specified in time units and determines how
+rapidly the temperature is relaxed. For example, a value of 100.0
+means to relax the temperature in a timespan of (roughly) 100 time
+units (tau or fmsec or psec - see the <A HREF = "units.html">units</A> command).
+The damp factor can be thought of as inversely related to the
+viscosity of the solvent. I.e. a small relaxation time implies a
+hi-viscosity solvent and vice versa. See the discussion about gamma
+and viscosity in the documentation for the <A HREF = "fix_viscous.html">fix
+viscous</A> command for more details.
+</P>
+<P>The random # <I>seed</I> must be a positive integer. A Marsaglia random
+number generator is used. Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+</P>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>The keyword <I>angmom</I> and <I>omega</I> keywords enable thermostatting of
+rotational degrees of freedom in addition to the usual translational
+degrees of freedom. This can only be done for finite-size particles.
+</P>
+<P>A simulation using atom_style sphere defines an omega for finite-size
+spheres. A simulation using atom_style ellipsoid defines a finite
+size and shape for aspherical particles and an angular momentum.
+The Langevin formulas for thermostatting the rotational degrees of
+freedom are the same as those above, where force is replaced by
+torque, m is replaced by the moment of inertia I, and v is replaced by
+omega (which is derived from the angular momentum in the case of
+aspherical particles).
+</P>
+<P>The rotational temperature of the particles can be monitored by the
+<A HREF = "compute_temp_sphere.html">compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
+temp/asphere</A> commands with their rotate
+options.
+</P>
+<P>For the <I>omega</I> keyword there is also a scale factor of 10.0/3.0 that
+is applied as a multiplier on the Ff (damping) term in the equation
+above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does
+not affect the thermostatting behaviour of the Langevin formalism but
+insures that the randomized rotational diffusivity of spherical
+particles is correct.
+</P>
+<P>For the <I>angmom</I> keyword a similar scale factor is needed which is
+10.0/3.0 for spherical particles, but is anisotropic for aspherical
+particles (e.g. ellipsoids). Currently LAMMPS only applies an
+isotropic scale factor, and you can choose its magnitude as the
+specified value of the <I>angmom</I> keyword. If your aspherical particles
+are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good
+choice. If they are highly aspherical, a value of 1.0 is as good a
+choice as any, since the effects on rotational diffusivity of the
+particles will be incorrect regardless. Note that for any reasonable
+scale factor, the thermostatting effect of the <I>angmom</I> keyword on the
+rotational temperature of the aspherical particles should still be
+valid.
+</P>
+<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
+the specified factor for atoms of that type. This can be useful when
+different atom types have different sizes or masses. It can be used
+multiple times to adjust damp for several atom types. Note that
+specifying a ratio of 2 increases the relaxation time which is
+equivalent to the solvent's viscosity acting on particles with 1/2 the
+diameter. This is the opposite effect of scale factors used by the
+<A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in fix
+<I>langevin</I> is inversely related to the gamma factor in fix <I>viscous</I>.
+Also note that the damping factor in fix <I>langevin</I> includes the
+particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass and size of
+different atom types should be accounted for in the choice of ratio
+values.
+</P>
+<P>The keyword <I>tally</I> enables the calculation of the cumulative energy
+added/subtracted to the atoms as they are thermostatted. Effectively
+it is the energy exchanged between the infinite thermal reservoir and
+the particles. As described below, this energy can then be printed
+out or added to the potential energy of the system to monitor energy
+conservation.
+</P>
+<P>IMPORTANT NOTE: this accumulated energy does NOT include kinetic
+energy removed by the <I>zero</I> flag. LAMMPS will print a warning when
+both options are active.
+</P>
+<P>The keyword <I>zero</I> can be used to eliminate drift due to the
+thermostat. Because the random forces on different atoms are
+independent, they do not sum exactly to zero. As a result, this fix
+applies a small random force to the entire system, and the
+center-of-mass of the system undergoes a slow random walk. If the
+keyword <I>zero</I> is set to <I>yes</I>, the total random force is set exactly
+to zero by subtracting off an equal part of it from each atom in the
+group. As a result, the center-of-mass of a system with zero initial
+momentum will not drift over time.
+</P>
+<P>The keyword <I>gjf</I> can be used to run the <A HREF = "#Gronbech-Jensen">Gronbech-Jensen/Farago
+</A> time-discretization of the Langevin model. As
+described in the papers cited below, the purpose of this method is to
+enable longer timesteps to be used (up to the numerical stability
+limit of the integrator), while still producing the correct Boltzmann
+distribution of atom positions. It is implemented within LAMMPS, by
+changing how the the random force is applied so that it is composed of
+the average of two random forces representing half-contributions from
+the previous and current time intervals.
+</P>
+<P>In common with all methods based on Verlet integration, the
+discretized velocities generated by this method in conjunction with
+velocity-Verlet time integration are not exactly conjugate to the
+positions. As a result the temperature (computed from the discretized
+velocities) will be systematically lower than the target temperature,
+by a small amount which grows with the timestep. Nonetheless, the
+distribution of atom positions will still be consistent with the
+target temperature.
+</P>
+<P>As an example of using the <I>gjf</I> keyword, for molecules containing C-H
+bonds, configurational properties generated with dt = 2.5 fs and tdamp
+= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity
+distribution systematically decreases with increasing timestep, the
+method should not be used to generate properties that depend on the
+velocity distribution, such as the velocity autocorrelation function
+(VACF). In this example, the velocity distribution at dt = 2.5fs
+generates an average temperature of 220 K, instead of 300 K.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place. However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. Note that use of this option requires
+setting the <I>tally</I> keyword to <I>yes</I>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive". Note that calculation of this
+quantity requires setting the <I>tally</I> keyword to <I>yes</I>.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
+viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "pair_dpd.html">pair_style
+dpd/tstat</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are angmom = no, omega = no, scale = 1.0 for all
+types, tally = no, zero = no, gjf = no.
+</P>
+<HR>
+
+<A NAME = "Dunweg"></A>
+
+<P><B>(Dunweg)</B> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
+</P>
+<A NAME = "Schneider"></A>
+
+<P><B>(Schneider)</B> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+</P>
+<A NAME = "Gronbech-Jensen"></A>
+
+<P><B>(Gronbech-Jensen)</B> Gronbech-Jensen and Farago, Mol Phys, 111, 983
+(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
+185, 524 (2014)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_langevin_drude.html b/doc/doc2/fix_langevin_drude.html
new file mode 100644
index 000000000..a118f323c
--- /dev/null
+++ b/doc/doc2/fix_langevin_drude.html
@@ -0,0 +1,280 @@
+<HTML>
+<script type="text/javascript"
+ src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix langevin/drude command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>langevin/drude = style name of this fix command
+
+<LI>Tcom = desired temperature of the centers of mass (temperature units)
+
+<LI>damp_com = damping parameter for the thermostat on centers of mass (time units)
+
+<LI>seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer)
+
+<LI>Tdrude = desired temperature of the Drude oscillators (temperature units)
+
+<LI>damp_drude = damping parameter for the thermostat on Drude oscillators (time units)
+
+<LI>seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>zero</I>
+
+<PRE> <I>zero</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not set total random force on centers of mass to zero
+ <I>yes</I> = set total random force on centers of mass to zero
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
+fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply two Langevin thermostats as described in <A HREF = "#Jiang">(Jiang)</A> for
+thermalizing the reduced degrees of freedom of Drude oscillators.
+This link describes how to use the <A HREF = "tutorial_drude.html">thermalized Drude oscillator
+model</A> in LAMMPS and polarizable models in LAMMPS
+are discussed in <A HREF = "Section_howto.html#howto_25">this Section</A>.
+</P>
+<P>Drude oscillators are a way to simulate polarizables atoms, by
+splitting them into a core and a Drude particle bound by a harmonic
+bond. The thermalization works by transforming the particles degrees
+of freedom by these equations. In these equations upper case denotes
+atomic or center of mass values and lower case denotes Drude particle
+or dipole values. Primes denote the transformed (reduced) values,
+while bare letters denote the original values.
+</P>
+Velocities:
+\begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation}
+\begin{equation} v' = v - V \end{equation}
+Masses:
+\begin{equation} M' = M + m \end{equation}
+\begin{equation} m' = \frac {M\, m } {M'} \end{equation}
+The Langevin forces are computed as
+\begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation}
+\begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation}
+\(F_r'\) is a random force proportional to
+\(\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'}
+ {\mathrm dt\, \mathtt{damp\_com} }
+ } \).
+<BR>
+\(f_r'\) is a random force proportional to
+\(\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'}
+ {\mathrm dt\, \mathtt{damp\_drude} }
+ } \).
+<BR>
+<P>Then the real forces acting on the particles are computed from the inverse
+transform:
+\begin{equation} F = \frac M {M'}\, F' - f' \end{equation}
+\begin{equation} f = \frac m {M'}\, F' + f' \end{equation}
+</P>
+<P>This fix also thermostates non-polarizable atoms in the group at
+temperature <I>Tcom</I>, as if they had a massless Drude partner. The
+Drude particles themselves need not be in the group. The center of
+mass and the dipole are thermostated iff the core atom is in the
+group.
+</P>
+<P>Note that the thermostat effect of this fix is applied to only the
+translational degrees of freedom of the particles, which is an
+important consideration if finite-size particles, which have
+rotational degrees of freedom, are being thermostated. The
+translational degrees of freedom can also have a bias velocity removed
+from them before thermostating takes place; see the description below.
+</P>
+<P>IMPORTANT NOTE: Like the <A HREF = "fix_langevin.html">fix langevin</A> command,
+this fix does NOT perform time integration. It only modifies forces to
+effect thermostating. Thus you must use a separate time integration
+fix, like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A> to actually
+update the velocities and positions of atoms using the modified
+forces. Likewise, this fix should not normally be used on atoms that
+also have their temperature controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix
+nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostating.
+</P>
+<HR>
+
+<P>This fix requires each atom know whether it is a Drude particle or
+not. You must therefore use the <A HREF = "fix_drude.html">fix drude</A> command to
+specify the Drude status of each atom type.
+</P>
+<P>IMPORTANT NOTE: only the Drude core atoms need to be in the group
+specified for this fix. A Drude electron will be transformed together
+with its cores even if it is not itself in the group. It is safe to
+include Drude electrons or non-polarizable atoms in the group. The
+non-polarizable atoms will simply not be thermostatted as if they had
+a massless Drude partner (electron).
+</P>
+<P>IMPORTANT NOTE: Ghost atoms need to know their velocity for this fix
+to act correctly. You must use the <A HREF = "comm_modify.html">comm_modify</A>
+command to enable this, e.g.
+</P>
+<PRE>comm_modify vel yes
+</PRE>
+<HR>
+
+<P><I>Tcom</I> is the target temperature of the centers of mass, which would
+be used to thermostate the non-polarizable atoms. <I>Tdrude</I> is the
+(normally low) target temperature of the core-Drude particle pairs
+(dipoles). <I>Tcom</I> and <I>Tdrude</I> can be specified as an equal-style
+<A HREF = "variable.html">variable</A>. If the value is a variable, it should be
+specified as v_name, where name is the variable name. In this case,
+the variable will be evaluated each timestep, and its value used to
+determine the target temperature.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent temperature.
+</P>
+<P>Like other fixes that perform thermostating, this fix can be used with
+<A HREF = "compute.html">compute commands</A> that remove a "bias" from the atom
+velocities. E.g. removing the center-of-mass velocity from a group of
+atoms. This is not done by default, but only if the
+<A HREF = "fix_modify.html">fix_modify</A> command is used to assign a temperature
+compute to this fix that includes such a bias term. See the doc pages
+for individual <A HREF = "compute.html">compute commands</A> to determine which ones
+include a bias. In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostating is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in. NOTE: this feature has not been tested.
+</P>
+<P>Note: The temperature thermostating the core-Drude particle pairs
+should be chosen low enough, so as to mimic as closely as possible the
+self-consistent minimization. It must however be high enough, so that
+the dipoles can follow the local electric field exerted by the
+neighbouring atoms. The optimal value probably depends on the
+temperature of the centers of mass and on the mass of the Drude
+particles.
+</P>
+<P><I>damp_com</I> is the characteristic time for reaching thermal equilibrium
+of the centers of mass. For example, a value of 100.0 means to relax
+the temperature of the centers of mass in a timespan of (roughly) 100
+time units (tau or fmsec or psec - see the <A HREF = "units.html">units</A>
+command). <I>damp_drude</I> is the characteristic time for reaching
+thermal equilibrium of the dipoles. It is typically a few timesteps.
+</P>
+<P>The number <I>seed_com</I> and <I>seed_drude</I> are positive integers. They set
+the seeds of the Marsaglia random number generators used for
+generating the random forces on centers of mass and on the
+dipoles. Each processor uses the input seed to generate its own unique
+seed and its own stream of random numbers. Thus the dynamics of the
+system will not be identical on two runs on different numbers of
+processors.
+</P>
+<P>The keyword <I>zero</I> can be used to eliminate drift due to the
+thermostat on centers of mass. Because the random forces on different
+centers of mass are independent, they do not sum exactly to zero. As
+a result, this fix applies a small random force to the entire system,
+and the momentum of the total center of mass of the system undergoes a
+slow random walk. If the keyword <I>zero</I> is set to <I>yes</I>, the total
+random force on the centers of mass is set exactly to zero by
+subtracting off an equal part of it from each center of mass in the
+group. As a result, the total center of mass of a system with zero
+initial momentum will not drift over time.
+</P>
+<P>The actual temperatures of cores and Drude particles, in
+center-of-mass and relatice coordinates, respectively, can be
+calculated using the <A HREF = "compute_temp_drude.html">compute temp/drude</A>
+command.
+</P>
+<HR>
+
+<P>Usage example for rigid bodies in the NPT ensemble:
+</P>
+<PRE>comm_modify vel yes
+fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
+fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
+fix NVE DRUDES nve
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TATOM c_TDRUDE f_TEMP[1] f_TEMP[2]
+</PRE>
+<P>Comments:
+</P>
+<UL><LI>Drude particles should not be in the rigid group, otherwise the Drude
+<LI>oscillators will be frozen and the system will lose its
+<LI>polarizability. <I>zero yes</I> avoids a drift of the center of mass of
+<LI>the system, but is a bit slower. use two different random seeds to
+<LI>avoid unphysical correlations. temperature is controlled by the fix
+<LI><I>langevin/drude</I>, so the time-integration fixes do not thermostate.
+<LI>don't forget to time-integrate both cores and Drude particles.
+<LI>pressure is time-integrated only once by using <I>nve</I> for Drude
+<LI>particles and <I>nph</I> for atoms/cores (or vice versa). Do not use <I>nph</I>
+<LI>for both. contrary to the alternative thermostating using Nose-Hoover
+<LI>thermostat fix <I>npt</I> and fix <I>drude/transform</I>, the <I>fix_modify</I>
+<LI>command is not required here, because the fix <I>nph</I> computes the
+<LI>global pressure even if its group is <I>ATOMS</I>. This is what we want. If
+<LI>we thermostated <I>ATOMS</I> using <I>npt</I>, the pressure should be the global
+<LI>one, but the temperature should be only that of the cores. That's why
+<LI>the command <I>fix_modify</I> should be called in that case. f_TEMP[1]
+<LI>and f_TEMP[2] contain the reduced temperatures of the cores/atoms
+<LI>and of the Drude particles (see below). They should be 300. and 1. on
+<LI>average here.
+</UL>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place. However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostating
+procedure, as described above. For consistency, the group used by the
+compute should include the group of this fix and the Drude particles.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>,
+<A HREF = "fix_drude.html">fix drude</A>,
+<A HREF = "fix_drude_transform.html">fix drude/transform</A>,
+<A HREF = "compute_temp_drude.html">compute temp/drude</A>,
+<A HREF = "pair_thole.html">pair_style thole</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are zero = no.
+</P>
+<HR>
+
+<A NAME = "Jiang"></A>
+
+<P><B>(Jiang)</B> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
+Phys Chem Lett, 2, 87-92 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_langevin_eff.html b/doc/doc2/fix_langevin_eff.html
new file mode 100644
index 000000000..c2b8617da
--- /dev/null
+++ b/doc/doc2/fix_langevin_eff.html
@@ -0,0 +1,128 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix langevin/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>langevin/eff = style name of this fix command
+
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+
+<LI>damp = damping parameter (time units)
+
+<LI>seed = random number seed to use for white noise (positive integer)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>scale</I> or <I>tally</I> or <I>zero</I>
+ <I>scale</I> values = type ratio
+ type = atom type (1-N)
+ ratio = factor by which to scale the damping coefficient
+ <I>tally</I> values = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not tally the energy added/subtracted to atoms
+ <I>yes</I> = do tally the energy added/subtracted to atoms
+</PRE>
+<PRE> <I>zero</I> value = <I>no</I> or <I>yes</I>
+ <I>no</I> = do not set total random force to zero
+ <I>yes</I> = set total random force to zero
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
+fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
+to a group of nuclei and electrons in the <A HREF = "pair_eff.html">electron force
+field</A> model. Used with <A HREF = "fix_nve_eff.html">fix nve/eff</A>,
+this command performs Brownian dynamics (BD), since the total force on
+each atom will have the form:
+</P>
+<PRE>F = Fc + Ff + Fr
+Ff = - (m / damp) v
+Fr is proportional to sqrt(Kb T m / (dt damp))
+</PRE>
+<P>Fc is the conservative force computed via the usual inter-particle
+interactions (<A HREF = "pair_style.html">pair_style</A>).
+</P>
+<P>The Ff and Fr terms are added by this fix on a per-particle basis.
+</P>
+<P>The operation of this fix is exactly like that described by the <A HREF = "fix_langevin.html">fix
+langevin</A> command, except that the thermostatting
+is also applied to the radial electron velocity for electron
+particles.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place. However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>. Note that use of this option requires
+setting the <I>tally</I> keyword to <I>yes</I>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive". Note that calculation of this
+quantity requires setting the <I>tally</I> keyword to <I>yes</I>.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P>This fix is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are scale = 1.0 for all types and tally = no.
+</P>
+<HR>
+
+<A NAME = "Dunweg"></A>
+
+<P><B>(Dunweg)</B> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
+</P>
+<A NAME = "Schneider"></A>
+
+<P><B>(Schneider)</B> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lb_fluid.html b/doc/doc2/fix_lb_fluid.html
new file mode 100644
index 000000000..090c68875
--- /dev/null
+++ b/doc/doc2/fix_lb_fluid.html
@@ -0,0 +1,388 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lb/fluid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>lb/fluid = style name of this fix command
+
+<LI>nevery = update the lattice-Boltzmann fluid every this many timesteps
+
+<LI>LBtype = 1 to use the standard finite difference LB integrator,
+2 to use the LB integrator of <A HREF = "#Ollila">Ollila et al.</A>
+
+<LI>viscosity = the fluid viscosity (units of mass/(time*length)).
+
+<LI>density = the fluid density.
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>setArea</I> or <I>setGamma</I> or <I>scaleGamma</I> or <I>dx</I> or <I>dm</I> or <I>a0</I> or <I>noise</I> or <I>calcforce</I> or <I>trilinear</I> or <I>D3Q19</I> or <I>read_restart</I> or <I>write_restart</I> or <I>zwall_velocity</I> or <I>bodyforce</I> or <I>printfluid</I>
+
+<PRE> <I>setArea</I> values = type node_area
+ type = atom type (1-N)
+ node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
+ <I>setGamma</I> values = gamma
+ gamma = user set value for the force coupling constant.
+ <I>scaleGamma</I> values = type gammaFactor
+ type = atom type (1-N)
+ gammaFactor = factor to scale the <I>setGamma</I> gamma value by, for the specified atom type.
+ <I>dx</I> values = dx_LB = the lattice spacing.
+ <I>dm</I> values = dm_LB = the lattice-Boltzmann mass unit.
+ <I>a0</I> values = a_0_real = the square of the speed of sound in the fluid.
+ <I>noise</I> values = Temperature seed
+ Temperature = fluid temperature.
+ seed = random number generator seed (positive integer)
+ <I>calcforce</I> values = N forcegroup-ID
+ N = output the force and torque every N timesteps
+ forcegroup-ID = ID of the particle group to calculate the force and torque of
+ <I>trilinear</I> values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
+ <I>D3Q19</I> values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
+ <I>read_restart</I> values = restart file = name of the restart file to use to restart a fluid run.
+ <I>write_restart</I> values = N = write a restart file every N MD timesteps.
+ <I>zwall_velocity</I> values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
+ <I>bodyforce</I> values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
+ <I>printfluid</I> values = N = print the fluid density and velocity at each grid point every N timesteps.
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
+fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS
+simulation domain. The MD particles described by <I>group-ID</I> apply a velocity
+dependent force to the fluid.
+</P>
+<P>The lattice-Boltzmann algorithm solves for the fluid motion governed by
+the Navier Stokes equations,
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_navierstokes.jpg">
+</CENTER>
+<P>with,
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_viscosity.jpg">
+</CENTER>
+<P>where rho is the fluid density, u is the local fluid velocity, sigma
+is the stress tensor, F is a local external force, and eta and Lambda
+are the shear and bulk viscosities respectively. Here, we have
+implemented
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_stress.jpg">
+</CENTER>
+<P>with a_0 set to 1/3 (dx/dt)^2 by default.
+</P>
+<P>The algorithm involves tracking the time evolution of a set of partial
+distribution functions which evolve according to a velocity
+discretized version of the Boltzmann equation,
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_boltzmann.jpg">
+</CENTER>
+<P>where the first term on the right hand side represents a single time
+relaxation towards the equilibrium distribution function, and tau is a
+parameter physically related to the viscosity. On a technical note,
+we have implemented a 15 velocity model (D3Q15) as default; however,
+the user can switch to a 19 velocity model (D3Q19) through the use of
+the <I>D3Q19</I> keyword. This fix provides the user with the choice of
+two algorithms to solve this equation, through the specification of
+the keyword <I>LBtype</I>. If <I>LBtype</I> is set equal to 1, the standard
+finite difference LB integrator is used. If <I>LBtype</I> is set equal to
+2, the algorithm of <A HREF = "#Ollila">Ollila et al.</A> is used.
+</P>
+<P>Physical variables are then defined in terms of moments of the distribution
+functions,
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_properties.jpg">
+</CENTER>
+<P>Full details of the lattice-Boltzmann algorithm used can be found in
+<A HREF = "#Mackay">Mackay et al.</A>.
+</P>
+<P>The fluid is coupled to the MD particles described by <I>group-ID</I>
+through a velocity dependent force. The contribution to the fluid
+force on a given lattice mesh site j due to MD particle alpha is
+calculated as:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_fluidforce.jpg">
+</CENTER>
+<P>where v_n is the velocity of the MD particle, u_f is the fluid
+velocity interpolated to the particle location, and gamma is the force
+coupling constant. Zeta is a weight assigned to the grid point,
+obtained by distributing the particle to the nearest lattice sites.
+For this, the user has the choice between a trilinear stencil, which
+provides a support of 8 lattice sites, or the immersed boundary method
+Peskin stencil, which provides a support of 64 lattice sites. While
+the Peskin stencil is seen to provide more stable results, the
+trilinear stencil may be better suited for simulation of objects close
+to walls, due to its smaller support. Therefore, by default, the
+Peskin stencil is used; however the user may switch to the trilinear
+stencil by specifying the keyword, <I>trilinear</I>.
+</P>
+<P>By default, the force coupling constant, gamma, is calculated according to
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_gammadefault.jpg">
+</CENTER>
+<P>Here, m_v is the mass of the MD particle, m_u is a representative
+fluid mass at the particle location, and dt_collision is a collision
+time, chosen such that tau/dt_collision = 1 (see <A HREF = "#Mackay2">Mackay and
+Denniston</A> for full details). In order to calculate m_u, the
+fluid density is interpolated to the MD particle location, and
+multiplied by a volume, node_area*dx_lb, where node_area represents
+the portion of the surface area of the composite object associated
+with a given MD particle. By default, node_area is set equal to
+dx_lb*dx_lb; however specific values for given atom types can be set
+using the <I>setArea</I> keyword.
+</P>
+<P>The user also has the option of specifying their own value for the
+force coupling constant, for all the MD particles associated with the
+fix, through the use of the <I>setGamma</I> keyword. This may be useful
+when modelling porous particles. See <A HREF = "#Mackay">Mackay et al.</A> for a
+detailed description of the method by which the user can choose an
+appropriate gamma value.
+</P>
+<P>IMPORTANT NOTE: while this fix applies the force of the particles on
+the fluid, it does not apply the force of the fluid to the particles.
+When the force coupling constant is set using the default method,
+there is only one option to include this hydrodynamic force on the
+particles, and that is through the use of the
+<A HREF = "fix_lb_viscous.html">lb/viscous</A> fix. This fix adds the hydrodynamic
+force to the total force acting on the particles, after which any of
+the built-in LAMMPS integrators can be used to integrate the particle
+motion. However, if the user specifies their own value for the force
+coupling constant, as mentioned in <A HREF = "#Mackay">Mackay et al.</A>, the
+built-in LAMMPS integrators may prove to be unstable. Therefore, we
+have included our own integrators <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A>, and <A HREF = "fix_lb_pc.html">fix
+lb/pc</A>, to solve for the particle motion in these
+cases. These integrators should not be used with the
+<A HREF = "fix_lb_viscous.html">lb/viscous</A> fix, as they add hydrodynamic forces
+to the particles directly. In addition, they can not be used if the
+force coupling constant has been set the default way.
+</P>
+<P>IMPORTANT NOTE: if the force coupling constant is set using the
+default method, and the <A HREF = "fix_lb_viscous.html">lb/viscous</A> fix is NOT
+used to add the hydrodynamic force to the total force acting on the
+particles, this physically corresponds to a situation in which an
+infinitely massive particle is moving through the fluid (since
+collisions between the particle and the fluid do not act to change the
+particle's velocity). Therefore, the user should set the mass of the
+particle to be significantly larger than the mass of the fluid at the
+particle location, in order to approximate an infinitely massive
+particle (see the dragforce test run for an example).
+</P>
+<HR>
+
+<P>Inside the fix, parameters are scaled by the lattice-Boltzmann
+timestep, dt, grid spacing, dx, and mass unit, dm. dt is set equal to
+(nevery*dt_MD), where dt_MD is the MD timestep. By default, dm is set
+equal to 1.0, and dx is chosen so that tau/(dt) =
+(3*eta*dt)/(rho*dx^2) is approximately equal to 1. However, the user
+has the option of specifying their own values for dm, and dx, by using
+the optional keywords <I>dm</I>, and <I>dx</I> respectively.
+</P>
+<P>IMPORTANT NOTE: Care must be taken when choosing both a value for dx,
+and a simulation domain size. This fix uses the same subdivision of
+the simulation domain among processors as the main LAMMPS program. In
+order to uniformly cover the simulation domain with lattice sites, the
+lengths of the individual LAMMPS subdomains must all be evenly
+divisible by dx. If the simulation domain size is cubic, with equal
+lengths in all dimensions, and the default value for dx is used, this
+will automatically be satisfied.
+</P>
+<P>Physical parameters describing the fluid are specified through
+<I>viscosity</I>, <I>density</I>, and <I>a0</I>. If the force coupling constant is
+set the default way, the surface area associated with the MD particles
+is specified using the <I>setArea</I> keyword. If the user chooses to
+specify a value for the force coupling constant, this is set using the
+<I>setGamma</I> keyword. These parameters should all be given in terms of
+the mass, distance, and time units chosen for the main LAMMPS run, as
+they are scaled by the LB timestep, lattice spacing, and mass unit,
+inside the fix.
+</P>
+<HR>
+
+<P>The <I>setArea</I> keyword allows the user to associate a surface area with
+a given atom type. For example if a spherical composite object of
+radius R is represented as a spherical shell of N evenly distributed
+MD particles, all of the same type, the surface area per particle
+associated with that atom type should be set equal to 4*pi*R^2/N.
+This keyword should only be used if the force coupling constant,
+gamma, is set the default way.
+</P>
+<P>The <I>setGamma</I> keyword allows the user to specify their own value for
+the force coupling constant, gamma, instead of using the default
+value.
+</P>
+<P>The <I>scaleGamma</I> keyword should be used in conjunction with the
+<I>setGamma</I> keyword, when the user wishes to specify different gamma
+values for different atom types. This keyword allows the user to
+scale the <I>setGamma</I> gamma value by a factor, gammaFactor, for a given
+atom type.
+</P>
+<P>The <I>dx</I> keyword allows the user to specify a value for the LB grid
+spacing.
+</P>
+<P>The <I>dm</I> keyword allows the user to specify the LB mass unit.
+</P>
+<P>If the <I>a0</I> keyword is used, the value specified is used for the
+square of the speed of sound in the fluid. If this keyword is not
+present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2.
+Setting a0 > (dx/dt)^2 is not allowed, as this may lead to
+instabilities.
+</P>
+<P>If the <I>noise</I> keyword is used, followed by a a positive temperature
+value, and a positive integer random number seed, a thermal
+lattice-Boltzmann algorithm is used. If <I>LBtype</I> is set equal to 1
+(i.e. the standard LB integrator is chosen), the thermal LB algorithm
+of <A HREF = "#Adhikari">Adhikari et al.</A> is used; however if <I>LBtype</I> is set
+equal to 2 both the LB integrator, and thermal LB algorithm described
+in <A HREF = "#Ollila">Ollila et al.</A> are used.
+</P>
+<P>If the <I>calcforce</I> keyword is used, both the fluid force and torque
+acting on the specified particle group are printed to the screen every
+N timesteps.
+</P>
+<P>If the keyword <I>trilinear</I> is used, the trilinear stencil is used to
+interpolate the particle nodes onto the fluid mesh. By default, the
+immersed boundary method, Peskin stencil is used. Both of these
+interpolation methods are described in <A HREF = "#Mackay">Mackay et al.</A>.
+</P>
+<P>If the keyword <I>D3Q19</I> is used, the 19 velocity (D3Q19) lattice is
+used by the lattice-Boltzmann algorithm. By default, the 15 velocity
+(D3Q15) lattice is used.
+</P>
+<P>If the keyword <I>write_restart</I> is used, followed by a positive
+integer, N, a binary restart file is printed every N LB timesteps.
+This restart file only contains information about the fluid.
+Therefore, a LAMMPS restart file should also be written in order to
+print out full details of the simulation.
+</P>
+<P>IMPORTANT NOTE: When a large number of lattice grid points are used,
+the restart files may become quite large.
+</P>
+<P>In order to restart the fluid portion of the simulation, the keyword
+<I>read_restart</I> is specified, followed by the name of the binary
+lb_fluid restart file to be used.
+</P>
+<P>If the <I>zwall_velocity</I> keyword is used y-velocities are assigned to
+the lower and upper walls. This keyword requires the presence of
+walls in the z-direction. This is set by assigning fixed boundary
+conditions in the z-direction. If fixed boundary conditions are
+present in the z-direction, and this keyword is not used, the walls
+are assumed to be stationary.
+</P>
+<P>If the <I>bodyforce</I> keyword is used, a constant body force is added to
+the fluid, defined by it's x, y and z components.
+</P>
+<P>If the <I>printfluid</I> keyword is used, followed by a positive integer, N,
+the fluid densities and velocities at each lattice site are printed to the
+screen every N timesteps.
+</P>
+<HR>
+
+<P>For further details, as well as descriptions and results of several
+test runs, see <A HREF = "#Mackay">Mackay et al.</A>. Please include a citation to
+this paper if the lb_fluid fix is used in work contributing to
+published research.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>Due to the large size of the fluid data, this fix writes it's own
+binary restart files, if requested, independent of the main LAMMPS
+<A HREF = "restart.html">binary restart files</A>; no information about <I>lb_fluid</I>
+is written to the main LAMMPS <A HREF = "restart.html">binary restart files</A>.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#4_15">output commands</A>. No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-LB package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix can only be used with an orthogonal simulation domain.
+</P>
+<P>Walls have only been implemented in the z-direction. Therefore, the
+boundary conditions, as specified via the main LAMMPS boundary command
+must be periodic for x and y, and either fixed or periodic for z.
+Shrink-wrapped boundary conditions are not permitted with this fix.
+</P>
+<P>This fix must be used before any of <A HREF = "fix_lb_viscous.html">fix
+lb/viscous</A>, <A HREF = "fix_lb_momentum.html">fix
+lb/momentum</A>, <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A>, and/ or <A HREF = "fix_lb_pc.html">fix
+lb/pc</A> , as the fluid needs to be initialized before
+any of these routines try to access its properties. In addition, in
+order for the hydrodynamic forces to be added to the particles, this
+fix must be used in conjunction with the
+<A HREF = "fix_lb_viscous.html">lb/viscous</A> fix if the force coupling constant is
+set by default, or either the <A HREF = "fix_lb_viscous.html">lb/viscous</A> fix or
+one of the <A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A> or
+<A HREF = "fix_lb_pc.html">lb/pc</A> integrators, if the user chooses to specifiy
+their own value for the force coupling constant.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_lb_viscous.html">fix lb/viscous</A>, <A HREF = "fix_lb_momentum.html">fix
+lb/momentum</A>, <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A>, <A HREF = "fix_lb_pc.html">fix
+lb/pc</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>By default, the force coupling constant is set according to
+</P>
+<CENTER><IMG SRC = "Eqs/fix_lb_fluid_gammadefault.jpg">
+</CENTER>
+<P>and an area of dx_lb^2 per node, used to calculate the fluid mass at
+the particle node location, is assumed.
+</P>
+<P>dx is chosen such that tau/(delta t_LB) =
+(3 eta dt_LB)/(rho dx_lb^2) is approximately equal to 1.
+dm is set equal to 1.0.
+a0 is set equal to (1/3)*(dx_lb/dt_lb)^2.
+The Peskin stencil is used as the default interpolation method.
+The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
+If walls are present, they are assumed to be stationary.
+</P>
+<HR>
+
+<A NAME = "Ollila"></A>
+
+<P><B>(Ollila et al.)</B> Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
+</P>
+<A NAME = "Mackay"></A>
+
+<P><B>(Mackay et al.)</B> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+</P>
+<A NAME = "Mackay2"></A>
+
+<P><B>(Mackay and Denniston)</B> Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298.
+</P>
+<A NAME = "Adhikari"></A>
+
+<P><B>(Adhikari et al.)</B> Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lb_momentum.html b/doc/doc2/fix_lb_momentum.html
new file mode 100644
index 000000000..7092c4e01
--- /dev/null
+++ b/doc/doc2/fix_lb_momentum.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lb/momentum command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lb/momentum nevery keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in the <A HREF = "fix.html">fix</A> command
+
+<LI>lb/momentum = style name of this fix command
+
+<LI>nevery = adjust the momentum every this many timesteps
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>linear</I>
+
+<PRE> <I>linear</I> values = xflag yflag zflag
+ xflag,yflag,zflag = 0/1 to exclude/include each dimension.
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 sphere lb/momentum
+fix 1 all lb/momentum linear 1 1 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix is based on the <A HREF = "fix_momentum.html">fix momentum</A> command, and
+was created to be used in place of that command, when a
+lattice-Boltzmann fluid is present.
+</P>
+<P>Zero the total linear momentum of the system, including both the atoms
+specified by group-ID and the lattice-Boltzmann fluid every nevery
+timesteps. This is accomplished by adjusting the particle velocities
+and the fluid velocities at each lattice site.
+</P>
+<P>NOTE: This fix only considers the linear momentum of the system.
+</P>
+<P>By default, the subtraction is performed for each dimension. This can
+be changed by specifying the keyword <I>linear</I>, along with a set of
+three flags set to 0/1 in order to exclude/ include the corresponding
+dimension.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+commands</A>. No parameter of this fix can be
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Can only be used if a lattice-Boltzmann fluid has been created via the
+<A HREF = "fix_lb_fluid.html">fix lb/fluid</A> command, and must come after this
+command.
+</P>
+<P>This fix is part of the USER-LB package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_momentum.html">fix momentum</A>, <A HREF = "fix_lb_fluid.html">fix lb/fluid</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>Zeros the total system linear momentum in each dimension.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lb_pc.html b/doc/doc2/fix_lb_pc.html
new file mode 100644
index 000000000..8fc22cf84
--- /dev/null
+++ b/doc/doc2/fix_lb_pc.html
@@ -0,0 +1,68 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lb/pc command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lb/pc
+</PRE>
+<UL><LI>ID, group-ID are documented in the <A HREF = "fix.html">fix</A> command
+<LI>lb/pc = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all lb/pc
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Update the positions and velocities of the individual particles
+described by <I>group-ID</I>, experiencing velocity-dependent hydrodynamic
+forces, using the integration algorithm described in <A HREF = "#Mackay">Mackay et
+al.</A>. This integration algorithm should only be used if a
+user-specified value for the force-coupling constant used in <A HREF = "fix_lb_fluid.html">fix
+lb/fluid</A> has been set; do not use this integration
+algorithm if the force coupling constant has been set by default.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+commands</A>. No parameter of this fix can be
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-LB package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Can only be used if a lattice-Boltzmann fluid has been created via the
+<A HREF = "fix_lb_fluid.html">fix lb/fluid</A> command, and must come after this
+command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A> <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A>
+</P>
+<P><B>Default:</B> None.
+</P>
+<HR>
+
+<A NAME = "Mackay"></A>
+
+<P><B>(Mackay et al.)</B> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lb_rigid_pc_sphere.html b/doc/doc2/fix_lb_rigid_pc_sphere.html
new file mode 100644
index 000000000..0debaa69d
--- /dev/null
+++ b/doc/doc2/fix_lb_rigid_pc_sphere.html
@@ -0,0 +1,158 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lb/rigid/pc/sphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>lb/rigid/pc/sphere = style name of this fix command
+
+<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
+
+<LI> <I>single</I> args = none
+ <I>molecule</I> args = none
+ <I>group</I> args = N groupID1 groupID2 ...
+ N = # of groups
+zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>force</I> or <I>torque</I> or <I>innerNodes</I>
+
+<PRE> <I>force</I> values = M xflag yflag zflag
+ M = which rigid body from 1-Nbody (see asterisk form below)
+ xflag,yflag,zflag = off/on if component of center-of-mass force is active
+ <I>torque</I> values = M xflag yflag zflag
+ M = which rigid body from 1-Nbody (see asterisk form below)
+ xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+ <I>innerNodes</I> values = innergroup-ID
+ innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 spheres lb/rigid/pc/sphere
+fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix is based on the <A HREF = "fix_rigid.html">fix rigid</A> command, and was
+created to be used in place of that fix, to integrate the equations of
+motion of spherical rigid bodies when a lattice-Boltzmann fluid is
+present with a user-specified value of the force-coupling constant.
+The fix uses the integration algorithm described in <A HREF = "#Mackay">Mackay et
+al.</A> to update the positions, velocities, and orientations of
+a set of spherical rigid bodies experiencing velocity dependent
+hydrodynamic forces. The spherical bodies are assumed to rotate as
+solid, uniform density spheres, with moments of inertia calculated
+using the combined sum of the masses of all the constituent particles
+(which are assumed to be point particles).
+</P>
+<HR>
+
+<P>By default, all of the atoms that this fix acts on experience a
+hydrodynamic force due to the presence of the lattice-Boltzmann fluid.
+However, the <I>innerNodes</I> keyword allows the user to specify atoms
+belonging to a rigid object which do not interact with the
+lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic
+force from the lattice-Boltzmann fluid). This can be used to
+distinguish between atoms on the surface of a non-porous object, and
+those on the inside.
+</P>
+<P>This feature can be used, for example, when implementing a hard sphere
+interaction between two spherical objects. Instead of interactions
+occurring between the particles on the surfaces of the two spheres, it
+is desirable simply to place an atom at the center of each sphere,
+which does not contribute to the hydrodynamic force, and have these
+central atoms interact with one another.
+</P>
+<HR>
+
+<P>Apart from the features described above, this fix is very similar to
+the rigid fix (although it includes fewer optional arguments, and
+assumes the constituent atoms are point particles); see
+<A HREF = "fix_rigid.html">fix_rigid</A> for a complete documentation.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about the <I>rigid</I> and <I>rigid/nve</I> fixes are written to
+<A HREF = "restart.html">binary restart files</A>.
+</P>
+<P>Similar to the <A HREF = "fix_rigid.html">fix_rigid</A> command: &quot; The rigid
+fix computes a global scalar which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar value calculated by
+these fixes is "intensive". The scalar is the current temperature of
+the collection of rigid bodies. This is averaged over all rigid
+bodies and their translational and rotational degrees of freedom. The
+translational energy of a rigid body is 1/2 m v^2, where m = total
+mass of the body and v = the velocity of its center of mass. The
+rotational energy of a rigid body is 1/2 I w^2, where I = the moment
+of inertia tensor of the body and w = its angular velocity. Degrees
+of freedom constrained by the <I>force</I> and <I>torque</I> keywords are
+removed from this calculation.&quot;
+</P>
+<P>&quot;All of these fixes compute a global array of values which can be
+accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+The number of rows in the array is equal to the number of rigid
+bodies. The number of columns is 15. Thus for each rigid body, 15
+values are stored: the xyz coords of the center of mass (COM), the xyz
+components of the COM velocity, the xyz components of the force acting
+on the COM, the xyz components of the torque acting on the COM, and
+the xyz image flags of the COM, which have the same meaning as image
+flags for atom positions (see the "dump" command). The force and
+torque values in the array are not affected by the <I>force</I> and
+<I>torque</I> keywords in the fix rigid command; they reflect values before
+any changes are made by those keywords.
+</P>
+<P>The ordering of the rigid bodies (by row in the array) is as follows.
+For the <I>single</I> keyword there is just one rigid body. For the
+<I>molecule</I> keyword, the bodies are ordered by ascending molecule ID.
+For the <I>group</I> keyword, the list of group IDs determines the ordering
+of bodies.
+</P>
+<P>The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
+</P>
+<P>No parameter of these fixes can be used with the <I>start/stop</I> keywords
+of the <A HREF = "run.html">run</A> command. These fixes are not invoked during
+<A HREF = "minimize.html">energy minimization</A>. &quot;
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-LB package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Can only be used if a lattice-Boltzmann fluid has been created via the
+<A HREF = "fix_lb_fluid.html">fix lb/fluid</A> command, and must come after this
+command. Should only be used if the force coupling constant used in
+<A HREF = "fix_lb_fluid.html">fix lb/fluid</A> has been set by the user; this
+integration fix cannot be used if the force coupling constant is set
+by default.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>, <A HREF = "fix_lb_pc.html">fix lb/pc</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The defaults are force * on on on, and torque * on on on.
+</P>
+<HR>
+
+<A NAME = "Mackay"></A>
+
+<P><B>(Mackay et al.)</B> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lb_viscous.html b/doc/doc2/fix_lb_viscous.html
new file mode 100644
index 000000000..d9c87884b
--- /dev/null
+++ b/doc/doc2/fix_lb_viscous.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lb/viscous command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lb/viscous
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>lb/viscous = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>fix 1 flow lb/viscous
+</P>
+<P><B>Description:</B>
+</P>
+<P>This fix is similar to the <A HREF = "fix_viscous.html">fix viscous</A> command, and
+is to be used in place of that command when a lattice-Boltzmann fluid
+is present, and the user wishes to integrate the particle motion using
+one of the built in LAMMPS integrators.
+</P>
+<P>This fix adds a force, F = - Gamma*(velocity-fluid_velocity), to each
+atom, where Gamma is the force coupling constant described in the <A HREF = "fix_lb_fluid.html">fix
+lb/fluid</A> command (which applies an equal and
+opposite force to the fluid).
+</P>
+<P>IMPORTANT NOTE: This fix should only be used in conjunction with one
+of the built in LAMMPS integrators; it should not be used with the
+<A HREF = "fix_lb_pc.html">fix lb/pc</A> or <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A> integrators, which
+already include the hydrodynamic forces. These latter fixes should
+only be used if the force coupling constant has been set by the user
+(instead of using the default value); if the default force coupling
+value is used, then this fix provides the only method for adding the
+hydrodynamic forces to the particles.
+</P>
+<HR>
+
+<P>For further details, as well as descriptions and results of several
+test runs, see <A HREF = "#Mackay">Mackay et al.</A>. Please include a citation to
+this paper if this fix is used in work contributing to published
+research.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>As described in the <A HREF = "fix_viscous.html">fix viscous</A> documentation:
+</P>
+<P>"No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. This fix should only
+be used with damped dynamics minimizers that allow for
+non-conservative forces. See the <A HREF = "min_style.html">min_style</A> command
+for details."
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-LB package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Can only be used if a lattice-Boltzmann fluid has been created via the
+<A HREF = "fix_lb_fluid.html">fix lb/fluid</A> command, and must come after this
+command.
+</P>
+<P>This fix should not be used if either the <A HREF = "fix_lb_pc.html">fix lb/pc</A>
+or <A HREF = "fix_lb_rigid_pc_sphere.html">fix lb/rigid/pc/sphere</A> integrator is
+used.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>, <A HREF = "fix_lb_pc.html">fix lb/pc</A>, <A HREF = "fix_lb_rigid_pc_sphere.html">fix
+lb/rigid/pc/sphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mackay"></A>
+
+<P><B>(Mackay et al.)</B> Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_lineforce.html b/doc/doc2/fix_lineforce.html
new file mode 100644
index 000000000..9c87f094e
--- /dev/null
+++ b/doc/doc2/fix_lineforce.html
@@ -0,0 +1,56 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix lineforce command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID lineforce x y z
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>lineforce = style name of this fix command
+<LI>x y z = direction of line as a 3-vector
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix hold boundary lineforce 0.0 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Adjust the forces on each atom in the group so that only the component
+of force along the linear direction specified by the vector (x,y,z)
+remains. This is done by subtracting out components of force in the
+plane perpendicular to the line.
+</P>
+<P>If the initial velocity of the atom is 0.0 (or along the line), then
+it should continue to move along the line thereafter.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_planeforce.html">fix planeforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_meso.html b/doc/doc2/fix_meso.html
new file mode 100644
index 000000000..81bb83334
--- /dev/null
+++ b/doc/doc2/fix_meso.html
@@ -0,0 +1,57 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix meso command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID meso
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>meso = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all meso
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform time integration to update position, velocity, internal energy
+and local density for atoms in the group each timestep. This fix is
+needed to time-integrate mesoscopic systems where particles carry
+internal variables such as SPH or DPDE.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P>"fix meso/stationary"
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_meso_stationary.html b/doc/doc2/fix_meso_stationary.html
new file mode 100644
index 000000000..cf339c256
--- /dev/null
+++ b/doc/doc2/fix_meso_stationary.html
@@ -0,0 +1,58 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix meso/stationary command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID meso/stationary
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>meso = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 boundary meso/stationary
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform time integration to update internal energy and local density,
+but not position or velocity for atoms in the group each timestep.
+This fix is needed for SPH simulations to correctly time-integrate
+fixed boundary particles which constrain a fluid to a given region in
+space.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P>"fix meso"
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_modify.html b/doc/doc2/fix_modify.html
new file mode 100644
index 000000000..d31aada56
--- /dev/null
+++ b/doc/doc2/fix_modify.html
@@ -0,0 +1,81 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix_modify fix-ID keyword value ...
+</PRE>
+<UL><LI>fix-ID = ID of the fix to modify
+
+<LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>temp</I> or <I>press</I> or <I>energy</I>
+
+<PRE> <I>temp</I> value = compute ID that calculates a temperature
+ <I>press</I> value = compute ID that calculates a pressure
+ <I>energy</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix_modify 3 temp myTemp press myPress
+fix_modify 1 energy yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Modify one or more parameters of a previously defined fix. Only
+specific fix styles support specific parameters. See the doc pages
+for individual fix commands for info on which ones support which
+fix_modify parameters.
+</P>
+<P>The <I>temp</I> keyword is used to determine how a fix computes
+temperature. The specified compute ID must have been previously
+defined by the user via the <A HREF = "compute.html">compute</A> command and it must
+be a style of compute that calculates a temperature. All fixes that
+compute temperatures define their own compute by default, as described
+in their documentation. Thus this option allows the user to override
+the default method for computing T.
+</P>
+<P>The <I>press</I> keyword is used to determine how a fix computes pressure.
+The specified compute ID must have been previously defined by the user
+via the <A HREF = "compute.html">compute</A> command and it must be a style of
+compute that calculates a pressure. All fixes that compute pressures
+define their own compute by default, as described in their
+documentation. Thus this option allows the user to override the
+default method for computing P.
+</P>
+<P>For fixes that calculate a contribution to the potential energy of the
+system, the <I>energy</I> keyword will include that contribution in
+thermodynamic output of potential energy. See the
+<A HREF = "thermo_style.html">thermo_style</A> command for info on how potential
+energy is output. The contribution by itself can be printed by using
+the keyword f_ID in the thermo_style custom command, where ID is the
+fix-ID of the appropriate fix. Note that you must use this setting
+for a fix if you are using it when performing an <A HREF = "minimize.html">energy
+minimization</A> and if you want the energy and forces it
+produces to be part of the optimization criteria.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix.html">fix</A>, <A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_pressure.html">compute
+pressure</A>, <A HREF = "thermo_style.html">thermo_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are temp = ID defined by fix, press = ID defined
+by fix, energy = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_momentum.html b/doc/doc2/fix_momentum.html
new file mode 100644
index 000000000..c17c44a3f
--- /dev/null
+++ b/doc/doc2/fix_momentum.html
@@ -0,0 +1,85 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix momentum command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID momentum N keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>momentum = style name of this fix command
+
+<LI>N = adjust the momentum every this many timesteps
+one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>linear</I> or <I>angular</I> or <I>rescale</I>
+
+<PRE> <I>linear</I> values = xflag yflag zflag
+ xflag,yflag,zflag = 0/1 to exclude/include each dimension
+ <I>angular</I> values = none
+</PRE>
+<PRE> <I>rescale</I> values = none
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all momentum 1 linear 1 1 0
+fix 1 all momentum 1 linear 1 1 1 rescale
+fix 1 all momentum 100 linear 1 1 1 angular
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Zero the linear and/or angular momentum of the group of atoms every N
+timesteps by adjusting the velocities of the atoms. One (or both) of
+the <I>linear</I> or <I>angular</I> keywords must be specified.
+</P>
+<P>If the <I>linear</I> keyword is used, the linear momentum is zeroed by
+subtracting the center-of-mass velocity of the group from each atom.
+This does not change the relative velocity of any pair of atoms. One
+or more dimensions can be excluded from this operation by setting the
+corresponding flag to 0.
+</P>
+<P>If the <I>angular</I> keyword is used, the angular momentum is zeroed by
+subtracting a rotational component from each atom.
+</P>
+<P>This command can be used to insure the entire collection of atoms (or
+a subset of them) does not drift or rotate during the simulation due
+to random perturbations (e.g. <A HREF = "fix_langevin.html">fix langevin</A>
+thermostatting).
+</P>
+<P>The <I>rescale</I> keyword enables conserving the kinetic energy of the group
+of atoms by rescaling the velocities after the momentum was removed.
+</P>
+<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
+initial velocities with zero aggregate linear and/or angular momentum.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_recenter.html">fix recenter</A>, <A HREF = "velocity.html">velocity</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_move.html b/doc/doc2/fix_move.html
new file mode 100644
index 000000000..099f269c8
--- /dev/null
+++ b/doc/doc2/fix_move.html
@@ -0,0 +1,234 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix move command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID move style args keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>move = style name of this fix command
+
+<LI>style = <I>linear</I> or <I>wiggle</I> or <I>rotate</I> or <I>variable</I>
+
+<PRE> <I>linear</I> args = Vx Vy Vz
+ Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+ <I>wiggle</I> args = Ax Ay Az period
+ Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+ period = period of oscillation (time units)
+ <I>rotate</I> args = Px Py Pz Rx Ry Rz period
+ Px,Py,Pz = origin point of axis of rotation (distance units)
+ Rx,Ry,Rz = axis of rotation vector
+ period = period of rotation (time units)
+ <I>variable</I> args = v_dx v_dy v_dz v_vx v_vy v_vz
+ v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+ v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>units</I>
+
+<PRE> <I>units</I> value = <I>box</I> or <I>lattice</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform updates of position and velocity for atoms in the group each
+timestep using the specified settings or formulas, without regard to
+forces on the atoms. This can be useful for boundary or other atoms,
+whose movement can influence nearby atoms.
+</P>
+<P>IMPORTANT NOTE: The atoms affected by this fix should not normally be
+time integrated by other fixes (e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix
+nvt</A>), since that will change their positions and
+velocities twice.
+</P>
+<P>IMPORTANT NOTE: As atoms move due to this fix, they will pass thru
+periodic boundaries and be remapped to the other side of the
+simulation box, just as they would during normal time integration
+(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command). It is up to you to
+decide whether periodic boundaries are appropriate with the kind of
+atom motion you are prescribing with this fix.
+</P>
+<P>IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their
+initial position at the time the fix is specified. These initial
+coordinates are stored by the fix in "unwrapped" form, by using the
+image flags associated with each atom. See the <A HREF = "dump.html">dump
+custom</A> command for a discussion of "unwrapped" coordinates.
+See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
+discussion of image flags and how they are set for each atom. You can
+reset the image flags (e.g. to 0) before invoking this fix by using
+the <A HREF = "set.html">set image</A> command.
+</P>
+<HR>
+
+<P>The <I>linear</I> style moves atoms at a constant velocity, so that their
+position <I>X</I> = (x,y,z) as a function of time is given in vector
+notation as
+</P>
+<PRE>X(t) = X0 + V * delta
+</PRE>
+<P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
+specified, <I>V</I> is the specified velocity vector with components
+(Vx,Vy,Vz), and <I>delta</I> is the time elapsed since the fix was
+specified. This style also sets the velocity of each atom to V =
+(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
+then the position and velocity of that component is time integrated
+the same as the <A HREF = "fix_nve.html">fix nve</A> command would perform, using
+the corresponding force component on the atom.
+</P>
+<P>Note that the <I>linear</I> style is identical to using the <I>variable</I>
+style with an <A HREF = "variable.html">equal-style variable</A> that uses the
+vdisplace() function. E.g.
+</P>
+<PRE>variable V equal 10.0
+variable x equal vdisplace(0.0,$V)
+fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
+</PRE>
+<P>The <I>wiggle</I> style moves atoms in an oscillatory fashion, so that
+their position <I>X</I> = (x,y,z) as a function of time is given in vector
+notation as
+</P>
+<PRE>X(t) = X0 + A sin(omega*delta)
+</PRE>
+<P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
+specified, <I>A</I> is the specified amplitude vector with components
+(Ax,Ay,Az), <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
+elapsed since the fix was specified. This style also sets the
+velocity of each atom to the time derivative of this expression. If
+any of the amplitude components is specified as NULL, then the
+position and velocity of that component is time integrated the same as
+the <A HREF = "fix_nve.html">fix nve</A> command would perform, using the
+corresponding force component on the atom.
+</P>
+<P>Note that the <I>wiggle</I> style is identical to using the <I>variable</I>
+style with <A HREF = "variable.html">equal-style variables</A> that use the
+swiggle() and cwiggle() functions. E.g.
+</P>
+<PRE>variable A equal 10.0
+variable T equal 5.0
+variable omega equal 2.0*PI/$T
+variable x equal swiggle(0.0,$A,$T)
+variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
+fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
+</PRE>
+<P>The <I>rotate</I> style rotates atoms around a rotation axis <I>R</I> =
+(Rx,Ry,Rz) that goes thru a point <I>P</I> = (Px,Py,Pz). The <I>period</I> of
+the rotation is also specified. This style also sets the velocity of
+each atom to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the atom. If the defined
+<A HREF = "atom_style.html">atom_style</A> assigns an angular velocity to each atom,
+then each atom's angular velocity is also set to omega. Note that the
+direction of rotation for the atoms around the rotation axis is
+consistent with the right-hand rule: if your right-hand's thumb points
+along <I>R</I>, then your fingers wrap around the axis in the direction of
+rotation.
+</P>
+<P>The <I>variable</I> style allows the position and velocity components of
+each atom to be set by formulas specified via the
+<A HREF = "variable.html">variable</A> command. Each of the 6 variables is
+specified as an argument to the fix as v_name, where name is the
+variable name that is defined elsewhere in the input script.
+</P>
+<P>Each variable must be of either the <I>equal</I> or <I>atom</I> style.
+<I>Equal</I>-style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+<I>Atom</I>-style variables compute a numeric quantity for each atom, that
+can be a function per-atom quantities, such as the atom's position, as
+well as of the timestep and other simulation values. Note that this
+fix stores the original coordinates of each atom (see note below) so
+that per-atom quantity can be used in an atom-style variable formula.
+See the <A HREF = "variable.html">variable</A> command for details.
+</P>
+<P>The first 3 variables (v_dx,v_dy,v_dz) specified for the <I>variable</I>
+style are used to calculate a displacement from the atom's original
+position at the time the fix was specified. The second 3 variables
+(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
+atom.
+</P>
+<P>Any of the 6 variables can be specified as NULL. If both the
+displacement and velocity variables for a particular x,y,z component
+are specified as NULL, then the position and velocity of that
+component is time integrated the same as the <A HREF = "fix_nve.html">fix nve</A>
+command would perform, using the corresponding force component on the
+atom. If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the atom, and its velocity component will not be changed. If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the atom,
+and the position of the atom will be time integrated using that
+velocity.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define the <I>linear</I> velocity and <I>wiggle</I> amplitude and <I>rotate</I>
+origin. This setting is ignored for the <I>variable</I> style. A <I>box</I>
+value selects standard units as defined by the <A HREF = "units.html">units</A>
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real. A <I>lattice</I> value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
+been previously used to define the lattice spacing. Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of moving atoms to <A HREF = "restart.html">binary
+restart files</A>, as well as the initial timestep, so that
+the motion can be continuous in a restarted simulation. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>IMPORTANNT NOTE: Because the move positions are a function of the
+current timestep and the initial timestep, you cannot reset the
+timestep to a different value after reading a restart file, if you
+expect a fix move command to work in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>This fix produces a per-atom array which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The number of columns
+for each atom is 3, and the columns store the original unwrapped x,y,z
+coords of each atom. The per-atom values can be accessed on any
+timestep.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix adjusts the
+position and velocity of atoms on the outermost rRESPA level.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "displace_atoms.html">displace_atoms</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<P>The option default is units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_msst.html b/doc/doc2/fix_msst.html
new file mode 100644
index 000000000..60f2daffe
--- /dev/null
+++ b/doc/doc2/fix_msst.html
@@ -0,0 +1,171 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3> fix msst command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID msst dir shockvel keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>msst = style name of this fix
+
+<LI>dir = <I>x</I> or <I>y</I> or <I>z</I>
+
+<LI>shockvel = shock velocity (strictly positive, distance/time units)
+
+<LI>zero or more keyword value pairs may be appended
+
+<LI>keyword = <I>q</I> or <I>mu</I> or <I>p0</I> or <I>v0</I> or <I>e0</I> or <I>tscale</I>
+
+<PRE> <I>q</I> value = cell mass-like parameter (mass^2/distance^4 units)
+ <I>mu</I> value = artificial viscosity (mass/length/time units)
+ <I>p0</I> value = initial pressure in the shock equations (pressure units)
+ <I>v0</I> value = initial simulation cell volume in the shock equations (distance^3 units)
+ <I>e0</I> value = initial total energy (energy units)
+ <I>tscale</I> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
+fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command performs the Multi-Scale Shock Technique (MSST)
+integration to update positions and velocities each timestep to mimic
+a compressive shock wave passing over the system. See <A HREF = "#Reed">(Reed)</A>
+for a detailed description of this method. The MSST varies the cell
+volume and temperature in such a way as to restrain the system to the
+shock Hugoniot and the Rayleigh line. These restraints correspond to
+the macroscopic conservation laws dictated by a shock
+front. <I>shockvel</I> determines the steady shock velocity that will be
+simulated.
+</P>
+<P>To perform a simulation, choose a value of <I>q</I> that provides volume
+compression on the timescale of 100 fs to 1 ps. If the volume is not
+compressing, either the shock speed is chosen to be below the material
+sound speed or <I>p0</I> has been chosen inaccurately. Volume compression
+at the start can be sped up by using a non-zero value of <I>tscale</I>. Use
+the smallest value of <I>tscale</I> that results in compression.
+</P>
+<P>Under some special high-symmetry conditions, the pressure (volume)
+and/or temperature of the system may oscillate for many cycles even
+with an appropriate choice of mass-like parameter <I>q</I>. Such
+oscillations have physical significance in some cases. The optional
+<I>mu</I> keyword adds an artificial viscosity that helps break the system
+symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
+rapidly in such cases.
+</P>
+<P><I>tscale</I> is a factor between 0 and 1 that determines what fraction of
+thermal kinetic energy is converted to compressive strain kinetic
+energy at the start of the simulation. Setting this parameter to a
+non-zero value may assist in compression at the start of simulations
+where it is slow to occur.
+</P>
+<P>If keywords <I>e0</I>, <I>p0</I>,or <I>v0</I> are not supplied, these quantities will
+be calculated on the first step, after the energy specified by
+<I>tscale</I> is removed. The value of <I>e0</I> is not used in the dynamical
+equations, but is used in calculating the deviation from the Hugoniot.
+</P>
+<P>Values of shockvel less than a critical value determined by the
+material response will not have compressive solutions. This will be
+reflected in lack of significant change of the volume in the MSST.
+</P>
+<P>For all pressure styles, the simulation box stays orthogonal in shape.
+Parrinello-Rahman boundary conditions (tilted box) are supported by
+LAMMPS, but are not implemented for MSST.
+</P>
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press". The group for the new computes is "all".
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of all internal variables to <A HREF = "restart.html">binary restart
+files</A>. See the <A HREF = "read_restart.html">read_restart</A> command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The progress of the MSST can be monitored by printing the global
+scalar and global vector quantities computed by the fix.
+</P>
+<P>The scalar is the cumulative energy change due to the fix. This is
+also the energy added to the potential energy by the
+<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> command. With this command, the
+thermo keyword <I>etotal</I> prints the conserved quantity of the MSST
+dynamic equations. This can be used to test if the MD timestep is
+sufficiently small for accurate integration of the dynamic
+equations. See also <A HREF = "thermo_style.html">thermo_style</A> command.
+</P>
+<P>The global vector contains four values in this order:
+</P>
+<P>[<I>dhugoniot</I>, <I>drayleigh</I>, <I>lagrangian_speed</I>, <I>lagrangian_position</I>]
+</P>
+<OL><LI><I>dhugoniot</I> is the departure from the Hugoniot (temperature units).
+<LI><I>drayleigh</I> is the departure from the Rayleigh line (pressure units).
+<LI><I>lagrangian_speed</I> is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
+<LI><I>lagrangian_position</I> is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front.
+</OL>
+<P>To print these quantities to the log file with descriptive column
+headers, the following LAMMPS commands are suggested:
+</P>
+<PRE>fix msst all msst z
+fix_modify msst energy yes
+variable dhug equal f_msst[1]
+variable dray equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+</PRE>
+<P>These fixes compute a global scalar and a global vector of 4
+quantities, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar values calculated
+by this fix are "extensive"; the vector values are "intensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the SHOCK package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>All cell dimensions must be periodic. This fix can not be used with a
+triclinic cell. The MSST fix has been tested only for the group-ID
+all.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nphug.html">fix nphug</A>, <A HREF = "fix_deform.html">fix deform</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
+are calculated on the first step.
+</P>
+<HR>
+
+<A NAME = "Reed"></A>
+
+<P><B>(Reed)</B> Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_neb.html b/doc/doc2/fix_neb.html
new file mode 100644
index 000000000..23a8b894d
--- /dev/null
+++ b/doc/doc2/fix_neb.html
@@ -0,0 +1,113 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix neb command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID neb Kspring
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>neb = style name of this fix command
+<LI>Kspring = inter-replica spring constant (force/distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 active neb 10.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add inter-replica forces to atoms in the group for a multi-replica
+simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
+elastic band (NEB) calculation for transition state finding. Hi-level
+explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
+<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual. The fix
+neb command must be used with the "neb" command to define how
+inter-replica forces are computed.
+</P>
+<P>Only the N atoms in the fix group experience inter-replica forces.
+Atoms in the two end-point replicas do not experience these forces,
+but those in intermediate replicas do. During the initial stage of
+NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
+on the atoms of each intermediate replica I is altered, as described
+in the <A HREF = "#Henkelman1">(Henkelman1)</A> paper, to become:
+</P>
+<PRE>Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
+</PRE>
+<P>Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
+coordinates of its neighbor replicas. That (t with a hat over it) is
+the unit "tangent" vector for replica I which is a function of Ri,
+Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
+roughly in the direction of (Ri+i - Ri-1); see the
+<A HREF = "#Henkelman1">(Henkelman1)</A> paper for details.
+</P>
+<P>The first two terms in the above equation are the component of the
+interatomic forces perpendicular to the tangent vector. The last term
+is a spring force between replica I and its neighbors, parallel to the
+tangent vector direction with the specified spring constant <I>Kspring</I>.
+</P>
+<P>The effect of the first two terms is to push the atoms of each replica
+toward the minimum energy path (MEP) of conformational states that
+transition over the energy barrier. The MEP for an energy barrier is
+defined as a sequence of 3N-dimensional states which cross the barrier
+at its saddle point, each of which has a potential energy gradient
+parallel to the MEP itself.
+</P>
+<P>The effect of the last term is to push each replica away from its two
+neighbors in a direction along the MEP, so that the final set of
+states are equidistant from each other.
+</P>
+<P>During the second stage of NEB, the forces on the N atoms in the
+replica nearest the top of the energy barrier are altered so that it
+climbs to the top of the barrier and finds the saddle point. The
+forces on atoms in this replica are described in the
+<A HREF = "#Henkelman2">(Henkelman2)</A> paper, and become:
+</P>
+<PRE>Fi = -Grad(V) + 2 (Grad(V) dot That) That
+</PRE>
+<P>The inter-replica forces for the other replicas are unchanged from the
+first equation.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+as invoked by the <A HREF = "minimize.html">minimize</A> command via the
+<A HREF = "neb.html">neb</A> command.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "neb.html">neb</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<A NAME = "Henkelman"></A>
+
+<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
+</P>
+<A NAME = "Henkelman"></A>
+
+<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
+</P>
+</HTML>
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+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt command
+</H3>
+<H3>fix nvt/cuda command
+</H3>
+<H3>fix nvt/omp command
+</H3>
+<H3>fix npt command
+</H3>
+<H3>fix npt/cuda command
+</H3>
+<H3>fix npt/omp command
+</H3>
+<H3>fix nph command
+</H3>
+<H3>fix nph/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style_name keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style_name = <I>nvt</I> or <I>npt</I> or <I>nph</I>
+
+<LI>one or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I> or <I>scalexy</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>flip</I> or <I>fixedpoint</I>
+ <I>temp</I> values = Tstart Tstop Tdamp
+ Tstart,Tstop = external temperature at start/end of run
+ Tdamp = temperature damping parameter (time units)
+ <I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+ Pdamp = stress damping parameter (time units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>tchain</I> value = N
+ N = length of thermostat chain (1 = single thermostat)
+ <I>pchain</I> values = N
+ N length of thermostat chain on barostat (0 = no thermostat)
+ <I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
+ <I>tloop</I> value = M
+ M = number of sub-cycles to perform on thermostat
+ <I>ploop</I> value = M
+ M = number of sub-cycles to perform on barostat thermostat
+ <I>nreset</I> value = reset reference cell every this many timesteps
+ <I>drag</I> value = Df
+ Df = drag factor added to barostat/thermostat (0.0 = no drag)
+ <I>dilate</I> value = dilate-group-ID
+ dilate-group-ID = only dilate atoms in this group due to barostat volume changes
+ <I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
+ <I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
+ <I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
+ <I>flip</I> value = <I>yes</I> or <I>no</I> = allow or disallow box flips when it becomes highly skewed
+ <I>fixedpoint</I> values = x y z
+ x,y,z = perform barostat dilation/contraction around this point (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt temp 300.0 300.0 100.0
+fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
+fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>These commands perform time integration on Nose-Hoover style
+non-Hamiltonian equations of motion which are designed to generate
+positions and velocities sampled from the canonical (nvt),
+isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This
+updates the position and velocity for atoms in the group each
+timestep.
+</P>
+<P>The thermostatting and barostatting is achieved by adding some dynamic
+variables which are coupled to the particle velocities
+(thermostatting) and simulation domain dimensions (barostatting). In
+addition to basic thermostatting and barostatting, these fixes can
+also create a chain of thermostats coupled to the particle thermostat,
+and another chain of thermostats coupled to the barostat
+variables. The barostat can be coupled to the overall box volume, or
+to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I> tilt
+dimensions. The external pressure of the barostat can be specified as
+either a scalar pressure (isobaric ensemble) or as components of a
+symmetric stress tensor (constant stress ensemble). When used
+correctly, the time-averaged temperature and stress tensor of the
+particles will match the target values specified by Tstart/Tstop and
+Pstart/Pstop.
+</P>
+<P>The equations of motion used are those of Shinoda et al in
+<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
+Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
+energy proposed by Parrinello and Rahman in
+<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
+follow the time-reversible measure-preserving Verlet and rRESPA
+integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
+</P>
+<HR>
+
+<P>The thermostat parameters for fix styles <I>nvt</I> and <I>npt</I> is specified
+using the <I>temp</I> keyword. Other thermostat-related keywords are
+<I>tchain</I>, <I>tloop</I> and <I>drag</I>, which are discussed below.
+</P>
+<P>The thermostat is applied to only the translational degrees of freedom
+for the particles. The translational degrees of freedom can also have
+a bias velocity removed before thermostatting takes place; see the
+description below. The desired temperature at each timestep is a
+ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
+parameter is specified in time units and determines how rapidly the
+temperature is relaxed. For example, a value of 10.0 means to relax
+the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+fmsec or psec - see the <A HREF = "units.html">units</A> command). The atoms in the
+fix group are the only ones whose velocities and positions are updated
+by the velocity/position update portion of the integration.
+</P>
+<P>IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for
+arbitrary values of <I>Tdamp</I>. If <I>Tdamp</I> is too small, the temperature
+can fluctuate wildly; if it is too large, the temperature will take a
+very long time to equilibrate. A good choice for many models is a
+<I>Tdamp</I> of around 100 timesteps. Note that this is NOT the same as
+100 time units for most <A HREF = "units.html">units</A> settings.
+</P>
+<HR>
+
+<P>The barostat parameters for fix styles <I>npt</I> and <I>nph</I> is specified
+using one or more of the <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>,
+<I>xz</I>, <I>yz</I>, and <I>couple</I> keywords. These keywords give you the
+ability to specify all 6 components of an external stress tensor, and
+to couple various of these components together so that the dimensions
+they represent are varied together during a constant-pressure
+simulation.
+</P>
+<P>Other barostat-related keywords are <I>pchain</I>, <I>mtk</I>, <I>ploop</I>,
+<I>nreset</I>, <I>drag</I>, and <I>dilate</I>, which are discussed below.
+</P>
+<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
+Triclinic (non-orthogonal) simulation boxes have 6 adjustable
+dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
+data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
+specify whether the simulation box is orthogonal or non-orthogonal
+(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
+</P>
+<P>The target pressures for each of the 6 components of the stress tensor
+can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>
+keywords, which correspond to the 6 simulation box dimensions. For
+each component, the external pressure or tensor component at each
+timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
+If a target pressure is specified for a component, then the
+corresponding box dimension will change during a simulation. For
+example, if the <I>y</I> keyword is used, the y-box length will change. If
+the <I>xy</I> keyword is used, the xy tilt factor will change. A box
+dimension will not change if that component is not specified, although
+you have the option to change that dimension via the <A HREF = "fix_deform.html">fix
+deform</A> command.
+</P>
+<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
+simulation box must be triclinic, even if its initial tilt factors are
+0.0.
+</P>
+<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
+<I>Tdamp</I> parameter, determining the time scale on which pressure is
+relaxed. For example, a value of 10.0 means to relax the pressure in
+a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+the <A HREF = "units.html">units</A> command).
+</P>
+<P>IMPORTANT NOTE: A Nose-Hoover barostat will not work well for
+arbitrary values of <I>Pdamp</I>. If <I>Pdamp</I> is too small, the pressure
+and volume can fluctuate wildly; if it is too large, the pressure will
+take a very long time to equilibrate. A good choice for many models
+is a <I>Pdamp</I> of around 1000 timesteps. Note that this is NOT the same
+as 1000 time units for most <A HREF = "units.html">units</A> settings.
+</P>
+<P>Regardless of what atoms are in the fix group (the only atoms which
+are time integrated), a global pressure or stress tensor is computed
+for all atoms. Similarly, when the size of the simulation box is
+changed, all atoms are re-scaled to new positions, unless the keyword
+<I>dilate</I> is specified with a <I>dilate-group-ID</I> for a group that
+represents a subset of the atoms. This can be useful, for example, to
+leave the coordinates of atoms in a solid substrate unchanged and
+controlling the pressure of a surrounding fluid. This option should
+be used with care, since it can be unphysical to dilate some atoms and
+not others, because it can introduce large, instantaneous
+displacements between a pair of atoms (one dilated, one not) that are
+far from the dilation origin. Also note that for atoms not in the fix
+group, a separate time integration fix like <A HREF = "fix_nve.html">fix nve</A> or
+<A HREF = "fix_nh.html">fix nvt</A> can be used on them, independent of whether they
+are dilated or not.
+</P>
+<HR>
+
+<P>The <I>couple</I> keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together. The value specified
+with the keyword determines which are coupled. For example, <I>xz</I>
+means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
+<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep. The
+<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
+be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
+dimension is simply ignored.
+</P>
+<HR>
+
+<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+</P>
+<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple xyz
+</PRE>
+<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
+independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple none
+</PRE>
+<P>The keyword <I>tri</I> means <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, and <I>yz</I> dimensions
+are controlled independently using their individual stress components
+as the driving forces, and the specified scalar pressure as the
+external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
+specifying these 7 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+xy 0.0 0.0 Pdamp
+yz 0.0 0.0 Pdamp
+xz 0.0 0.0 Pdamp
+couple none
+</PRE>
+<HR>
+
+<P>In some cases (e.g. for solids) the pressure (volume) and/or
+temperature of the system can oscillate undesirably when a Nose/Hoover
+barostat and thermostat is applied. The optional <I>drag</I> keyword will
+damp these oscillations, although it alters the Nose/Hoover equations.
+A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
+A non-zero value adds a drag term; the larger the value specified, the
+greater the damping effect. Performing a short run and monitoring the
+pressure and temperature is the best way to determine if the drag term
+is working. Typically a value between 0.2 to 2.0 is sufficient to
+damp oscillations after a few periods. Note that use of the drag
+keyword will interfere with energy conservation and will also change
+the distribution of positions and velocities so that they do not
+correspond to the nominal NVT, NPT, or NPH ensembles.
+</P>
+<P>An alternative way to control initial oscillations is to use chain
+thermostats. The keyword <I>tchain</I> determines the number of thermostats
+in the particle thermostat. A value of 1 corresponds to the original
+Nose-Hoover thermostat. The keyword <I>pchain</I> specifies the number of
+thermostats in the chain thermostatting the barostat degrees of
+freedom. A value of 0 corresponds to no thermostatting of the
+barostat variables.
+</P>
+<P>The <I>mtk</I> keyword controls whether or not the correction terms due to
+Martyna, Tuckerman, and Klein are included in the equations of motion
+<A HREF = "#Martyna">(Martyna)</A>. Specifying <I>no</I> reproduces the original
+Hoover barostat, whose volume probability distribution function
+differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
+using <I>yes</I> is more correct, but in many cases the difference is
+negligible.
+</P>
+<P>The keyword <I>tloop</I> can be used to improve the accuracy of integration
+scheme at little extra cost. The initial and final updates of the
+thermostat variables are broken up into <I>tloop</I> substeps, each of
+length <I>dt</I>/<I>tloop</I>. This corresponds to using a first-order
+Suzuki-Yoshida scheme <A HREF = "#Tuckerman2006">(Tuckerman2006)</A>. The keyword
+<I>ploop</I> does the same thing for the barostat thermostat.
+</P>
+<P>The keyword <I>nreset</I> controls how often the reference dimensions used
+to define the strain energy are reset. If this keyword is not used,
+or is given a value of zero, then the reference dimensions are set to
+those of the initial simulation domain and are never changed. If the
+simulation domain changes significantly during the simulation, then
+the final average pressure tensor will differ significantly from the
+specified values of the external stress tensor. A value of <I>nstep</I>
+means that every <I>nstep</I> timesteps, the reference dimensions are set
+to those of the current simulation domain.
+</P>
+<P>The <I>scaleyz</I>, <I>scalexz</I>, and <I>scalexy</I> keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when barostatting triclinic periodic cells. The default
+values <I>yes</I> will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape. Choosing
+<I>no</I> ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to <I>no</I>.
+</P>
+<P>The <I>flip</I> keyword allows the tilt factors for a triclinic box to
+exceed half the distance of the parallel box length, as discussed
+below. If the <I>flip</I> value is set to <I>yes</I>, the bound is enforced by
+flipping the box when it is exceeded. If the <I>flip</I> value is set to
+<I>no</I>, the tilt will continue to change without flipping. Note that if
+applied stress induces large deformations (e.g. in a liquid), this
+means the box shape can tilt dramatically and LAMMPS will run less
+efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+</P>
+<P>The <I>fixedpoint</I> keyword specifies the fixed point for barostat volume
+changes. By default, it is the center of the box. Whatever point is
+chosen will not move during the simulation. For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to <I>fixedpoint</I>, then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle trajectories are unaffected by the
+chosen value, except for a time-dependent constant translation of
+positions.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
+<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
+tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
+allows the tilt factors to grow a small amount beyond the normal limit
+of half the box length (0.6 times the box length), and then performs a
+box "flip" to an equivalent periodic cell. See the discussion of the
+<I>flip</I> keyword above, to allow this bound to be exceeded, if desired.
+</P>
+<P>The flip operation is described in more detail in the doc page for
+<A HREF = "fix_deform.html">fix deform</A>. Both the barostat dynamics and the atom
+trajectories are unaffected by this operation. However, if a tilt
+factor is incremented by a large amount (1.5 times the box length) on
+a single timestep, LAMMPS can not accomodate this event and will
+terminate the simulation with an error. This error typically indicates
+that there is something badly wrong with how the simulation was
+constructed, such as specifying values of <I>Pstart</I> that are too far
+from the current stress value, or specifying a timestep that is too
+large. Triclinic barostatting should be used with care. This also is
+true for other barostat styles, although they tend to be more
+forgiving of insults. In particular, it is important to recognize that
+equilibrium liquids can not support a shear stress and that
+equilibrium solids can not support shear stresses that exceed the
+yield stress.
+</P>
+<P>One exception to this rule is if the 1st dimension in the tilt factor
+(x for xy) is non-periodic. In that case, the limits on the tilt
+factor are not enforced, since flipping the box in that dimension does
+not change the atom positions due to non-periodicity. In this mode,
+if you tilt the system to extreme angles, the simulation will simply
+become inefficient due to the highly skewed simulation box.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A> command which performs
+thermostatting but NO time integration, these fixes perform
+thermostatting/barostatting AND time integration. Thus you should not
+use any other time integration fix, such as <A HREF = "fix_nve.html">fix nve</A> on
+atoms to which this fix is applied. Likewise, fix nvt and fix npt
+should not normally be used on atoms that also have their temperature
+controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix langevin</A> or <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+</P>
+<HR>
+
+<P>These fixes compute a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if one of these two sets of commands had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</PRE>
+<PRE>compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press". For fix nvt, the group for the new computes
+is the same as the fix group. For fix nph and fix npt, the group for
+the new computes is "all" since pressure is computed for the entire
+system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, fix nvt and fix npt can
+be used with <A HREF = "compute.html">compute commands</A> that calculate a
+temperature after removing a "bias" from the atom velocities.
+E.g. removing the center-of-mass velocity from a group of atoms or
+only calculating temperature on the x-component of velocity or only
+calculating temperature for atoms in a geometric region. This is not
+done by default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command
+is used to assign a temperature compute to this fix that includes such
+a bias term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>These fixes can be used with either the <I>verlet</I> or <I>respa</I>
+<A HREF = "run_style.html">integrators</A>. When using one of the barostat fixes
+with <I>respa</I>, LAMMPS uses an integrator constructed
+according to the following factorization of the Liouville propagator
+(for two rRESPA levels):
+</P>
+<CENTER><IMG SRC = "Eqs/fix_nh1.jpg">
+</CENTER>
+<P>This factorization differs somewhat from that of Tuckerman et al., in that
+the barostat is only updated at the outermost rRESPA level, whereas
+Tuckerman's factorization requires splitting the pressure into pieces
+corresponding to the forces computed at each rRESPA level. In theory, the
+latter method will exhibit better numerical stability. In practice,
+because Pdamp is normally chosen to be a large multiple of the
+outermost rRESPA timestep, the barostat dynamics are not the
+limiting factor for numerical stability. Both
+factorizations are time-reversible and can be shown to preserve the phase
+space measure of the underlying non-Hamiltonian equations of motion.
+</P>
+<HR>
+
+<P>The fix npt and fix nph commands can be used with rigid bodies or
+mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
+there are also <A HREF = "fix_rigid.html">fix rigid/npt</A> and <A HREF = "fix_rigid.html">fix
+rigid/nph</A> commands, which are typically a more natural
+choice. See the doc page for those commands for more discussion of
+the various ways to do this.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>These fixes writes the state of all the thermostat and barostat
+variables to <A HREF = "restart.html">binary restart files</A>. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by these fixes. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure. LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+</P>
+<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
+single thermo_modify command (or in two separate commands), then the
+order in which the keywords are specified is important. Note that a
+<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
+compute as an argument when it is specified. The <I>temp</I> keyword will
+override this (for the pressure compute being used by fix npt), but
+only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
+<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
+compute specified by the <I>press</I> keyword will be unaffected by the
+<I>temp</I> setting.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar value calculated by
+these fixes is "extensive"; the vector values are "intensive".
+</P>
+<P>The scalar is the cumulative energy change due to the fix.
+</P>
+<P>The vector stores internal Nose/Hoover thermostat and barostat
+variables. The number and meaning of the vector values depends on
+which fix is used and the settings for keywords <I>tchain</I> and <I>pchain</I>,
+which specify the number of Nose/Hoover chains for the thermostat and
+barostat. If no thermostatting is done, then <I>tchain</I> is 0. If no
+barostatting is done, then <I>pchain</I> is 0. In the following list,
+"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
+the barostat. Its value is 0 if no barostat is used, else its value
+is 6 if any off-diagonal stress tensor component is barostatted, else
+its value is 1 if <I>couple xyz</I> is used or <I>couple xy</I> for a 2d
+simulation, otherwise its value is 3.
+</P>
+<P>The order of values in the global vector and their meaning is as
+follows. The notation means there are tchain values for eta, followed
+by tchain for eta_dot, followed by ndof for omega, etc:
+</P>
+<UL><LI>eta[tchain] = particle thermostat displacements (unitless)
+<LI>eta_dot[tchain] = particle thermostat velocities (1/time units)
+<LI>omega[ndof] = barostat displacements (unitless)
+<LI>omega_dot[ndof] = barostat velocities (1/time units)
+<LI>etap[pchain] = barostat thermostat displacements (unitless)
+<LI>etap_dot[pchain] = barostat thermostat velocities (1/time units)
+<LI>PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units)
+<LI>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units)
+<LI>PE_omega[ndof] = potential energy of each barostat displacement (energy units)
+<LI>KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units)
+<LI>PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units)
+<LI>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units)
+<LI>PE_strain[1] = scalar strain energy (energy units)
+</UL>
+<P>These fixes can ramp their external temperature and pressure over
+multiple runs, using the <I>start</I> and <I>stop</I> keywords of the
+<A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for details of
+how to do this.
+</P>
+<P>These fixes are not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P><I>X</I>, <I>y</I>, <I>z</I> cannot be barostatted if the associated dimension is not
+periodic. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only be barostatted if the
+simulation domain is triclinic and the 2nd dimension in the keyword
+(<I>y</I> dimension in <I>xy</I>) is periodic. <I>Z</I>, <I>xz</I>, and <I>yz</I>, cannot be
+barostatted for 2D simulations. The <A HREF = "create_box.html">create_box</A>,
+<A HREF = "read_data.html">read data</A>, and <A HREF = "read_restart.html">read_restart</A>
+commands specify whether the simulation box is orthogonal or
+non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
+tilt factors.
+</P>
+<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
+make the external T = 0.0 at some timestep during the simulation which
+is not allowed in the Nose/Hoover formulation.
+</P>
+<P>The <I>scaleyz yes</I> and <I>scalexz yes</I> keyword/value pairs can not be used
+for 2D simulations. <I>scaleyz yes</I>, <I>scalexz yes</I>, and <I>scalexy yes</I> options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+<I>tri</I>, <I>yz</I>, <I>xz</I>, and <I>xy</I>.
+</P>
+<P>These fixes can be used with dynamic groups as defined by the
+<A HREF = "group.html">group</A> command. Likewise they can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation. However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms. You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_modify.html">fix_modify</A>,
+<A HREF = "run_style.html">run_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
+ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
+scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
+not coupled to barostat, otherwise no.
+</P>
+<HR>
+
+<A NAME = "Martyna"></A>
+
+<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
+</P>
+<A NAME = "Parrinello"></A>
+
+<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+</P>
+<A NAME = "Tuckerman"></A>
+
+<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
+Martyna, J Phys A: Math Gen, 39, 5629 (2006).
+</P>
+<A NAME = "Shinoda"></A>
+
+<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nh_eff.html b/doc/doc2/fix_nh_eff.html
new file mode 100644
index 000000000..7d159b4bd
--- /dev/null
+++ b/doc/doc2/fix_nh_eff.html
@@ -0,0 +1,158 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt/eff command
+</H3>
+<H3>fix npt/eff command
+</H3>
+<H3>fix nph/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style_name keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
+
+<PRE>one or more keyword value pairs may be appended
+keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
+ <I>temp</I> values = Tstart Tstop Tdamp
+ Tstart,Tstop = external temperature at start/end of run
+ Tdamp = temperature damping parameter (time units)
+ <I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+ Pdamp = stress damping parameter (time units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>tchain</I> value = length of thermostat chain (1 = single thermostat)
+ <I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
+ <I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
+ <I>tloop</I> value = number of sub-cycles to perform on thermostat
+ <I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
+ <I>nreset</I> value = reset reference cell every this many timesteps
+ <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
+ <I>dilate</I> value = <I>all</I> or <I>partial</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt/eff temp 300.0 300.0 0.1
+fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
+fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
+fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>These commands perform time integration on Nose-Hoover style
+non-Hamiltonian equations of motion for nuclei and electrons in the
+group for the <A HREF = "pair_eff.html">electron force field</A> model. The fixes
+are designed to generate positions and velocities sampled from the
+canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
+ensembles. This is achieved by adding some dynamic variables which
+are coupled to the particle velocities (thermostatting) and simulation
+domain dimensions (barostatting). In addition to basic thermostatting
+and barostatting, these fixes can also create a chain of thermostats
+coupled to the particle thermostat, and another chain of thermostats
+coupled to the barostat variables. The barostat can be coupled to the
+overall box volume, or to individual dimensions, including the <I>xy</I>,
+<I>xz</I> and <I>yz</I> tilt dimensions. The external pressure of the barostat
+can be specified as either a scalar pressure (isobaric ensemble) or as
+components of a symmetric stress tensor (constant stress ensemble).
+When used correctly, the time-averaged temperature and stress tensor
+of the particles will match the target values specified by
+Tstart/Tstop and Pstart/Pstop.
+</P>
+<P>The operation of these fixes is exactly like that described by the
+<A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands, except that the radius
+and radial velocity of electrons are also updated. Likewise the
+temperature and pressure calculated by the fix, using the computes it
+creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A>
+doc page), are performed with computes that include the eFF contribution
+to the temperature or kinetic energy from the electron radial velocity.
+</P>
+<P>IMPORTANT NOTE: there are two different pressures that can be reported
+for eFF when defining the pair_style (see <A HREF = "pair_eff_cut.html">pair
+eff/cut</A> to understand these settings), one
+(default) that considers electrons do not contribute radial virial
+components (i.e. electrons treated as incompressible 'rigid' spheres)
+and one that does. The radial electronic contributions to the virials
+are only tallied if the flexible pressure option is set, and this will
+affect both global and per-atom quantities. In principle, the true
+pressure of a system is somewhere in between the rigid and the
+flexible eFF pressures, but, for most cases, the difference between
+these two pressures will not be significant over long-term averaged
+runs (i.e. even though the energy partitioning changes, the total
+energy remains similar).
+</P>
+<P>IMPORTANT NOTE: currently, there is no available option for the user
+to set or create temperature distributions that include the radial
+electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A>
+command, so the the user must allow for these degrees of freedom to
+equilibrate (i.e. equi-partitioning of energy) through time
+integration.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>See the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands
+for details.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Other restriction discussed on the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and
+nph</A> commands also apply.
+</P>
+<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with
+only electrons and no nuclei is 0.0 (i.e. not defined) in the current
+temperature calculations, a practical example would be a uniform
+electron gas or a very hot plasma, where electrons remain delocalized
+from the nuclei. This is because, even though electron virials are
+included in the temperature calculation, these are averaged over the
+nuclear degrees of freedom only. In such cases a corrective term must
+be added to the pressure to get the correct kinetic contribution.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nh.html">fix npt</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
+ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
+</P>
+<HR>
+
+<A NAME = "Martyna"></A>
+
+<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
+</P>
+<A NAME = "Parrinello"></A>
+
+<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
+</P>
+<A NAME = "Tuckerman"></A>
+
+<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
+Martyna, J Phys A: Math Gen, 39, 5629 (2006).
+</P>
+<A NAME = "Shinoda"></A>
+
+<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nph_asphere.html b/doc/doc2/fix_nph_asphere.html
new file mode 100644
index 000000000..a6022e235
--- /dev/null
+++ b/doc/doc2/fix_nph_asphere.html
@@ -0,0 +1,159 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nph/asphere command
+</H3>
+<H3>fix nph/asphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nph/asphere args keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nph/asphere = style name of this fix command
+<LI>additional barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nph</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nph/asphere iso 0.0 0.0 1000.0
+fix 2 all nph/asphere x 5.0 5.0 1000.0
+fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2
+fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NPH integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover pressure
+barostat. P is pressure; H is enthalpy. This creates a system
+trajectory consistent with the isenthalpic ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix nph</A> command, which assumes
+point particles and only updates their position and velocity.
+</P>
+<P>Additional parameters affecting the barostat are specified by keywords
+and values documented with the <A HREF = "fix_nh.html">fix nph</A> command. See,
+for example, discussion of the <I>aniso</I>, and <I>dilate</I> keywords.
+</P>
+<P>The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPH integration.
+</P>
+<P>Regardless of what particles are in the fix group, a global pressure is
+computed for all particles. Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
+only the particles in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp/asphere" and
+"pressure", as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure. If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure. LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix nph</A> command.
+</P>
+<P>This fix can ramp its target pressure over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
+nvt_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
+npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nph_sphere.html b/doc/doc2/fix_nph_sphere.html
new file mode 100644
index 000000000..f1b4ef9fc
--- /dev/null
+++ b/doc/doc2/fix_nph_sphere.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nph/sphere command
+</H3>
+<H3>fix nph/sphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nph/sphere args keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nph/sphere = style name of this fix command
+<LI>additional barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nph</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nph/sphere iso 0.0 0.0 1000.0
+fix 2 all nph/sphere x 5.0 5.0 1000.0
+fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2
+fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NPH integration to update position, velocity, and
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover pressure barostat. P is pressure; H is
+enthalpy. This creates a system trajectory consistent with the
+isenthalpic ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix nph</A> command, which assumes
+point particles and only updates their position and velocity.
+</P>
+<P>Additional parameters affecting the barostat are specified by keywords
+and values documented with the <A HREF = "fix_nh.html">fix nph</A> command. See,
+for example, discussion of the <I>aniso</I>, and <I>dilate</I> keywords.
+</P>
+<P>The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPH integration.
+</P>
+<P>Regardless of what particles are in the fix group, a global pressure is
+computed for all particles. Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
+only the particles in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp/sphere" and
+"pressure", as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure. If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure. LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix nph</A> command.
+</P>
+<P>This fix can ramp its target pressure over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command.
+</P>
+<P>All particles in the group must be finite-size spheres. They cannot
+be point particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_sphere.html">fix
+nvt_sphere</A>, <A HREF = "fix_npt_sphere.html">fix npt_sphere</A>,
+<A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nphug.html b/doc/doc2/fix_nphug.html
new file mode 100644
index 000000000..9fb2140e7
--- /dev/null
+++ b/doc/doc2/fix_nphug.html
@@ -0,0 +1,239 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nphug command
+</H3>
+<H3>fix nphug/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nphug keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<PRE>one or more keyword value pairs may be appended
+keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</I>
+ <I>temp</I> values = Value1 Value2 Tdamp
+ Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat
+ Tdamp = temperature damping parameter (time units)
+ <I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressures, must be equal (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor components, must be equal (pressure units)
+ Pdamp = stress damping parameter (time units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>tchain</I> value = length of thermostat chain (1 = single thermostat)
+ <I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
+ <I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
+ <I>tloop</I> value = number of sub-cycles to perform on thermostat
+ <I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
+ <I>nreset</I> value = reset reference cell every this many timesteps
+ <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
+ <I>dilate</I> value = <I>all</I> or <I>partial</I>
+ <I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
+ <I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
+ <I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
+fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command is a variant of the Nose-Hoover
+<A HREF = "fix_nh.html">fix npt</A> fix style.
+It performs time integration of the Hugoniostat equations
+of motion developed by Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
+These equations compress the system to a state with average
+axial stress or pressure equal to the specified target value
+and that satisfies the Rankine-Hugoniot (RH)
+jump conditions for steady shocks.
+</P>
+<P>The compression can be performed
+either
+hydrostatically (using keyword <I>iso</I>, <I>aniso</I>, or <I>tri</I>) or uniaxially
+(using keywords <I>x</I>, <I>y</I>, or <I>z</I>). In the hydrostatic case,
+the cell dimensions change dynamically so that the average axial stress
+in all three directions converges towards the specified target value.
+In the uniaxial case, the chosen cell dimension changes dynamically
+so that the average
+axial stress in that direction converges towards the target value. The
+other two cell dimensions are kept fixed (zero lateral strain).
+</P>
+<P>This leads to the following additional restrictions on the keywords:
+</P>
+<UL><LI>One and only one of the following keywords should be used: <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>
+<LI>The specified initial and final target pressures must be the same.
+<LI>The keywords <I>xy</I>, <I>xz</I>, <I>yz</I> may not be used.
+<LI>The only admissible value for the couple keyword is <I>xyz</I>, which has the same effect as keyword <I>iso</I>
+<LI>The <I>temp</I> keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored.
+</UL>
+<P>Essentially, a Hugoniostat simulation is an NPT simulation in which the
+user-specified target temperature is replaced with a time-dependent
+target temperature Tt obtained from the following equation:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_nphug.jpg">
+</CENTER>
+<P>where T and Tt are the instantaneous and target temperatures,
+P and P0 are the instantaneous and reference pressures or axial stresses,
+depending on whether hydrostatic or uniaxial compression is being
+performed, V and V0 are the instantaneous and reference volumes,
+E and E0 are the instantaneous and reference internal energy (potential
+plus kinetic), Ndof is the number of degrees of freedom used in the
+definition of temperature, and kB is the Boltzmann constant. Delta is the
+negative deviation of the instantaneous temperature from the target temperature.
+When the system reaches a stable equilibrium, the value of Delta should
+fluctuate about zero.
+</P>
+<P>The values of E0, V0, and P0 are the instantaneous values at the start of
+the simulation. These can be overridden using the fix_modify keywords <I>e0</I>,
+<I>v0</I>, and <I>p0</I> described below.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A> command which performs
+thermostatting but NO time integration, this fix performs
+thermostatting/barostatting AND time integration. Thus you should not
+use any other time integration fix, such as <A HREF = "fix_nve.html">fix nve</A> on
+atoms to which this fix is applied. Likewise, this fix should not be
+used on atoms that have their temperature controlled by another fix
+- e.g. by <A HREF = "fix_nh.html">fix langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
+commands.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure at each timestep. To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if one of these two sets of commands had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</PRE>
+<PRE>compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press". The group for
+the new computes is "all" since pressure is computed for the entire
+system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the values of E0, V0, and P0, as well as the
+state of all the thermostat and barostat
+variables to <A HREF = "restart.html">binary restart files</A>. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>e0</I>, <I>v0</I> and <I>p0</I> keywords
+can be used to define the values of E0, V0, and P0. Note the
+the values for <I>e0</I> and <I>v0</I> are extensive, and so must correspond
+to the total energy and volume of the entire system, not energy and
+volume per atom. If any of these quantities are not specified, then the
+instantaneous value in the system at the start of the simulation is used.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by these fixes. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure. LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>. Either way, this energy is *not*
+included in the definition of internal energy E when calculating the value
+of Delta in the above equation.
+</P>
+<P>These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar value calculated by
+these fixes is "extensive"; the vector values are "intensive".
+</P>
+<P>The scalar is the cumulative energy change due to the fix.
+</P>
+<P>The vector stores three quantities unique to this fix (Delta, Us, and up),
+followed by all the internal Nose/Hoover thermostat and barostat
+variables defined for <A HREF = "fix_nh.html">fix_style npt</A>. Delta is the deviation
+of the temperature from the target temperature, given by the above equation.
+Us and up are the shock and particle velocity corresponding to a steady
+shock calculated from the RH conditions. They have units of distance/time.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the SHOCK package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>All the usual restrictions for <A HREF = "fix_nh.html">fix_style npt</A> apply,
+plus the additional ones mentioned above.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_msst.html">fix msst</A>, <A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are the same as those for <A HREF = "fix_nh.html">fix npt</A>
+</P>
+<HR>
+
+<A NAME = "Ravelo"></A>
+
+<P><B>(Ravelo)</B> Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_npt_asphere.html b/doc/doc2/fix_npt_asphere.html
new file mode 100644
index 000000000..f98e64f14
--- /dev/null
+++ b/doc/doc2/fix_npt_asphere.html
@@ -0,0 +1,183 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix npt/asphere command
+</H3>
+<H3>fix npt/asphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID npt/asphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>npt/asphere = style name of this fix command
+<LI>additional thermostat and barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix npt</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NPT integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover temperature
+thermostat and Nose/Hoover pressure barostat. P is pressure; T is
+temperature. This creates a system trajectory consistent with the
+isothermal-isobaric ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix npt</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P>The thermostat is applied to both the translational and rotational
+degrees of freedom for the aspherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below). The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>Additional parameters affecting the thermostat and barostat are
+specified by keywords and values documented with the <A HREF = "fix_nh.html">fix
+npt</A> command. See, for example, discussion of the <I>temp</I>,
+<I>iso</I>, <I>aniso</I>, and <I>dilate</I> keywords.
+</P>
+<P>The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPT integration.
+</P>
+<P>Regardless of what particles are in the fix group, a global pressure is
+computed for all particles. Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
+only the particles in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp/asphere" and
+"pressure", as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat and barostat
+to <A HREF = "restart.html">binary restart files</A>. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure. If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure. LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix npt</A> command.
+</P>
+<P>This fix can ramp its target temperature and pressure over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command. See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
+nvt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_npt_sphere.html b/doc/doc2/fix_npt_sphere.html
new file mode 100644
index 000000000..ff4949606
--- /dev/null
+++ b/doc/doc2/fix_npt_sphere.html
@@ -0,0 +1,178 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix npt/sphere command
+</H3>
+<H3>fix npt/sphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID npt/sphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>npt/sphere = style name of this fix command
+<LI>additional thermostat and barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix npt</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
+fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
+fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NPT integration to update position, velocity, and
+angular velocity each timestep for finite-sizex spherical particles in
+the group using a Nose/Hoover temperature thermostat and Nose/Hoover
+pressure barostat. P is pressure; T is temperature. This creates a
+system trajectory consistent with the isothermal-isobaric ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix npt</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P>The thermostat is applied to both the translational and rotational
+degrees of freedom for the spherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below). The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>Additional parameters affecting the thermostat and barostat are
+specified by keywords and values documented with the <A HREF = "fix_nh.html">fix
+npt</A> command. See, for example, discussion of the <I>temp</I>,
+<I>iso</I>, <I>aniso</I>, and <I>dilate</I> keywords.
+</P>
+<P>The particles in the fix group are the only ones whose velocities and
+positions are updated by the velocity/position update portion of the
+NPT integration.
+</P>
+<P>Regardless of what particles are in the fix group, a global pressure is
+computed for all particles. Similarly, when the size of the simulation
+box is changed, all particles are re-scaled to new positions, unless the
+keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
+only the particles in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of particles in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+</P>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp/sphere" and
+"pressure", as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is "all"
+since pressure is computed for the entire system.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat and barostat
+to <A HREF = "restart.html">binary restart files</A>. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure. If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure. LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix npt</A> command.
+</P>
+<P>This fix can ramp its target temperature and pressure over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command. See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command.
+</P>
+<P>All particles in the group must be finite-size spheres. They cannot
+be point particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_sphere.html">fix
+nvt_sphere</A>, <A HREF = "fix_npt_asphere.html">fix
+npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve.html b/doc/doc2/fix_nve.html
new file mode 100644
index 000000000..fbb452085
--- /dev/null
+++ b/doc/doc2/fix_nve.html
@@ -0,0 +1,81 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve command
+</H3>
+<H3>fix nve/cuda command
+</H3>
+<H3>fix nve/kk command
+</H3>
+<H3>fix nve/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position and velocity for
+atoms in the group each timestep. V is volume; E is energy. This
+creates a system trajectory consistent with the microcanonical
+ensemble.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix npt</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_asphere.html b/doc/doc2/fix_nve_asphere.html
new file mode 100644
index 000000000..8b5ea4a3f
--- /dev/null
+++ b/doc/doc2/fix_nve_asphere.html
@@ -0,0 +1,65 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/asphere command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/asphere
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/asphere = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/asphere
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for aspherical particles in the
+group each timestep. V is volume; E is energy. This creates a system
+trajectory consistent with the microcanonical ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_asphere_noforce.html b/doc/doc2/fix_nve_asphere_noforce.html
new file mode 100644
index 000000000..4dd6f31ad
--- /dev/null
+++ b/doc/doc2/fix_nve_asphere_noforce.html
@@ -0,0 +1,70 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/asphere/noforce command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/asphere/noforce
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/asphere/noforce = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>fix 1 all nve/asphere/noforce
+</P>
+<P><B>Description:</B>
+</P>
+<P>Perform updates of position and orientation, but not velocity or
+angular momentum for atoms in the group each timestep. In other
+words, the force and torque on the atoms is ignored and their velocity
+and angular momentum are not updated. The atom velocities and
+angularm momenta are used to update their positions and orientation.
+</P>
+<P>This is useful as an implicit time integrator for Fast Lubrication
+Dynamics, since the velocity and angular momentum are updated by the
+<A HREF = "pair_lubricateU.txt">pair_style lubricuteU</A> command.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve_noforce.html">fix nve/noforce</A>, <A HREF = "fix_nve_asphere.html">fix
+nve/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_body.html b/doc/doc2/fix_nve_body.html
new file mode 100644
index 000000000..fc7fe3dd6
--- /dev/null
+++ b/doc/doc2/fix_nve_body.html
@@ -0,0 +1,67 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/body command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/body
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/body = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/body
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for body particles in the group each
+timestep. V is volume; E is energy. This creates a system trajectory
+consistent with the microcanonical ensemble. See <A HREF = "Section_howto.html#howto_14">Section_howto
+14</A> of the manual and the <A HREF = "body.html">body</A>
+doc page for more details on using body particles.
+</P>
+<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the BODY package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style body</A>
+command.
+</P>
+<P>All particles in the group must be body particles. They cannot be
+point particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_sphere.html">fix nve/sphere</A>, <A HREF = "fix_nve_asphere.html">fix
+nve/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_eff.html b/doc/doc2/fix_nve_eff.html
new file mode 100644
index 000000000..80b150924
--- /dev/null
+++ b/doc/doc2/fix_nve_eff.html
@@ -0,0 +1,59 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/eff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/eff = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/eff
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position and velocity for
+nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron force
+field</A> model. V is volume; E is energy. This creates a
+system trajectory consistent with the microcanonical ensemble.
+</P>
+<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nve.html">fix
+nve</A> command, except that the radius and radial velocity
+of electrons are also updated.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_nh_eff.html">fix
+npt/eff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_limit.html b/doc/doc2/fix_nve_limit.html
new file mode 100644
index 000000000..13b40bb9e
--- /dev/null
+++ b/doc/doc2/fix_nve_limit.html
@@ -0,0 +1,91 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/limit command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/limit xmax
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve = style name of this fix command
+<LI>xmax = maximum distance an atom can move in one timestep (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/limit 0.1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE updates of position and velocity for atoms in the
+group each timestep. A limit is imposed on the maximum distance an
+atom can move in one timestep. This is useful when starting a
+simulation with a configuration containing highly overlapped atoms.
+Normally this would generate huge forces which would blow atoms out of
+the simulation box, causing LAMMPS to stop with an error.
+</P>
+<P>Using this fix can overcome that problem. Forces on atoms must still
+be computable (which typically means 2 atoms must have a separation
+distance > 0.0). But large velocities generated by large forces are
+reset to a value that corresponds to a displacement of length <I>xmax</I>
+in a single timestep. <I>Xmax</I> is specified in distance units; see the
+<A HREF = "units.html">units</A> command for details. The value of <I>xmax</I> should be
+consistent with the neighbor skin distance and the frequency of
+neighbor list re-building, so that pairwise interactions are not
+missed on successive timesteps as atoms move. See the
+<A HREF = "neighbor.html">neighbor</A> and <A HREF = "neigh_modify.html">neigh_modify</A> commands
+for details.
+</P>
+<P>Note that if a velocity reset occurs the integrator will not conserve
+energy. On steps where no velocity resets occur, this integrator is
+exactly like the <A HREF = "fix_nve.html">fix nve</A> command. Since forces are
+unaltered, pressures computed by thermodynamic output will still be
+very large for overlapped configurations.
+</P>
+<P>IMPORTANT NOTE: You should not use <A HREF = "fix_shake.html">fix shake</A> in
+conjunction with this fix. That is because fix shake applies
+contraint forces based on the predicted postitions of atoms after the
+next timestep. It has no way of knowing the timestep may change due
+to this fix, which will cause the constraint forces to be invalid. A
+better strategy is to turn off fix shake when performing initial
+dynamics that need this fix, then turn fix shake on when doing normal
+dynamics with a fixed-size timestep.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+count of how many updates of atom's velocity/position were limited by
+the maximum distance criterion. This should be roughly the number of
+atoms so affected, except that updates occur at both the beginning and
+end of a timestep in a velocity Verlet timestepping algorithm. This
+is a cumulative quantity for the current run, but is re-initialized to
+zero each time a run is performed. The scalar value calculated by
+this fix is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_noforce.html">fix nve/noforce</A>,
+<A HREF = "pair_soft.html">pair_style soft</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_line.html b/doc/doc2/fix_nve_line.html
new file mode 100644
index 000000000..9b18cfeaa
--- /dev/null
+++ b/doc/doc2/fix_nve_line.html
@@ -0,0 +1,62 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/line command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/line
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/line = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/line
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position, velocity,
+orientation, and angular velocity for line segment particles in the
+group each timestep. V is volume; E is energy. This creates a system
+trajectory consistent with the microcanonical ensemble. See
+<A HREF = "Section_howto.html">Section_howto 14</A> of the manual for an overview of
+using line segment particles.
+</P>
+<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that particles be line segments as defined by the
+<A HREF = "atom_style.html">atom_style line</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_noforce.html b/doc/doc2/fix_nve_noforce.html
new file mode 100644
index 000000000..8150e5668
--- /dev/null
+++ b/doc/doc2/fix_nve_noforce.html
@@ -0,0 +1,59 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/noforce command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/noforce = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 wall nve/noforce
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform updates of position, but not velocity for atoms in the group
+each timestep. In other words, the force on the atoms is ignored and
+their velocity is not updated. The atom velocities are used to update
+their positions.
+</P>
+<P>This can be useful for wall atoms, when you set their velocities, and
+want the wall to move (or stay stationary) in a prescribed fashion.
+</P>
+<P>This can also be accomplished via the <A HREF = "fix_setforce.html">fix setforce</A>
+command, but with fix nve/noforce, the forces on the wall atoms are
+unchanged, and can thus be printed by the <A HREF = "dump.html">dump</A> command or
+queried with an equal-style <A HREF = "variable.html">variable</A> that uses the
+fcm() group function to compute the total force on the group of atoms.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_sphere.html b/doc/doc2/fix_nve_sphere.html
new file mode 100644
index 000000000..4ac5df95a
--- /dev/null
+++ b/doc/doc2/fix_nve_sphere.html
@@ -0,0 +1,106 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/sphere command
+</H3>
+<H3>fix nve/sphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/sphere
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>nve/sphere = style name of this fix command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>update</I>
+
+<PRE> <I>update</I> value = <I>dipole</I>
+ dipole = update orientation of dipole moment during integration
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/sphere
+fix 1 all nve/sphere update dipole
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position, velocity, and
+angular velocity for finite-size spherical particles in the group each
+timestep. V is volume; E is energy. This creates a system trajectory
+consistent with the microcanonical ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P>If the <I>update</I> keyword is used with the <I>dipole</I> value, then the
+orientation of the dipole moment of each particle is also updated
+during the time integration. This option should be used for models
+where a dipole moment is assigned to particles via use of the
+<A HREF = "atom_style.html">atom_style dipole</A> command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command. If the <I>dipole</I> keyword is used, then they must also store a
+dipole moment as defined by the <A HREF = "atom_style.html">atom_style dipole</A>
+command.
+</P>
+<P>All particles in the group must be finite-size spheres. They cannot
+be point particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nve_tri.html b/doc/doc2/fix_nve_tri.html
new file mode 100644
index 000000000..de9d25b43
--- /dev/null
+++ b/doc/doc2/fix_nve_tri.html
@@ -0,0 +1,62 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nve/tri command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nve/tri
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nve/tri = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve/tri
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVE integration to update position, velocity,
+orientation, and angular momentum for triangular particles in the
+group each timestep. V is volume; E is energy. This creates a system
+trajectory consistent with the microcanonical ensemble. See
+<A HREF = "Section_howto.html">Section_howto 14</A> of the manual for an overview of
+using triangular particles.
+</P>
+<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that particles be triangles as defined by the
+<A HREF = "atom_style.html">atom_style tri</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nvt_asphere.html b/doc/doc2/fix_nvt_asphere.html
new file mode 100644
index 000000000..6320f401b
--- /dev/null
+++ b/doc/doc2/fix_nvt_asphere.html
@@ -0,0 +1,159 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt/asphere command
+</H3>
+<H3>fix nvt/asphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nvt/asphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nvt/asphere = style name of this fix command
+<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nvt</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt/asphere temp 300.0 300.0 100.0
+fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVT integration to update position, velocity,
+orientation, and angular velocity each timestep for aspherical or
+ellipsoidal particles in the group using a Nose/Hoover temperature
+thermostat. V is volume; T is temperature. This creates a system
+trajectory consistent with the canonical ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix nvt</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P>The thermostat is applied to both the translational and rotational
+degrees of freedom for the aspherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below). The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>Additional parameters affecting the thermostat are specified by
+keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
+command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
+keywords.
+</P>
+<P>This fix computes a temperature each timestep. To do this, the fix
+creates its own compute of style "temp/asphere", as if this command
+had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp/asphere
+</PRE>
+<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> command for
+details. Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires that atoms store torque and angular momementum and a
+quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
+command.
+</P>
+<P>All particles in the group must be finite-size. They cannot be point
+particles, but they can be aspherical or spherical as defined by their
+shape attribute.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
+npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nvt_sllod.html b/doc/doc2/fix_nvt_sllod.html
new file mode 100644
index 000000000..b4bca0eaf
--- /dev/null
+++ b/doc/doc2/fix_nvt_sllod.html
@@ -0,0 +1,187 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt/sllod command
+</H3>
+<H3>fix nvt/sllod/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nvt/sllod keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nvt/sllod = style name of this fix command
+<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nvt</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt/sllod temp 300.0 300.0 100.0
+fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVT integration to update positions and velocities
+each timestep for atoms in the group using a Nose/Hoover temperature
+thermostat. V is volume; T is temperature. This creates a system
+trajectory consistent with the canonical ensemble.
+</P>
+<P>This thermostat is used for a simulation box that is changing size
+and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
+The size/shape change is induced by use of the <A HREF = "fix_deform.html">fix
+deform</A> command, so each point in the simulation box
+can be thought of as having a "streaming" velocity. This
+position-dependent streaming velocity is subtracted from each atom's
+actual velocity to yield a thermal velocity which is used for
+temperature computation and thermostatting. For example, if the box
+is being sheared in x, relative to y, then points at the bottom of the
+box (low y) have a small x velocity, while points at the top of the
+box (hi y) have a large x velocity. These velocities do not
+contribute to the thermal "temperature" of the atom.
+</P>
+<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
+remapping either atom coordinates or velocities to the changing
+simulation box. To use fix nvt/sllod, fix deform should NOT remap
+atom positions, because fix nvt/sllod adjusts the atom positions and
+velocities to create a velocity profile that matches the changing box
+size/shape. Fix deform SHOULD remap atom velocities when atoms cross
+periodic boundaries since that is consistent with maintaining the
+velocity profile created by fix nvt/sllod. LAMMPS will give an
+error if this setting is not consistent.
+</P>
+<P>The SLLOD equations of motion, originally proposed by Hoover and Ladd
+(see <A HREF = "#Evans">(Evans and Morriss)</A>), were proven to be equivalent to
+Newton's equations of motion for shear flow by <A HREF = "#Evans">(Evans and
+Morriss)</A>. They were later shown to generate the desired
+velocity gradient and the correct production of work by stresses for
+all forms of homogeneous flow by <A HREF = "#Daivis">(Daivis and Todd)</A>. As
+implemented in LAMMPS, they are coupled to a Nose/Hoover chain
+thermostat in a velocity Verlet formulation, closely following the
+implementation used for the <A HREF = "fix_nh.html">fix nvt</A> command.
+</P>
+<P>Additional parameters affecting the thermostat are specified by
+keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
+command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
+keywords.
+</P>
+<P>This fix computes a temperature each timestep. To do this, the fix
+creates its own compute of style "temp/deform", as if this command had
+been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp/deform
+</PRE>
+<P>See the <A HREF = "compute_temp_deform.html">compute temp/deform</A> command for
+details. Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1. Setting tchain to larger values can result in poor
+equilibration.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>Same as <A HREF = "fix_nh.html">fix nvt</A>, except tchain = 1.
+</P>
+<HR>
+
+<A NAME = "Evans"></A>
+
+<P><B>(Evans and Morriss)</B> Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+</P>
+<A NAME = "Daivis"></A>
+
+<P><B>(Daivis and Todd)</B> Daivis and Todd, J Chem Phys, 124, 194103 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nvt_sllod_eff.html b/doc/doc2/fix_nvt_sllod_eff.html
new file mode 100644
index 000000000..072b12435
--- /dev/null
+++ b/doc/doc2/fix_nvt_sllod_eff.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt/sllod/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nvt/sllod/eff keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nvt/sllod/eff = style name of this fix command
+<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
+fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVT integration to update positions and velocities
+each timestep for nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron
+force field</A> model, using a Nose/Hoover temperature
+thermostat. V is volume; T is temperature. This creates a system
+trajectory consistent with the canonical ensemble.
+</P>
+<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nvt_sllod.html">fix
+nvt/sllod</A> command, except that the radius and
+radial velocity of electrons are also updated and thermostatted.
+Likewise the temperature calculated by the fix, using the compute it
+creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> doc
+page), is performed with a <A HREF = "compute_temp_deform_eff.html">compute
+temp/deform/eff</A> commmand that includes
+the eFF contribution to the temperature from the electron radial
+velocity.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix works best without Nose-Hoover chain thermostats, i.e. using
+tchain = 1. Setting tchain to larger values can result in poor
+equilibration.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_langevin_eff.html">fix
+langevin/eff</A>, <A HREF = "fix_nvt_sllod.html">fix
+nvt/sllod</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform_eff.html">compute
+temp/deform/eff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>Same as <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, except tchain = 1.
+</P>
+<HR>
+
+<A NAME = "Tuckerman"></A>
+
+<P><B>(Tuckerman)</B> Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
+106, 5615 (1997).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_nvt_sphere.html b/doc/doc2/fix_nvt_sphere.html
new file mode 100644
index 000000000..574a1a04c
--- /dev/null
+++ b/doc/doc2/fix_nvt_sphere.html
@@ -0,0 +1,155 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix nvt/sphere command
+</H3>
+<H3>fix nvt/sphere/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID nvt/sphere keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nvt/sphere = style name of this fix command
+<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nvt</A> command can be appended
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt/sphere temp 300.0 300.0 100.0
+fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform constant NVT integration to update position, velocity, and
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover temperature thermostat. V is volume; T
+is temperature. This creates a system trajectory consistent with the
+canonical ensemble.
+</P>
+<P>This fix differs from the <A HREF = "fix_nh.html">fix nvt</A> command, which
+assumes point particles and only updates their position and velocity.
+</P>
+<P>The thermostat is applied to both the translational and rotational
+degrees of freedom for the spherical particles, assuming a compute is
+used which calculates a temperature that includes the rotational
+degrees of freedom (see below). The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>Additional parameters affecting the thermostat are specified by
+keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
+command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
+keywords.
+</P>
+<P>This fix computes a temperature each timestep. To do this, the fix
+creates its own compute of style "temp/sphere", as if this command
+had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp/sphere
+</PRE>
+<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</A> command for
+details. Note that the ID of the new compute is the fix-ID +
+underscore + "temp", and the group for the new compute is the same as
+the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes the same global scalar and global vector of
+quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix requires that atoms store torque and angular velocity (omega)
+and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command.
+</P>
+<P>All particles in the group must be finite-size spheres. They cannot
+be point particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_asphere.html">fix
+nvt_asphere</A>, <A HREF = "fix_npt_sphere.html">fix
+npt_sphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_oneway.html b/doc/doc2/fix_oneway.html
new file mode 100644
index 000000000..9b48b802b
--- /dev/null
+++ b/doc/doc2/fix_oneway.html
@@ -0,0 +1,69 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix oneway command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID oneway N region-ID direction
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>oneway = style name of this fix command
+
+<LI>N = apply this fix every this many timesteps
+
+<LI>region-ID = ID of region where fix is active
+
+<LI>direction = <I>x</I> or <I>-x</I> or <I>y</I> or <I>-y</I> or <I>z</I> or <I>-z</I> = coordinate and direction of the oneway constraint
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix ions oneway 10 semi -x
+fix all oneway 1 left -z
+fix all oneway 1 right z
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Enforce that particles in the group and in a given region can only
+move in one direction. This is done by reversing a particle's
+velocity component, if it has the wrong sign in the specified
+dimension. The effect is that the particle moves in one direction
+only.
+</P>
+<P>This can be used, for example, as a simple model of a semi-permeable
+membrane, or as an implementation of Maxwell's demon.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+</HTML>
diff --git a/doc/doc2/fix_orient_fcc.html b/doc/doc2/fix_orient_fcc.html
new file mode 100644
index 000000000..f9d97dad8
--- /dev/null
+++ b/doc/doc2/fix_orient_fcc.html
@@ -0,0 +1,188 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix orient/fcc command
+</H3>
+<PRE>fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>nstats = print stats every this many steps, 0 = never
+<LI>dir = 0/1 for which crystal is used as reference
+<LI>alat = fcc cubic lattice constant (distance units)
+<LI>dE = energy added to each atom (energy units)
+<LI>cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi
+<LI>file0,file1 = files that specify orientation of each grain
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The fix applies an orientation-dependent force to atoms near a planar
+grain boundary which can be used to induce grain boundary migration
+(in the direction perpendicular to the grain boundary plane). The
+motivation and explanation of this force and its application are
+described in <A HREF = "#Janssens">(Janssens)</A>. The force is only applied to
+atoms in the fix group.
+</P>
+<P>The basic idea is that atoms in one grain (on one side of the
+boundary) have a potential energy dE added to them. Atoms in the
+other grain have 0.0 potential energy added. Atoms near the boundary
+(whose neighbor environment is intermediate between the two grain
+orientations) have an energy between 0.0 and dE added. This creates
+an effective driving force to reduce the potential energy of atoms
+near the boundary by pushing them towards one of the grain
+orientations. For dir = 1 and dE > 0, the boundary will thus move so
+that the grain described by file0 grows and the grain described by
+file1 shrinks. Thus this fix is designed for simulations of two-grain
+systems, either with one grain boundary and free surfaces parallel to
+the boundary, or a system with periodic boundary conditions and two
+equal and opposite grain boundaries. In either case, the entire
+system can displace during the simulation, and such motion should be
+accounted for in measuring the grain boundary velocity.
+</P>
+<P>The potential energy added to atom I is given by these formulas
+</P>
+<CENTER><IMG SRC = "Eqs/fix_orient_fcc.jpg">
+</CENTER>
+<P>which are fully explained in <A HREF = "#Janssens">(Janssens)</A>. The order
+parameter Xi for atom I in equation (1) is a sum over the 12 nearest
+neighbors of atom I. Rj is the vector from atom I to its neighbor J,
+and RIj is a vector in the reference (perfect) crystal. That is, if
+dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
+Equation (2) gives the expected value of the order parameter XiIJ in
+the other grain. Hi and lo cutoffs are defined in equations (3) and
+(4), using the input parameters <I>cutlo</I> and <I>cuthi</I> as thresholds to
+avoid adding grain boundary energy when the deviation in the order
+parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
+perfect crystal). The added potential energy Ui for atom I is given
+in equation (6) where it is interpolated between 0 and dE using the
+two threshold Xi values and the Wi value of equation (5).
+</P>
+<P>The derivative of this energy expression gives the force on each atom
+which thus depends on the orientation of its neighbors relative to the
+2 grain orientations. Only atoms near the grain boundary feel a net
+force which tends to drive them to one of the two grain orientations.
+</P>
+<P>In equation (1), the reference vector used for each neighbor is the
+reference vector closest to the actual neighbor position. This means
+it is possible two different neighbors will use the same reference
+vector. In such cases, the atom in question is far from a perfect
+orientation and will likely receive the full dE addition, so the
+effect of duplicate reference vector usage is small.
+</P>
+<P>The <I>dir</I> parameter determines which grain wants to grow at the
+expense of the other. A value of 0 means the first grain will shrink;
+a value of 1 means it will grow. This assumes that <I>dE</I> is positive.
+The reverse will be true if <I>dE</I> is negative.
+</P>
+<P>The <I>alat</I> parameter is the cubic lattice constant for the fcc
+material and is only used to compute a cutoff distance of 1.57 * alat
+/ sqrt(2) for finding the 12 nearest neighbors of each atom (which
+should be valid for an fcc crystal). A longer/shorter cutoff can be
+imposed by adjusting <I>alat</I>. If a particular atom has less than 12
+neighbors within the cutoff, the order parameter of equation (1) is
+effectively multiplied by 12 divided by the actual number of neighbors
+within the cutoff.
+</P>
+<P>The <I>dE</I> parameter is the maximum amount of additional energy added to
+each atom in the grain which wants to shrink.
+</P>
+<P>The <I>cutlo</I> and <I>cuthi</I> parameters are used to reduce the force added
+to bulk atoms in each grain far away from the boundary. An atom in
+the bulk surrounded by neighbors at the ideal grain orientation would
+compute an order parameter of 0 or 1 and have no force added.
+However, thermal vibrations in the solid will cause the order
+parameters to be greater than 0 or less than 1. The cutoff parameters
+mask this effect, allowing forces to only be added to atoms with
+order-parameters between the cutoff values.
+</P>
+<P><I>File0</I> and <I>file1</I> are filenames for the two grains which each
+contain 6 vectors (6 lines with 3 values per line) which specify the
+grain orientations. Each vector is a displacement from a central atom
+(0,0,0) to a nearest neighbor atom in an fcc lattice at the proper
+orientation. The vector lengths should all be identical since an fcc
+lattice has a coordination number of 12. Only 6 are listed due to
+symmetry, so the list must include one from each pair of
+equal-and-opposite neighbors. A pair of orientation files for a
+Sigma=5 tilt boundary are show below.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential energy of atom interactions with the grain
+boundary driving force to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix calculates a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+potential energy change due to this fix. The scalar value calculated
+by this fix is "extensive".
+</P>
+<P>This fix also calculates a per-atom array which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The array
+stores the order parameter Xi and normalized order parameter (0 to 1)
+for each atom. The per-atom values can be accessed on any timestep.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix should only be used with fcc lattices.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Janssens"></A>
+
+<P><B>(Janssens)</B> Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
+Materials, 5, 124-127 (2006).
+</P>
+<HR>
+
+<P>For illustration purposes, here are example files that specify a
+Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706
+Angs.
+</P>
+<P>file0:
+</P>
+<PRE> 0.798410432046075 1.785300000000000 1.596820864092150
+ -0.798410432046075 1.785300000000000 -1.596820864092150
+ 2.395231296138225 0.000000000000000 0.798410432046075
+ 0.798410432046075 0.000000000000000 -2.395231296138225
+ 1.596820864092150 1.785300000000000 -0.798410432046075
+ 1.596820864092150 -1.785300000000000 -0.798410432046075
+</PRE>
+<P>file1:
+</P>
+<PRE> -0.798410432046075 1.785300000000000 1.596820864092150
+ 0.798410432046075 1.785300000000000 -1.596820864092150
+ 0.798410432046075 0.000000000000000 2.395231296138225
+ 2.395231296138225 0.000000000000000 -0.798410432046075
+ 1.596820864092150 1.785300000000000 0.798410432046075
+ 1.596820864092150 -1.785300000000000 0.798410432046075
+</PRE>
+</HTML>
diff --git a/doc/doc2/fix_phonon.html b/doc/doc2/fix_phonon.html
new file mode 100644
index 000000000..3193e18d9
--- /dev/null
+++ b/doc/doc2/fix_phonon.html
@@ -0,0 +1,221 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix phonon command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>phonon = style name of this fix command
+
+<LI>N = measure the Green's function every this many timesteps
+
+<LI>Noutput = output the dynamical matrix every this many measurements
+
+<LI>Nwait = wait this many timesteps before measuring
+
+<LI>map_file = <I>file</I> or <I>GAMMA</I>
+
+<PRE> <I>file</I> is the file that contains the mapping info between atom ID and the lattice indices.
+</PRE>
+<PRE> <I>GAMMA</I> flags to treate the whole simulation box as a unit cell, so that the mapping
+ info can be generated internally. In this case, dynamical matrix at only the gamma-point
+ will/can be evaluated.
+</PRE>
+<LI>prefix = prefix for output files
+
+<LI>one or none keyword/value pairs may be appended
+
+<LI>keyword = <I>sysdim</I> or <I>nasr</I>
+
+<PRE> <I>sysdim</I> value = d
+ d = dimension of the system, usually the same as the MD model dimension
+ <I>nasr</I> value = n
+ n = number of iterations to enforce the acoustic sum rule
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
+fix 1 all phonon 20 5000 200000 map.in EAM3D
+fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Calculate the dynamical matrix from molecular dynamics simulations
+based on fluctuation-dissipation theory for a group of atoms.
+</P>
+<P>Consider a crystal with <I>N</I> unit cells in three dimensions labelled <I>l
+= (l<sub>1</sub>,l<sub>2</sub>,l<sub>3</sub>)</I> where <I>l<sub>i</sub></I>
+are integers. Each unit cell is defined by three linearly independent
+vectors <B>a</B><sub>1</sub>, <B>a</B><sub>2</sub>, <B>a</B><sub>3</sub> forming a
+parallelipiped, containing <I>K</I> basis atoms labelled <I>k</I>.
+</P>
+<P>Based on fluctuation-dissipation theory, the force constant
+coefficients of the system in reciprocal space are given by
+(<A HREF = "#Campana">Campa&ntilde;&aacute;</A> , <A HREF = "#Kong">Kong</A>)
+<center><b>&Phi;</b><sub>k&alpha;,k'&beta;</sub>(<b>q</b>) =
+k<sub>B</sub>T
+<b>G</b><sup>-1</sup><sub>k&alpha;,k'&beta;</sub>(<b>q</b>),</center>
+</P>
+<P>where <B>G</B> is the Green's functions coefficients given by
+</P>
+<center><b>G</b><sub>k&alpha;,k'&beta;</sub>(<b>q</b>) =
+<<b>u</b><sub>k&alpha;</sub>(<b>q</b>)&#149;<b>u</b><sub>k'&beta;</sub><sup>*</sup>(<b>q</b>)>,</center>
+
+<P>where <...> denotes the ensemble average, and
+<center><B>u</B><sub>k&alpha;</sub>(<b>q</b>) = &sum;<sub>l</sub>
+<b>u</b><sub>lk&alpha;</sub> exp(i<B>qr</B><sub>l</sub>)</center>
+</P>
+<P>is the &alpha; component of the atomic displacement for the <I>k</I>th atom
+in the unit cell in reciprocal space at <B>q</B>. In practice, the Green's
+functions coefficients can also be measured according to the following
+formula,
+</P>
+<center><b>G</b><sub>k&alpha;,k'&beta;</sub>(<b>q</b>) =
+<<b>R</b><sub>k&alpha;</sub>(<b>q</b>)&#149;<b>R</b><sup>*</sup><sub>k'&beta;</sub>(<b>q</b>)>
+- <<b>R</b>><sub>k&alpha;</sub>(<b>q</b>)&#149;<<b>R</b>><sup>*</sup><sub>k'&beta;</sub>(<b>q</b>),
+</center>
+
+<P>where <B>R</B> is the instantaneous positions of atoms, and <<B>R</B>> is the
+averaged atomic positions. It gives essentially the same results as
+the displacement method and is easier to implement in an MD code.
+</P>
+<P>Once the force constant matrix is known, the dynamical matrix <B>D</B> can
+then be obtained by
+</P>
+<center><b>D</b><sub>k&alpha;, k'&beta;</sub>(<b>q</b>) = (m<sub>k</sub>m<sub>k'</sub>)<sup>-1/2</sup> <b>&Phi;</b><sub>k&alpha;,k'&beta;</sub>(<b>q</b>)</center>
+
+<P>whose eigenvalues are exactly the phonon frequencies at <B>q</B>.
+</P>
+<P>This fix uses positions of atoms in the specified group and calculates
+two-point correlations. To achieve this. the positions of the atoms
+are examined every <I>Nevery</I> steps and are Fourier-transformed into
+reciprocal space, where the averaging process and correlation
+computation is then done. After every <I>Noutput</I> measurements, the
+matrix <B>G</B>(<B>q</B>) is calculated and inverted to obtain the elastic
+stiffness coefficients. The dynamical matrices are then constructed
+and written to <I>prefix</I>.bin.timestep files in binary format and to the
+file <I>prefix</I>.log for each wavevector <B>q</B>.
+</P>
+<P>A detailed description of this method can be found in
+(<A HREF = "#Kong2011">Kong2011</A>).
+</P>
+<P>The <I>sysdim</I> keyword is optional. If specified with a value smaller
+than the dimensionality of the LAMMPS simulation, its value is used
+for the dynamical matrix calculation. For example, using LAMMPS ot
+model a 2D or 3D system, the phonon dispersion of a 1D atomic chain
+can be computed using <I>sysdim</I> = 1.
+</P>
+<P>The <I>nasr</I> keyword is optional. An iterative procedure is employed to
+enforce the acoustic sum rule on &Phi; at &Gamma;, and the number
+provided by keyword <I>nasr</I> gives the total number of iterations. For a
+system whose unit cell has only one atom, <I>nasr</I> = 1 is sufficient;
+for other systems, <I>nasr</I> = 10 is typically sufficient.
+</P>
+<P>The <I>map_file</I> contains the mapping information between the lattice
+indices and the atom IDs, which tells the code which atom sits at
+which lattice point; the lattice indices start from 0. An auxiliary
+code, <A HREF = "http://code.google.com/p/latgen">latgen</A>, can be employed to
+generate the compatible map file for various crystals.
+</P>
+<P>In case one simulates an aperiodic system, where the whole simulation box
+is treated as a unit cell, one can set <I>map_file</I> as <I>GAMMA</I>, so that the mapping
+info will be generated internally and a file is not needed. In this case, the
+dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
+mind that fix-phonon is designed for cyrstals, it will be inefficient and
+even degrade the performance of lammps in case the unit cell is too large.
+</P>
+<P>The calculated dynamical matrix elements are written out in
+<A HREF = "units.html">energy/distance^2/mass</A> units. The coordinates for <I>q</I>
+points in the log file is in the units of the basis vectors of the
+corresponding reciprocal lattice.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to change the temperature compute from thermo_temp
+to the one that reflects the true temperature of atoms in the group.
+</P>
+<P>No global scalar or vector or per-atom quantities are stored by this
+fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
+</P>
+<P>Instead, this fix outputs its initialization information (including
+mapping information) and the calculated dynamical matrices to the file
+<I>prefix</I>.log, with the specified <I>prefix</I>. The dynamical matrices are
+also written to files <I>prefix</I>.bin.timestep in binary format. These
+can be read by the post-processing tool in tools/phonon to compute the
+phonon density of states and/or phonon dispersion curves.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords
+of the <A HREF = "run.html">run</A> command.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix assumes a crystalline system with periodical lattice. The
+temperature of the system should not exceed the melting temperature to
+keep the system in its solid state.
+</P>
+<P>This fix is part of the USER-PHONON package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix requires LAMMPS be built with an FFT library. See the
+<A HREF = "Section_start.html#start_2">Making LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_msd.html">compute msd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are sysdim = the same dimemsion as specified by
+the <A HREF = "dimension">dimension</A> command, and nasr = 20.
+</P>
+<HR>
+
+<A NAME = "Campana"></A>
+
+<P><B>(Campa&ntilde;&aacute;)</B> C. Campa&ntilde;&aacute; and
+M. H. M&uuml;ser, <I>Practical Green's function approach to the
+simulation of elastic semi-infinite solids</I>, <A HREF = "http://dx.doi.org/10.1103/PhysRevB.74.075420">Phys. Rev. B [74],
+075420 (2006)</A>
+</P>
+<A NAME = "Kong"></A>
+
+<P><B>(Kong)</B> L.T. Kong, G. Bartels, C. Campa&ntilde;&aacute;,
+C. Denniston, and Martin H. M&uuml;ser, <I>Implementation of Green's
+function molecular dynamics: An extension to LAMMPS</I>, <A HREF = "http://dx.doi.org/10.1016/j.cpc.2008.12.035">Computer
+Physics Communications [180](6):1004-1010
+(2009).</A>
+</P>
+<P>L.T. Kong, C. Denniston, and Martin H. M&uuml;ser,
+<I>An improved version of the Green's function molecular dynamics
+method</I>, <A HREF = "http://dx.doi.org/10.1016/j.cpc.2010.10.006">Computer Physics Communications [182](2):540-541
+(2011).</A>
+</P>
+<A NAME = "Kong2011"></A>
+
+<P><B>(Kong2011)</B> L.T. Kong, <I>Phonon dispersion measured directly from
+molecular dynamics simulations</I>, <A HREF = "http://dx.doi.org/10.1016/j.cpc.2011.04.019">Computer Physics Communications
+[182](10):2201-2207,
+(2011).</A>
+</P>
+</HTML>
diff --git a/doc/doc2/fix_pimd.html b/doc/doc2/fix_pimd.html
new file mode 100644
index 000000000..44da3e9b4
--- /dev/null
+++ b/doc/doc2/fix_pimd.html
@@ -0,0 +1,195 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix pimd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID pimd keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>pimd = style name of this fix command
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>method</I> or <I>fmass</I> or <I>sp</I> or <I>temp</I> or <I>nhc</I>
+
+<PRE> <I>method</I> value = <I>pimd</I> or <I>nmpimd</I> or <I>cmd</I>
+ <I>fmass</I> value = scaling factor on mass
+ <I>sp</I> value = scaling factor on Planck constant
+ <I>temp</I> value = temperature (temperarate units)
+ <I>nhc</I> value = Nc = number of chains in Nose-Hoover thermostat
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command performs quantum molecular dynamics simulations based on
+the Feynman path integral to include effects of tunneling and
+zero-point motion. In this formalism, the isomorphism of a quantum
+partition function for the original system to a classical partition
+function for a ring-polymer system is exploited, to efficiently sample
+configurations from the canonical ensemble <A HREF = "#Feynman">(Feynman)</A>.
+The classical partition function and its components are given
+by the following equations:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_pimd.jpg">
+</CENTER>
+<P>The interested user is referred to any of the numerous references on
+this methodology, but briefly, each quantum particle in a path
+integral simulation is represented by a ring-polymer of P quasi-beads,
+labeled from 1 to P. During the simulation, each quasi-bead interacts
+with beads on the other ring-polymers with the same imaginary time
+index (the second term in the effective potential above). The
+quasi-beads also interact with the two neighboring quasi-beads through
+the spring potential in imaginary-time space (first term in effective
+potential). To sample the canonical ensemble, a Nose-Hoover massive
+chain thermostat is applied <A HREF = "#Tuckerman">(Tuckerman)</A>. With the
+massive chain algorithm, a chain of NH thermostats is coupled to each
+degree of freedom for each quasi-bead. The keyword <I>temp</I> sets the
+target temperature for the system and the keyword <I>nhc</I> sets the
+number <I>Nc</I> of thermostats in each chain. For example, for a
+simulation of N particles with P beads in each ring-polymer, the total
+number of NH thermostats would be 3 x N x P x Nc.
+</P>
+<P>IMPORTANT NOTE: This fix implements a complete velocity-verlet
+integrator combined with NH massive chain thermostat, so no
+other time integration fix should be used.
+</P>
+<P>The <I>method</I> keyword determines what style of PIMD is performed. A
+value of <I>pimd</I> is standard PIMD. A value of <I>nmpimd</I> is for
+normal-mode PIMD. A value of <I>cmd</I> is for centroid molecular dynamics
+(CMD). The difference between the styles is as follows.
+</P>
+<P>In standard PIMD, the value used for a bead's fictitious mass is
+arbitrary. A common choice is to use Mi = m/P, which results in the
+mass of the entire ring-polymer being equal to the real quantum
+particle. But it can be difficult to efficiently integrate the
+equations of motion for the stiff harmonic interactions in the ring
+polymers.
+</P>
+<P>A useful way to resolve this issue is to integrate the equations of
+motion in a normal mode representation, using Normal Mode
+Path-Integral Molecular Dynamics (NMPIMD) <A HREF = "#Cao1">(Cao1)</A>. In NMPIMD,
+the NH chains are attached to each normal mode of the ring-polymer and
+the fictitious mass of each mode is chosen as Mk = the eigenvalue of
+the Kth normal mode for k > 0. The k = 0 mode, referred to as the
+zero-frequency mode or centroid, corresponds to overall translation of
+the ring-polymer and is assigned the mass of the real particle.
+</P>
+<P>Motion of the centroid can be effectively uncoupled from the other
+normal modes by scaling the fictitious masses to achieve a partial
+adiabatic separation. This is called a Centroid Molecular Dynamics
+(CMD) approximation <A HREF = "#Cao2">(Cao2)</A>. The time-evolution (and resulting
+dynamics) of the quantum particles can be used to obtain centroid time
+correlation functions, which can be further used to obtain the true
+quantum correlation function for the original system. The CMD method
+also uses normal modes to evolve the system, except only the k > 0
+modes are thermostatted, not the centroid degrees of freedom.
+</P>
+<P>The keyword <I>fmass</I> sets a further scaling factor for the fictitious
+masses of beads, which can be used for the Partial Adiabatic CMD
+<A HREF = "#Hone">(Hone)</A>, or to be set as P, which results in the fictitious
+masses to be equal to the real particle masses.
+</P>
+<P>The keyword <I>sp</I> is a scaling factor on Planck's constant, which can
+be useful for debugging or other purposes. The default value of 1.0
+is appropriate for most situations.
+</P>
+<P>The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
+as described in <A HREF = "#Calhoun">(Calhoun)</A>. In LAMMPS this is done by using
+<A HREF = "Section_howto.html#howto_5">multi-replica feature</A> in LAMMPS, where
+each quasi-particle system is stored and simulated on a separate
+partition of processors. The following diagram illustrates this
+approach. The original system with 2 ring polymers is shown in red.
+Since each ring has 4 quasi-beads (imaginary time slices), there are 4
+replicas of the system, each running on one of the 4 partitions of
+processors. Each replica (shown in green) owns one quasi-bead in each
+ring.
+</P>
+<CENTER><IMG SRC = "JPG/pimd.jpg">
+</CENTER>
+<P>To run a PIMD simulation with M quasi-beads in each ring polymer using
+N MPI tasks for each partition's domain-decomposition, you would use P
+= MxN processors (cores) and run the simulation as follows:
+</P>
+<PRE>mpirun -np P lmp_mpi -partition MxN -in script
+</PRE>
+<P>Note that in the LAMMPS input script for a multi-partition simulation,
+it is often very useful to define a <A HREF = "variable.html">uloop-style
+variable</A> such as
+</P>
+<PRE>variable ibead uloop M pad
+</PRE>
+<P>where M is the number of quasi-beads (partitions) used in the
+calculation. The uloop variable can then be used to manage I/O
+related tasks for each of the partitions, e.g.
+</P>
+<PRE>dump dcd all dcd 10 system_${ibead}.dcd
+restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
+read_restart system_${ibead}.restart2
+</PRE>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>A PIMD simulation can be initialized with a single data file read via
+the <A HREF = "read_data.html">read_data</A> command. However, this means all
+quasi-beads in a ring polymer will have identical positions and
+velocities, resulting in identical trajectories for all quasi-beads.
+To avoid this, users can simply initialize velocities with different
+random number seeds assigned to each partition, as defined by the
+uloop variable, e.g.
+</P>
+<PRE>velocity all create 300.0 1234${ibead} rot yes dist gaussian
+</PRE>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
+and nhc = 2.
+</P>
+<HR>
+
+<A NAME = "Feynman"></A>
+
+<P><B>(Feynman)</B> R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
+Path Integrals, McGraw-Hill, New York (1965).
+</P>
+<A NAME = "Tuckerman"></A>
+
+<P><B>(Tuckerman)</B> M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).
+</P>
+<A NAME = "Cao1"></A>
+
+<P><B>(Cao1)</B> J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
+</P>
+<A NAME = "Cao2"></A>
+
+<P><B>(Cao2)</B> J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).
+</P>
+<A NAME = "Hone"></A>
+
+<P><B>(Hone)</B> T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
+154103 (2006).
+</P>
+<A NAME = "Calhoun"></A>
+
+<P><B>(Calhoun)</B> A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
+415 (1996).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_planeforce.html b/doc/doc2/fix_planeforce.html
new file mode 100644
index 000000000..2ef66d5a0
--- /dev/null
+++ b/doc/doc2/fix_planeforce.html
@@ -0,0 +1,56 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix planeforce command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID planeforce x y z
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>planeforce = style name of this fix command
+<LI>x y z = 3-vector that is normal to the plane
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix hold boundary planeforce 1.0 0.0 0.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Adjust the forces on each atom in the group so that only the
+components of force in the plane specified by the normal vector
+(x,y,z) remain. This is done by subtracting out the component of
+force perpendicular to the plane.
+</P>
+<P>If the initial velocity of the atom is 0.0 (or in the plane), then it
+should continue to move in the plane thereafter.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_lineforce.html">fix lineforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_poems.html b/doc/doc2/fix_poems.html
new file mode 100644
index 000000000..0bc381f4e
--- /dev/null
+++ b/doc/doc2/fix_poems.html
@@ -0,0 +1,146 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix poems
+</H3>
+<P>Syntax:
+</P>
+<PRE>fix ID group-ID poems keyword values
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>poems = style name of this fix command
+
+<LI>keyword = <I>group</I> or <I>file</I> or <I>molecule</I>
+
+<PRE> <I>group</I> values = list of group IDs
+ <I>molecule</I> values = none
+ <I>file</I> values = filename
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 fluid poems group clump1 clump2 clump3
+fix 3 fluid poems file cluster.list
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Treats one or more sets of atoms as coupled rigid bodies. This means
+that each timestep the total force and torque on each rigid body is
+computed and the coordinates and velocities of the atoms are updated
+so that the collection of bodies move as a coupled set. This can be
+useful for treating a large biomolecule as a collection of connected,
+coarse-grained particles.
+</P>
+<P>The coupling, associated motion constraints, and time integration is
+performed by the software package <A HREF = "http://www.rpi.edu/~anderk5/lab">Parallelizable Open source
+Efficient Multibody Software (POEMS)</A> which computes the
+constrained rigid-body motion of articulated (jointed) multibody
+systems <A HREF = "#Anderson">(Anderson)</A>. POEMS was written and is distributed
+by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
+and other members of his group at Rensselaer Polytechnic Institute
+(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
+copyright information on POEMS and other details, please refer to the
+documents in the poems directory distributed with LAMMPS.
+</P>
+
+
+<P>This fix updates the positions and velocities of the rigid atoms with
+a constant-energy time integration, so you should not update the same
+atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
+</P>
+<P>Each body must have a non-degenerate inertia tensor, which means if
+must contain at least 3 non-collinear atoms. Which atoms are in which
+bodies can be defined via several options.
+</P>
+<P>For option <I>group</I>, each of the listed groups is treated as a rigid
+body. Note that only atoms that are also in the fix group are
+included in each rigid body.
+</P>
+<P>For option <I>molecule</I>, each set of atoms in the group with a different
+molecule ID is treated as a rigid body.
+</P>
+<P>For option <I>file</I>, sets of atoms are read from the specified file and
+each set is treated as a rigid body. Each line of the file specifies
+a rigid body in the following format:
+</P>
+<P>ID type atom1-ID atom2-ID atom3-ID ...
+</P>
+<P>ID as an integer from 1 to M (the number of rigid bodies). Type is
+any integer; it is not used by the fix poems command. The remaining
+arguments are IDs of atoms in the rigid body, each typically from 1 to
+N (the number of atoms in the system). Only atoms that are also in
+the fix group are included in each rigid body. Blank lines and lines
+that begin with '#' are skipped.
+</P>
+<P>A connection between a pair of rigid bodies is inferred if one atom is
+common to both bodies. The POEMS solver treats that atom as a
+spherical joint with 3 degrees of freedom. Currently, a collection of
+bodies can only be connected by joints as a linear chain. The entire
+collection of rigid bodies can represent one or more chains. Other
+connection topologies (tree, ring) are not allowed, but will be added
+later. Note that if no joints exist, it is more efficient to use the
+<A HREF = "fix_rigid.html">fix rigid</A> command to simulate the system.
+</P>
+<P>When the poems fix is defined, it will print out statistics on the
+total # of clusters, bodies, joints, atoms involved. A cluster in
+this context means a set of rigid bodies connected by joints.
+</P>
+<P>For computational efficiency, you should turn off pairwise and bond
+interactions within each rigid body, as they no longer contribute to
+the motion. The "neigh_modify exclude" and "delete_bonds" commands
+can be used to do this if each rigid body is a group.
+</P>
+<P>For computational efficiency, you should only define one fix poems
+which includes all the desired rigid bodies. LAMMPS will allow
+multiple poems fixes to be defined, but it is more expensive.
+</P>
+<P>The degrees-of-freedom removed by coupled rigid bodies are accounted
+for in temperature and pressure computations. Similarly, the rigid
+body contribution to the pressure virial is also accounted for. The
+latter is only correct if forces within the bodies have been turned
+off, and there is only a single fix poems defined.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the POEMS package. It is only enabled if LAMMPS
+was built with that package, which also requires the POEMS library be
+built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
+<A HREF = "neigh_modify.html">neigh_modify</A> exclude
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Anderson"></A>
+
+<P><B>(Anderson)</B> Anderson, Mukherjee, Critchley, Ziegler, and Lipton
+"POEMS: Parallelizable Open-source Efficient Multibody Software ",
+Engineering With Computers (2006). (<A HREF = "http://dx.doi.org/10.1007/s00366-006-0026-x">link to
+paper</A>)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_pour.html b/doc/doc2/fix_pour.html
new file mode 100644
index 000000000..7ce96622d
--- /dev/null
+++ b/doc/doc2/fix_pour.html
@@ -0,0 +1,242 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix pour command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID pour N type seed keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>pour = style name of this fix command
+
+<LI>N = # of atoms to insert
+
+<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
+
+<LI>seed = random # seed (positive integer)
+
+<LI>one or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I> or <I>mol</I> or <I>rigid</I> or <I>shake</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region to use as insertion volume
+ <I>diam</I> values = dstyle args
+ dstyle = <I>one</I> or <I>range</I> or <I>poly</I>
+ <I>one</I> args = D
+ D = single diameter for inserted particles (distance units)
+ <I>range</I> args = Dlo Dhi
+ Dlo,Dhi = range of diameters for inserted particles (distance units)
+ <I>poly</I> args = Npoly D1 P1 D2 P2 ...
+ Npoly = # of (D,P) pairs
+ D1,D2,... = diameter for subset of inserted particles (distance units)
+ P1,P2,... = percentage of inserted particles with this diameter (0-1)
+ <I>vol</I> values = fraction Nattempt
+ fraction = desired volume fraction for filling insertion volume
+ Nattempt = max # of insertion attempts per atom
+ <I>rate</I> value = V
+ V = z velocity (3d) or y velocity (2d) at which
+ insertion volume moves (velocity units)
+ <I>vel</I> values (3d) = vxlo vxhi vylo vyhi vz
+ <I>vel</I> values (2d) = vxlo vxhi vy
+ vxlo,vxhi = range of x velocities for inserted particles (velocity units)
+ vylo,vyhi = range of y velocities for inserted particles (velocity units)
+ vz = z velocity (3d) assigned to inserted particles (velocity units)
+ vy = y velocity (2d) assigned to inserted particles (velocity units)
+ <I>mol</I> value = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+ <I>molfrac</I> values = f1 f2 ... fN
+ f1 to fN = relative probability of creating each of N molecules in template-ID
+ <I>rigid</I> value = fix-ID
+ fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
+ <I>shake</I> value = fix-ID
+ fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 all pour 1000 2 29494 region myblock
+fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1
+fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
+fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Insert finite-size particles or molecules into the simulation box
+every few timesteps within a specified region until N particles or
+molecules have been inserted. This is typically used to model the
+pouring of granular particles into a container under the influence of
+gravity. For the remainder of this doc page, a single inserted atom
+or molecule is referred to as a "particle".
+</P>
+<P>If inserted particles are individual atoms, they are assigned the
+specified atom type. If they are molecules, the type of each atom in
+the inserted molecule is specified in the file read by the
+<A HREF = "molecule.html">molecule</A> command, and those values are added to the
+specified atom type. E.g. if the file specifies atom types 1,2,3, and
+those are the atom types you want for inserted molecules, then specify
+<I>type</I> = 0. If you specify <I>type</I> = 2, the in the inserted molecule
+will have atom types 3,4,5.
+</P>
+<P>All atoms in the inserted particle are assigned to two groups: the
+default group "all" and the group specified in the fix pour command
+(which can also be "all").
+</P>
+<P>This command must use the <I>region</I> keyword to define an insertion
+volume. The specified region must have been previously defined with a
+<A HREF = "region.html">region</A> command. It must be of type <I>block</I> or a z-axis
+<I>cylinder</I> and must be defined with side = <I>in</I>. The cylinder style
+of region can only be used with 3d simulations.
+</P>
+<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
+specifies a <I>template-ID</I> previously defined using the
+<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
+molecule. The coordinates, atom types, center-of-mass, moments of
+inertia, etc, as well as any bond/angle/etc and special neighbor
+information for the molecule can be specified in the molecule file.
+See the <A HREF = "molecule.html">molecule</A> command for details. The only
+settings required to be in this file are the coordinates and types of
+atoms in the molecule.
+</P>
+<P>If the molecule template contains more than one molecule, the relative
+probability of depositing each molecule can be specified by the
+<I>molfrac</I> keyword. N relative probablities, each from 0.0 to 1.0, are
+specified, where N is the number of molecules in the template. Each
+time a molecule is inserted, a random number is used to sample from
+the list of relative probabilities. The N values must sum to 1.0.
+</P>
+<P>If you wish to insert molecules via the <I>mol</I> keyword, that will be
+treated as rigid bodies, use the <I>rigid</I> keyword, specifying as its
+value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A>
+command which also appears in your input script.
+</P>
+<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
+their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
+specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
+shake</A> command which also appears in your input script.
+</P>
+<P>Each timestep particles are inserted, they are placed randomly inside
+the insertion volume so as to mimic a stream of poured particles. If
+they are molecules they are also oriented randomly. Each atom in the
+particle is tested for overlaps with existing particles, including
+effects due to periodic boundary conditions if applicable. If an
+overlap is detected, another random insertion attempt is made; see the
+<I>vol</I> keyword discussion below. The larger the volume of the
+insertion region, the more particles that can be inserted at any one
+timestep. Particles are inserted again after enough time has elapsed
+that the previously inserted particles fall out of the insertion
+volume under the influence of gravity. Insertions continue every so
+many timesteps until the desired # of particles has been inserted.
+</P>
+<P>All other keywords are optional with defaults as shown below.
+</P>
+<P>The <I>diam</I> option is only used when inserting atoms and specifes the
+diameters of inserted particles. There are 3 styles: <I>one</I>, <I>range</I>,
+or <I>poly</I>. For <I>one</I>, all particles will have diameter <I>D</I>. For
+<I>range</I>, the diameter of each particle will be chosen randomly and
+uniformly between the specified <I>Dlo</I> and <I>Dhi</I> bounds. For <I>poly</I>, a
+series of <I>Npoly</I> diameters is specified. For each diameter a
+percentage value from 0.0 to 1.0 is also specified. The <I>Npoly</I>
+percentages must sum to 1.0. For the example shown above with "diam 2
+0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7
+or 1.5. 40% of the particles will be small; 60% will be large.
+</P>
+<P>Note that for molecule insertion, the diameters of individual atoms in
+the molecule can be specified in the file read by the
+<A HREF = "molecule.html">molecule</A> command. If not specified, the diameter of
+each atom in the molecule has a default diameter of 1.0.
+</P>
+<P>The <I>dens</I> and <I>vel</I> options enable inserted particles to have a range
+of densities or xy velocities. The specific values for a particular
+inserted particle will be chosen randomly and uniformly between the
+specified bounds. The <I>vz</I> or <I>vy</I> value for option <I>vel</I> assigns a
+z-velocity (3d) or y-velocity (2d) to each inserted particle.
+</P>
+<P>The <I>vol</I> option specifies what volume fraction of the insertion
+volume will be filled with particles. For particles with a size
+specified by the <I>diam range</I> keyword, they are assumed to all be of
+maximum diamter <I>Dhi</I> for purposes of computing their contribution to
+the volume fraction.
+</P>
+<P>The higher the volume fraction value, the more particles are inserted
+each timestep. Since inserted particles cannot overlap, the maximum
+volume fraction should be no higher than about 0.6. Each timestep
+particles are inserted, LAMMPS will make up to a total of M tries to
+insert the new particles without overlaps, where M = # of inserted
+particles * Nattempt. If LAMMPS is unsuccessful at completing all
+insertions, it prints a warning.
+</P>
+<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
+or y direction (2d). This enables pouring particles from a
+successively higher height over time.
+</P>
+<P>IMPORTANT NOTE: If you are monitoring the temperature of a system
+where the particle count is changing due to adding particles, you
+typically should use the <A HREF = "compute_modify.html">compute_modify dynamic
+yes</A> command for the temperature compute you are
+using.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. This means you must be careful when restarting a
+pouring simulation, when the restart file was written in the middle of
+the pouring operation. Specifically, you should use a new fix pour
+command in the input script for the restarted simulation that
+continues the operation. You will need to adjust the arguments of the
+original fix pour command to do this.
+</P>
+<P>Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place. However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix pour parameters
+appropriately.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the GRANULAR package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>For 3d simulations, a gravity fix in the -z direction must be defined
+for use in conjunction with this fix. For 2d simulations, gravity
+must be defined in the -y direction.
+</P>
+<P>The specified insertion region cannot be a "dynamic" region, as
+defined by the <A HREF = "region.html">region</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_gravity.html">fix_gravity</A>,
+<A HREF = "region.html">region</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>Insertions are performed for individual particles, i.e. no <I>mol</I>
+setting is defined. If the <I>mol</I> keyword is used, the default for
+<I>molfrac</I> is an equal probabilities for all molecules in the template.
+Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
+0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_press_berendsen.html b/doc/doc2/fix_press_berendsen.html
new file mode 100644
index 000000000..673c1b343
--- /dev/null
+++ b/doc/doc2/fix_press_berendsen.html
@@ -0,0 +1,227 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix press/berendsen command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID press/berendsen keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>press/berendsen = style name of this fix command
+
+<PRE>one or more keyword value pairs may be appended
+keyword = <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>dilate</I> or <I>modulus</I>
+ <I>iso</I> or <I>aniso</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ <I>x</I> or <I>y</I> or <I>z</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+ Pdamp = stress damping parameter (time units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>modulus</I> value = bulk modulus of system (pressure units)
+ <I>dilate</I> value = <I>all</I> or <I>partial</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all press/berendsen iso 0.0 0.0 1000.0
+fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the pressure of the system by using a Berendsen barostat
+<A HREF = "#Berendsen">(Berendsen)</A>, which rescales the system volume and
+(optionally) the atoms coordinates within the simulation box every
+timestep.
+</P>
+<P>Regardless of what atoms are in the fix group, a global pressure is
+computed for all atoms. Similarly, when the size of the simulation
+box is changed, all atoms are re-scaled to new positions, unless the
+keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
+only the atoms in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of atoms in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_nh.html">fix
+nph</A> commands which perform Nose/Hoover barostatting AND
+time integration, this fix does NOT perform time integration. It only
+modifies the box size and atom coordinates to effect barostatting.
+Thus you must use a separate time integration fix, like <A HREF = "fix_nve.html">fix
+nve</A> or <A HREF = "fix_nh.html">fix nvt</A> to actually update the
+positions and velocities of atoms. This fix can be used in
+conjunction with thermostatting fixes to control the temperature, such
+as <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+</P>
+<HR>
+
+<P>The barostat is specified using one or more of the <I>iso</I>, <I>aniso</I>,
+<I>x</I>, <I>y</I>, <I>z</I>, and <I>couple</I> keywords. These keywords give you the
+ability to specify the 3 diagonal components of an external stress
+tensor, and to couple various of these components together so that the
+dimensions they represent are varied together during a
+constant-pressure simulation. Unlike the <A HREF = "fix_nh.html">fix npt</A> and
+<A HREF = "fix_nh.html">fix nph</A> commands, this fix cannot be used with triclinic
+(non-orthogonal) simulation boxes to control all 6 components of the
+general pressure tensor.
+</P>
+<P>The target pressures for each of the 3 diagonal components of the
+stress tensor can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>,
+keywords, which correspond to the 3 simulation box dimensions. For
+each component, the external pressure or tensor component at each
+timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
+If a target pressure is specified for a component, then the
+corresponding box dimension will change during a simulation. For
+example, if the <I>y</I> keyword is used, the y-box length will change. A
+box dimension will not change if that component is not specified,
+although you have the option to change that dimension via the <A HREF = "fix_deform.html">fix
+deform</A> command.
+</P>
+<P>For all barostat keywords, the <I>Pdamp</I> parameter determines the time
+scale on which pressure is relaxed. For example, a value of 1000.0
+means to relax the pressure in a timespan of (roughly) 1000 time units
+(tau or fmsec or psec - see the <A HREF = "units.html">units</A> command).
+</P>
+<P>IMPORTANT NOTE: The relaxation time is actually also a function of the
+bulk modulus of the system (inverse of isothermal compressibility).
+The bulk modulus has units of pressure and is the amount of pressure
+that would need to be applied (isotropically) to reduce the volume of
+the system by a factor of 2 (assuming the bulk modulus was a constant,
+independent of density, which it's not). The bulk modulus can be set
+via the keyword <I>modulus</I>. The <I>Pdamp</I> parameter is effectively
+multiplied by the bulk modulus, so if the pressure is relaxing faster
+than expected or desired, increasing the bulk modulus has the same
+effect as increasing <I>Pdamp</I>. The converse is also true. LAMMPS does
+not attempt to guess a correct value of the bulk modulus; it just uses
+10.0 as a default value which gives reasonable relaxation for a
+Lennard-Jones liquid, but will be way off for other materials and way
+too small for solids. Thus you should experiment to find appropriate
+values of <I>Pdamp</I> and/or the <I>modulus</I> when using this fix.
+</P>
+<HR>
+
+<P>The <I>couple</I> keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together. The value specified
+with the keyword determines which are coupled. For example, <I>xz</I>
+means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
+<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep. The
+<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
+be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
+dimension is simply ignored.
+</P>
+<HR>
+
+<P>The <I>iso</I> and <I>aniso</I> keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+</P>
+<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple xyz
+</PRE>
+<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
+independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple none
+</PRE>
+<HR>
+
+<P>This fix computes a temperature and pressure each timestep. To do
+this, the fix creates its own computes of style "temp" and "pressure",
+as if these commands had been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
+pressure</A> commands for details. Note that the
+IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is the same
+as the fix group.
+</P>
+<P>Note that these are NOT the computes used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
+and <I>thermo_press</I>. This means you can change the attributes of this
+fix's temperature or pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> or
+<I>thermo_press</I> will have no effect on this fix.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix. You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its temperature and pressure calculations. If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure. LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>No global or per-atom quantities are stored by this fix for access by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+</P>
+<P>This fix can ramp its target pressure over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension being adjusted by this fix must be periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nh.html">fix
+npt</A>, <A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>,
+<A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are dilate = all, modulus = 10.0 in units of
+pressure for whatever <A HREF = "units.html">units</A> are defined.
+</P>
+<HR>
+
+<A NAME = "Berendsen"></A>
+
+<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_print.html b/doc/doc2/fix_print.html
new file mode 100644
index 000000000..98b233769
--- /dev/null
+++ b/doc/doc2/fix_print.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix print command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID print N string keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>print = style name of this fix command
+
+<LI>N = print every N steps
+
+<LI>string = text string to print with optional variable names
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>file</I> or <I>append</I> or <I>screen</I> or <I>title</I>
+
+<PRE> <I>file</I> value = filename
+ <I>append</I> value = filename
+ <I>screen</I> value = <I>yes</I> or <I>no</I>
+ <I>title</I> value = string
+ string = text to print as 1st line of output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix extra all print 100 "Coords of marker atom = $x $y $z"
+fix extra all print 100 "Coords of marker atom = $x $y $z" file coord.txt
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Print a text string every N steps during a simulation run. This can
+be used for diagnostic purposes or as a debugging tool to monitor some
+quantity during a run. The text string must be a single argument, so
+it should be enclosed in double quotes if it is more than one word.
+If it contains variables it must be enclosed in double quotes to
+insure they are not evaluated when the input script line is read, but
+will instead be evaluated each time the string is printed.
+</P>
+<P>See the <A HREF = "variable.html">variable</A> command for a description of <I>equal</I>
+style variables which are the most useful ones to use with the fix
+print command, since they are evaluated afresh each timestep that the
+fix print line is output. Equal-style variables calculate formulas
+involving mathematical operations, atom properties, group properties,
+thermodynamic properties, global values calculated by a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>, or references to other
+<A HREF = "variable.html">variables</A>.
+</P>
+<P>If the <I>file</I> or <I>append</I> keyword is used, a filename is specified to
+which the output generated by this fix will be written. If <I>file</I> is
+used, then the filename is overwritten if it already exists. If
+<I>append</I> is used, then the filename is appended to if it already
+exists, or created if it does not exist.
+</P>
+<P>If the <I>screen</I> keyword is used, output by this fix to the screen and
+logfile can be turned on or off as desired.
+</P>
+<P>The <I>title</I> keyword allow specification of the string that will be
+printed as the first line of the output file, assuming the <I>file</I>
+keyword was used. By default, the title line is as follows:
+</P>
+<PRE># Fix print output for fix ID
+</PRE>
+<P>where ID is replaced with the fix-ID.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable</A>, <A HREF = "print.html">print</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are no file output, screen = yes, and title string
+as described above.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_property_atom.html b/doc/doc2/fix_property_atom.html
new file mode 100644
index 000000000..c17eb032c
--- /dev/null
+++ b/doc/doc2/fix_property_atom.html
@@ -0,0 +1,226 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix property/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID property/atom vec1 vec2 ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>property/atom = style name of this fix command
+
+<LI>vec1,vec2,... = <I>mol</I> or <I>q</I> or <I>i_name</I> or <I>d_name</I>
+
+<PRE> <I>mol</I> = molecule IDs
+ <I>q</I> = charge
+ <I>i_name</I> = new integer vector referenced by name
+ <I>d_name</I> = new floating-point vector referenced by name
+</PRE>
+<LI>zero of more keyword/value pairs may be appended
+
+<LI>keyword = <I>ghost</I>
+
+<PRE> <I>ghost</I> value = <I>no</I> or <I>yes</I> for whether ghost atom info in communicated
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all property/atom mol
+fix 1 all property/atom i_myflag1 i_myflag2
+fix 1 all property/atom d_sx d_sy d_sz
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Create one or more additional per-atom vectors to store information
+about atoms and to use during a simulation. The specified <I>group-ID</I>
+is ignored by this fix.
+</P>
+<P>The atom style used for a simulation defines a set of per-atom
+properties, as explained on the <A HREF = "atom_style.html">atom_style</A> and
+<A HREF = "read_data.html">read_data</A> doc pages. The latter command allows these
+properties to be defined for each atom in the system when a data file
+is read. This fix will augment the set of properties with new custom
+ones.
+</P>
+<P>This can be useful in at least two scenarios.
+</P>
+<P>If the atom style does not define molecule IDs or per-atom charge,
+they can be added using the <I>mol</I> or <I>q</I> keywords. This can be
+useful, e.g, to define "molecules" to use as rigid bodies with the
+<A HREF = "fix_rigid.html">fix rigid</A> command, or just to carry around an extra
+flag with the atoms (stored as a molecule ID). An alternative is to
+use an atom style that does define molecule IDs or charge or to use a
+hybrid atom style that combines two styles to allow for molecule IDs
+or charge, but that has 2 practical drawbacks. First it typically
+necessitates changing the format of the data file. And it may define
+additional properties that aren't needed such as bond lists, which has
+some overhead when there are no bonds.
+</P>
+<P>In the future, we may add additional per-atom properties similar to
+<I>mol</I> or <I>q</I>, which "turn-on" specific properties defined by some atom
+styles, so they can be used by atom styles that don't define them.
+</P>
+<P>More generally, the <I>i_name</I> and <I>d_name</I> vectors allow one or more
+new custom per-atom properties to be defined. Each name must be
+unique and can use alphanumeric or underscore characters. These
+vectors can store whatever values you decide are useful in your
+simulation. As explained below there are several ways to initialize
+and access and output these values, both via input script commands and
+in new code that you add to LAMMPS.
+</P>
+<P>This is effectively a simple way to add per-atom properties to a model
+without needing to write code for a new <A HREF = "atom_style.html">atom style</A>
+that defines the properties. Note however that implementing a new
+atom style allows new atom properties to be more tightly and
+seamlessly integrated with the rest of the code.
+</P>
+<P>The new atom properties encode values that migrate with atoms to new
+processors and are written to restart files. If you want the new
+properties to also be defined for ghost atoms, then use the <I>ghost</I>
+keyword with a value of <I>yes</I>. This will invoke extra communication
+when ghost atoms are created (at every re-neighboring) to insure the
+new properties are also defined for the ghost atoms.
+</P>
+<P>IMPORTANT NOTE: If you use this command with the <I>mol</I> or <I>charge</I>
+vectors than you most likely want to set <I>ghost</I> yes, since these
+properties are stored with ghost atoms if you use an
+<A HREF = "atom_style.html">atom_style</A> that defines them, and many LAMMPS
+operations that use molecule IDs or charge, such as neighbor lists and
+pair styles, will expect ghost atoms to have these valuse. LAMMPS
+will issue a warning it you define those vectors but do not set
+<I>ghost</I> yes.
+</P>
+<P>IMPORTANT NOTE: The properties for ghost atoms are not updated every
+timestep, but only once every few steps when neighbor lists are
+re-built. Thus the <I>ghost</I> keyword is suitable for static properties,
+like molecule IDs, but not for dynamic properties that change every
+step. For the latter, the code you add to LAMMPS to change the
+properties will also need to communicate their new values to/from
+ghost atoms, an operation that can be invoked from within a <A HREF = "pair_style.html">pair
+style</A> or <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A>
+that you write.
+</P>
+<HR>
+
+<P>This fix is one of a small number that can be defined in an input
+script before the simulation box is created or atoms are defined.
+This is so it can be used with the <A HREF = "read_data.html">read_data</A> command
+as described below.
+</P>
+<P>Per-atom properties that are defined by the <A HREF = "atom_style.html">atom
+style</A> are initialized when atoms are created, e.g. by
+the <A HREF = "read_data.html">read_data</A> or <A HREF = "create_atoms.html">create_atoms</A>
+commands. The per-atom properaties defined by this fix are not. So
+you need to initialize them explicitly. This can be done by the
+<A HREF = "read_data.html">read_data</A> command, using its <I>fix</I> keyword and
+passing it the fix-ID of this fix.
+</P>
+<P>Thus these commands:
+</P>
+<PRE>fix prop all property/atom mol d_flag
+read_data data.txt fix prop NULL Molecules
+</PRE>
+<P>would allow a data file to have a section like this:
+</P>
+<PRE>Molecules
+</PRE>
+<PRE>1 4 1.5
+2 4 3.0
+3 10 1.0
+4 10 1.0
+5 10 1.0
+...
+N 763 4.5
+</PRE>
+<P>where N is the number of atoms, and the first field on each line is
+the atom-ID, followed by a molecule-ID and a floating point value that
+will be stored in a new property called "flag". Note that the list of
+per-atom properties can be in any order.
+</P>
+<P>Another way of initializing the new properties is via the
+<A HREF = "set.html">set</A> command. For example, if you wanted molecules
+defined for every set of 10 atoms, based on their atom-IDs,
+these commands could be used:
+</P>
+<PRE>fix prop all property/atom mol
+variable cluster atom ((id-1)/10)+1
+set id * mol v_cluster
+</PRE>
+<P>The <A HREF = "variable.html">atom-style variable</A> will create values for atoms
+with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
+<A HREF = "set.html">set</A> commands assigns them to the molecule ID for each atom,
+they will be truncated to an integer value, so atoms 31-40 will all be
+assigned a molecule ID of 4.
+</P>
+<P>Note that <A HREF = "variable.html">atomfile-style variables</A> can also be used in
+place of atom-style variables, which means in this case that the
+molecule IDs could be read-in from a separate file and assinged by the
+<A HREF = "set.html">set</A> command. This allows you to initialize new per-atom
+properties in a completely general fashion.
+</P>
+<HR>
+
+<P>For new atom properties specified as <I>i_name</I> or <I>d_name</I>, the
+<A HREF = "compute_property_atom.html">compute property/atom</A> command can access
+their values. This means that the values can be output via the <A HREF = "dump.html">dump
+custom</A> command, accessed by fixes like <A HREF = "fix_ave_atom.html">fix
+ave/atom</A>, accessed by other computes like <A HREF = "compute_reduce.html">compute
+reduce</A>, or used in <A HREF = "variables">atom-style
+variables</A>.
+</P>
+<P>For example, these commands will output two new properties to a custom
+dump file:
+</P>
+<PRE>fix prop all property/atom i_flag1 d_flag2
+compute 1 all property/atom i_flag1 d_flag2
+dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
+</PRE>
+<HR>
+
+<P>If you wish to add new <A HREF = "pair_style.html">pair styles</A>,
+<A HREF = "fix.html">fixes</A>, or <A HREF = "compute.html">computes</A> that use the per-atom
+properties defined by this fix, see <A HREF = "Section_modify.html#mod_1">Section
+modify</A> of the manual which has some details
+on how the properties can be accessed from added classes.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the per-atom values it stores to <A HREF = "restart.html">binary restart
+files</A>, so that the values can be restored when a
+simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "set.html">set</A>, <A HREF = "compute_property_atom.html">compute
+property/atom</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default keyword values are ghost = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qbmsst.html b/doc/doc2/fix_qbmsst.html
new file mode 100644
index 000000000..376c73eed
--- /dev/null
+++ b/doc/doc2/fix_qbmsst.html
@@ -0,0 +1,232 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qbmsst command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID qbmsst dir shockvel keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>qbmsst = style name of this fix
+
+<LI>dir = <I>x</I> or <I>y</I> or <I>z</I>
+
+<LI>shockvel = shock velocity (strictly positive, velocity units)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>q</I> or <I>mu</I> or <I>p0</I> or <I>v0</I> or <I>e0</I> or <I>tscale</I> or <I>damp</I> or <I>seed</I>or <I>f_max</I> or <I>N_f</I> or <I>eta</I> or <I>beta</I> or <I>T_init</I>
+
+<PRE> <I>q</I> value = cell mass-like parameter (mass^2/distance^4 units)
+ <I>mu</I> value = artificial viscosity (mass/distance/time units)
+ <I>p0</I> value = initial pressure in the shock equations (pressure units)
+ <I>v0</I> value = initial simulation cell volume in the shock equations (distance^3 units)
+ <I>e0</I> value = initial total energy (energy units)
+ <I>tscale</I> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+ <I>damp</I> value = damping parameter (time units) inverse of friction <i>&gamma;</i>
+ <I>seed</I> value = random number seed (positive integer)
+ <I>f_max</I> value = upper cutoff frequency of the vibration spectrum (1/time units)
+ <I>N_f</I> value = number of frequency bins (positive integer)
+ <I>eta</I> value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
+ <I>beta</I> value = the quantum temperature is updated every beta time steps (positive integer)
+ <I>T_init</I> value = quantum temperature for the initial state (temperature units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
+fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
+</PRE>
+<P>Two example input scripts are given, including shocked alpha quartz
+and shocked liquid methane. The input script first equilibrate an
+initial state with the quantum thermal bath at the target temperature
+and then apply the qbmsst to simulate shock compression with quantum
+nuclear correction. The following two figures plot related quantities
+for shocked alpha quartz.
+</P>
+<CENTER><IMG SRC = "JPG/qbmsst_init.jpg">
+</CENTER>
+<P>Figure 1. Classical temperature <i>T</i><sup>cl</sup> = &sum;
+<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub> vs. time
+for coupling the alpha quartz initial state with the quantum thermal
+bath at target quantum temperature <i>T</i><sup>qm</sup> = 300 K. The
+NpH ensemble is used for time integration while QTB provides the
+colored random force. <i>T</i><sup>cl</sup> converges at the timescale
+of <I>damp</I> which is set to be 1 ps.
+</P>
+<CENTER><IMG SRC = "JPG/qbmsst_shock.jpg">
+</CENTER>
+<P>Figure 2. Quantum temperature and pressure vs. time for simulating
+shocked alpha quartz with the QBMSST. The shock propagates along the z
+direction. Restart of the QBMSST command is demonstrated in the
+example input script. Thermodynamic quantities stay continuous before
+and after the restart.
+</P>
+<P><B>Description:</B>
+</P>
+<P>This command performs the Quantum-Bath coupled Multi-Scale Shock
+Technique (QBMSST) integration. See <A HREF = "#Qi">(Qi)</A> for a detailed
+description of this method. The QBMSST provides description of the
+thermodynamics and kinetics of shock processes while incorporating
+quantum nuclear effects. The <I>shockvel</I> setting determines the steady
+shock velocity that will be simulated along direction <I>dir</I>.
+</P>
+<P>Quantum nuclear effects <A HREF = "fix_qtb.html">(fix qtb)</A> can be crucial
+especially when the temperature of the initial state is below the
+classical limit or there is a great change in the zero point energies
+between the initial and final states. Theoretical post processing
+quantum corrections of shock compressed water and methane have been
+reported as much as 30% of the temperatures <A HREF = "#Goldman">(Goldman)</A>. A
+self-consistent method that couples the shock to a quantum thermal
+bath described by a colored noise Langevin thermostat has been
+developed by Qi et al <A HREF = "#Qi">(Qi)</A> and applied to shocked methane. The
+onset of chemistry is reported to be at a pressure on the shock
+Hugoniot that is 40% lower than observed with classical molecular
+dynamics.
+</P>
+<P>It is highly recommended that the system be already in an equilibrium
+state with a quantum thermal bath at temperature of <I>T_init</I>. The fix
+command <A HREF = "fix_qtb.html">fix qtb</A> at constant temperature <I>T_init</I> could
+be used before applying this command to introduce self-consistent
+quantum nuclear effects into the initial state.
+</P>
+<P>The parameters <I>q</I>, <I>mu</I>, <I>e0</I>, <I>p0</I>, <I>v0</I> and <I>tscale</I> are described
+in the command <A HREF = "fix_msst.html">fix msst</A>. The values of <I>e0</I>, <I>p0</I>, or
+<I>v0</I> will be calculated on the first step if not specified. The
+parameter of <I>damp</I>, <I>f_max</I>, and <I>N_f</I> are described in the command
+<A HREF = "fix_qtb.html">fix qtb</A>.
+</P>
+<P>The fix qbmsst command couples the shock system to a quantum thermal
+bath with a rate that is proportional to the change of the total
+energy of the shock system, <i>etot</i> - <i>etot</i><sub>0</sub>.
+Here <i>etot</i> consists of both the system energy and a thermal
+term, see <A HREF = "#Qi">(Qi)</A>, and <i>etot</i><sub>0</sub> = <I>e0</I> is the
+initial total energy.
+</P>
+<P>The <I>eta</I> (<i>&eta;</i>) parameter is a unitless coupling constant
+between the shock system and the quantum thermal bath. A small <I>eta</I>
+value cannot adjust the quantum temperature fast enough during the
+temperature ramping period of shock compression while large <I>eta</I>
+leads to big temperature oscillation. A value of <I>eta</I> between 0.3 and
+1 is usually appropriate for simulating most systems under shock
+compression. We observe that different values of <I>eta</I> lead to almost
+the same final thermodynamic state behind the shock, as expected.
+</P>
+<P>The quantum temperature is updated every <I>beta</I> (<i>&beta;</i>) steps
+with an integration time interval <I>beta</I> times longer than the
+simulation time step. In that case, <i>etot</i> is taken as its
+average over the past <I>beta</I> steps. The temperature of the quantum
+thermal bath <i>T</i><sup>qm</sup> changes dynamically according to
+the following equation where &Delta;<i>t</i> is the MD time step and
+<i>&gamma;</i> is the friction constant which is equal to the inverse
+of the <I>damp</I> parameter.
+</P>
+<center><font size="4"> <i>dT</i><sup>qm</sup>/<i>dt =
+&gamma;&eta;</i>&sum;<i><sup>&beta;</sup><sub>l =
+1</sub></i>[<i>etot</i>(<i>t-l</i>&Delta;<i>t</i>)-<i>etot</i><sub>0</sub>]/<i>3&beta;Nk</i><sub>B</sub>
+</font></center>
+
+<P>The parameter <I>T_init</I> is the initial temperature of the quantum
+thermal bath and the system before shock loading.
+</P>
+<P>For all pressure styles, the simulation box stays orthorhombic in
+shape. Parrinello-Rahman boundary conditions (tilted box) are
+supported by LAMMPS, but are not implemented for QBMSST.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>Because the state of the random number generator is not written to
+<A HREF = "restart.html">binary restart files</A>, this fix cannot be restarted
+"exactly" in an uninterrupted fashion. However, in a statistical
+sense, a restarted simulation should produce similar behaviors of the
+system as if it is not interrupted. To achieve such a restart, one
+should write explicitly the same value for <I>q</I>, <I>mu</I>, <I>damp</I>, <I>f_max</I>,
+<I>N_f</I>, <I>eta</I>, and <I>beta</I> and set <I>tscale</I> = 0 if the system is
+compressed during the first run.
+</P>
+<P>The progress of the QBMSST can be monitored by printing the global
+scalar and global vector quantities computed by the fix. The global
+vector contains five values in this order:
+</P>
+<P>[<I>dhugoniot</I>, <I>drayleigh</I>, <I>lagrangian_speed</I>, <I>lagrangian_position</I>,
+<I>quantum_temperature</I>]
+</P>
+<OL><LI><I>dhugoniot</I> is the departure from the Hugoniot (temperature units).
+<LI><I>drayleigh</I> is the departure from the Rayleigh line (pressure units).
+<LI><I>lagrangian_speed</I> is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
+<LI><I>lagrangian_position</I> is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front.
+<LI><I>quantum_temperature</I> is the temperature of the quantum thermal bath <i>T</i><sup>qm</sup>.
+</OL>
+<P>To print these quantities to the log file with descriptive column
+headers, the following LAMMPS commands are suggested. Here the
+<A HREF = "fix_modify.html">fix_modify</A> energy command is also enabled to allow
+the thermo keyword <I>etotal</I> to print the quantity <i>etot</i>. See
+also the <A HREF = "thermo_style.html">thermo_style</A> command.
+</P>
+<PRE>fix fix_id all msst z
+fix_modify fix_id energy yes
+variable dhug equal f_fix_id[1]
+variable dray equal f_fix_id[2]
+variable lgr_vel equal f_fix_id[3]
+variable lgr_pos equal f_fix_id[4]
+variable T_qm equal f_fix_id[5]
+thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
+</PRE>
+<P>The global scalar under the entry f_fix_id is the quantity of thermo
+energy as an extra part of <i>etot</i>. This global scalar and the
+vector of 5 quantities can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. It is worth noting that the
+temp keyword under the <A HREF = "thermo_style.html">thermo_style</A> command print
+the instantaneous classical temperature <i>T</i><sup>cl</sup> as
+described in the command <A HREF = "fix_qtb.html">fix qtb</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the USER-QTB package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>All cell dimensions must be periodic. This fix can not be used with a
+triclinic cell. The QBMSST fix has been tested only for the group-ID
+all.
+</P>
+<HR>
+
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_qtb.html">fix qtb</A>, <A HREF = "fix_msst.html">fix msst</A>
+</P>
+<HR>
+
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed
+= 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and
+T_init=300.0. e0, p0, and v0 are calculated on the first step.
+</P>
+<HR>
+
+<A NAME = "Goldman"></A>
+
+<P><B>(Goldman)</B> Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
+</P>
+<A NAME = "Qi"></A>
+
+<P><B>(Qi)</B> Qi and Reed, J. Phys. Chem. A 116, 10451 (2012).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qeq.html b/doc/doc2/fix_qeq.html
new file mode 100644
index 000000000..e4abfa531
--- /dev/null
+++ b/doc/doc2/fix_qeq.html
@@ -0,0 +1,209 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qeq/point command
+</H3>
+<H3>fix qeq/shielded command
+</H3>
+<H3>fix qeq/slater command
+</H3>
+<H3>fix qeq/dynamic command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style Nevery cutoff tolerance maxiter qfile
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>style = <I>qeq/point</I> or <I>qeq/shielded</I> or <I>qeq/slater</I> or <I>qeq/dynamic</I>
+<LI>Nevery = perform charge equilibration every this many steps
+<LI>cutoff = global cutoff for charge-charge interactions (distance unit)
+<LI>tolerance = precision to which charges will be equilibrated
+<LI>maxiter = maximum iterations to perform charge equilibration
+<LI>qfile = a filename with QEq parameters
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
+fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
+fix 1 all qeq/slater 5 10 1.0e-6 100 params
+fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform the charge equilibration (QEq) method as described in <A HREF = "#Rappe">(Rappe
+and Goddard)</A> and formulated in <A HREF = "#Nakano">(Nakano)</A> (also known
+as the matrix inversion method) and in <A HREF = "#Rick">(Rick and Stuart)</A> (also
+known as the extended Lagrangian method) based on the
+electronegativity equilization principle.
+</P>
+<P>These fixes can be used with any <A HREF = "pair_style.html">pair style</A> in
+LAMMPS, so long as per-atom charges are defined. The most typical
+use-case is in conjunction with a <A HREF = "pair_style.html">pair style</A> that
+performs charge equilibration periodically (e.g. every timestep), such
+as the ReaxFF or Streitz-Mintmire potential (the latter is not yet
+implemented in LAMMPS). But these fixes can also be used with
+potentials that normally assume per-atom charges are fixed, e.g. a
+<A HREF = "pair_buck.html">Buckingham</A> or <A HREF = "pair_lj.html">LJ/Coulombic</A> potential.
+</P>
+<P>Because the charge equilibration calculation is effectively
+independent of the pair style, these fixes can also be used to perform
+a one-time assignment of charges to atoms. For example, you could
+define the QEq fix, perform a zero-timestep run via the <A HREF = "run.html">run</A>
+command without any pair style defined which would set per-atom
+charges (based on the current atom configuration), then remove the fix
+via the <A HREF = "unfix.html">unfix</A> command before performing further dynamics.
+</P>
+<P>IMPORTANT NOTE: Computing and using charge values different from
+published values defined for a fixed-charge potential like Buckingham
+or CHARMM or AMBER, can have a strong effect on energies and forces,
+and produces a different model than the published versions.
+</P>
+<P>IMPORTANT NOTE: The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command must
+still be used to perform charge equliibration with the <A HREF = "pair_comb.html">COMB
+potential</A>. The <A HREF = "fix_qeq_reax.html">fix qeq/reax</A>
+command can be used to perform charge equilibration with the <A HREF = "pair_reax_c.html">ReaxFF
+force field</A>, although fix qeq/shielded yields the
+same results as fix qeq/reax if <I>Nevery</I>, <I>cutoff</I>, and <I>tolerance</I> are
+the same. Eventually the fix qeq/reax command will be deprecated.
+</P>
+<P>The QEq method minimizes the electrostatic energy of the system (or
+equalizes the derivative of energy with respect to charge of all the
+atoms) by adjusting the partial charge on individual atoms based on
+interactions with their neighbors within <I>cutoff</I>. It reqires a few
+parameters, in <I>metal</I> units, for each atom type which provided in a
+file specified by <I>qfile</I>. The file has the following format
+</P>
+<PRE>1 chi eta gamma zeta qcore
+2 chi eta gamma zeta qcore
+...
+Ntype chi eta gamma zeta qcore
+</PRE>
+<P>There is one line per atom type with the following parameters.
+Only a subset of the parameters is used by each QEq style as descibed
+below, thus the others can be set to 0.0 if desired.
+</P>
+<UL><LI><I>chi</I> = electronegativity in energy units
+<LI><I>eta</I> = self-Coulomb potential in energy units
+<LI><I>gamma</I> = shielded Coulomb constant defined by <A HREF = "#vanDuin">ReaxFF force field</A> in distance units
+<LI><I>zeta</I> = Slater type orbital exponent defined by the <A HREF = "#Streitz">Streitz-Mintmire</A> potential in reverse distance units
+<LI><I>qcore</I> = charge of the nucleus defined by the <A HREF = "#Streitz">Streitz-Mintmire potential</A> potential in charge units
+</UL>
+<P>The <I>qeq/point</I> style describes partial charges on atoms as point
+charges. Interaction between a pair of charged particles is 1/r,
+which is the simplest description of the interaction between charges.
+Only the <I>chi</I> and <I>eta</I> parameters from the <I>qfile</I> file are used.
+Note that Coulomb catastrophe can occur if repulsion between the pair
+of charged particles is too weak. This style solves partial charges
+on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
+usually a good number.
+</P>
+<P>The <I>qeq/shielded</I> style describes partial charges on atoms also as
+point charges, but uses a shielded Coulomb potential to describe the
+interaction between a pair of charged particles. Interaction through
+the shielded Coulomb is given by equation (13) of the <A HREF = "#vanDuin">ReaxFF force
+field</A> paper. The shielding accounts for charge overlap
+between charged particles at small separation. This style is the same
+as <A HREF = "fix_qeq_reax.html">fix qeq/reax</A>, and can be used with <A HREF = "pair_reax_c.html">pair_style
+reax/c</A>. Only the <I>chi</I>, <I>eta</I>, and <I>gamma</I>
+parameters from the <I>qfile</I> file are used. This style solves partial
+charges on atoms via the matrix inversion method. A tolerance of
+1.0e-6 is usually a good number.
+</P>
+<P>The <I>qeq/slater</I> style describes partial charges on atoms as spherical
+charge densities centered around atoms via the Slater 1<I>s</I> orbital, so
+that the interaction between a pair of charged particles is the
+product of two Slater 1<I>s</I> orbitals. The expression for the Slater
+1<I>s</I> orbital is given under equation (6) of the
+<A HREF = "#Streitz">Streitz-Mintmire</A> paper. Only the <I>chi</I>, <I>eta</I>, <I>zeta</I>, and
+<I>qcore</I> parameters from the <I>qfile</I> file are used. This style solves
+partial charges on atoms via the matrix inversion method. A tolerance
+of 1.0e-6 is usually a good number.
+</P>
+<P>The <I>qeq/dynamic</I> style describes partial charges on atoms as point
+charges that interact through 1/r, but the extended Lagrangian method
+is used to solve partial charges on atoms. Only the <I>chi</I> and <I>eta</I>
+parameters from the <I>qfile</I> file are used. Note that Coulomb
+catastrophe can occur if repulsion between the pair of charged
+particles is too weak. A tolerance of 1.0e-3 is usually a good
+number.
+</P>
+<P>Note that <I>qeq/point</I>, <I>qeq/shielded</I>, and <I>qeq/slater</I> describe
+different charge models, whereas the matrix inversion method and the
+extended Lagrangian method (<I>qeq/dynamic</I>) are different solvers.
+</P>
+<P>Note that the <I>qeq/point</I> and the <I>qeq/dynamic</I> styles both describe
+charges as point charges that interact through 1/r relationship, but
+solve partial charges on atoms using different solvers. Styles
+<I>qeq/point</I> and the <I>qeq/dynamic</I> should yield comparable results if
+the QEq parameters and <I>Nevery</I>, <I>cutoff</I>, and <I>tolerance</I> are the
+same. Style <I>qeq/point</I> is typically faster, but <I>qeq/dynamic</I> scales
+better on larger sizes.
+</P>
+<P>IMPORTANT NOTE: To avoid the evaluation of the derivative of charge
+with respect to position, which is typically ill-defined, the system
+should have a zero net charge.
+</P>
+<P>IMPORTANT NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and
+qcore) is an "art". Charges on atoms are not guaranteed to
+equilibrate with arbitrary choices of these parameters. We do not
+develop these QEq paramters. See the examples/qeq directory for some
+examples.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about these fixes is written to <A HREF = "restart.html">binary restart
+files</A>. No global scalar or vector or per-atom
+quantities are stored by these fixes for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of these fixes
+can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.
+</P>
+<P>Thexe fixes are invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These fixes are part of the QEQ package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_qeq_reax.html">fix qeq/reax</A>, <A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Rappe"></A>
+
+<P><B>(Rappe and Goddard)</B> A. K. Rappe and W. A. Goddard III, J Physical
+Chemistry, 95, 3358-3363 (1991).
+</P>
+<A NAME = "Nakano"></A>
+
+<P><B>(Nakano)</B> A. Nakano, Computer Physics Communications, 104, 59-69 (1997).
+</P>
+<A NAME = "Rick"></A>
+
+<P><B>(Rick and Stuart)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
+101, 16141 (1994).
+</P>
+<A NAME = "Streitz"></A>
+
+<P><B>(Streitz-Mintmire)</B> F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
+16, 11996 (1994)
+</P>
+<A NAME = "vanDuin"></A>
+
+<P><B>(ReaxFF)</B> A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
+Physical Chemistry, 105, 9396-9049 (2001)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qeq_comb.html b/doc/doc2/fix_qeq_comb.html
new file mode 100644
index 000000000..4ae321f0f
--- /dev/null
+++ b/doc/doc2/fix_qeq_comb.html
@@ -0,0 +1,145 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qeq/comb command
+</H3>
+<H3>fix qeq/comb/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID qeq/comb Nevery precision keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>qeq/comb = style name of this fix command
+
+<LI>Nevery = perform charge equilibration every this many steps
+
+<LI>precision = convergence criterion for charge equilibration
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>file</I>
+
+<PRE> <I>file</I> value = filename
+ filename = name of file to write QEQ equilibration info to
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 surface qeq/comb 10 0.0001
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform charge equilibration (QeQ) in conjunction with the COMB
+(Charge-Optimized Many-Body) potential as described in
+<A HREF = "#COMB_1">(COMB_1)</A> and <A HREF = "#COMB_2">(COMB_2)</A>. It performs the charge
+equilibration portion of the calculation using the so-called QEq
+method, whereby the charge on each atom is adjusted to minimize the
+energy of the system. This fix can only be used with the COMB
+potential; see the <A HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for a QeQ
+calculation that can be used with any potential.
+</P>
+<P>Only charges on the atoms in the specified group are equilibrated.
+The fix relies on the pair style (COMB in this case) to calculate the
+per-atom electronegativity (effective force on the charges). An
+electronegativity equalization calculation (or QEq) is performed in an
+interative fashion, which in parallel requires communication at each
+iteration for processors to exchange charge information about nearby
+atoms with each other. See <A HREF = "#Rappe_and_Goddard">Rappe_and_Goddard</A> and
+<A HREF = "#Rick_and_Stuart">Rick_and_Stuart</A> for details.
+</P>
+<P>During a run, charge equilibration is peformed every <I>Nevery</I> time
+steps. Charge equilibration is also always enforced on the first step
+of each run. The <I>precision</I> argument controls the tolerance for the
+difference in electronegativity for all atoms during charge
+equilibration. <I>Precision</I> is a trade-off between the cost of
+performing charge equilibration (more iterations) and accuracy.
+</P>
+<P>If the <I>file</I> keyword is used, then information about each
+equilibration calculation is written to the specifed file.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a per-atom vector which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The vector stores the
+gradient of the charge on each atom. The per-atom values be accessed
+on any timestep.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>This fix can be invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix command currently only supports <A HREF = "pair_comb.html">pair style <I>comb</I></A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_comb.html">pair_style comb</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>No file output is performed.
+</P>
+<HR>
+
+<A NAME = "COMB_1"></A>
+
+<P><B>(COMB_1)</B> J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+</P>
+<A NAME = "COMB_2"></A>
+
+<P><B>(COMB_2)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
+Phillpot, Phys Rev B, 81, 125328 (2010).
+</P>
+<A NAME = "Rappe_and_Goddard"></A>
+
+<P><B>(Rappe_and_Goddard)</B> A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358
+(1991).
+</P>
+<A NAME = "Rick_and_Stuart"></A>
+
+<P><B>(Rick_and_Stuart)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys
+101, 16141 (1994).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qeq_reax.html b/doc/doc2/fix_qeq_reax.html
new file mode 100644
index 000000000..79f8340d5
--- /dev/null
+++ b/doc/doc2/fix_qeq_reax.html
@@ -0,0 +1,106 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qeq/reax command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>qeq/reax = style name of this fix command
+<LI>Nevery = perform QEq every this many steps
+<LI>cutlo,cuthi = lo and hi cutoff for Taper radius
+<LI>tolerance = precision to which charges will be equilibrated
+<LI>params = reax/c or a filename
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform the charge equilibration (QEq) method as described in <A HREF = "#Rappe">(Rappe
+and Goddard)</A> and formulated in <A HREF = "#Nakano">(Nakano)</A>. It is
+typically used in conjunction with the ReaxFF force field model as
+implemented in the <A HREF = "pair_reax_c.html">pair_style reax/c</A> command, but
+it can be used with any potential in LAMMPS, so long as it defines and
+uses charges on each atom. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
+command should be used to perform charge equliibration with the <A HREF = "pair_comb.html">COMB
+potential</A>. For more technical details about the
+charge equilibration performed by fix qeq/reax, see the
+<A HREF = "#Aktulga">(Aktulga)</A> paper.
+</P>
+<P>The QEq method minimizes the electrostatic energy of the system by
+adjusting the partial charge on individual atoms based on interactions
+with their neighbors. It reqires some parameters for each atom type.
+If the <I>params</I> setting above is the word "reax/c", then these are
+extracted from the <A HREF = "pair_reax_c.html">pair_style reax/c</A> command and
+the ReaxFF force field file it reads in. If a file name is specified
+for <I>params</I>, then the parameters are taken from the specified file
+and the file must contain one line for each atom type. The latter
+form must be used when performing QeQ with a non-ReaxFF potential.
+Each line should be formatted as follows:
+</P>
+<PRE>itype chi eta gamma
+</PRE>
+<P>where <I>itype</I> is the atom type from 1 to Ntypes, <I>chi</I> denotes the
+electronegativity in eV, <I>eta</I> denotes the self-Coulomb
+potential in eV, and <I>gamma</I> denotes the valence orbital
+exponent. Note that these 3 quantities are also in the ReaxFF
+potential file, except that eta is defined here as twice the eta value
+in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
+of this fix are hard-coded to be A, eV, and electronic charge.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. No global scalar or vector or per-atom
+quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>This fix is invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-REAXC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix does not correctly handle interactions
+involving multiple periodic images of the same atom. Hence, it should not
+be used for periodic cell dimensions less than 10 angstroms.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_reax_c.html">pair_style reax/c</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Rappe"></A>
+
+<P> <B>(Rappe)</B> Rappe and Goddard III, Journal of Physical Chemistry, 95,
+3358-3363 (1991).
+</P>
+<A NAME = "Nakano"></A>
+
+<P><B>(Nakano)</B> Nakano, Computer Physics Communications, 104, 59-69 (1997).
+</P>
+<A NAME = "Aktulga"></A>
+
+<P>(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+245-259 (2012).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qmmm.html b/doc/doc2/fix_qmmm.html
new file mode 100644
index 000000000..d10da4e27
--- /dev/null
+++ b/doc/doc2/fix_qmmm.html
@@ -0,0 +1,71 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qmmm command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID qmmm
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>qmmm = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<P>fix 1 qmol qmmm
+</P>
+<P><B>Description:</B>
+</P>
+<P>This fix provides functionality to enable a quantum
+mechanics/molecular mechanice (QM/MM) coupling of LAMMPS to a quantum
+mechanical code. The current implementation only supports an ONIOM
+style mechanical coupling to the <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> plane
+wave DFT package. Electrostatic coupling is in preparation and the
+interface has been written in a manner that coupling to other QM codes
+should be possible without changes to LAMMPS itself.
+</P>
+
+
+<P>The interface code for this is in the lib/qmmm directory of the LAMMPS
+distribution and is being made available at this early stage of
+development in order to encourage contributions for interfaces to
+other QM codes. This will allow the LAMMPS side of the implementation
+to be adapted if necessary before being finalized.
+</P>
+<P>Details about how to use this fix are currently documented in the
+description of the QM/MM interface code itself in lib/qmmm/README.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global scalar or vector or per-atom
+quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-QMMM package. It is only enabled if
+LAMMPS was built with that package. It also requires building a
+library provided with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The fix is only functional when LAMMPS is built as a library and
+linked with a compatible QM program and a QM/MM frontend into a QM/MM
+executable. See the lib/qmmm/README file for details.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_qtb.html b/doc/doc2/fix_qtb.html
new file mode 100644
index 000000000..45333c0bc
--- /dev/null
+++ b/doc/doc2/fix_qtb.html
@@ -0,0 +1,194 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix qtb command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID qtb keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>qtb = style name of this fix
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>temp</I> or <I>damp</I> or <I>seed</I> or <I>f_max</I> or <I>N_f</I>
+
+<PRE> <I>temp</I> value = target quantum temperature (temperature units)
+ <I>damp</I> value = damping parameter (time units) inverse of friction <i>&gamma</i>;
+ <I>seed</I> value = random number seed (positive integer)
+ <I>f_max</I> value = upper cutoff frequency of the vibration spectrum (1/time units)
+ <I>N_f</I> value = number of frequency bins (positive integer)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve
+fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+fix 2 all nph iso 1.01325 1.01325 1
+fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command performs the quantum thermal bath scheme proposed by
+<A HREF = "#Dammak">(Dammak)</A> to include self-consistent quantum nuclear effects,
+when used in conjunction with the <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix
+nph</A> commands.
+</P>
+<P>Classical molecular dynamics simulation does not include any quantum
+nuclear effect. Quantum treatment of the vibrational modes will
+introduce zero point energy into the system, alter the energy power
+spectrum and bias the heat capacity from the classical limit. Missing
+all the quantum nuclear effects, classical MD cannot model systems at
+temperatures lower than their classical limits. This effect is
+especially important for materials with a large population of hydrogen
+atoms and thus higher classical limits.
+</P>
+<P>The equation of motion implemented by this command follows a Langevin
+form:
+</P>
+<center><font size="4"><i> m<sub>i</sub>a<sub>i</sub> = f<sub>i</sub>
++ R<sub>i</sub> -
+m<sub>i</sub>&gamma;v<sub>i</sub>. </i></font></center>
+
+<P>Here <i>m<sub>i</sub></i>, <i>a<sub>i</sub></i>, <i>f<sub>i</sub>
+</i>, <i>R<sub>i</sub></i>, <i>&gamma;</i> and <i>v<sub>i</sub> </i>
+represent mass, acceleration, force exerted by all other atoms, random
+force, frictional coefficient (the inverse of damping parameter damp),
+and velocity. The random force <i>R<sub>i</sub></i> is "colored" so
+that any vibrational mode with frequency <i>&omega;</i> will have a
+temperature-sensitive energy <i>&theta;</i>(<i>&omega;,T</i>) which
+resembles the energy expectation for a quantum harmonic oscillator
+with the same natural frequency:
+</P>
+<center><font size="4"> <i>&theta;</i>(<i>&omega;,T</i>) =
+&#8463;&omega;/2 +
+&#8463;&omega;[</i>exp(<i>&#8463;&omega;/k</i><sub>B</sub><i>T</i>)<i>-1</i>]<i><sup>-1</sup></i>
+</font></center>
+
+<P>To efficiently generate the random forces, we employ the method
+of <A HREF = "#Barrat">(Barrat)</A>, that circumvents the need to generate all
+random forces for all times before the simulation. The memory
+requirement of this approach is less demanding and independent
+of the simulation duration. Since the total random force <i>R</i><sub>tot</sub>
+does not necessarily vanish for a finite number of atoms,
+<i>R<sub>i</sub></i> is replaced by <i>R<sub>i</sub></i> - <i>R</i><sub>tot</sub>/<i>N</i><sub>tot</sub>
+to avoid collective motion of the system.
+</P>
+<P>The <I>temp</I> parameter sets the target quantum temperature. LAMMPS will
+still have an output temperature in its thermo style. That is the
+instantaneous classical temperature <i>T</i><sup>cl</sup> derived from
+the atom velocities at thermal equilibrium. A non-zero
+<i>T</i><sup>cl</sup> will be present even when the quantum
+temperature approaches zero. This is associated with zero-point energy
+at low temperatures.
+</P>
+<center><font size="4"> <i>T</i><sup>cl</sup> = &sum;
+<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub>
+</font></center>
+
+<P>The <I>damp</I> parameter is specified in time units, and it equals the
+inverse of the frictional coefficient <i>&gamma;</i>. <i>&gamma;</i>
+should be as small as possible but slightly larger than the timescale
+of anharmonic coupling in the system which is about 10 ps to 100
+ps. When <i>&gamma;</i> is too large, it gives an energy spectrum that
+differs from the desired Bose-Einstein spectrum. When <i>&gamma;</i>
+is too small, the quantum thermal bath coupling to the system will be
+less significant than anharmonic effects, reducing to a classical
+limit. We find that setting <i>&gamma;</i> between 5 THz and 1 THz
+could be appropriate depending on the system.
+</P>
+<P>The random number <I>seed</I> is a positive integer used to initiate a
+Marsaglia random number generator. Each processor uses the input seed
+to generate its own unique seed and its own stream of random
+numbers. Thus the dynamics of the system will not be identical on two
+runs on different numbers of processors.
+</P>
+<P>The <I>f_max</I> parameter truncate the noise frequency domain so that
+vibrational modes with frequencies higher than <I>f_max</I> will not be
+modulated. If we denote &Delta;<i>t</i> as the time interval for the
+MD integration, <I>f_max</I> is always reset by the code to make
+<i>&alpha;</i> = (int)(2<I>f_max</I>&Delta;<i>t</i>)<sup><i>-1</i></sup> a
+positive integer and print out relative information. An appropriate
+value for the cutoff frequency <I>f_max</I> would be around 2~3
+<i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
+frequency.
+</P>
+<P>The <I>N_f</I> parameter is the frequency grid size, the number of points
+from 0 to <I>f_max</I> in the frequency domain that will be
+sampled. <i>3&times;2</i> <I>N_f</I> per-atom random numbers are required
+in the random force generation and there could be as many atoms as in
+the whole simulation that can migrate into every individual
+processor. A larger <I>N_f</I> provides a more accurate sampling of the
+spectrum while consumes more memory. With fixed <I>f_max</I> and
+<i>&gamma;</i>, <I>N_f</I> should be big enough to converge the classical
+temperature <i>T</i><sup>cl</sup> as a function of target quantum bath
+temperature. Memory usage per processor could be from 10 to 100
+Mbytes.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration. It only modifies forces to a
+colored thermostat. Thus you must use a separate time integration fix,
+like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A> to actually
+update the velocities and positions of atoms (as shown in the
+examples). Likewise, this fix should not normally be used with other
+fixes or commands that also specify system temperatures , e.g. <A HREF = "fix_nh.html">fix
+nvt</A> and <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimizie info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix. However, in a statistical sense, a restarted
+simulation should produce similar behaviors of the system.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the USER-QTB package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<HR>
+
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_langevin.html">fix
+langevin</A>, <A HREF = "fix_qbmsst.html">fix qbmsst</A>
+</P>
+<HR>
+
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are temp = 300, damp = 1, seed = 880302,
+f_max=200.0 and N_f = 100.
+</P>
+<HR>
+
+<A NAME = "Dammak"></A>
+
+<P><B>(Dammak)</B> Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev
+Lett, 103, 190601 (2009).
+</P>
+<A NAME = "Barrat"></A>
+
+<P><B>(Barrat)</B> Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_reax_bonds.html b/doc/doc2/fix_reax_bonds.html
new file mode 100644
index 000000000..dd25932e9
--- /dev/null
+++ b/doc/doc2/fix_reax_bonds.html
@@ -0,0 +1,73 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix reax/bonds command
+</H3>
+<H3>fix reax/c/bonds command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID reax/bonds Nevery filename
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>reax/bonds = style name of this fix command
+<LI>Nevery = output interval in timesteps
+<LI>filename = name of output file
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all reax/bonds 100 bonds.tatb
+fix 1 all reax/c/bonds 100 bonds.reaxc
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write out the bond information computed by the ReaxFF potential
+specified by <A HREF = "pair_reax.html">pair_style reax</A> or <A HREF = "pair_reax_c.html">pair_style
+reax/c</A> in the exact same format as the original
+stand-alone ReaxFF code of Adri van Duin. The bond information is
+written to <I>filename</I> on timesteps that are multiples of <I>Nevery</I>,
+including timestep 0. For time-averaged chemical species analysis,
+please see the <A HREF = "fix_species.html">fix species</A> command.
+</P>
+<P>The format of the output file should be self-explantory.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The fix reax/bonds command requires that the <A HREF = "pair_reax.html">pair_style
+reax</A> be invoked. This fix is part of the REAX
+package. It is only enabled if LAMMPS was built with that package,
+which also requires the REAX library be built and linked with LAMMPS.
+The fix reax/c/bonds command requires that the <A HREF = "pair_reax_c.html">pair_style
+reax/c</A> be invoked. This fix is part of the
+USER-REAXC package. It is only enabled if LAMMPS was built with that
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_reax.html">pair_style reax</A>, <A HREF = "pair_reax_c.html">pair_style
+reax/c</A>, <A HREF = "fix_reaxc_species.html">fix reax/c/species</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_reaxc_species.html b/doc/doc2/fix_reaxc_species.html
new file mode 100644
index 000000000..a507564a2
--- /dev/null
+++ b/doc/doc2/fix_reaxc_species.html
@@ -0,0 +1,165 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix reax/c/species command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>reax/c/species = style name of this command
+
+<LI>Nevery = sample bond-order every this many timesteps
+
+<LI>Nrepeat = # of bond-order samples used for calculating averages
+
+<LI>Nfreq = calculate average bond-order every this many timesteps
+
+<LI>filename = name of output file
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>cutoff</I> or <I>element</I> or <I>position</I>
+
+<PRE> <I>cutoff</I> value = I J Cutoff
+ I, J = atom types
+ Cutoff = Bond-order cutoff value for this pair of atom types
+ <I>element</I> value = Element1, Element2, ...
+ <I>position</I> value = posfreq filepos
+ posfreq = write position files every this many timestep
+ filepos = name of position output file
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all reax/c/species 10 10 100 species.out
+fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
+fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write out the chemical species information computed by the ReaxFF
+potential specified by <A HREF = "pair_reax_c.html">pair_style reax/c</A>.
+Bond-order values (either averaged or instantaneous, depending on
+value of <I>Nrepeat</I>) are used to determine chemical bonds. Every
+<I>Nfreq</I> timesteps, chemical species information is written to
+<I>filename</I> as a two line output. The first line is a header
+containing labels. The second line consists of the following:
+timestep, total number of molecules, total number of distinct species,
+number of molecules of each species. In this context, "species" means
+a unique molecule. The chemical formula of each species is given in
+the first line.
+</P>
+<P>Optional keyword <I>cutoff</I> can be assigned to change the minimum
+bond-order values used in identifying chemical bonds between pairs of
+atoms. Bond-order cutoffs should be carefully chosen, as bond-order
+cutoffs that are too small may include too many bonds (which will
+result in an error), while cutoffs that are too large will result in
+fragmented molecules. The default cutoff of 0.3 usually gives good
+results.
+</P>
+<P>The optional keyword <I>element</I> can be used to specify the chemical
+symbol printed for each LAMMPS atom type. The number of symbols must
+match the number of LAMMPS atom types and each symbol must consist of
+1 or 2 alphanumeric characters. Normally, these symbols should be
+chosen to match the chemical identity of each LAMMPS atom type, as
+specified using the <A HREF = "pair_reax_c.html">reax/c pair_coeff</A> command and
+the ReaxFF force field file.
+</P>
+<P>The optional keyword <I>position</I> writes center-of-mass positions of
+each identified molecules to file <I>filepos</I> every <I>posfreq</I> timesteps.
+The first line contains information on timestep, total number of
+molecules, total number of distinct species, and box dimensions. The
+second line is a header containing labels. From the third line
+downward, each molecule writes a line of output containing the
+following information: molecule ID, number of atoms in this molecule,
+chemical formula, total charge, and center-of-mass xyz positions of
+this molecule. The xyz positions are in fractional coordinates
+relative to the box dimensions.
+</P>
+<P>For the keyword <I>position</I>, the <I>filepos</I> is the name of the output
+file. It can contain the wildcard character "*". If the "*"
+character appears in <I>filepos</I>, then one file per snapshot is written
+at <I>posfreq</I> and the "*" character is replaced with the timestep
+value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
+</P>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the bond-order values are sampled to get the average bond
+order. The species analysis is performed using the average bond-order
+on timesteps that are a multiple of <I>Nfreq</I>. The average is over
+<I>Nrepeat</I> bond-order samples, computed in the preceding portion of the
+simulation every <I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of
+<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also,
+the timesteps contributing to the average bond-order cannot overlap,
+i.e. Nfreq > (Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
+values on timesteps 90,92,94,96,98,100 will be used to compute the
+average bond-order for the species analysis output on timestep 100.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes both a global vector of length 2 and a per-atom
+vector, either of which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The values in the global
+vector are "intensive".
+</P>
+<P>The 2 values in the global vector are as follows:
+</P>
+<UL><LI>1 = total number of molecules
+<LI>2 = total number of distinct species
+</UL>
+<P>The per-atom vector stores the molecule ID for each atom as identified
+by the fix. If an atom is not in a molecule, its ID will be 0.
+For atoms in the same molecule, the molecule ID for all of them
+will be the same and will be equal to the smallest atom ID of
+any atom in the molecule.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The fix species currently only works with
+<A HREF = "pair_reax_c.html">pair_style reax/c</A> and it requires that the <A HREF = "pair_reax_c.html">pair_style
+reax/c</A> be invoked. This fix is part of the
+USER-REAXC package. It is only enabled if LAMMPS was built with that
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P>It should be possible to extend it to other reactive pair_styles (such as
+<A HREF = "pair_airebo.html">rebo</A>, <A HREF = "pair_airebo.html">airebo</A>,
+<A HREF = "pair_comb.html">comb</A>, and <A HREF = "pair_bop.html">bop</A>), but this has not yet been done.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_reax_c.html">pair_style reax/c</A>, <A HREF = "fix_reax_bonds.html">fix
+reax/bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default values for bond-order cutoffs are 0.3 for all I-J pairs. The
+default element symbols are C, H, O, N. Position files are not written
+by default.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_recenter.html b/doc/doc2/fix_recenter.html
new file mode 100644
index 000000000..0213e1074
--- /dev/null
+++ b/doc/doc2/fix_recenter.html
@@ -0,0 +1,136 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix recenter command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID recenter x y z keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>recenter = style name of this fix command
+
+<LI>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>shift</I> or <I>units</I>
+
+<PRE> <I>shift</I> value = group-ID
+ group-ID = group of atoms whose coords are shifted
+ <I>units</I> value = <I>box</I> or <I>lattice</I> or <I>fraction</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all recenter 0.0 0.5 0.0
+fix 1 all recenter INIT INIT NULL
+fix 1 all recenter INIT 0.0 0.0 units box
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Constrain the center-of-mass position of a group of atoms by adjusting
+the coordinates of the atoms every timestep. This is simply a small
+shift that does not alter the dynamics of the system or change the
+relative coordinates of any pair of atoms in the group. This can be
+used to insure the entire collection of atoms (or a portion of them)
+do not drift during the simulation due to random perturbations
+(e.g. <A HREF = "fix_langevin.html">fix langevin</A> thermostatting).
+</P>
+<P>Distance units for the x,y,z values are determined by the setting of
+the <I>units</I> keyword, as discussed below. One or more x,y,z values can
+also be specified as NULL, which means exclude that dimension from
+this operation. Or it can be specified as INIT which means to
+constrain the center-of-mass to its initial value at the beginning of
+the run.
+</P>
+<P>The center-of-mass (COM) is computed for the group specified by the
+fix. If the current COM is different than the specified x,y,z, then a
+group of atoms has their coordinates shifted by the difference. By
+default the shifted group is also the group specified by the fix. A
+different group can be shifted by using the <I>shift</I> keyword. For
+example, the COM could be computed on a protein to keep it in the
+center of the simulation box. But the entire system (protein + water)
+could be shifted.
+</P>
+<P>If the <I>units</I> keyword is set to <I>box</I>, then the distance units of
+x,y,z are defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
+for <I>real</I> units. A <I>lattice</I> value means the distance units are in
+lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
+previously used to define the lattice spacing. A <I>fraction</I> value
+means a fractional distance between the lo/hi box boundaries, e.g. 0.5
+= middle of the box. The default is to use lattice units.
+</P>
+<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
+velocities with zero aggregate linear and/or angular momentum.
+</P>
+<P>IMPORTANT NOTE: This fix performs its operations at the same point in
+the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
+nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, or <A HREF = "fix_nh.html">fix npt</A>.
+Thus fix recenter should normally be the last such fix specified in
+the input script, since the adjustments it makes to atom coordinates
+should come after the changes made by time integration. LAMMPS will
+warn you if your fixes are not ordered this way.
+</P>
+<P>IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a
+molecule in solvent) without using the <I>shift</I> keyword to adjust the
+positions of all atoms in the system, then the results can be
+unpredictable. For example, if the molecule is pushed in one
+direction by the solvent, its velocity will increase. But its
+coordinates will be recentered, meaning it is pushed back towards the
+force. Thus over time, the velocity and temperature of the molecule
+could become very large (though it won't appear to be moving due to
+the recentering). If you are thermostatting the entire system, then
+the solvent would be cooled to compensate. A better solution for this
+simulation scenario is to use the <A HREF = "fix_spring.html">fix spring</A> command
+to tether the molecule in place.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+distance the group is moved by fix recenter.
+</P>
+<P>This fix also computes global 3-vector which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The 3
+quantities in the vector are xyz components of displacement applied to
+the group of atoms by the fix.
+</P>
+<P>The scalar and vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix should not be used with an x,y,z setting that causes a large
+shift in the system on the 1st timestep, due to the requested COM
+being very different from the initial COM. This could cause atoms to
+be lost, especially in parallel. Instead, use the
+<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used to
+move atoms a large distance.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_momentum.html">fix momentum</A>, <A HREF = "velocity.html">velocity</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are shift = fix group-ID, and units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_restrain.html b/doc/doc2/fix_restrain.html
new file mode 100644
index 000000000..6c0f498fa
--- /dev/null
+++ b/doc/doc2/fix_restrain.html
@@ -0,0 +1,193 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix restrain command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID restrain keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>restrain = style name of this fix command
+
+<LI>one or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I>
+
+<PRE> <I>bond</I> args = atom1 atom2 Kstart Kstop r0
+ atom1,atom2 = IDs of 2 atoms in bond
+ Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+ r0 = equilibrium bond distance (distance units)
+ <I>angle</I> args = atom1 atom2 atom3 Kstart Kstop theta0
+ atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
+ Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+ theta0 = equilibrium angle theta (degrees)
+ <I>dihedral</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
+ atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
+ Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+ phi0 = equilibrium dihedral angle phi (degrees)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Restrain the motion of the specified sets of atoms by making them part
+of a bond or angle or dihedral interaction whose strength can vary
+over time during a simulation. This is functionally equivalent to
+creating a bond or angle or dihedral for the same atoms in a data
+file, as specified by the <A HREF = "read_data.html">read_data</A> command, albeit
+with a time-varying pre-factor coefficient. For the purpose of
+forcefield parameter-fitting or mapping a molecular potential energy
+surface, this fix reduces the hassle and risk associated with
+modifying data files. In other words, use this fix to temporarily
+force a molecule to adopt a particular conformation. To create a
+permanent bond or angle or dihedral, you should modify the data file.
+</P>
+<P>The group-ID specified by this fix is ignored.
+</P>
+<P>The second example above applies a restraint to hold the dihedral
+angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
+restraint coefficient. The fourth example applies similar restraints
+to multiple dihedral angles using a restraint coefficient that
+increases from 0.0 to 2000.0 over the course of the run.
+</P>
+<P>IMPORTANT NOTE: Adding a force to atoms implies a change in their
+potential energy as they move due to the applied force field. For
+dynamics via the <A HREF = "run.html">run</A> command, this energy can be added to
+the system's potential energy for thermodynamic output (see below).
+For energy minimization via the <A HREF = "minimize.html">minimize</A> command, this
+energy must be added to the system's potential energy to formulate a
+self-consistent minimization problem (see below).
+</P>
+<P>In order for a restraint to be effective, the restraint force must
+typically be significantly larger than the forces associated with
+conventional forcefield terms. If the restraint is applied during a
+dynamics run (as opposed to during an energy minimization), a large
+restraint coefficient can significantly reduce the stable timestep
+size, especially if the atoms are initially far from the preferred
+conformation. You may need to experiment to determine what value of K
+works best for a given application.
+</P>
+<P>For the case of finding a minimum energy structure for a single
+molecule with particular restratins (e.g. for fitting forcefield
+parameters or constructing a potential energy surface), commands such
+as the following may be useful:
+</P>
+<PRE># minimize molecule energy with restraints
+velocity all create 600.0 8675309 mom yes rot yes dist gaussian
+fix NVE all nve
+fix TFIX all langevin 600.0 0.0 100 24601
+fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 0.0 5000.0 $<I>angle2</I>
+fix_modify REST energy yes
+run 10000
+fix TFIX all langevin 0.0 0.0 100 24601
+fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 5000.0 5000.0 $<I>angle2</I>
+fix_modify REST energy yes
+run 10000
+# sanity check for convergence
+minimize 1e-6 1e-9 1000 100000
+# report unrestrained energies
+unfix REST
+run 0
+</PRE>
+<HR>
+
+<P>The <I>bond</I> keyword applies a bond restraint to the specified atoms
+using the same functional form used by the <A HREF = "bond_harmonic.html">bond_style
+harmonic</A> command. The potential associated with
+the restraint is
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
+</CENTER>
+<P>with the following coefficients:
+</P>
+<UL><LI>K (energy/distance^2)
+<LI>r0 (distance)
+</UL>
+<P>K and r0 are specified with the fix. Note that the usual 1/2 factor
+is included in K.
+</P>
+<HR>
+
+<P>The <I>angle</I> keyword applies an angle restraint to the specified atoms
+using the same functional form used by the <A HREF = "angle_harmonic.html">angle_style
+harmonic</A> command. The potential associated with
+the restraint is
+</P>
+<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
+</CENTER>
+<P>with the following coefficients:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>theta0 (degrees)
+</UL>
+<P>K and theta0 are specified with the fix. Note that the usual 1/2
+factor is included in K.
+</P>
+<HR>
+
+<P>The <I>dihedral</I> keyword applies a dihedral restraint to the specified
+atoms using a simplified form of the function used by the
+<A HREF = "dihedral_charmm.html">dihedral_style charmm</A> command. The potential
+associated with the restraint is
+</P>
+<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
+</CENTER>
+<P>with the following coefficients:
+</P>
+<UL><LI>K (energy)
+<LI>n = 1
+<LI>d (degrees) = phi0 + 180
+</UL>
+<P>K and phi0 are specified with the fix. Note that the value of n is
+hard-wired to 1. Also note that the energy will be a minimum when the
+current dihedral angle phi is equal to phi0.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential energy associated with this fix to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
+with the added forces to be included in the total potential energy of
+the system (the quantity being minimized), you MUST enable the
+<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+</P>
+<P>This fix computes a global scalar, which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+potential energy for all the restraints as discussed above. The scalar
+value calculated by this fix is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_rigid.html b/doc/doc2/fix_rigid.html
new file mode 100644
index 000000000..971bfd479
--- /dev/null
+++ b/doc/doc2/fix_rigid.html
@@ -0,0 +1,814 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix rigid command
+</H3>
+<H3>fix rigid/nve command
+</H3>
+<H3>fix rigid/nvt command
+</H3>
+<H3>fix rigid/npt command
+</H3>
+<H3>fix rigid/nph command
+</H3>
+<H3>fix rigid/small command
+</H3>
+<H3>fix rigid/nve/small command
+</H3>
+<H3>fix rigid/nvt/small command
+</H3>
+<H3>fix rigid/npt/small command
+</H3>
+<H3>fix rigid/nph/small command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style bodystyle args keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I> or <I>rigid/nve/small</I> or <I>rigid/nvt/small</I> or <I>rigid/npt/small</I> or <I>rigid/nph/small</I>
+
+<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
+
+<PRE> <I>single</I> args = none
+ <I>molecule</I> args = none
+ <I>group</I> args = N groupID1 groupID2 ...
+ N = # of groups
+ groupID1, groupID2, ... = list of N group IDs
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I>
+
+<PRE> <I>langevin</I> values = Tstart Tstop Tperiod seed
+ Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+ Tdamp = temperature damping parameter (time units)
+ seed = random number seed to use for white noise (positive integer)
+ <I>temp</I> values = Tstart Tstop Tdamp
+ Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+ Tdamp = temperature damping parameter (time units)
+ <I>iso</I> or <I>aniso</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ <I>x</I> or <I>y</I> or <I>z</I> values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+ Pdamp = stress damping parameter (time units)
+ <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
+ <I>tparam</I> values = Tchain Titer Torder
+ Tchain = length of Nose/Hoover thermostat chain
+ Titer = number of thermostat iterations performed
+ Torder = 3 or 5 = Yoshida-Suzuki integration parameters
+ <I>pchain</I> values = Pchain
+ Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
+ <I>dilate</I> value = dilate-group-ID
+ dilate-group-ID = only dilate atoms in this group due to barostat volume changes
+ <I>force</I> values = M xflag yflag zflag
+ M = which rigid body from 1-Nbody (see asterisk form below)
+ xflag,yflag,zflag = off/on if component of center-of-mass force is active
+ <I>torque</I> values = M xflag yflag zflag
+ M = which rigid body from 1-Nbody (see asterisk form below)
+ xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+ <I>infile</I> filename
+ filename = file with per-body values of mass, center-of-mass, moments of inertia
+ <I>mol</I> value = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 clump rigid single
+fix 1 clump rigid/small molecule
+fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
+fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
+fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
+fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
+fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
+fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
+fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Treat one or more sets of atoms as independent rigid bodies. This
+means that each timestep the total force and torque on each rigid body
+is computed as the sum of the forces and torques on its constituent
+particles. The coordinates, velocities, and orientations of the atoms
+in each body are then updated so that the body moves and rotates as a
+single entity.
+</P>
+<P>Examples of large rigid bodies are a colloidal particle, or portions
+of a biomolecule such as a protein.
+</P>
+<P>Example of small rigid bodies are patchy nanoparticles, such as those
+modeled in <A HREF = "#Zhang">this paper</A> by Sharon Glotzer's group, clumps of
+granular particles, lipid molecules consiting of one or more point
+dipoles connected to other spheroids or ellipsoids, irregular
+particles built from line segments (2d) or triangles (3d), and
+coarse-grain models of nano or colloidal particles consisting of a
+small number of constituent particles. Note that the <A HREF = "fix_shake.html">fix
+shake</A> command can also be used to rigidify small
+molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
+the constituent atoms as point masses.
+</P>
+<P>These fixes also update the positions and velocities of the atoms in
+each rigid body via time integration, in the NVE, NVT, NPT, or NPH
+ensemble, as described below.
+</P>
+<P>There are two main variants of this fix, fix rigid and fix
+rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
+variants, as their style names indicate.
+</P>
+<P>IMPORTANT NOTE: Not all of the <I>bodystyle</I> options and keyword/value
+options are available for both the <I>rigid</I> and <I>rigid/small</I> variants.
+See details below.
+</P>
+<P>The <I>rigid</I> variant is typically the best choice for a system with a
+small number of large rigid bodies, each of which can extend across
+the domain of many processors. It operates by creating a single
+global list of rigid bodies, which all processors contribute to.
+MPI_Allreduce operations are performed each timestep to sum the
+contributions from each processor to the force and torque on all the
+bodies. This operation will not scale well in parallel if large
+numbers of rigid bodies are simulated.
+</P>
+<P>The <I>rigid/small</I> variant is typically best for a system with a large
+number of small rigid bodies. Each body is assigned to the atom
+closest to the geometrical center of the body. The fix operates using
+local lists of rigid bodies owned by each processor and information is
+exchanged and summed via local communication between neighboring
+processors when ghost atom info is accumlated.
+</P>
+<P>IMPORTANT NOTE: To use <I>rigid/small</I> the ghost atom cutoff must be
+large enough to span the distance between the atom that owns the body
+and every other atom in the body. This distance value is printed out
+when the rigid bodies are defined. If the
+<A HREF = "pair_style.html">pair_style</A> cutoff plus neighbor skin does not span
+this distance, then you should use the <A HREF = "comm_modify.html">comm_modify
+cutoff</A> command with a setting epsilon larger than
+the distance.
+</P>
+<P>Which of the two variants is faster for a particular problem is hard
+to predict. The best way to decide is to perform a short test run.
+Both variants should give identical numerical answers for short runs.
+Long runs should give statistically similar results, but round-off
+differences may accumulate to produce divergent trajectories.
+</P>
+<P>IMPORTANT NOTE: You should not update the atoms in rigid bodies via
+other time-integration fixes (e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix
+nvt</A>, <A HREF = "fix_npt.html">fix npt</A>), or you will be integrating
+their motion more than once each timestep. When performing a hybrid
+simulation with some atoms in rigid bodies, and some not, a separate
+time integration fix like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix
+nvt</A> should be used for the non-rigid particles.
+</P>
+<P>IMPORTANT NOTE: These fixes are overkill if you simply want to hold a
+collection of atoms stationary or have them move with a constant
+velocity. A simpler way to hold atoms stationary is to not include
+those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
+instead of "fix 1 all nve", where "mobile" is the group of atoms that
+you want to move. You can move atoms with a constant velocity by
+assigning them an initial velocity (via the <A HREF = "velocity.html">velocity</A>
+command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
+setforce</A> command), and integrating them as usual
+(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
+</P>
+<P>IMPORTANT NOTE: The aggregate properties of each rigid body are
+calculated one time at the start of the first simulation run after
+this fix is specified. The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia,
+and its angular momentum. This is done using the properties of the
+constituent atoms of the body at that point in time (or see the
+<I>infile</I> keyword option). Thereafter, changing properties of
+individual atoms in the body will have no effect on a rigid body's
+dynamics, unless they effect the <A HREF = "pair_style.html">pair_style</A>
+interactions that individual particles are part of. For example, you
+might think you could displace the atoms in a body or add a large
+velocity to each atom in a body to make it move in a desired direction
+before a 2nd run is performed, using the <A HREF = "set.html">set</A> or
+<A HREF = "displace_atoms.html">displace_atoms</A> or <A HREF = "velocity.html">velocity</A>
+command. But these commands will not affect the internal attributes
+of the body, and the position and velocity or individual atoms in the
+body will be reset when time integration starts.
+</P>
+<HR>
+
+<P>Each rigid body must have two or more atoms. An atom can belong to at
+most one rigid body. Which atoms are in which bodies can be defined
+via several options.
+</P>
+<P>IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
+<I>molecule</I>, you can define a system that has no rigid bodies
+initially. This is useful when you are using the <I>mol</I> keyword in
+conjunction with another fix that is adding rigid bodies on-the-fly,
+such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix pour</A>.
+</P>
+<P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
+rigid body. This option is only allowed for fix rigid and its
+sub-styles.
+</P>
+<P>For bodystyle <I>molecule</I>, each set of atoms in the fix group with a
+different molecule ID is treated as a rigid body. This option is
+allowed for fix rigid and fix rigid/small, and their sub-styles. Note
+that atoms with a molecule ID = 0 will be treated as a single rigid
+body. For a system with atomic solvent (typically this is atoms with
+molecule ID = 0) surrounding rigid bodies, this may not be what you
+want. Thus you should be careful to use a fix group that only
+includes atoms you want to be part of rigid bodies.
+</P>
+<P>For bodystyle <I>group</I>, each of the listed groups is treated as a
+separate rigid body. Only atoms that are also in the fix group are
+included in each rigid body. This option is only allowed for fix
+rigid and its sub-styles.
+</P>
+<P>IMPORTANT NOTE: To compute the initial center-of-mass position and
+other properties of each rigid body, the image flags for each atom in
+the body are used to "unwrap" the atom coordinates. Thus you must
+insure that these image flags are consistent so that the unwrapping
+creates a valid rigid body (one where the atoms are close together),
+particularly if the atoms in a single rigid body straddle a periodic
+boundary. This means the input data file or restart file must define
+the image flags for each atom consistently or that you have used the
+<A HREF = "set.html">set</A> command to specify them correctly. If a dimension is
+non-periodic then the image flag of each atom must be 0 in that
+dimension, else an error is generated.
+</P>
+<P>The <I>force</I> and <I>torque</I> keywords discussed next are only allowed for
+fix rigid and its sub-styles.
+</P>
+<P>By default, each rigid body is acted on by other atoms which induce an
+external force and torque on its center of mass, causing it to
+translate and rotate. Components of the external center-of-mass force
+and torque can be turned off by the <I>force</I> and <I>torque</I> keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+unaffected by interactions with other particles. Note that if you
+expect a rigid body not to move or rotate by using these keywords, you
+must insure its initial center-of-mass translational or angular
+velocity is 0.0. Otherwise the initial translational or angular
+momentum the body has will persist.
+</P>
+<P>An xflag, yflag, or zflag set to <I>off</I> means turn off the component of
+force of torque in that dimension. A setting of <I>on</I> means turn on
+the component, which is the default. Which rigid body(s) the settings
+apply to is determined by the first argument of the <I>force</I> and
+<I>torque</I> keywords. It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined. A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies. This takes the form "*" or "*n" or
+"n*" or "m*n". If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N. A leading
+asterisk means all bodies from 1 to n (inclusive). A trailing
+asterisk means all bodies from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive). Note that you can use the
+<I>force</I> or <I>torque</I> keywords as many times as you like. If a
+particular rigid body has its component flags set multiple times, the
+settings from the final keyword are used.
+</P>
+<P>IMPORTANT NOTE: For computational efficiency, you may wish to turn off
+pairwise and bond interactions within each rigid body, as they no
+longer contribute to the motion. The <A HREF = "neigh_modify.html">neigh_modify
+exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</A>
+commands are used to do this. If the rigid bodies have strongly
+overalapping atoms, you may need to turn off these interactions to
+avoid numerical problems due to large equal/opposite intra-body forces
+swamping the contribution of small inter-body forces.
+</P>
+<P>For computational efficiency, you should typically define one fix
+rigid or fix rigid/small command which includes all the desired rigid
+bodies. LAMMPS will allow multiple rigid fixes to be defined, but it
+is more expensive.
+</P>
+<HR>
+
+<P>The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheres or
+ellipsoids or line segments or triangles. See the <A HREF = "atom_style.html">atom_style sphere
+and ellipsoid and line and tri</A> commands for more
+details on these kinds of particles. Finite-size particles contribute
+differently to the moment of inertia of a rigid body than do point
+particles. Finite-size particles can also experience torque (e.g. due
+to <A HREF = "pair_gran.html">frictional granular interactions</A>) and have an
+orientation. These contributions are accounted for by these fixes.
+</P>
+<P>Forces between particles within a body do not contribute to the
+external force or torque on the body. Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body. The <A HREF = "neigh_modify.html">neigh_modify
+exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</A>
+commands are used to do this. For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
+</P>
+<HR>
+
+<P>The <I>rigid</I> and <I>rigid/small</I> and <I>rigid/nve</I> styles perform constant
+NVE time integration. The only difference is that the <I>rigid</I> and
+<I>rigid/small</I> styles use an integration technique based on Richardson
+iterations. The <I>rigid/nve</I> style uses the methods described in the
+paper by <A HREF = "#Miller">Miller</A>, which are thought to provide better energy
+conservation than an iterative approach.
+</P>
+<P>The <I>rigid/nvt</I> and <I>rigid/nvt/small</I> styles performs constant NVT
+integration using a Nose/Hoover thermostat with chains as described
+originally in <A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which
+thermostats both the translational and rotational degrees of freedom
+of the rigid bodies. The rigid-body algorithm used by <I>rigid/nvt</I>
+is described in the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
+</P>
+<P>The <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small counterparts) styles
+perform constant NPT or NPH integration using a Nose/Hoover barostat
+with chains. For the NPT case, the same Nose/Hoover thermostat is also
+used as with <I>rigid/nvt</I>.
+</P>
+<P>The barostat parameters are specified using one or more of the <I>iso</I>,
+<I>aniso</I>, <I>x</I>, <I>y</I>, <I>z</I> and <I>couple</I> keywords. These keywords give you
+the ability to specify 3 diagonal components of the external stress
+tensor, and to couple these components together so that the dimensions
+they represent are varied together during a constant-pressure
+simulation. The effects of these keywords are similar to those
+defined in <A HREF = "fix_nh.html">fix npt/nph</A>
+</P>
+<P>NOTE: Currently the <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small
+counterparts) styles do not support triclinic (non-orthongonal) boxes.
+</P>
+<P>The target pressures for each of the 6 components of the stress tensor
+can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I> keywords, which
+correspond to the 3 simulation box dimensions. For each component,
+the external pressure or tensor component at each timestep is a ramped
+value during the run from <I>Pstart</I> to <I>Pstop</I>. If a target pressure is
+specified for a component, then the corresponding box dimension will
+change during a simulation. For example, if the <I>y</I> keyword is used,
+the y-box length will change. A box dimension will not change if that
+component is not specified, although you have the option to change
+that dimension via the <A HREF = "fix_deform.html">fix deform</A> command.
+</P>
+<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
+<I>Tdamp</I> parameter, determining the time scale on which pressure is
+relaxed. For example, a value of 10.0 means to relax the pressure in
+a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+the <A HREF = "units.html">units</A> command).
+</P>
+<P>Regardless of what atoms are in the fix group (the only atoms which
+are time integrated), a global pressure or stress tensor is computed
+for all atoms. Similarly, when the size of the simulation box is
+changed, all atoms are re-scaled to new positions, unless the keyword
+<I>dilate</I> is specified with a <I>dilate-group-ID</I> for a group that
+represents a subset of the atoms. This can be useful, for example, to
+leave the coordinates of atoms in a solid substrate unchanged and
+controlling the pressure of a surrounding fluid. Another example is a
+system consisting of rigid bodies and point particles where the
+barostat is only coupled with the rigid bodies. This option should be
+used with care, since it can be unphysical to dilate some atoms and
+not others, because it can introduce large, instantaneous
+displacements between a pair of atoms (one dilated, one not) that are
+far from the dilation origin.
+</P>
+<P>The <I>couple</I> keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together. The value specified
+with the keyword determines which are coupled. For example, <I>xz</I>
+means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
+<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep. The
+<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
+be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
+dimension is simply ignored.
+</P>
+<P>The <I>iso</I> and <I>aniso</I> keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+</P>
+<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple xyz
+</PRE>
+<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
+independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+</P>
+<PRE>x Pstart Pstop Pdamp
+y Pstart Pstop Pdamp
+z Pstart Pstop Pdamp
+couple none
+</PRE>
+<HR>
+
+<P>The keyword/value option pairs are used in the following ways.
+</P>
+<P>The <I>langevin</I> and <I>temp</I> and <I>tparam</I> keywords perform thermostatting
+of the rigid bodies, altering both their translational and rotational
+degrees of freedom. What is meant by "temperature" of a collection of
+rigid bodies and how it can be monitored via the fix output is
+discussed below.
+</P>
+<P>The <I>langevin</I> keyword applies a Langevin thermostat to the constant
+NVE time integration performed by either the <I>rigid</I> or <I>rigid/small</I>
+or <I>rigid/nve</I> styles. It cannot be used with the <I>rigid/nvt</I> style.
+The desired temperature at each timestep is a ramped value during the
+run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed. For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command). The random # <I>seed</I> must be a positive
+integer.
+</P>
+<P>The way that Langevin thermostatting operates is explained on the <A HREF = "fix_langevin.html">fix
+langevin</A> doc page. If you wish to simply viscously
+damp the rotational motion without thermostatting, you can set
+<I>Tstart</I> and <I>Tstop</I> to 0.0, which means only the viscous drag term in
+the Langevin thermostat will be applied. See the discussion on the
+<A HREF = "doc/fix_viscous.html">fix viscous</A> doc page for details.
+</P>
+<P>IMPORTANT NOTE: When the <I>langevin</I> keyword is used with fix rigid
+versus fix rigid/small, different dynamics will result for parallel
+runs. This is because of the way random numbers are used in the two
+cases. The dynamics for the two cases should be statistically
+similar, but will not be identical, even for a single timestep.
+</P>
+<P>The <I>temp</I> and <I>tparam</I> keywords apply a Nose/Hoover thermostat to the
+NVT time integration performed by the <I>rigid/nvt</I> style. They cannot
+be used with the <I>rigid</I> or <I>rigid/small</I> or <I>rigid/nve</I> styles. The
+desired temperature at each timestep is a ramped value during the run
+from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in time
+units and determines how rapidly the temperature is relaxed. For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
+</P>
+<P>Nose/Hoover chains are used in conjunction with this thermostat. The
+<I>tparam</I> keyword can optionally be used to change the chain settings
+used. <I>Tchain</I> is the number of thermostats in the Nose Hoover chain.
+This value, along with <I>Tdamp</I> can be varied to dampen undesirable
+oscillations in temperature that can occur in a simulation. As a rule
+of thumb, increasing the chain length should lead to smaller
+oscillations. The keyword <I>pchain</I> specifies the number of
+thermostats in the chain thermostatting the barostat degrees of
+freedom.
+</P>
+<P>IMPORTANT NOTE: There are alternate ways to thermostat a system of
+rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> to treat
+the individual particles in the rigid bodies as effectively immersed
+in an implicit solvent, e.g. a Brownian dynamics model. For hybrid
+systems with both rigid bodies and solvent particles, you can
+thermostat only the solvent particles that surround one or more rigid
+bodies by appropriate choice of groups in the compute and fix commands
+for temperature and thermostatting. The solvent interactions with the
+rigid bodies should then effectively thermostat the rigid body
+temperature as well without use of the Langevin or Nose/Hoover options
+associated with the fix rigid commands.
+</P>
+<HR>
+
+<P>The <I>mol</I> keyword can only be used with fix rigid/small. It must be
+used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
+<A HREF = "fix_pour.html">fix pour</A>, add rigid bodies on-the-fly during a
+simulation. You specify a <I>template-ID</I> previously defined using the
+<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
+molecule. You must use the same <I>template-ID</I> that the other fix
+which is adding rigid bodies uses. The coordinates, atom types, atom
+diameters, center-of-mass, and moments of inertia can be specified in
+the molecule file. See the <A HREF = "molecule.html">molecule</A> command for
+details. The only settings required to be in this file are the
+coordinates and types of atoms in the molecule, in which case the
+molecule command calculates the other quantities itself.
+</P>
+<P>Note that these other fixes create new rigid bodies, in addition to
+those defined initially by this fix via the <I>bodystyle</I> setting.
+</P>
+<P>Also note that when using the <I>mol</I> keyword, extra restart information
+about all rigid bodies is written out whenever a restart file is
+written out. See the IMPORTANT NOTE in the next section for details.
+</P>
+<HR>
+
+<P>The <I>infile</I> keyword allows a file of rigid body attributes to be read
+in from a file, rather then having LAMMPS compute them. There are 5
+such attributes: the total mass of the rigid body, its center-of-mass
+position, its 6 moments of inertia, its center-of-mass velocity, and
+the 3 image flags of the center-of-mass position. For rigid bodies
+consisting of point particles or non-overlapping finite-size
+particles, LAMMPS can compute these values accurately. However, for
+rigid bodies consisting of finite-size particles which overlap each
+other, LAMMPS will ignore the overlaps when computing these 4
+attributes. The amount of error this induces depends on the amount of
+overlap. To avoid this issue, the values can be pre-computed
+(e.g. using Monte Carlo integration).
+</P>
+<P>The format of the file is as follows. Note that the file does not
+have to list attributes for every rigid body integrated by fix rigid.
+Only bodies which the file specifies will have their computed
+attributes overridden. The file can contain initial blank lines or
+comment lines starting with "#" which are ignored. The first
+non-blank, non-comment line should list N = the number of lines to
+follow. The N successive lines contain the following information:
+</P>
+<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+...
+IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+</PRE>
+<P>The rigid body IDs are all positive integers. For the <I>single</I>
+bodystyle, only an ID of 1 can be used. For the <I>group</I> bodystyle,
+IDs from 1 to Ng can be used where Ng is the number of specified
+groups. For the <I>molecule</I> bodystyle, use the molecule ID for the
+atoms in a specific rigid body as the rigid body ID.
+</P>
+<P>The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
+self-explanatory. The center-of-mass should be consistent with what
+is calculated for the position of the rigid body with all its atoms
+unwrapped by their respective image flags. If this produces a
+center-of-mass that is outside the simulation box, LAMMPS wraps it
+back into the box.
+</P>
+<P>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass. The values are with respect to the
+simulation box XYZ axes, not with respect to the prinicpal axes of the
+rigid body itself. LAMMPS performs the latter calculation internally.
+</P>
+<P>The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
+The (lx,ly,lz) values are the angular momentum of the body. The
+(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
+wish the body to have no initial motion.
+</P>
+<P>The (ixcm,iycm,izcm) values are the image flags of the center of mass
+of the body. For periodic dimensions, they specify which image of the
+simulation box the body is considered to be in. An image of 0 means
+it is inside the box as defined. A value of 2 means add 2 box lengths
+to get the true value. A value of -1 means subtract 1 box length to
+get the true value. LAMMPS updates these flags as the rigid bodies
+cross periodic boundaries during the simulation.
+</P>
+<P>IMPORTANT NOTE: If you use the <I>infile</I> or <I>mol</I> keywords and write
+restart files during a simulation, then each time a restart file is
+written, the fix also write an auxiliary restart file with the name
+rfile.rigid, where "rfile" is the name of the restart file,
+e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
+file is in the same format described above. Thus it can be used in a
+new input script that restarts the run and re-specifies a rigid fix
+using an <I>infile</I> keyword and the appropriate filename. Note that the
+auxiliary file will contain one line for every rigid body, even if the
+original file only listed a subset of the rigid bodies.
+</P>
+<HR>
+
+<P>If you use a <A HREF = "compute.html">temperature compute</A> with a group that
+includes particles in rigid bodies, the degrees-of-freedom removed by
+each rigid body are accounted for in the temperature (and pressure)
+computation, but only if the temperature group includes all the
+particles in a particular rigid body.
+</P>
+<P>A 3d rigid body has 6 degrees of freedom (3 translational, 3
+rotational), except for a collection of point particles lying on a
+straight line, which has only 5, e.g a dimer. A 2d rigid body has 3
+degrees of freedom (2 translational, 1 rotational).
+</P>
+<P>IMPORTANT NOTE: You may wish to explicitly subtract additional
+degrees-of-freedom if you use the <I>force</I> and <I>torque</I> keywords to
+eliminate certain motions of one or more rigid bodies. LAMMPS does
+not do this automatically.
+</P>
+<P>The rigid body contribution to the pressure of the system (virial) is
+also accounted for by this fix.
+</P>
+<HR>
+
+<P>If your simlulation is a hybrid model with a mixture of rigid bodies
+and non-rigid particles (e.g. solvent) there are several ways these
+rigid fixes can be used in tandem with <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix
+nvt</A>, <A HREF = "fix_nh.html">fix npt</A>, and <A HREF = "fix_nh.html">fix nph</A>.
+</P>
+<P>If you wish to perform NVE dynamics (no thermostatting or
+barostatting), use fix rigid or fix rigid/nve to integrate the rigid
+bodies, and <A HREF = "fix_nve.html">fix nve</A> to integrate the non-rigid
+particles.
+</P>
+<P>If you wish to perform NVT dynamics (thermostatting, but no
+barostatting), you can use fix rigid/nvt for the rigid bodies, and any
+thermostatting fix for the non-rigid particles (<A HREF = "fix_nh.html">fix nvt</A>,
+<A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_temp_berendsen.html">fix
+temp/berendsen</A>). You can also use fix rigid
+or fix rigid/nve for the rigid bodies and thermostat them using <A HREF = "fix_langevin.html">fix
+langevin</A> on the group that contains all the
+particles in the rigid bodies. The net force added by <A HREF = "fix_langevin.html">fix
+langevin</A> to each rigid body effectively thermostats
+its translational center-of-mass motion. Not sure how well it does at
+thermostatting its rotational motion.
+</P>
+<P>If you with to perform NPT or NPH dynamics (barostatting), you cannot
+use both <A HREF = "fix_nh.html">fix npt</A> and fix rigid/npt (or the nph
+variants). This is because there can only be one fix which monitors
+the global pressure and changes the simulation box dimensions. So you
+have 3 choices:
+</P>
+<UL><LI>Use fix rigid/npt for the rigid bodies. Use the <I>dilate</I> all option
+so that it will dilate the positions of the non-rigid particles as
+well. Use <A HREF = "fix_nh.html">fix nvt</A> (or any other thermostat) for the
+non-rigid particles.
+
+<LI>Use <A HREF = "fix_nh.html">fix npt</A> for the group of non-rigid particles. Use
+the <I>dilate</I> all option so that it will dilate the center-of-mass
+positions of the rigid bodies as well. Use fix rigid/nvt for the
+rigid bodies.
+
+<LI>Use <A HREF = "fix_press_berendsen.html">fix press/berendsen</A> to compute the
+pressure and change the box dimensions. Use fix rigid/nvt for the
+rigid bodies. Use <A HREF = "fix_nh.thml">fix nvt</A> (or any other thermostat) for
+the non-rigid particles.
+</UL>
+<P>In all case, the rigid bodies and non-rigid particles both contribute
+to the global pressure and the box is scaled the same by any of the
+barostatting fixes.
+</P>
+<P>You could even use the 2nd and 3rd options for a non-hybrid simulation
+consisting of only rigid bodies, assuming you give <A HREF = "fix_nh.html">fix
+npt</A> an empty group, though it's an odd thing to do. The
+barostatting fixes (<A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_press_berendsen.html">fix
+press/berensen</A>) will monitor the pressure
+and change the box dimensions, but not time integrate any particles.
+The integration of the rigid bodies will be performed by fix
+rigid/nvt.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about the <I>rigid</I> and <I>rigid/small</I> and <I>rigid/nve</I>
+fixes are written to <A HREF = "restart.html">binary restart files</A>. The
+exception is if the <I>infile</I> or <I>mol</I> keyword is used, in which case
+an auxiliary file is written out with rigid body information each time
+a restart file is written, as explained above for the <I>infile</I>
+keyword. For style <I>rigid/nvt</I> the state of the Nose/Hoover
+thermostat is written to <A HREF = "restart.html">binary restart files</A>. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by the
+rigid/nvt fix to add the energy change induced by the thermostatting
+to the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by the rigid/npt and rigid/nph fixes to change the computes used
+to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix
+does not use any external compute to compute instantaneous temperature.
+</P>
+<P>The <I>rigid</I> and <I>rigid/small</I> and <I>rigid/nve</I> fixes compute a global
+scalar which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar value calculated by
+these fixes is "intensive". The scalar is the current temperature of
+the collection of rigid bodies. This is averaged over all rigid
+bodies and their translational and rotational degrees of freedom. The
+translational energy of a rigid body is 1/2 m v^2, where m = total
+mass of the body and v = the velocity of its center of mass. The
+rotational energy of a rigid body is 1/2 I w^2, where I = the moment
+of inertia tensor of the body and w = its angular velocity. Degrees
+of freedom constrained by the <I>force</I> and <I>torque</I> keywords are
+removed from this calculation, but only for the <I>rigid</I> and
+<I>rigid/nve</I> fixes.
+</P>
+<P>The <I>rigid/nvt</I>, <I>rigid/npt</I>, and <I>rigid/nph</I> fixes compute a global
+scalar which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar value calculated by
+these fixes is "extensive". The scalar is the cumulative energy
+change due to the thermostatting and barostatting the fix performs.
+</P>
+<P>All of the <I>rigid</I> fixes except <I>rigid/small</I> compute a global array
+of values which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The number of rows in the
+array is equal to the number of rigid bodies. The number of columns
+is 15. Thus for each rigid body, 15 values are stored: the xyz coords
+of the center of mass (COM), the xyz components of the COM velocity,
+the xyz components of the force acting on the COM, the xyz components
+of the torque acting on the COM, and the xyz image flags of the COM.
+</P>
+<P>The center of mass (COM) for each body is similar to unwrapped
+coordinates written to a dump file. It will always be inside (or
+slightly outside) the simulation box. The image flags have the same
+meaning as image flags for atom positions (see the "dump" command).
+This means you can calculate the unwrapped COM by applying the image
+flags to the COM, the same as when unwrapped coordinates are written
+to a dump file.
+</P>
+<P>The force and torque values in the array are not affected by the
+<I>force</I> and <I>torque</I> keywords in the fix rigid command; they reflect
+values before any changes are made by those keywords.
+</P>
+<P>The ordering of the rigid bodies (by row in the array) is as follows.
+For the <I>single</I> keyword there is just one rigid body. For the
+<I>molecule</I> keyword, the bodies are ordered by ascending molecule ID.
+For the <I>group</I> keyword, the list of group IDs determines the ordering
+of bodies.
+</P>
+<P>The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
+</P>
+<P>No parameter of these fixes can be used with the <I>start/stop</I> keywords
+of the <A HREF = "run.html">run</A> command. These fixes are not invoked during
+<A HREF = "minimize.html">energy minimization</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These fixes are all part of the RIGID package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Assigning a temperature via the <A HREF = "velocity.html">velocity create</A>
+command to a system with <A HREF = "fix_rigid.html">rigid bodies</A> may not have
+the desired outcome for two reasons. First, the velocity command can
+be invoked before the rigid-body fix is invoked or initialized and the
+number of adjusted degrees of freedom (DOFs) is known. Thus it is not
+possible to compute the target temperature correctly. Second, the
+assigned velocities may be partially canceled when constraints are
+first enforced, leading to a different temperature than desired. A
+workaround for this is to perform a <A HREF = "run.html">run 0</A> command, which
+insures all DOFs are accounted for properly, and then rescale the
+temperature to the desired value before performing a simulation. For
+example:
+</P>
+<PRE>velocity all create 300.0 12345
+run 0 # temperature may not be 300K
+velocity all scale 300.0 # now it should be
+</PRE>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "neigh_modify.html">neigh_modify</A>
+exclude, <A HREF = "fix_shake.html">fix shake</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are force * on on on and torque * on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
+</P>
+<HR>
+
+<A NAME = "Hoover"></A>
+
+<P><B>(Hoover)</B> Hoover, Phys Rev A, 31, 1695 (1985).
+</P>
+<A NAME = "Kamberaj"></A>
+
+<P><B>(Kamberaj)</B> Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
+</P>
+<A NAME = "Martyna"></A>
+
+<P><B>(Martyna)</B> Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
+</P>
+<A NAME = "Miller"></A>
+
+<P><B>(Miller)</B> Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
+J Chem Phys, 116, 8649 (2002).
+</P>
+<A NAME = "Zhang"></A>
+
+<P><B>(Zhang)</B> Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_saed_vtk.html b/doc/doc2/fix_saed_vtk.html
new file mode 100644
index 000000000..25b281cb2
--- /dev/null
+++ b/doc/doc2/fix_saed_vtk.html
@@ -0,0 +1,199 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix saed/vtk command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>saed/vtk = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nrepeat = # of times to use input values for calculating averages
+
+<LI>Nfreq = calculate averages every this many timesteps
+
+<LI>c_ID = saed compute ID
+
+<PRE>keyword = <I>file</I> or <I>ave</I> or <I>start</I> or <I>file</I> or <I>overwrite</I>:l
+ <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+ one = output a new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+ <I>start</I> args = Nstart
+ Nstart = start averaging on this timestep
+ <I>file</I> arg = filename
+ filename = name of file to output time averages to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+</PRE>
+<PRE>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Time average computed intensities from <A HREF = "compute_saed.txt">compute_saed</A> and
+write output to a file in the 3rd generation vtk image data format for
+visualization directly in parallelized visualization software packages
+like ParaView and VisIt. Note that if no time averaging is done, this
+command can be used as a convenient way to simply output diffraction
+intensities at a single snapshot.
+</P>
+<P>To produce output in the image data vtk format ghost data is added
+outside the <I>Kmax</I> range assigned in the compute saed. The ghost data is
+assigned a value of -1 and can be removed setting a minimum isovolume
+of 0 within the vizualiziton software. SAED images can be created by
+visualizing a spherical slice of the data that is centered at
+R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.
+</P>
+<P>The group specified within this command is ignored. However, note that
+specified values may represent calculations performed by saed computes
+which store their own "group" definitions.
+</P>
+<P>Fix saed/vtk is designed to work only with <A HREF = "compute_saed.txt">compute_saed</A>
+values, e.g.
+</P>
+<PRE>compute 3 top saed 0.0251 Al O
+fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
+</PRE>
+<HR>
+
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the input values will be used in order to contribute to the
+average. The final averaged quantities are generated on timesteps
+that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
+quantities, computed in the preceding portion of the simulation every
+<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
+<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
+contributing to the average value cannot overlap, i.e. Nfreq >
+(Nrepeat-1)*Nevery is required.
+</P>
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
+timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
+averaging is done; values are simply generated on timesteps
+100,200,etc.
+</P>
+<HR>
+
+<P>The output for fix ave/time/saed is a file writen with the 3rd generation
+vtk image data formatting. The filename assigned by the <I>file</I> keyword is
+appended with _N.vtk where N is an index (0,1,2...) to account for multiple
+diffraction intensity outputs.
+</P>
+<P>By default the header contains the following information (with example data):
+</P>
+<PRE># vtk DataFile Version 3.0 c_SAED
+Image data set
+ASCII
+DATASET STRUCTURED_POINTS
+DIMENSIONS 337 219 209
+ASPECT_RATIO 0.00507953 0.00785161 0.00821458
+ORIGIN -0.853361 -0.855826 -0.854316
+POINT_DATA 15424827
+SCALARS intensity float
+LOOKUP_TABLE default
+...data
+</PRE>
+<P>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
+where the mesh spacing is approximately 0.005, 0.007, and 0.008
+inv(length) units in the k1, k2, and k3 directions, respectively.
+The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
+the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
+sampled in total.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
+</P>
+<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
+steps are averaged with values produced on previous steps that were
+multiples of <I>Nfreq</I>, before they are accessed by another output
+command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
+that are multiples of <I>Nfreq</I> are independent of each other; they are
+output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cumulative sense before being output. Each output value is thus the
+average of the value produced on that timestep with all preceding
+values. This running average begins when the fix is defined; it can
+only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
+command, or by re-defining the fix by re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000. Outputs on early steps will average over less than M
+values if they are not available.
+</P>
+<P>The <I>start</I> keyword specifies what timestep averaging will begin on.
+The default is step 0. Often input values can be 0.0 at time 0, so
+setting <I>start</I> to a larger value can avoid including a 0.0 in a
+running or windowed average.
+</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+steps, the vector of saed intensity data is written to a new file using
+the 3rd generation vtk format. The base of each file is assigned by
+the <I>file</I> keyword and this string is appended with _N.vtk where N is
+an index (0,1,2...) to account for situations with multiple diffraction
+intensity outputs.
+</P>
+<P>The <I>overwrite</I> keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output. This option can only be used with the <I>ave running</I> setting.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The attributes for fix_saed_vtk must match the values assigned in the
+associated <A HREF = "compute_saed.html">compute_saed</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_saed.html">compute_saed</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are ave = one, start = 0, no file output.
+</P>
+<HR>
+
+<A NAME = "Coleman"></A>
+
+<P><B>(Coleman)</B> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
+(2013).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_setforce.html b/doc/doc2/fix_setforce.html
new file mode 100644
index 000000000..da6ffb5d3
--- /dev/null
+++ b/doc/doc2/fix_setforce.html
@@ -0,0 +1,129 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix setforce command
+</H3>
+<H3>fix setforce/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID setforce fx fy fz keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>setforce = style name of this fix command
+
+<LI>fx,fy,fz = force component values
+
+<LI>any of fx,fy,fz can be a variable (see below)
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>region</I>
+
+<PRE> <I>region</I> value = region-ID
+ region-ID = ID of region atoms must be in to have added force
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix freeze indenter setforce 0.0 0.0 0.0
+fix 2 edge setforce NULL 0.0 0.0
+fix 2 edge setforce NULL 0.0 v_oscillate
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set each component of force on each atom in the group to the specified
+values fx,fy,fz. This erases all previously computed forces on the
+atom, though additional fixes could add new forces. This command can
+be used to freeze certain atoms in the simulation by zeroing their
+force, either for running dynamics or performing an energy
+minimization. For dynamics, this assumes their initial velocity is
+also zero.
+</P>
+<P>Any of the fx,fy,fz values can be specified as NULL which means do not
+alter the force component in that dimension.
+</P>
+<P>Any of the 3 quantities defining the force components can be specified
+as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
+<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+force component.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent force field.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent force
+field with optional time-dependence as well.
+</P>
+<P>If the <I>region</I> keyword is used, the atom must also be in the
+specified geometric <A HREF = "region.html">region</A> in order to have force added
+to it.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global 3-vector of forces, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix. The vector values calculated by this
+fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command, but you cannot set
+forces to any value besides zero when performing a minimization. Use
+the <A HREF = "fix_addforce.html">fix addforce</A> command if you want to apply a
+non-zero force to atoms during a minimization.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_addforce.html">fix addforce</A>, <A HREF = "fix_aveforce.html">fix aveforce</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_shake.html b/doc/doc2/fix_shake.html
new file mode 100644
index 000000000..064713a0e
--- /dev/null
+++ b/doc/doc2/fix_shake.html
@@ -0,0 +1,244 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix shake command
+</H3>
+<H3>fix shake/cuda command
+</H3>
+<H3>fix rattle command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style tol iter N constraint values ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style = shake or rattle = style name of this fix command
+
+<LI>tol = accuracy tolerance of SHAKE solution
+
+<LI>iter = max # of iterations in each SHAKE solution
+
+<LI>N = print SHAKE statistics every this many timesteps (0 = never)
+
+<LI>one or more constraint/value pairs are appended
+
+<LI>constraint = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
+
+<PRE> <I>b</I> values = one or more bond types
+ <I>a</I> values = one or more angle types
+ <I>t</I> values = one or more atom types
+ <I>m</I> value = one or more mass values
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>mol</I>
+
+<PRE> <I>mol</I> value = template-ID
+ template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
+fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
+fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
+fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31
+fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply bond and angle constraints to specified bonds and angles in the
+simulation by either the SHAKE or RATTLE algorithms. This typically
+enables a longer timestep.
+</P>
+<P><B>SHAKE vs RATTLE:</B>
+</P>
+<P>The SHAKE algorithm was invented for schemes such as standard Verlet
+timesteppnig, where only the coordinates are integrated and the
+velocities are approximated as finite differences to the trajectories
+(<A HREF = "#Ryckaert">Ryckaert et al. (1977)</A>). If the velocities are
+integrated explicitly, as with velocity Verlet which is what LAMMPS
+uses as an integration method, a second set of constraining forces is
+required in order to eliminate velocity components along the bonds
+(<A HREF = "#Andersen">Andersen (1983)</A>).
+</P>
+<P>In order to formulate individual constraints for SHAKE and RATTLE,
+focus on a single molecule whose bonds are constrained. Let Ri and Vi
+be the position and velocity of atom <I>i</I> at time <I>n</I>, for
+<I>i</I>=1,...,<I>N</I>, where <I>N</I> is the number of sites of our reference
+molecule. The distance vector between sites <I>i</I> and <I>j</I> is given by
+</P>
+<CENTER><IMG SRC = "Eqs/fix_rattle_rij.jpg">
+</CENTER>
+<P>The constraints can then be formulated as
+</P>
+<CENTER><IMG SRC = "Eqs/fix_rattle_constraints.jpg">
+</CENTER>
+<P>The SHAKE algorithm satisfies the first condition, i.e. the sites at
+time <I>n+1</I> will have the desired separations Dij immediately after the
+coordinates are integrated. If we also enforce the second condition,
+the velocity components along the bonds will vanish. RATTLE satisfies
+both conditions. As implemented in LAMMPS, fix rattle uses fix shake
+for satisfying the coordinate constraints. Therefore the settings and
+optional keywords are the same for both fixes, and all the information
+below about SHAKE is also relevant for RATTLE.
+</P>
+<P><B>SHAKE:</B>
+</P>
+<P>Each timestep the specified bonds and angles are reset to their
+equilibrium lengths and angular values via the SHAKE algorithm
+(<A HREF = "#Ryckaert">Ryckaert et al. (1977)</A>). This is done by applying an
+additional constraint force so that the new positions preserve the
+desired atom separations. The equations for the additional force are
+solved via an iterative method that typically converges to an accurate
+solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1
+part in 10000) and maximum # of iterations are specified as arguments.
+Setting the N argument will print statistics to the screen and log
+file about regarding the lengths of bonds and angles that are being
+constrained. Small delta values mean SHAKE is doing a good job.
+</P>
+<P>In LAMMPS, only small clusters of atoms can be constrained. This is
+so the constraint calculation for a cluster can be performed by a
+single processor, to enable good parallel performance. A cluster is
+defined as a central atom connected to others in the cluster by
+constrained bonds. LAMMPS allows for the following kinds of clusters
+to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
+one central atom bonded to 2 others and the angle between the 3 atoms
+also constrained. This means water molecules or CH2 or CH3 groups may
+be constrained, but not all the C-C backbone bonds of a long polymer
+chain.
+</P>
+<P>The <I>b</I> constraint lists bond types that will be constrained. The <I>t</I>
+constraint lists atom types. All bonds connected to an atom of the
+specified type will be constrained. The <I>m</I> constraint lists atom
+masses. All bonds connected to atoms of the specified masses will be
+constrained (within a fudge factor of MASSDELTA specified in
+fix_shake.cpp). The <I>a</I> constraint lists angle types. If both bonds
+in the angle are constrained then the angle will also be constrained
+if its type is in the list.
+</P>
+<P>For all constraints, a particular bond is only constrained if both
+atoms in the bond are in the group specified with the SHAKE fix.
+</P>
+<P>The degrees-of-freedom removed by SHAKE bonds and angles are accounted
+for in temperature and pressure computations. Similarly, the SHAKE
+contribution to the pressure of the system (virial) is also accounted
+for.
+</P>
+<P>IMPORTANT NOTE: This command works by using the current forces on
+atoms to caculate an additional constraint force which when added will
+leave the atoms in positions that satisfy the SHAKE constraints
+(e.g. bond length) after the next time integration step. If you
+define fixes (e.g. <A HREF = "fix_efield.html">fix efield</A>) that add additional
+force to the atoms after fix shake operates, then this fix will not
+take them into account and the time integration will typically not
+satisfy the SHAKE constraints. The solution for this is to make sure
+that fix shake is defined in your input script after any other fixes
+which add or change forces (to atoms that fix shake operates on).
+</P>
+<HR>
+
+<P>The <I>mol</I> keyword should be used when other commands, such as <A HREF = "fix_deposit.html">fix
+deposit</A> or <A HREF = "fix_pour.html">fix pour</A>, add molecules
+on-the-fly during a simulation, and you wish to contrain the new
+molecules via SHAKE. You specify a <I>template-ID</I> previously defined
+using the <A HREF = "molecule.html">molecule</A> command, which reads a file that
+defines the molecule. You must use the same <I>template-ID</I> that the
+command adding molecules uses. The coordinates, atom types, special
+bond restrictions, and SHAKE info can be specified in the molecule
+file. See the <A HREF = "molecule.html">molecule</A> command for details. The only
+settings required to be in this file (by this command) are the SHAKE
+info of atoms in the molecule.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>RATTLE:</B>
+</P>
+<P>The velocity constraints lead to a linear system of equations which
+can be solved analytically. The implementation of the algorithm in
+LAMMPS closely follows (<A HREF = "#Andersen">Andersen (1983)</A>).
+</P>
+<P>IMPORTANT NOTE: The fix rattle command modifies forces and velocities
+and thus should be defined after all other integration fixes in your
+input script. If you define other fixes that modify velocities or
+forces after fix rattle operates, then fix rattle will not take them
+into account and the overall time integration will typically not
+satisfy the RATTLE constraints. You can check whether the constraints
+work correctly by setting the value of RATTLE_DEBUG in
+src/fix_rattle.cpp to 1 and recompiling LAMMPS.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about these fixes is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to these fixes. No global or per-atom quantities are
+stored by these fixes for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of these fixes
+can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command. These fixes are not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These fixes are part of the RIGID package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>For computational efficiency, there can only be one shake or rattle
+fix defined in a simulation.
+</P>
+<P>If you use a tolerance that is too large or a max-iteration count that
+is too small, the constraints will not be enforced very strongly,
+which can lead to poor energy conservation. You can test for this in
+your system by running a constant NVE simulation with a particular set
+of SHAKE parameters and monitoring the energy versus time.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ryckaert"></A>
+
+<P><B>(Ryckaert)</B> J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
+J of Comp Phys, 23, 327-341 (1977).
+</P>
+<A NAME = "Andersen"></A>
+
+<P><B>(Andersen)</B> H. Andersen, J of Comp Phys, 52, 24-34 (1983).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_smd.html b/doc/doc2/fix_smd.html
new file mode 100644
index 000000000..ececffdc4
--- /dev/null
+++ b/doc/doc2/fix_smd.html
@@ -0,0 +1,162 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix smd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID smd type values keyword values
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>smd = style name of this fix command
+
+<LI>mode = <I>cvel</I> or <I>cfor</I> to select constant velocity or constant force SMD
+
+<PRE> <I>cvel</I> values = K vel
+ K = spring constant (force/distance units)
+ vel = velocity of pulling (distance/time units)
+ <I>cfor</I> values = force
+ force = pulling force (force units)
+</PRE>
+<LI>keyword = <I>tether</I> or <I>couple</I>
+
+<PRE> <I>tether</I> values = x y z R0
+ x,y,z = point to which spring is tethered
+ R0 = distance of end of spring from tether point (distance units)
+ <I>couple</I> values = group-ID2 x y z R0
+ group-ID2 = 2nd group to couple to fix group with a spring
+ x,y,z = direction of spring, automatically computed with 'auto'
+ R0 = distance of end of spring (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
+fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
+fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
+fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix implements several options of steered MD (SMD) as reviewed in
+<A HREF = "#Izrailev">(Izrailev)</A>, which allows to induce conformational changes
+in systems and to compute the potential of mean force (PMF) along the
+assumed reaction coordinate <A HREF = "#Park">(Park)</A> based on Jarzynski's
+equality <A HREF = "#Jarzynski">(Jarzynski)</A>. This fix borrows a lot from <A HREF = "fix_spring.html">fix
+spring</A> and <A HREF = "fix_setforce.html">fix setforce</A>.
+</P>
+<P>You can apply a moving spring force to a group of atoms (<I>tether</I>
+style) or between two groups of atoms (<I>couple</I> style). The spring
+can then be used in either constant velocity (<I>cvel</I>) mode or in
+constant force (<I>cfor</I>) mode to induce transitions in your systems.
+When running in <I>tether</I> style, you may need some way to fix some
+other part of the system (e.g. via <A HREF = "fix_spring_self.html">fix
+spring/self</A>)
+</P>
+<P>The <I>tether</I> style attaches a spring between a point at a distance of
+R0 away from a fixed point <I>x,y,z</I> and the center of mass of the fix
+group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
+applied to each atom in the group where <I>K</I> is the spring constant, Mi
+is the mass of the atom, and M is the total mass of all atoms in the
+group. Note that <I>K</I> thus represents the total force on the group of
+atoms, not a per-atom force.
+</P>
+<P>In <I>cvel</I> mode the distance R is incremented or decremented
+monotonously according to the pulling (or pushing) velocity.
+In <I>cfor</I> mode a constant force is added and the actual distance
+in direction of the spring is recorded.
+</P>
+<P>The <I>couple</I> style links two groups of atoms together. The first
+group is the fix group; the second is specified by group-ID2. The
+groups are coupled together by a spring that is at equilibrium when
+the two groups are displaced by a vector in direction <I>x,y,z</I> with
+respect to each other and at a distance R0 from that displacement.
+Note that <I>x,y,z</I> only provides a direction and will be internally
+normalized. But since it represents the <I>absolute</I> displacement of
+group-ID2 relative to the fix group, (1,1,0) is a different spring
+than (-1,-1,0). For each vector component, the displacement can be
+described with the <I>auto</I> parameter. In this case the direction is
+recomputed in every step, which can be useful for steering a local
+process where the whole object undergoes some other change. When the
+relative positions and distance between the two groups are not in
+equilibrium, the same spring force described above is applied to atoms
+in each of the two groups.
+</P>
+<P>For both the <I>tether</I> and <I>couple</I> styles, any of the x,y,z values can
+be specified as NULL which means do not include that dimension in the
+distance calculation or force application.
+</P>
+<P>For constant velocity pulling (<I>cvel</I> mode), the running integral
+over the pulling force in direction of the spring is recorded and
+can then later be used to compute the potential of mean force (PMF)
+by averaging over multiple independent trajectories along the same
+pulling path.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>The fix stores the direction of the spring, current pulling target
+distance and the running PMF to <A HREF = "restart.html">binary restart files</A>.
+See the <A HREF = "read_restart.html">read_restart</A> command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>This fix computes a vector list of 7 quantities, which can be accessed
+by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The
+quantities in the vector are in this order: the x-, y-, and
+z-component of the pulling force, the total force in direction of the
+pull, the equilibrium distance of the spring, the distance between the
+two reference points, and finally the accumulated PMF (the sum of
+pulling forces times displacement).
+</P>
+<P>The force is the total force on the group of atoms by the spring. In
+the case of the <I>couple</I> style, it is the force on the fix group
+(group-ID) or the negative of the force on the 2nd group (group-ID2).
+The vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring.html">fix spring</A>,
+<A HREF = "fix_spring_self.html">fix spring/self</A>,
+<A HREF = "fix_spring_rg.html">fix spring/rg</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Israilev"></A>
+
+<P><B>(Izrailev)</B> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
+Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
+Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
+Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
+</P>
+<P><B>(Park)</B>
+Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
+</P>
+<P><B>(Jarzynski)</B>
+Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_spring.html b/doc/doc2/fix_spring.html
new file mode 100644
index 000000000..80d6d695d
--- /dev/null
+++ b/doc/doc2/fix_spring.html
@@ -0,0 +1,151 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix spring command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID spring keyword values
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>spring = style name of this fix command
+
+<LI>keyword = <I>tether</I> or <I>couple</I>
+
+<PRE> <I>tether</I> values = K x y z R0
+ K = spring constant (force/distance units)
+ x,y,z = point to which spring is tethered
+ R0 = equilibrium distance from tether point (distance units)
+ <I>couple</I> values = group-ID2 K x y z R0
+ group-ID2 = 2nd group to couple to fix group with a spring
+ K = spring constant (force/distance units)
+ x,y,z = direction of spring
+ R0 = equilibrium distance of spring (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
+fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0
+fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0
+fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0
+fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0
+fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a spring force to a group of atoms or between two groups of
+atoms. This is useful for applying an umbrella force to a small
+molecule or lightly tethering a large group of atoms (e.g. all the
+solvent or a large molecule) to the center of the simulation box so
+that it doesn't wander away over the course of a long simulation. It
+can also be used to hold the centers of mass of two groups of atoms at
+a given distance or orientation with respect to each other.
+</P>
+<P>The <I>tether</I> style attaches a spring between a fixed point <I>x,y,z</I> and
+the center of mass of the fix group of atoms. The equilibrium
+position of the spring is R0. At each timestep the distance R from
+the center of mass of the group of atoms to the tethering point is
+computed, taking account of wrap-around in a periodic simulation box.
+A restoring force of magnitude K (R - R0) Mi / M is applied to each
+atom in the group where <I>K</I> is the spring constant, Mi is the mass of
+the atom, and M is the total mass of all atoms in the group. Note
+that <I>K</I> thus represents the total force on the group of atoms, not a
+per-atom force.
+</P>
+<P>The <I>couple</I> style links two groups of atoms together. The first
+group is the fix group; the second is specified by group-ID2. The
+groups are coupled together by a spring that is at equilibrium when
+the two groups are displaced by a vector <I>x,y,z</I> with respect to each
+other and at a distance R0 from that displacement. Note that <I>x,y,z</I>
+is the equilibrium displacement of group-ID2 relative to the fix
+group. Thus (1,1,0) is a different spring than (-1,-1,0). When the
+relative positions and distance between the two groups are not in
+equilibrium, the same spring force described above is applied to atoms
+in each of the two groups.
+</P>
+<P>For both the <I>tether</I> and <I>couple</I> styles, any of the x,y,z values can
+be specified as NULL which means do not include that dimension in the
+distance calculation or force application.
+</P>
+<P>The first example above pulls the ligand towards the point (0,0,0).
+The second example holds the ligand near the surface of a sphere of
+radius 5 around the point (0,0,0). The third example holds the ligand
+a distance 3 away from the z=2 plane (on either side).
+</P>
+<P>The fourth example holds 2 bilayers a distance 10 apart in z. For the
+last two examples, imagine a pore (a slab of atoms with a cylindrical
+hole cut out) oriented with the pore axis along z, and an ion moving
+within the pore. The fifth example holds the ion a distance of -20
+below the z = 0 center plane of the pore (umbrella sampling). The
+last example holds the ion a distance 5 away from the pore axis
+(assuming the center-of-mass of the pore in x,y is the pore axis).
+</P>
+<P>IMPORTANT NOTE: The center of mass of a group of atoms is calculated
+in "unwrapped" coordinates using atom image flags, which means that
+the group can straddle a periodic boundary. See the <A HREF = "dump.html">dump</A>
+doc page for a discussion of unwrapped coordinates. It also means
+that a spring connecting two groups or a group and the tether point
+can cross a periodic boundary and its length be calculated correctly.
+One exception is for rigid bodies, which should not be used with the
+fix spring command, if the rigid body will cross a periodic boundary.
+This is because image flags for rigid bodies are used in a different
+way, as explained on the <A HREF = "fix_rigid.html">fix rigid</A> doc page.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy stored in the spring to the system's potential
+energy as part of <A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+spring energy = 0.5 * K * r^2.
+</P>
+<P>This fix also computes global 4-vector which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The first 3
+quantities in the vector are xyz components of the total force added
+to the group of atoms by the spring. In the case of the <I>couple</I>
+style, it is the force on the fix group (group-ID) or the negative of
+the force on the 2nd group (group-ID2). The 4th quantity in the
+vector is the magnitude of the force added by the spring, as a
+positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This
+sign convention can be useful when using the spring force to compute a
+potential of mean force (PMF).
+</P>
+<P>The scalar and vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the spring energy to be included in the
+total potential energy of the system (the quantity being minimized),
+you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
+this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring_self.html">fix spring/self</A>,
+<A HREF = "fix_spring_rg.html">fix spring/rg</A>, <A HREF = "fix_smd.html">fix smd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_spring_rg.html b/doc/doc2/fix_spring_rg.html
new file mode 100644
index 000000000..535e088be
--- /dev/null
+++ b/doc/doc2/fix_spring_rg.html
@@ -0,0 +1,72 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix spring/rg command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID spring/rg K RG0
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>spring/rg = style name of this fix command
+<LI>K = harmonic force constant (force/distance units)
+<LI>RG0 = target radius of gyration to constrain to (distance units)
+</UL>
+<PRE> if RG0 = NULL, use the current RG as the target value
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 protein spring/rg 5.0 10.0
+fix 2 micelle spring/rg 5.0 NULL
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a harmonic restraining force to atoms in the group to affect
+their central moment about the center of mass (radius of gyration).
+This fix is useful to encourage a protein or polymer to fold/unfold
+and also when sampling along the radius of gyration as a reaction
+coordinate (i.e. for protein folding).
+</P>
+<P>The radius of gyration is defined as RG in the first formula. The
+energy of the constraint and associated force on each atom is given by
+the second and third formulas, when the group is at a different RG
+than the target value RG0.
+</P>
+<CENTER><IMG SRC = "Eqs/fix_spring_rg.jpg">
+</CENTER>
+<P>The (xi - center-of-mass) term is computed taking into account
+periodic boundary conditions, m_i is the mass of the atom, and M is
+the mass of the entire group. Note that K is thus a force constant
+for the aggregate force on the group of atoms, not a per-atom force.
+</P>
+<P>If RG0 is specified as NULL, then the RG of the group is computed at
+the time the fix is specified, and that value is used as the target.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_spring.html">fix spring</A>, <A HREF = "fix_spring_self.html">fix spring/self</A>
+<A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_smd.html">fix smd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_spring_self.html b/doc/doc2/fix_spring_self.html
new file mode 100644
index 000000000..7665abddd
--- /dev/null
+++ b/doc/doc2/fix_spring_self.html
@@ -0,0 +1,84 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix spring/self command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID spring/self K dir
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>spring/self = style name of this fix command
+<LI>K = spring constant (force/distance units)
+<LI>dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix tether boundary-atoms spring/self 10.0
+fix zrest move spring/self 10.0 z
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Apply a spring force independently to each atom in the group to tether
+it to its initial position. The initial position for each atom is its
+location at the time the fix command was issued. At each timestep,
+the magnitude of the force on each atom is -Kr, where r is the
+displacement of the atom from its current position to its initial
+position. The distance r correctly takes into account any crossings
+of periodic boundary by the atom since it was in its intitial
+position.
+</P>
+<P>With the (optional) dir flag, one can select in which direction the
+spring force is applied. By default, the restraint is applied in all
+directions, but it can be limited to the xy-, xz-, yz-plane and the
+x-, y-, or z-direction, thus restraining the atoms to a line or a
+plane, respectively.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of tethered atoms to <A HREF = "restart.html">binary
+restart files</A>, so that the spring effect will be the
+same in a restarted simulation. See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy stored in the per-atom springs to the system's
+potential energy as part of <A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is an
+energy which is the sum of the spring energy for each atom, where the
+per-atom energy is 0.5 * K * r^2. The scalar value calculated by this
+fix is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the per-atom spring energy to be included
+in the total potential energy of the system (the quantity being
+minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I>
+option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring.html">fix spring</A>,
+<A HREF = "fix_smd.html">fix smd</A>, <A HREF = "fix_spring_rg.html">fix spring/rg</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_srd.html b/doc/doc2/fix_srd.html
new file mode 100644
index 000000000..9c87160d7
--- /dev/null
+++ b/doc/doc2/fix_srd.html
@@ -0,0 +1,410 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix srd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>srd = style name of this fix command
+<LI>N = reset SRD particle velocities every this many timesteps
+<LI>groupbig-ID = ID of group of large particles that SRDs interact with
+<LI>Tsrd = temperature of SRD particles (temperature units)
+<LI>hgrid = grid spacing for SRD grouping (distance units)
+<LI>seed = random # seed (positive integer)
+</UL>
+<UL><LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>lamda</I> or <I>collision</I> or <I>overlap</I> or <I>inside</I> or <I>exact</I> or <I>radius</I> or <I>bounce</I> or <I>search</I> or <I>cubic</I> or <I>shift</I> or <I>tstat</I> or <I>rescale</I>
+
+<PRE> <I>lamda</I> value = mean free path of SRD particles (distance units)
+ <I>collision</I> value = <I>noslip</I> or <I>slip</I> = collision model
+ <I>overlap</I> value = <I>yes</I> or <I>no</I> = whether big particles may overlap
+ <I>inside</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I> = how SRD particles which end up inside a big particle are treated
+ <I>exact</I> value = <I>yes</I> or <I>no</I>
+ <I>radius</I> value = rfactor = scale collision radius by this factor
+ <I>bounce</I> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
+ <I>search</I> value = sgrid = grid spacing for collision partner searching (distance units)
+ <I>cubic</I> values = style tolerance
+ style = <I>error</I> or <I>warn</I>
+ tolerance = fractional difference allowed (0 <= tol <= 1)
+ <I>shift</I> values = flag shiftseed
+ flag = <I>yes</I> or <I>no</I> or <I>possible</I> = SRD bin shifting for better statistics
+ <I>yes</I> = perform bin shifting each time SRD velocities are rescaled
+ <I>no</I> = no shifting
+ <I>possible</I> = shift depending on mean free path and bin size
+ shiftseed = random # seed (positive integer)
+ <I>tstat</I> value = <I>yes</I> or <I>no</I> = thermostat SRD particles or not
+ <I>rescale</I> value = <I>yes</I> or <I>no</I> or <I>rotate</I> or <I>collide</I> = rescaling of SRD velocities
+ <I>yes</I> = rescale during velocity rotation and collisions
+ <I>no</I> = no rescaling
+ <I>rotate</I> = rescale during velocity rotation, but not collisions
+ <I>collide</I> = rescale during collisions, but not velocity rotation
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 srd srd 10 big 1.0 0.25 482984
+fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Treat a group of partilces as stochastic rotation dynamics (SRD)
+particles that serve as a background solvent when interacting with big
+(colloidal) particles in groupbig-ID. The SRD formalism is described
+in <A HREF = "#Hecht">(Hecht)</A>. The key idea behind using SRD particles as a
+cheap coarse-grained solvent is that SRD particles do not interact
+with each other, but only with the solute particles, which in LAMMPS
+can be spheroids, ellipsoids, or line segments, or triangles, or rigid
+bodies containing multiple spherioids or ellipsoids or line segments
+or triangles. The collision and rotation properties of the model
+imbue the SRD particles with fluid-like properties, including an
+effective viscosity. Thus simulations with large solute particles can
+be run more quickly, to measure solute propoerties like diffusivity
+and viscosity in a background fluid. The usual LAMMPS fixes for such
+simulations, such as <A HREF = "fix_deform.html">fix deform</A>, <A HREF = "fix_viscosity.html">fix
+viscosity</A>, and <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>,
+can be used in conjunction with the SRD model.
+</P>
+<P>For more details on how the SRD model is implemented in LAMMPS, <A HREF = "#Petersen">this
+paper</A> describes the implementation and usage of pure SRD
+fluids. <A HREF = "#Lechman">This paper</A>, which is nearly complete, describes
+the implementation and usage of mixture systems (solute particles in
+an SRD fluid). See the examples/srd directory for sample input
+scripts using SRD particles in both settings.
+</P>
+<P>This fix does 2 things:
+</P>
+<P>(1) It advects the SRD particles, performing collisions between SRD
+and big particles or walls every timestep, imparting force and torque
+to the big particles. Collisions also change the position and
+velocity of SRD particles.
+</P>
+<P>(2) It resets the velocity distribution of SRD particles via random
+rotations every N timesteps.
+</P>
+<P>SRD particles have a mass, temperature, characteristic timestep
+dt_SRD, and mean free path between collisions (lamda). The
+fundamental equation relating these 4 quantities is
+</P>
+<PRE>lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
+</PRE>
+<P>The mass of SRD particles is set by the <A HREF = "mass.html">mass</A> command
+elsewhere in the input script. The SRD timestep dt_SRD is N times the
+step dt defined by the <A HREF = "timestep.html">timestep</A> command. Big
+particles move in the normal way via a time integration <A HREF = "fix.html">fix</A>
+with a short timestep dt. SRD particles advect with a large timestep
+dt_SRD >= dt.
+</P>
+<P>If the <I>lamda</I> keyword is not specified, the the SRD temperature
+<I>Tsrd</I> is used in the above formula to compute lamda. If the <I>lamda</I>
+keyword is specified, then the <I>Tsrd</I> setting is ignored and the above
+equation is used to compute the SRD temperature.
+</P>
+<P>The characteristic length scale for the SRD fluid is set by <I>hgrid</I>
+which is used to bin SRD particles for purposes of resetting their
+velocities. Normally hgrid is set to be 1/4 of the big particle
+diameter or smaller, to adequately resolve fluid properties around the
+big particles.
+</P>
+<P>Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
+(unless the <I>shift</I> keyword is used, see below). The velocities of
+SRD particles are bounded by Vmax, which is set so that an SRD
+particle will not advect further than Dmax = 4*lamda in dt_SRD. This
+means that roughly speaking, Dmax should not be larger than a big
+particle diameter, else SRDs may pass thru big particles without
+colliding. A warning is generated if this is the case.
+</P>
+<P>Collisions between SRD particles and big particles or walls are
+modeled as a lightweight SRD point particle hitting a heavy big
+particle of given diameter or a wall at a point on its surface and
+bouncing off with a new velocity. The collision changes the momentum
+of the SRD particle. It imparts a force and torque to the big
+particle. It imparts a force to a wall. Static or moving SRD walls
+are setup via the <A HREF = "fix_wall_srd.html">fix wall/srd</A> command. For the
+remainder of this doc page, a collision of an SRD particle with a wall
+can be viewed as a collision with a big particle of infinite radius
+and mass.
+</P>
+<P>The <I>collision</I> keyword sets the style of collisions. The <I>slip</I>
+style means that the tangential component of the SRD particle momentum
+is preserved. Thus a force is imparted to a big particle, but no
+torque. The normal component of the new SRD velocity is sampled from
+a Gaussian distribution at temperature <I>Tsrd</I>.
+</P>
+<P>For the <I>noslip</I> style, both the normal and tangential components of
+the new SRD velocity are sampled from a Gaussian distribution at
+temperature <I>Tsrd</I>. Additionally, a new tangential direction for the
+SRD velocity is chosen randomly. This collision style imparts torque
+to a big particle. Thus a time integrator <A HREF = "fix.html">fix</A> that rotates
+the big particles appropriately should be used.
+</P>
+<HR>
+
+<P>The <I>overlap</I> keyword should be set to <I>yes</I> if two (or more) big
+particles can ever overlap. This depends on the pair potential
+interaction used for big-big interactions, or could be the case if
+multiple big particles are held together as rigid bodies via the <A HREF = "fix_rigid.html">fix
+rigid</A> command. If the <I>overlap</I> keyword is <I>no</I> and
+big particles do in fact overlap, then SRD/big collisions can generate
+an error if an SRD ends up inside two (or more) big particles at once.
+How this error is treated is determined by the <I>inside</I> keyword.
+Running with <I>overlap</I> set to <I>no</I> allows for faster collision
+checking, so it should only be set to <I>yes</I> if needed.
+</P>
+<P>The <I>inside</I> keyword determines how a collision is treated if the
+computation determines that the timestep started with the SRD particle
+already inside a big particle. If the setting is <I>error</I> then this
+generates an error message and LAMMPS stops. If the setting is <I>warn</I>
+then this generates a warning message and the code continues. If the
+setting is <I>ignore</I> then no message is generated. One of the output
+quantities logged by the fix (see below) tallies the number of such
+events, so it can be monitored. Note that once an SRD particle is
+inside a big particle, it may remain there for several steps until it
+drifts outside the big particle.
+</P>
+<P>The <I>exact</I> keyword determines how accurately collisions are computed.
+A setting of <I>yes</I> computes the time and position of each collision as
+SRD and big particles move together. A setting of <I>no</I> estimates the
+position of each collision based on the end-of-timestep positions of
+the SRD and big particle. If <I>overlap</I> is set to yes, the setting of
+the <I>exact</I> keyword is ignored since time-accurate collisions are
+needed.
+</P>
+<P>The <I>radius</I> keyword scales the effective size of big particles. If
+big particles will overlap as they undergo dynamics, then this keyword
+can be used to scale down their effective collision radius by an
+amount <I>rfactor</I>, so that SRD particle will only collide with one big
+particle at a time. For example, in a Lennard-Jones system at a
+temperature of 1.0 (in reduced LJ units), the minimum separation
+bewteen two big particles is as small as about 0.88 sigma. Thus an
+<I>rfactor</I> value of 0.85 should prevent dual collisions.
+</P>
+<P>The <I>bounce</I> keyword can be used to limit the maximum number of
+collisions an SRD particle undergoes in a single timestep as it
+bounces between nearby big particles. Note that if the limit is
+reached, the SRD can be left inside a big particle. A setting of 0 is
+the same as no limit.
+</P>
+<HR>
+
+<P>There are 2 kinds of bins created and maintained when running an SRD
+simulation. The first are "SRD bins" which are used to bin SRD
+particles and reset their velocities, as discussed above. The second
+are "search bins" which are used to identify SRD/big particle
+collisions.
+</P>
+<P>The <I>search</I> keyword can be used to choose a search bin size for
+identifying SRD/big particle collisions. The default is to use the
+<I>hgrid</I> parameter for SRD bins as the search bin size. Choosing a
+smaller or large value may be more efficient, depending on the
+problem. But, in a statistical sense, it should not change the
+simulation results.
+</P>
+<P>The <I>cubic</I> keyword can be used to generate an error or warning when
+the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
+different than the requested value of <I>hgrid</I> by a specified
+<I>tolerance</I>. Note that using non-cubic SRD bins can lead to
+undetermined behavior when rotating the velocities of SRD particles,
+hence LAMMPS tries to protect you from this problem.
+</P>
+<P>LAMMPS attempts to set the SRD bin size to exactly <I>hgrid</I>. However,
+there must be an integer number of bins in each dimension of the
+simulation box. Thus the actual bin size will depend on the size and
+shape of the overall simulation box. The actual bin size is printed
+as part of the SRD output when a simulation begins.
+</P>
+<P>If the actual bin size in non-cubic by an amount exceeding the
+tolerance, an error or warning is printed, depending on the style of
+the <I>cubic</I> keyword. Likewise, if the actual bin size differs from
+the requested <I>hgrid</I> value by an amount exceeding the tolerance, then
+an error or warning is printed. The <I>tolerance</I> is a fractional
+difference. E.g. a tolerance setting of 0.01 on the shape means that
+if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
+error or warning is generated. Similarly, if the ratio of any bin
+dimension with <I>hgrid</I> exceeds (1 +/- tolerance), then an error or
+warning is generated.
+</P>
+<P>IMPORTANT NOTE: The fix srd command can be used with simluations the
+size and/or shape of the simulation box changes. This can be due to
+non-periodic boundary conditions or the use of fixes such as the <A HREF = "fix_deform.html">fix
+deform</A> or <A HREF = "fix_wall_srd.html">fix wall/srd</A> commands
+to impose a shear on an SRD fluid or an interaction with an external
+wall. If the box size changes then the size of SRD bins must be
+recalculated every reneighboring. This is not necessary if only the
+box shape changes. This re-binning is always done so as to fit an
+integer number of bins in the current box dimension, whether it be a
+fixed, shrink-wrapped, or periodic boundary, as set by the
+<A HREF = "boundary.html">boundary</A> command. If the box size or shape changes,
+then the size of the search bins must be recalculated avery
+reneighboring. Note that changing the SRD bin size may alter the
+properties of the SRD fluid, such as its viscosity.
+</P>
+<P>The <I>shift</I> keyword determines whether the coordinates of SRD
+particles are randomly shifted when binned for purposes of rotating
+their velocities. When no shifting is performed, SRD particles are
+binned and the velocity distribution of the set of SRD particles in
+each bin is adjusted via a rotation operator. This is a statistically
+valid operation if SRD particles move sufficiently far between
+successive rotations. This is determined by their mean-free path
+lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
+is required. A shift means that all of the SRD particles are shifted
+by a vector whose coordinates are chosen randomly in the range [-1/2
+bin size, 1/2 bin size]. Note that all particles are shifted by the
+same vector. The specified random number <I>shiftseed</I> is used to
+generate these vectors. This operation sufficiently randomizes which
+SRD particles are in the same bin, even if lamda is small.
+</P>
+<P>If the <I>shift</I> flag is set to <I>no</I>, then no shifting is performed, but
+bin data will be communicated if bins overlap processor boundaries.
+An error will be generated if lamda < 0.6 of the SRD bin size. If the
+<I>shift</I> flag is set to <I>possible</I>, then shifting is performed only if
+lamda < 0.6 of the SRD bin size. A warning is generated to let you
+know this is occurring. If the <I>shift</I> flag is set to <I>yes</I> then
+shifting is performed regardless of the magnitude of lamda. Note that
+the <I>shiftseed</I> is not used if the <I>shift</I> flag is set to <I>no</I>, but
+must still be specified.
+</P>
+<P>Note that shifting of SRD coordinates requires extra communication,
+hence it should not normally be enabled unless required.
+</P>
+<P>The <I>tstat</I> keyword will thermostat the SRD particles to the specified
+<I>Tsrd</I>. This is done every N timesteps, during the velocity rotation
+operation, by rescaling the thermal velocity of particles in each SRD
+bin to the desired temperature. If there is a streaming velocity
+associated with the system, e.g. due to use of the <A HREF = "fix_deform.html">fix
+deform</A> command to perform a simulation undergoing
+shear, then that is also accounted for. The mean velocity of each bin
+of SRD particles is set to the position-dependent streaming velocity,
+based on the coordinates of the center of the SRD bin. Note that
+collisions of SRD particles with big particles or walls has a
+thermostatting effect on the colliding particles, so it may not be
+necessary to thermostat the SRD particles on a bin by bin basis in
+that case. Also note that for streaming simulations, if no
+thermostatting is performed (the default), then it may take a long
+time for the SRD fluid to come to equilibrium with a velocity profile
+that matches the simulation box deformation.
+</P>
+<P>The <I>rescale</I> keyword enables rescaling of an SRD particle's velocity
+if it would travel more than 4 mean-free paths in an SRD timestep. If
+an SRD particle exceeds this velocity it is possible it will be lost
+when migrating to other processors or that collisions with big
+particles will be missed, either of which will generate errors. Thus
+the safest mode is to run with rescaling enabled. However rescaling
+removes kinetic energy from the system (the particle's velocity is
+reduced). The latter will not typically be a problem if
+thermostatting is enabled via the <I>tstat</I> keyword or if SRD collisions
+with big particles or walls effectively thermostat the system. If you
+wish to turn off rescaling (on is the default), e.g. for a pure SRD
+system with no thermostatting so that the temperature does not decline
+over time, the <I>rescale</I> keyword can be used. The <I>no</I> value turns
+rescaling off during collisions and the per-bin velocity rotation
+operation. The <I>collide</I> and <I>rotate</I> values turn it on for
+one of the operations and off for the other.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: This fix is normally used for simulations with a huge
+number of SRD particles relative to the number of big particles,
+e.g. 100 to 1. In this scenario, computations that involve only big
+particles (neighbor list creation, communication, time integration)
+can slow down dramatically due to the large number of background SRD
+particles.
+</P>
+<P>Three other input script commands will largely overcome this effect,
+speeding up an SRD simulation by a significant amount. These are the
+<A HREF = "atom_modify.html">atom_modify first</A>, <A HREF = "neigh_modify.html">neigh_modify
+include</A>, and <A HREF = "comm_modify.html">comm_modify group</A>
+commands. Each takes a group-ID as an argument, which in this case
+should be the group-ID of the big solute particles.
+</P>
+<P>Additionally, when a <A HREF = "pair_style.html">pair_style</A> for big/big particle
+interactions is specified, the <A HREF = "pair_coeff.html">pair_coeff</A> command
+should be used to turn off big/SRD interactions, e.g. by setting their
+epsilon or cutoff length to 0.0.
+</P>
+<P>The "delete_atoms overlap" command may be useful in setting up an SRD
+simulation to insure there are no initial overlaps between big and SRD
+particles.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix tabulates several SRD statistics which are stored in a vector
+of length 12, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The vector values calculated
+by this fix are "intensive", meaning they do not scale with the size
+of the simulation. Technically, the first 8 do scale with the size of
+the simulation, but treating them as intensive means they are not
+scaled when printed as part of thermodyanmic output.
+</P>
+<P>These are the 12 quantities. All are values for the current timestep,
+except for quantity 5 and the last three, each of which are
+cummulative quantities since the beginning of the run.
+</P>
+<UL><LI>(1) # of SRD/big collision checks performed
+<LI>(2) # of SRDs which had a collision
+<LI>(3) # of SRD/big colllisions (including multiple bounces)
+<LI>(4) # of SRD particles inside a big particle
+<LI>(5) # of SRD particles whose velocity was rescaled to be < Vmax
+<LI>(6) # of bins for collision searching
+<LI>(7) # of bins for SRD velocity rotation
+<LI>(8) # of bins in which SRD temperature was computed
+<LI>(9) SRD temperature
+<LI>(10) # of SRD particles which have undergone max # of bounces
+<LI>(11) max # of bounces any SRD particle has had in a single step
+<LI>(12) # of reneighborings due to SRD particles moving too far
+</UL>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the SRD
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall_srd.html">fix wall/srd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are lamda inferred from Tsrd, collision = noslip,
+overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
+search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
+rescale = yes.
+</P>
+<HR>
+
+<A NAME = "Hecht"></A>
+
+<P><B>(Hecht)</B> Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
+</P>
+<A NAME = "Petersen"></A>
+
+<P><B>(Petersen)</B> Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
+Chem Phys, 132, 174106 (2010).
+</P>
+<A NAME = "Lechman"></A>
+
+<P><B>(Lechman)</B> Lechman, et al, in preparation (2010).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_store_force.html b/doc/doc2/fix_store_force.html
new file mode 100644
index 000000000..f73bdf65b
--- /dev/null
+++ b/doc/doc2/fix_store_force.html
@@ -0,0 +1,77 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix store/force command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID store/force
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>store/force = style name of this fix command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all store/force
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Store the forces on atoms in the group at the point during each
+timestep when the fix is invoked, as described below. This is useful
+for storing forces before constraints or other boundary conditions are
+computed which modify the forces, so that unmodified forces can be
+<A HREF = "dump.html">written to a dump file</A> or accessed by other <A HREF = "Section_howto.html#howto_15">output
+commands</A> that use per-atom quantities.
+</P>
+<P>This fix is invoked at the point in the velocity-Verlet timestepping
+immediately after <A HREF = "pair_style.html">pair</A>, <A HREF = "bond_style.html">bond</A>,
+<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
+<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
+forces have been calculated. It is the point in the timestep when
+various fixes that compute constraint forces are calculated and
+potentially modify the force on each atom. Examples of such fixes are
+<A HREF = "fix_shake.html">fix shake</A>, <A HREF = "fix_wall.html">fix wall</A>, and <A HREF = "fix_indent.html">fix
+indent</A>.
+</P>
+<P>IMPORTANT NOTE: The order in which various fixes are applied which
+operate at the same point during the timestep, is the same as the
+order they are specified in the input script. Thus normally, if you
+want to store per-atom forces due to force field interactions, before
+constraints are applied, you should list this fix first within that
+set of fixes, i.e. before other fixes that apply constraints.
+However, if you wish to include certain constraints (e.g. fix shake)
+in the stored force, then it could be specified after some fixes and
+before others.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a per-atom array which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The number of columns
+for each atom is 3, and the columns store the x,y,z forces on each
+atom. The per-atom values be accessed on any timestep.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_store_state.html">fix store_state</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_store_state.html b/doc/doc2/fix_store_state.html
new file mode 100644
index 000000000..641dbf7ea
--- /dev/null
+++ b/doc/doc2/fix_store_state.html
@@ -0,0 +1,143 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix store/state command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID store/state N input1 input2 ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>store/state = style name of this fix command
+
+<LI>N = store atom attributes every N steps, N = 0 for initial store only
+
+<LI>input = one or more atom attributes
+
+<PRE> possible attributes = id, mol, type, mass,
+ x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
+ q, mux, muy, muz,
+ radius, omegax, omegay, omegaz,
+ angmomx, angmomy, angmomz, tqx, tqy, tqz,
+ c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+ d_name, i_name
+</PRE>
+<PRE> id = atom ID
+ mol = molecule ID
+ type = atom type
+ mass = atom mass
+ x,y,z = unscaled atom coordinates
+ xs,ys,zs = scaled atom coordinates
+ xu,yu,zu = unwrapped atom coordinates
+ ix,iy,iz = box image that the atom is in
+ vx,vy,vz = atom velocities
+ fx,fy,fz = forces on atoms
+ q = atom charge
+ mux,muy,muz = orientation of dipolar atom
+ radius = radius of spherical particle
+ omegax,omegay,omegaz = angular velocity of spherical particle
+ angmomx,angmomy,angmomz = angular momentum of aspherical particle
+ tqx,tqy,tqz = torque on finite-size particles
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+ v_name = per-atom vector calculated by an atom-style variable with name
+ d_name = per-atom floating point vector name, managed by fix property/atom
+ i_name = per-atom integer vector name, managed by fix property/atom
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>com</I>
+
+<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all store/state 0 x y z
+fix 1 all store/state 0 xu yu zu com yes
+fix 2 all store/state 1000 vx vy vz
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a fix that stores attributes for each atom in the group at the
+time the fix is defined. If <I>N</I> is 0, then the values are never
+updated, so this is a way of archiving an atom attribute at a given
+time for future use in a calculation or output. See the discussion of
+<A HREF = "Section_howto.html#howto_15">output commands</A> that take fixes as
+inputs. And see for example, the <A HREF = "compute_reduce.html">compute
+reduce</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
+ave/histo</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
+and <A HREF = "variable.html">atom-style variable</A> commands.
+</P>
+<P>If <I>N</I> is not zero, then the attributes will be updated every <I>N</I>
+steps.
+</P>
+<P>IMPORTANT NOTE: Actually, only atom attributes specified by keywords
+like <I>xu</I> or <I>vy</I> are initially stored immediately at the point in
+your input script when the fix is defined. Attributes specified by a
+compute, fix, or variable are not initially stored until the first run
+following the fix definition begins. This is because calculating
+those attributes may require quantities that are not defined in
+between runs.
+</P>
+<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump
+custom</A> command, which describes their meaning.
+</P>
+<P>If the <I>com</I> keyword is set to <I>yes</I> then the <I>xu</I>, <I>yu</I>, and <I>zu</I>
+inputs store the position of each atom relative to the center-of-mass
+of the group of atoms, instead of storing the absolute position. This
+option is used by the <A HREF = "compute_msd.html">compute msd</A> command.
+</P>
+<P>The requested values are stored in a per-atom vector or array as
+discussed below. Zeroes are stored for atoms not in the specified
+group.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the per-atom values it stores to <A HREF = "restart.html">binary restart
+files</A>, so that the values can be restored when a
+simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>If a single input is specified, this fix produces a per-atom vector.
+If multiple inputs are specified, a per-atom array is produced where
+the number of columns for each atom is the number of inputs. These
+can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The per-atom values be
+accessed on any timestep.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>, <A HREF = "compute_property_atom.html">compute
+property/atom</A>,
+<A HREF = "fix_property_atom.html">fix property/atom</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is com = no.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_temp_berendsen.html b/doc/doc2/fix_temp_berendsen.html
new file mode 100644
index 000000000..6ae3f4ed9
--- /dev/null
+++ b/doc/doc2/fix_temp_berendsen.html
@@ -0,0 +1,190 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix temp/berendsen command
+</H3>
+<H3>fix temp/berendsen/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID temp/berendsen Tstart Tstop Tdamp
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>temp/berendsen = style name of this fix command
+
+<LI>Tstart,Tstop = desired temperature at start/end of run
+
+<PRE> Tstart can be a variable (see below)
+</PRE>
+<LI>Tdamp = temperature damping parameter (time units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all temp/berendsen 300.0 300.0 100.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the temperature of a group of atoms by using a Berendsen
+thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescales their velocities
+every timestep.
+</P>
+<P>The thermostat is applied to only the translational degrees of freedom
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix. The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>The desired temperature at each timestep is a ramped value during the
+run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed. For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
+</P>
+<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
+In this case, the <I>Tstop</I> setting is ignored. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent temperature.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration. It only modifies velocities to
+effect thermostatting. Thus you must use a separate time integration
+fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
+atoms using the modified velocities. Likewise, this fix should not
+normally be used on atoms that also have their temperature controlled
+by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
+langevin</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P>This fix computes a temperature each timestep. To do this, the fix
+creates its own compute of style "temp", as if this command had been
+issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
+that the ID of the new compute is the fix-ID + underscore + "temp",
+and the group for the new compute is the same as the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix can be used with dynamic groups as defined by the
+<A HREF = "group.html">group</A> command. Likewise it can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation. However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms. You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
+<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Berendsen"></A>
+
+<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_temp_csvr.html b/doc/doc2/fix_temp_csvr.html
new file mode 100644
index 000000000..41c6e7400
--- /dev/null
+++ b/doc/doc2/fix_temp_csvr.html
@@ -0,0 +1,182 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix temp/csvr command
+</H3>
+<H3>fix temp/csld command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
+</PRE>
+<PRE>fix ID group-ID temp/csld Tstart Tstop Tdamp seed
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>temp/csvr or temp/csld = style name of this fix command
+
+<LI>Tstart,Tstop = desired temperature at start/end of run
+
+<PRE> Tstart can be a variable (see below)
+</PRE>
+<LI>Tdamp = temperature damping parameter (time units)
+
+<LI>seed = random number seed to use for white noise (positive integer)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all temp/csvr 300.0 300.0 100.0 54324
+</PRE>
+<PRE>fix 1 all temp/csld 100.0 300.0 10.0 123321
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Adjust the temperature with a canonical sampling thermostat that uses
+global velocity rescaling with Hamiltonian dynamics (<I>temp/csvr</I>)
+<A HREF = "#Bussi1">(Bussi1)</A>, or Langevin dynamics (<I>temp/csld</I>)
+<A HREF = "#Bussi2">(Bussi2)</A>. In the case of <I>temp/csvr</I> the thermostat is
+similar to the empirical Berendsen thermostat in
+<A HREF = "fix_temp_berendsen.html">temp/berendsen</A>, but chooses the actual
+scaling factor from a suitably chosen (gaussian) distribution rather
+than having it determined from the time constant directly. In the case
+of <I>temp/csld</I> the velocities are updated to a linear combination of
+the current velocities with a gaussian distribution of velocities at
+the desired temperature. Both termostats are applied every timestep.
+</P>
+<P>The thermostat is applied to only the translational degrees of freedom
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with these fixes. The translational degrees of freedom
+can also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>The desired temperature at each timestep is a ramped value during the
+run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed. For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
+</P>
+<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
+In this case, the <I>Tstop</I> setting is ignored. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent temperature.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, these fixes
+do NOT perform time integration. They only modify velocities to effect
+thermostatting. Thus you must use a separate time integration fix,
+like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of atoms
+using the modified velocities. Likewise, these fixes should not
+normally be used on atoms that also have their temperature controlled
+by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
+langevin</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P>These fixes compute a temperature each timestep. To do this, the fix
+creates its own compute of style "temp", as if this command had been
+issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
+that the ID of the new compute is the fix-ID + underscore + "temp",
+and the group for the new compute is the same as the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, these fixes can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about these fixes are written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by these
+fixes. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to these fixes which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+these fixes and by the compute should be the same.
+</P>
+<P>These fixes can ramp its target temperature over multiple runs, using
+the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>These fixes are not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P>These fixes compute a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to the fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These fixes are not compatible with <A HREF = "fix_shake.html">fix shake</A>.
+</P>
+<P>The fix can be used with dynamic groups as defined by the
+<A HREF = "group.html">group</A> command. Likewise it can be used with groups to
+which atoms are added or deleted over time, e.g. a deposition
+simulation. However, the conservation properties of the thermostat
+and barostat are defined for systems with a static set of atoms. You
+may observe odd behavior if the atoms in a group vary dramatically
+over time or the atom count becomes very small.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
+<A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Bussi1"></A>
+
+<A NAME = "Bussi2"></A><B>(Bussi1)</B> Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
+
+
+<P><B>(Bussi2)</B> Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
+</P>
+</HTML>
diff --git a/doc/doc2/fix_temp_rescale.html b/doc/doc2/fix_temp_rescale.html
new file mode 100644
index 000000000..208a2de9d
--- /dev/null
+++ b/doc/doc2/fix_temp_rescale.html
@@ -0,0 +1,184 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix temp/rescale command
+</H3>
+<H3>fix temp/rescale/cuda command
+</H3>
+<H3>fix temp/rescale/limit/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>temp/rescale = style name of this fix command
+
+<LI>N = perform rescaling every N steps
+
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+
+<PRE> Tstart can be a variable (see below)
+</PRE>
+<LI>window = only rescale if temperature is outside this window (temperature units)
+
+<LI>fraction = rescale to target temperature by this fraction
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the temperature of a group of atoms by explicitly rescaling
+their velocities.
+</P>
+<P>The rescaling is applied to only the translational degrees of freedom
+for the particles, which is an important consideration if finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix. The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
+</P>
+<P>Rescaling is performed every N timesteps. The target temperature is a
+ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
+beginning and end of the run.
+</P>
+<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
+In this case, the <I>Tstop</I> setting is ignored. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value used to determine the target temperature.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent temperature.
+</P>
+<P>Rescaling is only performed if the difference between the current and
+desired temperatures is greater than the <I>window</I> value. The amount
+of rescaling that is applied is a <I>fraction</I> (from 0.0 to 1.0) of the
+difference between the actual and desired temperature. E.g. if
+<I>fraction</I> = 1.0, the temperature is reset to exactly the desired
+value.
+</P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration. It only modifies velocities to
+effect thermostatting. Thus you must use a separate time integration
+fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
+atoms using the modified velocities. Likewise, this fix should not
+normally be used on atoms that also have their temperature controlled
+by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
+langevin</A> commands.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
+<P>This fix computes a temperature each timestep. To do this, the fix
+creates its own compute of style "temp", as if one of this command had
+been issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> for details. Note that the
+ID of the new compute is the fix-ID + underscore + "temp", and the
+group for the new compute is the same as the fix group.
+</P>
+<P>Note that this is NOT the compute used by thermodynamic output (see
+the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+custom</A> command using the appropriate compute-ID.
+It also means that changing attributes of <I>thermo_temp</I> will have no
+effect on this fix.
+</P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities. E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region. This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term. See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias. In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_nh.html">fix nvt</A>,
+<A HREF = "fix_modify.html">fix_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_temp_rescale_eff.html b/doc/doc2/fix_temp_rescale_eff.html
new file mode 100644
index 000000000..038e18193
--- /dev/null
+++ b/doc/doc2/fix_temp_rescale_eff.html
@@ -0,0 +1,81 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix temp/rescale/eff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>temp/rescale/eff = style name of this fix command
+<LI>N = perform rescaling every N steps
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+<LI>window = only rescale if temperature is outside this window (temperature units)
+<LI>fraction = rescale to target temperature by this fraction
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the temperature of a group of nuclei and electrons in the
+<A HREF = "pair_eff.html">electron force field</A> model by explicitly rescaling
+their velocities.
+</P>
+<P>The operation of this fix is exactly like that described by the <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A> command, except that the rescaling
+is also applied to the radial electron velocity for electron
+particles.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above. For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the USER-EFF package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin_eff.html">fix langevin/eff</A>, <A HREF = "fix_nh_eff.html">fix
+nvt/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>,
+<A HREF = "fix_temp_rescale.html">fix_temp_rescale</A>,
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_tfmc.html b/doc/doc2/fix_tfmc.html
new file mode 100644
index 000000000..dd69b02f9
--- /dev/null
+++ b/doc/doc2/fix_tfmc.html
@@ -0,0 +1,168 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix tfmc command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID tfmc Delta Temp seed keyword value
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>tfmc = style name of this fix command
+
+<LI>Delta = maximal displacement length (distance units)
+
+<LI>Temp = imposed temperature of the system
+
+<LI>seed = random number seed (positive integer)
+
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>com</I> or <I>rot</I>
+
+<PRE> <I>com</I> args = xflag yflag zflag
+ xflag,yflag,zflag = 0/1 to exclude/include each dimension
+ <I>rot</I> args = none
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all tfmc 0.1 1000.0 159345
+fix 1 all tfmc 0.05 600.0 658943 com 1 1 0
+fix 1 all tfmc 0.1 750.0 387068 com 1 1 1 rot
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform uniform-acceptance force-bias Monte Carlo (fbMC) simulations,
+using the time-stamped force-bias Monte Carlo (tfMC) algorithm
+described in <A HREF = "#Mees">(Mees)</A> and <A HREF = "#Bal">(Bal)</A>.
+</P>
+<P>One successful use case of force-bias Monte Carlo methods is that they
+can be used to extend the time scale of atomistic simulations, in
+particular when long time scale relaxation effects must be considered;
+some interesting examples are given in the review by <A HREF = "#Neyts">(Neyts)</A>.
+An example of a typical use case would be the modelling of chemical
+vapour deposition (CVD) processes on a surface, in which impacts by
+gas-phase species can be performed using MD, but subsequent relaxation
+of the surface is too slow to be done using MD only. Using tfMC can
+allow for a much faster relaxation of the surface, so that higher
+fluxes can be used, effectively extending the time scale of the
+simulation. (Such an alternating simulation approach could be set up
+using a <A HREF = "jump.html">loop</A>.)
+</P>
+<P>The initial version of tfMC algorithm in <A HREF = "#Mees">(Mees)</A> contained an
+estimation of the effective time scale of such a simulation, but it
+was later shown that the speed-up one can gain from a tfMC simulation
+is system- and process-dependent, ranging from none to several orders
+of magnitude. In general, solid-state processes such as
+(re)crystallisation or growth can be accelerated by up to two or three
+orders of magnitude, whereas diffusion in the liquid phase is not
+accelerated at all. The observed pseudodynamics when using the tfMC
+method is not the actual dynamics one would obtain using MD, but the
+relative importance of processes can match the actual relative
+dynamics of the system quite well, provided <I>Delta</I> is chosen with
+care. Thus, the system's equilibrium is reached faster than in MD,
+along a path that is generally roughly similar to a typical MD
+simulation (but not necessarily so). See <A HREF = "#Bal">(Bal)</A> for details.
+</P>
+<P>Each step, all atoms in the selected group are displaced using the
+stochastic tfMC algorithm, which is designed to sample the canonical
+(NVT) ensemble at the temperature <I>Temp</I>. Although tfMC is a Monte
+Carlo algorithm and thus strictly speaking does not perform time
+integration, it is similar in the sense that it uses the forces on all
+atoms in order to update their positions. Therefore, it is implemented
+as a time integration fix, and no other fixes of this type (such as
+<A HREF = "fix_nve.html">fix nve</A>) should be used at the same time. Because
+velocities do not play a role in this kind of Monte Carlo simulations,
+instantaneous temperatures as calculated by <A HREF = "compute_temp.html">temperature
+computes</A> or <A HREF = "thermo_style.html">thermodynamic
+output</A> have no meaning: the only relevant
+temperature is the sampling temperature <I>Temp</I>. Similarly, performing
+tfMC simulations does not require setting a <A HREF = "timestep.html">timestep</A>
+and the <A HREF = "thermo_style.html">simulated time</A> as calculated by LAMMPS is
+meaningless.
+</P>
+<P>The critical parameter determining the success of a tfMC simulation is
+<I>Delta</I>, the maximal displacement length of the lightest element in
+the system: the larger it is, the longer the effective time scale of
+the simulation will be (there is an approximately quadratic
+dependence). However, <I>Delta</I> must also be chosen sufficiently small
+in order to comply with detailed balance; in general values between 5
+and 10 % of the nearest neighbor distance are found to be a good
+choice. For a more extensive discussion with specific examples, please
+refer to <A HREF = "#Bal">(Bal)</A>, which also describes how the code calculates
+element-specific maximal displacements from <I>Delta</I>, based on the
+fourth root of their mass.
+</P>
+<P>Because of the uncorrelated movements of the atoms, the center-of-mass
+of the fix group will not necessarily be stationary, just like its
+orientation. When the <I>com</I> keyword is used, all atom positions will
+be shifted (after every tfMC iteration) in order to fix the position
+of the center-of-mass along the included directions, by setting the
+corresponding flag to 1. The <I>rot</I> keyword does the same for the
+rotational component of the tfMC displacements after every iteration.
+</P>
+<P>IMPORTANT NOTE: the <I>com</I> and <I>rot</I> keywords should not be used if an
+external force is acting on the specified fix group, along the
+included directions. This can be either a true external force (e.g.
+through <A HREF = "fix_wall.html">fix wall</A>) or forces due to the interaction
+with atoms not included in the fix group. This is because in such
+cases, translations or rotations of the fix group could be induced by
+these external forces, and removing them will lead to a violation of
+detailed balance.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This fix is not compatible with <A HREF = "fix_shake.html">fix shake</A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_gcmc.html">fix gcmc</A>, <A HREF = "fix_nh.html">fix nvt</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option default is com = 0 0 0
+</P>
+<HR>
+
+<A NAME = "Bal"></A>
+
+<P><B>(Bal)</B> K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014).
+</P>
+<A NAME = "Mees"></A>
+
+<P><B>(Mees)</B> M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and
+A. Stesmans, Phys. Rev. B 85, 134301 (2012).
+</P>
+<A NAME = "Neyts"></A>
+
+<P><B>(Neyts)</B> E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320
+(2013).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_thermal_conductivity.html b/doc/doc2/fix_thermal_conductivity.html
new file mode 100644
index 000000000..ec5fcc040
--- /dev/null
+++ b/doc/doc2/fix_thermal_conductivity.html
@@ -0,0 +1,177 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix thermal/conductivity command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>thermal/conductivity = style name of this fix command
+
+<LI>N = perform kinetic energy exchange every N steps
+
+<LI>edim = <I>x</I> or <I>y</I> or <I>z</I> = direction of kinetic energy transfer
+
+<LI>Nbin = # of layers in edim direction (must be even number)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>swap</I>
+
+<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all thermal/conductivity 100 z 20
+fix 1 all thermal/conductivity 50 z 20 swap 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
+paper</A> to exchange kinetic energy between two particles
+in different regions of the simulation box every N steps. This
+induces a temperature gradient in the system. As described below this
+enables the thermal conductivity of a material to be calculated. This
+algorithm is sometimes called a reverse non-equilibrium MD (reverse
+NEMD) approach to computing thermal conductivity. This is because the
+usual NEMD approach is to impose a temperature gradient on the system
+and measure the response as the resulting heat flux. In the
+Muller-Plathe method, the heat flux is imposed, and the temperature
+gradient is the system's response.
+</P>
+<P>See the <A HREF = "compute_heat_flux.html">compute heat/flux</A> command for details
+on how to compute thermal conductivity in an alternate way, via the
+Green-Kubo formalism.
+</P>
+<P>The simulation box is divided into <I>Nbin</I> layers in the <I>edim</I>
+direction, where the layer 1 is at the low end of that dimension and
+the layer <I>Nbin</I> is at the high end. Every N steps, Nswap pairs of
+atoms are chosen in the following manner. Only atoms in the fix group
+are considered. The hottest Nswap atoms in layer 1 are selected.
+Similarly, the coldest Nswap atoms in the "middle" layer (see below)
+are selected. The two sets of Nswap atoms are paired up and their
+velocities are exchanged. This effectively swaps their kinetic
+energies, assuming their masses are the same. If the masses are
+different, an exchange of velocities relative to center of mass motion
+of the 2 atoms is performed, to conserve kinetic energy. Over time,
+this induces a temperature gradient in the system which can be
+measured using commands such as the following, which writes the
+temperature profile (assuming z = edim) to the file tmp.profile:
+</P>
+<PRE>compute ke all ke/atom
+variable temp atom c_ke/1.5
+fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
+ file tmp.profile units reduced
+</PRE>
+<P>Note that by default, Nswap = 1, though this can be changed by the
+optional <I>swap</I> keyword. Setting this parameter appropriately, in
+conjunction with the swap rate N, allows the heat flux to be adjusted
+across a wide range of values, and the kinetic energy to be exchanged
+in large chunks or more smoothly.
+</P>
+<P>The "middle" layer for velocity swapping is defined as the <I>Nbin</I>/2 +
+1 layer. Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
+This should lead to a symmetric temperature profile since the two
+layers are separated by the same distance in both directions in a
+periodic sense. This is why <I>Nbin</I> is restricted to being an even
+number.
+</P>
+<P>As described below, the total kinetic energy transferred by these
+swaps is computed by the fix and can be output. Dividing this
+quantity by time and the cross-sectional area of the simulation box
+yields a heat flux. The ratio of heat flux to the slope of the
+temperature profile is proportional to the thermal conductivity of the
+fluid, in appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe
+paper</A> for details.
+</P>
+<P>IMPORTANT NOTE: If your system is periodic in the direction of the
+heat flux, then the flux is going in 2 directions. This means the
+effective heat flux in one direction is reduced by a factor of 2. You
+will see this in the equations for thermal conductivity (kappa) in the
+Muller-Plathe paper. LAMMPS is simply tallying kinetic energy which
+does not account for whether or not your system is periodic; you must
+use the value appropriately to yield a kappa for your system.
+</P>
+<P>IMPORTANT NOTE: After equilibration, if the temperature gradient you
+observe is not linear, then you are likely swapping energy too
+frequently and are not in a regime of linear response. In this case
+you cannot accurately infer a thermal conductivity and should try
+increasing the Nevery parameter.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative kinetic energy transferred between the bottom and middle
+of the simulation box (in the <I>edim</I> direction) is stored as a scalar
+quantity by this fix. This quantity is zeroed when the fix is defined
+and accumlates thereafter, once every N steps. The units of the
+quantity are energy; see the <A HREF = "units.html">units</A> command for details.
+The scalar value calculated by this fix is "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Swaps conserve both momentum and kinetic energy, even if the masses of
+the swapped atoms are not equal. Thus you should not need to
+thermostat the system. If you do use a thermostat, you may want to
+apply it only to the non-swapped dimensions (other than <I>vdim</I>).
+</P>
+<P>LAMMPS does not check, but you should not use this fix to swap the
+kinetic energy of atoms that are in constrained molecules, e.g. via
+<A HREF = "fix_shake.html">fix shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is
+because application of the constraints will alter the amount of
+transferred momentum. You should, however, be able to use flexible
+molecules. See the <A HREF = "#Zhang">Zhang paper</A> for a discussion and results
+of this idea.
+</P>
+<P>When running a simulation with large, massive particles or molecules
+in a background solvent, you may want to only exchange kinetic energy
+bewteen solvent particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_viscosity.html">fix
+viscosity</A>, <A HREF = "compute_heat_flux.html">compute
+heat/flux</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are swap = 1.
+</P>
+<HR>
+
+<A NAME = "Muller-Plathe"></A>
+
+<P><B>(Muller-Plathe)</B> Muller-Plathe, J Chem Phys, 106, 6082 (1997).
+</P>
+<A NAME = "Zhang"></A>
+
+<P><B>(Zhang)</B> Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
+109, 15060-15067 (2005).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ti_rs.html b/doc/doc2/fix_ti_rs.html
new file mode 100644
index 000000000..c6f60635e
--- /dev/null
+++ b/doc/doc2/fix_ti_rs.html
@@ -0,0 +1,156 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ti/rs command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ti/rs = style name of this fix command
+
+<LI>lambda_initial/lambda_final = initial/final values of the coupling parameter
+
+<LI>t_switch/t_equil = number of steps of the switching/equilibration procedure
+
+<LI>keyword = <I>function</I>
+
+<PRE> <I>function</I> value = function-ID
+ function-ID = ID of the switching function (1, 2 or 3)
+</PRE>
+
+</UL>
+<P><B>Example:</B>
+</P>
+<PRE>fix ref all ti/rs 50.0 2000 1000
+fix vf vacancy ti/rs 10.0 70000 50000 function 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix allows you to compute the free energy temperature dependence
+by performing a thermodynamic integration procedure known as
+Reversible Scaling <A HREF = "#deKoning99">(de Koning99,</A> <A HREF = "#deKoning00a"">de
+Koning00a)</A>. The thermodynamic integration is performed
+using the nonequilibrium method of Adiabatic Switching
+<A HREF = "#Watanabe">(Watanabe,</A> <A HREF = "#deKoning96">de Koning96)</A>.
+</P>
+<P>The forces on the atoms are dynamically scaled during the simulation,
+the rescaling is done in the following manner:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_rs_force.jpg">
+</CENTER>
+<P>where F_int is the total force on the atoms due to the interatomic
+potential and lambda is the coupling parameter of the thermodynamic
+integration.
+</P>
+<P>The fix acts as follows: during the first <I>t_equil</I> steps after the
+fix is defined the value of lambda is <I>lambda_initial</I> , this is the
+period to equilibrate the system in the lambda = <I>lambda_initial</I>
+state. After this the value of lambda changes continuously from
+<I>lambda_initial</I> to <I>lambda_final</I> according to the function defined
+using the keyword <I>function</I> (described below), this is done in
+<I>t_switch</I> steps. Then comes the second equilibration period of
+<I>t_equil</I> to equilibrate the system in the lambda = <I>lambda_final</I>
+state. After that the switching back to the lambda = <I>lambda_initial</I>
+state is done using <I>t_switch</I> timesteps and following the same
+switching function. After this period the value of lambda is kept
+equal to <I>lambda_initial</I> indefinitely or until a <A HREF = "unfix.html">unfix</A>
+erase the fix.
+</P>
+<P>The description of thermodynamic integration in both directions is
+done in <A HREF = "#deKoning00b">de Koning00b</A>, the main reason is to try to
+eliminate the dissipated heat due to the nonequilibrium process.
+</P>
+<P>The <I>function</I> keyword allows the use of three different switching
+rates. The option <I>1</I> results in a constant rescaling where the lambda
+parameter changes at a constant rate during the switching time
+according to the switching function
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_1.jpg">
+</CENTER>
+<P>where tau is the scaled time variable t/t_switch. This switching
+function has the characteristic that the temperature scaling is faster
+at temperatures closer to the final temperature of the procedure. The
+option number <I>2</I> performs the switching at a rate defined by the
+following switching function
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_2.jpg">
+</CENTER>
+<P>This switching function has the characteristic that the temperature
+scaling occurs at a constant rate during all the procedure. The option
+number <I>3</I> performs the switching at a rate defined by the following
+switching function
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_3.jpg">
+</CENTER>
+<P>This switching function has the characteristic that the temperature
+scaling is faster at temperatures closer to the initial temperature of
+the procedure.
+</P>
+<P>An example script using this command is provided in the
+examples/USER/misc/ti directory.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>This fix computes a global vector quantitie which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector has
+2 positions, the first one is the coupling parameter lambda and the
+second one is the time derivative of lambda. The scalar and vector
+values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ti_spring.html">fix ti/spring</A>
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword default is function = 1.
+</P>
+<HR>
+
+<A NAME = "deKoning99"></A>
+
+<P><B>(de Koning 99)</B> M. de Koning, A. Antonelli and S. Yip, Phys Rev Lett, 83, 3973 (1999).
+</P>
+<A NAME = "Watanabe"></A>
+
+<P><B>(Watanabe)</B> M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990).
+</P>
+<A NAME = "deKoning96"></A>
+
+<P><B>(de Koning 96)</B> M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996).
+</P>
+<A NAME = "deKoning00a"></A>
+
+<P><B>(de Koning 00a)</B> M. de Koning, A. Antonelli and S. Yip, J Chem Phys, 115, 11025 (2000).
+</P>
+<A NAME = "deKoning00b"></A>
+
+<P><B>(de Koning 00b)</B> M. de Koning et al., Computing in Science & Engineering, 2, 88 (2000).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ti_spring.html b/doc/doc2/fix_ti_spring.html
new file mode 100644
index 000000000..7aa8255b4
--- /dev/null
+++ b/doc/doc2/fix_ti_spring.html
@@ -0,0 +1,175 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ti/spring command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ti/spring K t_switch t_equil keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ti/spring = style name of this fix command
+
+<LI>K = spring constant (force/distance units)
+
+<LI>t_switch/t_equil = number of steps of the switching/equilibration procedure
+
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>function</I>
+
+<PRE> <I>function</I> value = function-ID
+ function-ID = ID of the switching function (1 or 2)
+</PRE>
+
+</UL>
+<P><B>Example:</B>
+</P>
+<PRE>fix ref all ti/spring 50.0 2000 1000 function 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix allows you to compute the free energy of solids by performing
+a thermodynamic integration between the solid of interest and an
+Einstein crystal <A HREF = "#Frenkel">(Frenkel)</A>. The thermodynamic integration
+is performed using the nonequilibrium method of Adiabatic Switching
+<A HREF = "#Watanabe">(Watanabe,</A> <A HREF = "#deKoning96">de Koning96)</A>.
+</P>
+<P>A spring force is applied independently to each atom in the group to
+tether it to its initial position. The initial position for each atom
+is its location at the time the fix command was issued. More details
+about the springs are available in <A HREF = "fix_spring_self.html">fix
+spring/self</A>. The forces on the atoms are
+dynamically scaled during the simulation, the rescaling is done in the
+following manner:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_spring_force.jpg">
+</CENTER>
+<P>where F_harm is the force due to the springs, F_solid is the total
+force on the atoms due to the interatomic potential and lambda is the
+coupling parameter of the thermodynamic integration.
+</P>
+<P>The fix acts as follows: during the first <I>t_equil</I> steps after the
+fix is defined the value of lambda is zero, this is the period to
+equilibrate the system in the lambda = 0 state. After this the value
+of lambda changes continuously from 0 to 1 according to the function
+defined using the keyword <I>function</I> (described below), this is done
+in <I>t_switch</I> steps. Then comes the second equilibration period of
+<I>t_equil</I> to equilibrate the system in the lambda = 1 state. After
+that the switching back to the lambda = 0 state is made using
+<I>t_switch</I> timesteps and following the same switching function. After
+this period the value of lambda is kept equal to zero and the fix has
+no action in the dynamics of the system anymore.
+</P>
+<P>The description of thermodynamic integration in both directions is
+done in <A HREF = "#deKoning97">de Koning97</A>, the main reason is to try to
+eliminate the dissipated heat due to the nonequilibrium process.
+</P>
+<P>The <I>function</I> keyword allows the use of two different switching
+rates, the option <I>1</I> results in a constant rescaling where the lambda
+parameter changes at a constant rate during the switching time
+according to the switching function
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_spring_function_1.jpg">
+</CENTER>
+<P>where tau is the scaled time variable t/t_switch. The option number
+<I>2</I> performs the switching at a rate defined by the following
+switching function
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ti_spring_function_2.jpg">
+</CENTER>
+<P>This function has zero slope as lambda approaches its extreme values
+(0 and 1), according to (<A HREF = "#deKoning96">de Koning96)</A> this results in
+smaller fluctuations on the integral to be computed on the
+thermodynamic integration.
+</P>
+<P>IMPORTANT NOTE: It is importante to keep the center of mass fixed
+during the thermodynamic integration, a non-zero total velocity will
+result in divergencies during the integration due to the fact that the
+atoms are 'attatched' to its equilibrium positions by the Einstein
+crystal. Check the option <I>zero</I> of <A HREF = "fix_langevin_html">fix langevin</A>
+and <A HREF = "velocity.html">velocity</A>. The use of the Nose-Hoover thermostat
+(<A HREF = "fix_nvt.html">fix nvt</A>) is NOT recommended due to its well documented
+issues with the canonical sampling of harmonic degrees of freedom
+(notice that the <I>chain</I> option will NOT solve this problem). The
+Langevin thermostat (<A HREF = "fix_langevin.html"">fix langevin</A>) works fine.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of tethered atoms to <A HREF = "restart.html">binary
+restart files</A>, so that the spring effect will be the
+same in a restarted simulation. See the <A HREF = "read_restart.html">read
+restart</A> command for info on how to re-specify a fix
+in an input script that reads a restart file, so that the operation of
+the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix modify</A> <I>energy</I> option is supported by this
+fix to add the energy stored in the per-atom springs to the system's
+potential energy as part of <A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>This fix computes a global scalar and a global vector quantities which
+can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar is an energy which
+is the sum of the spring energy for each atom, where the per-atom
+energy is 0.5 * K * r^2. The vector has 2 positions, the first one is
+the coupling parameter lambda and the second one is the time
+derivative of lambda. The scalar and vector values calculated by this
+fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the per-atom spring energy to be included
+in the total potential energy of the system (the quantity being
+minimized), you MUST enable the <A HREF = "fix_modify.html">fix modify</A> <I>energy</I>
+option for this fix.
+</P>
+<P>An example script using this command is provided in the
+examples/USER/misc/ti directory.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_spring.html">fix spring</A>, <A HREF = "fix_ti_rs.html">fix ti/rs</A>
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword default is function = 1.
+</P>
+<HR>
+
+<A NAME = "Frenkel"></A>
+
+<P><B>(Frenkel)</B> Daan Frenkel and Anthony J. C. Ladd, J. Chem. Phys. 81, 3188
+(1984).
+</P>
+<A NAME = "Watanabe"></A>
+
+<P><B>(Watanabe)</B> M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990).
+</P>
+<A NAME = "deKoning96"></A>
+
+<P><B>(de Koning 96)</B> M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996).
+</P>
+<A NAME = "deKoning97"></A>
+
+<P><B>(de Koning 97)</B> M. de Koning and A. Antonelli, Phys Rev B, 55, 735 (1997).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_tmd.html b/doc/doc2/fix_tmd.html
new file mode 100644
index 000000000..c365365f4
--- /dev/null
+++ b/doc/doc2/fix_tmd.html
@@ -0,0 +1,138 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix tmd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID tmd rho_final file1 N file2
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>tmd = style name of this fix command
+<LI>rho_final = desired value of rho at the end of the run (distance units)
+<LI>file1 = filename to read target structure from
+<LI>N = dump TMD statistics every this many timesteps, 0 = no dump
+<LI>file2 = filename to write TMD statistics to (only needed if N > 0)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nve
+fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform targeted molecular dynamics (TMD) on a group of atoms. A
+holonomic constraint is used to force the atoms to move towards (or
+away from) the target configuration. The parameter "rho" is
+monotonically decreased (or increased) from its initial value to
+rho_final at the end of the run.
+</P>
+<P>Rho has distance units and is a measure of the root-mean-squared
+distance (RMSD) between the current configuration of the atoms in the
+group and the target coordinates listed in file1. Thus a value of
+rho_final = 0.0 means move the atoms all the way to the final
+structure during the course of the run.
+</P>
+<P>The target file1 can be ASCII text or a gzipped text file (detected by
+a .gz suffix). The format of the target file1 is as follows:
+</P>
+<PRE>0.0 25.0 xlo xhi
+0.0 25.0 ylo yhi
+0.0 25.0 zlo zhi
+125 24.97311 1.69005 23.46956 0 0 -1
+126 1.94691 2.79640 1.92799 1 0 0
+127 0.15906 3.46099 0.79121 1 0 0
+...
+</PRE>
+<P>The first 3 lines may or may not be needed, depending on the format of
+the atoms to follow. If image flags are included with the atoms, the
+1st 3 lo/hi lines must appear in the file. If image flags are not
+included, the 1st 3 lines should not appear. The 3 lines contain the
+simulation box dimensions for the atom coordinates, in the same format
+as in a LAMMPS data file (see the <A HREF = "read_data.html">read_data</A> command).
+</P>
+<P>The remaining lines each contain an atom ID and its target x,y,z
+coordinates. The atom lines (all or none of them) can optionally be
+followed by 3 integer values: nx,ny,nz. For periodic dimensions, they
+specify which image of the box the atom is considered to be in, i.e. a
+value of N (positive or negative) means add N times the box length to
+the coordinate to get the true value.
+</P>
+<P>The atom lines can be listed in any order, but every atom in the group
+must be listed in the file. Atoms not in the fix group may also be
+listed; they will be ignored.
+</P>
+<P>TMD statistics are written to file2 every N timesteps, unless N is
+specified as 0, which means no statistics.
+</P>
+<P>The atoms in the fix tmd group should be integrated (via a fix nve,
+nvt, npt) along with other atoms in the system.
+</P>
+<P>Restarts can be used with a fix tmd command. For example, imagine a
+10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a
+restart file was written after 2000 time steps, then the configuration
+in the file would have a rho value of 9. A new 8000 time step run
+could be performed with the same rho_final = 1 to complete the
+conformational change at the same transition rate. Note that for
+restarted runs, the name of the TMD statistics file should be changed
+to prevent it being overwritten.
+</P>
+<P>For more information about TMD, see <A HREF = "#Schlitter1">(Schlitter1)</A> and
+<A HREF = "#Schlitter2">(Schlitter2)</A>.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>.
+</P>
+<P>This fix can ramp its rho parameter over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>All TMD fixes must be listed in the input script after all integrator
+fixes (nve, nvt, npt) are applied. This ensures that atoms are moved
+before their positions are corrected to comply with the constraint.
+</P>
+<P>Atoms that have a TMD fix applied should not be part of a group to
+which a SHAKE fix is applied. This is because LAMMPS assumes there
+are not multiple competing holonomic constraints applied to the same
+atoms.
+</P>
+<P>To read gzipped target files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
+LAMMPS</A> section of the documentation.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Schlitter1"></A>
+
+<P><B>(Schlitter1)</B> Schlitter, Swegat, Mulders, "Distance-type reaction
+coordinates for modelling activated processes", J Molecular Modeling,
+7, 171-177 (2001).
+</P>
+<A NAME = "Schlitter2"></A>
+
+<P><B>(Schlitter2)</B> Schlitter and Klahn, "The free energy of a reaction
+coordinate at multiple constraints: a concise formulation", Molecular
+Physics, 101, 3439-3443 (2003).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_ttm.html b/doc/doc2/fix_ttm.html
new file mode 100644
index 000000000..ff7a39698
--- /dev/null
+++ b/doc/doc2/fix_ttm.html
@@ -0,0 +1,350 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ttm command
+</H3>
+<H3>fix ttm/mod command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
+fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style = <I>ttm</I> or <I>ttm_mod</I>
+
+<LI>seed = random number seed to use for white noise (positive integer)
+
+<LI>remaining arguments for fix ttm:
+
+<PRE> C_e = electronic specific heat (energy/(electron*temperature) units)
+ rho_e = electronic density (electrons/volume units)
+ kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
+ gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+ gamma_s = friction coefficient due to electronic stopping (mass/time units)
+ v_0 = electronic stopping critical velocity (velocity units)
+ Nx = number of thermal solve grid points in the x-direction (positive integer)
+ Ny = number of thermal solve grid points in the y-direction (positive integer)
+ Nz = number of thermal solve grid points in the z-direction (positive integer)
+ T_infile = filename to read initial electronic temperature from
+ N = dump TTM temperatures every this many timesteps, 0 = no dump
+ T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+</PRE>
+<LI>remaining arguments for fix ttm/mod:
+
+<PRE> init_file = file with the parameters to TTM
+ Nx = number of thermal solve grid points in the x-direction (positive integer)
+ Ny = number of thermal solve grid points in the y-direction (positive integer)
+ Nz = number of thermal solve grid points in the z-direction (positive integer)
+ T_infile = filename to read initial electronic temperature from
+ N = dump TTM temperatures every this many timesteps, 0 = no dump
+ T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
+fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
+fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use a two-temperature model (TTM) to represent heat transfer through
+and between electronic and atomic subsystems. LAMMPS models the
+atomic subsystem as usual with a molecular dynamics model and the
+classical force field specified by the user, but the electronic
+subsystem is modeled as a continuum, or a background "gas", on a
+regular grid. Energy can be transferred spatially within the grid
+representing the electrons. Energy can also be transferred between
+the electronic and the atomic subsystems. The algorithm underlying
+this fix was derived by D. M. Duffy and A. M. Rutherford and is
+discussed in two J Physics: Condensed Matter papers: <A HREF = "#Duffy">(Duffy)</A>
+and <A HREF = "#Rutherford">(Rutherford)</A>. They used this algorithm in cascade
+simulations where a primary knock-on atom (PKA) was initialized with a
+high velocity to simulate a radiation event.
+</P>
+<P>The description in this sub-section applies to both fix ttm and fix
+ttm/mod. Fix ttm/mod adds options to account for external heat
+sources (e.g. at a surface) and for specifying parameters that allow
+the electronic heat capacity to depend strongly on electronic
+temperature. It is more expensive computationally than fix ttm
+because it treats the thermal diffusion equation as non-linear. More
+details on fix ttm/mod are given below.
+</P>
+<P>Heat transfer between the electronic and atomic subsystems is carried
+out via an inhomogeneous Langevin thermostat. This thermostat differs
+from the regular Langevin thermostat (<A HREF = "fix_langevin.html">fix
+langevin</A>) in three important ways. First, the
+Langevin thermostat is applied uniformly to all atoms in the
+user-specified group for a single target temperature, whereas the TTM
+fix applies Langevin thermostatting locally to atoms within the
+volumes represented by the user-specified grid points with a target
+temperature specific to that grid point. Second, the Langevin
+thermostat couples the temperature of the atoms to an infinite heat
+reservoir, whereas the heat reservoir for fix TTM is finite and
+represents the local electrons. Third, the TTM fix allows users to
+specify not just one friction coefficient, but rather two independent
+friction coefficients: one for the electron-ion interactions
+(<I>gamma_p</I>), and one for electron stopping (<I>gamma_s</I>).
+</P>
+<P>When the friction coefficient due to electron stopping, <I>gamma_s</I>, is
+non-zero, electron stopping effects are included for atoms moving
+faster than the electron stopping critical velocity, <I>v_0</I>. For
+further details about this algorithm, see <A HREF = "#Duffy">(Duffy)</A> and
+<A HREF = "#Rutherford">(Rutherford)</A>.
+</P>
+<P>Energy transport within the electronic subsystem is solved according
+to the heat diffusion equation with added source terms for heat
+transfer between the subsystems:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ttm.jpg">
+</CENTER>
+<P>where C_e is the specific heat, rho_e is the density, kappa_e is the
+thermal conductivity, T is temperature, the "e" and "a" subscripts
+represent electronic and atomic subsystems respectively, g_p is the
+coupling constant for the electron-ion interaction, and g_s is the
+electron stopping coupling parameter. C_e, rho_e, and kappa_e are
+specified as parameters to the fix. The other quantities are derived.
+The form of the heat diffusion equation used here is almost the same
+as that in equation 6 of <A HREF = "#Duffy">(Duffy)</A>, with the exception that the
+electronic density is explicitly reprensented, rather than being part
+of the the specific heat parameter.
+</P>
+<P>Currently, fix ttm assumes that none of the user-supplied parameters
+will vary with temperature. Note that <A HREF = "#Duffy">(Duffy)</A> used a tanh()
+functional form for the temperature dependence of the electronic
+specific heat, but ignored temperature dependencies of any of the
+other parameters. See more discussion below for fix ttm/mod.
+</P>
+<P>These fixes require use of periodic boundary conditions and a 3D
+simulation. Periodic boundary conditions are also used in the heat
+equation solve for the electronic subsystem. This varies from the
+approach of <A HREF = "#Rutherford">(Rutherford)</A> where the atomic subsystem was
+embedded within a larger continuum representation of the electronic
+subsystem.
+</P>
+<P>The initial electronic temperature input file, <I>T_infile</I>, is a text
+file LAMMPS reads in with no header and with four numeric columns
+(ix,iy,iz,Temp) and with a number of rows equal to the number of
+user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node
+indices from 0 to nxnodes-1, etc. For example, the initial electronic
+temperatures on a 1 by 2 by 3 grid could be specified in a <I>T_infile</I>
+as follows:
+</P>
+<PRE>0 0 0 1.0
+0 0 1 1.0
+0 0 2 1.0
+0 1 0 2.0
+0 1 1 2.0
+0 1 2 2.0
+</PRE>
+<P>where the electronic temperatures along the y=0 plane have been set to
+1.0, and the electronic temperatures along the y=1 plane have been set
+to 2.0. The order of lines in this file is no important. If all the
+nodal values are not specified, LAMMPS will generate an error.
+</P>
+<P>The temperature output file, <I>T_oufile</I>, is created and written by
+this fix. Temperatures for both the electronic and atomic subsystems
+at every node and every N timesteps are output. If N is specified as
+zero, no output is generated, and no output filename is needed. The
+format of the output is as follows. One long line is written every
+output timestep. The timestep itself is given in the first column.
+The next Nx*Ny*Nz columns contain the temperatures for the atomic
+subsystem, and the final Nx*Ny*Nz columns contain the temperatures for
+the electronic subsystem. The ordering of the Nx*Ny*Nz columns is
+with the z index varing fastest, y the next fastest, and x the
+slowest.
+</P>
+<P>These fixes do not change the coordinates of their atoms; they only
+scales their velocities. Thus a time integration fix (e.g. <A HREF = "fix_nve.html">fix
+nve</A>) should still be used to time integrate the affected
+atoms. The fixes should not normally be used on atoms that have their
+temperature controlled by another fix - e.g. <A HREF = "fix_nh.html">fix nvt</A> or
+<A HREF = "fix_langevin.html">fix langevin</A>.
+</P>
+<P>IMPORTANT NOTE: The current implementations of these fixes create a
+copy of the electron grid that overlays the entire simulation domain,
+for each processor. Values on the grid are summed across all
+processors. Thus you should insure that this grid is not too large,
+else your simulation could incur high memory and communication costs.
+</P>
+<HR>
+
+<P><B>Additional details for fix ttm/mod</B>
+</P>
+<P>Fix ttm/mod uses the heat diffusion equation with possible external
+heat sources (e.g. laser heating in ablation simulations):
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ttm_mod.jpg">
+</CENTER>
+<P>where theta is the Heaviside step function, I_0 is the (absorbed)
+laser pulse intensity for ablation simulations, l_skin is the depth
+of skin-layer, and all other designations have the same meaning as in
+the former equation. The duration of the pulse is set by the parameter
+<I>tau</I> in the <I>init_file</I>.
+</P>
+<P>Fix ttm/mod also allows users to specify the dependencies of C_e and
+kappa_e on the electronic temperature. The specific heat is expressed
+as
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ttm_ce.jpg">
+</CENTER>
+<P>where <I>X</I> = T_e/1000, and the thermal conductivity is defined as
+kappa_e = D_e*rho_e*C_e, where D_e is the thermal diffusion
+coefficient.
+</P>
+<P>Electronic pressure effects are included in the TTM model to account
+for the blast force acting on ions because of electronic pressure
+gradient (see <A HREF = "Chen">(Chen)</A>, <A HREF = "#Norman">(Norman)</A>). The total force
+acting on an ion is:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ttm_blast.jpg">
+</CENTER>
+<P>where F_langevin is a force from Langevin thermostat simulating
+electron-phonon coupling, and nabla P_e/n_ion is the electron blast
+force.
+</P>
+<P>The electronic pressure is taken to be P_e = B*rho_e*C_e*T_e
+</P>
+<P>The current fix ttm/mod implementation allows TTM simulations with a
+vacuum. The vacuum region is defined as the grid cells with zero
+electronic temperature. The numerical scheme does not allow energy
+exchange with such cells. Since the material can expand to previously
+unoccupied region in some simulations, the vacuum border can be
+allowed to move. It is controlled by the <I>surface_movement</I> parameter
+in the <I>init_file</I>. If it is set to 1, then "vacuum" cells can be
+changed to "electron-filled" cells with the temperature <I>T_e_min</I> if
+atoms move into them (currently only implemented for the case of
+1-dimensional motion of flat surface normal to the X axis). The
+initial borders of vacuum can be set in the <I>init_file</I> via <I>lsurface</I>
+and <I>rsurface</I> parameters. In this case, electronic pressure gradient
+is calculated as
+</P>
+<CENTER><IMG SRC = "Eqs/fix_ttm_blast1.jpg">
+</CENTER>
+<P>where lambda is the electron mean free path (see <A HREF = "#Norman">(Norman)</A>,
+<A HREF = "#Pisarev">(Pisarev)</A>)
+</P>
+<P>The fix ttm/mod parameter file <I>init_file</I> has the following syntax/
+Every line with the odd number is considered as a comment and
+ignored. The lines with the even numbers are treated as follows:
+</P>
+<PRE>a_0, energy/(temperature*electron) units
+a_1, energy/(temperature^2*electron) units
+a_2, energy/(temperature^3*electron) units
+a_3, energy/(temperature^4*electron) units
+a_4, energy/(temperature^5*electron) units
+C_0, energy/(temperature*electron) units
+A, 1/temperature units
+rho_e, electrons/volume units
+D_e, length^2/time units
+gamma_p, mass/time units
+gamma_s, mass/time units
+v_0, length/time units
+I_0, energy/(time*length^2) units
+lsurface, electron grid units (positive integer)
+rsurface, electron grid units (positive integer)
+l_skin, length units
+tau, time units
+B, dimensionless
+lambda, length units
+n_ion, ions/volume units
+surface_movement: 0 to disable tracking of surface motion, 1 to enable
+T_e_min, temperature units
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>These fixes write the state of the electronic subsystem and the energy
+exchange between the subsystems to <A HREF = "restart.html">binary restart
+files</A>. See the <A HREF = "read_restart.html">read_restart</A> command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>Because the state of the random number generator is not saved in the
+restart files, this means you cannot do "exact" restarts with this
+fix, where the simulation continues on the same as if no restart had
+taken place. However, in a statistical sense, a restarted simulation
+should produce the same behavior.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to these
+fixes.
+</P>
+<P>Both fixes compute 2 output quantities stored in a vector of length 2,
+which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The first quantity is the
+total energy of the electronic subsystem. The second quantity is the
+energy transferred from the electronic to the atomic subsystem on that
+timestep. Note that the velocity verlet integrator applies the fix ttm
+forces to the atomic subsystem as two half-step velocity updates: one
+on the current timestep and one on the subsequent timestep.
+Consequently, the change in the atomic subsystem energy is lagged by
+half a timestep relative to the change in the electronic subsystem
+energy. As a result of this, users may notice slight fluctuations in
+the sum of the atomic and electronic subsystem energies reported at
+the end of the timestep.
+</P>
+<P>The vector values calculated are "extensive".
+</P>
+<P>No parameter of the fixes can be used with the <I>start/stop</I> keywords
+of the <A HREF = "run.html">run</A> command. The fixes are not invoked during
+<A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Fix <I>ttm</I> is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. Fix <I>ttm/mod</I> is part of the USER-MISC
+package. It is only enabled if LAMMPS was built with that package.
+See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more
+info.
+</P>
+<P>These fixes can only be used for 3d simulations and orthogonal
+simlulation boxes. You must also use periodic
+<A HREF = "boundary.html">boundary</A> conditions.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_dt_reset.html">fix dt/reset</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Duffy"></A>
+
+<P><B>(Duffy)</B> D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19,
+016207-016218 (2007).
+</P>
+<A NAME = "Rutherford"></A>
+
+<P><B>(Rutherford)</B> A M Rutherford and D M Duffy, J. Phys.:
+Condens. Matter, 19, 496201-496210 (2007).
+</P>
+<A NAME = "Chen"></A>
+
+<P><B>(Chen)</B> J Chen, D Tzou and J Beraun, Int. J. Heat
+Mass Transfer, 49, 307-316 (2006).
+</P>
+<A NAME = "Norman"></A>
+
+<P><B>(Norman)</B> G E Norman, S V Starikov, V V Stegailov et al., Contrib.
+Plasma Phys., 53, 129-139 (2013).
+</P>
+<A NAME = "Pisarev"></A>
+
+<P><B>(Pisarev)</B> V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26,
+475401 (2014).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_tune_kspace.html b/doc/doc2/fix_tune_kspace.html
new file mode 100644
index 000000000..2b21e12af
--- /dev/null
+++ b/doc/doc2/fix_tune_kspace.html
@@ -0,0 +1,109 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix tune/kspace command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID tune/kspace N
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>tune/kspace = style name of this fix command
+
+<LI>N = invoke this fix every N steps
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 2 all tune/kspace 100
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix tests each kspace style (Ewald, PPPM, and MSM), and
+automatically selects the fastest style to use for the remainder
+of the run. If the fastest style is Ewald or PPPM, the fix also
+adjusts the coulomb cutoff towards optimal speed. Future versions
+of this fix will automatically select other kspace parameters
+to use for maximum simulation speed. The kspace parameters may
+include the style, cutoff, grid points in each direction, order,
+Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc.
+</P>
+<P>The rationale for this fix is to provide the user with
+as-fast-as-possible simulations that include long-range electrostatics
+(kspace) while meeting the user-prescribed accuracy requirement. A
+simple heuristic could never capture the optimal combination of
+parameters for every possible run-time scenario. But by performing
+short tests of various kspace parameter sets, this fix allows
+parameters to be tailored specifically to the user's machine, MPI
+ranks, use of threading or accelerators, the simulated system, and the
+simulation details. In addition, it is possible that parameters could
+be evolved with the simulation on-the-fly, which is useful for systems
+that are dynamically evolving (e.g. changes in box size/shape or
+number of particles).
+</P>
+<P>When this fix is invoked, LAMMPS will perform short timed tests of
+various parameter sets to determine the optimal parameters. Tests are
+performed on-the-fly, with a new test initialized every N steps. N should
+be chosen large enough so that adequate CPU time lapses between tests,
+thereby providing statistically significant timings. But N should not be
+chosen to be so large that an unfortunate parameter set test takes an
+inordinate amount of wall time to complete. An N of 100 for most problems
+seems reasonable. Once an optimal parameter set is found, that set is
+used for the remainder of the run.
+</P>
+<P>This fix uses heristics to guide it's selection of parameter sets to test,
+but the actual timed results will be used to decide which set to use in the
+simulation.
+</P>
+<P>It is not necessary to discard trajectories produced using sub-optimal
+parameter sets, or a mix of various parameter sets, since the user-prescribed
+accuracy will have been maintained throughout. However, some users may prefer
+to use this fix only to discover the optimal parameter set for a given setup
+that can then be used on subsequent production runs.
+</P>
+<P>This fix starts with kspace parameters that are set by the user with the
+<A HREF = "kspace_style.html">kspace_style</A> and <A HREF = "kspace_modify.html">kspace_modify</A>
+commands. The prescribed accuracy will be maintained by this fix throughout
+the simulation.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the KSPACE package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Do not set "neigh_modify once yes" or else this fix will never be
+called. Reneighboring is required.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "boundary.html">boundary</A>
+<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
+lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
+lj/charmm/coul/long</A>, <A HREF = "pair_lj_long.html">pair_style
+lj/long</A>, <A HREF = "pair_lj_long.html">pair_style
+lj/long/coul/long</A>,
+<A HREF = "pair_buck.html">pair_style buck/coul/long</A>
+</P>
+<P><B>Default:</B>
+</P>
+<HR>
+
+</HTML>
diff --git a/doc/doc2/fix_vector.html b/doc/doc2/fix_vector.html
new file mode 100644
index 000000000..d35bae904
--- /dev/null
+++ b/doc/doc2/fix_vector.html
@@ -0,0 +1,171 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix vector command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID vector Nevery value1 value2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/time = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>one or more input values can be listed
+
+<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> c_ID = global scalar calculated by a compute with ID
+ c_ID[I] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID[I] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all vector 100 c_myTemp
+fix 1 all vector 5 c_myTemp v_integral
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more global values as inputs every few timesteps, and
+simply store them. For a single specified value, the values are
+stored as a global vector of growing length. For multiple specified
+values, they are stored as rows in a global array, whose number of
+rows is growing. The resulting vector or array can be used by other
+<A HREF = "Section_howto.html#howto_15">output commands</A>.
+</P>
+<P>One way to to use this command is to accumulate a vector that is
+time-integrated using the <A HREF = "variable.html">variable trap()</A> function.
+For example the velocity auto-correlation function (VACF) can be
+time-integrated, to yield a diffusion coefficient, as follows:
+</P>
+<PRE>compute 2 all vacf
+fix 5 all vector 1 c_2[4]
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff
+</PRE>
+<P>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+</P>
+<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
+<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.
+And the global quantity must be a scalar, not a vector or array.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
+do not have the word <I>atom</I> in their style name. Only a few
+<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
+individual fixes for info on which ones produce such values.
+<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
+be used with this fix. Variables of style <I>atom</I> cannot be used,
+since they produce per-atom values.
+</P>
+<P>The <I>Nevery</I> argument specifies on what timesteps the input values
+will be used in order to be stored. Only timesteps that are a
+multiple of <I>Nevery</I>, including timestep 0, will contribute values.
+</P>
+<P>Note that if you perform multiple runs, using the "pre no" option of
+the <A HREF = "run.html">run</A> command to avoid initialization on subsequent runs,
+then you need to use the <I>stop</I> keyword with the first <A HREF = "run.html">run</A>
+command with a timestep value that encompasses all the runs. This is
+so that the vector or array stored by this fix can be allocated to a
+sufficient size.
+</P>
+<HR>
+
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the compute is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.
+</P>
+<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix vector. Or it can be a compute defined
+not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
+output</A> or other fixes such as <A HREF = "fix_nh.html">fix nvt</A>
+or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See the doc pages for
+these commands which give the IDs of these computes. Users can also
+write code for their own compute styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the fix is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.
+</P>
+<P>Note that some fixes only produce their values on certain timesteps,
+which must be compatible with <I>Nevery</I>, else an error will result.
+Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Only equal-style
+variables can be referenced. See the <A HREF = "variable.html">variable</A> command
+for details. Note that variables of style <I>equal</I> define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to be stored by fix vector.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a global vector or global array which can be
+accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+The values can only be accessed on timesteps that are multiples of
+<I>Nevery</I>.
+</P>
+<P>A vector is produced if only a single input value is specified.
+An array is produced if multiple input values are specified.
+The length of the vector or the number of rows in the array grows
+by 1 every <I>Nevery</I> timesteps.
+</P>
+<P>If the fix prouduces a vector, then the entire vector will be either
+"intensive" or "extensive", depending on whether the values stored in
+the vector are "intensive" or "extensive". If the fix produces an
+array, then all elements in the array must be the same, either
+"intensive" or "extensive". If a compute or fix provides the value
+stored, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
+</P>
+<P>This fix can allocate storage for stored values accumulated over
+multiple runs, using the <I>start</I> and <I>stop</I> keywords of the
+<A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for details of
+how to do this. If using the <A HREF = "run.html">run pre no</A> command option,
+this is required to allow the fix to allocate sufficient storage for
+stored values.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_viscosity.html b/doc/doc2/fix_viscosity.html
new file mode 100644
index 000000000..eb96df8cb
--- /dev/null
+++ b/doc/doc2/fix_viscosity.html
@@ -0,0 +1,184 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix viscosity command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>viscosity = style name of this fix command
+
+<LI>N = perform momentum exchange every N steps
+
+<LI>vdim = <I>x</I> or <I>y</I> or <I>z</I> = which momentum component to exchange
+
+<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer
+
+<LI>Nbin = # of layers in pdim direction (must be even number)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>swap</I> or <I>target</I>
+
+<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
+ <I>vtarget</I> value = V or INF = target velocity of swap partners (velocity units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all viscosity 100 x z 20
+fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
+paper</A> to exchange momenta between two particles in
+different regions of the simulation box every N steps. This induces a
+shear velocity profile in the system. As described below this enables
+a viscosity of the fluid to be calculated. This algorithm is
+sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
+to computing viscosity. This is because the usual NEMD approach is to
+impose a shear velocity profile on the system and measure the response
+via an off-diagonal component of the stress tensor, which is
+proportional to the momentum flux. In the Muller-Plathe method, the
+momentum flux is imposed, and the shear velocity profile is the
+system's response.
+</P>
+<P>The simulation box is divided into <I>Nbin</I> layers in the <I>pdim</I>
+direction, where the layer 1 is at the low end of that dimension and
+the layer <I>Nbin</I> is at the high end. Every N steps, Nswap pairs of
+atoms are chosen in the following manner. Only atoms in the fix group
+are considered. Nswap atoms in layer 1 with positive velocity
+components in the <I>vdim</I> direction closest to the target value <I>V</I> are
+selected. Similarly, Nswap atoms in the "middle" layer (see below) with
+negative velocity components in the <I>vdim</I> direction closest to the
+negative of the target value <I>V</I> are selected. The two sets of Nswap
+atoms are paired up and their <I>vdim</I> momenta components are swapped
+within each pair. This resets their velocities, typically in opposite
+directions. Over time, this induces a shear velocity profile in the
+system which can be measured using commands such as the following,
+which writes the profile to the file tmp.profile:
+</P>
+<PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
+ file tmp.profile units reduced
+</PRE>
+<P>Note that by default, Nswap = 1 and vtarget = INF, though this can be
+changed by the optional <I>swap</I> and <I>vtarget</I> keywords. When vtarget =
+INF, one or more atoms with the most positive and negative velocity
+components are selected. Setting these parameters appropriately, in
+conjunction with the swap rate N, allows the momentum flux rate to be
+adjusted across a wide range of values, and the momenta to be
+exchanged in large chunks or more smoothly.
+</P>
+<P>The "middle" layer for momenta swapping is defined as the <I>Nbin</I>/2 + 1
+layer. Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
+This should lead to a symmetric velocity profile since the two layers
+are separated by the same distance in both directions in a periodic
+sense. This is why <I>Nbin</I> is restricted to being an even number.
+</P>
+<P>As described below, the total momentum transferred by these velocity
+swaps is computed by the fix and can be output. Dividing this
+quantity by time and the cross-sectional area of the simulation box
+yields a momentum flux. The ratio of momentum flux to the slope of
+the shear velocity profile is proportional to the viscosity of the
+fluid, in appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe
+paper</A> for details.
+</P>
+<P>IMPORTANT NOTE: If your system is periodic in the direction of the
+momentum flux, then the flux is going in 2 directions. This means the
+effective momentum flux in one direction is reduced by a factor of 2.
+You will see this in the equations for viscosity in the Muller-Plathe
+paper. LAMMPS is simply tallying momentum which does not account for
+whether or not your system is periodic; you must use the value
+appropriately to yield a viscosity for your system.
+</P>
+<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
+observe is not linear, then you are likely swapping momentum too
+frequently and are not in a regime of linear response. In this case
+you cannot accurately infer a viscosity and should try increasing
+the Nevery parameter.
+</P>
+<P>An alternative method for calculating a viscosity is to run a NEMD
+simulation, as described in <A HREF = "Section_howto.html#howto_13">Section_howto
+13</A> of the manual. NEMD simulations
+deform the simmulation box via the <A HREF = "fix_deform.html">fix deform</A>
+command. Thus they cannot be run on a charged system using a <A HREF = "kspace_style.html">PPPM
+solver</A> since PPPM does not currently support
+non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
+thus it does not suffer from this limitation.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
+cummulative momentum transferred between the bottom and middle of the
+simulation box (in the <I>pdim</I> direction) is stored as a scalar
+quantity by this fix. This quantity is zeroed when the fix is defined
+and accumlates thereafter, once every N steps. The units of the
+quantity are momentum = mass*velocity. The scalar value calculated by
+this fix is "intensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Swaps conserve both momentum and kinetic energy, even if the masses of
+the swapped atoms are not equal. Thus you should not need to
+thermostat the system. If you do use a thermostat, you may want to
+apply it only to the non-swapped dimensions (other than <I>vdim</I>).
+</P>
+<P>LAMMPS does not check, but you should not use this fix to swap
+velocities of atoms that are in constrained molecules, e.g. via <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
+application of the constraints will alter the amount of transferred
+momentum. You should, however, be able to use flexible molecules.
+See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algorithm
+in a computation of alcohol molecule properties.
+</P>
+<P>When running a simulation with large, massive particles or molecules
+in a background solvent, you may want to only exchange momenta bewteen
+solvent particles.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_thermal_conductivity.html">fix
+thermal/conductivity</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are swap = 1 and vtarget = INF.
+</P>
+<HR>
+
+<A NAME = "Muller-Plathe"></A>
+
+<P><B>(Muller-Plathe)</B> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
+</P>
+<A NAME = "Maginn"></A>
+
+<P><B>(Maginn)</B> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
+260, 218-231 (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_viscous.html b/doc/doc2/fix_viscous.html
new file mode 100644
index 000000000..9d890a071
--- /dev/null
+++ b/doc/doc2/fix_viscous.html
@@ -0,0 +1,134 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix viscous command
+</H3>
+<H3>fix viscous/cuda command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID viscous gamma keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>viscous = style name of this fix command
+
+<LI>gamma = damping coefficient (force/velocity units)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>scale</I>
+ <I>scale</I> values = type ratio
+ type = atom type (1-N)
+ ratio = factor to scale the damping coefficient by
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 flow viscous 0.1
+fix 1 damp viscous 0.5 scale 3 2.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Add a viscous damping force to atoms in the group that is proportional
+to the velocity of the atom. The added force can be thought of as a
+frictional interaction with implicit solvent, i.e. the no-slip Stokes
+drag on a spherical particle. In granular simulations this can be
+useful for draining the kinetic energy from the system in a controlled
+fashion. If used without additional thermostatting (to add kinetic
+energy to the system), it has the effect of slowly (or rapidly)
+freezing the system; hence it can also be used as a simple energy
+minimization technique.
+</P>
+<P>The damping force F is given by F = - gamma * velocity. The larger
+the coefficient, the faster the kinetic energy is reduced. If the
+optional keyword <I>scale</I> is used, gamma can scaled up or down by the
+specified factor for atoms of that type. It can be used multiple
+times to adjust gamma for several atom types.
+</P>
+<P>IMPORTANT NOTE: You should specify gamma in force/velocity units.
+This is not the same as mass/time units, at least for some of the
+LAMMPS <A HREF = "units.html">units</A> options like "real" or "metal" that are not
+self-consistent.
+</P>
+<P>In a Brownian dynamics context, gamma = Kb T / D, where Kb =
+Boltzmann's constant, T = temperature, and D = particle diffusion
+coefficient. D can be written as Kb T / (3 pi eta d), where eta =
+dynamic viscosity of the frictional fluid and d = diameter of
+particle. This means gamma = 3 pi eta d, and thus is proportional to
+the viscosity of the fluid and the particle diameter.
+</P>
+<P>In the current implementation, rather than have the user specify a
+viscosity, gamma is specified directly in force/velocity units. If
+needed, gamma can be adjusted for atoms of different sizes
+(i.e. sigma) by using the <I>scale</I> keyword.
+</P>
+<P>Note that Brownian dynamics models also typically include a randomized
+force term to thermostat the system at a chosen temperature. The <A HREF = "fix_langevin.html">fix
+langevin</A> command does this. It has the same
+viscous damping term as fix viscous and adds a random force to each
+atom. The random force term is proportional to the sqrt of the chosen
+thermostatting temperature. Thus if you use fix langevin with a
+target T = 0, its random force term is zero, and you are essentially
+performing the same operation as fix viscous. Also note that the
+gamma of fix viscous is related to the damping parameter of <A HREF = "fix_langevin.html">fix
+langevin</A>, however the former is specified in units
+of force/velocity and the latter in units of time, so that it can more
+easily be used as a thermostat.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I> suffix are functionally the same as the
+corresponding style without the suffix. They have been optimized to
+run faster, depending on your available hardware, as discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
+accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command. This fix should only
+be used with damped dynamics minimizers that allow for
+non-conservative forces. See the <A HREF = "min_style.html">min_style</A> command
+for details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_langevin.html">fix langevin</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall.html b/doc/doc2/fix_wall.html
new file mode 100644
index 000000000..891863492
--- /dev/null
+++ b/doc/doc2/fix_wall.html
@@ -0,0 +1,310 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/lj93 command
+</H3>
+<H3>fix wall/lj126 command
+</H3>
+<H3>fix wall/lj1043 command
+</H3>
+<H3>fix wall/colloid command
+</H3>
+<H3>fix wall/harmonic command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID style face args ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>style = <I>wall/lj93</I> or <I>wall/lj126</I> or <I>wall/lj1043</I> or <I>wall/colloid</I> or <I>wall/harmonic</I>
+
+<LI>one or more face/arg pairs may be appended
+
+<LI>face = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
+
+<PRE> args = coord epsilon sigma cutoff
+ coord = position of wall = EDGE or constant or variable
+ EDGE = current lo or hi edge of simulation box
+ constant = number like 0.0 or -30.0 (distance units)
+ variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
+ epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+ epsilon can be a variable (see below)
+ sigma = size factor for wall-particle interaction (distance units)
+ sigma can be a variable (see below)
+ cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>units</I> or <I>fld</I>
+
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the wall position is defined in lattice units
+ <I>box</I> = the wall position is defined in simulation box units
+ <I>fld</I> value = <I>yes</I> or <I>no</I>
+ <I>yes</I> = invoke the wall constraint to be compatible with implicit FLD
+ <I>no</I> = invoke the wall constraint in the normal way
+ <I>pbc</I> value = <I>yes</I> or <I>no</I>
+ <I>yes</I> = allow periodic boundary in a wall dimension
+ <I>no</I> = require non-perioidic boundaries in any wall dimension
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
+fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
+fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Bound the simulation domain on one or more of its faces with a flat
+wall that interacts with the atoms in the group by generating a force
+on the atom in a direction perpendicular to the wall. The energy of
+wall-particle interactions depends on the style.
+</P>
+<P>For style <I>wall/lj93</I>, the energy E is given by the 9/3 potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_lj93.jpg">
+</CENTER>
+<P>For style <I>wall/lj126</I>, the energy E is given by the 12/6 potential:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>For style <I>wall/lj1043</I>, the energy E is given by the 10/4/3 potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_lj1043.jpg">
+</CENTER>
+<P>For style <I>wall/colloid</I>, the energy E is given by an integrated form
+of the <A HREF = "pair_colloid.html">pair_style colloid</A> potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_colloid.jpg">
+</CENTER>
+<P>For style <I>wall/harmonic</I>, the energy E is given by a harmonic spring
+potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_harmonic.jpg">
+</CENTER>
+<P>In all cases, <I>r</I> is the distance from the particle to the wall at
+position <I>coord</I>, and Rc is the <I>cutoff</I> distance at which the
+particle and wall no longer interact. The energy of the wall
+potential is shifted so that the wall-particle interaction energy is
+0.0 at the cutoff distance.
+</P>
+<P>Up to 6 walls or faces can be specified in a single command: <I>xlo</I>,
+<I>xhi</I>, <I>ylo</I>, <I>yhi</I>, <I>zlo</I>, <I>zhi</I>. A <I>lo</I> face interacts with
+particles near the lower side of the simulation box in that dimension.
+A <I>hi</I> face interacts with particles near the upper side of the
+simulation box in that dimension.
+</P>
+<P>The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable. If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used. If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z). In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v_name,
+where name is an <A HREF = "variable.html">equal-style variable</A> name. In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall. Equal-style variables
+can specify formulas with various mathematical functions, and include
+<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
+box parameters and timestep and elapsed time. Thus it is easy to
+specify a time-dependent wall position. See examples below.
+</P>
+<P>For the <I>wall/lj93</I> and <I>wall/lj126</I> and <I>wall/lj1043</I> styles,
+<I>epsilon</I> and <I>sigma</I> are the usual Lennard-Jones parameters, which
+determine the strength and size of the particle as it interacts with
+the wall. Epsilon has energy units. Note that this <I>epsilon</I> and
+<I>sigma</I> may be different than any <I>epsilon</I> or <I>sigma</I> values defined
+for a pair style that computes particle-particle interactions.
+</P>
+<P>The <I>wall/lj93</I> interaction is derived by integrating over a 3d
+half-lattice of Lennard-Jones 12/6 particles. The <I>wall/lj126</I>
+interaction is effectively a harder, more repulsive wall interaction.
+The <I>wall/lj1043</I> interaction is yet a different form of wall
+interaction, described in Magda et al in <A HREF = "#Magda">(Magda)</A>.
+</P>
+<P>For the <I>wall/colloid</I> style, <I>R</I> is the radius of the colloid
+particle, <I>D</I> is the distance from the surface of the colloid particle
+to the wall (r-R), and <I>sigma</I> is the size of a constituent LJ
+particle inside the colloid particle and wall. Note that the cutoff
+distance Rc in this case is the distance from the colloid particle
+center to the wall. The prefactor <I>epsilon</I> can be thought of as an
+effective Hamaker constant with energy units for the strength of the
+colloid-wall interaction. More specifically, the <I>epsilon</I> pre-factor
+= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon
+and sigma are the LJ parameters for the constituent LJ
+particles. Rho_wall and rho_colloid are the number density of the
+constituent particles, in the wall and colloid respectively, in units
+of 1/volume.
+</P>
+<P>The <I>wall/colloid</I> interaction is derived by integrating over
+constituent LJ particles of size <I>sigma</I> within the colloid particle
+and a 3d half-lattice of Lennard-Jones 12/6 particles of size <I>sigma</I>
+in the wall. As mentioned in the preceeding paragraph, the density of
+particles in the wall and colloid can be different, as specified by
+the <I>epsilon</I> pre-factor.
+</P>
+<P>For the <I>wall/harmonic</I> style, <I>epsilon</I> is effectively the spring
+constant K, and has units (energy/distance^2). The input parameter
+<I>sigma</I> is ignored. The minimum energy position of the harmonic
+spring is at the <I>cutoff</I>. This is a repulsive-only spring since the
+interaction is truncated at the <I>cutoff</I>
+</P>
+<P>For any wall, the <I>epsilon</I> and/or <I>sigma</I> parameter can be specified
+as an <A HREF = "variable.html">equal-style variable</A>, in which case it should be
+specified as v_name, where name is the variable name. As with a
+variable wall position, the variable is evaluated each timestep and
+the result becomes the current epsilon or sigma of the wall.
+Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent wall interaction.
+</P>
+<P>IMPORTANT NOTE: For all of the styles, you must insure that r is
+always > 0 for all particles in the group, or LAMMPS will generate an
+error. This means you cannot start your simulation with particles at
+the wall position <I>coord</I> (r = 0) or with particles on the wrong side
+of the wall (r < 0). For the <I>wall/lj93</I> and <I>wall/lj126</I> styles, the
+energy of the wall/particle interaction (and hence the force on the
+particle) blows up as r -> 0. The <I>wall/colloid</I> style is even more
+restrictive, since the energy blows up as D = r-R -> 0. This means
+the finite-size particles of radius R must be a distance larger than R
+from the wall position <I>coord</I>. The <I>harmonic</I> style is a softer
+potential and does not blow up as r -> 0, but you must use a large
+enough <I>epsilon</I> that particles always reamin on the correct side of
+the wall (r > 0).
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant or
+variable is used. It is not relevant when EDGE is used to specify a
+face position. In the variable case, the variable is assumed to
+produce a value compatible with the <I>units</I> setting you specify.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings.
+</P>
+<P>The <I>fld</I> keyword can be used with a <I>yes</I> setting to invoke the wall
+constraint before pairwise interactions are computed. This allows an
+implicit FLD model using <A HREF = "pair_lubricateU.html">pair_style lubricateU</A>
+to include the wall force in its calculations. If the setting is
+<I>no</I>, wall forces are imposed after pairwise interactions, in the
+usual manner.
+</P>
+<P>The <I>pbc</I> keyword can be used with a <I>yes</I> setting to allow walls to
+be specified in a periodic dimension. See the
+<A HREF = "boundary.html">boundary</A> command for options on simulation box
+boundaries. The default for <I>pbc</I> is <I>no</I>, which means the system
+must be non-periodic when using a wall. But you may wish to use a
+periodic box. E.g. to allow some particles to interact with the wall
+via the fix group-ID, and others to pass through it and wrap around a
+periodic box. In this case you should insure that the wall if
+sufficiently far enough away from the box boundary. If you do not,
+then particles may interact with both the wall and with periodic
+images on the other side of the box, which is probably not what you
+want.
+</P>
+<HR>
+
+<P>Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+<A HREF = "variable.html">variables</A>. The wall interaction parameters (epsilon,
+sigma) could be varied with additional variable definitions.
+</P>
+<PRE>variable ramp equal ramp(0,10)
+fix 1 all wall xlo v_ramp 1.0 1.0 2.5
+</PRE>
+<PRE>variable linear equal vdisplace(0,20)
+fix 1 all wall xlo v_linear 1.0 1.0 2.5
+</PRE>
+<PRE>variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+</PRE>
+<PRE>variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+</PRE>
+<P>The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run. The vdisplace(c0,velocity) function does
+something similar using the equation position = c0 + velocity*delta,
+where delta is the elapsed time.
+</P>
+<P>The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+</P>
+<PRE>position = c0 + A sin(omega*delta)
+</PRE>
+<P>The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+</P>
+<PRE>position = c0 + A (1 - cos(omega*delta))
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and each wall to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar energy and a global vector of
+forces, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. Note that the scalar energy is
+the sum of interactions with all defined walls. If you want the
+energy on a per-wall basis, you need to use multiple fix wall
+commands. The length of the vector is equal to the number of walls
+defined by the fix. Each vector value is the normal force on a
+specific wall. Note that an outward force on a wall will be a
+negative value for <I>lo</I> walls and a positive value for <I>hi</I> walls.
+The scalar and vector values calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall_reflect.html">fix wall/reflect</A>,
+<A HREF = "fix_wall_gran.html">fix wall/gran</A>,
+<A HREF = "fix_wall_region.html">fix wall/region</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults units = lattice, fld = no, and pbc = no.
+</P>
+<HR>
+
+<A NAME = "Magda"></A>
+
+<P><B>(Magda)</B> Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985);
+erratum in JCP 84, 2901 (1986).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall_gran.html b/doc/doc2/fix_wall_gran.html
new file mode 100644
index 000000000..032beac91
--- /dev/null
+++ b/doc/doc2/fix_wall_gran.html
@@ -0,0 +1,176 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/gran command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID wall/gran Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>wall/gran = style name of this fix command
+
+<LI>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+
+<LI>Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+
+<LI>gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+
+<LI>gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+
+<LI>xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+
+<LI>dampflag = 0 or 1 if tangential damping force is excluded or included
+
+<LI>wallstyle = <I>xplane</I> or <I>yplane</I> or <I>zplane</I> or <I>zcylinder</I>
+
+<LI>args = list of arguments for a particular style
+
+<PRE> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
+ lo,hi = position of lower and upper plane (distance units), either can be NULL)
+ <I>zcylinder</I> args = radius
+ radius = cylinder radius (distance units)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended to args
+
+<LI>keyword = <I>wiggle</I> or <I>shear</I>
+
+<PRE> <I>wiggle</I> values = dim amplitude period
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ amplitude = size of oscillation (distance units)
+ period = time of oscillation (time units)
+ <I>shear</I> values = dim vshear
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ vshear = magnitude of shear velocity (velocity units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
+fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
+fix 2 all wall/gran 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Bound the simulation domain of a granular system with a frictional
+wall. All particles in the group interact with the wall when they are
+close enough to touch it.
+</P>
+<P>The first set of parameters (Kn, Kt, gamma_n, gamma_t, xmu, and
+dampflag) have the same meaning as those specified with the
+<A HREF = "pair_gran.html">pair_style granular</A> force fields. This means a NULL
+can be used for either Kt or gamma_t as described on that page. If a
+NULL is used for Kt, then a default value is used where Kt = 2/7 Kn.
+If a NULL is used for gamma_t, then a default value is used where
+gamma_t = 1/2 gamma_n.
+</P>
+<P>The nature of the wall/particle interactions are determined by which
+pair_style is used in your input script: <I>hooke</I>, <I>hooke/history</I>, or
+<I>hertz/history</I>. The equation for the force between the wall and
+particles touching it is the same as the corresponding equation on the
+<A HREF = "pair_gran.html">pair_style granular</A> doc page, in the limit of one of
+the two particles going to infinite radius and mass (flat wall).
+I.e. delta = radius - r = overlap of particle with wall, m_eff = mass
+of particle, and sqrt(RiRj/Ri+Rj) becomes sqrt(radius of particle).
+The units for Kn, Kt, gamma_n, and gamma_t are as described on that
+doc page. The meaning of xmu and dampflag are also as described on
+that page. Note that you can choose different values for these 6
+wall/particle coefficients than for particle/particle interactions, if
+you wish your wall to interact differently with the particles, e.g. if
+the wall is a different material.
+</P>
+<P>IMPORTANT NOTE: As discussed on the doc page for <A HREF = "pair_gran.html">pair_style
+granular</A>, versions of LAMMPS before 9Jan09 used a
+different equation for Hertzian interactions. This means Hertizian
+wall/particle interactions have also changed. They now include a
+sqrt(radius) term which was not present before. Also the previous
+versions used Kn and Kt from the pairwise interaction and hardwired
+dampflag to 1, rather than letting them be specified directly. This
+means you can set the values of the wall/particle coefficients
+appropriately in the current code to reproduce the results of a
+prevoius Hertzian monodisperse calculation. For example, for the
+common case of a monodisperse system with particles of diameter 1, Kn,
+Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
+previously.
+</P>
+<P>The <I>wallstyle</I> can be planar or cylindrical. The 3 planar options
+specify a pair of walls in a dimension. Wall positions are given by
+<I>lo</I> and <I>hi</I>. Either of the values can be specified as NULL if a
+single wall is desired. For a <I>zcylinder</I> wallstyle, the cylinder's
+axis is at x = y = 0.0, and the radius of the cylinder is specified.
+</P>
+<P>Optionally, the wall can be moving, if the <I>wiggle</I> or <I>shear</I>
+keywords are appended. Both keywords cannot be used together.
+</P>
+<P>For the <I>wiggle</I> keyword, the wall oscillates sinusoidally, similar to
+the oscillations of particles which can be specified by the
+<A HREF = "fix_move.html">fix_move</A> command. This is useful in packing
+simulations of granular particles. The arguments to the <I>wiggle</I>
+keyword specify a dimension for the motion, as well as it's
+<I>amplitude</I> and <I>period</I>. Note that if the dimension is in the plane
+of the wall, this is effectively a shearing motion. If the dimension
+is perpendicular to the wall, it is more of a shaking motion. A
+<I>zcylinder</I> wall can only be wiggled in the z dimension.
+</P>
+<P>Each timestep, the position of a wiggled wall in the appropriate <I>dim</I>
+is set according to this equation:
+</P>
+<PRE>position = coord + A - A cos (omega * delta)
+</PRE>
+<P>where <I>coord</I> is the specified initial position of the wall, <I>A</I> is
+the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
+elapsed since the fix was specified. The velocity of the wall is set
+to the derivative of this expression.
+</P>
+<P>For the <I>shear</I> keyword, the wall moves continuously in the specified
+dimension with velocity <I>vshear</I>. The dimension must be tangential to
+walls with a planar <I>wallstyle</I>, e.g. in the <I>y</I> or <I>z</I> directions for
+an <I>xplane</I> wall. For <I>zcylinder</I> walls, a dimension of <I>z</I> means the
+cylinder is moving in the z-direction along it's axis. A dimension of
+<I>x</I> or <I>y</I> means the cylinder is spinning around the z-axis, either in
+the clockwise direction for <I>vshear</I> > 0 or counter-clockwise for
+<I>vshear</I> < 0. In this case, <I>vshear</I> is the tangential velocity of
+the wall at whatever <I>radius</I> has been defined.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the shear friction state of atoms interacting with the
+wall to <A HREF = "restart.html">binary restart files</A>, so that a simulation can
+continue correctly if granular potentials with shear "history" effects
+are being used. See the <A HREF = "read_restart.html">read_restart</A> command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix is part of the GRANULAR package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Any dimension (xyz) that has a granular wall must be non-periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_move.html">fix_move</A>, <A HREF = "pair_gran.html">pair_style granular</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall_piston.html b/doc/doc2/fix_wall_piston.html
new file mode 100644
index 000000000..b76361ce9
--- /dev/null
+++ b/doc/doc2/fix_wall_piston.html
@@ -0,0 +1,131 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/piston command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID wall/piston face ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>wall/piston = style name of this fix command
+
+<LI>face = <I>zlo</I>
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>pos</I> or <I>vel</I> or <I>ramp</I> or <I>units</I>
+
+<PRE> <I>pos</I> args = z
+ z = z coordinate at which the piston begins (distance units)
+ <I>vel</I> args = vz
+ vz = final velocity of the piston (velocity units)
+ <I>ramp</I> = use a linear velocity ramp from 0 to vz
+ <I>temp</I> args = target damp seed extent
+ target = target velocity for region immediately ahead of the piston
+ damp = damping paramter (time units)
+ seed = random number seed for langevin kicks
+ extent = extent of thermostated region (distance units)
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the wall position is defined in lattice units
+ <I>box</I> = the wall position is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix xwalls all wall/piston zlo
+fix walls all wall/piston zlo pos 1.0 vel 10.0 units box
+fix top all wall/piston zlo vel 10.0 ramp
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Bound the simulation with a moving wall which reflect particles in the
+specified group and drive the system with an effective infinite-mass
+piston capable of driving shock waves.
+</P>
+<P>A momentum mirror technique is used, which means that if an atom (or
+the wall) moves such that an atom is outside the wall on a timestep by
+a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is put
+back inside the face by the same delta, and the velocity relative to
+the moving wall is flipped in z. For instance, a stationary particle
+hit with a piston wall with velocity vz, will end the timestep with a
+velocity of 2*vz.
+</P>
+<P>Currently the <I>face</I> keyword can only be <I>zlo</I>. This creates a piston
+moving in the positive z direction. Particles with z coordinate less
+than the wall position are reflected to a z coordinate greater than
+the wall position. If the piston velocity is vpz and the particle
+velocity before reflection is vzi, the particle velocity after
+reflection is -vzi + 2*vpz.
+</P>
+<P>The initial position of the wall can be specified by the <I>pos</I> keyword.
+</P>
+<P>The final velocity of the wall can be specified by the <I>vel</I> keyword
+</P>
+<P>The <I>ramp</I> keyword will cause the wall/piston to adjust the velocity
+linearly from zero velocity to <I>vel</I> over the course of the run. If
+the <I>ramp</I> keyword is omitted then the wall/piston moves at a constant
+velocity defined by <I>vel</I>.
+</P>
+<P>The <I>temp</I> keyword will cause the region immediately in front of the
+wall/piston to be thermostated with a Langevin thermostat. This
+region moves with the piston. The damping and kicking are measured in
+the reference frame of the piston. So, a temperature of zero would
+mean all particles were moving at exactly the speed of the
+wall/piston.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howoto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This fix style is part of the SHOCK package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The face that has the wall/piston must be boundary type 's'
+(shrink-wrapped). The opposing face can be
+any boundary type other than periodic.
+</P>
+<P>A wall/piston should not be used with rigid bodies such as those
+defined by a "fix rigid" command. This is because the wall/piston
+displaces atoms directly rather than exerting a force on them.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall.html">fix wall/reflect</A> command, <A HREF = "fix_append_atoms.html">fix
+append/atoms</A> command
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are pos = 0, vel = 0, units = lattice.
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall_reflect.html b/doc/doc2/fix_wall_reflect.html
new file mode 100644
index 000000000..8e87e80db
--- /dev/null
+++ b/doc/doc2/fix_wall_reflect.html
@@ -0,0 +1,174 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/reflect command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID wall/reflect face arg ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>wall/reflect = style name of this fix command
+
+<LI>one or more face/arg pairs may be appended
+
+<LI>face = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
+
+<PRE> <I>xlo</I>,<I>ylo</I>,<I>zlo</I> arg = EDGE or constant or variable
+ EDGE = current lo edge of simulation box
+ constant = number like 0.0 or -30.0 (distance units)
+ variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
+ <I>xhi</I>,<I>yhi</I>,<I>zhi</I> arg = EDGE or constant or variable
+ EDGE = current hi edge of simulation box
+ constant = number like 50.0 or 100.3 (distance units)
+ variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>units</I>
+
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the wall position is defined in lattice units
+ <I>box</I> = the wall position is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix xwalls all wall/reflect xlo EDGE xhi EDGE
+fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
+fix top all wall/reflect zhi v_pressdown
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Bound the simulation with one or more walls which reflect particles
+in the specified group when they attempt to move thru them.
+</P>
+<P>Reflection means that if an atom moves outside the wall on a timestep
+by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is
+put back inside the face by the same delta, and the sign of the
+corresponding component of its velocity is flipped.
+</P>
+<P>When used in conjunction with <A HREF = "fix_nve.html">fix nve</A> and <A HREF = "run_style.html">run_style
+verlet</A>, the resultant time-integration algorithm is
+equivalent to the primitive splitting algorithm (PSA) described by
+<A HREF = "#Bond">Bond</A>. Because each reflection event divides
+the corresponding timestep asymmetrically, energy conservation is only
+satisfied to O(dt), rather than to O(dt^2) as it would be for
+velocity-Verlet integration without reflective walls.
+</P>
+<P>Up to 6 walls or faces can be specified in a single command: <I>xlo</I>,
+<I>xhi</I>, <I>ylo</I>, <I>yhi</I>, <I>zlo</I>, <I>zhi</I>. A <I>lo</I> face reflects particles
+that move to a coordinate less than the wall position, back in the
+<I>hi</I> direction. A <I>hi</I> face reflects particles that move to a
+coordinate higher than the wall position, back in the <I>lo</I> direction.
+</P>
+<P>The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable. If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used. If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z). In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v_name,
+where name is an <A HREF = "variable.html">equal-style variable</A> name. In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall. Equal-style variables
+can specify formulas with various mathematical functions, and include
+<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
+box parameters and timestep and elapsed time. Thus it is easy to
+specify a time-dependent wall position.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant or
+variable is used. It is not relevant when EDGE is used to specify a
+face position. In the variable case, the variable is assumed to
+produce a value compatible with the <I>units</I> setting you specify.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings.
+</P>
+<HR>
+
+<P>Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+<A HREF = "variable.html">variables</A>.
+</P>
+<PRE>variable ramp equal ramp(0,10)
+fix 1 all wall/reflect xlo v_ramp
+</PRE>
+<PRE>variable linear equal vdisplace(0,20)
+fix 1 all wall/reflect xlo v_linear
+</PRE>
+<PRE>variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+</PRE>
+<PRE>variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+</PRE>
+<P>The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run. The vdisplace(c0,velocity) function does
+something similar using the equation position = c0 + velocity*delta,
+where delta is the elapsed time.
+</P>
+<P>The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+</P>
+<PRE>position = c0 + A sin(omega*delta)
+</PRE>
+<P>The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+</P>
+<PRE>position = c0 + A (1 - cos(omega*delta))
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. No parameter of this fix can
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension (xyz) that has a reflecting wall must be non-periodic.
+</P>
+<P>A reflecting wall should not be used with rigid bodies such as those
+defined by a "fix rigid" command. This is because the wall/reflect
+displaces atoms directly rather than exerts a force on them. For
+rigid bodies, use a soft wall instead, such as <A HREF = "fix_wall.html">fix
+wall/lj93</A>. LAMMPS will flag the use of a rigid
+fix with fix wall/reflect with a warning, but will not generate an
+error.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall.html">fix wall/lj93</A>, <A HREF = "fix_oneway.html">fix oneway</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Bond"></A>
+
+<P><B>(Bond)</B> Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall_region.html b/doc/doc2/fix_wall_region.html
new file mode 100644
index 000000000..9f4a5d06c
--- /dev/null
+++ b/doc/doc2/fix_wall_region.html
@@ -0,0 +1,210 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/region command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID wall/region region-ID style epsilon sigma cutoff
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>wall/region = style name of this fix command
+<LI>region-ID = region whose boundary will act as wall
+<LI>style = <I>lj93</I> or <I>lj126</I> or <I>colloid</I> or <I>harmonic</I>
+<LI>epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+<LI>sigma = size factor for wall-particle interaction (distance units)
+<LI>cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix wall all wall/region mySphere lj93 1.0 1.0 2.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Treat the surface of the geometric region defined by the <I>region-ID</I>
+as a bounding wall which interacts with nearby particles according to
+the specified style. The distance between a particle and the surface
+is the distance to the nearest point on the surface and the force the
+wall exerts on the particle is along the direction between that point
+and the particle, which is the direction normal to the surface at that
+point. Note that if the region surface is comprised of multiple
+"faces", then each face can exert a force on the particle if it is
+close enough. E.g. for <A HREF = "region.html">region_style block</A>, a particle
+in the interior, near a corner of the block, could feel wall forces
+from 1, 2, or 3 faces of the block.
+</P>
+<P>Regions are defined using the <A HREF = "region.html">region</A> command. Note that
+the region volume can be interior or exterior to the bounding surface,
+which will determine in which direction the surface interacts with
+particles, i.e. the direction of the surface normal. Regions can
+either be primitive shapes (block, sphere, cylinder, etc) or
+combinations of primitive shapes specified via the <I>union</I> or
+<I>intersect</I> region styles. These latter styles can be used to
+construct particle containers with complex shapes. Regions can also
+change over time via the <A HREF = "region.html">region</A> command keywords (move)
+and <I>rotate</I>. If such a region is used with this fix, then the of
+region surface will move over time in the corresponding manner.
+</P>
+<P>IMPORTANT NOTE: As discussed on the <A HREF = "region.html">region</A> command doc
+page, regions in LAMMPS do not get wrapped across periodic boundaries.
+It is up to you to insure that periodic or non-periodic boundaries are
+specified appropriately via the <A HREF = "boundary.html">boundary</A> command when
+using a region as a wall that bounds particle motion. This also means
+that if you embed a region in your simulation box and want it to
+repulse particles from its surface (using the "side out" option in the
+<A HREF = "region.html">region</A> command), that its repulsive force will not be
+felt across a periodic boundary.
+</P>
+<P>IMPORTANT NOTE: For primitive regions with sharp corners and/or edges
+(e.g. a block or cylinder), wall/particle forces are computed
+accurately for both interior and exterior regions. For <I>union</I> and
+<I>intersect</I> regions, additional sharp corners and edges may be present
+due to the intersection of the surfaces of 2 or more primitive
+volumes. These corners and edges can be of two types: concave or
+convex. Concave points/edges are like the corners of a cube as seen
+by particles in the interior of a cube. Wall/particle forces around
+these features are computed correctly. Convex points/edges are like
+the corners of a cube as seen by particles exterior to the cube,
+i.e. the points jut into the volume where particles are present.
+LAMMPS does NOT compute the location of these convex points directly,
+and hence wall/particle forces in the cutoff volume around these
+points suffer from inaccuracies. The basic problem is that the
+outward normal of the surface is not continuous at these points. This
+can cause particles to feel no force (they don't "see" the wall) when
+in one location, then move a distance epsilon, and suddenly feel a
+large force because they now "see" the wall. In a worst-case
+scenario, this can blow particles out of the simulation box. Thus, as
+a general rule you should not use the fix wall/region command with
+<I>union</I> or <I>interesect</I> regions that have convex points or edges.
+</P>
+<P>IMPORTANT NOTE: Similarly, you should not define <I>union</I> or
+<I>intersert</I> regions for use with this command that share a common
+face, even if the face is smooth. E.g. two regions of style block in
+a <I>union</I> region, where the two blocks have the same face. This is
+because LAMMPS discards points that are part of multiple sub-regions
+when calculating wall/particle interactions, to avoid double-counting
+the interaction. Having two coincident faces could cause the face to
+become invisible to the particles. The solution is to make the two
+faces differ by epsilon in their position.
+</P>
+<P>The energy of wall-particle interactions depends on the specified
+style.
+</P>
+<P>For style <I>lj93</I>, the energy E is given by the 9/3 potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_lj93.jpg">
+</CENTER>
+<P>For style <I>lj126</I>, the energy E is given by the 12/6 potential:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>For style <I>colloid</I>, the energy E is given by an integrated form of
+the <A HREF = "pair_colloid.html">pair_style colloid</A> potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_colloid.jpg">
+</CENTER>
+<P>For style <I>wall/harmonic</I>, the energy E is given by a harmonic spring
+potential:
+</P>
+<CENTER><IMG SRC = "Eqs/fix_wall_harmonic.jpg">
+</CENTER>
+<P>In all cases, <I>r</I> is the distance from the particle to the region
+surface, and Rc is the <I>cutoff</I> distance at which the particle and
+surface no longer interact. The energy of the wall potential is
+shifted so that the wall-particle interaction energy is 0.0 at the
+cutoff distance.
+</P>
+<P>For the <I>lj93</I> and <I>lj126</I> styles, <I>epsilon</I> and <I>sigma</I> are the usual
+Lennard-Jones parameters, which determine the strength and size of the
+particle as it interacts with the wall. Epsilon has energy units.
+Note that this <I>epsilon</I> and <I>sigma</I> may be different than any
+<I>epsilon</I> or <I>sigma</I> values defined for a pair style that computes
+particle-particle interactions.
+</P>
+<P>The <I>lj93</I> interaction is derived by integrating over a 3d
+half-lattice of Lennard-Jones 12/6 particles. The <I>lj126</I> interaction
+is effectively a harder, more repulsive wall interaction.
+</P>
+<P>For the <I>colloid</I> style, <I>epsilon</I> is effectively a Hamaker constant
+with energy units for the colloid-wall interaction, <I>R</I> is the radius
+of the colloid particle, <I>D</I> is the distance from the surface of the
+colloid particle to the wall (r-R), and <I>sigma</I> is the size of a
+constituent LJ particle inside the colloid particle. Note that the
+cutoff distance Rc in this case is the distance from the colloid
+particle center to the wall.
+</P>
+<P>The <I>colloid</I> interaction is derived by integrating over constituent
+LJ particles of size <I>sigma</I> within the colloid particle and a 3d
+half-lattice of Lennard-Jones 12/6 particles of size <I>sigma</I> in the
+wall.
+</P>
+<P>For the <I>wall/harmonic</I> style, <I>epsilon</I> is effectively the spring
+constant K, and has units (energy/distance^2). The input parameter
+<I>sigma</I> is ignored. The minimum energy position of the harmonic
+spring is at the <I>cutoff</I>. This is a repulsive-only spring since the
+interaction is truncated at the <I>cutoff</I>
+</P>
+<P>IMPORTANT NOTE: For all of the styles, you must insure that r is
+always > 0 for all particles in the group, or LAMMPS will generate an
+error. This means you cannot start your simulation with particles on
+the region surface (r = 0) or with particles on the wrong side of the
+region surface (r < 0). For the <I>wall/lj93</I> and <I>wall/lj126</I> styles,
+the energy of the wall/particle interaction (and hence the force on
+the particle) blows up as r -> 0. The <I>wall/colloid</I> style is even
+more restrictive, since the energy blows up as D = r-R -> 0. This
+means the finite-size particles of radius R must be a distance larger
+than R from the region surface. The <I>harmonic</I> style is a softer
+potential and does not blow up as r -> 0, but you must use a large
+enough <I>epsilon</I> that particles always reamin on the correct side of
+the region surface (r > 0).
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar energy and a global 3-length vector
+of forces, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar energy is the sum
+of energy interactions for all particles interacting with the wall
+represented by the region surface. The 3 vector quantities are the
+x,y,z components of the total force acting on the wall due to the
+particles. The scalar and vector values calculated by this fix are
+"extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_wall.html">fix wall/lj93</A>,
+<A HREF = "fix_wall.html">fix wall/lj126</A>,
+<A HREF = "fix_wall.html">fix wall/colloid</A>,
+<A HREF = "fix_wall_gran.html">fix wall/gran</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/fix_wall_srd.html b/doc/doc2/fix_wall_srd.html
new file mode 100644
index 000000000..ea3f64c68
--- /dev/null
+++ b/doc/doc2/fix_wall_srd.html
@@ -0,0 +1,203 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix wall/srd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID wall/srd face arg ... keyword value ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>wall/srd = style name of this fix command
+
+<LI>one or more face/arg pairs may be appended
+
+<LI>face = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
+
+<PRE> <I>xlo</I>,<I>ylo</I>,<I>zlo</I> arg = EDGE or constant or variable
+ EDGE = current lo edge of simulation box
+ constant = number like 0.0 or -30.0 (distance units)
+ variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
+ <I>xhi</I>,<I>yhi</I>,<I>zhi</I> arg = EDGE or constant or variable
+ EDGE = current hi edge of simulation box
+ constant = number like 50.0 or 100.3 (distance units)
+ variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>units</I>
+
+<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the wall position is defined in lattice units
+ <I>box</I> = the wall position is defined in simulation box units
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix xwalls all wall/srd xlo EDGE xhi EDGE
+fix walls all wall/srd xlo 0.0 ylo 10.0 units box
+fix top all wall/srd zhi v_pressdown
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Bound the simulation with one or more walls which interact with
+stochastic reaction dynamics (SRD) particles as slip (smooth) or
+no-slip (rough) flat surfaces. The wall interaction is actually
+invoked via the <A HREF = "fix_srd.html">fix srd</A> command, only on the group of
+SRD particles it defines, so the group setting for the fix wall/srd
+command is ignored.
+</P>
+<P>A particle/wall collision occurs if an SRD particle moves outside the
+wall on a timestep. This alters the position and velocity of the SRD
+particle and imparts a force to the wall.
+</P>
+<P>The <I>collision</I> and <I>Tsrd</I> settings specified via the <A HREF = "fix_srd.html">fix
+srd</A> command affect the SRD/wall collisions. A <I>slip</I>
+setting for the <I>collision</I> keyword means that the tangential
+component of the SRD particle momentum is preserved. Thus only a
+normal force is imparted to the wall. The normal component of the new
+SRD velocity is sampled from a Gaussian distribution at temperature
+<I>Tsrd</I>.
+</P>
+<P>For a <I>noslip</I> setting of the <I>collision</I> keyword, both the normal and
+tangential components of the new SRD velocity are sampled from a
+Gaussian distribution at temperature <I>Tsrd</I>. Additionally, a new
+tangential direction for the SRD velocity is chosen randomly. This
+collision style imparts both a normal and tangential force to the
+wall.
+</P>
+<P>Up to 6 walls or faces can be specified in a single command: <I>xlo</I>,
+<I>xhi</I>, <I>ylo</I>, <I>yhi</I>, <I>zlo</I>, <I>zhi</I>. A <I>lo</I> face reflects particles
+that move to a coordinate less than the wall position, back in the
+<I>hi</I> direction. A <I>hi</I> face reflects particles that move to a
+coordinate higher than the wall position, back in the <I>lo</I> direction.
+</P>
+<P>The position of each wall can be specified in one of 3 ways: as the
+EDGE of the simulation box, as a constant value, or as a variable. If
+EDGE is used, then the corresponding boundary of the current
+simulation box is used. If a numeric constant is specified then the
+wall is placed at that position in the appropriate dimension (x, y, or
+z). In both the EDGE and constant cases, the wall will never move.
+If the wall position is a variable, it should be specified as v_name,
+where name is an <A HREF = "variable.html">equal-style variable</A> name. In this
+case the variable is evaluated each timestep and the result becomes
+the current position of the reflecting wall. Equal-style variables
+can specify formulas with various mathematical functions, and include
+<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
+box parameters and timestep and elapsed time. Thus it is easy to
+specify a time-dependent wall position.
+</P>
+<P>IMPORTANT NOTE: Because the trajectory of the SRD particle is tracked
+as it collides with the wall, you must insure that r = distance of the
+particle from the wall, is always > 0 for SRD particles, or LAMMPS
+will generate an error. This means you cannot start your simulation
+with SRD particles at the wall position <I>coord</I> (r = 0) or with
+particles on the wrong side of the wall (r < 0).
+</P>
+<P>IMPORTANT NOTE: If you have 2 or more walls that come together at an
+edge or corner (e.g. walls in the x and y dimensions), then be sure to
+set the <I>overlap</I> keyword to <I>yes</I> in the <A HREF = "fix_srd.html">fix srd</A>
+command, since the walls effectively overlap when SRD particles
+collide with them. LAMMPS will issue a warning if you do not do this.
+</P>
+<P>IMPORTANT NOTE: The walls of this fix only interact with SRD
+particles, as defined by the <A HREF = "fix_srd.html">fix srd</A> command. If you
+are simulating a mixture containing other kinds of particles, then you
+should typically use <A HREF = "fix_wall.html">another wall command</A> to act on
+the other particles. Since SRD particles will be colliding both with
+the walls and the other particles, it is important to insure that the
+other particle's finite extent does not overlap an SRD wall. If you
+do not do this, you may generate errors when SRD particles end up
+"inside" another particle or a wall at the beginning of a collision
+step.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define a wall position, but only when a numeric constant is used.
+It is not relevant when EDGE or a variable is used to specify a face
+position.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings.
+</P>
+<HR>
+
+<P>Here are examples of variable definitions that move the wall position
+in a time-dependent fashion using equal-style
+<A HREF = "variable.html">variables</A>.
+</P>
+<PRE>variable ramp equal ramp(0,10)
+fix 1 all wall/srd xlo v_ramp
+</PRE>
+<PRE>variable linear equal vdisplace(0,20)
+fix 1 all wall/srd xlo v_linear
+</PRE>
+<PRE>variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+</PRE>
+<PRE>variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+</PRE>
+<P>The ramp(lo,hi) function adjusts the wall position linearly from lo to
+hi over the course of a run. The displace(c0,velocity) function does
+something similar using the equation position = c0 + velocity*delta,
+where delta is the elapsed time.
+</P>
+<P>The swiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, where omega = 2 PI
+/ period:
+</P>
+<PRE>position = c0 + A sin(omega*delta)
+</PRE>
+<P>The cwiggle(c0,A,period) function causes the wall position to
+oscillate sinusoidally according to this equation, which will have an
+initial wall velocity of 0.0, and thus may impose a gentler
+perturbation on the particles:
+</P>
+<PRE>position = c0 + A (1 - cos(omega*delta))
+</PRE>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix computes a global array of values which can be accessed by
+various <A HREF = "Section_howto.html#howto_15">output commands</A>. The number of
+rows in the array is equal to the number of walls defined by the fix.
+The number of columns is 3, for the x,y,z components of force on each
+wall.
+</P>
+<P>Note that an outward normal force on a wall will be a negative value
+for <I>lo</I> walls and a positive value for <I>hi</I> walls. The array values
+calculated by this fix are "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension (xyz) that has an SRD wall must be non-periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_srd.html">fix srd</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html
new file mode 100644
index 000000000..b92abe245
--- /dev/null
+++ b/doc/doc2/genindex.html
@@ -0,0 +1,2090 @@
+
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+ <meta charset="utf-8">
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+ <title>Index &mdash; LAMMPS 15 May 2015 version documentation</title>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+
+
+
+ <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+
+
+
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
+
+
+ <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+ <div class="wy-grid-for-nav">
+
+
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-nav-search">
+
+
+
+ <a href="Manual.html" class="icon icon-home"> LAMMPS
+
+
+
+ </a>
+
+
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+
+
+ </div>
+
+ <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+ <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+
+
+
+ </div>
+ &nbsp;
+ </nav>
+
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+ <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+ <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+ <a href="Manual.html">LAMMPS</a>
+ </nav>
+
+
+
+ <div class="wy-nav-content">
+ <div class="rst-content">
+ <div role="navigation" aria-label="breadcrumbs navigation">
+ <ul class="wy-breadcrumbs">
+ <li><a href="Manual.html">Docs</a> &raquo;</li>
+
+ <li></li>
+ <li class="wy-breadcrumbs-aside">
+
+
+ <a href="http://lammps.sandia.gov">Homepage</a>
+ <a href="Section_commands.html#comm">Commands</a>
+
+ </li>
+ </ul>
+ <hr/>
+</div>
+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#J"><strong>J</strong></a>
+ | <a href="#K"><strong>K</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#Q"><strong>Q</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="angle_coeff.html#index-0">angle_coeff</a>
+ </dt>
+
+
+ <dt><a href="angle_style.html#index-0">angle_style</a>
+ </dt>
+
+
+ <dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
+ </dt>
+
+
+ <dt><a href="angle_class2.html#index-0">angle_style class2</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
+ </dt>
+
+
+ <dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
+ </dt>
+
+
+ <dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
+ </dt>
+
+
+ <dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
+ </dt>
+
+
+ <dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
+ </dt>
+
+
+ <dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
+ </dt>
+
+
+ <dt><a href="angle_none.html#index-0">angle_style none</a>
+ </dt>
+
+
+ <dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
+ </dt>
+
+
+ <dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
+ </dt>
+
+
+ <dt><a href="angle_table.html#index-0">angle_style table</a>
+ </dt>
+
+
+ <dt><a href="atom_modify.html#index-0">atom_modify</a>
+ </dt>
+
+
+ <dt><a href="atom_style.html#index-0">atom_style</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="balance.html#index-0">balance</a>
+ </dt>
+
+
+ <dt><a href="bond_coeff.html#index-0">bond_coeff</a>
+ </dt>
+
+
+ <dt><a href="bond_style.html#index-0">bond_style</a>
+ </dt>
+
+
+ <dt><a href="bond_class2.html#index-0">bond_style class2</a>
+ </dt>
+
+
+ <dt><a href="bond_fene.html#index-0">bond_style fene</a>
+ </dt>
+
+
+ <dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
+ </dt>
+
+
+ <dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
+ </dt>
+
+
+ <dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
+ </dt>
+
+
+ <dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
+ </dt>
+
+
+ <dt><a href="bond_morse.html#index-0">bond_style morse</a>
+ </dt>
+
+
+ <dt><a href="bond_none.html#index-0">bond_style none</a>
+ </dt>
+
+
+ <dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
+ </dt>
+
+
+ <dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
+ </dt>
+
+
+ <dt><a href="bond_table.html#index-0">bond_style table</a>
+ </dt>
+
+
+ <dt><a href="boundary.html#index-0">boundary</a>
+ </dt>
+
+
+ <dt><a href="box.html#index-0">box</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="change_box.html#index-0">change_box</a>
+ </dt>
+
+
+ <dt><a href="clear.html#index-0">clear</a>
+ </dt>
+
+
+ <dt><a href="comm_modify.html#index-0">comm_modify</a>
+ </dt>
+
+
+ <dt><a href="comm_style.html#index-0">comm_style</a>
+ </dt>
+
+
+ <dt><a href="compute.html#index-0">compute</a>
+ </dt>
+
+
+ <dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
+ </dt>
+
+
+ <dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_body_local.html#index-0">compute body/local</a>
+ </dt>
+
+
+ <dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
+ </dt>
+
+
+ <dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_com.html#index-0">compute com</a>
+ </dt>
+
+
+ <dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
+ </dt>
+
+
+ <dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
+ </dt>
+
+
+ <dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
+ </dt>
+
+
+ <dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
+ </dt>
+
+
+ <dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
+ </dt>
+
+
+ <dt><a href="compute_fep.html#index-0">compute fep</a>
+ </dt>
+
+
+ <dt><a href="compute_group_group.html#index-0">compute group/group</a>
+ </dt>
+
+
+ <dt><a href="compute_gyration.html#index-0">compute gyration</a>
+ </dt>
+
+
+ <dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
+ </dt>
+
+
+ <dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
+ </dt>
+
+
+ <dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_ke.html#index-0">compute ke</a>
+ </dt>
+
+
+ <dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
+ </dt>
+
+
+ <dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
+ </dt>
+
+
+ <dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
+ </dt>
+
+
+ <dt><a href="compute_meso_e_atom.html#index-0">compute meso_e/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_meso_rho_atom.html#index-0">compute meso_rho/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_meso_t_atom.html#index-0">compute meso_t/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_msd.html#index-0">compute msd</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
+ </dt>
+
+
+ <dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_pair.html#index-0">compute pair</a>
+ </dt>
+
+
+ <dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
+ </dt>
+
+
+ <dt><a href="compute_pe.html#index-0">compute pe</a>
+ </dt>
+
+
+ <dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_pressure.html#index-0">compute pressure</a>
+ </dt>
+
+
+ <dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_property_local.html#index-0">compute property/local</a>
+ </dt>
+
+
+ <dt><a href="compute_rdf.html#index-0">compute rdf</a>
+ </dt>
+
+
+ <dt><a href="compute_reduce.html#index-0">compute reduce</a>
+ </dt>
+
+
+ <dt><a href="compute_saed.html#index-0">compute saed</a>
+ </dt>
+
+
+ <dt><a href="compute_slice.html#index-0">compute slice</a>
+ </dt>
+
+
+ <dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_temp.html#index-0">compute temp</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
+ </dt>
+
+
+ <dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
+ </dt>
+
+
+ <dt><a href="compute_ti.html#index-0">compute ti</a>
+ </dt>
+
+
+ <dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_vacf.html#index-0">compute vacf</a>
+ </dt>
+
+
+ <dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
+ </dt>
+
+
+ <dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
+ </dt>
+
+
+ <dt><a href="compute_xrd.html#index-0">compute xrd</a>
+ </dt>
+
+
+ <dt><a href="compute_modify.html#index-0">compute_modify</a>
+ </dt>
+
+
+ <dt><a href="create_atoms.html#index-0">create_atoms</a>
+ </dt>
+
+
+ <dt><a href="create_bonds.html#index-0">create_bonds</a>
+ </dt>
+
+
+ <dt><a href="create_box.html#index-0">create_box</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="delete_atoms.html#index-0">delete_atoms</a>
+ </dt>
+
+
+ <dt><a href="delete_bonds.html#index-0">delete_bonds</a>
+ </dt>
+
+
+ <dt><a href="dielectric.html#index-0">dielectric</a>
+ </dt>
+
+
+ <dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
+ </dt>
+
+
+ <dt><a href="dihedral_style.html#index-0">dihedral_style</a>
+ </dt>
+
+
+ <dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
+ </dt>
+
+
+ <dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
+ </dt>
+
+
+ <dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
+ </dt>
+
+
+ <dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
+ </dt>
+
+
+ <dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
+ </dt>
+
+
+ <dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
+ </dt>
+
+
+ <dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
+ </dt>
+
+
+ <dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
+ </dt>
+
+
+ <dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
+ </dt>
+
+
+ <dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
+ </dt>
+
+
+ <dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
+ </dt>
+
+
+ <dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
+ </dt>
+
+
+ <dt><a href="dimension.html#index-0">dimension</a>
+ </dt>
+
+
+ <dt><a href="displace_atoms.html#index-0">displace_atoms</a>
+ </dt>
+
+
+ <dt><a href="dump.html#index-0">dump</a>
+ </dt>
+
+
+ <dt><a href="dump_image.html#index-0">dump image</a>
+ </dt>
+
+
+ <dt><a href="dump_molfile.html#index-0">dump molfile</a>
+ </dt>
+
+
+ <dt><a href="dump_modify.html#index-0">dump_modify</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="echo.html#index-0">echo</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="fix.html#index-0">fix</a>
+ </dt>
+
+
+ <dt><a href="fix_adapt.html#index-0">fix adapt</a>
+ </dt>
+
+
+ <dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
+ </dt>
+
+
+ <dt><a href="fix_addforce.html#index-0">fix addforce</a>
+ </dt>
+
+
+ <dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
+ </dt>
+
+
+ <dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
+ </dt>
+
+
+ <dt><a href="fix_atc.html#index-0">fix atc</a>
+ </dt>
+
+
+ <dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
+ </dt>
+
+
+ <dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
+ </dt>
+
+
+ <dt><a href="fix_balance.html#index-0">fix balance</a>
+ </dt>
+
+
+ <dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
+ </dt>
+
+
+ <dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
+ </dt>
+
+
+ <dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
+ </dt>
+
+
+ <dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
+ </dt>
+
+
+ <dt><a href="fix_colvars.html#index-0">fix colvars</a>
+ </dt>
+
+
+ <dt><a href="fix_deform.html#index-0">fix deform</a>
+ </dt>
+
+
+ <dt><a href="fix_deposit.html#index-0">fix deposit</a>
+ </dt>
+
+
+ <dt><a href="fix_drag.html#index-0">fix drag</a>
+ </dt>
+
+
+ <dt><a href="fix_drude.html#index-0">fix drude</a>
+ </dt>
+
+
+ <dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
+ </dt>
+
+
+ <dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
+ </dt>
+
+
+ <dt><a href="fix_efield.html#index-0">fix efield</a>
+ </dt>
+
+
+ <dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
+ </dt>
+
+
+ <dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
+ </dt>
+
+
+ <dt><a href="fix_external.html#index-0">fix external</a>
+ </dt>
+
+
+ <dt><a href="fix_freeze.html#index-0">fix freeze</a>
+ </dt>
+
+
+ <dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
+ </dt>
+
+
+ <dt><a href="fix_gld.html#index-0">fix gld</a>
+ </dt>
+
+
+ <dt><a href="fix_gle.html#index-0">fix gle</a>
+ </dt>
+
+
+ <dt><a href="fix_gravity.html#index-0">fix gravity</a>
+ </dt>
+
+
+ <dt><a href="fix_heat.html#index-0">fix heat</a>
+ </dt>
+
+
+ <dt><a href="fix_imd.html#index-0">fix imd</a>
+ </dt>
+
+
+ <dt><a href="fix_indent.html#index-0">fix indent</a>
+ </dt>
+
+
+ <dt><a href="fix_ipi.html#index-0">fix ipi</a>
+ </dt>
+
+
+ <dt><a href="fix_langevin.html#index-0">fix langevin</a>
+ </dt>
+
+
+ <dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
+ </dt>
+
+
+ <dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
+ </dt>
+
+
+ <dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
+ </dt>
+
+
+ <dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
+ </dt>
+
+
+ <dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
+ </dt>
+
+
+ <dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
+ </dt>
+
+
+ <dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
+ </dt>
+
+
+ <dt><a href="fix_meso.html#index-0">fix meso</a>
+ </dt>
+
+
+ <dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
+ </dt>
+
+
+ <dt><a href="fix_momentum.html#index-0">fix momentum</a>
+ </dt>
+
+
+ <dt><a href="fix_move.html#index-0">fix move</a>
+ </dt>
+
+
+ <dt><a href="fix_msst.html#index-0">fix msst</a>
+ </dt>
+
+
+ <dt><a href="fix_neb.html#index-0">fix neb</a>
+ </dt>
+
+
+ <dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nphug.html#index-0">fix nphug</a>
+ </dt>
+
+
+ <dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
+ </dt>
+
+
+ <dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nve.html#index-0">fix nve</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
+ </dt>
+
+
+ <dt><a href="fix_nh.html#index-0">fix nvt</a>
+ </dt>
+
+
+ <dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
+ </dt>
+
+
+ <dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
+ </dt>
+
+
+ <dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
+ </dt>
+
+
+ <dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
+ </dt>
+
+
+ <dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
+ </dt>
+
+
+ <dt><a href="fix_oneway.html#index-0">fix oneway</a>
+ </dt>
+
+
+ <dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
+ </dt>
+
+
+ <dt><a href="fix_phonon.html#index-0">fix phonon</a>
+ </dt>
+
+
+ <dt><a href="fix_pimd.html#index-0">fix pimd</a>
+ </dt>
+
+
+ <dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
+ </dt>
+
+
+ <dt><a href="fix_pour.html#index-0">fix pour</a>
+ </dt>
+
+
+ <dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
+ </dt>
+
+
+ <dt><a href="fix_print.html#index-0">fix print</a>
+ </dt>
+
+
+ <dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
+ </dt>
+
+
+ <dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
+ </dt>
+
+
+ <dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
+ </dt>
+
+
+ <dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
+ </dt>
+
+
+ <dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
+ </dt>
+
+
+ <dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
+ </dt>
+
+
+ <dt><a href="fix_qtb.html#index-0">fix qtb</a>
+ </dt>
+
+
+ <dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
+ </dt>
+
+
+ <dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
+ </dt>
+
+
+ <dt><a href="fix_recenter.html#index-0">fix recenter</a>
+ </dt>
+
+
+ <dt><a href="fix_restrain.html#index-0">fix restrain</a>
+ </dt>
+
+
+ <dt><a href="fix_rigid.html#index-0">fix rigid</a>
+ </dt>
+
+
+ <dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
+ </dt>
+
+
+ <dt><a href="fix_setforce.html#index-0">fix setforce</a>
+ </dt>
+
+
+ <dt><a href="fix_shake.html#index-0">fix shake</a>
+ </dt>
+
+
+ <dt><a href="fix_smd.html#index-0">fix smd</a>
+ </dt>
+
+
+ <dt><a href="fix_spring.html#index-0">fix spring</a>
+ </dt>
+
+
+ <dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
+ </dt>
+
+
+ <dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
+ </dt>
+
+
+ <dt><a href="fix_srd.html#index-0">fix srd</a>
+ </dt>
+
+
+ <dt><a href="fix_store_force.html#index-0">fix store/force</a>
+ </dt>
+
+
+ <dt><a href="fix_store_state.html#index-0">fix store/state</a>
+ </dt>
+
+
+ <dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
+ </dt>
+
+
+ <dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
+ </dt>
+
+
+ <dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
+ </dt>
+
+
+ <dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
+ </dt>
+
+
+ <dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
+ </dt>
+
+
+ <dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
+ </dt>
+
+
+ <dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
+ </dt>
+
+
+ <dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
+ </dt>
+
+
+ <dt><a href="fix_tmd.html#index-0">fix tmd</a>
+ </dt>
+
+
+ <dt><a href="fix_ttm.html#index-0">fix ttm</a>
+ </dt>
+
+
+ <dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
+ </dt>
+
+
+ <dt><a href="fix_vector.html#index-0">fix vector</a>
+ </dt>
+
+
+ <dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
+ </dt>
+
+
+ <dt><a href="fix_viscous.html#index-0">fix viscous</a>
+ </dt>
+
+
+ <dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
+ </dt>
+
+
+ <dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
+ </dt>
+
+
+ <dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
+ </dt>
+
+
+ <dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
+ </dt>
+
+
+ <dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
+ </dt>
+
+
+ <dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
+ </dt>
+
+
+ <dt><a href="fix_modify.html#index-0">fix_modify</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="group.html#index-0">group</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="group2ndx.html#index-0">group2ndx</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="if.html#index-0">if</a>
+ </dt>
+
+
+ <dt><a href="improper_coeff.html#index-0">improper_coeff</a>
+ </dt>
+
+
+ <dt><a href="improper_style.html#index-0">improper_style</a>
+ </dt>
+
+
+ <dt><a href="improper_class2.html#index-0">improper_style class2</a>
+ </dt>
+
+
+ <dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
+ </dt>
+
+
+ <dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
+ </dt>
+
+
+ <dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
+ </dt>
+
+
+ <dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
+ </dt>
+
+
+ <dt><a href="improper_none.html#index-0">improper_style none</a>
+ </dt>
+
+
+ <dt><a href="improper_ring.html#index-0">improper_style ring</a>
+ </dt>
+
+
+ <dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
+ </dt>
+
+
+ <dt><a href="include.html#index-0">include</a>
+ </dt>
+
+
+ <dt><a href="info.html#index-0">info</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="J">J</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="jump.html#index-0">jump</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="kspace_modify.html#index-0">kspace_modify</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="kspace_style.html#index-0">kspace_style</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="label.html#index-0">label</a>
+ </dt>
+
+
+ <dt><a href="lattice.html#index-0">lattice</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="log.html#index-0">log</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="mass.html#index-0">mass</a>
+ </dt>
+
+
+ <dt><a href="min_modify.html#index-0">min_modify</a>
+ </dt>
+
+
+ <dt><a href="min_style.html#index-0">min_style</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="minimize.html#index-0">minimize</a>
+ </dt>
+
+
+ <dt><a href="molecule.html#index-0">molecule</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="neb.html#index-0">neb</a>
+ </dt>
+
+
+ <dt><a href="neigh_modify.html#index-0">neigh_modify</a>
+ </dt>
+
+
+ <dt><a href="neighbor.html#index-0">neighbor</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="newton.html#index-0">newton</a>
+ </dt>
+
+
+ <dt><a href="next.html#index-0">next</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="package.html#index-0">package</a>
+ </dt>
+
+
+ <dt><a href="pair_coeff.html#index-0">pair_coeff</a>
+ </dt>
+
+
+ <dt><a href="pair_modify.html#index-0">pair_modify</a>
+ </dt>
+
+
+ <dt><a href="pair_style.html#index-0">pair_style</a>
+ </dt>
+
+
+ <dt><a href="pair_adp.html#index-0">pair_style adp</a>
+ </dt>
+
+
+ <dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
+ </dt>
+
+
+ <dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_beck.html#index-0">pair_style beck</a>
+ </dt>
+
+
+ <dt><a href="pair_body.html#index-0">pair_style body</a>
+ </dt>
+
+
+ <dt><a href="pair_bop.html#index-0">pair_style bop</a>
+ </dt>
+
+
+ <dt><a href="pair_born.html#index-0">pair_style born</a>
+ </dt>
+
+
+ <dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
+ </dt>
+
+
+ <dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
+ </dt>
+
+
+ <dt><a href="pair_buck.html#index-0">pair_style buck</a>
+ </dt>
+
+
+ <dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
+ </dt>
+
+
+ <dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
+ </dt>
+
+
+ <dt><a href="pair_comb.html#index-0">pair_style comb</a>
+ </dt>
+
+
+ <dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
+ </dt>
+
+
+ <dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
+ </dt>
+
+
+ <dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
+ </dt>
+
+
+ <dt><a href="pair_eam.html#index-0">pair_style eam</a>
+ </dt>
+
+
+ <dt><a href="pair_edip.html#index-0">pair_style edip</a>
+ </dt>
+
+
+ <dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_eim.html#index-0">pair_style eim</a>
+ </dt>
+
+
+ <dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
+ </dt>
+
+
+ <dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
+ </dt>
+
+
+ <dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
+ </dt>
+
+
+ <dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
+ </dt>
+
+
+ <dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
+ </dt>
+
+
+ <dt><a href="pair_kim.html#index-0">pair_style kim</a>
+ </dt>
+
+
+ <dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
+ </dt>
+
+
+ <dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
+ </dt>
+
+
+ <dt><a href="pair_list.html#index-0">pair_style list</a>
+ </dt>
+
+
+ <dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
+ </dt>
+
+
+ <dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
+ </dt>
+
+
+ <dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
+ </dt>
+
+
+ <dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
+ </dt>
+
+
+ <dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
+ </dt>
+
+
+ <dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
+ </dt>
+
+
+ <dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
+ </dt>
+
+
+ <dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
+ </dt>
+
+
+ <dt><a href="pair_meam.html#index-0">pair_style meam</a>
+ </dt>
+
+
+ <dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_morse.html#index-0">pair_style morse</a>
+ </dt>
+
+
+ <dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
+ </dt>
+
+
+ <dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
+ </dt>
+
+
+ <dt><a href="pair_none.html#index-0">pair_style none</a>
+ </dt>
+
+
+ <dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
+ </dt>
+
+
+ <dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
+ </dt>
+
+
+ <dt><a href="pair_quip.html#index-0">pair_style quip</a>
+ </dt>
+
+
+ <dt><a href="pair_reax.html#index-0">pair_style reax</a>
+ </dt>
+
+
+ <dt><a href="pair_reax_c.html#index-0">pair_style reax/c</a>
+ </dt>
+
+
+ <dt><a href="pair_resquared.html#index-0">pair_style resquared</a>
+ </dt>
+
+
+ <dt><a href="pair_snap.html#index-0">pair_style snap</a>
+ </dt>
+
+
+ <dt><a href="pair_soft.html#index-0">pair_style soft</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_heatconduction.html#index-0">pair_style sph/heatconduction</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_idealgas.html#index-0">pair_style sph/idealgas</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_lj.html#index-0">pair_style sph/lj</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_rhosum.html#index-0">pair_style sph/rhosum</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_taitwater.html#index-0">pair_style sph/taitwater</a>
+ </dt>
+
+
+ <dt><a href="pair_sph_taitwater_morris.html#index-0">pair_style sph/taitwater/morris</a>
+ </dt>
+
+
+ <dt><a href="pair_srp.html#index-0">pair_style srp</a>
+ </dt>
+
+
+ <dt><a href="pair_sw.html#index-0">pair_style sw</a>
+ </dt>
+
+
+ <dt><a href="pair_table.html#index-0">pair_style table</a>
+ </dt>
+
+
+ <dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
+ </dt>
+
+
+ <dt><a href="pair_tersoff_mod.html#index-0">pair_style tersoff/mod</a>
+ </dt>
+
+
+ <dt><a href="pair_tersoff_zbl.html#index-0">pair_style tersoff/zbl</a>
+ </dt>
+
+
+ <dt><a href="pair_thole.html#index-0">pair_style thole</a>
+ </dt>
+
+
+ <dt><a href="pair_tri_lj.html#index-0">pair_style tri/lj</a>
+ </dt>
+
+
+ <dt><a href="pair_yukawa.html#index-0">pair_style yukawa</a>
+ </dt>
+
+
+ <dt><a href="pair_yukawa_colloid.html#index-0">pair_style yukawa/colloid</a>
+ </dt>
+
+
+ <dt><a href="pair_zbl.html#index-0">pair_style zbl</a>
+ </dt>
+
+
+ <dt><a href="pair_write.html#index-0">pair_write</a>
+ </dt>
+
+
+ <dt><a href="partition.html#index-0">partition</a>
+ </dt>
+
+
+ <dt><a href="prd.html#index-0">prd</a>
+ </dt>
+
+
+ <dt><a href="print.html#index-0">print</a>
+ </dt>
+
+
+ <dt><a href="processors.html#index-0">processors</a>
+ </dt>
+
+
+ <dt><a href="python.html#index-0">python</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="Q">Q</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="quit.html#index-0">quit</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="read_data.html#index-0">read_data</a>
+ </dt>
+
+
+ <dt><a href="read_dump.html#index-0">read_dump</a>
+ </dt>
+
+
+ <dt><a href="read_restart.html#index-0">read_restart</a>
+ </dt>
+
+
+ <dt><a href="region.html#index-0">region</a>
+ </dt>
+
+
+ <dt><a href="replicate.html#index-0">replicate</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="rerun.html#index-0">rerun</a>
+ </dt>
+
+
+ <dt><a href="reset_timestep.html#index-0">reset_timestep</a>
+ </dt>
+
+
+ <dt><a href="restart.html#index-0">restart</a>
+ </dt>
+
+
+ <dt><a href="run.html#index-0">run</a>
+ </dt>
+
+
+ <dt><a href="run_style.html#index-0">run_style</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="set.html#index-0">set</a>
+ </dt>
+
+
+ <dt><a href="shell.html#index-0">shell</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="special_bonds.html#index-0">special_bonds</a>
+ </dt>
+
+
+ <dt><a href="suffix.html#index-0">suffix</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="tad.html#index-0">tad</a>
+ </dt>
+
+
+ <dt><a href="temper.html#index-0">temper</a>
+ </dt>
+
+
+ <dt><a href="thermo.html#index-0">thermo</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="thermo_modify.html#index-0">thermo_modify</a>
+ </dt>
+
+
+ <dt><a href="thermo_style.html#index-0">thermo_style</a>
+ </dt>
+
+
+ <dt><a href="timestep.html#index-0">timestep</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="uncompute.html#index-0">uncompute</a>
+ </dt>
+
+
+ <dt><a href="undump.html#index-0">undump</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="unfix.html#index-0">unfix</a>
+ </dt>
+
+
+ <dt><a href="units.html#index-0">units</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="variable.html#index-0">variable</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="velocity.html#index-0">velocity</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="write_data.html#index-0">write_data</a>
+ </dt>
+
+
+ <dt><a href="write_dump.html#index-0">write_dump</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="write_restart.html#index-0">write_restart</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+
+
+ </div>
+ </div>
+ <footer>
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\ No newline at end of file
diff --git a/doc/doc2/group.html b/doc/doc2/group.html
new file mode 100644
index 000000000..53347eefc
--- /dev/null
+++ b/doc/doc2/group.html
@@ -0,0 +1,289 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>group command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>group ID style args
+</PRE>
+<UL><LI>ID = user-defined name of the group
+
+<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>variable</I> or <I>include</I> or <I>subtract</I> or <I>union</I> or <I>intersect</I> or <I>dynamic</I> or <I>static</I>
+
+<PRE> <I>delete</I> = no args
+ <I>clear</I> = no args
+ <I>region</I> args = region-ID
+ <I>type</I> or <I>id</I> or <I>molecule</I>
+ args = list of one or more atom types, atom IDs, or molecule IDs
+ any entry in list can be a sequence formatted as A:B or A:B:C where
+ A = starting index, B = ending index,
+ C = increment between indices, 1 if not specified
+ args = logical value
+ logical = "<" or "<=" or ">" or ">=" or "==" or "!="
+ value = an atom type or atom ID or molecule ID (depending on <I>style</I>)
+ args = logical value1 value2
+ logical = "<>"
+ value1,value2 = atom types or atom IDs or molecule IDs (depending on <I>style</I>)
+ <I>variable</I> args = variable-name
+ <I>include</I> args = molecule
+ molecule = add atoms to group with same molecule ID as atoms already in group
+ <I>subtract</I> args = two or more group IDs
+ <I>union</I> args = one or more group IDs
+ <I>intersect</I> args = two or more group IDs
+ <I>dynamic</I> args = parent-ID keyword value ...
+ one or more keyword/value pairs may be appended
+ keyword = <I>region</I> or <I>var</I> or <I>every</I>
+ <I>region</I> value = region-ID
+ <I>var</I> value = name of variable
+ <I>every</I> value = N = update group every this many timesteps
+ <I>static</I> = no args
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>group edge region regstrip
+group water type 3 4
+group sub id 10 25 50
+group sub id 10 25 50 500:1000
+group sub id 100:10000:10
+group sub id <= 150
+group polyA molecule <> 50 250
+group hienergy variable eng
+group hienergy include molecule
+group boundary subtract all a2 a3
+group boundary union lower upper
+group boundary intersect upper flow
+group boundary delete
+group mine dynamic all region myRegion every 100
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Identify a collection of atoms as belonging to a group. The group ID
+can then be used in other commands such as <A HREF = "fix.html">fix</A>,
+<A HREF = "compute.html">compute</A>, <A HREF = "dump.html">dump</A>, or <A HREF = "velocity.html">velocity</A>
+to act on those atoms together.
+</P>
+<P>If the group ID already exists, the group command adds the specified
+atoms to the group.
+</P>
+<P>IMPORTANT NOTE: By default groups are static, meaning the atoms are
+permanently assigned to the group. For example, if the <I>region</I> style
+is used to assign atoms to a group, the atoms will remain in the group
+even if they later move out of the region. As explained below, the
+<I>dynamic</I> style can be used to make a group dynamic so that a periodic
+determination is made as to which atoms are in the group. Since many
+LAMMPS commands operate on groups of atoms, you should think carefully
+about whether making a group dynamic makes sense for your model.
+</P>
+<P>A group with the ID <I>all</I> is predefined. All atoms belong to this
+group. This group cannot be deleted, or made dynamic.
+</P>
+<P>The <I>delete</I> style removes the named group and un-assigns all atoms
+that were assigned to that group. Since there is a restriction (see
+below) that no more than 32 groups can be defined at any time, the
+<I>delete</I> style allows you to remove groups that are no longer needed,
+so that more can be specified. You cannot delete a group if it has
+been used to define a current <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A>
+or <A HREF = "dump.html">dump</A>.
+</P>
+<P>The <I>clear</I> style un-assigns all atoms that were assigned to that
+group. This may be dangerous to do during a simulation run,
+e.g. using the <A HREF = "run.html">run every</A> command if a fix or compute or
+other operation expects the atoms in the group to remain constant, but
+LAMMPS does not check for this.
+</P>
+<P>The <I>region</I> style puts all atoms in the region volume into the group.
+Note that this is a static one-time assignment. The atoms remain
+assigned (or not assigned) to the group even in they later move out of
+the region volume.
+</P>
+<P>The <I>type</I>, <I>id</I>, and <I>molecule</I> styles put all atoms with the
+specified atom types, atom IDs, or molecule IDs into the group. These
+3 styles can use arguments specified in one of two formats.
+</P>
+<P>The first format is a list of values (types or IDs). For example, the
+2nd command in the examples above puts all atoms of type 3 or 4 into
+the group named <I>water</I>. Each entry in the list can be a
+colon-separated sequence A:B or A:B:C, as in two of the examples
+above. A "sequence" generates a sequence of values (types or IDs),
+with an optional increment. The first example with 500:1000 has the
+default increment of 1 and would add all atom IDs from 500 to 1000
+(inclusive) to the group sub, along with 10,25,50 since they also
+appear in the list of values. The second example with 100:10000:10
+uses an increment of 10 and would thus would add atoms IDs
+100,110,120, ... 9990,10000 to the group sub.
+</P>
+<P>The second format is a <I>logical</I> followed by one or two values (type
+or ID). The 7 valid logicals are listed above. All the logicals
+except <> take a single argument. The 3rd example above adds all
+atoms with IDs from 1 to 150 to the group named <I>sub</I>. The logical <>
+means "between" and takes 2 arguments. The 4th example above adds all
+atoms belonging to molecules with IDs from 50 to 250 (inclusive) to
+the group named polyA.
+</P>
+<P>The <I>variable</I> style evaluates a variable to determine which atoms to
+add to the group. It must be an <A HREF = "variable.html">atom-style variable</A>
+previously defined in the input script. If the variable evaluates
+to a non-zero value for a particular atom, then that atom is added
+to the specified group.
+</P>
+<P>Atom-style variables can specify formulas that include thermodynamic
+quantities, per-atom values such as atom coordinates, or per-atom
+quantities calculated by computes, fixes, or other variables. They
+can also include Boolean logic where 2 numeric values are compared to
+yield a 1 or 0 (effectively a true or false). Thus using the
+<I>variable</I> style, is a general way to flag specific atoms to include
+or exclude from a group.
+</P>
+<P>For example, these lines define a variable "eatom" that calculates the
+potential energy of each atom and includes it in the group if its
+potential energy is above the threshhold value -3.0.
+</P>
+<PRE>compute 1 all pe/atom
+compute 2 all reduce sum c_1
+thermo_style custom step temp pe c_2
+run 0
+</PRE>
+<PRE>variable eatom atom "c_1 > -3.0"
+group hienergy variable eatom
+</PRE>
+<P>Note that these lines
+</P>
+<PRE>compute 2 all reduce sum c_1
+thermo_style custom step temp pe c_2
+run 0
+</PRE>
+<P>are necessary to insure that the "eatom" variable is current when the
+group command invokes it. Because the eatom variable computes the
+per-atom energy via the pe/atom compute, it will only be current if a
+run has been performed which evaluated pairwise energies, and the
+pe/atom compute was actually invoked during the run. Printing the
+thermodyanmic info for compute 2 insures that this is the case, since
+it sums the pe/atom compute values (in the reduce compute) to output
+them to the screen. See the "Variable Accuracy" section of the
+<A HREF = "variable.html">variable</A> doc page for more details on insuring that
+variables are current when they are evaluated between runs.
+</P>
+<P>The <I>include</I> style with its arg <I>molecule</I> adds atoms to a group that
+have the same molecule ID as atoms already in the group. The molecule
+ID = 0 is ignored in this operation, since it is assumed to flag
+isolated atoms that are not part of molecules. An example of where
+this operation is useful is if the <I>region</I> style has been used
+previously to add atoms to a group that are within a geometric region.
+If molecules straddle the region boundary, then atoms outside the
+region that are part of molecules with atoms inside the region will
+not be in the group. Using the group command a 2nd time with <I>include
+molecule</I> will add those atoms that are outside the region to the
+group.
+</P>
+<P>IMPORTANT NOTE: The <I>include molecule</I> operation is relatively
+expensive in a parallel sense. This is because it requires
+communication of relevant molecule IDs between all the processors and
+each processor to loop over its atoms once per processor, to compare
+its atoms to the list of molecule IDs from every other processor.
+Hence it scales as N, rather than N/P as most of the group operations
+do, where N is the number of atoms, and P is the number of processors.
+</P>
+<P>The <I>subtract</I> style takes a list of two or more existing group names
+as arguments. All atoms that belong to the 1st group, but not to any
+of the other groups are added to the specified group.
+</P>
+<P>The <I>union</I> style takes a list of one or more existing group names as
+arguments. All atoms that belong to any of the listed groups are
+added to the specified group.
+</P>
+<P>The <I>intersect</I> style takes a list of two or more existing group names
+as arguments. Atoms that belong to every one of the listed groups are
+added to the specified group.
+</P>
+<HR>
+
+<P>The <I>dynamic</I> style flags an existing or new group as dynamic. This
+means atoms will be (re)assigned to the group periodically as a
+simulation runs. This is in contrast to static groups where atoms are
+permanently assigned to the group. The way the assignment occurs is
+as follows. Only atoms in the group specified as the parent group via
+the parent-ID are assigned to the dynamic group before the following
+conditions are applied. If the <I>region</I> keyword is used, atoms not in
+the specified region are removed from the dynamic group. If the <I>var</I>
+keyword is used, the variable name must be an atom-style or
+atomfile-style variable. The variable is evaluated and atoms whose
+per-atom values are 0.0, are removed from the dynamic group.
+</P>
+<P>The assignment of atoms to a dynamic group is done at the beginning of
+each run and on every timestep that is a multiple of <I>N</I>, which is the
+argument for the <I>every</I> keyword (N = 1 is the default). For an
+energy minimization, via the <A HREF = "minimize.html">minimize</A> command, an
+assignement is made at the beginning of the minimization, but not
+during the iterations of the minimizer.
+</P>
+<P>The point in the timestep at which atoms are assigned to a dynamic
+group is after the initial stage of velocity Verlet time integration
+has been performed, and before neighbor lists or forces are computed.
+This is the point in the timestep where atom positions have just
+changed due to the time integration, so the region criterion should be
+accurate, if applied.
+</P>
+<P>IMPORTANT NOTE: If the <I>region</I> keyword is used to determine what
+atoms are in the dynamic group, atoms can move outside of the
+simulation box between reneighboring events. Thus if you want to
+include all atoms on the left side of the simulation box, you probably
+want to set the left boundary of the region to be outside the
+simulation box by some reasonable amount (e.g. up to the cutoff of the
+potential), else they may be excluded from the dynamic region.
+</P>
+<P>Here is an example of using a dynamic group to shrink the set of atoms
+being integrated by using a spherical region with a variable radius
+(shrinking from 18 to 5 over the course of the run). This could be
+used to model a quench of the system, freezing atoms outside the
+shrinking sphere, then converting the remaining atoms to a static
+group and running further.
+</P>
+<PRE>variable nsteps equal 5000
+variable rad equal 18-(step/v_nsteps)*(18-5)
+region ss sphere 20 20 0 v_rad
+group mobile dynamic all region ss
+fix 1 mobile nve
+run ${nsteps}
+group mobile static
+run ${nsteps}
+</PRE>
+<P>IMPORTANT NOTE: All fixes and computes take a group ID as an argument,
+but they do not all allow for use of a dynamic group. If you get an
+error message that this is not allowed, but feel that it should be for
+the fix or compute in question, then please post your reasoning to the
+LAMMPS mail list and we can change it.
+</P>
+<P>The <I>static</I> style removes the setting for a dynamic group, converting
+it to a static group (the default). The atoms in the static group are
+those currently in the dynamic group.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>There can be no more than 32 groups defined at one time, including
+"all".
+</P>
+<P>The parent group of a dynamic group cannot itself be a dynamic group.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "fix.html">fix</A>, <A HREF = "region.html">region</A>,
+<A HREF = "velocity.html">velocity</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>All atoms belong to the "all" group.
+</P>
+</HTML>
diff --git a/doc/doc2/group2ndx.html b/doc/doc2/group2ndx.html
new file mode 100644
index 000000000..3fb0670fc
--- /dev/null
+++ b/doc/doc2/group2ndx.html
@@ -0,0 +1,58 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>group2ndx command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>group2ndx file group-ID ...
+</PRE>
+<UL><LI>file = name of index file to write out
+
+<LI>zero or more group IDs may be appended
+
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>group2ndx allindex.ndx
+group2ndx someindex.ndx upper lower mobile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write a Gromacs style index file in text format that associates atom IDs
+with the corresponding group definitions. This index file can be used
+with in combination with Gromacs analysis tools or to import group
+definitions into the <A HREF = "fix_colvars.html">fix colvars</A> input file.
+</P>
+<P>Without specifying any group IDs, all groups will be written to the index
+file. When specifying group IDs, only those groups will be written to the
+index file. In order to follow the Gromacs conventions, the group <I>all</I>
+will be renamed to <I>System</I> in the index file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command requires that atoms have atom IDs, since this is the
+information that is written to the index file.
+</P>
+<P>This fix is part of the USER-COLVARS package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "group.html">group</A>, <A HREF = "dump.html">dump</A>, <A HREF = "fix_colvars.html">fix colvars</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/if.html b/doc/doc2/if.html
new file mode 100644
index 000000000..ba4f5de6d
--- /dev/null
+++ b/doc/doc2/if.html
@@ -0,0 +1,194 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>if command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ...
+</PRE>
+<UL><LI>boolean = a Boolean expression evaluated as TRUE or FALSE (see below)
+<LI>then = required word
+<LI>t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes
+<LI>elif = optional word, can appear multiple times
+<LI>f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments)
+<LI>else = optional argument
+<LI>e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>if "${steps} > 1000" then quit
+if "${myString} == a10" then quit
+if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
+if "(${eng} > 0.0) || ($n < 1000)" then &
+ "timestep 0.005" &
+elif $n<10000 &
+ "timestep 0.01" &
+else &
+ "timestep 0.02" &
+ "print 'Max step reached'"
+if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command provides an if-then-else capability within an input
+script. A Boolean expression is evaluted and the result is TRUE or
+FALSE. Note that as in the examples above, the expression can contain
+variables, as defined by the <A HREF = "variable.html">variable</A> command, which
+will be evaluated as part of the expression. Thus a user-defined
+formula that reflects the current state of the simulation can be used
+to issue one or more new commands.
+</P>
+<P>If the result of the Boolean expression is TRUE, then one or more
+commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean
+expressions associated with successive elif keywords are evaluated
+until one is found to be true, in which case its commands (f1, f2,
+..., fN) are executed. If no Boolean expression is TRUE, then the
+commands associated with the else keyword, namely (e1, e2, ..., eN),
+are executed. The elif and else keywords and their associated
+commands are optional. If they aren't specified and the initial
+Boolean expression is FALSE, then no commands are executed.
+</P>
+<P>The syntax for Boolean expressions is described below.
+</P>
+<P>Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
+command, except an <A HREF = "include.html">include</A> command, which is not
+allowed. If the command is more than one word, it must enclosed in
+quotes, so it will be treated as a single argument, as in the examples
+above.
+</P>
+<P>IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
+<A HREF = "print.html">print</A> command), then double and single quotes can be used
+and nested in the usual manner, as in the examples above and below.
+See <A HREF = "Section_commands.html#cmd_2">Section_commands 2</A> of the manual for
+more details on using quotes in arguments. Only one of level of
+nesting is allowed, but that should be sufficient for most use cases.
+</P>
+<P>Note that by using the line continuation character "&", the if command
+can be spread across many lines, though it is still a single command:
+</P>
+<PRE>if "$a < $b" then &
+ "print 'Minimum value = $a'" &
+ "run 1000" &
+else &
+ 'print "Minimum value = $b"' &
+ "minimize 0.001 0.001 1000 10000"
+</PRE>
+<P>Note that if one of the commands to execute is <A HREF = "quit.html">quit</A>, as in
+the first example above, then executing the command will cause LAMMPS
+to halt.
+</P>
+<P>Note that by jumping to a label in the same input script, the if
+command can be used to break out of a loop. See the <A HREF = "variable.html">variable
+delete</A> command for info on how to delete the associated
+loop variable, so that it can be re-used later in the input script.
+</P>
+<P>Here is an example of a loop which checks every 1000 steps if the
+system temperature has reached a certain value, and if so, breaks out
+of the loop to finish the run. Note that any variable could be
+checked, so long as it is current on the timestep when the run
+completes. As explained on the <A HREF = "variable.html">variable</A> doc page,
+this can be insured by includig the variable in thermodynamic output.
+</P>
+<PRE>variable myTemp equal temp
+label loop
+variable a loop 1000
+run 1000
+if "${myTemp} < 300.0" then "jump SELF break"
+next a
+jump SELF loop
+label break
+print "ALL DONE"
+</PRE>
+<P>Here is an example of a double loop which uses the if and
+<A HREF = "jump.html">jump</A> commands to break out of the inner loop when a
+condition is met, then continues iterating thru the outer loop.
+</P>
+<PRE>label loopa
+variable a loop 5
+ label loopb
+ variable b loop 5
+ print "A,B = $a,$b"
+ run 10000
+ if "$b > 2" then "jump SELF break"
+ next b
+ jump in.script loopb
+label break
+variable b delete
+next a
+jump SELF loopa
+</PRE>
+<HR>
+
+<P>The Boolean expressions for the if and elif keywords have a C-like
+syntax. Note that each expression is a single argument within the if
+command. Thus if you want to include spaces in the expression for
+clarity, you must enclose the entire expression in quotes.
+</P>
+<P>An expression is built out of numbers (which start with a digit or
+period or minus sign) or strings (which start with a letter and can
+contain alphanumeric characters or underscores):
+</P>
+<PRE>0.2, 100, 1.0e20, -15.4, etc
+InP, myString, a123, ab_23_cd, etc
+</PRE>
+<P>and Boolean operators:
+</P>
+<PRE>A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A
+</PRE>
+<P>Each A and B is a number or string or a variable reference like $a or
+${abc}, or A or B can be another Boolean expression.
+</P>
+<P>If a variable is used it can produce a number when evaluated, like an
+<A HREF = "variable.html">equal-style variable</A>. Or it can produce a string,
+like an <A HREF = "variable.html">index-style variable</A>. For an individual
+Boolean operator, A and B must both be numbers or must both be
+strings. You cannot compare a number to a string.
+</P>
+<P>Expressions are evaluated left to right and have the usual C-style
+precedence: the unary logical NOT operator "!" has the highest
+precedence, the 4 relational operators "<", "<=", ">", and ">=" are
+next; the two remaining relational operators "==" and "!=" are next;
+then the logical AND operator "&&"; and finally the logical OR
+operator "||" has the lowest precedence. Parenthesis can be used to
+group one or more portions of an expression and/or enforce a different
+order of evaluation than what would occur with the default precedence.
+</P>
+<P>When the 6 relational operators (first 6 in list above) compare 2
+numbers, they return either a 1.0 or 0.0 depending on whether the
+relationship between A and B is TRUE or FALSE. When the 6 relational
+operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or
+FALSE, but the comparison is done by the C function strcmp().
+</P>
+<P>When the 3 logical operators (last 3 in list above) compare 2 numbers,
+they also return either a 1.0 or 0.0 depending on whether the
+relationship between A and B is TRUE or FALSE (or just A). The
+logical AND operator will return 1.0 if both its arguments are
+non-zero, else it returns 0.0. The logical OR operator will return
+1.0 if either of its arguments is non-zero, else it returns 0.0. The
+logical NOT operator returns 1.0 if its argument is 0.0, else it
+returns 0.0. The 3 logical operators can only be used to operate on
+numbers, not on strings.
+</P>
+<P>The overall Boolean expression produces a TRUE result if the result is
+non-zero. If the result is zero, the expression result is FALSE.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable</A>, <A HREF = "print.html">print</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_class2.html b/doc/doc2/improper_class2.html
new file mode 100644
index 000000000..da32179c3
--- /dev/null
+++ b/doc/doc2/improper_class2.html
@@ -0,0 +1,131 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style class2 command
+</H3>
+<H3>improper_style class2/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style class2
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style class2
+improper_coeff 1 100.0 0
+improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>class2</I> improper style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/improper_class2.jpg">
+</CENTER>
+<P>where Ei is the improper term and Eaa is an angle-angle term. The 3 X
+terms in Ei are an average over 3 out-of-plane angles.
+</P>
+<P>The 4 atoms in an improper quadruplet (listed in the data file read by
+the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L. X_IJKL
+refers to the angle between the plane of I,J,K and the plane of J,K,L,
+and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK.
+Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X
+terms. Thus J (the 2nd atom in the quadruplet) is the atom of
+symmetry in the 3 X angles.
+</P>
+<P>The subscripts on the various theta's refer to different combinations
+of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL
+is the angle formed by atoms I,J,L with J in the middle. Theta1,
+theta2, theta3 are the equilibrium positions of those angles. Again,
+atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the
+theta angles, since it is always the center atom.
+</P>
+<P>Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
+would exist for an improper to be defined between the 4 atoms, but
+this is not required.
+</P>
+<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
+</P>
+<P>Coefficients for the Ei and Eaa formulas must be defined for each
+improper type via the <A HREF = "improper_coeff.html">improper_coeff</A> command as
+in the example above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>These are the 2 coefficients for the Ei formula:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>X0 (degrees)
+</UL>
+<P>X0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<P>For the Eaa formula, each line in a
+<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script lists
+7 coefficients, the first of which is "aa" to indicate they are
+AngleAngle coefficients. In a data file, these coefficients should be
+listed under a "AngleAngle Coeffs" heading and you must leave out the
+"aa", i.e. only list 6 coefficients after the improper type.
+</P>
+<UL><LI>aa
+<LI>M1 (energy/distance)
+<LI>M2 (energy/distance)
+<LI>M3 (energy/distance)
+<LI>theta1 (degrees)
+<LI>theta2 (degrees)
+<LI>theta3 (degrees)
+</UL>
+<P>The theta values are specified in degrees, but LAMMPS converts them to
+radians internally; hence the units of M are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+CLASS2 package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/improper_coeff.html b/doc/doc2/improper_coeff.html
new file mode 100644
index 000000000..bd67c5f64
--- /dev/null
+++ b/doc/doc2/improper_coeff.html
@@ -0,0 +1,102 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_coeff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_coeff N args
+</PRE>
+<UL><LI>N = improper type (see asterisk form below)
+<LI>args = coefficients for one or more improper types
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_coeff 1 300.0 0.0
+improper_coeff * 80.2 -1 2
+improper_coeff *4 80.2 -1 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Specify the improper force field coefficients for one or more improper
+types. The number and meaning of the coefficients depends on the
+improper style. Improper coefficients can also be set in the data
+file read by the <A HREF = "read_data.html">read_data</A> command or in a restart
+file.
+</P>
+<P>N can be specified in one of two ways. An explicit numeric value can
+be used, as in the 1st example above. Or a wild-card asterisk can be
+used to set the coefficients for multiple improper types. This takes
+the form "*" or "*n" or "n*" or "m*n". If N = the number of improper
+types, then an asterisk with no numeric values means all types from 1
+to N. A leading asterisk means all types from 1 to n (inclusive). A
+trailing asterisk means all types from n to N (inclusive). A middle
+asterisk means all types from m to n (inclusive).
+</P>
+<P>Note that using an improper_coeff command can override a previous
+setting for the same improper type. For example, these commands set
+the coeffs for all improper types, then overwrite the coeffs for just
+improper type 2:
+</P>
+<PRE>improper_coeff * 300.0 0.0
+improper_coeff 2 50.0 0.0
+</PRE>
+<P>A line in a data file that specifies improper coefficients uses the
+exact same format as the arguments of the improper_coeff command in an
+input script, except that wild-card asterisks should not be used since
+coefficients for all N types must be listed in the file. For example,
+under the "Improper Coeffs" section of a data file, the line that
+corresponds to the 1st example above would be listed as
+</P>
+<PRE>1 300.0 0.0
+</PRE>
+<P>The <A HREF = "improper_class2.html">improper_style class2</A> is an exception to
+this rule, in that an additional argument is used in the input script
+to allow specification of the cross-term coefficients. See its doc
+page for details.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of improper styles defined in LAMMPS. Click on
+the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A> command.
+</P>
+<P>Note that there are also additional improper styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the improper section of
+<A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
+<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
+</UL>
+<UL><LI><A HREF = "improper_class2.html">improper_style class2</A> - COMPASS (class 2) improper
+<LI><A HREF = "improper_cvff.html">improper_style cvff</A> - CVFF improper
+<LI><A HREF = "improper_harmonic.html">improper_style harmonic</A> - harmonic improper
+<LI><A HREF = "improper_umbrella.html">improper_style umbrella</A> - DREIDING improper
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>An improper style must be defined before any improper coefficients are
+set, either in the input script or in a data file.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_style.html">improper_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_cossq.html b/doc/doc2/improper_cossq.html
new file mode 100644
index 000000000..6bdb36927
--- /dev/null
+++ b/doc/doc2/improper_cossq.html
@@ -0,0 +1,95 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style cossq command
+</H3>
+<H3>improper_style cossq/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style cossq
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style cossq
+improper_coeff 1 4.0 0.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cossq</I> improper style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/improper_cossq.jpg">
+</CENTER>
+<P>where x is the improper angle, x0 is its equilibrium value, and K is a
+prefactor.
+</P>
+<P>If the 4 atoms in an improper quadruplet (listed in the data file read
+by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then X
+is the angle between the plane of I,J,K and the plane of J,K,L.
+Alternatively, you can think of atoms J,K,L as being in a plane, and
+atom I above the plane, and X as a measure of how far out-of-plane I
+is with respect to the other 3 atoms.
+</P>
+<P>Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>X0 (degrees)
+</UL>
+<P>X0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_cvff.html b/doc/doc2/improper_cvff.html
new file mode 100644
index 000000000..b437e7c02
--- /dev/null
+++ b/doc/doc2/improper_cvff.html
@@ -0,0 +1,92 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style cvff command
+</H3>
+<H3>improper_style cvff/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style cvff
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style cvff
+improper_coeff 1 80.0 -1 4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>cvff</I> improper style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/improper_cvff.jpg">
+</CENTER>
+<P>where phi is the improper dihedral angle.
+</P>
+<P>If the 4 atoms in an improper quadruplet (listed in the data file read
+by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then
+the improper dihedral angle is between the plane of I,J,K and the
+plane of J,K,L. Note that because this is effectively a dihedral
+angle, the formula for this improper style is the same as for
+<A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A>.
+</P>
+<P>Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy)
+<LI>d (+1 or -1)
+<LI>n (0,1,2,3,4,6)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_fourier.html b/doc/doc2/improper_fourier.html
new file mode 100644
index 000000000..5b3478deb
--- /dev/null
+++ b/doc/doc2/improper_fourier.html
@@ -0,0 +1,87 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style fourier command
+</H3>
+<H3>improper_style fourier/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style fourier
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style fourier
+improper_coeff 1 100.0 180.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>fourier</I> improper style uses the following potential:
+</P>
+<CENTER><IMG SRC = "Eqs/improper_fourier.jpg">
+</CENTER>
+<P>where K is the force constant and omega is the angle between the IL
+axis and the IJK plane:
+</P>
+<CENTER><IMG SRC = "Eqs/umbrella.jpg">
+</CENTER>
+<P>If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy)
+<LI>C0 (real)
+<LI>C1 (real)
+<LI>C2 (real)
+<LI>all (integer >= 0)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_harmonic.html b/doc/doc2/improper_harmonic.html
new file mode 100644
index 000000000..771d27faa
--- /dev/null
+++ b/doc/doc2/improper_harmonic.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style harmonic command
+</H3>
+<H3>improper_style harmonic/kk command
+</H3>
+<H3>improper_style harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style harmonic
+improper_coeff 1 100.0 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>harmonic</I> improper style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/improper_harmonic.jpg">
+</CENTER>
+<P>where X is the improper angle, X0 is its equilibrium value, and K is a
+prefactor. Note that the usual 1/2 factor is included in K.
+</P>
+<P>If the 4 atoms in an improper quadruplet (listed in the data file read
+by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then X
+is the angle between the plane of I,J,K and the plane of J,K,L.
+Alternatively, you can think of atoms J,K,L as being in a plane, and
+atom I above the plane, and X as a measure of how far out-of-plane I
+is with respect to the other 3 atoms.
+</P>
+<P>Note that defining 4 atoms to interact in this way, does not mean that
+bonds necessarily exist between I-J, J-K, or K-L, as they would in a
+linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
+improper to be defined between the 4 atoms.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>X0 (degrees)
+</UL>
+<P>X0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_hybrid.html b/doc/doc2/improper_hybrid.html
new file mode 100644
index 000000000..c0903b607
--- /dev/null
+++ b/doc/doc2/improper_hybrid.html
@@ -0,0 +1,75 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style hybrid command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style hybrid style1 style2 ...
+</PRE>
+<UL><LI>style1,style2 = list of one or more improper styles
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style hybrid harmonic helix
+improper_coeff 1 harmonic 120.0 30
+improper_coeff 2 cvff 20.0 -1 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hybrid</I> style enables the use of multiple improper styles in one
+simulation. An improper style is assigned to each improper type. For
+example, impropers in a polymer flow (of improper type 1) could be
+computed with a <I>harmonic</I> potential and impropers in the wall
+boundary (of improper type 2) could be computed with a <I>cvff</I>
+potential. The assignment of improper type to style is made via the
+<A HREF = "improper_coeff.html">improper_coeff</A> command or in the data file.
+</P>
+<P>In the improper_coeff command, the first coefficient sets the improper
+style and the remaining coefficients are those appropriate to that
+style. In the example above, the 2 improper_coeff commands would set
+impropers of improper type 1 to be computed with a <I>harmonic</I>
+potential with coefficients 120.0, 30 for K, X0. Improper type 2
+would be computed with a <I>cvff</I> potential with coefficients 20.0, -1,
+2 for K, d, n.
+</P>
+<P>If the improper <I>class2</I> potential is one of the hybrid styles, it
+requires additional AngleAngle coefficients be specified in the data
+file. These lines must also have an additional "class2" argument
+added after the improper type. For improper types which are assigned
+to other hybrid styles, use the style name (e.g. "harmonic")
+appropriate to that style. The AngleAngle coeffs for that improper
+type will then be ignored.
+</P>
+<P>An improper style of <I>none</I> can be specified as the 2nd argument to
+the improper_coeff command, if you desire to turn off certain improper
+types.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P>Unlike other improper styles, the hybrid improper style does not store
+improper coefficient info for individual sub-styles in a <A HREF = "restart.html">binary
+restart files</A>. Thus when retarting a simulation from a
+restart file, you need to re-specify improper_coeff commands.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_none.html b/doc/doc2/improper_none.html
new file mode 100644
index 000000000..bfd664f38
--- /dev/null
+++ b/doc/doc2/improper_none.html
@@ -0,0 +1,34 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style none command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style none
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Using an improper style of none means improper forces are not
+computed, even if quadruplets of improper atoms were listed in the
+data file read by the <A HREF = "read_data.html">read_data</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/improper_ring.html b/doc/doc2/improper_ring.html
new file mode 100644
index 000000000..9e1ab3c26
--- /dev/null
+++ b/doc/doc2/improper_ring.html
@@ -0,0 +1,102 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style ring command
+</H3>
+<H3>improper_style ring/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style ring
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style ring
+improper_coeff 1 8000 70.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>ring</I> improper style uses the potential
+</P>
+<CENTER><IMG SRC = "Eqs/improper_ring.jpg">
+</CENTER>
+<P>where K is a prefactor, theta is the angle formed by the atoms
+specified by (i,j,k,l) indices and theta0 its equilibrium value.
+</P>
+<P>If the 4 atoms in an improper quadruplet (listed in the data file read
+by the <A HREF = "read_data.html">read_data</A> command) are ordered i,j,k,l then
+theta_<I>ijl</I> is the angle between atoms i,j and l, theta_<I>ijk</I> is the
+angle between atoms i,j and k, theta_<I>kjl</I> is the angle between atoms
+j,k, and l.
+</P>
+<P>The "ring" improper style implements the improper potential introduced
+by Destree et al., in Equation (9) of <A HREF = "#Destree">(Destree)</A>. This
+potential does not affect small amplitude vibrations but is used in an
+ad-hoc way to prevent the onset of accidentially large amplitude
+fluctuations leading to the occurrence of a planar conformation of the
+three bonds i-j, j-k and j-l, an intermediate conformation toward the
+chiral inversion of a methine carbon. In the "Impropers" section of
+data file four atoms: i, j, k and l are specified with i,j and l lying
+on the backbone of the chain and k specifying the chirality of j.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy/radian^2)
+<LI>theta0 (degrees)
+</UL>
+<P>theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<A NAME = "Destree"></A>
+
+<P><B>(Destree)</B> M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert,
+J Chem Phys, 112, 9632 (2000).
+</P>
+</HTML>
diff --git a/doc/doc2/improper_style.html b/doc/doc2/improper_style.html
new file mode 100644
index 000000000..c7deed3da
--- /dev/null
+++ b/doc/doc2/improper_style.html
@@ -0,0 +1,99 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style style
+</PRE>
+<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>cvff</I> or <I>harmonic</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style harmonic
+improper_style cvff
+improper_style hybrid cvff harmonic
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the formula(s) LAMMPS uses to compute improper interactions
+between quadruplets of atoms, which remain in force for the duration
+of the simulation. The list of improper quadruplets is read in by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
+from a data or restart file. Note that the ordering of the 4 atoms in
+an improper quadruplet determines the the definition of the improper
+angle used in the formula for each style. See the doc pages of
+individual styles for details.
+</P>
+<P>Hybrid models where impropers are computed using different improper
+potentials can be setup using the <I>hybrid</I> improper style.
+</P>
+<P>The coefficients associated with an improper style can be specified in
+a data or restart file or via the <A HREF = "improper_coeff.html">improper_coeff</A>
+command.
+</P>
+<P>All improper potentials store their coefficient data in binary restart
+files which means improper_style and
+<A HREF = "improper_coeff.html">improper_coeff</A> commands do not need to be
+re-specified in an input script that restarts a simulation. See the
+<A HREF = "read_restart.html">read_restart</A> command for details on how to do
+this. The one exception is that improper_style <I>hybrid</I> only stores
+the list of sub-styles in the restart file; improper coefficients need
+to be re-specified.
+</P>
+<P>IMPORTANT NOTE: When both an improper and pair style is defined, the
+<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between a group of 4 bonded atoms.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of improper styles defined in LAMMPS.
+Click on the style to display the formula it computes and coefficients
+specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A>
+command.
+</P>
+<P>Note that there are also additional improper styles submitted by users
+which are included in the LAMMPS distribution. The list of these with
+links to the individual styles are given in the improper section of
+<A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
+<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
+</UL>
+<UL><LI><A HREF = "improper_class2.html">improper_style class2</A> - COMPASS (class 2) improper
+<LI><A HREF = "improper_cvff.html">improper_style cvff</A> - CVFF improper
+<LI><A HREF = "improper_harmonic.html">improper_style harmonic</A> - harmonic improper
+<LI><A HREF = "improper_umbrella.html">improper_style umbrella</A> - DREIDING improper
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Improper styles can only be set for atom_style choices that allow
+impropers to be defined.
+</P>
+<P>Most improper styles are part of the MOLECULE package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual improper potentials tell if it is part of
+a package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>improper_style none
+</PRE>
+</HTML>
diff --git a/doc/doc2/improper_umbrella.html b/doc/doc2/improper_umbrella.html
new file mode 100644
index 000000000..2774452ae
--- /dev/null
+++ b/doc/doc2/improper_umbrella.html
@@ -0,0 +1,97 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>improper_style umbrella command
+</H3>
+<H3>improper_style umbrella/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>improper_style umbrella
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>improper_style umbrella
+improper_coeff 1 100.0 180.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>umbrella</I> improper style uses the following potential, which is
+commonly referred to as a classic inversion and used in the
+<A HREF = "Section_howto.html#howto_4">DREIDING</A> force field:
+</P>
+<CENTER><IMG SRC = "Eqs/improper_umbrella.jpg">
+</CENTER>
+<P>where K is the force constant and omega is the angle between the IL
+axis and the IJK plane:
+</P>
+<CENTER><IMG SRC = "Eqs/umbrella.jpg">
+</CENTER>
+<P>If omega0 = 0 the potential term has a minimum for the planar
+structure. Otherwise it has two minima at +/- omega0, with a barrier
+in between.
+</P>
+<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field.
+</P>
+<P>The following coefficients must be defined for each improper type via
+the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>K (energy)
+<LI>omega0 (degrees)
+</UL>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This improper style can only be used if LAMMPS was built with the
+MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "improper_coeff.html">improper_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mayo"></A>
+
+<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990),
+</P>
+</HTML>
diff --git a/doc/doc2/include.html b/doc/doc2/include.html
new file mode 100644
index 000000000..f7ba914ea
--- /dev/null
+++ b/doc/doc2/include.html
@@ -0,0 +1,45 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>include command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>include file
+</PRE>
+<UL><LI>file = filename of new input script to switch to
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>include newfile
+include in.run2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command opens a new input script file and begins reading LAMMPS
+commands from that file. When the new file is finished, the original
+file is returned to. Include files can be nested as deeply as
+desired. If input script A includes script B, and B includes A, then
+LAMMPS could run for a long time.
+</P>
+<P>If the filename is a variable (see the <A HREF = "variable.html">variable</A>
+command), different processor partitions can run different input
+scripts.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable</A>, <A HREF = "jump.html">jump</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/info.html b/doc/doc2/info.html
new file mode 100644
index 000000000..0a9dec096
--- /dev/null
+++ b/doc/doc2/info.html
@@ -0,0 +1,85 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>info command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>info args
+</PRE>
+<P>args = one or more of the following keywords: <I>out</I>, <I>all</I>, <I>system</I>, <I>computes</I>, <I>dumps</I>, <I>fixes</I>, <I>groups</I>, <I>regions</I>, <I>variables</I>, <I>time</I>, or <I>configuration</I>
+ <I>out</I> values = <I>screen</I>, <I>log</I>, <I>append</I> filename, <I>overwrite</I> filename:ul
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>info system
+info groups computes variables
+info all out log
+info all out append info.txt
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Print out information about the current internal state of the running
+LAMMPS process. This can be helpful when debugging or validating
+complex input scripts. Several output categories are available and
+one or more output category may be requested.
+</P>
+<P>The <I>out</I> flag controls where the output is sent. It can only be sent
+to one target. By default this is the screen, if it is active. The
+<I>log</I> argument selects the log file instead. With the <I>append</I> and
+<I>overwrite</I> option, followed by a filename, the output is written
+to that file, which is either appended to or overwritten, respectively.
+</P>
+<P>The <I>all</I> flag activates printing all categories listed below.
+</P>
+<P>The <I>system</I> category prints a general system overview listing. This
+includes the unit style, atom style, number of atoms, bonds, angles,
+dihedrals, and impropers and the number of the respective types, box
+dimensions and properties, force computing styles and more.
+</P>
+<P>The <I>computes</I> category prints a list of all currently defined
+computes, their IDs and styles and groups they operate on.
+</P>
+<P>The <I>dumps</I> category prints a list of all currently active dumps,
+their IDs, styles, filenames, groups, and dump frequencies.
+</P>
+<P>The <I>fixes</I> category prints a list of all currently defined fixes,
+their IDs and styles and groups they operate on.
+</P>
+<P>The <I>groups</I> category prints a list of all currently defined groups.
+</P>
+<P>The <I>regions</I> category prints a list of all currently defined regions,
+their IDs and styles and whether "inside" or "outside" atoms are
+selected.
+</P>
+<P>The <I>variables</I> category prints a list of all currently defined
+variables, their names, styles, definition and last computed value, if
+available.
+</P>
+<P>The <I>time</I> category prints the accumulated CPU and wall time for the
+process that writes output (usually MPI rank 0).
+</P>
+<P>The <I>configuration</I> command prints some information about the LAMMPS
+version and architection and OS it is run on. Where supported, also
+information about the memory consumption provided by the OS is
+reported.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "print.html">print</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The <I>out</I> option has the default <I>screen</I>.
+</P>
+</HTML>
diff --git a/doc/doc2/jump.html b/doc/doc2/jump.html
new file mode 100644
index 000000000..5fa724662
--- /dev/null
+++ b/doc/doc2/jump.html
@@ -0,0 +1,136 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>jump command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>jump file label
+</PRE>
+<UL><LI>file = filename of new input script to switch to
+<LI>label = optional label within file to jump to
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>jump newfile
+jump in.run2 runloop
+jump SELF runloop
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command closes the current input script file, opens the file with
+the specified name, and begins reading LAMMPS commands from that file.
+Unlike the <A HREF = "include.html">include</A> command, the original file is not
+returned to, although by using multiple jump commands it is possible
+to chain from file to file or back to the original file.
+</P>
+<P>If the word "SELF" is used for the filename, then the current input
+script is re-opened and read again.
+</P>
+<P>IMPORTANT NOTE: The SELF option is not guaranteed to work when the
+current input script is being read through stdin (standard input),
+e.g.
+</P>
+<PRE>lmp_g++ < in.script
+</PRE>
+<P>since the SELF option invokes the C-library rewind() call, which may
+not be supported for stdin on some systems or by some MPI
+implementations. This can be worked around by using the <A HREF = "Section_start.html#start_7">-in
+command-line argument</A>, e.g.
+</P>
+<PRE>lmp_g++ -in in.script
+</PRE>
+<P>or by using the <A HREF = "Section_start.html#start_7">-var command-line
+argument</A> to pass the script name as a
+variable to the input script. In the latter case, a
+<A HREF = "variable.html">variable</A> called "fname" could be used in place of
+SELF, e.g.
+</P>
+<PRE>lmp_g++ -var fname in.script < in.script
+</PRE>
+<P>The 2nd argument to the jump command is optional. If specified, it is
+treated as a label and the new file is scanned (without executing
+commands) until the label is found, and commands are executed from
+that point forward. This can be used to loop over a portion of the
+input script, as in this example. These commands perform 10 runs,
+each of 10000 steps, and create 10 dump files named file.1, file.2,
+etc. The <A HREF = "next.html">next</A> command is used to exit the loop after 10
+iterations. When the "a" variable has been incremented for the tenth
+time, it will cause the next jump command to be skipped.
+</P>
+<PRE>variable a loop 10
+label loop
+dump 1 all atom 100 file.$a
+run 10000
+undump 1
+next a
+jump in.lj loop
+</PRE>
+<P>If the jump <I>file</I> argument is a variable, the jump command can be
+used to cause different processor partitions to run different input
+scripts. In this example, LAMMPS is run on 40 processors, with 4
+partitions of 10 procs each. An in.file containing the example
+variable and jump command will cause each partition to run a different
+simulation.
+</P>
+<PRE>mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
+</PRE>
+<PRE>variable f world script.1 script.2 script.3 script.4
+jump $f
+</PRE>
+<P>Here is an example of a loop which checks every 1000 steps if the
+system temperature has reached a certain value, and if so, breaks out
+of the loop to finish the run. Note that any variable could be
+checked, so long as it is current on the timestep when the run
+completes. As explained on the <A HREF = "variable.html">variable</A> doc page,
+this can be insured by includig the variable in thermodynamic output.
+</P>
+<PRE>variable myTemp equal temp
+label loop
+variable a loop 1000
+run 1000
+if "${myTemp} < 300.0" then "jump SELF break"
+next a
+jump SELF loop
+label break
+print "ALL DONE"
+</PRE>
+<P>Here is an example of a double loop which uses the if and
+<A HREF = "jump.html">jump</A> commands to break out of the inner loop when a
+condition is met, then continues iterating thru the outer loop.
+</P>
+<PRE>label loopa
+variable a loop 5
+ label loopb
+ variable b loop 5
+ print "A,B = $a,$b"
+ run 10000
+ if "$b > 2" then "jump SELF break"
+ next b
+ jump in.script loopb
+label break
+variable b delete
+next a
+jump SELF loopa
+</PRE>
+<P><B>Restrictions:</B>
+</P>
+<P>If you jump to a file and it does not contain the specified label,
+LAMMPS will come to the end of the file and exit.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable</A>, <A HREF = "include.html">include</A>, <A HREF = "label.html">label</A>,
+<A HREF = "next.html">next</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/kspace_modify.html b/doc/doc2/kspace_modify.html
new file mode 100644
index 000000000..25693a130
--- /dev/null
+++ b/doc/doc2/kspace_modify.html
@@ -0,0 +1,350 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>kspace_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>kspace_modify keyword value ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be listed
+
+<PRE>keyword = <I>mesh</I> or <I>order</I> or <I>order/disp</I> or <I>mix/disp</I> or <I>overlap</I> or <I>minorder</I> or <I>force</I> or <I>gewald</I> or <I>gewald/disp</I> or <I>slab</I> or (nozforce</I> or <I>compute</I> or <I>cutoff/adjust</I> or <I>fftbench</I> or <I>collective</I> or <I>diff</I> or <I>kmax/ewald</I> or <I>force/disp/real</I> or <I>force/disp/kspace</I> or <I>splittol</I> or <I>disp/auto</I>:l
+ <I>mesh</I> value = x y z
+ x,y,z = grid size in each dimension for long-range Coulombics
+ <I>mesh/disp</I> value = x y z
+ x,y,z = grid size in each dimension for 1/r^6 dispersion
+ <I>order</I> value = N
+ N = extent of Gaussian for PPPM or MSM mapping of charge to grid
+ <I>order/disp</I> value = N
+ N = extent of Gaussian for PPPM mapping of dispersion term to grid
+ <I>mix/disp</I> value = <I>pair</I> or <I>geom</I> or <I>none</I>
+ <I>overlap</I> = <I>yes</I> or <I>no</I> = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
+ <I>minorder</I> value = M
+ M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
+ <I>force</I> value = accuracy (force units)
+ <I>gewald</I> value = rinv (1/distance units)
+ rinv = G-ewald parameter for Coulombics
+ <I>gewald/disp</I> value = rinv (1/distance units)
+ rinv = G-ewald parameter for dispersion
+ <I>slab</I> value = volfactor or <I>nozforce</I>
+ volfactor = ratio of the total extended volume used in the
+ 2d approximation compared with the volume of the simulation domain
+ <I>nozforce</I> turns off kspace forces in the z direction
+ <I>compute</I> value = <I>yes</I> or <I>no</I>
+ <I>cutoff/adjust</I> value = <I>yes</I> or <I>no</I>
+ <I>pressure/scalar</I> value = <I>yes</I> or <I>no</I>
+ <I>fftbench</I> value = <I>yes</I> or <I>no</I>
+ <I>collective</I> value = <I>yes</I> or <I>no</I>
+ <I>diff</I> value = <I>ad</I> or <I>ik</I> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
+ <I>kmax/ewald</I> value = kx ky kz
+ kx,ky,kz = number of Ewald sum kspace vectors in each dimension
+ <I>force/disp/real</I> value = accuracy (force units)
+ <I>force/disp/kspace</I> value = accuracy (force units)
+ <I>splittol</I> value = tol
+ tol = relative size of two eigenvalues (see discussion below)
+ <I>disp/auto</I> value = yes or no
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>kspace_modify mesh 24 24 30 order 6
+kspace_modify slab 3.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set parameters used by the kspace solvers defined by the
+<A HREF = "kspace_style.html">kspace_style</A> command. Not all parameters are
+relevant to all kspace styles.
+</P>
+<P>The <I>mesh</I> keyword sets the grid size for kspace style <I>pppm</I> or
+<I>msm</I>. In the case of PPPM, this is the FFT mesh, and each dimension
+must be factorizable into powers of 2, 3, and 5. In the case of MSM,
+this is the finest scale real-space mesh, and each dimension must be
+factorizable into powers of 2. When this option is not set, the PPPM
+or MSM solver chooses its own grid size, consistent with the
+user-specified accuracy and pairwise cutoff. Values for x,y,z of
+0,0,0 unset the option.
+</P>
+<P>The <I>mesh/disp</I> keyword sets the grid size for kspace style
+<I>pppm/disp</I>. This is the FFT mesh for long-range dispersion and ach
+dimension must be factorizable into powers of 2, 3, and 5. When this
+option is not set, the PPPM solver chooses its own grid size,
+consistent with the user-specified accuracy and pairwise cutoff.
+Values for x,y,z of 0,0,0 unset the option.
+</P>
+<P>The <I>order</I> keyword determines how many grid spacings an atom's charge
+extends when it is mapped to the grid in kspace style <I>pppm</I> or <I>msm</I>.
+The default for this parameter is 5 for PPPM and 8 for MSM, which
+means each charge spans 5 or 8 grid cells in each dimension,
+respectively. For the LAMMPS implementation of MSM, the order can
+range from 4 to 10 and must be even. For PPPM, the minimum allowed
+setting is 2 and the maximum allowed setting is 7. The larger the
+value of this parameter, the smaller that LAMMPS will set the grid
+size, to achieve the requested accuracy. Conversely, the smaller the
+order value, the larger the grid size will be. Note that there is an
+inherent trade-off involved: a small grid will lower the cost of FFTs
+or MSM direct sum, but a larger order parameter will increase the cost
+of interpolating charge/fields to/from the grid.
+</P>
+<P>The <I>order/disp</I> keyword determines how many grid spacings an atom's
+dispersion term extends when it is mapped to the grid in kspace style
+<I>pppm/disp</I>. It has the same meaning as the <I>order</I> setting for
+Coulombics.
+</P>
+<P>The <I>overlap</I> keyword can be used in conjunction with the <I>minorder</I>
+keyword with the PPPM styles to adjust the amount of communication
+that occurs when values on the FFT grid are exchangeed between
+processors. This communication is distinct from the communication
+inherent in the parallel FFTs themselves, and is required because
+processors interpolate charge and field values using grid point values
+owned by neighboring processors (i.e. ghost point communication). If
+the <I>overlap</I> keyword is set to <I>yes</I> then this communication is
+allowed to extend beyond nearest-neighbor processors, e.g. when using
+lots of processors on a small problem. If it is set to <I>no</I> then the
+communication will be limited to nearest-neighbor processors and the
+<I>order</I> setting will be reduced if necessary, as explained by the
+<I>minorder</I> keyword discussion. The <I>overlap</I> keyword is always set to
+<I>yes</I> in MSM.
+</P>
+<P>The <I>minorder</I> keyword allows LAMMPS to reduce the <I>order</I> setting if
+necessary to keep the communication of ghost grid point limited to
+exchanges between nearest-neighbor processors. See the discussion of
+the <I>overlap</I> keyword for details. If the <I>overlap</I> keyword is set to
+<I>yes</I>, which is the default, this is never needed. If it set to <I>no</I>
+and overlap occurs, then LAMMPS will reduce the order setting, one
+step at a time, until the ghost grid overlap only extends to nearest
+neighbor processors. The <I>minorder</I> keyword limits how small the
+<I>order</I> setting can become. The minimum allowed value for PPPM is 2,
+which is the default. If <I>minorder</I> is set to the same value as
+<I>order</I> then no reduction is allowed, and LAMMPS will generate an
+error if the grid communcation is non-nearest-neighbor and <I>overlap</I>
+is set to <I>no</I>. The <I>minorder</I> keyword is not currently supported in
+MSM.
+</P>
+<P>The PPPM order parameter may be reset by LAMMPS when it sets up the
+FFT grid if the implied grid stencil extends beyond the grid cells
+owned by neighboring processors. Typically this will only occur when
+small problems are run on large numbers of processors. A warning will
+be generated indicating the order parameter is being reduced to allow
+LAMMPS to run the problem. Automatic adjustment of the order parameter
+is not supported in MSM.
+</P>
+<P>The <I>force</I> keyword overrides the relative accuracy parameter set by
+the <A HREF = "kspace_style.html">kspace_style</A> command with an absolute
+accuracy. The accuracy determines the RMS error in per-atom forces
+calculated by the long-range solver and is thus specified in force
+units. A negative value for the accuracy setting means to use the
+relative accuracy parameter. The accuracy setting is used in
+conjunction with the pairwise cutoff to determine the number of
+K-space vectors for style <I>ewald</I>, the FFT grid size for style
+<I>pppm</I>, or the real space grid size for style <I>msm</I>.
+</P>
+<P>The <I>gewald</I> keyword sets the value of the Ewald or PPPM G-ewald
+parameter for charge as <I>rinv</I> in reciprocal distance units. Without
+this setting, LAMMPS chooses the parameter automatically as a function
+of cutoff, precision, grid spacing, etc. This means it can vary from
+one simulation to the next which may not be desirable for matching a
+KSpace solver to a pre-tabulated pairwise potential. This setting can
+also be useful if Ewald or PPPM fails to choose a good grid spacing
+and G-ewald parameter automatically. If the value is set to 0.0,
+LAMMPS will choose the G-ewald parameter automatically. MSM does not
+use the <I>gewald</I> parameter.
+</P>
+<P>The <I>gewald/disp</I> keyword sets the value of the Ewald or PPPM G-ewald
+parameter for dispersion as <I>rinv</I> in reciprocal distance units. It
+has the same meaning as the <I>gewald</I> setting for Coulombics.
+</P>
+<P>The <I>slab</I> keyword allows an Ewald or PPPM solver to be used for a
+systems that are periodic in x,y but non-periodic in z - a
+<A HREF = "boundary.html">boundary</A> setting of "boundary p p f". This is done by
+treating the system as if it were periodic in z, but inserting empty
+volume between atom slabs and removing dipole inter-slab interactions
+so that slab-slab interactions are effectively turned off. The
+volfactor value sets the ratio of the extended dimension in z divided
+by the actual dimension in z. The recommended value is 3.0. A larger
+value is inefficient; a smaller value introduces unwanted slab-slab
+interactions. The use of fixed boundaries in z means that the user
+must prevent particle migration beyond the initial z-bounds, typically
+by providing a wall-style fix. The methodology behind the <I>slab</I>
+option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>. The <I>slab</I> option
+is also extended to non-neutral systems
+<A HREF = "#Ballenegger">(Ballenegger)</A>. An alternative slab option can be
+invoked with the <I>nozforce</I> keyword in lieu of the volfactor. This
+turns off all kspace forces in the z direction. The <I>nozforce</I> option
+is not supported by MSM. For MSM, any combination of periodic,
+non-periodic, or shrink-wrapped boundaries can be set using
+<A HREF = "boundary.html">boundary</A> (the slab approximation in not needed). The
+<I>slab</I> keyword is not currently supported by Ewald or PPPM when using
+a triclinic simulation cell. The slab correction has also been
+extended to point dipole interactions <A HREF = "#Klapp">(Klapp)</A> in
+<A HREF = "kspace_style.html">kspace_style</A> <I>ewald/disp</I>.
+</P>
+<P>The <I>compute</I> keyword allows Kspace computations to be turned off,
+even though a <A HREF = "kspace_style.html">kspace_style</A> is defined. This is
+not useful for running a real simulation, but can be useful for
+debugging purposes or for computing only partial forces that do not
+include the Kspace contribution. You can also do this by simply not
+defining a <A HREF = "kspace_style.html">kspace_style</A>, but a Kspace-compatible
+<A HREF = "pair_style.html">pair_style</A> requires a kspace style to be defined.
+This keyword gives you that option.
+</P>
+<P>The <I>cutoff/adjust</I> keyword applies only to MSM. If this option is
+turned on, the Coulombic cutoff will be automatically adjusted at the
+beginning of the run to give the desired estimated error. Other
+cutoffs such as LJ will not be affected. If the grid is not set using
+the <I>mesh</I> command, this command will also attempt to use the optimal
+grid that minimizes cost using an estimate given by
+<A HREF = "#Hardy">(Hardy)</A>. Note that this cost estimate is not exact, somewhat
+experimental, and still may not yield the optimal parameters.
+</P>
+<P>The <I>pressure/scalar</I> keyword applies only to MSM. If this option is
+turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
+be computed, which can be used, for example, to run an isotropic barostat.
+Computing the full pressure tensor with MSM is expensive, and this option
+provides a faster alternative. The scalar pressure is computed using a
+relationship between the Coulombic energy and pressure <A HREF = "#Hummer">(Hummer)</A>
+instead of using the virial equation. This option cannot be used to access
+individual components of the pressure tensor, to compute per-atom virial,
+or with suffix kspace/pair styles of MSM, like OMP or GPU.
+</P>
+<P>The <I>fftbench</I> keyword applies only to PPPM. It is on by default. If
+this option is turned off, LAMMPS will not take the time at the end
+of a run to give FFT benchmark timings, and will finish a few seconds
+faster than it would if this option were on.
+</P>
+<P>The <I>collective</I> keyword applies only to PPPM. It is set to <I>no</I> by
+default, except on IBM BlueGene machines. If this option is set to
+<I>yes</I>, LAMMPS will use MPI collective operations to remap data for
+3d-FFT operations instead of the default point-to-point communication.
+This is faster on IBM BlueGene machines, and may also be faster on
+other machines if they have an efficient implementation of MPI
+collective operations and adequate hardware.
+</P>
+<P>The <I>diff</I> keyword specifies the differentiation scheme used by the
+PPPM method to compute forces on particles given electrostatic
+potentials on the PPPM mesh. The <I>ik</I> approach is the default for
+PPPM and is the original formulation used in <A HREF = "#Hockney">(Hockney)</A>. It
+performs differentiation in Kspace, and uses 3 FFTs to transfer each
+component of the computed fields back to real space for total of 4
+FFTs per timestep.
+</P>
+<P>The analytic differentiation <I>ad</I> approach uses only 1 FFT to transfer
+information back to real space for a total of 2 FFTs per timestep. It
+then performs analytic differentiation on the single quantity to
+generate the 3 components of the electric field at each grid point.
+This is sometimes referred to as "smoothed" PPPM. This approach
+requires a somewhat larger PPPM mesh to achieve the same accuracy as
+the <I>ik</I> method. Currently, only the <I>ik</I> method (default) can be
+used for a triclinic simulation cell with PPPM. The <I>ad</I> method is
+always used for MSM.
+</P>
+<P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I>
+option. Support for those PPPM variants will be added later.
+</P>
+<P>The <I>kmax/ewald</I> keyword sets the number of kspace vectors in each
+dimension for kspace style <I>ewald</I>. The three values must be positive
+integers, or else (0,0,0), which unsets the option. When this option
+is not set, the Ewald sum scheme chooses its own kspace vectors,
+consistent with the user-specified accuracy and pairwise cutoff. In
+any case, if kspace style <I>ewald</I> is invoked, the values used are
+printed to the screen and the log file at the start of the run.
+</P>
+<P>With the <I>mix/disp</I> keyword one can select the mixing rule for the
+dispersion coefficients. With <I>pair</I>, the dispersion coefficients of
+unlike types are computed as indicated with
+<A HREF = "pair_modify.html">pair_modify</A>. With <I>geom</I>, geometric mixing is
+enforced on the dispersion coefficients in the kspace
+coefficients. When using the arithmetic mixing rule, this will
+speed-up the simulations but introduces some error in the force
+computations, as shown in <A HREF = "#Wennberg">(Wennberg)</A>. With <I>none</I>, it is
+assumed that no mixing rule is applicable. Splitting of the dispersion
+coefficients will be performed as described in
+<A HREF = "#Isele-Holder">(Isele-Holder)</A>. This splitting can be influenced with
+the <I>splittol</I> keywords. Only the eigenvalues that are larger than tol
+compared to the largest eigenvalues are included. Using this keywords
+the original matrix of dispersion coefficients is approximated. This
+leads to faster computations, but the accuracy in the reciprocal space
+computations of the dispersion part is decreased.
+</P>
+<P>The <I>force/disp/real</I> and <I>force/disp/kspace</I> keywords set the force
+accuracy for the real and space computations for the dispersion part
+of pppm/disp. As shown in <A HREF = "#Isele-Holder">(Isele-Holder)</A>, optimal
+performance and accuracy in the results is obtained when these values
+are different.
+</P>
+<P>The <I>disp/auto</I> option controlls whether the pppm/disp is allowed to
+generate PPPM parameters automatically. If set to <I>no</I>, parameters have
+to be specified using the <I>gewald/disp</I>, <I>mesh/disp</I>,
+<I>force/disp/real</I> or <I>force/disp/kspace</I> keywords, or
+the code will stop with an error message. When this option is set to
+<I>yes</I>, the error message will not appear and the simulation will start.
+For a typical application, using the automatic parameter generation will provide
+simulations that are either inaccurate or slow. Using this option is thus not
+recommended. For guidelines on how to obtain good parameters, see the <A HREF = "Section_howto.html#howto_23">How-To</A> discussion.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "boundary.html">boundary</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
+5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
+gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
+yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
+(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
+split = 0, tol = 1.0e-6, and disp/auto = no.
+</P>
+<HR>
+
+<A NAME = "Hockney"></A>
+
+<P><B>(Hockney)</B> Hockney and Eastwood, Computer Simulation Using Particles,
+Adam Hilger, NY (1989).
+</P>
+<A NAME = "Yeh"></A>
+
+<P><B>(Yeh)</B> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
+</P>
+<A NAME = "Ballenegger"></A>
+
+<P><B>(Ballenegger)</B> Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
+(2009).
+</P>
+<A NAME = "Klapp"></A>
+
+<P><B>(Klapp)</B> Klapp, Schoen, J Chem Phys, 117, 8050 (2002).
+</P>
+<A NAME = "Hardy"></A>
+
+<P><B>(Hardy)</B> David Hardy thesis: Multilevel Summation for the Fast
+Evaluation of Forces for the Simulation of Biomolecules, University of
+Illinois at Urbana-Champaign, (2006).
+</P>
+<A NAME = "Hummer"></A>
+
+<P><B>(Hummer)</B> Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
+</P>
+<A NAME = "Isele-Holder"></A>
+
+<P><B>(Isele-Holder)</B> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
+Chem Theory Comput, 9, 5412 (2013).
+</P>
+<A NAME = "Wennberg"></A>
+
+<P><B>(Wennberg)</B> Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
+9, 3527 (2013).
+</P>
+</HTML>
diff --git a/doc/doc2/kspace_style.html b/doc/doc2/kspace_style.html
new file mode 100644
index 000000000..36b55dc1d
--- /dev/null
+++ b/doc/doc2/kspace_style.html
@@ -0,0 +1,394 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>kspace_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>kspace_style style value
+</PRE>
+<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>ewald/disp</I> or <I>ewald/omp</I> or <I>pppm</I> or <I>pppm/cg</I> or <I>pppm/disp</I> or <I>pppm/tip4p</I> or <I>pppm/stagger</I> or <I>pppm/disp/tip4p</I> or <I>pppm/gpu</I> or <I>pppm/omp</I> or <I>pppm/cg/omp</I> or <I>pppm/tip4p/omp</I> or <I>msm</I> or <I>msm/cg</I> or <I>msm/omp</I> or <I>msm/cg/omp</I>
+
+<PRE> <I>none</I> value = none
+ <I>ewald</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>ewald/disp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>ewald/omp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/cg</I> value = accuracy (smallq)
+ accuracy = desired relative error in forces
+ smallq = cutoff for charges to be considered (optional) (charge units)
+ <I>pppm/disp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/tip4p</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/disp/tip4p</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/gpu</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/omp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/cg/omp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/tip4p/omp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>pppm/stagger</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>msm</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>msm/cg</I> value = accuracy (smallq)
+ accuracy = desired relative error in forces
+ smallq = cutoff for charges to be considered (optional) (charge units)
+ <I>msm/omp</I> value = accuracy
+ accuracy = desired relative error in forces
+ <I>msm/cg/omp</I> value = accuracy (smallq)
+ accuracy = desired relative error in forces
+ smallq = cutoff for charges to be considered (optional) (charge units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>kspace_style pppm 1.0e-4
+kspace_style pppm/cg 1.0e-5 1.0e-6
+kspace style msm 1.0e-4
+kspace_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a long-range solver for LAMMPS to use each timestep to compute
+long-range Coulombic interactions or long-range 1/r^6 interactions.
+Most of the long-range solvers perform their computation in K-space,
+hence the name of this command.
+</P>
+<P>When such a solver is used in conjunction with an appropriate pair
+style, the cutoff for Coulombic or 1/r^N interactions is effectively
+infinite. If the Coulombic case, this means each charge in the system
+interacts with charges in an infinite array of periodic images of the
+simulation domain.
+</P>
+<P>Note that using a long-range solver requires use of a matching <A HREF = "pair.html">pair
+style</A> to perform consistent short-range pairwise
+calculations. This means that the name of the pair style contains a
+matching keyword to the name of the KSpace style, as in this table:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD >Pair style </TD><TD > KSpace style </TD></TR>
+<TR ALIGN="center"><TD >coul/long </TD><TD > ewald or pppm</TD></TR>
+<TR ALIGN="center"><TD >coul/msm </TD><TD > msm</TD></TR>
+<TR ALIGN="center"><TD >lj/long or buck/long </TD><TD > disp (for dispersion)</TD></TR>
+<TR ALIGN="center"><TD >tip4p/long </TD><TD > tip4p
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<P>The <I>ewald</I> style performs a standard Ewald summation as described in
+any solid-state physics text.
+</P>
+<P>The <I>ewald/disp</I> style adds a long-range dispersion sum option for
+1/r^6 potentials and is useful for simulation of interfaces
+<A HREF = "#Veld">(Veld)</A>. It also performs standard Coulombic Ewald summations,
+but in a more efficient manner than the <I>ewald</I> style. The 1/r^6
+capability means that Lennard-Jones or Buckingham potentials can be
+used without a cutoff, i.e. they become full long-range potentials.
+The <I>ewald/disp</I> style can also be used with point-dipoles
+<A HREF = "#Toukmaji">(Toukmaji)</A> and is currently the only kspace solver in
+LAMMPS with this capability.
+</P>
+<HR>
+
+<P>The <I>pppm</I> style invokes a particle-particle particle-mesh solver
+<A HREF = "#Hockney">(Hockney)</A> which maps atom charge to a 3d mesh, uses 3d FFTs
+to solve Poisson's equation on the mesh, then interpolates electric
+fields on the mesh points back to the atoms. It is closely related to
+the particle-mesh Ewald technique (PME) <A HREF = "#Darden">(Darden)</A> used in
+AMBER and CHARMM. The cost of traditional Ewald summation scales as
+N^(3/2) where N is the number of atoms in the system. The PPPM solver
+scales as Nlog(N) due to the FFTs, so it is almost always a faster
+choice <A HREF = "#Pollock">(Pollock)</A>.
+</P>
+<P>The <I>pppm/cg</I> style is identical to the <I>pppm</I> style except that it
+has an optimization for systems where most particles are uncharged.
+Similarly the <I>msm/cg</I> style implements the same optimization for <I>msm</I>.
+The optional <I>smallq</I> argument defines the cutoff for the absolute
+charge value which determines whether a particle is considered charged
+or not. Its default value is 1.0e-5.
+</P>
+<P>The <I>pppm/tip4p</I> style is identical to the <I>pppm</I> style except that it
+adds a charge at the massless 4th site in each TIP4P water molecule.
+It should be used with <A HREF = "pair_style.html">pair styles</A> with a
+<I>tip4p/long</I> in their style name.
+</P>
+<P>The <I>pppm/stagger</I> style performs calculations using two different
+meshes, one shifted slightly with respect to the other. This can
+reduce force aliasing errors and increase the accuracy of the method
+for a given mesh size. Or a coarser mesh can be used for the same
+target accuracy, which saves CPU time. However, there is a trade-off
+since FFTs on two meshes are now performed which increases the
+compuation required. See <A HREF = "#Cerutti">(Cerutti)</A>, <A HREF = "#Neelov">(Neelov)</A>,
+and <A HREF = "#Hockney">(Hockney)</A> for details of the method.
+</P>
+<P>For high relative accuracy, using staggered PPPM allows the mesh size
+to be reduced by a factor of 2 in each dimension as compared to
+regular PPPM (for the same target accuracy). This can give up to a 4x
+speedup in the KSpace time (8x less mesh points, 2x more expensive).
+However, for low relative accuracy, the staggered PPPM mesh size may
+be essentially the same as for regular PPPM, which means the method
+will be up to 2x slower in the KSpace time (simply 2x more expensive).
+For more details and timings, see
+<A HREF = "Section_accelerate.html">Section_accelerate</A>.
+</P>
+<P>IMPORTANT NOTE: Using <I>pppm/stagger</I> may not give the same increase in
+the accuracy of energy and pressure as it does in forces, so some
+caution must be used if energy and/or pressure are quantities of
+interest, such as when using a barostat.
+</P>
+<HR>
+
+<P>The <I>pppm/disp</I> and <I>pppm/disp/tip4p</I> styles add a mesh-based long-range
+dispersion sum option for 1/r^6 potentials <A HREF = "#Isele-Holder">(Isele-Holder)</A>,
+similar to the <I>ewald/disp</I> style. The 1/r^6 capability means
+that Lennard-Jones or Buckingham potentials can be used without a cutoff,
+i.e. they become full long-range potentials.
+</P>
+<P>For these styles, you will possibly want to adjust the default choice of
+parameters by using the <A HREF = "kspace_modify.html">kspace_modify</A> command.
+This can be done by either choosing the Ewald and grid parameters, or
+by specifying separate accuracies for the real and kspace
+calculations. When not making any settings, the simulation will stop with
+an error message. Further information on the influence of the parameters
+and how to choose them is described in <A HREF = "#Isele-Holder">(Isele-Holder)</A>,
+<A HREF = "#Isele-Holder2">(Isele-Holder2)</A> and the
+<A HREF = "Section_howto.html#howto_24">How-To</A> discussion.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: All of the PPPM styles can be used with
+single-precision FFTs by using the compiler switch -DFFT_SINGLE for
+the FFT_INC setting in your lo-level Makefile. This setting also
+changes some of the PPPM operations (e.g. mapping charge to mesh and
+interpolating electric fields to particles) to be performed in single
+precision. This option can speed-up long-range calulations,
+particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag
+is discussed in <A HREF = "Section_start.html#start_2_4">this section</A> of the
+manual. MSM does not currently support the -DFFT_SINGLE compiler switch.
+</P>
+<HR>
+
+<P>The <I>msm</I> style invokes a multi-level summation method MSM solver,
+<A HREF = "#Hardy">(Hardy)</A> or <A HREF = "#Hardy2">(Hardy2)</A>, which maps atom charge to a 3d
+mesh, and uses a multi-level hierarchy of coarser and coarser meshes
+on which direct coulomb solves are done. This method does not use
+FFTs and scales as N. It may therefore be faster than the other
+K-space solvers for relatively large problems when running on large
+core counts. MSM can also be used for non-periodic boundary conditions and
+for mixed periodic and non-periodic boundaries.
+</P>
+<P>MSM is most competitive versus Ewald and PPPM when only relatively
+low accuracy forces, about 1e-4 relative error or less accurate,
+are needed. Note that use of a larger coulomb cutoff (i.e. 15
+angstroms instead of 10 angstroms) provides better MSM accuracy for
+both the real space and grid computed forces.
+</P>
+<P>Currently calculation of the full pressure tensor in MSM is expensive.
+Using the <A HREF = "kspace_modify.html">kspace_modify</A> <I>pressure/scalar yes</I>
+command provides a less expensive way to compute the scalar pressure
+(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
+to run an isotropic barostat. If the full pressure tensor is needed,
+then calculating the pressure at every timestep or using a fixed
+pressure simulation with MSM will cause the code to run slower.
+</P>
+<HR>
+
+<P>The specified <I>accuracy</I> determines the relative RMS error in per-atom
+forces calculated by the long-range solver. It is set as a
+dimensionless number, relative to the force that two unit point
+charges (e.g. 2 monovalent ions) exert on each other at a distance of
+1 Angstrom. This reference value was chosen as representative of the
+magnitude of electrostatic forces in atomic systems. Thus an accuracy
+value of 1.0e-4 means that the RMS error will be a factor of 10000
+smaller than the reference force.
+</P>
+<P>The accuracy setting is used in conjunction with the pairwise cutoff
+to determine the number of K-space vectors for style <I>ewald</I> or the
+grid size for style <I>pppm</I> or <I>msm</I>.
+</P>
+<P>Note that style <I>pppm</I> only computes the grid size at the beginning of
+a simulation, so if the length or triclinic tilt of the simulation
+cell increases dramatically during the course of the simulation, the
+accuracy of the simulation may degrade. Likewise, if the
+<A HREF = "kspace_modify.html">kspace_modify slab</A> option is used with
+shrink-wrap boundaries in the z-dimension, and the box size changes
+dramatically in z. For example, for a triclinic system with all three
+tilt factors set to the maximum limit, the PPPM grid should be
+increased roughly by a factor of 1.5 in the y direction and 2.0 in the
+z direction as compared to the same system using a cubic orthogonal
+simulation cell. One way to ensure the accuracy requirement is being
+met is to run a short simulation at the maximum expected tilt or
+length, note the required grid size, and then use the
+<A HREF = "kspace_modify.html">kspace_modify</A> <I>mesh</I> command to manually set the
+PPPM grid size to this value.
+</P>
+<P>RMS force errors in real space for <I>ewald</I> and <I>pppm</I> are estimated
+using equation 18 of <A HREF = "#Kolafa">(Kolafa)</A>, which is also referenced as
+equation 9 of <A HREF = "#Petersen">(Petersen)</A>. RMS force errors in K-space for
+<I>ewald</I> are estimated using equation 11 of <A HREF = "#Petersen">(Petersen)</A>,
+which is similar to equation 32 of <A HREF = "#Kolafa">(Kolafa)</A>. RMS force
+errors in K-space for <I>pppm</I> are estimated using equation 38 of
+<A HREF = "#Deserno">(Deserno)</A>. RMS force errors for <I>msm</I> are estimated
+using ideas from chapter 3 of <A HREF = "#Hardy">(Hardy)</A>, with equation 3.197
+of particular note. When using <I>msm</I> with non-periodic boundary
+conditions, it is expected that the error estimation will be too
+pessimistic. RMS force errors for dipoles when using <I>ewald/disp</I>
+are estimated using equations 33 and 46 of <A HREF = "#Wang">(Wang)</A>.
+</P>
+<P>See the <A HREF = "kspace_modify.html">kspace_modify</A> command for additional
+options of the K-space solvers that can be set, including a <I>force</I>
+option for setting an absoulte RMS error in forces, as opposed to a
+relative RMS error.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>More specifically, the <I>pppm/gpu</I> style performs charge assignment and
+force interpolation calculations on the GPU. These processes are
+performed either in single or double precision, depending on whether
+the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
+discussed above. The FFTs themselves are still calculated on the CPU.
+If <I>pppm/gpu</I> is used with a GPU-enabled pair style, part of the PPPM
+calculation can be performed concurrently on the GPU while other
+calculations for non-bonded and bonded force calculation are performed
+on the CPU.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP, and OPT packages respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>Note that the long-range electrostatic solvers in LAMMPS assume conducting
+metal (tinfoil) boundary conditions for both charge and dipole
+interactions. Vacuum boundary conditions are not currently supported.
+</P>
+<P>The <I>ewald/disp</I>, <I>ewald</I>, <I>pppm</I>, and <I>msm</I> styles support
+non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic
+simulation cells may not yet be supported by suffix versions of these
+styles (such as <I>pppm/cuda</I>).
+</P>
+<P>All of the kspace styles are part of the KSPACE package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. Note that
+the KSPACE package is installed by default.
+</P>
+<P>For MSM, a simulation must be 3d and one can use any combination of
+periodic, non-periodic, or shrink-wrapped boundaries (specified using
+the <A HREF = "boundary.html">boundary</A> command).
+</P>
+<P>For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
+The only exception is if the slab option is set with <A HREF = "kspace_modify.html">kspace_modify</A>,
+in which case the xy dimensions must be periodic and the z dimension must be
+non-periodic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
+lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
+lj/charmm/coul/long</A>, <A HREF = "pair_lj_long.html">pair_style
+lj/long/coul/long</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>kspace_style none
+</PRE>
+<HR>
+
+<A NAME = "Darden"></A>
+
+<P><B>(Darden)</B> Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
+</P>
+<A NAME = "Deserno"></A>
+
+<P><B>(Deserno)</B> Deserno and Holm, J Chem Phys, 109, 7694 (1998).
+</P>
+<A NAME = "Hockney"></A>
+
+<P><B>(Hockney)</B> Hockney and Eastwood, Computer Simulation Using Particles,
+Adam Hilger, NY (1989).
+</P>
+<A NAME = "Kolafa"></A>
+
+<P><B>(Kolafa)</B> Kolafa and Perram, Molecular Simualtion, 9, 351 (1992).
+</P>
+<A NAME = "Petersen"></A>
+
+<P><B>(Petersen)</B> Petersen, J Chem Phys, 103, 3668 (1995).
+</P>
+<A NAME = "Wang"></A>
+
+<P><B>(Wang)</B> Wang and Holm, J Chem Phys, 115, 6277 (2001).
+</P>
+<A NAME = "Pollock"></A>
+
+<P><B>(Pollock)</B> Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
+</P>
+<A NAME = "Cerutti"></A>
+
+<P><B>(Cerutti)</B> Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
+and Computation 5, 2322 (2009)
+</P>
+<A NAME = "Neelov"></A>
+
+<P><B>(Neelov)</B> Neelov, Holm, J Chem Phys 132, 234103 (2010)
+</P>
+<A NAME = "Veld"></A>
+
+<P><B>(Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
+</P>
+<A NAME = "Toukmaji"></A>
+
+<P><B>(Toukmaji)</B> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
+10913 (2000).
+</P>
+<A NAME = "Isele-Holder"></A>
+
+<P><B>(Isele-Holder)</B> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
+</P>
+<A NAME = "Isele-Holder2"></A>
+
+<P><B>(Isele-Holder2)</B> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
+Comput 9, 5412 (2013).
+</P>
+<A NAME = "Hardy"></A>
+
+<P><B>(Hardy)</B> David Hardy thesis: Multilevel Summation for the Fast
+Evaluation of Forces for the Simulation of Biomolecules, University of
+Illinois at Urbana-Champaign, (2006).
+</P>
+<A NAME = "Hardy2"></A>
+
+<P><B>(Hardy)</B> Hardy, Stone, Schulten, Parallel Computing 35 (2009)
+164-177.
+</P>
+</HTML>
diff --git a/doc/doc2/label.html b/doc/doc2/label.html
new file mode 100644
index 000000000..70030e6d3
--- /dev/null
+++ b/doc/doc2/label.html
@@ -0,0 +1,41 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>label command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>label ID
+</PRE>
+<UL><LI>ID = string used as label name
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>label xyz
+label loop
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Label this line of the input script with the chosen ID. Unless a jump
+command was used previously, this does nothing. But if a
+<A HREF = "jump.html">jump</A> command was used with a label argument to begin
+invoking this script file, then all command lines in the script prior
+to this line will be ignored. I.e. execution of the script will begin
+at this line. This is useful for looping over a section of the input
+script as discussed in the <A HREF = "jump.html">jump</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/lattice.html b/doc/doc2/lattice.html
new file mode 100644
index 000000000..2e75e2157
--- /dev/null
+++ b/doc/doc2/lattice.html
@@ -0,0 +1,267 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>lattice command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>lattice style scale keyword values ...
+</PRE>
+<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>hcp</I> or <I>diamond</I> or <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>custom</I>
+
+<LI>scale = scale factor between lattice and simulation box
+
+<PRE> scale = reduced density rho* (for LJ units)
+ scale = lattice constant in distance units (for all other units)
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>origin</I> or <I>orient</I> or <I>spacing</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I>
+
+<PRE> <I>origin</I> values = x y z
+ x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
+ <I>orient</I> values = dim i j k
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ i,j,k = integer lattice directions
+ <I>spacing</I> values = dx dy dz
+ dx,dy,dz = lattice spacings in the x,y,z box directions
+ <I>a1</I>,<I>a2</I>,<I>a3</I> values = x y z
+ x,y,z = primitive vector components that define unit cell
+ <I>basis</I> values = x y z
+ x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>lattice fcc 3.52
+lattice hex 0.85
+lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
+lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+ basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+lattice none 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a lattice for use by other commands. In LAMMPS, a lattice is
+simply a set of points in space, determined by a unit cell with basis
+atoms, that is replicated infinitely in all dimensions. The arguments
+of the lattice command can be used to define a wide variety of
+crystallographic lattices.
+</P>
+<P>A lattice is used by LAMMPS in two ways. First, the
+<A HREF = "create_atoms.html">create_atoms</A> command creates atoms on the lattice
+points inside the simulation box. Note that the
+<A HREF = "create_atoms.html">create_atoms</A> command allows different atom types
+to be assigned to different basis atoms of the lattice. Second, the
+lattice spacing in the x,y,z dimensions implied by the lattice, can be
+used by other commands as distance units
+(e.g. <A HREF = "create_box.html">create_box</A>, <A HREF = "region.html">region</A> and
+<A HREF = "velocity.html">velocity</A>), which are often convenient to use when the
+underlying problem geometry is atoms on a lattice.
+</P>
+<P>The lattice style must be consistent with the dimension of the
+simulation - see the <A HREF = "dimension.html">dimension</A> command. Styles <I>sc</I>
+or <I>bcc</I> or <I>fcc</I> or <I>hcp</I> or <I>diamond</I> are for 3d problems. Styles
+<I>sq</I> or <I>sq2</I> or <I>hex</I> are for 2d problems. Style <I>custom</I> can be
+used for either 2d or 3d problems.
+</P>
+<P>A lattice consists of a unit cell, a set of basis atoms within that
+cell, and a set of transformation parameters (scale, origin, orient)
+that map the unit cell into the simulation box. The vectors a1,a2,a3
+are the edge vectors of the unit cell. This is the nomenclature for
+"primitive" vectors in solid-state crystallography, but in LAMMPS the
+unit cell they determine does not have to be a "primitive cell" of
+minimum volume.
+</P>
+<P>Note that the lattice command can be used multiple times in an input
+script. Each time it is invoked, the lattice attributes are
+re-defined and are used for all subsequent commands (that use lattice
+attributes). For example, a sequence of lattice,
+<A HREF = "region.html">region</A>, and <A HREF = "create_atoms.html">create_atoms</A> commands
+can be repeated multiple times to build a poly-crystalline model with
+different geometric regions populated with atoms in different lattice
+orientations.
+</P>
+<HR>
+
+<P>A lattice of style <I>none</I> does not define a unit cell and basis set,
+so it cannot be used with the <A HREF = "create_atoms.html">create_atoms</A>
+command. However it does define a lattice spacing via the specified
+scale parameter. As explained above the lattice spacings in x,y,z can
+be used by other commands as distance units. No additional
+keyword/value pairs can be specified for the <I>none</I> style. By
+default, a "lattice none 1.0" is defined, which means the lattice
+spacing is the same as one distance unit, as defined by the
+<A HREF = "units.html">units</A> command.
+</P>
+<P>Lattices of style <I>sc</I>, <I>fcc</I>, <I>bcc</I>, and <I>diamond</I> are 3d lattices
+that define a cubic unit cell with edge length = 1.0. This means a1 =
+1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style <I>hcp</I> has a1 = 1 0 0, a2 = 0
+sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms
+within the unit cell are described in any solid-state physics text. A
+<I>sc</I> lattice has 1 basis atom at the lower-left-bottom corner of the
+cube. A <I>bcc</I> lattice has 2 basis atoms, one at the corner and one at
+the center of the cube. A <I>fcc</I> lattice has 4 basis atoms, one at the
+corner and 3 at the cube face centers. A <I>hcp</I> lattice has 4 basis
+atoms, two in the z = 0 plane and 2 in the z = 0.5 plane. A <I>diamond</I>
+lattice has 8 basis atoms.
+</P>
+<P>Lattices of style <I>sq</I> and <I>sq2</I> are 2d lattices that define a square
+unit cell with edge length = 1.0. This means a1 = 1 0 0 and a2 = 0 1
+0. A <I>sq</I> lattice has 1 basis atom at the lower-left corner of the
+square. A <I>sq2</I> lattice has 2 basis atoms, one at the corner and one
+at the center of the square. A <I>hex</I> style is also a 2d lattice, but
+the unit cell is rectangular, with a1 = 1 0 0 and a2 = 0 sqrt(3) 0.
+It has 2 basis atoms, one at the corner and one at the center of the
+rectangle.
+</P>
+<P>A lattice of style <I>custom</I> allows you to specify a1, a2, a3, and a
+list of basis atoms to put in the unit cell. By default, a1 and a2
+and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you
+can specify them to be of any length and non-orthogonal to each other,
+so that they describe a tilted parallelepiped. Via the <I>basis</I>
+keyword you add atoms, one at a time, to the unit cell. Its arguments
+are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector
+x of a basis atom within the unit cell is thus a linear combination of
+the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
+where bx,by,bz are the 3 values specified for the <I>basis</I> keyword.
+</P>
+<HR>
+
+<P>This sub-section discusses the arguments that determine how the
+idealized unit cell is transformed into a lattice of points within the
+simulation box.
+</P>
+<P>The <I>scale</I> argument determines how the size of the unit cell will be
+scaled when mapping it into the simulation box. I.e. it determines a
+multiplicative factor to apply to the unit cell, to convert it to a
+lattice of the desired size and distance units in the simulation box.
+The meaning of the <I>scale</I> argument depends on the <A HREF = "units.html">units</A>
+being used in your simulation.
+</P>
+<P>For all unit styles except <I>lj</I>, the scale argument is specified in
+the distance units defined by the unit style. For example, in <I>real</I>
+or <I>metal</I> units, if the unit cell is a unit cube with edge length
+1.0, specifying scale = 3.52 would create a cubic lattice with a
+spacing of 3.52 Angstroms. In <I>cgs</I> units, the spacing would be 3.52
+cm.
+</P>
+<P>For unit style <I>lj</I>, the scale argument is the Lennard-Jones reduced
+density, typically written as rho*. LAMMPS converts this value into
+the multiplicative factor via the formula "factor^dim = rho/rho*",
+where rho = N/V with V = the volume of the lattice unit cell and N =
+the number of basis atoms in the unit cell (described below), and dim
+= 2 or 3 for the dimensionality of the simulation. Effectively, this
+means that if LJ particles of size sigma = 1.0 are used in the
+simulation, the lattice of particles will be at the desired reduced
+density.
+</P>
+<P>The <I>origin</I> option specifies how the unit cell will be shifted or
+translated when mapping it into the simulation box. The x,y,z values
+are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice
+by a fraction of the lattice spacing in each dimension. The meaning
+of "lattice spacing" is discussed below.
+</P>
+<P>The <I>orient</I> option specifies how the unit cell will be rotated when
+mapping it into the simulation box. The <I>dim</I> argument is one of the
+3 coordinate axes in the simulation box. The other 3 arguments are
+the crystallographic direction in the lattice that you want to orient
+along that axis, specified as integers. E.g. "orient x 2 1 0" means
+the x-axis in the simulation box will be the [210] lattice
+direction, and similarly for y and z. The 3 lattice directions you
+specify do not have to be unit vectors, but they must be mutually
+orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
+the Z direction.
+</P>
+<P>IMPORTANT NOTE: The preceding paragraph describing lattice directions
+is only valid for orthogonal cubic unit cells (or square in 2d). If
+you are using a <I>hcp</I> or <I>hex</I> lattice or the more general lattice
+style <I>custom</I> with non-orthogonal a1,a2,a3 vectors, then you should
+think of the 3 <I>orient</I> vectors as creating a 3x3 rotation matrix
+which is applied to a1,a2,a3 to rotate the original unit cell to a new
+orientation in the simulation box.
+</P>
+<HR>
+
+<P>Several LAMMPS commands have the option to use distance units that are
+inferred from "lattice spacings" in the x,y,z box directions.
+E.g. the <A HREF = "region.html">region</A> command can create a block of size
+10x20x20, where 10 means 10 lattice spacings in the x direction.
+</P>
+<P>IMPORTANT NOTE: Though they are called lattice spacings, all the
+commands that have a "units lattice" option, simply use the 3 values
+as scale factors on the distance units defined by the
+<A HREF = "units.html">units</A> command. Thus if you do not like the lattice
+spacings computed by LAMMPS (e.g. for a non-orthogonal or rotated unit
+cell), you can define the 3 values to be whatever you wish, via the
+<I>spacing</I> option.
+</P>
+<P>If the <I>spacing</I> option is not specified, the lattice spacings are
+computed by LAMMPS in the following way. A unit cell of the lattice
+is mapped into the simulation box (scaled and rotated), so that it now
+has (perhaps) a modified size and orientation. The lattice spacing in
+X is defined as the difference between the min/max extent of the x
+coordinates of the 8 corner points of the modified unit cell (4 in
+2d). Similarly, the Y and Z lattice spacings are defined as the
+difference in the min/max of the y and z coordinates.
+</P>
+<P>Note that if the unit cell is orthogonal with axis-aligned edges (no
+rotation via the <I>orient</I> keyword), then the lattice spacings in each
+dimension are simply the scale factor (described above) multiplied by
+the length of a1,a2,a3. Thus a <I>hex</I> style lattice with a scale
+factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
+3*sqrt(3.0) in y.
+</P>
+<P>IMPORTANT NOTE: For non-orthogonal unit cells and/or when a rotation
+is applied via the <I>orient</I> keyword, then the lattice spacings
+computed by LAMMPS are typically less intuitive. In particular, in
+these cases, there is no guarantee that a particular lattice spacing
+is an integer multiple of the periodicity of the lattice in that
+direction. Thus, if you create an orthogonal periodic simulation box
+whose size in a dimension is a multiple of the lattice spacing, and
+then fill it with atoms via the <A HREF = "create_atoms.html">create_atoms</A>
+command, you will NOT necessarily create a periodic system.
+I.e. atoms may overlap incorrectly at the faces of the simulation box.
+</P>
+<P>The <I>spacing</I> option sets the 3 lattice spacings directly. All must
+be non-zero (use 1.0 for dz in a 2d simulation). The specified values
+are multiplied by the multiplicative factor described above that is
+associated with the scale factor. Thus a spacing of 1.0 means one
+unit cell edge length independent of the scale factor. As mentioned
+above, this option can be useful if the spacings LAMMPS computes are
+inconvenient to use in subsequent commands, which can be the case for
+non-orthogonal or rotated lattices.
+</P>
+<P>Note that whenever the lattice command is used, the values of the
+lattice spacings LAMMPS calculates are printed out. Thus their effect
+in commands that use the spacings should be decipherable.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>custom</I>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dimension.html">dimension</A>, <A HREF = "create_atoms.html">create_atoms</A>,
+<A HREF = "region.html">region</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>lattice none 1.0
+</PRE>
+<P>For other lattice styles, the option defaults are origin = 0.0 0.0
+0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0,
+a2 = 0 1 0, and a3 = 0 0 1.
+</P>
+</HTML>
diff --git a/doc/doc2/log.html b/doc/doc2/log.html
new file mode 100644
index 000000000..e583a10ea
--- /dev/null
+++ b/doc/doc2/log.html
@@ -0,0 +1,51 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>log command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>log file keyword
+</PRE>
+<UL><LI>file = name of new logfile
+<LI>keyword = <I>append</I> if output should be appended to logfile (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>log log.equil
+log log.equil append
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command closes the current LAMMPS log file, opens a new file with
+the specified name, and begins logging information to it. If the
+specified file name is <I>none</I>, then no new log file is opened. If the
+optional keyword <I>append</I> is specified, then output will be appended
+to an existing log file, instead of overwriting it.
+</P>
+<P>If multiple processor partitions are being used, the file name should
+be a variable, so that different processors do not attempt to write to
+the same log file.
+</P>
+<P>The file "log.lammps" is the default log file for a LAMMPS run. The
+name of the initial log file can also be set by the command-line
+switch -log. See <A HREF = "Section_start.html#start_7">Section_start 6</A> for
+details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default LAMMPS log file is named log.lammps
+</P>
+</HTML>
diff --git a/doc/doc2/mass.html b/doc/doc2/mass.html
new file mode 100644
index 000000000..1fa0e4377
--- /dev/null
+++ b/doc/doc2/mass.html
@@ -0,0 +1,89 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>mass command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>mass I value
+</PRE>
+<UL><LI>I = atom type (see asterisk form below)
+<LI>value = mass
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>mass 1 1.0
+mass * 62.5
+mass 2* 62.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the mass for all atoms of one or more atom types. Per-type mass
+values can also be set in the <A HREF = "read_data.html">read_data</A> data file
+using the "Masses" keyword. See the <A HREF = "units.html">units</A> command for
+what mass units to use.
+</P>
+<P>The I index can be specified in one of two ways. An explicit numeric
+value can be used, as in the 1st example above. Or a wild-card
+asterisk can be used to set the mass for multiple atom types. This
+takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+</P>
+<P>A line in a <A HREF = "read_data.html">data file</A> that follows the "Masses"
+keyword specifies mass using the same format as the arguments of the
+mass command in an input script, except that no wild-card asterisk can
+be used. For example, under the "Masses" section of a data file, the
+line that corresponds to the 1st example above would be listed as
+</P>
+<PRE>1 1.0
+</PRE>
+<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom
+style</A> requires per-type atom mass to be set.
+Currently, all but the <I>sphere</I> and <I>ellipsoid</I> and <I>peri</I> styles do.
+They require mass to be set for individual particles, not types.
+Per-atom masses are defined in the data file read by the
+<A HREF = "read_data.html">read_data</A> command, or set to default values by the
+<A HREF = "create_atoms.html">create_atoms</A> command. Per-atom masses can also be
+set to new values by the <A HREF = "set.html">set mass</A> or <A HREF = "set.html">set density</A>
+commands.
+</P>
+<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> and <A HREF = "pair_bop.html">pair_style
+bop</A> commands define the masses of atom types in their
+respective potential files, in which case the mass command is normally
+not used.
+</P>
+<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
+(or more) sub-styles which require per-type mass and one (or more)
+sub-styles which require per-atom mass, then you must define both.
+However, in this case the per-type mass will be ignored; only the
+per-atom mass will be used by LAMMPS.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>All masses must be defined before a simulation is run. They must also
+all be defined before a <A HREF = "velocity.html">velocity</A> or <A HREF = "fix_shake.html">fix
+shake</A> command is used.
+</P>
+<P>The mass assigned to any type or atom must be > 0.0.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/min_modify.html b/doc/doc2/min_modify.html
new file mode 100644
index 000000000..d9298f9b6
--- /dev/null
+++ b/doc/doc2/min_modify.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>min_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>min_modify keyword values ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be listed
+
+<PRE>keyword = <I>dmax</I> or <I>line</I>
+ <I>dmax</I> value = max
+ max = maximum distance for line search to move (distance units)
+ <I>line</I> value = <I>backtrack</I> or <I>quadratic</I> or <I>forcezero</I>
+ backtrack,quadratic,forcezero = style of linesearch to use
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>min_modify dmax 0.2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets parameters that affect the energy minimization
+algorithms selected by the <A HREF = "min_style.html">min_style</A> command. The
+various settings may affect the convergence rate and overall number of
+force evaluations required by a minimization, so users can experiment
+with these parameters to tune their minimizations.
+</P>
+<P>The <I>cg</I> and <I>sd</I> minimization styles have an outer iteration and an
+inner iteration which is steps along a one-dimensional line search in
+a particular search direction. The <I>dmax</I> parameter is how far any
+atom can move in a single line search in any dimension (x, y, or z).
+For the <I>quickmin</I> and <I>fire</I> minimization styles, the <I>dmax</I> setting
+is how far any atom can move in a single iteration (timestep). Thus a
+value of 0.1 in real <A HREF = "units.html">units</A> means no atom will move
+further than 0.1 Angstroms in a single outer iteration. This prevents
+highly overlapped atoms from being moved long distances (e.g. through
+another atom) due to large forces.
+</P>
+<P>The choice of line search algorithm for the <I>cg</I> and <I>sd</I> minimization
+styles can be selected via the <I>line</I> keyword.
+The default <I>quadratic</I> line search algorithm starts out using
+the robust backtracking method described below. However, once
+the system gets close to a local
+minimum and the linesearch steps get small, so that the energy
+is approximately quadratic in the step length, it uses the
+estimated location of zero gradient as the linesearch step,
+provided the energy change is downhill.
+This becomes more efficient than backtracking
+for highly-converged relaxations. The <I>forcezero</I>
+line search algorithm is similar to <I>quadratic</I>.
+It may be more efficient than <I>quadratic</I> on some systems.
+</P>
+<P>The backtracking search is robust and should always find a local energy
+minimum. However, it will "converge" when it can no longer reduce the
+energy of the system. Individual atom forces may still be larger than
+desired at this point, because the energy change is measured as the
+difference of two large values (energy before and energy after) and
+that difference may be smaller than machine epsilon even if atoms
+could move in the gradient direction to reduce forces further.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "min_style.html">min_style</A>, <A HREF = "minimize.html">minimize</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are dmax = 0.1 and line = quadratic.
+</P>
+</HTML>
diff --git a/doc/doc2/min_style.html b/doc/doc2/min_style.html
new file mode 100644
index 000000000..740ca261e
--- /dev/null
+++ b/doc/doc2/min_style.html
@@ -0,0 +1,104 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Page</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>min_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>min_style style
+</PRE>
+<UL><LI>style = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>quickmin</I> or <I>fire</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>min_style cg
+min_style fire
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Choose a minimization algorithm to use when a <A HREF = "minimize.html">minimize</A>
+command is performed.
+</P>
+<P>Style <I>cg</I> is the Polak-Ribiere version of the conjugate gradient (CG)
+algorithm. At each iteration the force gradient is combined with the
+previous iteration information to compute a new search direction
+perpendicular (conjugate) to the previous search direction. The PR
+variant affects how the direction is chosen and how the CG method is
+restarted when it ceases to make progress. The PR variant is thought
+to be the most effective CG choice for most problems.
+</P>
+<P>Style <I>hftn</I> is a Hessian-free truncated Newton algorithm. At each
+iteration a quadratic model of the energy potential is solved by a
+conjugate gradient inner iteration. The Hessian (second derivatives)
+of the energy is not formed directly, but approximated in each
+conjugate search direction by a finite difference directional
+derivative. When close to an energy minimum, the algorithm behaves
+like a Newton method and exhibits a quadratic convergence rate to high
+accuracy. In most cases the behavior of <I>hftn</I> is similar to <I>cg</I>,
+but it offers an alternative if <I>cg</I> seems to perform poorly. This
+style is not affected by the <A HREF = "min_modify.html">min_modify</A> command.
+</P>
+<P>Style <I>sd</I> is a steepest descent algorithm. At each iteration, the
+search direction is set to the downhill direction corresponding to the
+force vector (negative gradient of energy). Typically, steepest
+descent will not converge as quickly as CG, but may be more robust in
+some situations.
+</P>
+<P>Style <I>quickmin</I> is a damped dynamics method described in
+<A HREF = "#Sheppard">(Sheppard)</A>, where the damping parameter is related to the
+projection of the velocity vector along the current force vector for
+each atom. The velocity of each atom is initialized to 0.0 by this
+style, at the beginning of a minimization.
+</P>
+<P>Style <I>fire</I> is a damped dynamics method described in
+<A HREF = "#Bitzek">(Bitzek)</A>, which is similar to <I>quickmin</I> but adds a variable
+timestep and alters the projection operation to maintain components of
+the velocity non-parallel to the current force vector. The velocity
+of each atom is initialized to 0.0 by this style, at the beginning of
+a minimization.
+</P>
+<P>Either the <I>quickmin</I> and <I>fire</I> styles are useful in the context of
+nudged elastic band (NEB) calculations via the <A HREF = "neb.html">neb</A> command.
+</P>
+<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
+you have defined via the <A HREF = "timestep.html">timestep</A> command. Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+</P>
+<P>IMPORTANT NOTE: The <I>quickmin</I> and <I>fire</I> styles do not yet support
+the use of the <A HREF = "fix_box_relax.html">fix box/relax</A> command or
+minimizations involving the electron radius in <A HREF = "pair_eff.html">eFF</A>
+models.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "min_modify.html">min_modify</A>, <A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>min_style cg
+</PRE>
+<HR>
+
+<A NAME = "Sheppard"></A>
+
+<P><B>(Sheppard)</B> Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
+(2008). See ref 1 in this paper for original reference to Qmin in
+Jonsson, Mills, Jacobsen.
+</P>
+<A NAME = "Bitzek"></A>
+
+<P><B>(Bitzek)</B> Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+97, 170201 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/minimize.html b/doc/doc2/minimize.html
new file mode 100644
index 000000000..16f8be7b4
--- /dev/null
+++ b/doc/doc2/minimize.html
@@ -0,0 +1,279 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>minimize command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>minimize etol ftol maxiter maxeval
+</PRE>
+<UL><LI>etol = stopping tolerance for energy (unitless)
+<LI>ftol = stopping tolerance for force (force units)
+<LI>maxiter = max iterations of minimizer
+<LI>maxeval = max number of force/energy evaluations
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>minimize 1.0e-4 1.0e-6 100 1000
+minimize 0.0 1.0e-8 1000 100000
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform an energy minimization of the system, by iteratively adjusting
+atom coordinates. Iterations are terminated when one of the stopping
+criteria is satisfied. At that point the configuration will hopefully
+be in local potential energy minimum. More precisely, the
+configuration should approximate a critical point for the objective
+function (see below), which may or may not be a local minimum.
+</P>
+<P>The minimization algorithm used is set by the
+<A HREF = "min_style.html">min_style</A> command. Other options are set by the
+<A HREF = "min_modify.html">min_modify</A> command. Minimize commands can be
+interspersed with <A HREF = "run.html">run</A> commands to alternate between
+relaxation and dynamics. The minimizers bound the distance atoms move
+in one iteration, so that you can relax systems with highly overlapped
+atoms (large energies and forces) by pushing the atoms off of each
+other.
+</P>
+<P>Alternate means of relaxing a system are to run dynamics with a small
+or <A HREF = "fix_nve_limit.html">limited timestep</A>. Or dynamics can be run
+using <A HREF = "fix_viscous.html">fix viscous</A> to impose a damping force that
+slowly drains all kinetic energy from the system. The <A HREF = "pair_soft.html">pair_style
+soft</A> potential can be used to un-overlap atoms while
+running dynamics.
+</P>
+<P>Note that you can minimize some atoms in the system while holding the
+coordiates of other atoms fixed by applying <A HREF = "fix_setforce.html">fix
+setforce</A> to the other atoms. See a fuller
+discussion of using fixes while minimizing below.
+</P>
+<P>The <A HREF = "min_style.html">minimization styles</A> <I>cg</I>, <I>sd</I>, and <I>hftn</I>
+involves an outer iteration loop which sets the search direction along
+which atom coordinates are changed. An inner iteration is then
+performed using a line search algorithm. The line search typically
+evaluates forces and energies several times to set new coordinates.
+Currently, a backtracking algorithm is used which may not be optimal
+in terms of the number of force evaulations performed, but appears to
+be more robust than previous line searches we've tried. The
+backtracking method is described in Nocedal and Wright's Numerical
+Optimization (Procedure 3.1 on p 41).
+</P>
+<P>The <A HREF = "min_style.html">minimization styles</A> <I>quickmin</I> and <I>fire</I> perform
+damped dynamics using an Euler integration step. Thus they require a
+<A HREF = "timestep.html">timestep</A> be defined.
+</P>
+<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
+you have defined via the <A HREF = "timestep.html">timestep</A> command. Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+</P>
+<HR>
+
+<P>In all cases, the objective function being minimized is the total
+potential energy of the system as a function of the N atom
+coordinates:
+</P>
+<CENTER><IMG SRC = "Eqs/min_energy.jpg">
+</CENTER>
+<P>where the first term is the sum of all non-bonded <A HREF = "pair_style.html">pairwise
+interactions</A> including <A HREF = "kspace_style.html">long-range Coulombic
+interactions</A>, the 2nd thru 5th terms are
+<A HREF = "bond_style.html">bond</A>, <A HREF = "angle_style.html">angle</A>,
+<A HREF = "dihedral_style.html">dihedral</A>, and <A HREF = "improper_style.html">improper</A>
+interactions respectively, and the last term is energy due to
+<A HREF = "fix.html">fixes</A> which can act as constraints or apply force to atoms,
+such as thru interaction with a wall. See the discussion below about
+how fix commands affect minimization.
+</P>
+<P>The starting point for the minimization is the current configuration
+of the atoms.
+</P>
+<HR>
+
+<P>The minimization procedure stops if any of several criteria are met:
+</P>
+<UL><LI>the change in energy between outer iterations is less than <I>etol</I>
+<LI>the 2-norm (length) of the global force vector is less than the <I>ftol</I>
+<LI>the line search fails because the step distance backtracks to 0.0
+<LI>the number of outer iterations or timesteps exceeds <I>maxiter</I>
+<LI>the number of total force evaluations exceeds <I>maxeval</I>
+</UL>
+<P>For the first criterion, the specified energy tolerance <I>etol</I> is
+unitless; it is met when the energy change between successive
+iterations divided by the energy magnitude is less than or equal to
+the tolerance. For example, a setting of 1.0e-4 for <I>etol</I> means an
+energy tolerance of one part in 10^4. For the damped dynamics
+minimizers this check is not performed for a few steps after
+velocities are reset to 0, otherwise the minimizer would prematurely
+converge.
+</P>
+<P>For the second criterion, the specified force tolerance <I>ftol</I> is in
+force units, since it is the length of the global force vector for all
+atoms, e.g. a vector of size 3N for N atoms. Since many of the
+components will be near zero after minimization, you can think of
+<I>ftol</I> as an upper bound on the final force on any component of any
+atom. For example, a setting of 1.0e-4 for <I>ftol</I> means no x, y, or z
+component of force on any atom will be larger than 1.0e-4 (in force
+units) after minimization.
+</P>
+<P>Either or both of the <I>etol</I> and <I>ftol</I> values can be set to 0.0, in
+which case some other criterion will terminate the minimization.
+</P>
+<P>During a minimization, the outer iteration count is treated as a
+timestep. Output is triggered by this timestep, e.g. thermodynamic
+output or dump and restart files.
+</P>
+<P>Using the <A HREF = "thermo_style.html">thermo_style custom</A> command with the
+<I>fmax</I> or <I>fnorm</I> keywords can be useful for monitoring the progress
+of the minimization. Note that these outputs will be calculated only
+from forces on the atoms, and will not include any extra degrees of
+freedom, such as from the <A HREF = "fix_box_relax.html">fix box/relax</A> command.
+</P>
+<P>Following minimization, a statistical summary is printed that lists
+which convergence criterion caused the minimizer to stop, as well as
+information about the energy, force, final line search, and
+iteration counts. An example is as follows:
+</P>
+<PRE>Minimization stats:
+ Stopping criterion = max iterations
+ Energy initial, next-to-last, final =
+ -0.626828169302 -2.82642039062 -2.82643549739
+ Force two-norm initial, final = 2052.1 91.9642
+ Force max component initial, final = 346.048 9.78056
+ Final line search alpha, max atom move = 2.23899e-06 2.18986e-05
+ Iterations, force evaluations = 2000 12724
+</PRE>
+<P>The 3 energy values are for before and after the minimization and on
+the next-to-last iteration. This is what the <I>etol</I> parameter checks.
+</P>
+<P>The two-norm force values are the length of the global force vector
+before and after minimization. This is what the <I>ftol</I> parameter
+checks.
+</P>
+<P>The max-component force values are the absolute value of the largest
+component (x,y,z) in the global force vector, i.e. the infinity-norm
+of the force vector.
+</P>
+<P>The alpha parameter for the line-search, when multiplied by the max
+force component (on the last iteration), gives the max distance any
+atom moved during the last iteration. Alpha will be 0.0 if the line
+search could not reduce the energy. Even if alpha is non-zero, if the
+"max atom move" distance is tiny compared to typical atom coordinates,
+then it is possible the last iteration effectively caused no atom
+movement and thus the evaluated energy did not change and the
+minimizer terminated. Said another way, even with non-zero forces,
+it's possible the effect of those forces is to move atoms a distance
+less than machine precision, so that the energy cannot be further
+reduced.
+</P>
+<P>The iterations and force evaluation values are what is checked by the
+<I>maxiter</I> and <I>maxeval</I> parameters.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: There are several force fields in LAMMPS which have
+discontinuities or other approximations which may prevent you from
+performing an energy minimization to high tolerances. For example,
+you should use a <A HREF = "pair_style.html">pair style</A> that goes to 0.0 at the
+cutoff distance when performing minimization (even if you later change
+it when running dynamics). If you do not do this, the total energy of
+the system will have discontinuities when the relative distance
+between any pair of atoms changes from cutoff+epsilon to
+cutoff-epsilon and the minimizer may behave poorly. Some of the
+manybody potentials use splines and other internal cutoffs that
+inherently have this problem. The <A HREF = "kspace_style.html">long-range Coulombic
+styles</A> (PPPM, Ewald) are approximate to within the
+user-specified tolerance, which means their energy and forces may not
+agree to a higher precision than the Kspace-specified tolerance. In
+all these cases, the minimizer may give up and stop before finding a
+minimum to the specified energy or force tolerance.
+</P>
+<P>Note that a cutoff Lennard-Jones potential (and others) can be shifted
+so that its energy is 0.0 at the cutoff via the
+<A HREF = "pair_modify.html">pair_modify</A> command. See the doc pages for
+inidividual <A HREF = "pair_style.html">pair styles</A> for details. Note that
+Coulombic potentials always have a cutoff, unless versions with a
+long-range component are used (e.g. <A HREF = "pair_lj.html">pair_style
+lj/cut/coul/long</A>). The CHARMM potentials go to 0.0 at
+the cutoff (e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A>),
+as do the GROMACS potentials (e.g. <A HREF = "pair_gromacs.html">pair_style
+lj/gromacs</A>).
+</P>
+<P>If a soft potential (<A HREF = "pair_soft.html">pair_style soft</A>) is used the
+Astop value is used for the prefactor (no time dependence).
+</P>
+<P>The <A HREF = "fix_box_relax.html">fix box/relax</A> command can be used to apply an
+external pressure to the simulation box and allow it to shrink/expand
+during the minimization.
+</P>
+<P>Only a few other fixes (typically those that apply force constraints)
+are invoked during minimization. See the doc pages for individual
+<A HREF = "fix.html">fix</A> commands to see which ones are relevant. Current
+examples of fixes that can be used include:
+</P>
+<UL><LI><A HREF = "fix_addforce.html">fix addforce</A>
+<LI><A HREF = "fix_addtorque.html">fix addtorque</A>
+<LI><A HREF = "fix_efield.html">fix efield</A>
+<LI><A HREF = "fix_enforce2d.html">fix enforce2d</A>
+<LI><A HREF = "fix_indent.html">fix indent</A>
+<LI><A HREF = "fix_lineforce.html">fix lineforce</A>
+<LI><A HREF = "fix_planeforce.html">fix planeforce</A>
+<LI><A HREF = "fix_setforce.html">fix setforce</A>
+<LI><A HREF = "fix_spring.html">fix spring</A>
+<LI><A HREF = "fix_spring_self.html">fix spring/self</A>
+<LI><A HREF = "fix_viscous.html">fix viscous</A>
+<LI><A HREF = "fix_wall.html">fix wall</A>
+<LI><A HREF = "fix_wall_region.html">fix wall/region</A>
+</UL>
+<P>IMPORTANT NOTE: Some fixes which are invoked during minimization have
+an associated potential energy. For that energy to be included in the
+total potential energy of the system (the quantity being minimized),
+you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
+that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
+specify if this should be done.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Features that are not yet implemented are listed here, in case someone
+knows how they could be coded:
+</P>
+<P>It is an error to use <A HREF = "fix_shake.html">fix shake</A> with minimization
+because it turns off bonds that should be included in the potential
+energy of the system. The effect of a fix shake can be approximated
+during a minimization by using stiff spring constants for the bonds
+and/or angles that would normally be constrained by the SHAKE
+algorithm.
+</P>
+<P><A HREF = "fix_rigid.html">Fix rigid</A> is also not supported by minimization. It
+is not an error to have it defined, but the energy minimization will
+not keep the defined body(s) rigid during the minimization. Note that
+if bonds, angles, etc internal to a rigid body have been turned off
+(e.g. via <A HREF = "neigh_modify.html">neigh_modify exclude</A>), they will not
+contribute to the potential energy which is probably not what is
+desired.
+</P>
+<P>Pair potentials that produce torque on a particle (e.g. <A HREF = "pair_gran.html">granular
+potentials</A> or the <A HREF = "pair_gayberne.html">GayBerne
+potential</A> for ellipsoidal particles) are not
+relaxed by a minimization. More specifically, radial relaxations are
+induced, but no rotations are induced by a minimization, so such a
+system will not fully relax.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
+<A HREF = "run_style.html">run_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/molecule.html b/doc/doc2/molecule.html
new file mode 100644
index 000000000..15f8df52c
--- /dev/null
+++ b/doc/doc2/molecule.html
@@ -0,0 +1,444 @@
+<HTML>
+<CENTER><<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>molecule command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>molecule ID file1 file2 ... keyword values ...
+</PRE>
+<UL><LI>ID = user-assigned name for the molecule template
+
+<LI>file1,file2,... = names of files containing molecule descriptions
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>offset</I>
+
+<PRE> <I>offset</I> values = toff boff aoff doff ioff
+ toff = offset to add to atom types
+ boff = offset to add to bond types
+ aoff = offset to add to angle types
+ doff = offset to add to dihedral types
+ ioff = offset to add to improper types
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>molecule 1 mymol
+molecule 1 co2.txt h2o.txt
+molecule CO2 co2.txt
+molecule 1 mymol offset 6 9 18 23 14
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a molecule template that can be used as part of other LAMMPS
+commands, typically to define a collection of particles as a bonded
+molecule or a rigid body. Commands that currently use molecule
+templates include:
+</P>
+<UL><LI><A HREF = "fix_deposit.html">fix deposit</A>
+<LI><A HREF = "fix_pour.html">fix pour</A>
+<LI><A HREF = "fix_rigid.html">fix rigid/small</A>
+<LI><A HREF = "fix_shake.html">fix shake</A>
+<LI><A HREF = "fix_gcmc.html">fix gcmc</A>
+<LI><A HREF = "create_atoms.html">create_atoms</A>
+<LI><A HREF = "atom_style.html">atom_style template</A>
+</UL>
+<P>The ID of a molecule template can only contain alphanumeric characters
+and underscores.
+</P>
+<P>A single template can contain multiple molecules, listed one per file.
+Many of the commands listed above currently use only the first
+molecule in the template, and will issue a warning if the template
+contains multiple molecules. The <A HREF = "atom_style.html">atom_style
+template</A> command allows multiple-molecule templates
+to define a system with more than one templated molecule.
+</P>
+<P>The optional <I>offset</I> keyword adds the specified offset values to the
+atom types, bond types, angle types, dihedral types, and improper
+types as they are read from the molecule file. E.g. if <I>toff</I> = 2,
+and the file uses atom types 1,2,3, then each created molecule will
+have atom types 3,4,5. This is to make it easy to use the same
+molecule template file in different simulations. Note that the same
+offsets are applied to the molecules in all specified files. All five
+offset values must be speicified, but individual values will be
+ignored if the molecule template does not use that attribute (e.g. no
+bonds).
+</P>
+<P>IMPORTANT NOTE: This command can be used to define molecules with
+bonds, angles, dihedrals, imporopers, or special bond lists of
+neighbors within a molecular topology, so that you can later add the
+molecules to your simulation, via one or more of the commands listed
+above. If such molecules do not already exist when LAMMPS creates the
+simulation box, via the <A HREF = "create_box.html">create_box</A> or
+<A HREF = "read_data.html">read_data</A> command, when you later add them you may
+overflow the pre-allocated data structures which store molecular
+topology information with each atom, and an error will be generated.
+Both the <A HREF = "create_box.html">create_box</A> command and the data files read
+by the <A HREF = "read_data.html">read_data</A> command have "extra" options which
+insure space is allocated for storing topology info for molecules that
+are added later.
+</P>
+<P>The format of an individual molecule file is similar to the data file
+read by the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
+</P>
+<P>A molecule file has a header and a body. The header appears first.
+The first line of the header is always skipped; it typically contains
+a description of the file. Then lines are read one at a time. Lines
+can have a trailing comment starting with '#' that is ignored. If the
+line is blank (only whitespace after comment is deleted), it is
+skipped. If the line contains a header keyword, the corresponding
+value(s) is read from the line. If it doesn't contain a header
+keyword, the line begins the body of the file.
+</P>
+<P>The body of the file contains zero or more sections. The first line
+of a section has only a keyword. The next line is skipped. The
+remaining lines of the section contain values. The number of lines
+depends on the section keyword as described below. Zero or more blank
+lines can be used between sections. Sections can appear in any order,
+with a few exceptions as noted below.
+</P>
+<P>These are the recognized header keywords. Header lines can come in
+any order. The numeric value(s) are read from the beginning of the
+line. The keyword should appear at the end of the line. All these
+settings have default values, as explained below. A line need only
+appear if the value(s) are different than the default.
+</P>
+<UL><LI>N <I>atoms</I> = # of atoms N in molecule, default = 0
+<LI>Nb <I>bonds</I> = # of bonds Nb in molecule, default = 0
+<LI>Na <I>angles</I> = # of angles Na in molecule, default = 0
+<LI>Nd <I>dihedrals</I> = # of dihedrals Nd in molecule, default = 0
+<LI>Ni <I>impropers</I> = # of impropers Ni in molecule, default = 0
+<LI>Mtotal <I>mass</I> = total mass of molecule
+<LI>Xc Yc Zc <I>com</I> = coordinates of center-of-mass of molecule
+<LI>Ixx Iyy Izz Ixy Ixz Iyz <I>inertia</I> = 6 components of inertia tensor of molecule
+</UL>
+<P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
+calculate this quantity itself if needed, assuming the molecules
+consists of a set of point particles or finite-size particles (with a
+non-zero diameter) that do not overlap. If finite-size particles in
+the molecule do overlap, LAMMPS will not account for the overlap
+effects when calculating any of these 3 quantities, so you should
+pre-compute them yourself and list the values in the file.
+</P>
+<P>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
+self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
+should be the values consistent with the current orientation of the
+rigid body around its center of mass. The values are with respect to
+the simulation box XYZ axes, not with respect to the prinicpal axes of
+the rigid body itself. LAMMPS performs the latter calculation
+internally.
+</P>
+<P>These are the allowed section keywords for the body of the file.
+</P>
+<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
+<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
+<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
+<LI><I>Shake Flags, Shake Atoms, Shake Bond Types</I> = SHAKE info
+</UL>
+<P>If a Bonds section is specified then the Special Bond Counts and
+Special Bonds sections can also be used, if desired, to explicitly
+list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
+details below). This is optional since if these sections are not
+included, LAMMPS will auto-generate this information. Note that
+LAMMPS uses this info to properly exclude or weight bonded pairwise
+interactions between bonded atoms. See the
+<A HREF = "special_bonds.html">special_bonds</A> command for more details. One
+reason to list the special bond info explicitly is for the
+<A HREF = "tutorial_drude.html">thermalized Drude oscillator model</A> which treats
+the bonds between nuclear cores and Drude electrons in a different
+manner.
+</P>
+<P>IMPORTANT NOTE: Whether a section is required depends on how the
+molecule template is used by other LAMMPS commands. For example, to
+add a molecule via the <A HREF = "fix_deposit.html">fix deposit</A> command, the
+Coords and Types sections are required. To add a rigid body via the
+<A HREF = "fix_pout.html">fix pour</A> command, the Bonds (Angles, etc) sections are
+not required, since the molecule will be treated as a rigid body.
+Some sections are optional. For example, the <A HREF = "fix_pour.html">fix pour</A>
+command can be used to add "molecules" which are clusters of
+finite-size granular particles. If the Diameters section is not
+specified, each particle in the molecule will have a default diameter
+of 1.0. See the doc pages for LAMMPS commands that use molecule
+templates for more details.
+</P>
+<P>Each section is listed below in alphabetic order. The format of each
+section is described including the number of lines it must contain and
+rules (if any) for whether it can appear in the data file. In each
+case the ID is ignored; it is simply included for readability, and
+should be a number from 1 to Nlines for the section, indicating which
+atom (or bond, etc) the entry applies to. The lines are assumed to be
+listed in order from 1 to Nlines, but LAMMPS does not check for this.
+</P>
+<HR>
+
+<P><I>Coords</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID x y z
+<LI>x,y,z = coordinate of atom
+</UL>
+<HR>
+
+<P><I>Types</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID type
+<LI>type = atom type of atom
+</UL>
+<HR>
+
+<P><I>Charges</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID q
+<LI>q = charge on atom
+</UL>
+<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
+support charge. If this section is not included, the default charge
+on each atom in the molecule is 0.0.
+</P>
+<HR>
+
+<P><I>Diameters</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID diam
+<LI>diam = diameter of atom
+</UL>
+<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
+support finite-size spherical particles, e.g. atom_style sphere. If
+not listed, the default diameter of each atom in the molecule is 1.0.
+</P>
+<HR>
+
+<P><I>Masses</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID mass
+<LI>mass = mass of atom
+</UL>
+<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
+support per-atom mass, as opposed to per-type mass. See the
+<A HREF = "mass.html">mass</A> command for details. If this section is not
+included, the default mass for each atom is derived from its volume
+(see Diameters section) and a default density of 1.0, in
+<A HREF = "units.html">units</A> of mass/volume.
+</P>
+<HR>
+
+<P><I>Bonds</I> section:
+</P>
+<UL><LI>one line per bond
+<LI>line syntax: ID type atom1 atom2
+<LI>type = bond type (1-Nbondtype)
+<LI>atom1,atom2 = IDs of atoms in bond
+</UL>
+<P>The IDs for the two atoms in each bond should be values
+from 1 to Natoms, where Natoms = # of atoms in the molecule.
+</P>
+<HR>
+
+<P><I>Angles</I> section:
+</P>
+<UL><LI>one line per angle
+<LI>line syntax: ID type atom1 atom2 atom3
+<LI>type = angle type (1-Nangletype)
+<LI>atom1,atom2,atom3 = IDs of atoms in angle
+</UL>
+<P>The IDs for the three atoms in each angle should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
+ordered linearly within the angle. Thus the central atom (around
+which the angle is computed) is the atom2 in the list.
+</P>
+<HR>
+
+<P><I>Dihedrals</I> section:
+</P>
+<UL><LI>one line per dihedral
+<LI>line syntax: ID type atom1 atom2 atom3 atom4
+<LI>type = dihedral type (1-Ndihedraltype)
+<LI>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
+</UL>
+<P>The IDs for the four atoms in each dihedral should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
+ordered linearly within the dihedral.
+</P>
+<HR>
+
+<P><I>Impropers</I> section:
+</P>
+<UL><LI>one line per improper
+<LI>line syntax: ID type atom1 atom2 atom3 atom4
+<LI>type = improper type (1-Nimpropertype)
+<LI>atom1,atom2,atom3,atom4 = IDs of atoms in improper
+</UL>
+<P>The IDs for the four atoms in each improper should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule. The ordering of
+the 4 atoms determines the definition of the improper angle used in
+the formula for the defined <A HREF = "improper_style.html">improper style</A>. See
+the doc pages for individual styles for details.
+</P>
+<HR>
+
+<P><I>Special Bond Counts</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID N1 N2 N3
+<LI>N1 = # of 1-2 bonds
+<LI>N2 = # of 1-3 bonds
+<LI>N3 = # of 1-4 bonds
+</UL>
+<P>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
+this atom within the topology of the molecule. See the
+<A HREF = "special_bonds.html">special_bonds</A> doc page for more discussion of
+1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
+section must also appear. If this section is not specied, the
+atoms in the molecule will have no special bonds.
+</P>
+<HR>
+
+<P><I>Special Bonds</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID a b c d ...
+<LI>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds
+</UL>
+<P>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
+1-4 neighbors of this atom. The IDs should be values from 1 to
+Natoms, where Natoms = # of atoms in the molecule. The first N1
+values should be the 1-2 neighbors, the next N2 should be the 1-3
+neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
+appear more than once. See the <A HREF = "special_bonds.html">special_bonds</A> doc
+page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
+appears, the Special Bond Counts section must also appear. If this
+section is not specied, the atoms in the molecule will have no special
+bonds.
+</P>
+<HR>
+
+<P><I>Shake Flags</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID flag
+<LI>flag = 0,1,2,3,4
+</UL>
+<P>This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command. The other
+two Shake sections must also appear in the file, following this one.
+</P>
+<P>The meaning of the flag for each atom is as follows. See the <A HREF = "fix_shake.html">fix
+shake</A> doc page for a further description of SHAKE
+clusters.
+</P>
+<UL><LI>0 = not part of a SHAKE cluster
+<LI>1 = part of a SHAKE angle cluster (two bonds and the angle they form)
+<LI>2 = part of a 2-atom SHAKE cluster with a single bond
+<LI>3 = part of a 3-atom SHAKE cluster with two bonds
+<LI>4 = part of a 4-atom SHAKE cluster with three bonds
+</UL>
+<HR>
+
+<P><I>Shake Atoms</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID a b c d
+<LI>a,b,c,d = IDs of atoms in cluster
+</UL>
+<P>This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command. The other
+two Shake sections must also appear in the file.
+</P>
+<P>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
+in the SHAKE cluster that this atom belongs to. The number of values
+that must appear is determined by the shake flag for the atom (see the
+Shake Flags section above). All atoms in a particular cluster should
+list their a,b,c,d values identically.
+</P>
+<P>If flag = 0, no a,b,c,d values are listed on the line, just the
+(ignored) ID.
+</P>
+<P>If flag = 1, a,b,c are listed, where a = ID of central atom in the
+angle, and b,c the other two atoms in the angle.
+</P>
+<P>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
+lowest ID, and b = ID of atom in bond with the highest ID.
+</P>
+<P>If flag = 3, a,b,c are listed, where a = ID of central atom,
+and b,c = IDs of other two atoms bonded to the central atom.
+</P>
+<P>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
+and b,c,d = IDs of other three atoms bonded to the central atom.
+</P>
+<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
+of SHAKE clusters.
+</P>
+<HR>
+
+<P><I>Shake Bond Types</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: ID a b c
+<LI>a,b,c = bond types (or angle type) of bonds (or angle) in cluster
+</UL>
+<P>This section is only needed when molecules created using the template
+will be constrained by SHAKE via the "fix shake" command. The other
+two Shake sections must also appear in the file.
+</P>
+<P>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
+in the SHAKE cluster that this atom belongs to. The number of values
+that must appear is determined by the shake flag for the atom (see the
+Shake Flags section above). All atoms in a particular cluster should
+list their a,b,c values identically.
+</P>
+<P>If flag = 0, no a,b,c values are listed on the line, just the
+(ignored) ID.
+</P>
+<P>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), b = bondtype of the bond between the central atom and
+the 2nd non-central atom (value c in the Shake Atoms section), and c =
+the angle type (1 to Nangletypes) of the angle between the 3 atoms.
+</P>
+<P>If flag = 2, only a is listed, where a = bondtype of the bond between
+the 2 atoms in the cluster.
+</P>
+<P>If flag = 3, a,b are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), and b = bondtype of the bond between the central atom
+and the 2nd non-central atom (value c in the Shake Atoms section).
+</P>
+<P>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
+the central atom and the first non-central atom (value b in the Shake
+Atoms section), b = bondtype of the bond between the central atom and
+the 2nd non-central atom (value c in the Shake Atoms section), and c =
+bondtype of the bond between the central atom and the 3rd non-central
+atom (value d in the Shake Atoms section).
+</P>
+<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
+of SHAKE clusters.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>,
+<A HREF = "fix_gcmc.html">fix_gcmc</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default keyword value is offset 0 0 0 0 0.
+</P>
+</HTML>
diff --git a/doc/doc2/neb.html b/doc/doc2/neb.html
new file mode 100644
index 000000000..ae2fe0cdb
--- /dev/null
+++ b/doc/doc2/neb.html
@@ -0,0 +1,442 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>neb command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>neb etol ftol N1 N2 Nevery file-style arg
+</PRE>
+<UL><LI>etol = stopping tolerance for energy (energy units)
+
+<LI>ftol = stopping tolerance for force (force units)
+
+<LI>N1 = max # of iterations (timesteps) to run initial NEB
+
+<LI>N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+
+<LI>Nevery = print replica energies and reaction coordinates every this many timesteps
+
+<LI>file-style= <I>final</I> or <I>each</I> or <I>none</I>
+
+<PRE> <I>final</I> arg = filename
+ filename = file with initial coords for final replica
+ coords for intermediate replicas are linearly interpolated between first and last replica
+ <I>each</I> arg = filename
+ filename = unique filename for each replica (except first) with its initial coords
+ <I>none</I> arg = no argument
+ all replicas assumed to already have their initial coords
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>neb 0.1 0.0 1000 500 50 final coords.final
+neb 0.0 0.001 1000 500 50 each coords.initial.$i
+neb 0.0 0.001 1000 500 50 none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform a nudged elastic band (NEB) calculation using multiple
+replicas of a system. Two or more replicas must be used; the first
+and last are the end points of the transition path.
+</P>
+<P>NEB is a method for finding both the atomic configurations and height
+of the energy barrier associated with a transition state, e.g. for an
+atom to perform a diffusive hop from one energy basin to another in a
+coordinated fashion with its neighbors. The implementation in LAMMPS
+follows the discussion in these 3 papers: <A HREF = "#Henkelman1">(Henkelman1)</A>,
+<A HREF = "#Henkelman2">(Henkelman2)</A>, and <A HREF = "#Nakano">(Nakano)</A>.
+</P>
+<P>Each replica runs on a partition of one or more processors. Processor
+partitions are defined at run-time using the -partition command-line
+switch; see <A HREF = "Section_start.html#start_7">Section_start 7</A> of the
+manual. Note that if you have MPI installed, you can run a
+multi-replica simulation with more replicas (partitions) than you have
+physical processors, e.g you can run a 10-replica simulation on just
+one or two processors. You will simply not get the performance
+speed-up you would see with one or more physical processors per
+replica. See <A HREF = "Section_howto.html#howto_5">this section</A> of the manual
+for further discussion.
+</P>
+<P>IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
+there to be one processor per replica.
+</P>
+<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped
+dynamics minimization across all the replicas. The mimimizer uses
+whatever timestep you have defined in your input script, via the
+<A HREF = "timestep.html">timestep</A> command. Often NEB will converge more
+quickly if you use a timestep about 10x larger than you would normally
+use for dynamics simulations.
+</P>
+<P>When a NEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of atoms, the interaction
+potentials, and the starting configuration when the neb command is
+issued should be the same for every replica.
+</P>
+<P>In a NEB calculation each atom in a replica is connected to the same
+atom in adjacent replicas by springs, which induce inter-replica
+forces. These forces are imposed by the <A HREF = "fix_neb.html">fix neb</A>
+command, which must be used in conjunction with the neb command. The
+group used to define the fix neb command defines the NEB atoms which
+are the only ones that inter-replica springs are applied to. If the
+group does not include all atoms, then non-NEB atoms have no
+inter-replica springs and the forces they feel and their motion is
+computed in the usual way due only to other atoms within their
+replica. Conceptually, the non-NEB atoms provide a background force
+field for the NEB atoms. They can be allowed to move during the NEB
+minimiation procedure (which will typically induce different
+coordinates for non-NEB atoms in different replicas), or held fixed
+using other LAMMPS commands such as <A HREF = "fix_setforce">fix setforce</A>. Note
+that the <A HREF = "partition.html">partition</A> command can be used to invoke a
+command on a subset of the replicas, e.g. if you wish to hold NEB or
+non-NEB atoms fixed in only the end-point replicas.
+</P>
+<P>The initial atomic configuration for each of the replicas can be
+specified in different manners via the <I>file-style</I> setting, as
+discussed below. Only atoms whose initial coordinates should differ
+from the current configuration need be specified.
+</P>
+<P>Conceptually, the initial configuration for the first replica should
+be a state with all the atoms (NEB and non-NEB) having coordinates on
+one side of the energy barrier. A perfect energy minimum is not
+required, since atoms in the first replica experience no spring forces
+from the 2nd replica. Thus the damped dynamics minimizaiton will
+drive the first replica to an energy minimum if it is not already
+there. However, you will typically get better convergence if the
+initial state is already at a minimum. For example, for a system with
+a free surface, the surface should be fully relaxed before attempting
+a NEB calculation.
+</P>
+<P>Likewise, the initial configuration of the final replica should be a
+state with all the atoms (NEB and non-NEB) on the other side of the
+energy barrier. Again, a perfect energy minimum is not required,
+since the atoms in the last replica also experience no spring forces
+from the next-to-last replica, and thus the damped dynamics
+minimization will drive it to an energy minimum.
+</P>
+<P>As explained below, the initial configurations of intermediate
+replicas can be atomic coordinates interpolated in a linear fashion
+between the first and last replicas. This is often adequate state for
+simple transitions. For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial configuration. In this case, you will want to
+generate initial states for the intermediate replicas that are
+geometrically closer to the MEP and read them in.
+</P>
+<HR>
+
+<P>For a <I>file-style</I> setting of <I>final</I>, a filename is specified which
+contains atomic coordinates for zero or more atoms, in the format
+described below. For each atom that appears in the file, the new
+coordinates are assigned to that atom in the final replica. Each
+intermediate replica also assigns a new position to that atom in an
+interpolated manner. This is done by using the current position of
+the atom as the starting point and the read-in position as the final
+point. The distance between them is calculated, and the new position
+is assigned to be a fraction of the distance. E.g. if there are 10
+replicas, the 2nd replica will assign a position that is 10% of the
+distance along a line between the starting and final point, and the
+9th replica will assign a position that is 90% of the distance along
+the line. Note that this procedure to produce consistent coordinates
+across all the replicas, the current coordinates need to be the same
+in all replicas. LAMMPS does not check for this, but invalid initial
+configurations will likely result if it is not the case.
+</P>
+<P>NOTE: The "distance" between the starting and final point is
+calculated in a minimum-image sense for a periodic simulation box.
+This means that if the two positions are on opposite sides of a box
+(periodic in that dimension), the distance between them will be small,
+because the periodic image of one of the atoms is close to the other.
+Similarly, even if the assigned position resulting from the
+interpolation is outside the periodic box, the atom will be wrapped
+back into the box when the NEB calculation begins.
+</P>
+<P>For a <I>file-style</I> setting of <I>each</I>, a filename is specified which is
+assumed to be unique to each replica. This can be done by
+using a variable in the filename, e.g.
+</P>
+<PRE>variable i equal part
+neb 0.0 0.001 1000 500 50 each coords.initial.$i
+</PRE>
+<P>which in this case will substitute the partition ID (0 to N-1) for the
+variable I, which is also effectively the replica ID. See the
+<A HREF = "variable.html">variable</A> command for other options, such as using
+world-, universe-, or uloop-style variables.
+</P>
+<P>Each replica (except the first replica) will read its file, formatted
+as described below, and for any atom that appears in the file, assign
+the specified coordinates to its atom. The various files do not need
+to contain the same set of atoms.
+</P>
+<P>For a <I>file-style</I> setting of <I>none</I>, no filename is specified. Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued. This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the <A HREF = "read_data.html">read_data</A>,
+<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "read_dump.html">read_dump</A>
+commands. The replica-specific names of these files can be specified
+as in the discussion above for the <I>each</I> file-style. Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+</P>
+<P>IMPORTANT NOTE: None of the <I>file-style</I> settings change the initial
+configuration of any atom in the first replica. The first replica
+must thus be in the correct initial configuration at the time the neb
+command is issued.
+</P>
+<HR>
+
+<P>A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics. To enable
+this, you must first define a damped dynamics
+<A HREF = "min_style.html">min_style</A>, such as <I>quickmin</I> or <I>fire</I>. The <I>cg</I>,
+<I>sd</I>, and <I>hftn</I> styles cannot be used, since they perform iterative
+line searches in their inner loop, which cannot be easily synchronized
+across multiple replicas.
+</P>
+<P>The minimizer tolerances for energy and force are set by <I>etol</I> and
+<I>ftol</I>, the same as for the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>A non-zero <I>etol</I> means that the NEB calculation will terminate if the
+energy criterion is met by every replica. The energies being compared
+to <I>etol</I> do not include any contribution from the inter-replica
+forces, since these are non-conservative. A non-zero <I>ftol</I> means
+that the NEB calculation will terminate if the force criterion is met
+by every replica. The forces being compared to <I>ftol</I> include the
+inter-replica forces between an atom and its images in adjacent
+replicas.
+</P>
+<P>The maximum number of iterations in each stage is set by <I>N1</I> and
+<I>N2</I>. These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+<A HREF = "run.html">run</A>. During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+<I>Nevery</I> timesteps. The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative distance (normalized
+by the total cumulative distance) between adjacent replicas, where
+"distance" is defined as the length of the 3N-vector of differences in
+atomic coordinates, where N is the number of NEB atoms involved in the
+transition. These outputs allow you to monitor NEB's progress in
+finding a good energy barrier. <I>N1</I> and <I>N2</I> must both be multiples
+of <I>Nevery</I>.
+</P>
+<P>In the first stage of NEB, the set of replicas should converge toward
+the minimum energy path (MEP) of conformational states that transition
+over the barrier. The MEP for a barrier is defined as a sequence of
+3N-dimensional states that cross the barrier at its saddle point, each
+of which has a potential energy gradient parallel to the MEP itself.
+The replica states will also be roughly equally spaced along the MEP
+due to the inter-replica spring force added by the <A HREF = "fix_neb.html">fix
+neb</A> command.
+</P>
+<P>In the second stage of NEB, the replica with the highest energy
+is selected and the inter-replica forces on it are converted to a
+force that drives its atom coordinates to the top or saddle point of
+the barrier, via the barrier-climbing calculation described in
+<A HREF = "#Hinkelman2">(Henkelman2)</A>. As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+</P>
+<P>When both stages are complete, if the NEB calculation was successful,
+one of the replicas should be an atomic configuration at the top or
+saddle point of the barrier, the potential energies for the set of
+replicas should represent the energy profile of the barrier along the
+MEP, and the configurations of the replicas should be a sequence of
+configurations along the MEP.
+</P>
+<HR>
+
+<P>A few other settings in your input script are required or advised to
+perform a NEB calculation. See the IMPORTANT NOTE about the choice of
+timestep at the beginning of this doc page.
+</P>
+<P>An atom map must be defined which it is not by default for <A HREF = "atom_style.html">atom_style
+atomic</A> problems. The <A HREF = "atom_modify.html">atom_modify
+map</A> command can be used to do this.
+</P>
+<P>The "atom_modify sort 0 0.0" command should be used to turn off atom
+sorting.
+</P>
+<P>NOTE: This sorting restriction will be removed in a future version of
+NEB in LAMMPS.
+</P>
+<P>The minimizers in LAMMPS operate on all atoms in your system, even
+non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
+during the minimization, you should use the <A HREF = "fix_setforce.html">fix
+setforce</A> command to set the force on each of those
+atoms to 0.0. This is not required, and may not even be desired in
+some cases, but if those atoms move too far (e.g. because the initial
+state of your system was not well-minimized), it can cause problems
+for the NEB procedure.
+</P>
+<P>The damped dynamics <A HREF = "min_style.html">minimizers</A>, such as <I>quickmin</I>
+and <I>fire</I>), adjust the position and velocity of the atoms via an
+Euler integration step. Thus you must define an appropriate
+<A HREF = "timestep.html">timestep</A> to use with NEB. As mentioned above, NEB
+will often converge more quickly if you use a timestep about 10x
+larger than you would normally use for dynamics simulations.
+</P>
+<HR>
+
+<P>Each file read by the neb command containing atomic coordinates used
+to initialize one or more replicas must be formatted as follows.
+</P>
+<P>The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix). The file can contain initial blank lines or comment lines
+starting with "#" which are ignored. The first non-blank, non-comment
+line should list N = the number of lines to follow. The N successive
+lines contain the following information:
+</P>
+<PRE>ID1 x1 y1 z1
+ID2 x2 y2 z2
+...
+IDN xN yN zN
+</PRE>
+<P>The fields are the the atom ID, followed by the x,y,z coordinates.
+The lines can be listed in any order. Additional trailing information
+on the line is OK, such as a comment.
+</P>
+<P>Note that for a typical NEB calculation you do not need to specify
+initial coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier. Typically only new coordinates for atoms
+geometrically near the barrier need be specified.
+</P>
+<P>Also note there is no requirement that the atoms in the file
+correspond to the NEB atoms in the group defined by the <A HREF = "fix_neb.html">fix
+neb</A> command. Not every NEB atom need be in the file,
+and non-NEB atoms can be listed in the file.
+</P>
+<HR>
+
+<P>Four kinds of output can be generated during a NEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+</P>
+<P>When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every <I>Nevery</I> timesteps. It
+contains the timestep, the maximum force per replica, the maximum
+force per atom (in any replica), potential gradients in the initial,
+ final, and climbing replicas,
+the forward and backward energy barriers,
+the total reaction coordinate (RDT), and
+the normalized reaction coordinate and potential energy of each replica.
+</P>
+<P>The "maximum force per replica" is
+the two-norm of the 3N-length force vector for the atoms in each
+replica, maximized across replicas, which is what the <I>ftol</I> setting
+is checking against. In this case, N is all the atoms in each
+replica. The "maximum force per atom" is the maximum force component
+of any atom in any replica. The potential gradients are the two-norm
+of the 3N-length force vector solely due to the interaction potential i.e.
+without adding in inter-replica forces. Note that inter-replica forces
+are zero in the initial and final replicas, and only affect
+the direction in the climbing replica. For this reason, the "maximum
+force per replica" is often equal to the potential gradient in the
+climbing replica. In the first stage of NEB, there is no climbing
+replica, and so the potential gradient in the highest energy replica
+is reported, since this replica will become the climbing replica
+in the second stage of NEB.
+</P>
+<P>The "reaction coordinate" (RD) for each
+replica is the two-norm of the 3N-length vector of distances between
+its atoms and the preceding replica's atoms, added to the RD of the
+preceding replica. The RD of the first replica RD1 = 0.0;
+the RD of the final replica RDN = RDT, the total reaction coordinate.
+The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence
+from zero to one. When computing RD, N only includes the atoms
+being operated on by the fix neb command.
+</P>
+<P>The forward (reverse) energy barrier is the potential energy of the highest
+replica minus the energy of the first (last) replica.
+</P>
+<P>When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
+NEB calculation, these contain the thermodynamic output for each
+replica.
+</P>
+<P>If <A HREF = "dump.html">dump</A> commands in the input script define a filename
+that includes a <I>universe</I> or <I>uloop</I> style <A HREF = "variable.html">variable</A>,
+then one dump file (per dump command) will be created for each
+replica. At the end of the NEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier. Earlier snapshots will show the
+convergence of the replicas to the MEP.
+</P>
+<P>Likewise, <A HREF = "restart.html">restart</A> filenames can be specified with a
+<I>universe</I> or <I>uloop</I> style <A HREF = "variable.html">variable</A>, to generate
+restart files for each replica. These may be useful if the NEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+</P>
+<P>There are 2 Python scripts provided in the tools/python directory,
+neb_combine.py and neb_final.py, which are useful in analyzing output
+from a NEB calculation. Assume a NEB simulation with M replicas, and
+the NEB atoms labelled with a specific atom type.
+</P>
+<P>The neb_combine.py script extracts atom coords for the NEB atoms from
+all M dump files and creates a single dump file where each snapshot
+contains the NEB atoms from all the replicas and one copy of non-NEB
+atoms from the first replica (presumed to be identical in other
+replicas). This can be visualized/animated to see how the NEB atoms
+relax as the NEB calculation proceeds.
+</P>
+<P>The neb_final.py script extracts the final snapshot from each of the M
+dump files to create a single dump file with M snapshots. This can be
+visualized to watch the system make its transition over the energy
+barrier.
+</P>
+<P>To illustrate, here are images from the final snapshot produced by the
+neb_combine.py script run on the dump files produced by the two
+example input scripts in examples/neb. Click on them to see a larger
+image.
+</P>
+<A HREF = "JPG/hop1.jpg"><IMG SRC = "JPG/hop1_small.jpg"></A>
+
+<A HREF = "JPG/hop2.jpg"><IMG SRC = "JPG/hop2_small.jpg"></A>
+
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "prd.html">prd</A>, <A HREF = "temper.html">temper</A>, <A HREF = "fix_langevin.html">fix
+langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Henkelman1"></A>
+
+<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
+</P>
+<A NAME = "Henkelman2"></A>
+
+<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
+</P>
+<A NAME = "Nakano"></A>
+
+<P><B>(Nakano)</B> Nakano, Comp Phys Comm, 178, 280-289 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/neigh_modify.html b/doc/doc2/neigh_modify.html
new file mode 100644
index 000000000..38e8f15f6
--- /dev/null
+++ b/doc/doc2/neigh_modify.html
@@ -0,0 +1,219 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>neigh_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>neigh_modify keyword values ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be listed
+
+<PRE>keyword = <I>delay</I> or <I>every</I> or <I>check</I> or <I>once</I> or <I>cluster</I> or <I>include</I> or <I>exclude</I> or <I>page</I> or <I>one</I> or <I>binsize</I>
+ <I>delay</I> value = N
+ N = delay building until this many steps since last build
+ <I>every</I> value = M
+ M = build neighbor list every this many steps
+ <I>check</I> value = <I>yes</I> or <I>no</I>
+ <I>yes</I> = only build if some atom has moved half the skin distance or more
+ <I>no</I> = always build on 1st step that <I>every</I> and <I>delay</I> are satisfied
+ <I>once</I>
+ <I>yes</I> = only build neighbor list once at start of run and never rebuild
+ <I>no</I> = rebuild neighbor list according to other settings
+ <I>cluster</I>
+ <I>yes</I> = check bond,angle,etc neighbor list for nearby clusters
+ <I>no</I> = do not check bond,angle,etc neighbor list for nearby clusters
+ <I>include</I> value = group-ID
+ group-ID = only build pair neighbor lists for atoms in this group
+ <I>exclude</I> values:
+ type M N
+ M,N = exclude if one atom in pair is type M, other is type N
+ group group1-ID group2-ID
+ group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
+ molecule group-ID
+ groupname = exclude if both atoms are in the same molecule and in the same group
+ none
+ delete all exclude settings
+ <I>page</I> value = N
+ N = number of pairs stored in a single neighbor page
+ <I>one</I> value = N
+ N = max number of neighbors of one atom
+ <I>binsize</I> value = size
+ size = bin size for neighbor list construction (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>neigh_modify every 2 delay 10 check yes page 100000
+neigh_modify exclude type 2 3
+neigh_modify exclude group frozen frozen check no
+neigh_modify exclude group residue1 chain3
+neigh_modify exclude molecule rigid
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets parameters that affect the building and use of
+pairwise neighbor lists. Depending on what pair interactions and
+other commands are defined, a simulation may require one or more
+neighbor lists.
+</P>
+<P>The <I>every</I>, <I>delay</I>, <I>check</I>, and <I>once</I> options affect how often
+lists are built as a simulation runs. The <I>delay</I> setting means never
+build new lists until at least N steps after the previous build. The
+<I>every</I> setting means build lists every M steps (after the delay has
+passed). If the <I>check</I> setting is <I>no</I>, the lists are built on the
+first step that satisfies the <I>delay</I> and <I>every</I> settings. If the
+<I>check</I> setting is <I>yes</I>, then the <I>every</I> and <I>delay</I> settings
+determine when a build may possibly be performed, but an actual build
+only occurs if some atom has moved more than half the skin distance
+(specified in the <A HREF = "neighbor.html">neighbor</A> command) since the last
+build.
+</P>
+<P>If the <I>once</I> setting is yes, then the neighbor list is only built
+once at the beginning of each run, and never rebuilt, except on steps
+when a restart file is written, or steps when a fix forces a rebuild
+to occur (e.g. fixes that create or delete atoms, such as <A HREF = "fix_deposit.html">fix
+deposit</A> or <A HREF = "fix_evaporate.html">fix evaporate</A>).
+This setting should only be made if you are certain atoms will not
+move far enough that the neighbor list should be rebuilt, e.g. running
+a simulation of a cold crystal. Note that it is not that expensive to
+check if neighbor lists should be rebuilt.
+</P>
+<P>When the rRESPA integrator is used (see the <A HREF = "run_style.html">run_style</A>
+command), the <I>every</I> and <I>delay</I> parameters refer to the longest
+(outermost) timestep.
+</P>
+<P>The <I>cluster</I> option does a sanity test every time neighbor lists are
+built for bond, angle, dihedral, and improper interactions, to check
+that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It
+does this by computing the distance between pairs of atoms in the
+interaction and insuring they are not further apart than half the
+periodic box length. If they are, an error is generated, since the
+interaction would be computed between far-away atoms instead of their
+nearby periodic images. The only way this should happen is if the
+pairwise cutoff is so short that atoms that are part of the same
+interaction are not communicated as ghost atoms. This is an unusual
+model (e.g. no pair interactions at all) and the problem can be fixed
+by use of the <A HREF = "comm_modify.html">comm_modify cutoff</A> command. Note
+that to save time, the default <I>cluster</I> setting is <I>no</I>, so that this
+check is not performed.
+</P>
+<P>The <I>include</I> option limits the building of pairwise neighbor lists to
+atoms in the specified group. This can be useful for models where a
+large portion of the simulation is particles that do not interact with
+other particles or with each other via pairwise interactions. The
+group specified with this option must also be specified via the
+<A HREF = "atom_modify.html">atom_modify first</A> command.
+</P>
+<P>The <I>exclude</I> option turns off pairwise interactions between certain
+pairs of atoms, by not including them in the neighbor list. These are
+sample scenarios where this is useful:
+</P>
+<UL><LI>In crack simulations, pairwise interactions can be shut off between 2
+slabs of atoms to effectively create a crack.
+
+<LI>When a large collection of atoms is treated as frozen, interactions
+between those atoms can be turned off to save needless
+computation. E.g. Using the <A HREF = "fix_setforce.html">fix setforce</A> command
+to freeze a wall or portion of a bio-molecule.
+
+<LI>When one or more rigid bodies are specified, interactions within each
+body can be turned off to save needless computation. See the <A HREF = "fix_rigid.html">fix
+rigid</A> command for more details.
+</UL>
+<P>The <I>exclude type</I> option turns off the pairwise interaction if one
+atom is of type M and the other of type N. M can equal N. The
+<I>exclude group</I> option turns off the interaction if one atom is in the
+first group and the other is the second. Group1-ID can equal
+group2-ID. The <I>exclude molecule</I> option turns off the interaction if
+both atoms are in the specified group and in the same molecule, as
+determined by their molecule ID.
+</P>
+<P>Each of the exclude options can be specified multiple times. The
+<I>exclude type</I> option is the most efficient option to use; it requires
+only a single check, no matter how many times it has been specified.
+The other exclude options are more expensive if specified multiple
+times; they require one check for each time they have been specified.
+</P>
+<P>Note that the exclude options only affect pairwise interactions; see
+the <A HREF = "delete_bonds.html">delete_bonds</A> command for information on
+turning off bond interactions.
+</P>
+<P>IMPORTANT NOTE: Excluding pairwise interactions will not work
+correctly when also using a long-range solver via the
+<A HREF = "kspace_style.html">kspace_style</A> command. LAMMPS will give a warning
+to this effect. This is because the short-range pairwise interaction
+needs to subtract off a term from the total energy for pairs whose
+short-range interaction is excluded, to compensate for how the
+long-range solver treats the interaction. This is done correctly for
+pairwise interactions that are excluded (or weighted) via the
+<A HREF = "special_bonds.html">special_bonds</A> command. But it is not done for
+interactions that are excluded via these neigh_modify exclude options.
+</P>
+<P>The <I>page</I> and <I>one</I> options affect how memory is allocated for the
+neighbor lists. For most simulations the default settings for these
+options are fine, but if a very large problem is being run or a very
+long cutoff is being used, these parameters can be tuned. The indices
+of neighboring atoms are stored in "pages", which are allocated one
+after another as they fill up. The size of each page is set by the
+<I>page</I> value. A new page is allocated when the next atom's neighbors
+could potentially overflow the list. This threshold is set by the
+<I>one</I> value which tells LAMMPS the maximum number of neighbor's one
+atom can have.
+</P>
+<P>IMPORTANT NOTE: LAMMPS can crash without an error message if the
+number of neighbors for a single particle is larger than the <I>page</I>
+setting, which means it is much, much larger than the <I>one</I> setting.
+This is because LAMMPS doesn't error check these limits for every
+pairwise interaction (too costly), but only after all the particle's
+neighbors have been found. This problem usually means something is
+very wrong with the way you've setup your problem (particle spacing,
+cutoff length, neighbor skin distance, etc). If you really expect
+that many neighbors per particle, then boost the <I>one</I> and <I>page</I>
+settings accordingly.
+</P>
+<P>The <I>binsize</I> option allows you to specify what size of bins will be
+used in neighbor list construction to sort and find neighboring atoms.
+By default, for <A HREF = "neighbor.html">neighbor style bin</A>, LAMMPS uses bins
+that are 1/2 the size of the maximum pair cutoff. For <A HREF = "neighbor.html">neighbor style
+multi</A>, the bins are 1/2 the size of the minimum pair
+cutoff. Typically these are good values values for minimizing the
+time for neighbor list construction. This setting overrides the
+default. If you make it too big, there is little overhead due to
+looping over bins, but more atoms are checked. If you make it too
+small, the optimal number of atoms is checked, but bin overhead goes
+up. If you set the binsize to 0.0, LAMMPS will use the default
+binsize of 1/2 the cutoff.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>If the "delay" setting is non-zero, then it must be a multiple of the
+"every" setting.
+</P>
+<P>The exclude molecule option can only be used with atom styles that
+define molecule IDs.
+</P>
+<P>The value of the <I>page</I> setting must be at least 10x larger than the
+<I>one</I> setting. This insures neighbor pages are not mostly empty
+space.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "neighbor.html">neighbor</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are delay = 10, every = 1, check = yes, once = no,
+cluster = no, include = all, exclude = none, page = 100000, one =
+2000, and binsize = 0.0.
+</P>
+</HTML>
diff --git a/doc/doc2/neighbor.html b/doc/doc2/neighbor.html
new file mode 100644
index 000000000..9618531ee
--- /dev/null
+++ b/doc/doc2/neighbor.html
@@ -0,0 +1,88 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>neighbor command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>neighbor skin style
+</PRE>
+<UL><LI>skin = extra distance beyond force cutoff (distance units)
+<LI>style = <I>bin</I> or <I>nsq</I> or <I>multi</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>neighbor 0.3 bin
+neighbor 2.0 nsq
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets parameters that affect the building of pairwise
+neighbor lists. All atom pairs within a neighbor cutoff distance
+equal to the their force cutoff plus the <I>skin</I> distance are stored in
+the list. Typically, the larger the skin distance, the less often
+neighbor lists need to be built, but more pairs must be checked for
+possible force interactions every timestep. The default value for
+<I>skin</I> depends on the choice of units for the simulation; see the
+default values below.
+</P>
+<P>The <I>skin</I> distance is also used to determine how often atoms migrate
+to new processors if the <I>check</I> option of the
+<A HREF = "neigh_modify.html">neigh_modify</A> command is set to <I>yes</I>. Atoms are
+migrated (communicated) to new processors on the same timestep that
+neighbor lists are re-built.
+</P>
+<P>The <I>style</I> value selects what algorithm is used to build the list.
+The <I>bin</I> style creates the list by binning which is an operation that
+scales linearly with N/P, the number of atoms per processor where N =
+total number of atoms and P = number of processors. It is almost
+always faster than the <I>nsq</I> style which scales as (N/P)^2. For
+unsolvated small molecules in a non-periodic box, the <I>nsq</I> choice can
+sometimes be faster. Either style should give the same answers.
+</P>
+<P>The <I>multi</I> style is a modified binning algorithm that is useful for
+systems with a wide range of cutoff distances, e.g. due to different
+size particles. For the <I>bin</I> style, the bin size is set to 1/2 of
+the largest cutoff distance between any pair of atom types and a
+single set of bins is defined to search over for all atom types. This
+can be inefficient if one pair of types has a very long cutoff, but
+other type pairs have a much shorter cutoff. For style <I>multi</I> the
+bin size is set to 1/2 of the shortest cutoff distance and multiple
+sets of bins are defined to search over for different atom types.
+This imposes some extra setup overhead, but the searches themselves
+may be much faster for the short-cutoff cases. See the <A HREF = "comm_modify.html">comm_modify
+mode multi</A> command for a communication option option
+that may also be beneficial for simulations of this kind.
+</P>
+<P>The <A HREF = "neigh_modify.html">neigh_modify</A> command has additional options
+that control how often neighbor lists are built and which pairs are
+stored in the list.
+</P>
+<P>When a run is finished, counts of the number of neighbors stored in
+the pairwise list and the number of times neighbor lists were built
+are printed to the screen and log file. See <A HREF = "Section_start.html#start_8">this
+section</A> for details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "units.html">units</A>,
+<A HREF = "cmom_modify.html">comm_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+0.3 bin for units = lj, skin = 0.3 sigma<BR>
+2.0 bin for units = real or metal, skin = 2.0 Angstroms<BR>
+0.001 bin for units = si, skin = 0.001 meters = 1.0 mm<BR>
+0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm <BR>
+
+</HTML>
diff --git a/doc/doc2/newton.html b/doc/doc2/newton.html
new file mode 100644
index 000000000..94e20608e
--- /dev/null
+++ b/doc/doc2/newton.html
@@ -0,0 +1,67 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>newton command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>newton flag
+newton flag1 flag2
+</PRE>
+<UL><LI>flag = <I>on</I> or <I>off</I> for both pairwise and bonded interactions
+<LI>flag1 = <I>on</I> or <I>off</I> for pairwise interactions
+<LI>flag2 = <I>on</I> or <I>off</I> for bonded interactions
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>newton off
+newton on off
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command turns Newton's 3rd law <I>on</I> or <I>off</I> for pairwise and
+bonded interactions. For most problems, setting Newton's 3rd law to
+<I>on</I> means a modest savings in computation at the cost of two times
+more communication. Whether this is faster depends on problem size,
+force cutoff lengths, a machine's compute/communication ratio, and how
+many processors are being used.
+</P>
+<P>Setting the pairwise newton flag to <I>off</I> means that if two
+interacting atoms are on different processors, both processors compute
+their interaction and the resulting force information is not
+communicated. Similarly, for bonded interactions, newton <I>off</I> means
+that if a bond, angle, dihedral, or improper interaction contains
+atoms on 2 or more processors, the interaction is computed by each
+processor.
+</P>
+<P>LAMMPS should produce the same answers for any newton flag settings,
+except for round-off issues.
+</P>
+<P>With <A HREF = "run_style.html">run_style</A> <I>respa</I> and only bonded interactions
+(bond, angle, etc) computed in the innermost timestep, it may be
+faster to turn newton <I>off</I> for bonded interactions, to avoid extra
+communication in the innermost loop.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The newton bond setting cannot be changed after the simulation box is
+defined by a <A HREF = "read_data.html">read_data</A> or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "run_style.html">run_style</A> respa
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>newton on
+</PRE>
+</HTML>
diff --git a/doc/doc2/next.html b/doc/doc2/next.html
new file mode 100644
index 000000000..ed8effb53
--- /dev/null
+++ b/doc/doc2/next.html
@@ -0,0 +1,148 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>next command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>next variables
+</PRE>
+<UL><LI>variables = one or more variable names
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>next x
+next a t x myTemp
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command is used with variables defined by the
+<A HREF = "variable.html">variable</A> command. It assigns the next value to the
+variable from the list of values defined for that variable by the
+<A HREF = "variable.html">variable</A> command. Thus when that variable is
+subsequently substituted for in an input script command, the new value
+is used.
+</P>
+<P>See the <A HREF = "variable.html">variable</A> command for info on how to define and
+use different kinds of variables in LAMMPS input scripts. If a
+variable name is a single lower-case character from "a" to "z", it can
+be used in an input script command as $a or $z. If it is multiple
+letters, it can be used as ${myTemp}.
+</P>
+<P>If multiple variables are used as arguments to the <I>next</I> command,
+then all must be of the same variable style: <I>index</I>, <I>loop</I>, <I>file</I>,
+<I>universe</I>, or <I>uloop</I>. An exception is that <I>universe</I>- and
+<I>uloop</I>-style variables can be mixed in the same <I>next</I> command.
+</P>
+<P>All the variables specified with the next command are incremented by
+one value from their respective list of values. A <I>file</I>-style
+variable reads the next line from its associated file. An
+<I>atomfile</I>-style variable reads the next set of lines (one per atom)
+from its associated file. <I>String-</I> or <I>atom</I>- or <I>equal</I>- or
+<I>world</I>-style variables cannot be used with the the next command,
+since they only store a single value.
+</P>
+<P>When any of the variables in the next command has no more values, a
+flag is set that causes the input script to skip the next
+<A HREF = "jump.html">jump</A> command encountered. This enables a loop containing
+a next command to exit. As explained in the <A HREF = "variable.html">variable</A>
+command, the variable that has exhausted its values is also deleted.
+This allows it to be used and re-defined later in the input script.
+<I>File</I>-style and <I>atomfile</I>-style variables are exhausted when the
+end-of-file is reached.
+</P>
+<P>When the next command is used with <I>index</I>- or <I>loop</I>-style variables,
+the next value is assigned to the variable for all processors. When
+the next command is used with <I>file</I>-style variables, the next line is
+read from its file and the string assigned to the variable. When the
+next command is used with <I>atomfile</I>-style variables, the next set of
+per-atom values is read from its file and assigned to the variable.
+</P>
+<P>When the next command is used with <I>universe</I>- or <I>uloop</I>-style
+variables, all <I>universe</I>- or <I>uloop</I>-style variables must be listed
+in the next command. This is because of the manner in which the
+incrementing is done, using a single lock file for all variables. The
+next value (for each variable) is assigned to whichever processor
+partition executes the command first. All processors in the partition
+are assigned the same value(s). Running LAMMPS on multiple partitions
+of processors via the "-partition" command-line switch is described in
+<A HREF = "Section_start.html#start_7">this section</A> of the manual. <I>Universe</I>-
+and <I>uloop</I>-style variables are incremented using the files
+"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
+see in your directory during and after such a LAMMPS run.
+</P>
+<P>Here is an example of running a series of simulations using the next
+command with an <I>index</I>-style variable. If this input script is named
+in.polymer, 8 simulations would be run using data files from
+directories run1 thru run8.
+</P>
+<PRE>variable d index run1 run2 run3 run4 run5 run6 run7 run8
+shell cd $d
+read_data data.polymer
+run 10000
+shell cd ..
+clear
+next d
+jump in.polymer
+</PRE>
+<P>If the variable "d" were of style <I>universe</I>, and the same in.polymer
+input script were run on 3 partitions of processors, then the first 3
+simulations would begin, one on each set of processors. Whichever
+partition finished first, it would assign variable "d" the 4th value
+and run another simulation, and so forth until all 8 simulations were
+finished.
+</P>
+<P>Jump and next commands can also be nested to enable multi-level loops.
+For example, this script will run 15 simulations in a double loop.
+</P>
+<PRE>variable i loop 3
+ variable j loop 5
+ clear
+ ...
+ read_data data.polymer.$i$j
+ print Running simulation $i.$j
+ run 10000
+ next j
+ jump in.script
+next i
+jump in.script
+</PRE>
+<P>Here is an example of a double loop which uses the <A HREF = "if.html">if</A> and
+<A HREF = "jump.html">jump</A> commands to break out of the inner loop when a
+condition is met, then continues iterating thru the outer loop.
+</P>
+<PRE>label loopa
+variable a loop 5
+ label loopb
+ variable b loop 5
+ print "A,B = $a,$b"
+ run 10000
+ if $b > 2 then "jump in.script break"
+ next b
+ jump in.script loopb
+label break
+variable b delete
+</PRE>
+<PRE>next a
+jump in.script loopa
+</PRE>
+<P><B>Restrictions:</B>
+</P>
+<P>As described above.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "jump.html">jump</A>, <A HREF = "include.html">include</A>, <A HREF = "shell.html">shell</A>,
+<A HREF = "variable.html">variable</A>,
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/package.html b/doc/doc2/package.html
new file mode 100644
index 000000000..5c0dd866d
--- /dev/null
+++ b/doc/doc2/package.html
@@ -0,0 +1,666 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>package command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>package style args
+</PRE>
+<UL><LI>style = <I>cuda</I> or <I>gpu</I> or <I>intel</I> or <I>kokkos</I> or <I>omp</I>
+
+<LI>args = arguments specific to the style
+
+<PRE> <I>cuda</I> args = Ngpu keyword value ...
+ Ngpu = # of GPUs per node
+ zero or more keyword/value pairs may be appended
+ keywords = <I>newton</I> or <I>gpuID</I> or <I>timing</I> or <I>test</I> or <I>thread</I>
+ <I>newton</I> = <I>off</I> or <I>on</I>
+ off = set Newton pairwise and bonded flags off (default)
+ on = set Newton pairwise and bonded flags on
+ <I>gpuID</I> values = gpu1 .. gpuN
+ gpu1 .. gpuN = IDs of the Ngpu GPUs to use
+ <I>timing</I> values = none
+ <I>test</I> values = id
+ id = atom-ID of a test particle
+ <I>thread</I> = auto or tpa or bpa
+ auto = test whether tpa or bpa is faster
+ tpa = one thread per atom
+ bpa = one block per atom
+ <I>gpu</I> args = Ngpu keyword value ...
+ Ngpu = # of GPUs per node
+ zero or more keyword/value pairs may be appended
+ keywords = <I>neigh</I> or <I>newton</I> or <I>binsize</I> or <I>split</I> or <I>gpuID</I> or <I>tpa</I> or <I>device</I>
+ <I>neigh</I> value = <I>yes</I> or <I>no</I>
+ yes = neighbor list build on GPU (default)
+ no = neighbor list build on CPU
+ <I>newton</I> = <I>off</I> or <I>on</I>
+ off = set Newton pairwise flag off (default and required)
+ on = set Newton pairwise flag on (currently not allowed)
+ <I>binsize</I> value = size
+ size = bin size for neighbor list construction (distance units)
+ <I>split</I> = fraction
+ fraction = fraction of atoms assigned to GPU (default = 1.0)
+ <I>gpuID</I> values = first last
+ first = ID of first GPU to be used on each node
+ last = ID of last GPU to be used on each node
+ <I>tpa</I> value = Nthreads
+ Nthreads = # of GPU threads used per atom
+ <I>device</I> value = device_type
+ device_type = <I>kepler</I> or <I>fermi</I> or <I>cypress</I> or <I>generic</I>
+ <I>intel</I> args = NPhi keyword value ...
+ Nphi = # of coprocessors per node
+ zero or more keyword/value pairs may be appended
+ keywords = <I>omp</I> or <I>mode</I> or <I>balance</I> or <I>ghost</I> or <I>tpc</I> or <I>tptask</I> or <I>no_affinity</I>
+ <I>omp</I> value = Nthreads
+ Nthreads = number of OpenMP threads to use on CPU (default = 0)
+ <I>mode</I> value = <I>single</I> or <I>mixed</I> or <I>double</I>
+ single = perform force calculations in single precision
+ mixed = perform force calculations in mixed precision
+ double = perform force calculations in double precision
+ <I>balance</I> value = split
+ split = fraction of work to offload to coprocessor, -1 for dynamic
+ <I>ghost</I> value = <I>yes</I> or <I>no</I>
+ yes = include ghost atoms for offload
+ no = do not include ghost atoms for offload
+ <I>tpc</I> value = Ntpc
+ Ntpc = max number of coprocessor threads per coprocessor core (default = 4)
+ <I>tptask</I> value = Ntptask
+ Ntptask = max number of coprocessor threads per MPI task (default = 240)
+ <I>no_affinity</I> values = none
+ <I>kokkos</I> args = keyword value ...
+ zero or more keyword/value pairs may be appended
+ keywords = <I>neigh</I> or <I>newton</I> or <I>binsize</I> or <I>comm</I> or <I>comm/exchange</I> or <I>comm/forward</I>
+ <I>neigh</I> value = <I>full</I> or <I>half/thread</I> or <I>half</I> or <I>n2</I> or <I>full/cluster</I>
+ full = full neighbor list
+ half/thread = half neighbor list built in thread-safe manner
+ half = half neighbor list, not thread-safe, only use when 1 thread/MPI task
+ n2 = non-binning neighbor list build, O(N^2) algorithm
+ full/cluster = full neighbor list with clustered groups of atoms
+ <I>newton</I> = <I>off</I> or <I>on</I>
+ off = set Newton pairwise and bonded flags off (default)
+ on = set Newton pairwise and bonded flags on
+ <I>binsize</I> value = size
+ size = bin size for neighbor list construction (distance units)
+ <I>comm</I> value = <I>no</I> or <I>host</I> or <I>device</I>
+ use value for both comm/exchange and comm/forward
+ <I>comm/exchange</I> value = <I>no</I> or <I>host</I> or <I>device</I>
+ <I>comm/forward</I> value = <I>no</I> or <I>host</I> or <I>device</I>
+ no = perform communication pack/unpack in non-KOKKOS mode
+ host = perform pack/unpack on host (e.g. with OpenMP threading)
+ device = perform pack/unpack on device (e.g. on GPU)
+ <I>omp</I> args = Nthreads keyword value ...
+ Nthread = # of OpenMP threads to associate with each MPI process
+ zero or more keyword/value pairs may be appended
+ keywords = <I>neigh</I>
+ <I>neigh</I> value = <I>yes</I> or <I>no</I>
+ yes = threaded neighbor list build (default)
+ no = non-threaded neighbor list build
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>package gpu 1
+package gpu 1 split 0.75
+package gpu 2 split -1.0
+package cuda 2 gpuID 0 2
+package cuda 1 test 3948
+package kokkos neigh half/thread comm device
+package omp 0 neigh no
+package omp 4
+package intel 1
+package intel 2 omp 4 mode mixed balance 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command invokes package-specific settings for the various
+accelerator packages available in LAMMPS. Currently the following
+packages use settings from this command: USER-CUDA, GPU, USER-INTEL,
+KOKKOS, and USER-OMP.
+</P>
+<P>If this command is specified in an input script, it must be near the
+top of the script, before the simulation box has been defined. This
+is because it specifies settings that the accelerator packages use in
+their intialization, before a simultion is defined.
+</P>
+<P>This command can also be specified from the command-line when
+launching LAMMPS, using the "-pk" <A HREF = "Section_start.html#start_7">command-line
+switch</A>. The syntax is exactly the same as
+when used in an input script.
+</P>
+<P>Note that all of the accelerator packages require the package command
+to be specified (except the OPT package), if the package is to be used
+in a simulation (LAMMPS can be built with an accelerator package
+without using it in a particular simulation). However, in all cases,
+a default version of the command is typically invoked by other
+accelerator settings.
+</P>
+<P>The USER-CUDA and KOKKOS packages require a "-c on" or "-k on"
+<A HREF = "Section_start.html#start_7">command-line switch</A> respectively, which
+invokes a "package cuda" or "package kokkos" command with default
+settings.
+</P>
+<P>For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
+intel" or "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A>
+is used to auto-append accelerator suffixes to various styles in the
+input script, then those switches also invoke a "package gpu",
+"package intel", or "package omp" command with default settings.
+</P>
+<P>IMPORTANT NOTE: A package command for a particular style can be
+invoked multiple times when a simulation is setup, e.g. by the "-c
+on", "-k on", "-sf", and "-pk" <A HREF = "Section_start.html#start_7">command-line
+switches</A>, and by using this command in an
+input script. Each time it is used all of the style options are set,
+either to default values or to specified settings. I.e. settings from
+previous invocations do not persist across multiple invocations.
+</P>
+<P>See the <A HREF = "Section_accelerate.html">Section Accelerate</A> section of the
+manual for more details about using the various accelerator packages
+for speeding up LAMMPS simulations.
+</P>
+<HR>
+
+<P>The <I>cuda</I> style invokes settings associated with the use of the
+USER-CUDA package.
+</P>
+<P>The <I>Ngpus</I> argument sets the number of GPUs per node. There must be
+exactly one MPI task per GPU, as set by the mpirun or mpiexec command.
+</P>
+<P>Optional keyword/value pairs can also be specified. Each has a
+default value as listed below.
+</P>
+<P>The <I>newton</I> keyword sets the Newton flags for pairwise and bonded
+interactions to <I>off</I> or <I>on</I>, the same as the <A HREF = "newton.html">newton</A>
+command allows. The default is <I>off</I> because this will almost always
+give better performance for the USER-CUDA package. This means
+more computation is done, but less communication.
+</P>
+<P>The <I>gpuID</I> keyword allows selection of which GPUs on each node will
+be used for a simulation. GPU IDs range from 0 to N-1 where N is the
+physical number of GPUs/node. An ID is specified for each of the
+Ngpus being used. For example if you have three GPUs on a machine,
+one of which is used for the X-Server (the GPU with the ID 1) while
+the others (with IDs 0 and 2) are used for computations you would
+specify:
+</P>
+<PRE>package cuda 2 gpuID 0 2
+</PRE>
+<P>The purpose of the <I>gpuID</I> keyword is to allow two (or more)
+simulations to be run on one workstation. In that case one could set
+the first simulation to use GPU 0 and the second to use GPU 1. This is
+not necessary however, if the GPUs are in what is called <I>compute
+exclusive</I> mode. Using that setting, every process will get its own
+GPU automatically. This <I>compute exclusive</I> mode can be set as root
+using the <I>nvidia-smi</I> tool which is part of the CUDA installation.
+</P>
+<P>Also note that if the <I>gpuID</I> keyword is not used, the USER-CUDA
+package sorts existing GPUs on each node according to their number of
+multiprocessors. This way, compute GPUs will be priorized over
+X-Server GPUs.
+</P>
+<P>If the <I>timing</I> keyword is specified, detailed timing information for
+various subroutines will be output.
+</P>
+<P>If the <I>test</I> keyword is specified, information for the specified atom
+with atom-ID will be output at several points during each timestep.
+This is mainly usefull for debugging purposes. Note that the
+simulation slow down dramatically if this option is used.
+</P>
+<P>The <I>thread</I> keyword can be used to specify how GPU threads are
+assigned work during pair style force evaluation. If the value =
+<I>tpa</I>, one thread per atom is used. If the value = <I>bpa</I>, one block
+per atom is used. If the value = <I>auto</I>, a short test is performed at
+the beginning of each run to determing where <I>tpa</I> or <I>bpa</I> mode is
+faster. The result of this test is output. Since <I>auto</I> is the
+default value, it is usually not necessary to use this keyword.
+</P>
+<HR>
+
+<P>The <I>gpu</I> style invokes settings associated with the use of the GPU
+package.
+</P>
+<P>The <I>Ngpu</I> argument sets the number of GPUs per node. There must be
+at least as many MPI tasks per node as GPUs, as set by the mpirun or
+mpiexec command. If there are more MPI tasks (per node)
+than GPUs, multiple MPI tasks will share each GPU.
+</P>
+<P>Optional keyword/value pairs can also be specified. Each has a
+default value as listed below.
+</P>
+<P>The <I>neigh</I> keyword specifies where neighbor lists for pair style
+computation will be built. If <I>neigh</I> is <I>yes</I>, which is the default,
+neighbor list building is performed on the GPU. If <I>neigh</I> is <I>no</I>,
+neighbor list building is performed on the CPU. GPU neighbor list
+building currently cannot be used with a triclinic box. GPU neighbor
+list calculation currently cannot be used with
+<A HREF = "pair_hybrid.html">hybrid</A> pair styles. GPU neighbor lists are not
+compatible with comannds that are not GPU-enabled. When a non-GPU
+enabled command requires a neighbor list, it will also be built on the
+CPU. In these cases, it will typically be more efficient to only use
+CPU neighbor list builds.
+</P>
+<P>The <I>newton</I> keyword sets the Newton flags for pairwise (not bonded)
+interactions to <I>off</I> or <I>on</I>, the same as the <A HREF = "newton.html">newton</A>
+command allows. Currently, only an <I>off</I> value is allowed, since all
+the GPU package pair styles require this setting. This means more
+computation is done, but less communication. In the future a value of
+<I>on</I> may be allowed, so the <I>newton</I> keyword is included as an option
+for compatibility with the package command for other accelerator
+styles. Note that the newton setting for bonded interactions is not
+affected by this keyword.
+</P>
+<P>The <I>binsize</I> keyword sets the size of bins used to bin atoms in
+neighbor list builds performed on the GPU, if <I>neigh</I> = <I>yes</I> is set.
+If <I>binsize</I> is set to 0.0 (the default), then bins = the size of the
+pairwise cutoff + neighbor skin distance. This is 2x larger than the
+LAMMPS default used for neighbor list building on the CPU. This will
+be close to optimal for the GPU, so you do not normally need to use
+this keyword. Note that if you use a longer-than-usual pairwise
+cutoff, e.g. to allow for a smaller fraction of KSpace work with a
+<A HREF = "kspace_style.html">long-range Coulombic solver</A> because the GPU is
+faster at performing pairwise interactions, then it may be optimal to
+make the <I>binsize</I> smaller than the default. For example, with a
+cutoff of 20*sigma in LJ <A HREF = "units.html">units</A> and a neighbor skin
+distance of sigma, a <I>binsize</I> = 5.25*sigma can be more efficient than
+the default.
+</P>
+<P>The <I>split</I> keyword can be used for load balancing force calculations
+between CPU and GPU cores in GPU-enabled pair styles. If 0 < <I>split</I> <
+1.0, a fixed fraction of particles is offloaded to the GPU while force
+calculation for the other particles occurs simulataneously on the CPU.
+If <I>split</I> < 0.0, the optimal fraction (based on CPU and GPU timings)
+is calculated every 25 timesteps, i.e. dynamic load-balancing across
+the CPU and GPU is performed. If <I>split</I> = 1.0, all force
+calculations for GPU accelerated pair styles are performed on the GPU.
+In this case, other <A HREF = "pair_hybrid.html">hybrid</A> pair interactions,
+<A HREF = "bond_style.html">bond</A>, <A HREF = "angle_style.html">angle</A>,
+<A HREF = "dihedral_style.html">dihedral</A>, <A HREF = "improper_style.html">improper</A>, and
+<A HREF = "kspace_style.html">long-range</A> calculations can be performed on the
+CPU while the GPU is performing force calculations for the GPU-enabled
+pair style. If all CPU force computations complete before the GPU
+completes, LAMMPS will block until the GPU has finished before
+continuing the timestep.
+</P>
+<P>As an example, if you have two GPUs per node and 8 CPU cores per node,
+and would like to run on 4 nodes (32 cores) with dynamic balancing of
+force calculation across CPU and GPU cores, you could specify
+</P>
+<PRE>mpirun -np 32 -sf gpu -in in.script # launch command
+package gpu 2 split -1 # input script command
+</PRE>
+<P>In this case, all CPU cores and GPU devices on the nodes would be
+utilized. Each GPU device would be shared by 4 CPU cores. The CPU
+cores would perform force calculations for some fraction of the
+particles at the same time the GPUs performed force calculation for
+the other particles.
+</P>
+<P>The <I>gpuID</I> keyword allows selection of which GPUs on each node will
+be used for a simulation. The <I>first</I> and <I>last</I> values specify the
+GPU IDs to use (from 0 to Ngpu-1). By default, first = 0 and last =
+Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
+of physical GPUs. If you only wish to use a subset, set Ngpu to a
+smaller number and first/last to a sub-range of the available GPUs.
+</P>
+<P>The <I>tpa</I> keyword sets the number of GPU thread per atom used to
+perform force calculations. With a default value of 1, the number of
+threads will be chosen based on the pair style, however, the value can
+be set explicitly with this keyword to fine-tune performance. For
+large cutoffs or with a small number of particles per GPU, increasing
+the value can improve performance. The number of threads per atom must
+be a power of 2 and currently cannot be greater than 32.
+</P>
+<P>The <I>device</I> keyword can be used to tune parameters optimized for a
+specific accelerator, when using OpenCL. For CUDA, the <I>device</I>
+keyword is ignored. Currently, the device type is limited to NVIDIA
+Kepler, NVIDIA Fermi, AMD Cypress, or a generic device. More devices
+may be added later. The default device type can be specified when
+building LAMMPS with the GPU library, via settings in the
+lib/gpu/Makefile that is used.
+</P>
+<HR>
+
+<P>The <I>intel</I> style invokes settings associated with the use of the
+USER-INTEL package. All of its settings, except the <I>omp</I> and <I>mode</I>
+keywords, are ignored if LAMMPS was not built with Xeon Phi
+coprocessor support. All of its settings, including the <I>omp</I> and
+<I>mode</I> keyword are applicable if LAMMPS was built with coprocessor
+support.
+</P>
+<P>The <I>Nphi</I> argument sets the number of coprocessors per node.
+This can be set to any value, including 0, if LAMMPS was not
+built with coprocessor support.
+</P>
+<P>Optional keyword/value pairs can also be specified. Each has a
+default value as listed below.
+</P>
+<P>The <I>omp</I> keyword determines the number of OpenMP threads allocated
+for each MPI task when any portion of the interactions computed by a
+USER-INTEL pair style are run on the CPU. This can be the case even
+if LAMMPS was built with coprocessor support; see the <I>balance</I>
+keyword discussion below. If you are running with less MPI tasks/node
+than there are CPUs, it can be advantageous to use OpenMP threading on
+the CPUs.
+</P>
+<P>IMPORTANT NOTE: The <I>omp</I> keyword has nothing to do with coprocessor
+threads on the Xeon Phi; see the <I>tpc</I> and <I>tptask</I> keywords below for
+a discussion of coprocessor threads.
+</P>
+<P>The <I>Nthread</I> value for the <I>omp</I> keyword sets the number of OpenMP
+threads allocated for each MPI task. Setting <I>Nthread</I> = 0 (the
+default) instructs LAMMPS to use whatever value is the default for the
+given OpenMP environment. This is usually determined via the
+<I>OMP_NUM_THREADS</I> environment variable or the compiler runtime, which
+is usually a value of 1.
+</P>
+<P>For more details, including examples of how to set the OMP_NUM_THREADS
+environment variable, see the discussion of the <I>Nthreads</I> setting on
+this doc page for the "package omp" command. Nthreads is a required
+argument for the USER-OMP package. Its meaning is exactly the same
+for the USER-INTEL pacakge.
+</P>
+<P>IMPORTANT NOTE: If you build LAMMPS with both the USER-INTEL and
+USER-OMP packages, be aware that both packages allow setting of the
+<I>Nthreads</I> value via their package commands, but there is only a
+single global <I>Nthreads</I> value used by OpenMP. Thus if both package
+commands are invoked, you should insure the two values are consistent.
+If they are not, the last one invoked will take precedence, for both
+packages. Also note that if the "-sf intel" <A HREF = <A HREF = "Section_start.html#start_7">command-line"></A>
+switch</A> is used, it invokes a "package
+intel" command, followed by a "package omp" command, both with a
+setting of <I>Nthreads</I> = 0.
+</P>
+<P>The <I>mode</I> keyword determines the precision mode to use for
+computing pair style forces, either on the CPU or on the coprocessor,
+when using a USER-INTEL supported <A HREF = "pair_style.html">pair style</A>. It
+can take a value of <I>single</I>, <I>mixed</I> which is the default, or
+<I>double</I>. <I>Single</I> means single precision is used for the entire
+force calculation. <I>Mixed</I> means forces between a pair of atoms are
+computed in single precision, but accumulated and stored in double
+precision, including storage of forces, torques, energies, and virial
+quantities. <I>Double</I> means double precision is used for the entire
+force calculation.
+</P>
+<P>The <I>balance</I> keyword sets the fraction of <A HREF = "pair_style.html">pair
+style</A> work offloaded to the coprocessor for split
+values between 0.0 and 1.0 inclusive. While this fraction of work is
+running on the coprocessor, other calculations will run on the host,
+including neighbor and pair calculations that are not offloaded, as
+well as angle, bond, dihedral, kspace, and some MPI communications.
+If <I>split</I> is set to -1, the fraction of work is dynamically adjusted
+automatically throughout the run. This typically give performance
+within 5 to 10 percent of the optimal fixed fraction.
+</P>
+<P>The <I>ghost</I> keyword determines whether or not ghost atoms, i.e. atoms
+at the boundaries of proessor sub-domains, are offloaded for neighbor
+and force calculations. When the value = "no", ghost atoms are not
+offloaded. This option can reduce the amount of data transfer with
+the coprocessor and can also overlap MPI communication of forces with
+computation on the coprocessor when the <A HREF = "newton.html">newton pair</A>
+setting is "on". When the value = "yes", ghost atoms are offloaded.
+In some cases this can provide better performance, especially if the
+<I>balance</I> fraction is high.
+</P>
+<P>The <I>tpc</I> keyword sets the max # of coprocessor threads <I>Ntpc</I> that
+will run on each core of the coprocessor. The default value = 4,
+which is the number of hardware threads per core supported by the
+current generation Xeon Phi chips.
+</P>
+<P>The <I>tptask</I> keyword sets the max # of coprocessor threads (Ntptask</I>
+assigned to each MPI task. The default value = 240, which is the
+total # of threads an entire current generation Xeon Phi chip can run
+(240 = 60 cores * 4 threads/core). This means each MPI task assigned
+to the Phi will enough threads for the chip to run the max allowed,
+even if only 1 MPI task is assigned. If 8 MPI tasks are assigned to
+the Phi, each will run with 30 threads. If you wish to limit the
+number of threads per MPI task, set <I>tptask</I> to a smaller value.
+E.g. for <I>tptask</I> = 16, if 8 MPI tasks are assigned, each will run
+with 16 threads, for a total of 128.
+</P>
+<P>Note that the default settings for <I>tpc</I> and <I>tptask</I> are fine for
+most problems, regardless of how many MPI tasks you assign to a Phi.
+</P>
+<P>The <I>no_affinity</I> keyword will turn off automatic setting of core
+affinity for MPI tasks and OpenMP threads on the host when using
+offload to a coprocessor. Affinity settings are used when possible
+to prevent MPI tasks and OpenMP threads from being on separate NUMA
+domains and to prevent offload threads from interfering with other
+processes/threads used for LAMMPS.
+</P>
+<HR>
+
+<P>The <I>kokkos</I> style invokes settings associated with the use of the
+KOKKOS package.
+</P>
+<P>All of the settings are optional keyword/value pairs. Each has a
+default value as listed below.
+</P>
+<P>The <I>neigh</I> keyword determines how neighbor lists are built. A value
+of <I>half</I> uses half-neighbor lists, the same as used by most pair
+styles in LAMMPS. A value of <I>half/thread</I> uses a thread-safe variant
+of the half-neighbor list. It should be used instead of <I>half</I> when
+running with more than 1 threads per MPI task on a CPU. A value of
+<I>n2</I> uses an O(N^2) algorithm to build the neighbor list without
+binning, where N = # of atoms on a processor. It is typically slower
+than the other methods, which use binning.
+</P>
+<P>A value of <I>full</I> uses a full neighbor lists and is the default. This
+performs twice as much computation as the <I>half</I> option, however that
+is often a win because it is thread-safe and doesn't require atomic
+operations in the calculation of pair forces. For that reason, <I>full</I>
+is the default setting. However, when running in MPI-only mode with 1
+thread per MPI task, <I>half</I> neighbor lists will typically be faster,
+just as it is for non-accelerated pair styles.
+</P>
+<P>A value of <I>full/cluster</I> is an experimental neighbor style, where
+particles interact with all particles within a small cluster, if at
+least one of the clusters particles is within the neighbor cutoff
+range. This potentially allows for better vectorization on
+architectures such as the Intel Phi. If also reduces the size of the
+neighbor list by roughly a factor of the cluster size, thus reducing
+the total memory footprint considerably.
+</P>
+<P>The <I>newton</I> keyword sets the Newton flags for pairwise and bonded
+interactions to <I>off</I> or <I>on</I>, the same as the <A HREF = "newton.html">newton</A>
+command allows. The default is <I>off</I> because this will almost always
+give better performance for the KOKKOS package. This means more
+computation is done, but less communication. However, when running in
+MPI-only mode with 1 thread per MPI task, a value of <I>on</I> will
+typically be faster, just as it is for non-accelerated pair styles.
+</P>
+<P>The <I>binsize</I> keyword sets the size of bins used to bin atoms in
+neighbor list builds. The same value can be set by the <A HREF = "neigh_modify.html">neigh_modify
+binsize</A> command. Making it an option in the
+package kokkos command allows it to be set from the command line. The
+default value is 0.0, which means the LAMMPS default will be used,
+which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
+distance. This is fine when neighbor lists are built on the CPU. For
+GPU builds, a 2x larger binsize equal to the pairwise cutoff +
+neighbor skin, is often faster, which can be set by this keyword.
+Note that if you use a longer-than-usual pairwise cutoff, e.g. to
+allow for a smaller fraction of KSpace work with a <A HREF = "kspace_style.html">long-range
+Coulombic solver</A> because the GPU is faster at
+performing pairwise interactions, then this rule of thumb may give too
+large a binsize.
+</P>
+<P>The <I>comm</I> and <I>comm/exchange</I> and <I>comm/forward</I> keywords determine
+whether the host or device performs the packing and unpacking of data
+when communicating per-atom data between processors. "Exchange"
+communication happens only on timesteps that neighbor lists are
+rebuilt. The data is only for atoms that migrate to new processors.
+"Forward" communication happens every timestep. The data is for atom
+coordinates and any other atom properties that needs to be updated for
+ghost atoms owned by each processor.
+</P>
+<P>The <I>comm</I> keyword is simply a short-cut to set the same value
+for both the <I>comm/exchange</I> and <I>comm/forward</I> keywords.
+</P>
+<P>The value options for all 3 keywords are <I>no</I> or <I>host</I> or <I>device</I>.
+A value of <I>no</I> means to use the standard non-KOKKOS method of
+packing/unpacking data for the communication. A value of <I>host</I> means
+to use the host, typically a multi-core CPU, and perform the
+packing/unpacking in parallel with threads. A value of <I>device</I> means
+to use the device, typically a GPU, to perform the packing/unpacking
+operation.
+</P>
+<P>The optimal choice for these keywords depends on the input script and
+the hardware used. The <I>no</I> value is useful for verifying that the
+Kokkos-based <I>host</I> and <I>device</I> values are working correctly. It may
+also be the fastest choice when using Kokkos styles in MPI-only mode
+(i.e. with a thread count of 1).
+</P>
+<P>When running on CPUs or Xeon Phi, the <I>host</I> and <I>device</I> values work
+identically. When using GPUs, the <I>device</I> value will typically be
+optimal if all of your styles used in your input script are supported
+by the KOKKOS package. In this case data can stay on the GPU for many
+timesteps without being moved between the host and GPU, if you use the
+<I>device</I> value. This requires that your MPI is able to access GPU
+memory directly. Currently that is true for OpenMPI 1.8 (or later
+versions), Mvapich2 1.9 (or later), and CrayMPI. If your script uses
+styles (e.g. fixes) which are not yet supported by the KOKKOS package,
+then data has to be move between the host and device anyway, so it is
+typically faster to let the host handle communication, by using the
+<I>host</I> value. Using <I>host</I> instead of <I>no</I> will enable use of
+multiple threads to pack/unpack communicated data.
+</P>
+<HR>
+
+<P>The <I>omp</I> style invokes settings associated with the use of the
+USER-OMP package.
+</P>
+<P>The <I>Nthread</I> argument sets the number of OpenMP threads allocated for
+each MPI task. For example, if your system has nodes with dual
+quad-core processors, it has a total of 8 cores per node. You could
+use two MPI tasks per node (e.g. using the -ppn option of the mpirun
+command in MPICH or -npernode in OpenMPI), and set <I>Nthreads</I> = 4.
+This would use all 8 cores on each node. Note that the product of MPI
+tasks * threads/task should not exceed the physical number of cores
+(on a node), otherwise performance will suffer.
+</P>
+<P>Setting <I>Nthread</I> = 0 instructs LAMMPS to use whatever value is the
+default for the given OpenMP environment. This is usually determined
+via the <I>OMP_NUM_THREADS</I> environment variable or the compiler
+runtime. Note that in most cases the default for OpenMP capable
+compilers is to use one thread for each available CPU core when
+<I>OMP_NUM_THREADS</I> is not explicitly set, which can lead to poor
+performance.
+</P>
+<P>Here are examples of how to set the environment variable when
+launching LAMMPS:
+</P>
+<PRE>env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
+env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
+mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
+</PRE>
+<P>or you can set it permanently in your shell's start-up script.
+All three of these examples use a total of 4 CPU cores.
+</P>
+<P>Note that different MPI implementations have different ways of passing
+the OMP_NUM_THREADS environment variable to all MPI processes. The
+2nd example line above is for MPICH; the 3rd example line with -x is
+for OpenMPI. Check your MPI documentation for additional details.
+</P>
+<P>What combination of threads and MPI tasks gives the best performance
+is difficult to predict and can depend on many components of your
+input. Not all features of LAMMPS support OpenMP threading via the
+USER-OMP packaage and the parallel efficiency can be very different,
+too.
+</P>
+<P>Optional keyword/value pairs can also be specified. Each has a
+default value as listed below.
+</P>
+<P>The <I>neigh</I> keyword specifies whether neighbor list building will be
+multi-threaded in addition to force calculations. If <I>neigh</I> is set
+to <I>no</I> then neighbor list calculation is performed only by MPI tasks
+with no OpenMP threading. If <I>mode</I> is <I>yes</I> (the default), a
+multi-threaded neighbor list build is used. Using <I>neigh</I> = <I>yes</I> is
+almost always faster and should produce idential neighbor lists at the
+expense of using more memory. Specifically, neighbor list pages are
+allocated for all threads at the same time and each thread works
+within its own pages.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
+</P>
+<P>The cuda style of this command can only be invoked if LAMMPS was built
+with the USER-CUDA package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The gpu style of this command can only be invoked if LAMMPS was built
+with the GPU package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The intel style of this command can only be invoked if LAMMPS was
+built with the USER-INTEL package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The kk style of this command can only be invoked if LAMMPS was built
+with the KOKKOS package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The omp style of this command can only be invoked if LAMMPS was built
+with the USER-OMP package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "suffix.html">suffix</A>, "-pk" <A HREF = "Section_start.html#start_7">command-line
+setting</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>For the USER-CUDA package, the default is Ngpu = 1 and the option
+defaults are newton = off, gpuID = 0 to Ngpu-1, timing = not enabled,
+test = not enabled, and thread = auto. These settings are made
+automatically by the required "-c on" <A HREF = "Section_start.html#start_7">command-line
+switch</A>. You can change them bu using the
+package cuda command in your input script or via the "-pk cuda"
+<A HREF = "Section_start.html#start_7">command-line switch</A>.
+</P>
+<P>For the GPU package, the default is Ngpu = 1 and the option defaults
+are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
+to Ngpu-1, tpa = 1, and device = not used. These settings are made
+automatically if the "-sf gpu" <A HREF = "Section_start.html#start_7">command-line
+switch</A> is used. If it is not used, you
+must invoke the package gpu command in your input script or via the
+"-pk gpu" <A HREF = "Section_start.html#start_7">command-line switch</A>.
+</P>
+<P>For the USER-INTEL package, the default is Nphi = 1 and the option
+defaults are omp = 0, mode = mixed, balance = -1, tpc = 4, tptask =
+240. The default ghost option is determined by the pair style being
+used. This value is output to the screen in the offload report at the
+end of each run. Note that all of these settings, except "omp" and
+"mode", are ignored if LAMMPS was not built with Xeon Phi coprocessor
+support. These settings are made automatically if the "-sf intel"
+<A HREF = "Section_start.html#start_7">command-line switch</A> is used. If it is
+not used, you must invoke the package intel command in your input
+script or or via the "-pk intel" <A HREF = "Section_start.html#start_7">command-line
+switch</A>.
+</P>
+<P>For the KOKKOS package, the option defaults neigh = full, newton =
+off, binsize = 0.0, and comm = host. These settings are made
+automatically by the required "-k on" <A HREF = "Section_start.html#start_7">command-line
+switch</A>. You can change them bu using the
+package kokkos command in your input script or via the "-pk kokkos"
+<A HREF = "Section_start.html#start_7">command-line switch</A>.
+</P>
+<P>For the OMP package, the default is Nthreads = 0 and the option
+defaults are neigh = yes. These settings are made automatically if
+the "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A> is
+used. If it is not used, you must invoke the package omp command in
+your input script or via the "-pk omp" <A HREF = "Section_start.html#start_7">command-line
+switch</A>.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_adp.html b/doc/doc2/pair_adp.html
new file mode 100644
index 000000000..bbce04db0
--- /dev/null
+++ b/doc/doc2/pair_adp.html
@@ -0,0 +1,194 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style adp command
+</H3>
+<H3>pair_style adp/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style adp
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style adp
+pair_coeff * * Ta.adp Ta
+pair_coeff * * ../potentials/AlCu.adp Al Al Cu
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>adp</I> computes pairwise interactions for metals and metal alloys
+using the angular dependent potential (ADP) of <A HREF = "#Mishin">(Mishin)</A>,
+which is a generalization of the <A HREF = "pair_eam.html">embedded atom method (EAM)
+potential</A>. The LAMMPS implementation is discussed in
+<A HREF = "#Singh">(Singh)</A>. The total energy Ei of an atom I is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_adp.jpg">
+</CENTER>
+<P>where F is the embedding energy which is a function of the atomic
+electron density rho, phi is a pair potential interaction, alpha and
+beta are the element types of atoms I and J, and s and t = 1,2,3 and
+refer to the cartesian coordinates. The mu and lambda terms represent
+the dipole and quadruple distortions of the local atomic environment
+which extend the original EAM framework by introducing angular forces.
+</P>
+<P>Note that unlike for other potentials, cutoffs for ADP potentials are
+not set in the pair_style or pair_coeff command; they are specified in
+the ADP potential files themselves. Likewise, the ADP potential files
+list atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
+command to specify them.
+</P>
+<P>The NIST WWW site distributes and documents ADP potentials:
+</P>
+<PRE>http://www.ctcms.nist.gov/potentials
+</PRE>
+<P>Note that these must be converted into the extended DYNAMO <I>setfl</I>
+format discussed below.
+</P>
+<P>The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
+who is good resource for info on interatomic potentials and file
+formats.
+</P>
+<HR>
+
+<P>Only a single pair_coeff command is used with the <I>adp</I> style which
+specifies an extended DYNAMO <I>setfl</I> file, which contains information
+for M elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of extended <I>setfl</I> elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways to
+specify the path for the potential file.
+</P>
+<P>As an example, the potentials/AlCu.adp file, included in the
+potentials directory of the LAMMPS distrbution, is an extended <I>setfl</I>
+file which has tabulated ADP values for w elements and their alloy
+interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
+and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
+the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * AlCu.adp Al Al Al Cu
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
+element in the extended <I>setfl</I> file. The final Cu argument maps
+LAMMPS atom type 4 to the Al element in the extended <I>setfl</I> file.
+Note that there is no requirement that your simulation use all the
+elements specified by the extended <I>setfl</I> file.
+</P>
+<P>If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an <I>adp</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P><I>Adp</I> files in the <I>potentials</I> directory of the LAMMPS distribution
+have an ".adp" suffix. A DYNAMO <I>setfl</I> file extended for ADP is
+formatted as follows. Basically it is the standard <I>setfl</I> format
+with additional tabulated functions u and w added to the file after
+the tabulated pair potentials. See the <A HREF = "pair_eam.html">pair_eam</A>
+command for further details on the <I>setfl</I> format.
+</P>
+<UL><LI>lines 1,2,3 = comments (ignored)
+<LI>line 4: Nelements Element1 Element2 ... ElementN
+<LI>line 5: Nrho, drho, Nr, dr, cutoff
+</UL>
+<P>Following the 5 header lines are Nelements sections, one for each
+element, each with the following format:
+</P>
+<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+<LI>embedding function F(rho) (Nrho values)
+<LI>density function rho(r) (Nr values)
+</UL>
+<P>Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed for all i,j element pairs in the same format
+as other arrays. Since these interactions are symmetric (i,j = j,i)
+only phi arrays with i >= j are listed, in the following order: i,j =
+(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
+Nelements). The tabulated values for each phi function are listed as
+r*phi (in units of eV-Angstroms), since they are for atom pairs, the
+same as for <A HREF = "pair_eam.html">other EAM files</A>.
+</P>
+<P>After the phi(r) arrays, each of the u(r) arrays are listed in the
+same order with the same assumptions of symmetry. Directly following
+the u(r), the w(r) arrays are listed. Note that phi(r) is the only
+array tabulated with a scaling by r.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, no special mixing rules are needed, since
+the ADP potential files specify alloy interactions explicitly.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_eam.html">pair_eam</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mishin"></A>
+
+<P><B>(Mishin)</B> Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029
+(2005).
+</P>
+<A NAME = "Singh"></A>
+
+<P><B>(Singh)</B> Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
+</P>
+</HTML>
diff --git a/doc/doc2/pair_airebo.html b/doc/doc2/pair_airebo.html
new file mode 100644
index 000000000..898b04d7a
--- /dev/null
+++ b/doc/doc2/pair_airebo.html
@@ -0,0 +1,203 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style airebo command
+</H3>
+<H3>pair_style airebo/omp command
+</H3>
+<H3>pair_style rebo command
+</H3>
+<H3>pair_style rebo/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style cutoff LJ_flag TORSION_flag
+</PRE>
+<UL><LI>style = <I>airebo</I> or <I>rebo</I>
+<LI>cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
+<LI>LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
+<LI>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style airebo 3.0
+pair_style airebo 2.5 1 0
+pair_coeff * * ../potentials/CH.airebo H C
+</PRE>
+<PRE>pair_style rebo
+pair_coeff * * ../potentials/CH.airebo H C
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>airebo</I> pair style computes the Adaptive Intermolecular Reactive
+Empirical Bond Order (AIREBO) Potential of <A HREF = "#Stuart">(Stuart)</A> for a
+system of carbon and/or hydrogen atoms. Note that this is the initial
+formulation of AIREBO from 2000, not the later formulation. The
+<I>rebo</I> pair style computes the Reactive Empirical Bond Order (REBO)
+Potential of <A HREF = "#Brenner">(Brenner)</A>. Note that this is the so-called
+2nd generation REBO from 2002, not the original REBO from 1990. As
+discussed below, 2nd generation REBO is closely related to the intial
+AIREBO; it is just a subset of the potential energy terms.
+</P>
+<P>The AIREBO potential consists of three terms:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_airebo.jpg">
+</CENTER>
+<P>By default, all three terms are included. For the <I>airebo</I> style, if
+the two optional flag arguments to the pair_style command are
+included, the LJ and torsional terms can be turned off. Note that
+both or neither of the flags must be included. If both of the LJ an
+torsional terms are turned off, it becomes the 2nd-generation REBO
+potential, with a small caveat on the spline fitting procedure
+mentioned below. This can be specified directly as pair_style rebo
+with no additional arguments.
+</P>
+<P>The detailed formulas for this potential are given in
+<A HREF = "#Stuart">(Stuart)</A>; here we provide only a brief description.
+</P>
+<P>The E_REBO term has the same functional form as the hydrocarbon REBO
+potential developed in <A HREF = "#Brenner">(Brenner)</A>. The coefficients for
+E_REBO in AIREBO are essentially the same as Brenner's potential, but
+a few fitted spline values are slightly different. For most cases the
+E_REBO term in AIREBO will produce the same energies, forces and
+statistical averages as the original REBO potential from which it was
+derived. The E_REBO term in the AIREBO potential gives the model its
+reactive capabilities and only describes short-ranged C-C, C-H and H-H
+interactions (r < 2 Angstroms). These interactions have strong
+coordination-dependence through a bond order parameter, which adjusts
+the attraction between the I,J atoms based on the position of other
+nearby atoms and thus has 3- and 4-body dependence.
+</P>
+<P>The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a
+form similar to the standard <A HREF = "pair_lj.html">Lennard Jones potential</A>.
+The E_LJ term in AIREBO contains a series of switching functions so
+that the short-ranged LJ repulsion (1/r^12) does not interfere with
+the energetics captured by the E_REBO term. The extent of the E_LJ
+interactions is determined by the <I>cutoff</I> argument to the pair_style
+command which is a scale factor. For each type pair (C-C, C-H, H-H)
+the cutoff is obtained by multiplying the scale factor by the sigma
+value defined in the potential file for that type pair. In the
+standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
+factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
+would be 10.2 Angstroms.
+</P>
+<P>The E_TORSION term is an explicit 4-body potential that describes
+various dihedral angle preferences in hydrocarbon configurations.
+</P>
+<HR>
+
+<P>Only a single pair_coeff command is used with the <I>airebo</I> or <I>rebo</I>
+style which specifies an AIREBO potential file with parameters for C
+and H. Note that the <I>rebo</I> style in LAMMPS uses the same
+AIREBO-formatted potential file. These are mapped to LAMMPS atom
+types by specifying N additional arguments after the filename in the
+pair_coeff command, where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of AIREBO elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C, and the 4th to be H, you would use the following
+pair_coeff command:
+</P>
+<PRE>pair_coeff * * CH.airebo C C C H
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three C arguments map LAMMPS atom types 1,2,3 to the C
+element in the AIREBO file. The final H argument maps LAMMPS atom
+type 4 to the H element in the SW file. If a mapping value is
+specified as NULL, the mapping is not performed. This can be used
+when a <I>airebo</I> potential is used as part of the <I>hybrid</I> pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
+</P>
+<P>The parameters/coefficients for the AIREBO potentials are listed in
+the CH.airebo file to agree with the original <A HREF = "#Stuart">(Stuart)</A>
+paper. Thus the parameters are specific to this potential and the way
+it was fit, so modifying the file should be done cautiously.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the MANYBODY package. They are only
+enabled if LAMMPS was built with that package (which it is by
+default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P>These pair potentials require the <A HREF = "newton.html">newton</A> setting to be
+"on" for pair interactions.
+</P>
+<P>The CH.airebo potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal <A HREF = "units.html">units</A>. You can use
+the AIREBO or REBO potential with any LAMMPS units, but you would need
+to create your own AIREBO potential file with coefficients listed in
+the appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Stuart"></A>
+
+<P><B>(Stuart)</B> Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
+(2000).
+</P>
+<A NAME = "Brenner"></A>
+
+<P><B>(Brenner)</B> Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
+Physics: Condensed Matter, 14, 783-802 (2002).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_awpmd.html b/doc/doc2/pair_awpmd.html
new file mode 100644
index 000000000..7ab6be867
--- /dev/null
+++ b/doc/doc2/pair_awpmd.html
@@ -0,0 +1,130 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style awpmd/cut command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style awpmd/cut Rc keyword value ...
+</PRE>
+<UL><LI>Rc = global cutoff, -1 means cutoff of half the shortest box length
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>hartree</I> or <I>dproduct</I> or <I>uhf</I> or <I>free</I> or <I>pbc</I> or <I>fix</I> or <I>harm</I> or <I>ermscale</I> or <I>flex_press</I>
+
+<PRE> <I>hartree</I> value = none
+ <I>dproduct</I> value = none
+ <I>uhf</I> value = none
+ <I>free</I> value = none
+ <I>pbc</I> value = Plen
+ Plen = periodic width of electron = -1 or positive value (distance units)
+ <I>fix</I> value = Flen
+ Flen = fixed width of electron = -1 or positive value (distance units)
+ <I>harm</I> value = width
+ width = harmonic width constraint
+ <I>ermscale</I> value = factor
+ factor = scaling between electron mass and width variable mass
+ <I>flex_press</I> value = none
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style awpmd/cut -1
+pair_style awpmd/cut 40.0 uhf free
+pair_coeff * *
+pair_coeff 2 2 20.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This pair style contains an implementation of the Antisymmetrized Wave
+Packet Molecular Dynamics (AWPMD) method. Need citation here. Need
+basic formulas here. Could be links to other documents.
+</P>
+<P>Rc is the cutoff.
+</P>
+<P>The pair_style command allows for several optional keywords
+to be specified.
+</P>
+<P>The <I>hartree</I>, <I>dproduct</I>, and <I>uhf</I> keywords specify the form of the
+initial trial wave function for the system. If the <I>hartree</I> keyword
+is used, then a Hartree multielectron trial wave function is used. If
+the <I>dproduct</I> keyword is used, then a trial function which is a
+product of two determinants for each spin type is used. If the <I>uhf</I>
+keyword is used, then an unrestricted Hartree-Fock trial wave function
+is used.
+</P>
+<P>The <I>free</I>, <I>pbc</I>, and <I>fix</I> keywords specify a width constraint on
+the electron wavepackets. If the <I>free</I> keyword is specified, then there is no
+constraint. If the <I>pbc</I> keyword is used and <I>Plen</I> is specified as
+-1, then the maximum width is half the shortest box length. If <I>Plen</I>
+is a positive value, then the value is the maximum width. If the
+<I>fix</I> keyword is used and <I>Flen</I> is specified as -1, then electrons
+have a constant width that is read from the data file. If <I>Flen</I> is a
+positive value, then the constant width for all electrons is set to
+<I>Flen</I>.
+</P>
+<P>The <I>harm</I> keyword allow oscillations in the width of the
+electron wavepackets. More details are needed.
+</P>
+<P>The <I>ermscale</I> keyword specifies a unitless scaling factor
+between the electron masses and the width variable mass. More
+details needed.
+</P>
+<P>If the <I>flex_press</I> keyword is used, then a contribution from the
+electrons is added to the total virial and pressure of the system.
+</P>
+<P>This potential is designed to be used with <A HREF = "atom_style.html">atom_style
+wavepacket</A> definitions, in order to handle the
+description of systems with interacting nuclei and explicit electrons.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutoff (distance units)
+</UL>
+<P>For <I>awpmd/cut</I>, the cutoff coefficient is optional. If it is not
+used (as in some of the examples above), the default global value
+specified in the pair_style command is used.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options
+are not relevant for this pair style.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>These are the defaults for the pair_style keywords: <I>hartree</I> for the
+initial wavefunction, <I>free</I> for the wavepacket width.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_beck.html b/doc/doc2/pair_beck.html
new file mode 100644
index 000000000..e804eb066
--- /dev/null
+++ b/doc/doc2/pair_beck.html
@@ -0,0 +1,117 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style beck command
+</H3>
+<H3>pair_style beck/gpu command
+</H3>
+<H3>pair_style beck/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style beck Rc
+</PRE>
+<UL><LI>Rc = cutoff for interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style beck 8.0
+pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
+pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>beck</I> computes interactions based on the potential by
+<A HREF = "#Beck">(Beck)</A>, originally designed for simulation of Helium. It
+includes truncation at a cutoff distance Rc.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_beck.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<UL><LI>A (energy units)
+<LI>B (energy-distance^6 units)
+<LI>a (distance units)
+<LI>alpha (1/distance units)
+<LI>beta (1/distance^6 units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+Rc is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, coeffiecients must be specified.
+No default miture rules are used.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Beck"></A>
+
+<P><B>(Beck)</B> Beck, Molecular Physics, 14, 311 (1968).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_body.html b/doc/doc2/pair_body.html
new file mode 100644
index 000000000..b83a52bdc
--- /dev/null
+++ b/doc/doc2/pair_body.html
@@ -0,0 +1,124 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style body command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style body cutoff
+</PRE>
+<P>cutoff = global cutoff for interactions (distance units)
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style body 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>body</I> is for use with body particles and calculates pairwise
+body/body interactions as well as interactions between body and
+point-particles. See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
+of the manual and the <A HREF = "body.html">body</A> doc page for more details on
+using body particles.
+</P>
+<P>This pair style is designed for use with the "nparticle" body style,
+which is specified as an argument to the "atom-style body" command.
+See the <A HREF = "body.html">body</A> doc page for more details about the body
+styles LAMMPS supports. The "nparticle" style treats a body particle
+as a rigid body composed of N sub-particles.
+</P>
+<P>The coordinates of a body particle are its center-of-mass (COM). If
+the COMs of a pair of body particles are within the cutoff (global or
+type-specific, as specified above), then all interactions between
+pairs of sub-particles in the two body particles are computed.
+E.g. if the first body particle has 3 sub-particles, and the second
+has 10, then 30 interactions are computed and summed to yield the
+total force and torque on each body particle.
+</P>
+<P>IMPORTANT NOTE: In the example just described, all 30 interactions are
+computed even if the distance between a particular pair of
+sub-particles is greater than the cutoff. Likewise, no interaction
+between two body particles is computed if the two COMs are further
+apart than the cutoff, even if the distance between some pairs of
+their sub-particles is within the cutoff. Thus care should be used in
+defining the cutoff distances for body particles, depending on their
+shape and size.
+</P>
+<P>Similar rules apply for a body particle interacting with a point
+particle. The distance between the two particles is calculated using
+the COM of the body particle and the position of the point particle.
+If the distance is within the cutoff and the body particle has N
+sub-particles, then N interactions with the point particle are
+computed and summed. If the distance is not within the cutoff, no
+interactions between the body and point particle are computed.
+</P>
+<P>The interaction between two sub-particles, or a sub-particle and point
+particle, or betwee two point particles is computed as a Lennard-Jones
+interaction, using the standard formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>where Rc is the cutoff. As explained above, an interaction involving
+one or two body sub-particles may be computed even for r > Rc.
+</P>
+<P>For style <I>body</I>, the following coefficients must be defined for each
+pair of atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in
+the examples above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+is used.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of this pair style can be mixed. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the BODY package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Defining particles to be bodies so they participate in body/body or
+body/particle interactions requires the use of the <A HREF = "atom_style.html">atom_style
+body</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_rigid.html">fix_rigid</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_bop.html b/doc/doc2/pair_bop.html
new file mode 100644
index 000000000..0952ed896
--- /dev/null
+++ b/doc/doc2/pair_bop.html
@@ -0,0 +1,460 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style bop command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style bop keyword ...
+</PRE>
+<LI>zero or more keywords may be appended
+
+<LI>keyword = <I>save</I>
+
+<PRE> save = pre-compute and save some values
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style bop
+pair_coeff * * ../potentials/CdTe_bop Cd Te
+pair_style bop save
+pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
+comm_modify cutoff 14.70
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>bop</I> pair style computes Bond-Order Potentials (BOP) based on
+quantum mechanical theory incorporating both sigma and pi bondings.
+By analytically deriving the BOP from quantum mechanical theory its
+transferability to different phases can approach that of quantum
+mechanical methods. This potential is similar to the original BOP
+developed by Pettifor (<A HREF = "#Pettifor_1">Pettifor_1</A>,
+<A HREF = "#Pettifor_2">Pettifor_2</A>, <A HREF = "#Pettifor_3">Pettifor_3</A>) and later updated
+by Murdick, Zhou, and Ward (<A HREF = "#Murdick">Murdick</A>, <A HREF = "#Ward">Ward</A>).
+Currently, BOP potential files for these systems are provided with
+LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with
+only a subset of these elements, including a single element (e.g. C or
+Cu or Al or Ga or Zn or CdZn), can also be modeled by using the
+appropriate alloy file and assigning all atom types to the
+singleelement or subset of elements via the pair_coeff command, as
+discussed below.
+</P>
+<P>The BOP potential consists of three terms:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_bop.jpg">
+</CENTER>
+<P>where phi_ij(r_ij) is a short-range two-body function representing the
+repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and
+beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals,
+THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and
+U_prom is the promotion energy for sp-valent systems.
+</P>
+<P>The detailed formulas for this potential are given in Ward
+(<A HREF = "#Ward">Ward</A>); here we provide only a brief description.
+</P>
+<P>The repulsive energy phi_ij(r_ij) and the bond integrals
+beta_(sigma,ij)(r_ij) and beta_(phi,ij)(r_ij) are functions of the
+interatomic distance r_ij between atom i and j. Each of these
+potentials has a smooth cutoff at a radius of r_(cut,ij). These
+smooth cutoffs ensure stable behavior at situations with high sampling
+near the cutoff such as melts and surfaces.
+</P>
+<P>The bond-orders can be viewed as environment-dependent local variables
+that are ij bond specific. The maximum value of the sigma bond-order
+(THETA_sigma) is 1, while that of the pi bond-order (THETA_pi) is 2,
+attributing to a maximum value of the total bond-order
+(THETA_sigma+THETA_pi) of 3. The sigma and pi bond-orders reflect the
+ubiquitous single-, double-, and triple- bond behavior of
+chemistry. Their analytical expressions can be derived from tight-
+binding theory by recursively expanding an inter-site Green's function
+as a continued fraction. To accurately represent the bonding with a
+computationally efficient potential formulation suitable for MD
+simulations, the derived BOP only takes (and retains) the first two
+levels of the recursive representations for both the sigma and the pi
+bond-orders. Bond-order terms can be understood in terms of molecular
+orbital hopping paths based upon the Cyrot-Lackmann theorem
+(<A HREF = "#Pettifor_1">Pettifor_1</A>). The sigma bond-order with a half-full
+valence shell is used to interpolate the bond-order expressiont that
+incorporated explicite valance band filling. This pi bond-order
+expression also contains also contains a three-member ring term that
+allows implementation of an asymmetric density of states, which helps
+to either stabilize or destabilize close-packed structures. The pi
+bond-order includes hopping paths of length 4. This enables the
+incorporation of dihedral angles effects.
+</P>
+<P>IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP
+potentials are not set in the pair_style or pair_coeff command; they
+are specified in the BOP potential files themselves. Likewise, the
+BOP potential files list atomic masses; thus you do not need to use
+the <A HREF = "mass.html">mass</A> command to specify them. Note that for BOP
+potentials with hydrogen, you will likely want to set the mass of H
+atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
+You can do this by using the <A HREF = "mass.html">mass</A> command after using the
+<A HREF = "doc/pair_coeff.html">pair_coeff</A> command to read the BOP potential
+file.
+</P>
+<P>One option can be specified as a keyword with the pair_style command.
+</P>
+<P>The <I>save</I> keyword gives you the option to calculate in advance and
+store a set of distances, angles, and derivatives of angles. The
+default is to not do this, but to calculate them on-the-fly each time
+they are needed. The former may be faster, but takes more memory.
+The latter requires less memory, but may be slower. It is best to
+test this option to optimize the speed of BOP for your particular
+system configuration.
+</P>
+<HR>
+
+<P>Only a single pair_coeff command is used with the <I>bop</I> style which
+specifies a BOP potential file, with parameters for all needed
+elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of BOP elements to atom types
+</UL>
+<P>As an example, imagine the CdTe.bop file has BOP values for Cd
+and Te. If your LAMMPS simulation has 4 atoms types and you want the
+1st 3 to be Cd, and the 4th to be Te, you would use the following
+pair_coeff command:
+</P>
+<PRE>pair_coeff * * CdTe Cd Cd Cd Te
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
+element in the BOP file. The final Te argument maps LAMMPS atom type
+4 to the Te element in the BOP file.
+</P>
+<P>BOP files in the <I>potentials</I> directory of the LAMMPS distribution
+have a ".bop" suffix. The potentials are in tabulated form containing
+pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij),
+and beta_pi,ij)(r_ij).
+</P>
+<P>The parameters/coefficients format for the different kinds of BOP
+files are given below with variables matching the formulation of Ward
+(<A HREF = "#Ward">Ward</A>) and Zhou (<A HREF = "#Zhou">Zhou</A>). Each header line containing a
+":" is preceded by a blank line.
+</P>
+<HR>
+
+<P><B>No angular table file format</B>:
+</P>
+<P>The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (<A HREF = "#Ward">Ward</A>). This format also
+assumes the angular functions have the formulation of (<A HREF = "#Ward">Ward</A>).
+</P>
+<UL><LI>Line 1: # elements N
+</UL>
+<P>The first line is followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+</P>
+<P>Following the definition of the elements several global variables for
+the tabulated functions are given.
+</P>
+<UL><LI>Line 1: nr, nBOt (nr is the number of divisions the radius is broken
+into for function tables and MUST be a factor of 5; nBOt is the number
+of divisions for the tabulated values of THETA_(S,ij)
+
+<LI>Line 2: delta_1-delta_7 (if all are not used in the particular
+
+<LI>formulation, set unused values to 0.0)
+</UL>
+<P>Following this N lines for e_1-e_N containing p_pi.
+</P>
+<UL><LI>Line 3: p_pi (for e_1)
+<LI>Line 4: p_pi (for e_2 and continues to e_N)
+</UL>
+<P>The next section contains several pair constants for the number of
+interaction types e_i-e_j, with i=1->N, j=i->N
+</P>
+<UL><LI>Line 1: r_cut (for e_1-e_1 interactions)
+
+<LI>Line 2: c_sigma, a_sigma, c_pi, a_pi
+
+<LI>Line 3: delta_sigma, delta_pi
+
+<LI>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
+the previous section but is interaction type dependent)
+</UL>
+<P>The next section contains a line for each three body interaction type
+e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
+</P>
+<UL><LI>Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for
+g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. <A HREF = "#Ward">Ward</A>
+contains the full expressions for the constants as functions of
+b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk))
+
+<LI>Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2)
+</UL>
+<P>The next section contains a block for each interaction type for the
+phi_ij(r_ij). Each block has nr entries with 5 entries per line.
+</P>
+<UL><LI>Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1
+interaction type)
+
+<LI>Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
+until nr)
+
+<LI>...
+
+<LI>Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
+e_1-e_1 interaction type)
+</UL>
+<P>The next section contains a block for each interaction type for the
+beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per
+line.
+</P>
+<UL><LI>Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4),
+beta_sigma(r5) (for the e_1-e_1 interaction type)
+
+<LI>Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9),
+beta_sigma(r10) (this continues until nr)
+
+<LI>...
+
+<LI>Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3),
+beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type)
+</UL>
+<P>The next section contains a block for each interaction type for
+beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line.
+</P>
+<UL><LI>Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5)
+(for the e_1-e_1 interaction type)
+
+<LI>Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9),
+beta_pi(r10) (this continues until nr)
+
+<LI>...
+
+<LI>Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4),
+beta_pi(r5) (for the e_1-e_2 interaction type)
+</UL>
+<P>The next section contains a block for each interaction type for the
+THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has
+nBOt entries with 5 entries per line.
+</P>
+<UL><LI>Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
+THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type)
+
+<LI>Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8),
+THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt)
+
+<LI>...
+
+<LI>Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
+THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type)
+</UL>
+<P>The next section contains a block of N lines for e_1-e_N
+</P>
+<UL><LI>Line 1: delta^mu (for e_1)
+<LI>Line 2: delta^mu (for e_2 and repeats to e_N)
+</UL>
+<P>The last section contains more constants for e_i-e_j interactions with
+i=0->N, j=i->N
+</P>
+<UL><LI>Line 1: (A_ij)^(mu*nu) (for e1-e1)
+<LI>Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above)
+</UL>
+<HR>
+
+<P><B>Angular spline table file format</B>:
+</P>
+<P>The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (<A HREF = "#Ward">Ward</A>). This format also
+assumes the angular functions have the formulation of (<A HREF = "#Zhou">Zhou</A>).
+</P>
+<UL><LI>Line 1: # elements N
+</UL>
+<P>The first line is followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+</P>
+<P>Following the definition of the elements several global variables for
+the tabulated functions are given.
+</P>
+<UL><LI>Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
+into for function tables and MUST be a factor of 5; ntheta is the power of the
+power of the spline used to fit the angular function; nBOt is the number
+of divisions for the tabulated values of THETA_(S,ij)
+
+<LI>Line 2: delta_1-delta_7 (if all are not used in the particular
+
+<LI>formulation, set unused values to 0.0)
+</UL>
+<P>Following this N lines for e_1-e_N containing p_pi.
+</P>
+<UL><LI>Line 3: p_pi (for e_1)
+<LI>Line 4: p_pi (for e_2 and continues to e_N)
+</UL>
+<P>The next section contains several pair constants for the number of
+interaction types e_i-e_j, with i=1->N, j=i->N
+</P>
+<UL><LI>Line 1: r_cut (for e_1-e_1 interactions)
+
+<LI>Line 2: c_sigma, a_sigma, c_pi, a_pi
+
+<LI>Line 3: delta_sigma, delta_pi
+
+<LI>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
+the previous section but is interaction type dependent)
+</UL>
+<P>The next section contains a line for each three body interaction type
+e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
+</P>
+<LI>Line 1: g0, g1, g2... (These are coefficients for the angular spline
+of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
+function can contain up to 10 term thus 10 constants. The first line
+can contain up to five constants. If the spline has more than five
+terms the second line will contain the remaining constants The
+following lines will then contain the constants for the remainaing g0,
+g1, g2... (for e_1-e_1-e_2) and the other three body
+interactions
+</UL>
+<P>The rest of the table has the same structure as the previous section
+(see above).
+</P>
+<HR>
+
+<P><B>Angular no-spline table file format</B>:
+</P>
+<P>The parameters/coefficients format for the BOP potentials input file
+containing pre-tabulated functions of g is given below with variables
+matching the formulation of Ward (<A HREF = "#Ward">Ward</A>). This format also
+assumes the angular functions have the formulation of (<A HREF = "#Zhou">Zhou</A>).
+</P>
+<UL><LI>Line 1: # elements N
+</UL>
+<P>The first two lines are followed by N lines containing the atomic
+number, mass, and element symbol of each element.
+</P>
+<P>Following the definition of the elements several global variables for
+the tabulated functions are given.
+</P>
+<UL><LI>Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
+into for function tables and MUST be a factor of 5; ntheta is the number of
+divisions for the tabulated values of the g angular function; nBOt is the number
+of divisions for the tabulated values of THETA_(S,ij)
+
+<LI>Line 2: delta_1-delta_7 (if all are not used in the particular
+
+<LI>formulation, set unused values to 0.0)
+</UL>
+<P>Following this N lines for e_1-e_N containing p_pi.
+</P>
+<UL><LI>Line 3: p_pi (for e_1)
+<LI>Line 4: p_pi (for e_2 and continues to e_N)
+</UL>
+<P>The next section contains several pair constants for the number of
+interaction types e_i-e_j, with i=1->N, j=i->N
+</P>
+<UL><LI>Line 1: r_cut (for e_1-e_1 interactions)
+
+<LI>Line 2: c_sigma, a_sigma, c_pi, a_pi
+
+<LI>Line 3: delta_sigma, delta_pi
+
+<LI>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
+the previous section but is interaction type dependent)
+</UL>
+<P>The next section contains a line for each three body interaction type
+e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
+</P>
+<UL><LI>Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1
+interaction type)
+
+<LI>Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
+until ntheta)
+
+<LI>...
+
+<LI>Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
+e_1-e_1-e_2 interaction type)
+</UL>
+<P>The rest of the table has the same structure as the previous section (see above).
+</P>
+<HR>
+
+<P><B>Mixing, shift, table tail correction, restart</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the MANYBODY package. They are only
+enabled if LAMMPS was built with that package (which it is by default).
+See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more
+info.
+</P>
+<P>These pair potentials require the <A HREF = "newton.html">newtion</A> setting to be
+"on" for pair interactions.
+</P>
+<P>The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
+You can use the BOP potential with any LAMMPS units, but you would need
+to create your own BOP potential file with coefficients listed in the
+appropriate units if your simulation does not use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>non-tabulated potential file, a_0 is non-zero.
+</P>
+<HR>
+
+<A NAME = "Pettofor_1"></A>
+
+<P><B>(Pettifor_1)</B> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
+(1999).
+</P>
+<A NAME = "Pettofor_2"></A>
+
+<P><B>(Pettifor_2)</B> D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
+4124 (2000).
+</P>
+<A NAME = "Pettofor_3"></A>
+
+<P><B>(Pettifor_3)</B> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
+(2002).
+</P>
+<A NAME = "Murdick"></A>
+
+<P><B>(Murdick)</B> D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R.
+Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).
+</P>
+<A NAME = "Ward"></A>
+
+<P><B>(Ward)</B> D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A.
+Zimmerman, Phys. Rev. B, 85,115206 (2012).
+</P>
+<A NAME = "Zhou"></A>
+
+<P><B>(Zhou)</B> X.W. Zhou, D.K. Ward, M. Foster (TBP).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_born.html b/doc/doc2/pair_born.html
new file mode 100644
index 000000000..bd2ba588f
--- /dev/null
+++ b/doc/doc2/pair_born.html
@@ -0,0 +1,210 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style born command
+</H3>
+<H3>pair_style born/omp command
+</H3>
+<H3>pair_style born/gpu command
+</H3>
+<H3>pair_style born/coul/long command
+</H3>
+<H3>pair_style born/coul/long/cs command
+</H3>
+<H3>pair_style born/coul/long/cuda command
+</H3>
+<H3>pair_style born/coul/long/gpu command
+</H3>
+<H3>pair_style born/coul/long/omp command
+</H3>
+<H3>pair_style born/coul/msm command
+</H3>
+<H3>pair_style born/coul/msm/omp command
+</H3>
+<H3>pair_style born/coul/wolf command
+</H3>
+<H3>pair_style born/coul/wolf/gpu command
+</H3>
+<H3>pair_style born/coul/wolf/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>born</I> or <I>born/coul/long</I> or <I>born/coul/long/cs</I> or <I>born/coul/msm</I> or <I>born/coul/wolf</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>born</I> args = cutoff
+ cutoff = global cutoff for non-Coulombic interactions (distance units)
+ <I>born/coul/long</I> or <I>born/coul/long/cs</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>born/coul/msm</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>born/coul/wolf</I> args = alpha cutoff (cutoff2)
+ alpha = damping parameter (inverse distance units)
+ cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style born 10.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</PRE>
+<PRE>pair_style born/coul/long 10.0
+pair_style born/coul/long/cs 10.0
+pair_style born/coul/long 10.0 8.0
+pair_style born/coul/long/cs 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</PRE>
+<PRE>pair_style born/coul/msm 10.0
+pair_style born/coul/msm 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</PRE>
+<PRE>pair_style born/coul/wolf 0.25 10.0
+pair_style born/coul/wolf 0.25 10.0 9.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>born</I> style computes the Born-Mayer-Huggins or Tosi/Fumi
+potential described in <A HREF = "#FumiTosi">(Fumi and Tosi)</A>, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_born.jpg">
+</CENTER>
+<P>where sigma is an interaction-dependent length parameter, rho is an
+ionic-pair dependent length parameter, and Rc is the cutoff.
+</P>
+<P>The styles with <I>coul/long</I> or <I>coul/msm</I> add a Coulombic term as
+described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles. An additional
+damping factor is applied to the Coulombic term so it can be used in
+conjunction with the <A HREF = "kspace_style.html">kspace_style</A> command and its
+<I>ewald</I> or <I>pppm</I> of <I>msm</I> option. The Coulombic cutoff specified for
+this style means that pairwise interactions within this distance are
+computed directly; interactions outside that distance are computed in
+reciprocal space.
+</P>
+<P>If one cutoff is specified for the <I>born/coul/long</I> and
+<I>born/coul/msm</I> style, it is used for both the A,C,D and Coulombic
+terms. If two cutoffs are specified, the first is used as the cutoff
+for the A,C,D terms, and the second is the cutoff for the Coulombic
+term.
+</P>
+<P>The <I>born/coul/wolf</I> style adds a Coulombic term as described for the
+Wolf potential in the <A HREF = "pair_coul.html">coul/wolf</A> pair style.
+</P>
+<P>Style <I>born/coul/long/cs</I> is identical to <I>born/coul/long</I> except that
+a term is added for the <A HREF = "Section_howto.html#howto_25">core/shell model</A>
+to allow charges on core and shell particles to be separated by r =
+0.0.
+</P>
+<P>Note that these potentials are related to the <A HREF = "pair_buck.html">Buckingham
+potential</A>.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>A (energy units)
+<LI>rho (distance units)
+<LI>sigma (distance units)
+<LI>C (energy units * distance units^6)
+<LI>D (energy units * distance units^8)
+<LI>cutoff (distance units)
+</UL>
+<P>The second coefficient, rho, must be greater than zero.
+</P>
+<P>The last coefficient is optional. If not specified, the global A,C,D
+cutoff specified in the pair_style command is used.
+</P>
+<P>For <I>born/coul/long</I> and <I>born/coul/wolf</I> no Coulombic cutoff can be
+specified for an individual I,J type pair. All type pairs use the
+same global Coulombic cutoff specified in the pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
+for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
+interaction.
+</P>
+<P>The <I>born/coul/long</I> pair style supports the
+<A HREF = "pair_modify.html">pair_modify</A> table option ti tabulate the
+short-range portion of the long-range Coulombic interaction.
+</P>
+<P>These styles support the pair_modify tail option for adding long-range
+tail corrections to energy and pressure.
+</P>
+<P>Thess styles writes thei information to binary <A HREF = "restart.html">restart</A>
+files, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
+</P>
+<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. They do not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>born/coul/long</I> style is part of the KSPACE package. It is only
+enabled if LAMMPS was built with that package (which it is by
+default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_buck.html">pair_style buck</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "FumiTosi"></A>
+
+<P>Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964),
+Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_brownian.html b/doc/doc2/pair_brownian.html
new file mode 100644
index 000000000..be855698d
--- /dev/null
+++ b/doc/doc2/pair_brownian.html
@@ -0,0 +1,150 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style brownian command
+</H3>
+<H3>pair_style brownian/omp command
+</H3>
+<H3>pair_style brownian/poly command
+</H3>
+<H3>pair_style brownian/poly/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
+</PRE>
+<UL><LI>style = <I>brownian</I> or <I>brownian/poly</I>
+<LI>mu = dynamic viscosity (dynamic viscosity units)
+<LI>flaglog = 0/1 log terms in the lubrication approximation on/off
+<LI>flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
+<LI>cutinner = inner cutoff distance (distance units)
+<LI>cutoff = outer cutoff for interactions (distance units)
+<LI>t_target = target temp of the system (temperature units)
+<LI>seed = seed for the random number generator (positive integer)
+<LI>flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
+<LI>flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Styles <I>brownian</I> and <I>brownain/poly</I> compute Brownian forces and
+torques on finite-size particles. The former requires monodisperse
+spherical particles; the latter allows for polydisperse spherical
+particles.
+</P>
+<P>These pair styles are designed to be used with either the <A HREF = "pair_lubricate.html">pair_style
+lubricate</A> or <A HREF = "pair_lubricateU.html">pair_style
+lubricateU</A> commands to provide thermostatting
+when dissipative lubrication forces are acting. Thus the parameters
+<I>mu</I>, <I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, and <I>cutoff</I> should be
+specified consistent with the settings in the lubrication pair styles.
+For details, refer to either of the lubrication pair styles.
+</P>
+<P>The <I>t_target</I> setting is used to specify the target temperature of
+the system. The random number <I>seed</I> is used to generate random
+numbers for the thermostatting procedure.
+</P>
+<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
+used, or both must be defined.
+</P>
+<HR>
+
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutinner (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The two coefficients are optional. If neither is specified, the two
+cutoffs specified in the pair_style command are used. Otherwise both
+must be specified.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">this section</A> of
+the manual. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
+instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed. The default mix value is <I>geometric</I>. See
+the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These styles are part of the FLD package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Only spherical monodisperse particles are allowed for pair_style
+brownian.
+</P>
+<P>Only spherical particles are allowed for pair_style brownian/poly.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricate.html">pair_style
+lubricate</A>, <A HREF = "pair_lubricateU.html">pair_style
+lubricateU</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_buck.html b/doc/doc2/pair_buck.html
new file mode 100644
index 000000000..046d2f712
--- /dev/null
+++ b/doc/doc2/pair_buck.html
@@ -0,0 +1,220 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style buck command
+</H3>
+<H3>pair_style buck/cuda command
+</H3>
+<H3>pair_style buck/gpu command
+</H3>
+<H3>pair_style buck/kk command
+</H3>
+<H3>pair_style buck/omp command
+</H3>
+<H3>pair_style buck/coul/cut command
+</H3>
+<H3>pair_style buck/coul/cut/cuda command
+</H3>
+<H3>pair_style buck/coul/cut/gpu command
+</H3>
+<H3>pair_style buck/coul/cut/kk command
+</H3>
+<H3>pair_style buck/coul/cut/omp command
+</H3>
+<H3>pair_style buck/coul/long command
+</H3>
+<H3>pair_style buck/coul/long/cs command
+</H3>
+<H3>pair_style buck/coul/long/cuda command
+</H3>
+<H3>pair_style buck/coul/long/gpu command
+</H3>
+<H3>pair_style buck/coul/long/kk command
+</H3>
+<H3>pair_style buck/coul/long/omp command
+</H3>
+<H3>pair_style buck/coul/msm command
+</H3>
+<H3>pair_style buck/coul/msm/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>buck</I> or <I>buck/coul/cut</I> or <I>buck/coul/long</I> or <I>buck/coul/long/cs</I> or <I>buck/coul/msm</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>buck</I> args = cutoff
+ cutoff = global cutoff for Buckingham interactions (distance units)
+ <I>buck/coul/cut</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>buck/coul/long</I> or <I>buck/coul/long/cs</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>buck/coul/msm</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style buck 2.5
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff * * 100.0 1.5 200.0 3.0
+</PRE>
+<PRE>pair_style buck/coul/cut 10.0
+pair_style buck/coul/cut 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
+</PRE>
+<PRE>pair_style buck/coul/long 10.0
+pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long 10.0 8.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</PRE>
+<PRE>pair_style buck/coul/msm 10.0
+pair_style buck/coul/msm 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>buck</I> style computes a Buckingham potential (exp/6 instead of
+Lennard-Jones 12/6) given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_buck.jpg">
+</CENTER>
+<P>where rho is an ionic-pair dependent length parameter, and Rc is the
+cutoff on both terms.
+</P>
+<P>The styles with <I>coul/cut</I> or <I>coul/long</I> or <I>coul/msm</I> add a
+Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles.
+For <I>buck/coul/long</I> and <I>buc/coul/msm</I>, an additional damping factor
+is applied to the Coulombic term so it can be used in conjunction with
+the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
+or <I>msm</I> option. The Coulombic cutoff specified for this style means
+that pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+</P>
+<P>If one cutoff is specified for the <I>born/coul/cut</I> and
+<I>born/coul/long</I> and <I>born/coul/msm</I> styles, it is used for both the
+A,C and Coulombic terms. If two cutoffs are specified, the first is
+used as the cutoff for the A,C terms, and the second is the cutoff for
+the Coulombic term.
+</P>
+<P>Style <I>buck/coul/long/cs</I> is identical to <I>buck/coul/long</I> except that
+a term is added for the <A HREF = "Section_howto.html#howto_25">core/shell model</A>
+to allow charges on core and shell particles to be separated by r =
+0.0.
+</P>
+<P>Note that these potentials are related to the <A HREF = "pair_born.html">Born-Mayer-Huggins
+potential</A>.
+</P>
+<P>IMPORTANT NOTE: For all these pair styles, the terms with A and C are
+always cutoff. The additional Coulombic term can be cutoff or
+long-range (no cutoff) depending on whether the style name includes
+coul/cut or coul/long or coul/msm. If you wish the C/r^6 term to be
+long-range (no cutoff), then see the <A HREF = "pair_buck_long.html">pair_style
+buck/long/coul/long</A> command.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>A (energy units)
+<LI>rho (distance units)
+<LI>C (energy-distance^6 units)
+<LI>cutoff (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The second coefficient, rho, must be greater than zero.
+</P>
+<P>The latter 2 coefficients are optional. If not specified, the global
+A,C and Coulombic cutoffs are used. If only one cutoff is specified,
+it is used as the cutoff for both A,C and Coulombic interactions for
+this type pair. If both coefficients are specified, they are used as
+the A,C and Coulombic cutoffs for this type pair. You cannot specify
+2 cutoffs for style <I>buck</I>, since it has no Coulombic terms.
+</P>
+<P>For <I>buck/coul/long</I> only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
+for the energy of the exp() and 1/r^6 portion of the pair interaction.
+</P>
+<P>The <I>buck/coul/long</I> pair style supports the
+<A HREF = "pair_modify.html">pair_modify</A> table option to tabulate the
+short-range portion of the long-range Coulombic interaction.
+</P>
+<P>These styles support the pair_modify tail option for adding long-range
+tail corrections to energy and pressure for the A,C terms in the
+pair interaction.
+</P>
+<P>These styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. They do not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>buck/coul/long</I> style is part of the KSPACE package. The
+<I>buck/coul/long/cs</I> style is part of the CORESHELL package. They are
+only enabled if LAMMPS was built with that package (which it is by
+default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_born.html">pair_style born</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_buck_long.html b/doc/doc2/pair_buck_long.html
new file mode 100644
index 000000000..77c8a3884
--- /dev/null
+++ b/doc/doc2/pair_buck_long.html
@@ -0,0 +1,182 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style buck/long/coul/long command
+</H3>
+<H3>pair_style buck/long/coul/long/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
+</PRE>
+<UL><LI>flag_buck = <I>long</I> or <I>cut</I>
+
+<PRE> <I>long</I> = use Kspace long-range summation for the dispersion term 1/r^6
+ <I>cut</I> = use a cutoff
+</PRE>
+<LI>flag_coul = <I>long</I> or <I>off</I>
+
+<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
+ <I>off</I> = omit the Coulombic term
+</PRE>
+<LI>cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)
+
+<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style buck/long/coul/long cut off 2.5
+pair_style buck/long/coul/long cut long 2.5 4.0
+pair_style buck/long/coul/long long long 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>buck/long/coul/long</I> style computes a Buckingham potential (exp/6
+instead of Lennard-Jones 12/6) and Coulombic potential, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_buck.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
+</CENTER>
+<P>Rc is the cutoff. If one cutoff is specified in the pair_style
+command, it is used for both the Buckingham and Coulombic terms. If
+two cutoffs are specified, they are used as cutoffs for the Buckingham
+and Coulombic terms respectively.
+</P>
+<P>The purpose of this pair style is to capture long-range interactions
+resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r
+interactions. This is done by use of the <I>flag_buck</I> and <I>flag_coul</I>
+settings. The "<A HREF = "#Ismail">Ismail</A> paper has more details on when it is
+appropriate to include long-range 1/r^6 interactions, using this
+potential.
+</P>
+<P>If <I>flag_buck</I> is set to <I>long</I>, no cutoff is used on the Buckingham
+1/r^6 dispersion term. The long-range portion can be calculated by
+using the <A HREF = "kspace_style.html">kspace_style ewald/disp or pppm/disp</A>
+commands. The specified Buckingham cutoff then determines which
+portion of the Buckingham interactions are computed directly by the
+pair potential versus which part is computed in reciprocal space via
+the Kspace style. If <I>flag_buck</I> is set to <I>cut</I>, the Buckingham
+interactions are simply cutoff, as with <A HREF = "pair_buck.html">pair_style
+buck</A>.
+</P>
+<P>If <I>flag_coul</I> is set to <I>long</I>, no cutoff is used on the Coulombic
+interactions. The long-range portion can calculated by using any of
+several <A HREF = "kspace_style.html">kspace_style</A> command options such as
+<I>pppm</I> or <I>ewald</I>. Note that if <I>flag_buck</I> is also set to long, then
+the <I>ewald/disp</I> or <I>pppm/disp</I> Kspace style needs to be used to
+perform the long-range calculations for both the Buckingham and
+Coulombic interactions. If <I>flag_coul</I> is set to <I>off</I>, Coulombic
+interactions are not computed.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>A (energy units)
+<LI>rho (distance units)
+<LI>C (energy-distance^6 units)
+<LI>cutoff (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The second coefficient, rho, must be greater than zero.
+</P>
+<P>The latter 2 coefficients are optional. If not specified, the global
+Buckingham and Coulombic cutoffs specified in the pair_style command
+are used. If only one cutoff is specified, it is used as the cutoff
+for both Buckingham and Coulombic interactions for this type pair. If
+both coefficients are specified, they are used as the Buckingham and
+Coulombic cutoffs for this type pair. Note that if you are using
+<I>flag_buck</I> set to <I>long</I>, you cannot specify a Buckingham cutoff for
+an atom type pair, since only one global Buckingham cutoff is allowed.
+Similarly, if you are using <I>flag_coul</I> set to <I>long</I>, you cannot
+specify a Coulombic cutoff for an atom type pair, since only one
+global Coulombic cutoff is allowed.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair styles does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the exp() and 1/r^6 portion of the pair
+interaction, assuming <I>flag_buck</I> is <I>cut</I>.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the Buckingham portion of the pair
+interaction.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> table and
+table/disp options since they can tabulate the short-range portion of
+the long-range Coulombic and dispersion interactions.
+</P>
+<P>This pair style write its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
+keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
+details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the KSPACE package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. Note that
+the KSPACE package is installed by default.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ismail"></A>
+
+<P><B>(Ismail)</B> Ismail, Tsige, In 't Veld, Grest, Molecular Physics
+(accepted) (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_charmm.html b/doc/doc2/pair_charmm.html
new file mode 100644
index 000000000..a36e85267
--- /dev/null
+++ b/doc/doc2/pair_charmm.html
@@ -0,0 +1,219 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/charmm/coul/charmm command
+</H3>
+<H3>pair_style lj/charmm/coul/charmm/cuda command
+</H3>
+<H3>pair_style lj/charmm/coul/charmm/omp command
+</H3>
+<H3>pair_style lj/charmm/coul/charmm/implicit command
+</H3>
+<H3>pair_style lj/charmm/coul/charmm/implicit/cuda command
+</H3>
+<H3>pair_style lj/charmm/coul/charmm/implicit/omp command
+</H3>
+<H3>pair_style lj/charmm/coul/long command
+</H3>
+<H3>pair_style lj/charmm/coul/long/cuda command
+</H3>
+<H3>pair_style lj/charmm/coul/long/gpu command
+</H3>
+<H3>pair_style lj/charmm/coul/long/intel command
+</H3>
+<H3>pair_style lj/charmm/coul/long/opt command
+</H3>
+<H3>pair_style lj/charmm/coul/long/omp command
+</H3>
+<H3>pair_style lj/charmm/coul/msm command
+</H3>
+<H3>pair_style lj/charmm/coul/msm/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/msm</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
+ inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+ inner2, outer2 = global switching cutoffs for Coulombic (optional)
+ <I>lj/charmm/coul/charmm/implicit</I> args = inner outer (inner2) (outer2)
+ inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+ inner2, outer2 = global switching cutoffs for Coulombic (optional)
+ <I>lj/charmm/coul/long</I> args = inner outer (cutoff)
+ inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+ cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+ <I>lj/charmm/coul/msm</I> args = inner outer (cutoff)
+ inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+ cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/charmm/coul/charmm 8.0 10.0
+pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</PRE>
+<PRE>pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
+pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</PRE>
+<PRE>pair_style lj/charmm/coul/long 8.0 10.0
+pair_style lj/charmm/coul/long 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</PRE>
+<PRE>pair_style lj/charmm/coul/msm 8.0 10.0
+pair_style lj/charmm/coul/msm 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/charmm</I> styles compute LJ and Coulombic interactions with an
+additional switching function S(r) that ramps the energy and force
+smoothly to zero between an inner and outer cutoff. It is a widely
+used potential in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A> MD code.
+See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
+field.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_charmm.jpg">
+</CENTER>
+<P>Both the LJ and Coulombic terms require an inner and outer cutoff.
+They can be the same for both formulas or different depending on
+whether 2 or 4 arguments are used in the pair_style command. In each
+case, the inner cutoff distance must be less than the outer cutoff.
+It it typical to make the difference between the 2 cutoffs about 1.0
+Angstrom.
+</P>
+<P>Style <I>lj/charmm/coul/charmm/implicit</I> computes the same formulas as
+style <I>lj/charmm/coul/charmm</I> except that an additional 1/r term is
+included in the Coulombic formula. The Coulombic energy thus varies
+as 1/r^2. This is effectively a distance-dependent dielectric term
+which is a simple model for an implicit solvent with additional
+screening. It is designed for use in a simulation of an unsolvated
+biomolecule (no explicit water molecules).
+</P>
+<P>Styles <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/msm</I> compute the same
+formulas as style <I>lj/charmm/coul/charmm</I> except that an additional
+damping factor is applied to the Coulombic term, as described for the
+<A HREF = "pair_lj.html">lj/cut</A> pair styles. Only one Coulombic cutoff is
+specified for <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/msm</I>; if only
+2 arguments are used in the pair_style command, then the outer LJ
+cutoff is used as the single Coulombic cutoff.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>epsilon_14 (energy units)
+<LI>sigma_14 (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2^(1/6)
+sigma.
+</P>
+<P>The latter 2 coefficients are optional. If they are specified, they
+are used in the LJ formula between 2 atoms of these types which are
+also first and fourth atoms in any dihedral. No cutoffs are specified
+because this CHARMM force field does not allow varying cutoffs for
+individual atom pairs; all pairs use the global cutoff(s) specified in
+the pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
+and sigma_14 coefficients for all of the lj/charmm pair styles can be
+mixed. The default mix value is <I>arithmetic</I> to coincide with the
+usual settings for the CHARMM force field. See the "pair_modify"
+command for details.
+</P>
+<P>None of the lj/charmm pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
+portion of the pair interaction is smoothed to 0.0 at the cutoff.
+</P>
+<P>The <I>lj/charmm/coul/long</I> style supports the
+<A HREF = "pair_modify.html">pair_modify</A> table option since it can tabulate the
+short-range portion of the long-range Coulombic interaction.
+</P>
+<P>None of the lj/charmm pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
+corrections to energy and pressure, since the Lennard-Jones portion of
+the pair interaction is smoothed to 0.0 at the cutoff.
+</P>
+<P>All of the lj/charmm pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>The lj/charmm/coul/long pair style supports the use of the <I>inner</I>,
+<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
+command, meaning the pairwise forces can be partitioned by distance at
+different levels of the rRESPA hierarchy. The other styles only
+support the <I>pair</I> keyword of run_style respa. See the
+<A HREF = "run_style.html">run_style</A> command for details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
+styles are part of the MOLECULE package. The <I>lj/charmm/coul/long</I>
+style is part of the KSPACE package. They are only enabled if LAMMPS
+was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. Note that
+the MOLECULE and KSPACE packages are installed by default.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "MacKerell"></A>
+
+<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_class2.html b/doc/doc2/pair_class2.html
new file mode 100644
index 000000000..58c66b927
--- /dev/null
+++ b/doc/doc2/pair_class2.html
@@ -0,0 +1,193 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/class2 command
+</H3>
+<H3>pair_style lj/class2/cuda command
+</H3>
+<H3>pair_style lj/class2/gpu command
+</H3>
+<H3>pair_style lj/class2/kk command
+</H3>
+<H3>pair_style lj/class2/omp command
+</H3>
+<H3>pair_style lj/class2/coul/cut command
+</H3>
+<H3>pair_style lj/class2/coul/cut/cuda command
+</H3>
+<H3>pair_style lj/class2/coul/cut/kk command
+</H3>
+<H3>pair_style lj/class2/coul/cut/omp command
+</H3>
+<H3>pair_style lj/class2/coul/long command
+</H3>
+<H3>pair_style lj/class2/coul/long/cuda command
+</H3>
+<H3>pair_style lj/class2/coul/long/gpu command
+</H3>
+<H3>pair_style lj/class2/coul/long/kk command
+</H3>
+<H3>pair_style lj/class2/coul/long/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/class2</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/class2</I> args = cutoff
+ cutoff = global cutoff for class 2 interactions (distance units)
+ <I>lj/class2/coul/cut</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/class2/coul/long</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/class2 10.0
+pair_coeff * * 100.0 2.5
+pair_coeff 1 2* 100.0 2.5 9.0
+</PRE>
+<PRE>pair_style lj/class2/coul/cut 10.0
+pair_style lj/class2/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+</PRE>
+<PRE>pair_style lj/class2/coul/long 10.0
+pair_style lj/class2/coul/long 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/class2</I> styles compute a 6/9 Lennard-Jones potential given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_class2.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
+Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles.
+</P>
+<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The latter 2 coefficients are optional. If not specified, the global
+class 2 and Coulombic cutoffs are used. If only one cutoff is
+specified, it is used as the cutoff for both class 2 and Coulombic
+interactions for this type pair. If both coefficients are specified,
+they are used as the class 2 and Coulombic cutoffs for this type pair.
+You cannot specify 2 cutoffs for style <I>lj/class2</I>, since it has no
+Coulombic terms.
+</P>
+<P>For <I>lj/class2/coul/long</I> only the class 2 cutoff can be specified
+since a Coulombic cutoff cannot be specified for an individual I,J
+type pair. All type pairs use the same global Coulombic cutoff
+specified in the pair_style command.
+</P>
+<HR>
+
+<P>If the pair_coeff command is not used to define coefficients for a
+particular I != J type pair, the mixing rule for epsilon and sigma for
+all class2 potentials is to use the <I>sixthpower</I> formulas documented
+by the <A HREF = "pair_modify.html">pair_modify</A> command. The <A HREF = "pair_modify.html">pair_modify
+mix</A> setting is thus ignored for class2 potentials
+for epsilon and sigma. However it is still followed for mixing the
+cutoff distance.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/class2 pair styles can be mixed.
+Epsilon and sigma are always mixed with the value <I>sixthpower</I>. The
+cutoff distance is mixed by whatever option is set by the pair_modify
+command (default = geometric). See the "pair_modify" command for
+details.
+</P>
+<P>All of the lj/class2 pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+</P>
+<P>The <I>lj/class2/coul/long</I> pair style does not support the
+<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
+capability has not yet been added to this potential.
+</P>
+<P>All of the lj/class2 pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
+tail correction to the energy and pressure of the Lennard-Jones
+portion of the pair interaction.
+</P>
+<P>All of the lj/class2 pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>All of the lj/class2 pair styles can only be used via the <I>pair</I>
+keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
+support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These styles are part of the CLASS2 package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_coeff.html b/doc/doc2/pair_coeff.html
new file mode 100644
index 000000000..fed17fdca
--- /dev/null
+++ b/doc/doc2/pair_coeff.html
@@ -0,0 +1,150 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_coeff command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_coeff I J args
+</PRE>
+<UL><LI>I,J = atom types (see asterisk form below)
+<LI>args = coefficients for one or more pairs of atom types
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_coeff 1 2 1.0 1.0 2.5
+pair_coeff 2 * 1.0 1.0
+pair_coeff 3* 1*2 1.0 1.0 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff * * nialhjea 1 1 2
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Specify the pairwise force field coefficients for one or more pairs of
+atom types. The number and meaning of the coefficients depends on the
+pair style. Pair coefficients can also be set in the data file read
+by the <A HREF = "read_data.html">read_data</A> command or in a restart file.
+</P>
+<P>I and J can be specified in one of two ways. Explicit numeric values
+can be used for each, as in the 1st example above. I <= J is
+required. LAMMPS sets the coefficients for the symmetric J,I
+interaction to the same values.
+</P>
+<P>A wildcard asterisk can be used in place of or in conjunction with the
+I,J arguments to set the coefficients for multiple pairs of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means all
+types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive). Note that only type pairs with I <= J are considered; if
+asterisks imply type pairs where J < I, they are ignored.
+</P>
+<P>Note that a pair_coeff command can override a previous setting for the
+same I,J pair. For example, these commands set the coeffs for all I,J
+pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
+</P>
+<PRE>pair_coeff * * 1.0 1.0 2.5
+pair_coeff 2 3 2.0 1.0 1.12
+</PRE>
+<P>A line in a data file that specifies pair coefficients uses the exact
+same format as the arguments of the pair_coeff command in an input
+script, with the exception of the I,J type arguments. In each line of
+the "Pair Coeffs" section of a data file, only a single type I is
+specified, which sets the coefficients for type I interacting with
+type I. This is because the section has exactly N lines, where N =
+the number of atom types. For this reason, the wild-card asterisk
+should also not be used as part of the I argument. Thus in a data
+file, the line corresponding to the 1st example above would be listed
+as
+</P>
+<PRE>2 1.0 1.0 2.5
+</PRE>
+<P>For many potentials, if coefficients for type pairs with I != J are
+not set explicitly by a pair_coeff command, the values are inferred
+from the I,I and J,J settings by mixing rules; see the
+<A HREF = "pair_modify.html">pair_modify</A> command for a discussion. Details on
+this option as it pertains to individual potentials are described on
+the doc page for the potential.
+</P>
+<P>Many pair styles, typically for many-body potentials, use tabulated
+potential files as input, when specifying the pair_coeff command.
+Potential files provided with LAMMPS are in the potentials directory
+of the distribution. For some potentials, such as EAM, other archives
+of suitable files can be found on the Web. They can be used with
+LAMMPS so long as they are in the format LAMMPS expects, as discussed
+on the individual doc pages.
+</P>
+<P>When a pair_coeff command using a potential file is specified, LAMMPS
+looks for the potential file in 2 places. First it looks in the
+location specified. E.g. if the file is specified as "niu3.eam", it
+is looked for in the current working directory. If it is specified as
+"../potentials/niu3.eam", then it is looked for in the potentials
+directory, assuming it is a sister directory of the current working
+directory. If the file is not found, it is then looked for in the
+directory specified by the LAMMPS_POTENTIALS environment variable.
+Thus if this is set to the potentials directory in the LAMMPS distro,
+then you can use those files from anywhere on your system, without
+copying them into your working directory. Environment variables are
+set in different ways for different shells. Here are example settings
+for
+</P>
+<PRE>csh, tcsh:
+% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
+</PRE>
+<PRE>bash:
+% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
+</PRE>
+<PRE>Windows:
+% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials
+</PRE>
+<HR>
+
+<P>The alphabetic list of pair styles defined in LAMMPS is given on the
+<A HREF = "pair_style.html">pair_style</A> doc page. They are also given in more
+compact form in the pair section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<P>Click on the style to display the formula it computes, arguments
+specified in the pair_style command, and coefficients specified by the
+associated <A HREF = "pair_coeff.html">pair_coeff</A> command.
+</P>
+<P>Note that there are also additional pair styles (not listed on the
+<A HREF = "pair_style.html">pair_style</A> doc page) submitted by users which are
+included in the LAMMPS distribution. The list of these with links to
+the individual styles are given in the pair section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<P>There are also additional accelerated pair styles (not listed on the
+<A HREF = "pair_style.html">pair_style</A> doc page) included in the LAMMPS
+distribution for faster performance on CPUs and GPUs. The list of
+these with links to the individual styles are given in the pair
+section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_modify.html">pair_modify</A>,
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "pair_write.html">pair_write</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_colloid.html b/doc/doc2/pair_colloid.html
new file mode 100644
index 000000000..3f8f006ba
--- /dev/null
+++ b/doc/doc2/pair_colloid.html
@@ -0,0 +1,213 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style colloid command
+</H3>
+<H3>pair_style colloid/gpu command
+</H3>
+<H3>pair_style colloid/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style colloid cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for colloidal interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style colloid 10.0
+pair_coeff * * 25 1.0 10.0 10.0
+pair_coeff 1 1 144 1.0 0.0 0.0 3.0
+pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
+pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>colloid</I> computes pairwise interactions between large colloidal
+particles and small solvent particles using 3 formulas. A colloidal
+particle has a size > sigma; a solvent particle is the usual
+Lennard-Jones particle of size sigma.
+</P>
+<P>The colloid-colloid interaction energy is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_colloid_cc.jpg">
+</CENTER>
+<P>where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
+colloidal particles, and Rc is the cutoff. This equation results from
+describing each colloidal particle as an integrated collection of
+Lennard-Jones particles of size sigma and is derived in
+<A HREF = "#Everaers">(Everaers)</A>.
+</P>
+<P>The colloid-solvent interaction energy is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_colloid_cs.jpg">
+</CENTER>
+<P>where A_cs is the Hamaker constant, a is the radius of the colloidal
+particle, and Rc is the cutoff. This formula is derived from the
+colloid-colloid interaction, letting one of the particle sizes go to
+zero.
+</P>
+<P>The solvent-solvent interaction energy is given by the usual
+Lennard-Jones formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_colloid_ss.jpg">
+</CENTER>
+<P>with A_ss set appropriately, which results from letting both particle
+sizes go to zero.
+</P>
+<P>When used in combination with <A HREF = "pair_colloid.html">pair_style
+yukawa/colloid</A>, the two terms become the so-called
+DLVO potential, which combines electrostatic repulsion and van der
+Waals attraction.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>A (energy units)
+<LI>sigma (distance units)
+<LI>d1 (distance units)
+<LI>d2 (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>A is the Hamaker energy prefactor and should typically be set as
+follows:
+</P>
+<UL><LI>A_cc = colloid/colloid = 4 pi^2 = 39.5
+<LI>A_cs = colloid/solvent = sqrt(A_cc*A_ss)
+<LI>A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4)
+</UL>
+<P>Sigma is the size of the solvent particle or the constituent particles
+integrated over in the colloidal particle and should typically be set
+as follows:
+</P>
+<UL><LI>Sigma_cc = colloid/colloid = 1.0
+<LI>Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma
+<LI>Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is
+</UL>
+<P>Thus typically Sigma_cs = 1.0, unless the solvent particle's size !=
+1.0.
+</P>
+<P>D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in
+the formulas above. Both d1 and d2 must be values >= 0. If d1 > 0
+and d2 > 0, then the pair interacts via the colloid-colloid formula
+above. If d1 = 0 and d2 = 0, then the pair interacts via the
+solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones
+particle of size sigma. If either d1 = 0 or d2 = 0 and the other is
+larger, then the pair interacts via the colloid-solvent formula.
+</P>
+<P>Note that the diameter of a particular particle type may appear in
+multiple pair_coeff commands, as it interacts with other particle
+types. You should insure the particle diameter is specified
+consistently each time it appears.
+</P>
+<P>The last coefficient is optional. If not specified, the global cutoff
+specified in the pair_style command is used. However, you typically
+want different cutoffs for interactions between different particle
+sizes. E.g. if colloidal particles of diameter 10 are used with
+solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
+would correspond to a colloid-colloid cutoff of 25. A good
+rule-of-thumb is to use a colloid-solvent cutoff that is half the big
+diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
+colloid-solvent cutoff in this case.
+</P>
+<P>IMPORTANT NOTE: When using pair_style colloid for a mixture with 2 (or
+more) widely different particles sizes (e.g. sigma=10 colloids in a
+background sigam=1 LJ fluid), you will likely want to use these
+commands for efficiency: <A HREF = "neighbor.html">neighbor multi</A> and
+<A HREF = "comm_modify.html">comm_modify multi</A>.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed. A
+is an energy value mixed like a LJ epsilon. D1 and d2 are distance
+values and are mixed like sigma. The default mix value is
+<I>geometric</I>. See the "pair_modify" command for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the COLLOID package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Normally, this pair style should be used with finite-size particles
+which have a diameter, e.g. see the <A HREF = "atom_style.html">atom_style
+sphere</A> command. However, this is not a requirement,
+since the only definition of particle size is via the pair_coeff
+parameters for each type. In other words, the physical radius of the
+particle is ignored. Thus you should insure that the d1,d2 parameters
+you specify are consistent with the physical size of the particles of
+that type.
+</P>
+<P>Per-particle polydispersity is not yet supported by this pair style;
+only per-type polydispersity is enabled via the pair_coeff parameters.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Everaers"></A>
+
+<P><B>(Everaers)</B> Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_comb.html b/doc/doc2/pair_comb.html
new file mode 100644
index 000000000..3812b2592
--- /dev/null
+++ b/doc/doc2/pair_comb.html
@@ -0,0 +1,204 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style comb command
+</H3>
+<H3>pair_style comb/omp command
+</H3>
+<H3>pair_style comb3 command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style comb
+pair_style comb3 keyword
+</PRE>
+<PRE>keyword = <I>polar</I>
+ <I>polar</I> value = <I>polar_on</I> or <I>polar_off</I> = whether or not to include atomic polarization
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style comb
+pair_coeff * * ../potentials/ffield.comb Si
+pair_coeff * * ../potentials/ffield.comb Hf Si O
+</PRE>
+<PRE>pair_style comb3 polar_off
+pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>comb</I> computes the second-generation variable charge COMB
+(Charge-Optimized Many-Body) potential. Style <I>comb3</I> computes the
+third-generation COMB potential. These COMB potentials are described
+in <A HREF = "#COMB">(COMB)</A> and <A HREF = "#COMB3">(COMB3)</A>. Briefly, the total energy
+<I>E<sub>T</sub></I> of a system of atoms is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
+</CENTER>
+<P>where <I>E<sub>i</sub><sup>self</sup></I> is the self-energy of atom <I>i</I>
+(including atomic ionization energies and electron affinities),
+<I>E<sub>ij</sub><sup>short</sup></I> is the bond-order potential between
+atoms <I>i</I> and <I>j</I>,
+<I>E<sub>ij</sub><sup>Coul</sup></I> is the Coulomb interactions,
+<I>E<sup>polar</sup></I> is the polarization term for organic systems
+(style <I>comb3</I> only),
+<I>E<sup>vdW</sup></I> is the van der Waals energy (style <I>comb3</I> only),
+<I>E<sup>barr</sup></I> is a charge barrier function, and
+<I>E<sup>corr</sup></I> are angular correction terms.
+</P>
+<P>The COMB potentials (styles <I>comb</I> and <I>comb3</I>) are variable charge
+potentials. The equilibrium charge on each atom is calculated by the
+electronegativity equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for
+further details. This is implemented by the <A HREF = "fix_qeq_comb.html">fix
+qeq/comb</A> command, which should normally be
+specified in the input script when running a model with the COMB
+potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command has options
+that determine how often charge equilibration is performed, its
+convergence criterion, and which atoms are included in the
+calculation.
+</P>
+<P>Only a single pair_coeff command is used with the <I>comb</I> and <I>comb3</I>
+styles which specifies the COMB potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the potential file in the pair_coeff
+command, where N is the number of LAMMPS atom types.
+</P>
+<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
+HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
+last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
+use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
+</PRE>
+<P>The first two arguments must be * * so as to span all LAMMPS atom
+types. The first and last Si arguments map LAMMPS atom types 1 and 4
+to the Si element in the <I>ffield.comb</I> file. The second Hf argument
+maps LAMMPS atom type 2 to the Hf element, and the third O argument
+maps LAMMPS atom type 3 to the O element in the potential file. If a
+mapping value is specified as NULL, the mapping is not performed.
+This can be used when a <I>comb</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P>For style <I>comb</I>, the provided potential file <I>ffield.comb</I> contains
+all currently-available 2nd generation COMB parameterizations: for Si,
+Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
+<I>comb3</I>, the potential file <I>ffield.comb3</I> contains all
+currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
+H, Ti, Zn and Zr. The status of the optimization of the compounds, for
+example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
+following table:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
+</CENTER>
+<P>For style <I>comb3</I>, in addition to ffield.comb3, a special parameter
+file, <I>lib.comb3</I>, that is exclusively used for C/O/H systems, will be
+automatically loaded if carbon atom is detected in LAMMPS input
+structure. This file must be in your working directory or in the
+directory pointed to by the environment variable LAMMPS_POTENTIALS, as
+described on the <A HREF = "pair_coeff.html">pair_coeff</A> command doc page.
+</P>
+<P>Keyword <I>polar</I> indicates whether the force field includes
+the atomic polarization. Since the equilibration of the polarization
+has not yet been implemented, it can only set polar_off at present.
+</P>
+<P>IMPORTANT NOTE: You can not use potential file <I>ffield.comb</I> with
+style <I>comb3</I>, nor file <I>ffield.comb3</I> with style <I>comb</I>.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>These pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>These pair styles do not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
+qeq/comb</A> commands in an input script that reads a
+restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>These pair styles requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The COMB potentials in the <I>ffield.comb</I> and <I>ffield.comb3</I> files provided
+with LAMMPS (see the potentials directory) are parameterized for metal
+<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
+units, but you would need to create your own COMB potential file with
+coefficients listed in the appropriate units if your simulation
+doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "COMB"></A>
+
+<P><B>(COMB)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
+S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
+</P>
+<A NAME = "COMB3"></A>
+
+<P><B>(COMB3)</B> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
+Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
+255-279 (2013).
+</P>
+<A NAME = "Rick"></A>
+
+<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+(1994).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_coul.html b/doc/doc2/pair_coul.html
new file mode 100644
index 000000000..db95f8848
--- /dev/null
+++ b/doc/doc2/pair_coul.html
@@ -0,0 +1,373 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style coul/cut command
+</H3>
+<H3>pair_style coul/cut/gpu command
+</H3>
+<H3>pair_style coul/cut/kk command
+</H3>
+<H3>pair_style coul/cut/omp command
+</H3>
+<H3>pair_style coul/debye command
+</H3>
+<H3>pair_style coul/debye/gpu command
+</H3>
+<H3>pair_style coul/debye/kk command
+</H3>
+<H3>pair_style coul/debye/omp command
+</H3>
+<H3>pair_style coul/dsf command
+</H3>
+<H3>pair_style coul/dsf/gpu command
+</H3>
+<H3>pair_style coul/dsf/kk command
+</H3>
+<H3>pair_style coul/dsf/omp command
+</H3>
+<H3>pair_style coul/long command
+</H3>
+<H3>pair_style coul/long/cs command
+</H3>
+<H3>pair_style coul/long/omp command
+</H3>
+<H3>pair_style coul/long/gpu command
+</H3>
+<H3>pair_style coul/long/kk command
+</H3>
+<H3>pair_style coul/msm command
+</H3>
+<H3>pair_style coul/msm/omp command
+</H3>
+<H3>pair_style coul/streitz command
+</H3>
+<H3>pair_style coul/wolf command
+</H3>
+<H3>pair_style coul/wolf/kk command
+</H3>
+<H3>pair_style coul/wolf/omp command
+</H3>
+<H3>pair_style tip4p/cut command
+</H3>
+<H3>pair_style tip4p/long command
+</H3>
+<H3>pair_style tip4p/cut/omp command
+</H3>
+<H3>pair_style tip4p/long/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style coul/cut cutoff
+pair_style coul/debye kappa cutoff
+pair_style coul/dsf alpha cutoff
+pair_style coul/long cutoff
+pair_style coul/long/cs cutoff
+pair_style coul/long/gpu cutoff
+pair_style coul/wolf alpha cutoff
+pair_style coul/streitz cutoff keyword alpha
+pair_style tip4p/cut otype htype btype atype qdist cutoff
+pair_style tip4p/long otype htype btype atype qdist cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for Coulombic interactions
+<LI>kappa = Debye length (inverse distance units)
+<LI>alpha = damping parameter (inverse distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style coul/cut 2.5
+pair_coeff * *
+pair_coeff 2 2 3.5
+</PRE>
+<PRE>pair_style coul/debye 1.4 3.0
+pair_coeff * *
+pair_coeff 2 2 3.5
+</PRE>
+<PRE>pair_style coul/dsf 0.05 10.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style coul/long 10.0
+pair_style coul/long/cs 10.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style coul/msm 10.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style coul/wolf 0.2 9.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style coul/streitz 12.0 ewald
+pair_style coul/streitz 12.0 wolf 0.30
+pair_coeff * * AlO.streitz Al O
+</PRE>
+<PRE>pair_style tip4p/cut 1 2 7 8 0.15 12.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style tip4p/long 1 2 7 8 0.15 10.0
+pair_coeff * *
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>coul/cut</I> style computes the standard Coulombic interaction
+potential given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
+</CENTER>
+<P>where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the <A HREF = "dielectric.html">dielectric</A> command. The cutoff Rc truncates
+the interaction distance.
+</P>
+<HR>
+
+<P>Style <I>coul/debye</I> adds an additional exp() damping factor to the
+Coulombic term, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
+</CENTER>
+<P>where kappa is the Debye length. This potential is another way to
+mimic the screening effect of a polar solvent.
+</P>
+<HR>
+
+<P>Style <I>coul/dsf</I> computes Coulombic interactions via the damped
+shifted force model described in <A HREF = "#Fennell">Fennell</A>, given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coul_dsf.jpg">
+</CENTER>
+<P>where <I>alpha</I> is the damping parameter and erfc() is the
+complementary error-function. The potential corrects issues in the
+Wolf model (described below) to provide consistent forces and energies
+(the Wolf potential is not differentiable at the cutoff) and smooth
+decay to zero.
+</P>
+<HR>
+
+<P>Style <I>coul/wolf</I> computes Coulombic interactions via the Wolf
+summation method, described in <A HREF = "#Wolf">Wolf</A>, given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coul_wolf.jpg">
+</CENTER>
+<P>where <I>alpha</I> is the damping parameter, and erc() and erfc() are
+error-fuction and complementary error-function terms. This potential
+is essentially a short-range, spherically-truncated,
+charge-neutralized, shifted, pairwise <I>1/r</I> summation. With a
+manipulation of adding and substracting a self term (for i = j) to the
+first and second term on the right-hand-side, respectively, and a
+small enough <I>alpha</I> damping parameter, the second term shrinks and
+the potential becomes a rapidly-converging real-space summation. With
+a long enough cutoff and small enough alpha parameter, the energy and
+forces calcluated by the Wolf summation method approach those of the
+Ewald sum. So it is a means of getting effective long-range
+interactions with a short-range potential.
+</P>
+<HR>
+
+<P>Style <I>coul/streitz</I> is the Coulomb pair interaction defined as part
+of the Streitz-Mintmire potential, as described in <A HREF = "#Streitz">this
+paper</A>, in which charge distribution about an atom is modeled
+as a Slater 1<I>s</I> orbital. More details can be found in the referenced
+paper. To fully reproduce the published Streitz-Mintmire potential,
+which is a variable charge potential, style <I>coul/streitz</I> must be
+used with <A HREF = "pair_eam.html">pair_style eam/alloy</A> (or some other
+short-range potential that has been parameterized appropriately) via
+the <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command. Likewise,
+charge equilibration must be performed via the <A HREF = "fix_qeq.html">fix
+qeq/slater</A> command. For example:
+</P>
+<PRE>pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+</PRE>
+<P>The keyword <I>wolf</I> in the coul/streitz command denotes computing
+Coulombic interactions via Wolf summation. An additional damping
+parameter is required for the Wolf summation, as described for the
+coul/wolf potential above. Alternatively, Coulombic interactions can
+be computed via an Ewald summation. For example:
+</P>
+<PRE>pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+kspace_style ewald 1e-6
+</PRE>
+<P>Keyword <I>ewald</I> does not need a damping parameter, but a
+<A HREF = "kspace_style.html">kspace_style</A> must be defined, which can be style
+<I>ewald</I> or <I>pppm</I>. The Ewald method was used in Streitz and
+Mintmire's original paper, but a Wolf summation offers a speed-up in
+some cases.
+</P>
+<P>For the fix qeq/slater command, the <I>qfile</I> can be a filename that
+contains QEq parameters as discussed on the <A HREF = "fix_qeq.html">fix qeq</A>
+command doc page. Alternatively <I>qfile</I> can be replaced by
+"coul/streitz", in which case the fix will extract QEq parameters from
+the coul/streitz pair style itself.
+</P>
+<P>See the examples/strietz directory for an example input script that
+uses the Streitz-Mintmire potential. The potentials directory has the
+AlO.eam.alloy and AlO.streitz potential files used by the example.
+</P>
+<P>Note that the Streiz-Mintmire potential is generally used for oxides,
+but there is no conceptual problem with extending it to nitrides and
+carbides (such as SiC, TiN). Pair coul/strietz used by itself or with
+any other pair style such as EAM, MEAM, Tersoff, or LJ in
+hybrid/overlay mode. To do this, you would need to provide a
+Streitz-Mintmire parameterizaion for the material being modeled.
+</P>
+<HR>
+
+<P>Styles <I>coul/long</I> and <I>coul/msm</I> compute the same Coulombic
+interactions as style <I>coul/cut</I> except that an additional damping
+factor is applied so it can be used in conjunction with the
+<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
+option. The Coulombic cutoff specified for this style means that
+pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+</P>
+<P>Style <I>coul/long/cs</I> is identical to <I>coul/long</I> except that a term is
+added for the <A HREF = "Section_howto.html#howto_25">core/shell model</A> to allow
+charges on core and shell particles to be separated by r = 0.0.
+</P>
+<P>Styles <I>tip4p/cut</I> and <I>tip4p/long</I> implement the coulomb part of
+the TIP4P water model of <A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces
+a massless site located a short distance away from the oxygen atom
+along the bisector of the HOH angle. The atomic types of the oxygen and
+hydrogen atoms, the bond and angle types for OH and HOH interactions,
+and the distance to the massless charge site are specified as
+pair_style arguments. Style <I>tip4p/cut</I> uses a global cutoff for
+Coulomb interactions; style <I>tip4p/long</I> is for use with a long-range
+Coulombic solver (Ewald or PPPM).
+</P>
+<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
+IDs for the O and 2 H atoms must be consecutive, with the O atom
+first. This is to enable LAMMPS to "find" the 2 H atoms associated
+with each O atom. For example, if the atom ID of an O atom in a TIP4P
+water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+</P>
+<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
+information on how to use the TIP4P pair styles and lists of
+parameters to set. Note that the neighobr list cutoff for Coulomb
+interactions is effectively extended by a distance 2*qdist when using
+the TIP4P pair style, to account for the offset distance of the
+fictitious charges on O atoms in water molecules. Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
+to slightly larger cost for the long-range calculation, so you can
+test the trade-off for your model.
+</P>
+<HR>
+
+<P>Note that these potentials are designed to be combined with other pair
+potentials via the <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
+command. This is because they have no repulsive core. Hence if they
+are used by themselves, there will be no repulsion to keep two
+oppositely charged particles from moving arbitrarily close to each
+other.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutoff (distance units)
+</UL>
+<P>For <I>coul/cut</I> and <I>coul/debye</I>, the cutoff coefficient is optional.
+If it is not used (as in some of the examples above), the default
+global value specified in the pair_style command is used.
+</P>
+<P>For <I>coul/long</I> and <I>coul/msm</I> no cutoff can be specified for an
+individual I,J type pair via the pair_coeff command. All type pairs
+use the same global Coulombic cutoff specified in the pair_style
+command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the cutoff distance for the
+<I>coul/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
+See the "pair_modify" command for details.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant
+for these pair styles.
+</P>
+<P>The <I>coul/long</I> style supports the <A HREF = "pair_modify.html">pair_modify</A>
+table option for tabulation of the short-range portion of the
+long-range Coulombic interaction.
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>coul/long</I>, <I>coul/msm</I> and <I>tip4p/long</I> styles are part of the
+KSPACE package. The <I>coul/long/cs</I> style is part of the CORESHELL
+package. They are only enabled if LAMMPS was built with that package
+(which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_hybrid.html">pair_style,
+hybrid/overlay</A>, <A HREF = "kspace_style.html">kspace_style</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Wolf"></A>
+
+<P><B>(Wolf)</B> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
+Phys, 110, 8254 (1999).
+</P>
+<A NAME = "Fennell"></A>
+
+<P><B>(Fennell)</B> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
+234104 (2006).
+</P>
+<A NAME = "Streitz"></A>
+
+<P><B>(Streitz)</B> F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
+(1994).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_coul_diel.html b/doc/doc2/pair_coul_diel.html
new file mode 100644
index 000000000..a5f97bce4
--- /dev/null
+++ b/doc/doc2/pair_coul_diel.html
@@ -0,0 +1,120 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style coul/diel command
+</H3>
+<H3>pair_style coul/diel/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style coul/diel cutoff
+</PRE>
+<P>cutoff = global cutoff (distance units)
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style coul/diel 3.5
+pair_coeff 1 4 78. 1.375 0.112
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>coul/diel</I> computes a Coulomb correction for implict solvent
+ion interactions in which the dielectric perimittivity is distance dependent.
+The dielectric permittivity epsilon_D(r) connects to limiting regimes:
+One limit is defined by a small dielectric permittivity (close to vacuum)
+at or close to contact seperation between the ions. At larger separations
+the dielectric permittivity reaches a bulk value used in the regular Coulomb
+interaction coul/long or coul/cut.
+The transition is modeled by a hyperbolic function which is incorporated
+in the Coulomb correction term for small ion separations as follows
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coul_diel.jpg">
+</CENTER>
+<P>where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope
+defining length scale. C is the same Coulomb conversion factor as in the
+pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
+interaction between ions is corrected at small distances r. The lower
+limit of epsilon_D(r->0)=5.2 due to dielectric saturation <A HREF = "#Stiles">(Stiles)</A>
+while the Coulomb interaction reaches its bulk limit by setting
+epsilon_D(r->\infty)=epsilon, the bulk value of the solvent which is 78
+for water at 298K.
+</P>
+<P>Examples of the use of this type of Coulomb interaction include implicit
+solvent simulations of salt ions
+<A HREF = "#Lenart">(Lenart)</A> and of ionic surfactants <A HREF = "#Jusufi">(Jusufi)</A>.
+Note that this potential is only reasonable for implicit solvent simulations
+and in combiantion with coul/cut or coul/long. It is also usually combined
+with gauss/cut, see <A HREF = "#Lenart">(Lenart)</A> or <A HREF = "#Jusufi">(Jusufi)</A>.
+</P>
+<P>The following coefficients must be defined for each pair of atom
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>epsilon (no units)
+<LI>r_me (distance units)
+<LI>sigma_e (distance units)
+</UL>
+<P>The global cutoff (r_c) specified in the pair_style command is used.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the "user-misc" package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+<A HREF = "pair_gauss.html">pair_style gauss/cut</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Stiles"></A>
+
+<P><B>(Stiles)</B> Stiles , Hubbard, and Kayser, J Chem Phys, 77,
+6189 (1982).
+</P>
+<A NAME = "Lenart"></A>
+
+<P><B>(Lenart)</B> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
+044509 (2007).
+</P>
+<A NAME = "Jusufi"></A>
+
+<P><B>(Jusufi)</B> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
+13783 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_cs.html b/doc/doc2/pair_cs.html
new file mode 100644
index 000000000..8cc7b4f09
--- /dev/null
+++ b/doc/doc2/pair_cs.html
@@ -0,0 +1,91 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style born/coul/long/cs command
+</H3>
+<H3>pair_style buck/coul/long/cs command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>born/coul/long/cs</I> or <I>buck/coul/long/cs</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>born/coul/long/cs</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>buck/coul/long/cs</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style born/coul/long/cs 10.0 8.0
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</PRE>
+<PRE>pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>These pair styles are designed to be used with the adiabatic
+core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
+<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
+overview of the model as implemented in LAMMPS.
+</P>
+<P>These pair styles are identical to the <A HREF = "pair_born.html">pair_style
+born/coul/long</A> and <A HREF = "pair_buck.html">pair_style
+buck/coul/long</A> styles, except they correctly treat the
+special case where the distance between two charged core and shell
+atoms in the same core/shell pair approach r = 0.0. This needs
+special treatment when a long-range solver for Coulombic interactions
+is also used, i.e. via the <A HREF = "kspace_style.html">kspace_style</A> command.
+</P>
+<P>More specifically, the short-range Coulomb interaction between a core
+and its shell should be turned off using the
+<A HREF = "special_bonds.html">special_bonds</A> command by setting the 1-2 weight
+to 0.0, which works because the core and shell atoms are bonded to
+each other. This induces a long-range correction approximation which
+fails at small distances (~< 10e-8). Therefore, the Coulomb term which
+is used to calculate the correction factor is extended by a minimal
+distance (r_min = 1.0-6) when the interaction between a core/shell
+pair is treated, as follows
+</P>
+<CENTER><IMG SRC = "Eqs/pair_cs.jpg">
+</CENTER>
+<P>where C is an energy-conversion constant, Qi and Qj are the charges on
+the core and shell, epsilon is the dielectric constant and r_min is the
+minimal distance.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the CORESHELL package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_born.html">pair_style born</A>,
+<A HREF = "pair_buck.html">pair_style buck</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "MitchellFinchham"></A>
+
+<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_dipole.html b/doc/doc2/pair_dipole.html
new file mode 100644
index 000000000..6bce1d0de
--- /dev/null
+++ b/doc/doc2/pair_dipole.html
@@ -0,0 +1,286 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/cut/dipole/cut command
+</H3>
+<H3>pair_style lj/cut/dipole/cut/gpu command
+</H3>
+<H3>pair_style lj/cut/dipole/cut/omp command
+</H3>
+<H3>pair_style lj/sf/dipole/sf command
+</H3>
+<H3>pair_style lj/sf/dipole/sf/gpu command
+</H3>
+<H3>pair_style lj/sf/dipole/sf/omp command
+</H3>
+<H3>pair_style lj/cut/dipole/long command
+</H3>
+<H3>pair_style lj/long/dipole/long command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/cut/dipole/cut cutoff (cutoff2)
+pair_style lj/sf/dipole/sf cutoff (cutoff2)
+pair_style lj/cut/dipole/long cutoff (cutoff2)
+pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
+</PRE>
+<UL><LI>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)
+
+<LI>cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)
+
+<LI>flag_lj = <I>long</I> or <I>cut</I> or <I>off</I>
+
+<PRE> <I>long</I> = use long-range damping on dispersion 1/r^6 term
+ <I>cut</I> = use a cutoff on dispersion 1/r^6 term
+ <I>off</I> = omit disperion 1/r^6 term entirely
+</PRE>
+<LI>flag_coul = <I>long</I> or <I>off</I>
+
+<PRE> <I>long</I> = use long-range damping on Coulombic 1/r and point-dipole terms
+ <I>off</I> = omit Coulombic and point-dipole terms entirely
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cut/dipole/cut 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</PRE>
+<PRE>pair_style lj/sf/dipole/sf 9.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</PRE>
+<PRE>pair_style lj/cut/dipole/long 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</PRE>
+<PRE>pair_style lj/long/dipole/long long long 3.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/cut/dipole/cut</I> computes interactions between pairs of particles
+that each have a charge and/or a point dipole moment. In addition to
+the usual Lennard-Jones interaction between the particles (Elj) the
+charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
+interactions are computed by these formulas for the energy (E), force
+(F), and torque (T) between particles I and J.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_dipole.jpg">
+</CENTER>
+<P>where qi and qj are the charges on the two particles, pi and pj are
+the dipole moment vectors of the two particles, r is their separation
+distance, and the vector r = Ri - Rj is the separation vector between
+the two particles. Note that Eqq and Fqq are simply Coulombic energy
+and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
+torques do not act symmetrically. These formulas are discussed in
+<A HREF = "#Allen">(Allen)</A> and in <A HREF = "#Toukmaji">(Toukmaji)</A>.
+</P>
+<P>Style <I>lj/sf/dipole/sf</I> computes "shifted-force" interactions between
+pairs of particles that each have a charge and/or a point dipole
+moment. In general, a shifted-force potential is a (sligthly) modified
+potential containing extra terms that make both the energy and its
+derivative go to zero at the cutoff distance; this removes
+(cutoff-related) problems in energy conservation and any numerical
+instability in the equations of motion <A HREF = "#Allen">(Allen)</A>. Shifted-force
+interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
+charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
+potentials are computed by these formulas for the energy (E), force
+(F), and torque (T) between particles I and J:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_dipole_sf.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/pair_dipole_sf2.jpg">
+</CENTER>
+<P>where epsilon and sigma are the standard LJ parameters, r_c is the
+cutoff, qi and qj are the charges on the two particles, pi and pj are
+the dipole moment vectors of the two particles, r is their separation
+distance, and the vector r = Ri - Rj is the separation vector between
+the two particles. Note that Eqq and Fqq are simply Coulombic energy
+and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
+torques do not act symmetrically. The shifted-force formula for the
+Lennard-Jones potential is reported in <A HREF = "#Stoddard">(Stoddard)</A>. The
+original (unshifted) formulas for the electrostatic potentials, forces
+and torques can be found in <A HREF = "#Price">(Price)</A>. The shifted-force
+electrostatic potentials have been obtained by applying equation 5.13
+of <A HREF = "#Allen">(Allen)</A>. The formulas for the corresponding forces and
+torques have been obtained by applying the 'chain rule' as in appendix
+C.3 of <A HREF = "#Allen">(Allen)</A>.
+</P>
+<P>If one cutoff is specified in the pair_style command, it is used for
+both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
+they are used as cutoffs for the LJ and Coulombic (q,p) terms
+respectively.
+</P>
+<P>Style <I>lj/cut/dipole/long</I> computes long-range point-dipole
+interactions as discussed in <A HREF = "#Toukmaji">(Toukmaji)</A>. Dipole-dipole,
+dipole-charge, and charge-charge interactions are all supported, along
+with the standard 12/6 Lennard-Jones interactions, which are computed
+with a cutoff. A <A HREF = "kspace_style.html">kspace_style</A> must be defined to
+use this pair style. Currently, only <A HREF = "kspace_style.html">kspace_style
+ewald/disp</A> support long-range point-dipole
+interactions.
+</P>
+<P>Style <I>lj/long/dipole/long</I> also computes point-dipole interactions as
+discussed in <A HREF = "#Toukmaji">(Toukmaji)</A>. Long-range dipole-dipole,
+dipole-charge, and charge-charge interactions are all supported, along
+with the standard 12/6 Lennard-Jones interactions. LJ interactions
+can be cutoff or long-ranged.
+</P>
+<P>For style <I>lj/long/dipole/long</I>, if <I>flag_lj</I> is set to <I>long</I>, no
+cutoff is used on the LJ 1/r^6 dispersion term. The long-range
+portion is calculated by using the <A HREF = "kspace_style.html">kspace_style
+ewald_disp</A> command. The specified LJ cutoff then
+determines which portion of the LJ interactions are computed directly
+by the pair potential versus which part is computed in reciprocal
+space via the Kspace style. If <I>flag_lj</I> is set to <I>cut</I>, the LJ
+interactions are simply cutoff, as with <A HREF = "pair_lj.html">pair_style
+lj/cut</A>. If <I>flag_lj</I> is set to <I>off</I>, LJ interactions
+are not computed at all.
+</P>
+<P>If <I>flag_coul</I> is set to <I>long</I>, no cutoff is used on the Coulombic or
+dipole interactions. The long-range portion is calculated by using
+<I>ewald_disp</I> of the <A HREF = "kspace_style.html">kspace_style</A> command. If
+<I>flag_coul</I> is set to <I>off</I>, Coulombic and dipole interactions are not
+computed at all.
+</P>
+<P>Atoms with dipole moments should be integrated using the <A HREF = "fix_nve_sphere.html">fix
+nve/sphere update dipole</A> command to rotate the
+dipole moments. The <I>omega</I> option on the <A HREF = "fix_langevin.html">fix
+langevin</A> command can be used to thermostat the
+rotational motion. The <A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
+command can be used to monitor the temperature, since it includes
+rotational degrees of freedom. The <A HREF = "atom_style.html">atom_style
+dipole</A> command should be used since it defines the
+point dipoles and their rotational state. The magnitude of the dipole
+moment for each type of particle can be defined by the
+<A HREF = "dipole.html">dipole</A> command or in the "Dipoles" section of the data
+file read in by the <A HREF = "read_data.html">read_data</A> command. Their initial
+orientation can be defined by the <A HREF = "set.html">set dipole</A> command or in
+the "Atoms" section of the data file.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The latter 2 coefficients are optional. If not specified, the global
+LJ and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distances for this pair style can be mixed. The default
+mix value is <I>geometric</I>. See the "pair_modify" command for details.
+</P>
+<P>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed. A
+is an energy value mixed like a LJ epsilon. D1 and d2 are distance
+values and are mixed like sigma. The default mix value is
+<I>geometric</I>. See the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the Lennard-Jones portion of the pair
+interaction; such energy goes to zero at the cutoff by construction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>lj/cut/dipole/cut</I>, <I>lj/cut/dipole/long</I>, and
+<I>lj/long/dipole/long</I> styles are part of the DIPOLE package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The <I>lj/sf/dipole/sf</I> style is part of the USER-MISC package. It is
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Using dipole pair styles with <I>electron</I> <A HREF = "units.html">units</A> is not
+currently supported.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Allen"></A>
+
+<P><B>(Allen)</B> Allen and Tildesley, Computer Simulation of Liquids,
+Clarendon Press, Oxford, 1987.
+</P>
+<A NAME = "Toukmaji"></A>
+
+<P><B>(Toukmaji)</B> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
+10913 (2000).
+</P>
+<A NAME = "Stoddard"></A>
+
+<P><B>(Stoddard)</B> Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
+</P>
+<A NAME = "Price"></A>
+
+<P><B>(Price)</B> Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_dpd.html b/doc/doc2/pair_dpd.html
new file mode 100644
index 000000000..91d610c71
--- /dev/null
+++ b/doc/doc2/pair_dpd.html
@@ -0,0 +1,221 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style dpd command
+</H3>
+<H3>pair_style dpd/gpu command
+</H3>
+<H3>pair_style dpd/omp command
+</H3>
+<H3>pair_style dpd/tstat command
+</H3>
+<H3>pair_style dpd/tstat/gpu command
+</H3>
+<H3>pair_style dpd/tstat/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style dpd T cutoff seed
+pair_style dpd/tstat Tstart Tstop cutoff seed
+</PRE>
+<UL><LI>T = temperature (temperature units)
+<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
+<LI>cutoff = global cutoff for DPD interactions (distance units)
+<LI>seed = random # seed (positive integer)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style dpd 1.0 2.5 34387
+pair_coeff * * 3.0 1.0
+pair_coeff 1 1 3.0 1.0 1.0
+</PRE>
+<PRE>pair_style dpd/tstat 1.0 1.0 2.5 34387
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>dpd</I> computes a force field for dissipative particle dynamics
+(DPD) following the exposition in <A HREF = "#Groot">(Groot)</A>.
+</P>
+<P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions,
+which is equivalent to the non-conservative portion of the DPD force
+field. This pair-wise thermostat can be used in conjunction with any
+<A HREF = "pair_style.html">pair style</A>, and in leiu of per-particle thermostats
+like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like
+Nose Hoover as implemented by <A HREF = "fix_nh.html">fix nvt</A>. To use
+<I>dpd/stat</I> as a thermostat for another pair style, use the <A HREF = "pair_hybrid.html">pair_style
+hybrid/overlay</A> command to compute both the desired
+pair interaction and the thermostat for each pair of particles.
+</P>
+<P>For style <I>dpd</I>, the force on atom I due to atom J is given as a sum
+of 3 terms
+</P>
+<CENTER><IMG SRC = "Eqs/pair_dpd.jpg">
+</CENTER>
+<P>where Fc is a conservative force, Fd is a dissipative force, and Fr is
+a random force. Rij is a unit vector in the direction Ri - Rj, Vij is
+the vector difference in velocities of the two atoms = Vi - Vj, alpha
+is a Gaussian random number with zero mean and unit variance, dt is
+the timestep size, and w(r) is a weighting factor that varies between
+0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma),
+where Kb is the Boltzmann constant and T is the temperature parameter
+in the pair_style command.
+</P>
+<P>For style <I>dpd/tstat</I>, the force on atom I due to atom J is the same
+as the above equation, except that the conservative Fc term is
+dropped. Also, during the run, T is set each timestep to a ramped
+value from Tstart to Tstop.
+</P>
+<P>For style <I>dpd</I>, the pairwise energy associated with style <I>dpd</I> is
+only due to the conservative force term Fc, and is shifted to be zero
+at the cutoff distance Rc. The pairwise virial is calculated using
+all 3 terms. For style <I>dpd/tstat</I> there is no pairwise energy, but
+the last two terms of the formula make a contribution to the virial.
+</P>
+<P>For style <I>dpd</I>, the following coefficients must be defined for each
+pair of atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in
+the examples above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>A (force units)
+<LI>gamma (force/velocity units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global DPD
+cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
+where T is the temperature set by the <A HREF = "pair_style.html">pair_style</A>
+command so it does not need to be specified.
+</P>
+<P>For style <I>dpd/tstat</I>, the coefficiencts defined for each pair of
+atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command is the same,
+except that A is not included.
+</P>
+<P>The GPU-accelerated versions of these styles are implemented based on
+the work of <A HREF = "#Afshar">(Afshar)</A> and <A HREF = "#Phillips">(Phillips)</A>.
+</P>
+<P>IMPORTANT NOTE: If you are modeling DPD polymer chains, you may want
+to use the <A HREF = "pair_srp.html">pair_style srp</A> command in conjuction with
+these pair styles. It is a soft segmental repulsive potential (SRP)
+that can prevent DPD polymer chains from crossing each other.
+</P>
+<P>IMPORTANT NOTE: The virial calculation for pressure when using this
+pair style includes all the components of force listed above,
+including the random force.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction. Note that as
+discussed above, the energy due to the conservative Fc term is already
+shifted to be 0.0 at the cutoff distance Rc.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for these pair styles.
+</P>
+<P>These pair style do not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>These pair styles writes their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file. Note
+that the user-specified random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+initially. This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P>The <I>dpd/tstat</I> style can ramp its target temperature over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command. See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The default frequency for rebuilding neighbor lists is every 10 steps
+(see the <A HREF = "neigh_modify.html">neigh_modify</A> command). This may be too
+infrequent for style <I>dpd</I> simulations since particles move rapidly
+and can overlap by large amounts. If this setting yields a non-zero
+number of "dangerous" reneighborings (printed at the end of a
+simulation), you should experiment with forcing reneighboring more
+often and see if system energies/trajectories change.
+</P>
+<P>These pair styles requires you to use the <A HREF = "comm_modify.html">comm_modify vel
+yes</A> command so that velocites are stored by ghost
+atoms.
+</P>
+<P>These pair styles will not restart exactly when using the
+<A HREF = "read_restart.html">read_restart</A> command, though they should provide
+statistically similar results. This is because the forces they
+compute depend on atom velocities. See the
+<A HREF = "read_restart.html">read_restart</A> command for more details.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
+langevin</A>, <A HREF = "pair_srp.html">pair_style srp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Groot"></A>
+
+<P><B>(Groot)</B> Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+</P>
+<A NAME = "Afshar"></A>
+
+<P><B>(Afshar)</B> Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
+Comm, 184, 1119-1128 (2013).
+</P>
+<A NAME = "Phillips"></A>
+
+<P><B>(Phillips)</B> C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
+Phys Comm, 230, 7191-7201 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_dsmc.html b/doc/doc2/pair_dsmc.html
new file mode 100644
index 000000000..f21cefe8c
--- /dev/null
+++ b/doc/doc2/pair_dsmc.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style dsmc command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
+</PRE>
+<UL><LI>max_cell_size = global maximum cell size for DSMC interactions (distance units)
+<LI>seed = random # seed (positive integer)
+<LI>weighting = macroparticle weighting
+<LI>Tref = reference temperature (temperature units)
+<LI>Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
+<LI>Nsample = sample this many times in recomputing v*sigma_max
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style dsmc 2.5 34387 10 1.0 100 20
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>dsmc</I> computes collisions between pairs of particles for a
+direct simulation Monte Carlo (DSMC) model following the exposition in
+<A HREF = "#Bird">(Bird)</A>. Each collision resets the velocities of the two
+particles involved. The number of pairwise collisions for each pair
+or particle types and the length scale within which they occur are
+determined by the parameters of the pair_style and pair_coeff
+commands.
+</P>
+<P>Stochastic collisions are performed using the variable hard sphere
+(VHS) approach, with the user-defined <I>max_cell_size</I> value used as
+the maximum DSMC cell size, and reference cross-sections for
+collisions given using the pair_coeff command.
+</P>
+<P>There is no pairwise energy or virial contributions associated with
+this pair style.
+</P>
+<P>The following coefficient must be defined for each pair of atoms types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>sigma (area units, i.e. distance-squared)
+</UL>
+<P>The global DSMC <I>max_cell_size</I> determines the maximum cell length
+used in the DSMC calculation. A structured mesh is overlayed on the
+simulation box such that an integer number of cells are created in
+each direction for each processor's sub-domain. Cell lengths are
+adjusted up to the user-specified maximum cell size.
+</P>
+<HR>
+
+<P>To perform a DSMC simulation with LAMMPS, several additional options
+should be set in your input script, though LAMMPS does not check for
+these settings.
+</P>
+<P>Since this pair style does not compute particle forces, you should use
+the "fix nve/noforce" time integration fix for the DSMC particles,
+e.g.
+</P>
+<PRE>fix 1 all nve/noforce
+</PRE>
+<P>This pair style assumes that all particles will communicated to
+neighboring processors every timestep as they move. This makes it
+possible to perform all collisions between pairs of particles that are
+on the same processor. To ensure this occurs, you should use
+these commands:
+</P>
+<PRE>neighbor 0.0 bin
+neigh_modify every 1 delay 0 check no
+atom_modify sort 0 0.0
+communicate single cutoff 0.0
+</PRE>
+<P>These commands ensure that LAMMPS communicates particles to
+neighboring processors every timestep and that no ghost atoms are
+created. The output statistics for a simulation run should indicate
+there are no ghost particles or neighbors.
+</P>
+<P>In order to get correct DSMC collision statistics, users should
+specify a Gaussian velocity distribution when populating the
+simulation domain. Note that the default velocity distribution is
+uniform, which will not give good DSMC collision rates. Specify
+"dist gaussian" when using the <A HREF = "velocity.html">velocity</A> command
+as in the following:
+</P>
+<PRE>velocity all create 594.6 87287 loop geom dist gaussian
+</PRE>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file. Note
+that the user-specified random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+initially. This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the MC package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_noforce.html">fix nve/noforce</A>,
+<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
+<A HREF = "comm_modify.html">comm_modify</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Bird"></A>
+
+<P><B>(Bird)</B> G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation
+of Gas Flows" (1994).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_eam.html b/doc/doc2/pair_eam.html
new file mode 100644
index 000000000..3bb2cb901
--- /dev/null
+++ b/doc/doc2/pair_eam.html
@@ -0,0 +1,480 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style eam command
+</H3>
+<H3>pair_style eam/cuda command
+</H3>
+<H3>pair_style eam/gpu command
+</H3>
+<H3>pair_style eam/kk command
+</H3>
+<H3>pair_style eam/omp command
+</H3>
+<H3>pair_style eam/opt command
+</H3>
+<H3>pair_style eam/alloy command
+</H3>
+<H3>pair_style eam/alloy/cuda command
+</H3>
+<H3>pair_style eam/alloy/gpu command
+</H3>
+<H3>pair_style eam/alloy/kk command
+</H3>
+<H3>pair_style eam/alloy/omp command
+</H3>
+<H3>pair_style eam/alloy/opt command
+</H3>
+<H3>pair_style eam/cd command
+</H3>
+<H3>pair_style eam/cd/omp command
+</H3>
+<H3>pair_style eam/fs command
+</H3>
+<H3>pair_style eam/fs/cuda command
+</H3>
+<H3>pair_style eam/fs/gpu command
+</H3>
+<H3>pair_style eam/fs/kk command
+</H3>
+<H3>pair_style eam/fs/omp command
+</H3>
+<H3>pair_style eam/fs/opt command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style
+</PRE>
+<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/cd</I> or <I>eam/fs</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style eam
+pair_coeff * * cuu3
+pair_coeff 1*3 1*3 niu3.eam
+</PRE>
+<PRE>pair_style eam/alloy
+pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
+</PRE>
+<PRE>pair_style eam/cd
+pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
+</PRE>
+<PRE>pair_style eam/fs
+pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>eam</I> computes pairwise interactions for metals and metal alloys
+using embedded-atom method (EAM) potentials <A HREF = "#Daw">(Daw)</A>. The total
+energy Ei of an atom I is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_eam.jpg">
+</CENTER>
+<P>where F is the embedding energy which is a function of the atomic
+electron density rho, phi is a pair potential interaction, and alpha
+and beta are the element types of atoms I and J. The multi-body
+nature of the EAM potential is a result of the embedding energy term.
+Both summations in the formula are over all neighbors J of atom I
+within the cutoff distance.
+</P>
+<P>The cutoff distance and the tabulated values of the functionals F,
+rho, and phi are listed in one or more files which are specified by
+the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
+in a DYNAMO-style format which is described below. DYNAMO was the
+original serial EAM MD code, written by the EAM originators. Several
+DYNAMO potential files for different metals are included in the
+"potentials" directory of the LAMMPS distribution. All of these files
+are parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
+</P>
+<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
+the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
+can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>. For the
+alloy case LAMMPS mixes the single-element potentials to produce alloy
+potentials, the same way that DYNAMO does. Alternatively, a single
+DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
+to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/cd</I> or
+<I>eam/fs</I> styles as described below. These files require no mixing
+since they specify alloy interactions explicitly.
+</P>
+<P>IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for EAM
+potentials are not set in the pair_style or pair_coeff command; they
+are specified in the EAM potential files themselves. Likewise, the
+EAM potential files list atomic masses; thus you do not need to use
+the <A HREF = "mass.html">mass</A> command to specify them.
+</P>
+<P>There are several WWW sites that distribute and document EAM
+potentials stored in DYNAMO or other formats:
+</P>
+<PRE>http://www.ctcms.nist.gov/potentials
+http://cst-www.nrl.navy.mil/ccm6/ap
+http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
+</PRE>
+<P>These potentials should be usable with LAMMPS, though the alternate
+formats would need to be converted to the DYNAMO format used by LAMMPS
+and described on this page. The NIST site is maintained by Chandler
+Becker (cbecker at nist.gov) who is good resource for info on
+interatomic potentials and file formats.
+</P>
+<HR>
+
+<P>For style <I>eam</I>, potential values are read from a file that is in the
+DYNAMO single-element <I>funcfl</I> format. If the DYNAMO file was created
+by a Fortran program, it cannot have "D" values in it for exponents.
+C only recognizes "e" or "E" for scientific notation.
+</P>
+<P>Note that unlike for other potentials, cutoffs for EAM potentials are
+not set in the pair_style or pair_coeff command; they are specified in
+the EAM potential files themselves.
+</P>
+<P>For style <I>eam</I> a potential file must be assigned to each I,I pair of
+atom types by using one or more pair_coeff commands, each with a
+single argument:
+</P>
+<UL><LI>filename
+</UL>
+<P>Thus the following command
+</P>
+<PRE>pair_coeff *2 1*2 cuu3.eam
+</PRE>
+<P>will read the cuu3 potential file and use the tabulated Cu values for
+F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
+1,2 and 2,1 are ignored). See the <A HREF = "pair_coeff.html">pair_coeff</A> doc
+page for alternate ways to specify the path for the potential file.
+In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
+Different single-element files can be assigned to different atom types
+to model an alloy system. The mixing to create alloy potentials for
+type pairs with I != J is done automatically the same way that the
+serial DYNAMO code originally did it; you do not need to specify
+coefficients for these type pairs.
+</P>
+<P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
+distribution have an ".eam" suffix. A DYNAMO single-element <I>funcfl</I>
+file is formatted as follows:
+</P>
+<UL><LI>line 1: comment (ignored)
+<LI>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
+<LI>line 3: Nrho, drho, Nr, dr, cutoff
+</UL>
+<P>On line 2, all values but the mass are ignored by LAMMPS. The mass is
+in mass <A HREF = "units.html">units</A>, e.g. mass number or grams/mole for metal
+units. The cubic lattice constant is in Angstroms. On line 3, Nrho
+and Nr are the number of tabulated values in the subsequent arrays,
+drho and dr are the spacing in density and distance space for the
+values in those arrays, and the specified cutoff becomes the pairwise
+cutoff used by LAMMPS for the potential. The units of dr are
+Angstroms; I'm not sure of the units for drho - some measure of
+electron density.
+</P>
+<P>Following the three header lines are three arrays of tabulated values:
+</P>
+<UL><LI>embedding function F(rho) (Nrho values)
+<LI>effective charge function Z(r) (Nr values)
+<LI>density function rho(r) (Nr values)
+</UL>
+<P>The values for each array can be listed as multiple values per line,
+so long as each array starts on a new line. For example, the
+individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
+</P>
+<P>The units for the embedding function F are eV. The units for the
+density function rho are the same as for drho (see above, electron
+density). The units for the effective charge Z are "atomic charge" or
+sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
+by LAMMPS to compute the pair potential term in the EAM energy
+expression as r*phi, in units of eV-Angstroms, via the formula
+</P>
+<PRE>r*phi = 27.2 * 0.529 * Zi * Zj
+</PRE>
+<P>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
+</P>
+<HR>
+
+<P>Style <I>eam/alloy</I> computes pairwise interactions using the same
+formula as style <I>eam</I>. However the associated
+<A HREF = "pair_coeff.html">pair_coeff</A> command reads a DYNAMO <I>setfl</I> file
+instead of a <I>funcfl</I> file. <I>Setfl</I> files can be used to model a
+single-element or alloy system. In the alloy case, as explained
+above, <I>setfl</I> files contain explicit tabulated values for alloy
+interactions. Thus they allow more generality than <I>funcfl</I> files for
+modeling alloys.
+</P>
+<P>For style <I>eam/alloy</I>, potential values are read from a file that is
+in the DYNAMO multi-element <I>setfl</I> format, except that element names
+(Ni, Cu, etc) are added to one of the lines in the file. If the
+DYNAMO file was created by a Fortran program, it cannot have "D"
+values in it for exponents. C only recognizes "e" or "E" for
+scientific notation.
+</P>
+<P>Only a single pair_coeff command is used with the <I>eam/alloy</I> style
+which specifies a DYNAMO <I>setfl</I> file, which contains information for
+M elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of <I>setfl</I> elements to atom types
+</UL>
+<P>As an example, the potentials/NiAlH_jea.eam.alloy file is a <I>setfl</I>
+file which has tabulated EAM values for 3 elements and their alloy
+interactions: Ni, Al, and H. See the <A HREF = "pair_coeff.html">pair_coeff</A> doc
+page for alternate ways to specify the path for the potential file.
+If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
+be Ni, and the 4th to be Al, you would use the following pair_coeff
+command:
+</P>
+<PRE>pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
+element in the <I>setfl</I> file. The final Al argument maps LAMMPS atom
+type 4 to the Al element in the <I>setfl</I> file. Note that there is no
+requirement that your simulation use all the elements specified by the
+<I>setfl</I> file.
+</P>
+<P>If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an <I>eam/alloy</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P><I>Setfl</I> files in the <I>potentials</I> directory of the LAMMPS distribution
+have an ".eam.alloy" suffix. A DYNAMO multi-element <I>setfl</I> file is
+formatted as follows:
+</P>
+<UL><LI>lines 1,2,3 = comments (ignored)
+<LI>line 4: Nelements Element1 Element2 ... ElementN
+<LI>line 5: Nrho, drho, Nr, dr, cutoff
+</UL>
+<P>In a DYNAMO <I>setfl</I> file, line 4 only lists Nelements = the # of
+elements in the <I>setfl</I> file. For LAMMPS, the element name (Ni, Cu,
+etc) of each element must be added to the line, in the order the
+elements appear in the file.
+</P>
+<P>The meaning and units of the values in line 5 is the same as for the
+<I>funcfl</I> file described above. Note that the cutoff (in Angstroms) is
+a global value, valid for all pairwise interactions for all element
+pairings.
+</P>
+<P>Following the 5 header lines are Nelements sections, one for each
+element, each with the following format:
+</P>
+<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+<LI>embedding function F(rho) (Nrho values)
+<LI>density function rho(r) (Nr values)
+</UL>
+<P>As with the <I>funcfl</I> files, only the mass (in mass <A HREF = "units.html">units</A>,
+e.g. mass number or grams/mole for metal units) is used by LAMMPS from
+the 1st line. The cubic lattice constant is in Angstroms. The F and
+rho arrays are unique to a single element and have the same format and
+units as in a <I>funcfl</I> file.
+</P>
+<P>Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed for all i,j element pairs in the same format
+as other arrays. Since these interactions are symmetric (i,j = j,i)
+only phi arrays with i >= j are listed, in the following order: i,j =
+(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
+Nelements). Unlike the effective charge array Z(r) in <I>funcfl</I> files,
+the tabulated values for each phi function are listed in <I>setfl</I> files
+directly as r*phi (in units of eV-Angstroms), since they are for atom
+pairs.
+</P>
+<HR>
+
+<P>Style <I>eam/cd</I> is similar to the <I>eam/alloy</I> style, except that it
+computes alloy pairwise interactions using the concentration-dependent
+embedded-atom method (CD-EAM). This model can reproduce the enthalpy
+of mixing of alloys over the full composition range, as described in
+<A HREF = "#Stukowski">(Stukowski)</A>.
+</P>
+<P>The pair_coeff command is specified the same as for the <I>eam/alloy</I>
+style. However the DYNAMO <I>setfl</I> file must has two
+lines added to it, at the end of the file:
+</P>
+<UL><LI>line 1: Comment line (ignored)
+<LI>line 2: N Coefficient0 Coefficient1 ... CoeffincientN
+</UL>
+<P>The last line begins with the degree <I>N</I> of the polynomial function
+<I>h(x)</I> that modifies the cross interaction between A and B elements.
+Then <I>N+1</I> coefficients for the terms of the polynomial are then
+listed.
+</P>
+<P>Modified EAM <I>setfl</I> files used with the <I>eam/cd</I> style must contain
+exactly two elements, i.e. in the current implementation the <I>eam/cd</I>
+style only supports binary alloys. The first and second elements in
+the input EAM file are always taken as the <I>A</I> and <I>B</I> species.
+</P>
+<P><I>CD-EAM</I> files in the <I>potentials</I> directory of the LAMMPS
+distribution have a ".cdeam" suffix.
+</P>
+<HR>
+
+<P>Style <I>eam/fs</I> computes pairwise interactions for metals and metal
+alloys using a generalized form of EAM potentials due to Finnis and
+Sinclair <A HREF = "#Finnis">(Finnis)</A>. The total energy Ei of an atom I is
+given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_eam_fs.jpg">
+</CENTER>
+<P>This has the same form as the EAM formula above, except that rho is
+now a functional specific to the atomic types of both atoms I and J,
+so that different elements can contribute differently to the total
+electron density at an atomic site depending on the identity of the
+element at that atomic site.
+</P>
+<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
+reads a DYNAMO <I>setfl</I> file that has been extended to include
+additional rho_alpha_beta arrays of tabulated values. A discussion of
+how FS EAM differs from conventional EAM alloy potentials is given in
+<A HREF = "#Ackland1">(Ackland1)</A>. An example of such a potential is the same
+author's Fe-P FS potential <A HREF = "#Ackland2">(Ackland2)</A>. Note that while FS
+potentials always specify the embedding energy with a square root
+dependence on the total density, the implementation in LAMMPS does not
+require that; the user can tabulate any functional form desired in the
+FS potential files.
+</P>
+<P>For style <I>eam/fs</I>, the form of the pair_coeff command is exactly the
+same as for style <I>eam/alloy</I>, e.g.
+</P>
+<PRE>pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
+</PRE>
+<P>where there are N additional arguments after the filename, where N is
+the number of LAMMPS atom types. See the <A HREF = "pair_coeff.html">pair_coeff</A>
+doc page for alternate ways to specify the path for the potential
+file. The N values determine the mapping of LAMMPS atom types to EAM
+elements in the file, as described above for style <I>eam/alloy</I>. As
+with <I>eam/alloy</I>, if a mapping value is NULL, the mapping is not
+performed. This can be used when an <I>eam/fs</I> potential is used as
+part of the <I>hybrid</I> pair style. The NULL values are used as
+placeholders for atom types that will be used with other potentials.
+</P>
+<P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
+files read by <I>eam/alloy</I>, in that i,j density functionals for all
+pairs of elements are included as needed by the Finnis/Sinclair
+formulation of the EAM.
+</P>
+<P>FS EAM files in the <I>potentials</I> directory of the LAMMPS distribution
+have an ".eam.fs" suffix. They are formatted as follows:
+</P>
+<UL><LI>lines 1,2,3 = comments (ignored)
+<LI>line 4: Nelements Element1 Element2 ... ElementN
+<LI>line 5: Nrho, drho, Nr, dr, cutoff
+</UL>
+<P>The 5-line header section is identical to an EAM <I>setfl</I> file.
+</P>
+<P>Following the header are Nelements sections, one for each element I,
+each with the following format:
+</P>
+<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
+<LI>embedding function F(rho) (Nrho values)
+<LI>density function rho(r) for element I at element 1 (Nr values)
+<LI>density function rho(r) for element I at element 2
+<LI>...
+<LI>density function rho(r) for element I at element Nelement
+</UL>
+<P>The units of these quantities in line 1 are the same as for <I>setfl</I>
+files. Note that the rho(r) arrays in Finnis/Sinclair can be
+asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
+file.
+</P>
+<P>Following the Nelements sections, Nr values for each pair potential
+phi(r) array are listed in the same manner (r*phi, units of
+eV-Angstroms) as in EAM <I>setfl</I> files. Note that in Finnis/Sinclair,
+the phi(r) arrays are still symmetric, so only phi arrays for i >= j
+are listed.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accerlate</A> of the manual for more
+instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above with the individual styles. You never need to specify
+a pair_coeff command with I != J arguments for the eam styles.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>The eam pair styles do not write their information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+</P>
+<P>The eam pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>All of these styles except the <I>eam/cd</I> style are part of the MANYBODY
+package. They are only enabled if LAMMPS was built with that package
+(which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The <I>eam/cd</I> style is part of the USER-MISC package and also requires
+the MANYBODY package. It is only enabled if LAMMPS was built with
+those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ackland1"></A>
+
+<P><B>(Ackland1)</B> Ackland, Condensed Matter (2005).
+</P>
+<A NAME = "Ackland2"></A>
+
+<P><B>(Ackland2)</B> Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
+of Physics: Condensed Matter, 16, S2629 (2004).
+</P>
+<A NAME = "Daw"></A>
+
+<P><B>(Daw)</B> Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
+Daw, Baskes, Phys Rev B, 29, 6443 (1984).
+</P>
+<A NAME = "Finnis"></A>
+
+<P><B>(Finnis)</B> Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
+</P>
+<A NAME = "Stukowski"></A>
+
+<P><B>(Stukowski)</B> Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
+Materials Science & Engineering, 7, 075005 (2009).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_edip.html b/doc/doc2/pair_edip.html
new file mode 100644
index 000000000..fcf1b3ec4
--- /dev/null
+++ b/doc/doc2/pair_edip.html
@@ -0,0 +1,174 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style edip command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style edip
+</PRE>
+<PRE>pair_style edip/omp
+</PRE>
+<P><B>Examples:</B>
+</P>
+<P>pair_style edip
+pair_coeff * * Si.edip Si
+</P>
+<P><B>Description:</B>
+</P>
+<P>The <I>edip</I> style computes a 3-body <A HREF = "#EDIP">EDIP</A> potential which is
+popular for modeling silicon materials where it can have advantages
+over other models such as the <A HREF = "pair_sw.html">Stillinger-Weber</A> or
+<A HREF = "pair_tersoff.html">Tersoff</A> potentials. In EDIP, the energy E of a
+system of atoms is
+</P>
+<CENTER><IMG SRC = "Eqs/pair_edip.jpg">
+</CENTER>
+<P>where phi2 is a two-body term and phi3 is a three-body term. The
+summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = a.
+Both terms depend on the local environment of atom I through its
+effective coordination number defined by Z, which is unity for a
+cutoff distance < c and gently goes to 0 at distance = a.
+</P>
+<P>Only a single pair_coeff command is used with the <I>edip</I> style which
+specifies a EDIP potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of EDIP elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine a file Si.edip has EDIP values for Si.
+</P>
+<P>EDIP files in the <I>potentials</I> directory of the LAMMPS
+distribution have a ".edip" suffix. Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements. The parameters in a single entry correspond to the two-body
+and three-body coefficients in the formula above:
+</P>
+<UL><LI>element 1 (the center atom in a 3-body interaction)
+<LI>element 2
+<LI>element 3
+<LI>A (energy units)
+<LI>B (distance units)
+<LI>cutoffA (distance units)
+<LI>cutoffC (distance units)
+<LI>alpha
+<LI>beta
+<LI>eta
+<LI>gamma (distance units)
+<LI>lambda (energy units)
+<LI>mu
+<LI>tho
+<LI>sigma (distance units)
+<LI>Q0
+<LI>u1
+<LI>u2
+<LI>u3
+<LI>u4
+</UL>
+<P>The A, B, beta, sigma parameters are used only for two-body interactions.
+The eta, gamma, lambda, mu, Q0 and all u1 to u4 parameters are used only
+for three-body interactions. The alpha and cutoffC parameters are used
+for the coordination environment function only.
+</P>
+<P>The EDIP potential file must contain entries for all the
+elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify EDIP parameters for all permutations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 27
+entries would be required, etc.
+</P>
+<P>At the moment, only a single element parametrization is
+implemented. However, the author is not aware of other
+multi-element EDIP parametrizations. If you know any and
+you are interest in that, please contact the author of
+the EDIP package.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This angle style can only be used if LAMMPS was built with the
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The EDIP potential files provided with LAMMPS (see the potentials directory)
+are parameterized for metal <A HREF = "units.html">units</A>.
+You can use the SW potential with any LAMMPS units, but you would need
+to create your own EDIP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "EDIP"></A>
+
+<P><B>(EDIP)</B> J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_eff.html b/doc/doc2/pair_eff.html
new file mode 100644
index 000000000..1e3b5391c
--- /dev/null
+++ b/doc/doc2/pair_eff.html
@@ -0,0 +1,325 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style eff/cut command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style eff/cut cutoff keyword args ...
+</PRE>
+<UL><LI>cutoff = global cutoff for Coulombic interactions
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>limit/eradius</I> or <I>pressure/evirials</I> or <I>ecp</I>
+ <I>limit/eradius</I> args = none
+ <I>pressure/evirials</I> args = none
+ <I>ecp</I> args = type element type element ...
+ type = LAMMPS atom type (1 to Ntypes)
+ element = element symbol (e.g. H, Si)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style eff/cut 39.7
+pair_style eff/cut 40.0 limit/eradius
+pair_style eff/cut 40.0 limit/eradius pressure/evirials
+pair_style eff/cut 40.0 ecp 1 Si 3 C
+pair_coeff * *
+pair_coeff 2 2 20.0
+pair_coeff 1 s 0.320852 2.283269 0.814857
+pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This pair style contains a LAMMPS implementation of the electron Force
+Field (eFF) potential currently under development at Caltech, as
+described in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>. The eFF for Z<6
+was first introduced by <A HREF = "#Su">(Su)</A> in 2007. It has been extended to
+higher Zs by using effective core potentials (ECPs) that now cover up
+to 2nd and 3rd row p-block elements of the periodic table.
+</P>
+<P>eFF can be viewed as an approximation to QM wave packet dynamics and
+Fermionic molecular dynamics, combining the ability of electronic
+structure methods to describe atomic structure, bonding, and chemistry
+in materials, and of plasma methods to describe nonequilibrium
+dynamics of large systems with a large number of highly excited
+electrons. Yet, eFF relies on a simplification of the electronic
+wavefunction in which electrons are described as floating Gaussian
+wave packets whose position and size respond to the various dynamic
+forces between interacting classical nuclear particles and spherical
+Gaussian electron wavepackets. The wavefunction is taken to be a
+Hartree product of the wave packets. To compensate for the lack of
+explicit antisymmetry in the resulting wavefunction, a spin-dependent
+Pauli potential is included in the Hamiltonian. Substituting this
+wavefunction into the time-dependent Schrodinger equation produces
+equations of motion that correspond - to second order - to classical
+Hamiltonian relations between electron position and size, and their
+conjugate momenta. The N-electron wavefunction is described as a
+product of one-electron Gaussian functions, whose size is a dynamical
+variable and whose position is not constrained to a nuclear
+center. This form allows for straightforward propagation of the
+wavefunction, with time, using a simple formulation from which the
+equations of motion are then integrated with conventional MD
+algorithms. In addition to this spin-dependent Pauli repulsion
+potential term between Gaussians, eFF includes the electron kinetic
+energy from the Gaussians. These two terms are based on
+first-principles quantum mechanics. On the other hand, nuclei are
+described as point charges, which interact with other nuclei and
+electrons through standard electrostatic potential forms.
+</P>
+<P>The full Hamiltonian (shown below), contains then a standard
+description for electrostatic interactions between a set of
+delocalized point and Gaussian charges which include, nuclei-nuclei
+(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
+mixed QM-classical mechanics method rather than a conventional force
+field method (in which electron motions are averaged out into ground
+state nuclear motions, i.e a single electronic state, and particle
+interactions are described via empirically parameterized interatomic
+potential functions). This makes eFF uniquely suited to simulate
+materials over a wide range of temperatures and pressures where
+electronically excited and ionized states of matter can occur and
+coexist. Furthermore, the interactions between particles -nuclei and
+electrons- reduce to the sum of a set of effective pairwise potentials
+in the eFF formulation. The <I>eff/cut</I> style computes the pairwise
+Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
+and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
+potentials between electrons (E_KE) for a total energy expression
+given as,
+</P>
+<CENTER><IMG SRC = "Eqs/eff_energy_expression.jpg">
+</CENTER>
+<P>The individual terms are defined as follows:
+</P>
+<CENTER><IMG SRC = "Eqs/eff_KE.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/eff_NN.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/eff_Ne.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/eff_ee.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/eff_Pauli.jpg">
+</CENTER>
+<P>where, s_i correspond to the electron sizes, the sigmas i's to the
+fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
+to the distances between the nuclei or the nuclei and electrons, and
+r_ij to the distances between electrons. For additional details see
+<A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
+</P>
+<P>The overall electrostatics energy is given in Hartree units of energy
+by default and can be modified by an energy-conversion constant,
+according to the units chosen (see <A HREF = "units.html">electron_units</A>). The
+cutoff Rc, given in Bohrs (by default), truncates the interaction
+distance. The recommended cutoff for this pair style should follow
+the minimum image criterion, i.e. half of the minimum unit cell
+length.
+</P>
+<P>Style <I>eff/long</I> (not yet available) computes the same interactions as
+style <I>eff/cut</I> except that an additional damping factor is applied so
+it can be used in conjunction with the
+<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
+option. The Coulombic cutoff specified for this style means that
+pairwise interactions within this distance are computed directly;
+interactions outside that distance are computed in reciprocal space.
+</P>
+<P>This potential is designed to be used with <A HREF = "atom_style.html">atom_style
+electron</A> definitions, in order to handle the
+description of systems with interacting nuclei and explicit electrons.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutoff (distance units)
+</UL>
+<P>For <I>eff/cut</I>, the cutoff coefficient is optional. If it is not used
+(as in some of the examples above), the default global value specified
+in the pair_style command is used.
+</P>
+<P>For <I>eff/long</I> (not yet available) no cutoff will be specified for an
+individual I,J type pair via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
+All type pairs use the same global cutoff specified in the pair_style
+command.
+</P>
+<HR>
+
+<P>The <I>limit/eradius</I> and <I>pressure/evirials</I> keywrods are optional.
+Neither or both must be specified. If not specified they are unset.
+</P>
+<P>The <I>limit/eradius</I> keyword is used to restrain electron size from
+becoming excessively diffuse at very high temperatures were the
+Gaussian wave packet representation breaks down, and from expanding as
+free particles to infinite size. If unset, electron radius is free to
+increase without bounds. If set, a restraining harmonic potential of
+the form E = 1/2k_ss^2 for s > L_box/2, where k_s = 1 Hartrees/Bohr^2,
+is applied on the electron radius.
+</P>
+<P>The <I>pressure/evirials</I> keyword is used to control between two types
+of pressure computation: if unset, the computed pressure does not
+include the electronic radial virials contributions to the total
+pressure (scalar or tensor). If set, the computed pressure will
+include the electronic radial virial contributions to the total
+pressure (scalar and tensor).
+</P>
+<P>The <I>ecp</I> keyword is used to associate an ECP representation for a
+particular atom type. The ECP captures the orbital overlap between a
+core pseudo particle and valence electrons within the Pauli repulsion.
+A list of type:element-symbol pairs may be provided for all ECP
+representations, after the "ecp" keyword.
+</P>
+<P>IMPORTANT NOTE: Default ECP parameters are provided for C, N, O, Al,
+and Si. Users can modify these using the pair_coeff command as
+exemplified above. For this, the User must distinguish between two
+different functional forms supported, one that captures the orbital
+overlap assuming the s-type core interacts with an s-like valence
+electron (s-s) and another that assumes the interaction is s-p. For
+systems that exhibit significant p-character (e.g. C, N, O) the s-p
+form is recommended. The "s" ECP form requires 3 parameters and the
+"p" 5 parameters.
+</P>
+<P>IMPORTANT NOTE: there are two different pressures that can be reported
+for eFF when defining this pair_style, one (default) that considers
+electrons do not contribute radial virial components (i.e. electrons
+treated as incompressible 'rigid' spheres) and one that does. The
+radial electronic contributions to the virials are only tallied if the
+flexible pressure option is set, and this will affect both global and
+per-atom quantities. In principle, the true pressure of a system is
+somewhere in between the rigid and the flexible eFF pressures, but,
+for most cases, the difference between these two pressures will not be
+significant over long-term averaged runs (i.e. even though the energy
+partitioning changes, the total energy remains similar).
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: This implemention of eFF gives a reasonably accurate
+description for systems containing nuclei from Z = 1-6 in "all
+electron" representations. For systems with increasingly
+non-spherical electrons, Users should use the ECP representations.
+ECPs are now supported and validated for most of the 2nd and 3rd row
+elements of the p-block. Predefined parameters are provided for C, N,
+O, Al, and Si. The ECP captures the orbital overlap between the core
+and valence electrons (i.e. Pauli repulsion) with one of the
+functional forms:
+</P>
+<CENTER><IMG SRC = "Eqs/eff_ECP1.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/eff_ECP2.jpg">
+</CENTER>
+<P>Where the 1st form correspond to core interactions with s-type valence
+electrons and the 2nd to core interactions with p-type valence
+electrons.
+</P>
+<P>The current version adds full support for models with fixed-core and
+ECP definitions. to enable larger timesteps (i.e. by avoiding the
+high frequency vibrational modes -translational and radial- of the 2 s
+electrons), and in the ECP case to reduce the increased orbital
+complexity in higher Z elements (up to Z<18). A fixed-core should be
+defined with a mass that includes the corresponding nuclear mass plus
+the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a
+radius equivalent to that of minimized 1s electrons (see examples
+under /examples/USER/eff/fixed-core). An pseudo-core should be
+described with a mass that includes the corresponding nuclear mass,
+plus all the core electrons (i.e no outer shell electrons), and a
+radius equivalent to that of a corresponding minimized full-electron
+system. The charge for a pseudo-core atom should be given by the
+number of outer shell electrons.
+</P>
+<P>In general, eFF excels at computing the properties of materials in
+extreme conditions and tracing the system dynamics over multi-picosend
+timescales; this is particularly relevant where electron excitations
+can change significantly the nature of bonding in the system. It can
+capture with surprising accuracy the behavior of such systems because
+it describes consistently and in an unbiased manner many different
+kinds of bonds, including covalent, ionic, multicenter, ionic, and
+plasma, and how they interconvert and/or change when they become
+excited. eFF also excels in computing the relative thermochemistry of
+isodemic reactions and conformational changes, where the bonds of the
+reactants are of the same type as the bonds of the products. eFF
+assumes that kinetic energy differences dominate the overall exchange
+energy, which is true when the electrons present are nearly spherical
+and nodeless and valid for covalent compounds such as dense hydrogen,
+hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
+metals (e.g. beryllium) and semimetals such as boron; and various
+compounds containing ionic and/or multicenter bonds, such as boron
+dihydride.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the cutoff distance for the
+<I>eff/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
+See the "pair_modify" command for details.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant for
+these pair styles.
+</P>
+<P>The <I>eff/long</I> (not yet available) style supports the
+<A HREF = "pair_modify.html">pair_modify</A> table option for tabulation of the
+short-range portion of the long-range Coulombic interaction.
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles will only be enabled if LAMMPS is built with the
+USER-EFF package. It will only be enabled if LAMMPS was built with
+that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info.
+</P>
+<P>These pair styles require that particles store electron attributes
+such as radius, radial velocity, and radital force, as defined by the
+<A HREF = "atom_style.html">atom_style</A>. The <I>electron</I> atom style does all of
+this.
+</P>
+<P>Thes pair styles require you to use the <A HREF = "comm_modify.html">comm_modify vel
+yes</A> command so that velocites are stored by ghost
+atoms.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>If not specified, limit_eradius = 0 and pressure_with_evirials = 0.
+</P>
+<HR>
+
+<A NAME = "Su"></A>
+
+<P><B>(Su)</B> Su and Goddard, Excited Electron Dynamics Modeling of Warm
+Dense Matter, Phys Rev Lett, 99:185003 (2007).
+</P>
+<A NAME = "Jaramillo-Botero"></A>
+
+<P><B>(Jaramillo-Botero)</B> Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
+Long-term Non-adiabatic Electron Molecular Dynamics for Describing
+Material Properties and Phenomena in Extreme Environments, J Comp
+Chem, 32, 497-512 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_eim.html b/doc/doc2/pair_eim.html
new file mode 100644
index 000000000..01867a598
--- /dev/null
+++ b/doc/doc2/pair_eim.html
@@ -0,0 +1,181 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style eim command
+</H3>
+<H3>pair_style eim/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style
+</PRE>
+<UL><LI>style = <I>eim</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style eim
+pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
+pair_coeff * * Na Cl ffield.eim Na Na Na Cl
+pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>eim</I> computes pairwise interactions for ionic compounds
+using embedded-ion method (EIM) potentials <A HREF = "#Zhou">(Zhou)</A>. The
+energy of the system E is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_eim1.jpg">
+</CENTER>
+<P>The first term is a double pairwise sum over the J neighbors of all I
+atoms, where phi_ij is a pair potential. The second term sums over
+the embedding energy E_i of atom I, which is a function of its charge
+q_i and the electrical potential sigma_i at its location. E_i, q_i,
+and sigma_i are calculated as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_eim2.jpg">
+</CENTER>
+<P>where eta_ji is a pairwise function describing electron flow from atom
+I to atom J, and psi_ij is another pairwise function. The multi-body
+nature of the EIM potential is a result of the embedding energy term.
+A complete list of all the pair functions used in EIM is summarized
+below
+</P>
+<CENTER><IMG SRC = "Eqs/pair_eim3.jpg">
+</CENTER>
+<P>Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi),
+r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type
+p are parameters, with subscripts ij indicating the two species of
+atoms in the atomic pair.
+</P>
+<P>IMPORTANT NOTE: Even though the EIM potential is treating atoms as
+charged ions, you should not use a LAMMPS <A HREF = "atom_style.html">atom_style</A>
+that stores a charge on each atom and thus requires you to assign a
+charge to each atom, e.g. the <I>charge</I> or <I>full</I> atom styles. This is
+because the EIM potential infers the charge on an atom from the
+equation above for q_i; you do not assign charges explicitly.
+</P>
+<HR>
+
+<P>All the EIM parameters are listed in a potential file which is
+specified by the <A HREF = "pair_coeff.html">pair_coeff</A> command. This is an
+ASCII text file in a format described below. The "ffield.eim" file
+included in the "potentials" directory of the LAMMPS distribution
+currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
+A system with any combination of these elements can be modeled. This
+file is parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
+</P>
+<P>Note that unlike other potentials, cutoffs for EIM potentials are not
+set in the pair_style or pair_coeff command; they are specified in the
+EIM potential file itself. Likewise, the EIM potential file lists
+atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
+command to specify them.
+</P>
+<P>Only a single pair_coeff command is used with the <I>eim</I> style which
+specifies an EIM potential file and the element(s) to extract
+information for. The EIM elements are mapped to LAMMPS atom types by
+specifying N additional arguments after the filename in the pair_coeff
+command, where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>Elem1, Elem2, ...
+<LI>EIM potential file
+<LI>N element names = mapping of EIM elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example like one of those above, suppose you want to model a
+system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
+types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
+use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * Na Cl ffield.eim Na Na Na Cl
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The filename is the EIM potential file. The Na and Cl arguments
+(before the file name) are the two elements for which info will be
+extracted from the potentail file. The first three trailing Na
+arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
+final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
+</P>
+<P>If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when an <I>eim</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P>The ffield.eim file in the <I>potentials</I> directory of the LAMMPS
+distribution is formated as follows:
+</P>
+<P>Lines starting with # are comments and are ignored by LAMMPS. Lines
+starting with "global:" include three global values. The first value
+divides the cations from anions, i.e., any elements with
+electronegativity above this value are viewed as anions, and any
+elements with electronegativity below this value are viewed as
+cations. The second and third values are related to the cutoff
+function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
+equation can be derived from these values.
+</P>
+<P>Lines starting with "element:" are formatted as follows: name of
+element, atomic number, atomic mass, electronic negativity, atomic
+radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
+energy (LAMMPS ignores it), and q0 (must be 0).
+</P>
+<P>Lines starting with "pair:" are entered as: element 1, element 2,
+r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e,
+alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta,
+r_(s,psi), and p.
+</P>
+<P>The lines in the file can be in any order; LAMMPS extracts the info it
+needs.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the MANYBODY package. It is only enabled if
+LAMMPS was built with that package (which it is by default).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Zhou"></A>
+
+<P><B>(Zhou)</B> Zhou, submitted for publication (2010). Please contact
+Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_gauss.html b/doc/doc2/pair_gauss.html
new file mode 100644
index 000000000..a3753aab3
--- /dev/null
+++ b/doc/doc2/pair_gauss.html
@@ -0,0 +1,172 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style gauss command
+</H3>
+<H3>pair_style gauss/gpu command
+</H3>
+<H3>pair_style gauss/omp command
+</H3>
+<H3>pair_style gauss/cut command
+</H3>
+<H3>pair_style gauss/cut/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style gauss cutoff
+pair_style gauss/cut cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for Gauss interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style gauss 12.0
+pair_coeff * * 1.0 0.9
+pair_coeff 1 4 1.0 0.9 10.0
+</PRE>
+<PRE>pair_style gauss/cut 3.5
+pair_coeff 1 4 0.2805 1.45 0.112
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>gauss</I> computes a tethering potential of the form
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gauss.jpg">
+</CENTER>
+<P>between an atom and its corresponding tether site which will typically
+be a frozen atom in the simulation. Rc is the cutoff.
+</P>
+<P>The following coefficients must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>A (energy units)
+<LI>B (1/distance^2 units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+is used.
+</P>
+<P>Style <I>gauss/cut</I> computes a generalized Gaussian interaction potential
+between pairs of particles:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gauss_cut.jpg">
+</CENTER>
+<P>where H determines together with the standard deviation sigma_h the
+peak height of the Gaussian function, and r_mh the peak position.
+Examples of the use of the Gaussian potentials include implicit
+solvent simulations of salt ions <A HREF = "#Lenart">(Lenart)</A> and of surfactants
+<A HREF = "#Jusufi">(Jusufi)</A>. In these instances the Gaussian potential mimics
+the hydration barrier between a pair of particles. The hydration
+barrier is located at r_mh and has a width of sigma_h. The prefactor
+determines the hight of the potential barrier.
+</P>
+<P>The following coefficients must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>H (energy * distance units)
+<LI>r_mh (distance units)
+<LI>sigma_h (distance units)
+</UL>
+<P>The global cutoff (r_c) specified in the pair_style command is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>The <I>gauss</I> style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option. There is no effect due to the Gaussian well beyond the
+cutoff; hence reasonable cutoffs need to be specified.
+</P>
+<P>The <I>gauss/cut</I> style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Gauss-potential portion of the pair
+interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for these pair styles.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P>The <I>gauss</I> pair style tallies an "occupancy" count of how many Gaussian-well
+sites have an atom within the distance at which the force is a maximum
+= sqrt(0.5/b). This quantity can be accessed via the <A HREF = "compute_pair.html">compute
+pair</A> command as a vector of values of length 1.
+</P>
+<P>To print this quantity to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+</P>
+<PRE>compute gauss all pair gauss
+variable occ equal c_gauss[1]
+thermo_style custom step temp epair v_occ
+</PRE>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>gauss/cut</I> style is part of the "user-misc" package. It is only
+enabled if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "pair_coul_diel.html">pair_style coul/diel</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<A NAME = "Lenart"></A>
+
+<P><B>(Lenart)</B> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
+044509 (2007).
+</P>
+<A NAME = "Jusufi"></A>
+
+<P><B>(Jusufi)</B> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
+13783 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_gayberne.html b/doc/doc2/pair_gayberne.html
new file mode 100644
index 000000000..27de23053
--- /dev/null
+++ b/doc/doc2/pair_gayberne.html
@@ -0,0 +1,243 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style gayberne command
+</H3>
+<H3>pair_style gayberne/gpu command
+</H3>
+<H3>pair_style gayberne/intel command
+</H3>
+<H3>pair_style gayberne/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style gayberne gamma upsilon mu cutoff
+</PRE>
+<UL><LI>gamma = shift for potential minimum (typically 1)
+<LI>upsilon = exponent for eta orientation-dependent energy function
+<LI>mu = exponent for chi orientation-dependent energy function
+<LI>cutoff = global cutoff for interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
+pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>gayberne</I> styles compute a Gay-Berne anisotropic LJ interaction
+<A HREF = "#Berardi">(Berardi)</A> between pairs of ellipsoidal particles or an
+ellipsoidal and spherical particle via the formulas
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
+</CENTER>
+<P>where A1 and A2 are the transformation matrices from the simulation
+box frame to the body frame and r12 is the center to center vector
+between the particles. Ur controls the shifted distance dependent
+interaction based on the distance of closest approach of the two
+particles (h12) and the user-specified shift parameter gamma. When
+both particles are spherical, the formula reduces to the usual
+Lennard-Jones interaction (see details below for when Gay-Berne treats
+a particle as "spherical").
+</P>
+<P>For large uniform molecules it has been shown that the energy
+parameters are approximately representable in terms of local contact
+curvatures <A HREF = "#Everaers">(Everaers)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gayberne2.jpg">
+</CENTER>
+<P>The variable names utilized as potential parameters are for the most
+part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
+the <A HREF = "pair_resquared.html">RE-squared pair potential</A>. Details on the
+upsilon and mu parameters are given
+<A HREF = "PDF/pair_resquared_extra.pdf">here</A>.
+</P>
+<P>More details of the Gay-Berne formulation are given in the references
+listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
+document</A>.
+</P>
+<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
+<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
+order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
+ellipsoid</A> should be used since it defines the
+rotational state and the size and shape of each ellipsoidal particle.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon = well depth (energy units)
+<LI>sigma = minimum effective particle radii (distance units)
+<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
+<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
+<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
+<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
+<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
+<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global
+cutoff specified in the pair_style command is used.
+</P>
+<P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
+minimum of the 3 shape diameters of the particles involved in an I,I
+interaction, though this is not required. Note that this is a
+different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
+resquared</A> potential uses.
+</P>
+<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
+types, not for pairs of atom types. Thus, in a series of pair_coeff
+commands, they only need to be specified once for each atom type.
+</P>
+<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
+non-zero, the three values are assigned to atom type I. If all the
+epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
+epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
+to atom type J. If all three epsilon_j values are zero, they are
+ignored. Thus the typical way to define the epsilon_i and epsilon_j
+coefficients is to list their values in "pair_coeff I J" commands when
+I = J, but set them to 0.0 when I != J. If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair_coeff commands, since only the last setting will be in effect.
+</P>
+<P>Note that if this potential is being used as a sub-style of
+<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
+setting made for Gay-Berne for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type. e.g. in a "pair_coeff I J" command.
+</P>
+<P>IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the
+shape of the particle itself is spherical, meaning its 3 shape
+parameters are all the same, then the particle is treated as an LJ
+sphere by the Gay-Berne potential. This is significant because if two
+LJ spheres interact, then the simple Lennard-Jones formula is used to
+compute their interaction energy/force using the specified epsilon and
+sigma as the standard LJ parameters. This is much cheaper to compute
+than the full Gay-Berne formula. To treat the particle as a LJ sphere
+with sigma = D, you should normally set epsilon a = b = c = 1.0, set
+the pair_coeff sigma = D, and also set the 3 shape parameters for the
+particle to D. The one exception is that if the 3 shape parameters
+are set to 0.0, which is a valid way in LAMMPS to specify a point
+particle, then the Gay-Berne potential will treat that as shape
+parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
+requires finite-size particles. In this case you should still set the
+pair_coeff sigma to 1.0 as well.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed. The default mix
+value is <I>geometric</I>. See the "pair_modify" command for details.
+</P>
+<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions. There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>gayberne</I> style is part of the ASPHERE package. It is only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>These pair style require that atoms store torque and a quaternion to
+represent their orientation, as defined by the
+<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
+<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
+diameter.
+</P>
+<P>This pair style requires that atoms be ellipsoids as defined by the
+<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
+</P>
+<P>Particles acted on by the potential can be finite-size aspherical or
+spherical particles, or point particles. Spherical particles have all
+3 of their shape parameters equal to each other. Point particles have
+all 3 of their shape parameters equal to 0.0.
+</P>
+<P>The Gay-Berne potential does not become isotropic as r increases
+<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
+approximation used by LAMMPS becomes less accurate when high-aspect
+ratio ellipsoids are used.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
+<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_resquared.html">pair_style
+resquared</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Everaers"></A>
+
+<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+</P>
+<A NAME = "Berardi"></A>
+
+<P><B>(Berardi)</B> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
+Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
+</P>
+<A NAME = "Perram"></A>
+
+<P><B>(Perram)</B> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
+</P>
+<A NAME = "Allen"></A>
+
+<P><B>(Allen)</B> Allen and Germano, Mol Phys 104, 3225-3235 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_gran.html b/doc/doc2/pair_gran.html
new file mode 100644
index 000000000..281d2246e
--- /dev/null
+++ b/doc/doc2/pair_gran.html
@@ -0,0 +1,279 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style gran/hooke command
+</H3>
+<H3>pair_style gran/cuda command
+</H3>
+<H3>pair_style gran/omp command
+</H3>
+<H3>pair_style gran/hooke/history command
+</H3>
+<H3>pair_style gran/hooke/history/omp command
+</H3>
+<H3>pair_style gran/hertz/history command
+</H3>
+<H3>pair_style gran/hertz/history/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style Kn Kt gamma_n gamma_t xmu dampflag
+</PRE>
+<UL><LI>style = <I>gran/hooke</I> or <I>gran/hooke/history</I> or <I>gran/hertz/history</I>
+
+<LI>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+
+<LI>Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+
+<LI>gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+
+<LI>gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+
+<LI>xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+
+<LI>dampflag = 0 or 1 if tangential damping force is excluded or included
+</UL>
+<P>IMPORTANT NOTE: Versions of LAMMPS before 9Jan09 had different style
+names for granular force fields. This is to emphasize the fact that
+the Hertzian equation has changed to model polydispersity more
+accurately. A side effect of the change is that the Kn, Kt, gamma_n,
+and gamma_t coefficients in the pair_style command must be specified
+with different values in order to reproduce calculations made with
+earlier versions of LAMMPS, even for monodisperse systems. See the
+NOTE below for details.
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
+pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>gran</I> styles use the following formulas for the frictional force
+between two granular particles, as described in
+<A HREF = "#Brilliantov">(Brilliantov)</A>, <A HREF = "#Silbert">(Silbert)</A>, and
+<A HREF = "#Zhang">(Zhang)</A>, when the distance r between two particles of radii
+Ri and Rj is less than their contact distance d = Ri + Rj. There is
+no force between the particles when r > d.
+</P>
+<P>The two Hookean styles use this formula:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gran_hooke.jpg">
+</CENTER>
+<P>The Hertzian style uses this formula:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gran_hertz.jpg">
+</CENTER>
+<P>In both equations the first parenthesized term is the normal force
+between the two particles and the second parenthesized term is the
+tangential force. The normal force has 2 terms, a contact force and a
+damping force. The tangential force also has 2 terms: a shear force
+and a damping force. The shear force is a "history" effect that
+accounts for the tangential displacement between the particles for the
+duration of the time they are in contact. This term is included in
+pair styles <I>hooke/history</I> and <I>hertz/history</I>, but is not included
+in pair style <I>hooke</I>. The tangential damping force term is included
+in all three pair styles if <I>dampflag</I> is set to 1; it is not included
+if <I>dampflag</I> is set to 0.
+</P>
+<P>The other quantities in the equations are as follows:
+</P>
+<UL><LI>delta = d - r = overlap distance of 2 particles
+<LI>Kn = elastic constant for normal contact
+<LI>Kt = elastic constant for tangential contact
+<LI>gamma_n = viscoelastic damping constant for normal contact
+<LI>gamma_t = viscoelastic damping constant for tangential contact
+<LI>m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj
+<LI>Delta St = tangential displacement vector between 2 spherical particles which is truncated to satisfy a frictional yield criterion
+<LI>n_ij = unit vector along the line connecting the centers of the 2 particles
+<LI>Vn = normal component of the relative velocity of the 2 particles
+<LI>Vt = tangential component of the relative velocity of the 2 particles
+</UL>
+<P>The Kn, Kt, gamma_n, and gamma_t coefficients are specified as
+parameters to the pair_style command. If a NULL is used for Kt, then
+a default value is used where Kt = 2/7 Kn. If a NULL is used for
+gamma_t, then a default value is used where gamma_t = 1/2 gamma_n.
+</P>
+<P>The interpretation and units for these 4 coefficients are different in
+the Hookean versus Hertzian equations.
+</P>
+<P>The Hookean model is one where the normal push-back force for two
+overlapping particles is a linear function of the overlap distance.
+Thus the specified Kn is in units of (force/distance). Note that this
+push-back force is independent of absolute particle size (in the
+monodisperse case) and of the relative sizes of the two particles (in
+the polydisperse case). This model also applies to the other terms in
+the force equation so that the specified gamma_n is in units of
+(1/time), Kt is in units of (force/distance), and gamma_t is in units
+of (1/time).
+</P>
+<P>The Hertzian model is one where the normal push-back force for two
+overlapping particles is proportional to the area of overlap of the
+two particles, and is thus a non-linear function of overlap distance.
+Thus Kn has units of force per area and is thus specified in units of
+(pressure). The effects of absolute particle size (monodispersity)
+and relative size (polydispersity) are captured in the radii-dependent
+pre-factors. When these pre-factors are carried through to the other
+terms in the force equation it means that the specified gamma_n is in
+units of (1/(time*distance)), Kt is in units of (pressure), and
+gamma_t is in units of (1/(time*distance)).
+</P>
+<P>Note that in the Hookean case, Kn can be thought of as a linear spring
+constant with units of force/distance. In the Hertzian case, Kn is
+like a non-linear spring constant with units of force/area or
+pressure, and as shown in the <A HREF = "#Zhang">(Zhang)</A> paper, Kn = 4G /
+(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E /
+(2(1+nu)), and E = Young's modulus. Similarly, Kt = 4G / (2-nu).
+(NOTE: in an earlier version of the manual, we incorrectly stated that
+Kt = 8G / (2-nu).)
+</P>
+<P>Thus in the Hertzian case Kn and Kt can be set to values that
+corresponds to properties of the material being modeled. This is also
+true in the Hookean case, except that a spring constant must be chosen
+that is appropriate for the absolute size of particles in the model.
+Since relative particle sizes are not accounted for, the Hookean
+styles may not be a suitable model for polydisperse systems.
+</P>
+<P>IMPORTANT NOTE: In versions of LAMMPS before 9Jan09, the equation for
+Hertzian interactions did not include the sqrt(RiRj/Ri+Rj) term and
+thus was not as accurate for polydisperse systems. For monodisperse
+systems, sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales
+all 4 coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the
+values of these 4 coefficients appropriately in the current code to
+reproduce the results of a previous Hertzian monodisperse calculation.
+For example, for the common case of a monodisperse system with
+particles of diameter 1, all 4 of these coefficients should now be set
+2x larger than they were previously.
+</P>
+<P>Xmu is also specified in the pair_style command and is the upper limit
+of the tangential force through the Coulomb criterion Ft = xmu*Fn,
+where Ft and Fn are the total tangential and normal force components
+in the formulas above. Thus in the Hookean case, the tangential force
+between 2 particles grows according to a tangential spring and
+dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until
+the particles lose contact. In the Hertzian case, a similar analogy
+holds, though the spring is no longer linear.
+</P>
+<P>IMPORTANT NOTE: Normally, xmu should be specified as a fractional
+value between 0.0 and 1.0, however LAMMPS allows large values (up to
+1.0e4) to allow for modeling of systems which can sustain very large
+tangential forces.
+</P>
+<P>For granular styles there are no additional coefficients to set for
+each pair of atom types via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
+All settings are global and are made via the pair_style command.
+However you must still use the <A HREF = "pair_coeff.html">pair_coeff</A> for all
+pairs of granular atom types. For example the command
+</P>
+<PRE>pair_coeff * *
+</PRE>
+<P>should be used if all atoms in the simulation interact via a granular
+potential (i.e. one of the pair styles above is used). If a granular
+potential is used as a sub-style of <A HREF = "pair_hybrid.html">pair_style
+hybrid</A>, then specific atom types can be used in the
+pair_coeff command to determine which atoms interact via a granular
+potential.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options
+are not relevant for granular pair styles.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so a pair_style command does not need to be
+specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P>The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials. It also returns only the normal component of
+the pairwise interaction force. However, the single() function also
+calculates 4 extra pairwise quantities. The first 3 are the
+components of the tangential force between particles I and J, acting
+on particle I. <I>P4</I> is the magnitude of this tangential force. These
+extra quantites can be accessed by the <A HREF = "compute_pair_local.html">compute
+pair/local</A> command, as <I>p1</I>, <I>p2</I>, <I>p3</I>,
+<I>p4</I>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P>All the granular pair styles are part of the GRANULAR package. It is
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>These pair styles require that atoms store torque and angular velocity
+(omega) as defined by the <A HREF = "atom_style.html">atom_style</A>. They also
+require a per-particle radius is stored. The <I>sphere</I> atom style does
+all of this.
+</P>
+<P>This pair style requires you to use the <A HREF = "comm_modify.html">comm_modify vel
+yes</A> command so that velocites are stored by ghost
+atoms.
+</P>
+<P>These pair styles will not restart exactly when using the
+<A HREF = "read_restart.html">read_restart</A> command, though they should provide
+statistically similar results. This is because the forces they
+compute depend on atom velocities. See the
+<A HREF = "read_restart.html">read_restart</A> command for more details.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Brilliantov"></A>
+
+<P><B>(Brilliantov)</B> Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53,
+p 5382-5392 (1996).
+</P>
+<A NAME = "Silbert"></A>
+
+<P><B>(Silbert)</B> Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev
+E, 64, p 051302 (2001).
+</P>
+<A NAME = "Zhang"></A>
+
+<P><B>(Zhang)</B> Zhang and Makse, Phys Rev E, 72, p 011301 (2005).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_gromacs.html b/doc/doc2/pair_gromacs.html
new file mode 100644
index 000000000..eb74024b8
--- /dev/null
+++ b/doc/doc2/pair_gromacs.html
@@ -0,0 +1,170 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/gromacs command
+</H3>
+<H3>pair_style lj/gromacs/cuda command
+</H3>
+<H3>pair_style lj/gromacs/gpu command
+</H3>
+<H3>pair_style lj/gromacs/omp command
+</H3>
+<H3>pair_style lj/gromacs/coul/gromacs command
+</H3>
+<H3>pair_style lj/gromacs/coul/gromacs/cuda command
+</H3>
+<H3>pair_style lj/gromacs/coul/gromacs/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/gromacs</I> or <I>lj/gromacs/coul/gromacs</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/gromacs</I> args = inner outer
+ inner, outer = global switching cutoffs for Lennard Jones
+ <I>lj/gromacs/coul/gromacs</I> args = inner outer (inner2) (outer2)
+ inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+ inner2, outer2 = global switching cutoffs for Coulombic (optional)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/gromacs 9.0 12.0
+pair_coeff * * 100.0 2.0
+pair_coeff 2 2 100.0 2.0 8.0 10.0
+</PRE>
+<PRE>pair_style lj/gromacs/coul/gromacs 9.0 12.0
+pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/gromacs</I> styles compute shifted LJ and Coulombic interactions
+with an additional switching function S(r) that ramps the energy and force
+smoothly to zero between an inner and outer cutoff. It is a commonly
+used potential in the <A HREF = "http://www.gromacs.org">GROMACS</A> MD code and for
+the coarse-grained models of <A HREF = "#Marrink">(Marrink)</A>.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_gromacs.jpg">
+</CENTER>
+<P>r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
+and C are computed by LAMMPS to perform the shifting and smoothing.
+The function
+S(r) is actually applied once to each term of the LJ formula and once
+to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
+depending on which pair_style is used. The boundary conditions
+applied to the smoothing function are as follows: S'(r1) = S''(r1) = 0,
+S(rc) = -E(rc), S'(rc) = -E'(rc), and S''(rc) = -E''(rc),
+where E(r) is the corresponding term
+in the LJ or Coulombic potential energy function.
+Single and double primes denote first and second
+derivatives with respect to r, respectively.
+</P>
+<P>The inner and outer cutoff for the LJ and Coulombic terms can be the
+same or different depending on whether 2 or 4 arguments are used in
+the pair_style command. The inner LJ cutoff must be > 0, but the
+inner Coulombic cutoff can be >= 0.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>inner (distance units)
+<LI>outer (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2^(1/6)
+sigma.
+</P>
+<P>The last 2 coefficients are optional inner and outer cutoffs for style
+<I>lj/gromacs</I>. If not specified, the global <I>inner</I> and <I>outer</I> values
+are used.
+</P>
+<P>The last 2 coefficients cannot be used with style
+<I>lj/gromacs/coul/gromacs</I> because this force field does not allow
+varying cutoffs for individual atom pairs; all pairs use the global
+cutoff(s) specified in the pair_style command.
+</P>
+<HR>
+
+<P>Styles <I>intel</I>, <I>kk</I>, with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>None of the GROMACS pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
+portion of the pair interaction is already smoothed to 0.0 at the
+cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>None of the GROMACS pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
+corrections to energy and pressure, since there are no corrections for
+a potential that goes to 0.0 at the cutoff.
+</P>
+<P>All of the GROMACS pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>All of the GROMACS pair styles can only be used via the <I>pair</I>
+keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
+support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Marrink"></A>
+
+<P><B>(Marrink)</B> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_hbond_dreiding.html b/doc/doc2/pair_hbond_dreiding.html
new file mode 100644
index 000000000..617d0fa3f
--- /dev/null
+++ b/doc/doc2/pair_hbond_dreiding.html
@@ -0,0 +1,255 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style hbond/dreiding/lj command
+</H3>
+<H3>pair_style hbond/dreiding/lj/omp command
+</H3>
+<H3>pair_style hbond/dreiding/morse command
+</H3>
+<H3>pair_style hbond/dreiding/morse/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
+</PRE>
+<UL><LI>style = <I>hbond/dreiding/lj</I> or <I>hbond/dreiding/morse</I>
+<LI>n = cosine angle periodicity
+<LI>inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)
+<LI>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
+<LI>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
+<LI>interactions (degrees)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
+</PRE>
+<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hbond/dreiding</I> styles compute the Acceptor-Hydrogen-Donor (AHD)
+3-body hydrogen bond interaction for the
+<A HREF = "Section_howto.html#howto_4">DREIDING</A> force field, given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_hbond_dreiding.jpg">
+</CENTER>
+<P>where Rin is the inner spline distance cutoff, Rout is the outer
+distance cutoff, theta_c is the angle cutoff, and n is the cosine
+periodicity.
+</P>
+<P>Here, <I>r</I> is the radial distance between the donor (D) and acceptor
+(A) atoms and <I>theta</I> is the bond angle between the acceptor, the
+hydrogen (H) and the donor atoms:
+</P>
+<CENTER><IMG SRC = "Eqs/dreiding_hbond.jpg">
+</CENTER>
+<P>These 3-body interactions can be defined for pairs of acceptor and
+donor atoms, based on atom types. For each donor/acceptor atom pair,
+the 3rd atom in the interaction is a hydrogen permanently bonded to
+the donor atom, e.g. in a bond list read in from a data file via the
+<A HREF = "read_data.html">read_data</A> command. The atom types of possible
+hydrogen atoms for each donor/acceptor type pair are specified by the
+<A HREF = "pair_coeff.html">pair_coeff</A> command (see below).
+</P>
+<P>Style <I>hbond/dreiding/lj</I> is the original DREIDING potential of
+<A HREF = "#Mayo">(Mayo)</A>. It uses a LJ 12/10 functional for the Donor-Acceptor
+interactions. To match the results in the original paper, use n = 4.
+</P>
+<P>Style <I>hbond/dreiding/morse</I> is an improved version using a Morse
+potential for the Donor-Acceptor interactions. <A HREF = "#Liu">(Liu)</A> showed
+that the Morse form gives improved results for Dendrimer simulations,
+when n = 2.
+</P>
+<P>See this <A HREF = "Section_howto.html#howto_4">howto section</A> of the manual for
+more information on the DREIDING forcefield.
+</P>
+<P>IMPORTANT NOTE: Because the Dreiding hydrogen bond potential is only
+one portion of an overall force field which typically includes other
+pairwise interactions, it is common to use it as a sub-style in a
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command, where another
+pair style provides the repulsive core interaction between pairs of
+atoms, e.g. a 1/r^12 Lennard-Jones repulsion.
+</P>
+<P>IMPORTANT NOTE: When using the hbond/dreiding pair styles with
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>, you should explicitly
+define pair interactions between the donor atom and acceptor atoms,
+(as well as between these atoms and ALL other atoms in your system).
+Whenever <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> is used,
+ordinary mixing rules are not applied to atoms like the donor and
+acceptor atoms because they are typically referenced in multiple pair
+styles. Neglecting to do this can cause difficult-to-detect physics
+problems.
+</P>
+<P>IMPORTANT NOTE: In the original Dreiding force field paper 1-4
+non-bonded interactions ARE allowed. If this is desired for your
+model, use the special_bonds command (e.g. "special_bonds lj 0.0 0.0
+1.0") to turn these interactions on.
+</P>
+<HR>
+
+<P>The following coefficients must be defined for pairs of eligible
+donor/acceptor types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as
+in the examples above.
+</P>
+<P>IMPORTANT NOTE: Unlike other pair styles and their associated
+<A HREF = "pair_coeff.html">pair_coeff</A> commands, you do not need to specify
+pair_coeff settings for all possible I,J type pairs. Only I,J type
+pairs for atoms which act as joint donors/acceptors need to be
+specified; all other type pairs are assumed to be inactive.
+</P>
+<P>IMPORTANT NOTE: A <A HREF = "pair_coeff.html">pair_coeff</A> command can be
+speficied multiple times for the same donor/acceptor type pair. This
+enables multiple hydrogen types to be assigned to the same
+donor/acceptor type pair. For other pair_styles, if the pair_coeff
+command is re-used for the same I.J type pair, the settings for that
+type pair are overwritten. For the hydrogen bond potentials this is
+not the case; the settings are cummulative. This means the only way
+to turn off a previous setting, is to re-use the pair_style command
+and start over.
+</P>
+<P>For the <I>hbond/dreiding/lj</I> style the list of coefficients is as
+follows:
+</P>
+<UL><LI>K = hydrogen atom type = 1 to Ntypes
+<LI>donor flag = <I>i</I> or <I>j</I>
+<LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>n = exponent in formula above
+<LI>distance cutoff Rin (distance units)
+<LI>distance cutoff Rout (distance units)
+<LI>angle cutoff (degrees)
+</UL>
+<P>For the <I>hbond/dreiding/morse</I> style the list of coefficients is as
+follows:
+</P>
+<UL><LI>K = hydrogen atom type = 1 to Ntypes
+<LI>donor flag = <I>i</I> or <I>j</I>
+<LI>D0 (energy units)
+<LI>alpha (1/distance units)
+<LI>r0 (distance units)
+<LI>n = exponent in formula above
+<LI>distance cutoff Rin (distance units)
+<LI>distance cutoff Rout (distance units)
+<LI>angle cutoff (degrees)
+</UL>
+<P>A single hydrogen atom type K can be specified, or a wild-card
+asterisk can be used in place of or in conjunction with the K
+arguments to select multiple types as hydrogens. This takes the form
+"*" or "*n" or "n*" or "m*n". See the <A HREF = "pair_coeff">pair_coeff</A> command
+doc page for details.
+</P>
+<P>If the donor flag is <I>i</I>, then the atom of type I in the pair_coeff
+command is treated as the donor, and J is the acceptor. If the donor
+flag is <I>j</I>, then the atom of type J in the pair_coeff command is
+treated as the donor and I is the donor. This option is required
+because the <A HREF = "pair_coeff.html">pair_coeff</A> command requires that I <= J.
+</P>
+<P>Epsilon and sigma are settings for the hydrogen bond potential based
+on a Lennard-Jones functional form. Note that sigma is defined as the
+zero-crossing distance for the potential, not as the energy minimum at
+2^(1/6) sigma.
+</P>
+<P>D0 and alpha and r0 are settings for the hydrogen bond potential based
+on a Morse functional form.
+</P>
+<P>The last 3 coefficients for both styles are optional. If not
+specified, the global n, distance cutoff, and angle cutoff specified
+in the pair_style command are used. If you wish to only override the
+2nd or 3rd optional parameter, you must also specify the preceding
+optional parameters.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. You must explicitly identify
+each donor/acceptor type pair.
+</P>
+<P>These styles do not support the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the interactions.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
+these pair styles.
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands need to be
+re-specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P>These pair styles tally a count of how many hydrogen bonding
+interactions they calculate each timestep and the hbond energy. These
+quantities can be accessed via the <A HREF = "compute_pair.html">compute pair</A>
+command as a vector of values of length 2.
+</P>
+<P>To print these quantities to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+</P>
+<PRE>compute hb all pair hbond/dreiding/lj
+variable n_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom step temp epair v_E_hbond
+</PRE>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mayo"></A>
+
+<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+</P>
+<A NAME = "Liu"></A>
+
+<P><B>(Liu)</B> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
+2798 (2009)
+</P>
+</HTML>
diff --git a/doc/doc2/pair_hybrid.html b/doc/doc2/pair_hybrid.html
new file mode 100644
index 000000000..0403530f0
--- /dev/null
+++ b/doc/doc2/pair_hybrid.html
@@ -0,0 +1,354 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style hybrid command
+</H3>
+<H3>pair_style hybrid/omp command
+</H3>
+<H3>pair_style hybrid/overlay command
+</H3>
+<H3>pair_style hybrid/overlay/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style hybrid style1 args style2 args ...
+pair_style hybrid/overlay style1 args style2 args ...
+</PRE>
+<UL><LI>style1,style2 = list of one or more pair styles and their arguments
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
+pair_coeff 1*2 1*2 eam niu3
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.5 1.2
+</PRE>
+<PRE>pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * coul/long
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>hybrid</I> and <I>hybrid/overlay</I> styles enable the use of multiple
+pair styles in one simulation. With the <I>hybrid</I> style, exactly one
+pair style is assigned to each pair of atom types. With the
+<I>hybrid/overlay</I> style, one or more pair styles can be assigned to
+each pair of atom types. The assignment of pair styles to type pairs
+is made via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
+</P>
+<P>Here are two examples of hybrid simulations. The <I>hybrid</I> style could
+be used for a simulation of a metal droplet on a LJ surface. The
+metal atoms interact with each other via an <I>eam</I> potential, the
+surface atoms interact with each other via a <I>lj/cut</I> potential, and
+the metal/surface interaction is also computed via a <I>lj/cut</I>
+potential. The <I>hybrid/overlay</I> style could be used as in the 2nd
+example above, where multiple potentials are superposed in an additive
+fashion to compute the interaction between atoms. In this example,
+using <I>lj/cut</I> and <I>coul/long</I> together gives the same result as if
+the <I>lj/cut/coul/long</I> potential were used by itself. In this case,
+it would be more efficient to use the single combined potential, but
+in general any combination of pair potentials can be used together in
+to produce an interaction that is not encoded in any single pair_style
+file, e.g. adding Coulombic forces between granular particles.
+</P>
+<P>All pair styles that will be used are listed as "sub-styles" following
+the <I>hybrid</I> or <I>hybrid/overlay</I> keyword, in any order. Each
+sub-style's name is followed by its usual arguments, as illustrated in
+the example above. See the doc pages of individual pair styles for a
+listing and explanation of the appropriate arguments.
+</P>
+<P>Note that an individual pair style can be used multiple times as a
+sub-style. For efficiency this should only be done if your model
+requires it. E.g. if you have different regions of Si and C atoms and
+wish to use a Tersoff potential for pure Si for one set of atoms, and
+a Tersoff potetnial for pure C for the other set (presumably with some
+3rd potential for Si-C interactions), then the sub-style <I>tersoff</I>
+could be listed twice. But if you just want to use a Lennard-Jones or
+other pairwise potential for several different atom type pairs in your
+model, then you should just list the sub-style once and use the
+pair_coeff command to assign parameters for the different type pairs.
+</P>
+<P>IMPORTANT NOTE: An exception to this option to list an individual pair
+style multiple times are the pair styles implemented as Fortran
+libraries: <A HREF = "pair_meam.html">pair_style meam</A> and <A HREF = "pair_reax.html">pair_style
+reax</A> (<A HREF = "pair_reax_c.html">pair_style reax/c</A> is OK).
+This is because unlike a C++ class, they can not be instantiated
+multiple times, due to the manner in which they were coded in Fortran.
+</P>
+<P>In the pair_coeff commands, the name of a pair style must be added
+after the I,J type specification, with the remaining coefficients
+being those appropriate to that style. If the pair style is used
+multiple times in the pair_style command, then an additional numeric
+argument must also be specified which is a number from 1 to M where M
+is the number of times the sub-style was listed in the pair style
+command. The extra number indicates which instance of the sub-style
+these coefficients apply to.
+</P>
+<P>For example, consider a simulation with 3 atom types: types 1 and 2
+are Ni atoms, type 3 are LJ atoms with charges. The following
+commands would set up a hybrid simulation:
+</P>
+<PRE>pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
+pair_coeff * * eam/alloy nialhjea Ni Ni NULL
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.8 1.3
+</PRE>
+<P>As an example of using the same pair style multiple times, consider a
+simulation with 2 atom types. Type 1 is Si, type 2 is C. The
+following commands would model the Si atoms with Tersoff, the C atoms
+with Tersoff, and the cross-interactions with Lennard-Jones:
+</P>
+<PRE>pair_style hybrid lj/cut 2.5 tersoff tersoff
+pair_coeff * * tersoff 1 Si.tersoff Si NULL
+pair_coeff * * tersoff 2 C.tersoff NULL C
+pair_coeff 1 2 lj/cut 1.0 1.5
+</PRE>
+<P>If pair coefficients are specified in the data file read via the
+<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
+E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for
+each line in the "Pair Coeffs" section, e.g.
+</P>
+<PRE>Pair Coeffs
+</PRE>
+<PRE>1 lj/cut/coul/cut 1.0 1.0
+...
+</PRE>
+<P>Note that the pair_coeff command for some potentials such as
+<A HREF = "pair_eam.html">pair_style eam/alloy</A> includes a mapping specification
+of elements to all atom types, which in the hybrid case, can include
+atom types not assigned to the <I>eam/alloy</I> potential. The NULL
+keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
+etc), to denote an atom type that will be assigned to a different
+sub-style.
+</P>
+<P>For the <I>hybrid</I> style, each atom type pair I,J is assigned to exactly
+one sub-style. Just as with a simulation using a single pair style,
+if you specify the same atom type pair in a second pair_coeff command,
+the previous assignment will be overwritten.
+</P>
+<P>For the <I>hybrid/overlay</I> style, each atom type pair I,J can be
+assigned to one or more sub-styles. If you specify the same atom type
+pair in a second pair_coeff command with a new sub-style, then the
+second sub-style is added to the list of potentials that will be
+calculated for two interacting atoms of those types. If you specify
+the same atom type pair in a second pair_coeff command with a
+sub-style that has already been defined for that pair of atoms, then
+the new pair coefficients simply override the previous ones, as in the
+normal usage of the pair_coeff command. E.g. these two sets of
+commands are the same:
+</P>
+<PRE>pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 2 2 1.5 0.8
+</PRE>
+<PRE>pair_style hybrid/overlay lj/cut 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 2 2 lj/cut 1.5 0.8
+</PRE>
+<P>Coefficients must be defined for each pair of atoms types via the
+<A HREF = "pair_coeff.html">pair_coeff</A> command as described above, or in the
+data file or restart files read by the <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> commands, or by mixing as described
+below.
+</P>
+<P>For both the <I>hybrid</I> and <I>hybrid/overlay</I> styles, every atom type
+pair I,J (where I <= J) must be assigned to at least one sub-style via
+the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or
+in the data file read by the <A HREF = "read_data.html">read_data</A>, or by mixing
+as described below.
+</P>
+<P>If you want there to be no interactions between a particular pair of
+atom types, you have 3 choices. You can assign the type pair to some
+sub-style and use the <A HREF = "neigh_modify.html">neigh_modify exclude type</A>
+command. You can assign it to some sub-style and set the coefficients
+so that there is effectively no interaction (e.g. epsilon = 0.0 in a
+LJ potential). Or, for <I>hybrid</I> and <I>hybrid/overlay</I> simulations, you
+can use this form of the pair_coeff command in your input script:
+</P>
+<PRE>pair_coeff 2 3 none
+</PRE>
+<P>or this form in the "Pair Coeffs" section of the data file:
+</P>
+<PRE>3 none
+</PRE>
+<P>If an assignment to <I>none</I> is made in a simulation with the
+<I>hybrid/overlay</I> pair style, it wipes out all previous assignments of
+that atom type pair to sub-styles.
+</P>
+<P>Note that you may need to use an <A HREF = "atom_style.html">atom_style</A> hybrid
+command in your input script, if atoms in the simulation will need
+attributes from several atom styles, due to using multiple pair
+potentials.
+</P>
+<HR>
+
+<P>Different force fields (e.g. CHARMM vs AMBER) may have different rules
+for applying weightings that change the strength of pairwise
+interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
+neighbors in the molecular bond topology, as normally set by the
+<A HREF = "special_bonds.html">special_bonds</A> command. Different weights can be
+assigned to different pair hybrid sub-styles via the <A HREF = "pair_modify.html">pair_modify
+special</A> command. This allows multiple force fields
+to be used in a model of a hybrid system. See the
+<A HREF = "pair_modify.html">pair_modify</A> doc page for details.
+</P>
+<P>The potential energy contribution to the overall system due to an
+individual sub-style can be accessed and output via the <A HREF = "compute_pair.html">compute
+pair</A> command.
+</P>
+<HR>
+
+<P>IMPORTANT: Several of the potentials defined via the pair_style
+command in LAMMPS are really many-body potentials, such as Tersoff,
+AIREBO, MEAM, ReaxFF, etc. The way to think about using these
+potentials in a hybrid setting is as follows.
+</P>
+<P>A subset of atom types is assigned to the many-body potential with a
+single <A HREF = "pair_coeff.html">pair_coeff</A> command, using "* *" to include
+all types and the NULL keywords described above to exclude specific
+types not assigned to that potential. If types 1,3,4 were assigned in
+that way (but not type 2), this means that all many-body interactions
+between all atoms of types 1,3,4 will be computed by that potential.
+Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
+2-3, 2-4 to be specified for computation by other pair styles. You
+could even add a second interaction for 1-1 to be computed by another
+pair style, assuming pair_style hybrid/overlay is used.
+</P>
+<P>But you should not, as a general rule, attempt to exclude the
+many-body interactions for some subset of the type pairs within the
+set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
+is not conceptually well-defined for many-body interactions, since the
+potential will typically calculate energies and foces for small groups
+of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
+find the additional atoms in the group. It is typically non-physical
+to think of excluding an interaction between a particular pair of
+atoms when the potential computes 3-body or 4-body interactions.
+</P>
+<P>However, you can still use the pair_coeff none setting or the
+<A HREF = "neigh_modify.html">neigh_modify exclude</A> command to exclude certain
+type pairs from the neighbor list that will be passed to a manybody
+sub-style. This will alter the calculations made by a many-body
+potential, since it builds its list of 3-body, 4-body, etc
+interactions from the pair list. You will need to think carefully as
+to whether it produces a physically meaningful result for your model.
+</P>
+<P>For example, imagine you have two atom types in your model, type 1 for
+atoms in one surface, and type 2 for atoms in the other, and you wish
+to use a Tersoff potential to compute interactions within each
+surface, but not between surfaces. Then either of these two command
+sequences would implement that model:
+</P>
+<PRE>pair_style hybrid tersoff
+pair_coeff * * tersoff SiC.tersoff C C
+pair_coeff 1 2 none
+</PRE>
+<PRE>pair_style tersoff
+pair_coeff * * SiC.tersoff C C
+neigh_modify exclude type 1 2
+</PRE>
+<P>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
+passed to the Tersoff potential, which means it would compute no
+3-body interactions containing both type 1 and 2 atoms.
+</P>
+<P>Here is another example, using hybrid/overlay, to use 2 many-body
+potentials together, in an overlapping manner. Imagine you have CNT
+(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
+interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
+atoms are type 2. Something like this will work:
+</P>
+<PRE>pair_style hybrid/overlay tersoff airebo 3.0
+pair_coeff * * tersoff SiC.tersoff.custom Si C
+pair_coeff * * airebo CH.airebo NULL C
+</PRE>
+<P>Note that to prevent the Tersoff potential from computing C/C
+interactions, you would need to modify the SiC.tersoff file to turn
+off C/C interaction, i.e. by setting the appropriate coefficients to
+0.0.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual.
+</P>
+<P>Since the <I>hybrid</I> and <I>hybrid/overlay</I> styles delegate computation
+to the individual sub-styles, the suffix versions of the <I>hybrid</I>
+and <I>hybrid/overlay</I> styles are used to propagate the corresponding
+suffix to all sub-styles, if those versions exist. Otherwise the
+non-accelerated version will be used.
+</P>
+<P>The individual accelerated sub-styles are part of the USER-CUDA, GPU,
+USER-OMP and OPT packages, respectively. They are only enabled if
+LAMMPS was built with those packages. See the
+<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>Any pair potential settings made via the
+<A HREF = "pair_modify.html">pair_modify</A> command are passed along to all
+sub-styles of the hybrid potential.
+</P>
+<P>For atom type pairs I,J and I != J, if the sub-style assigned to I,I
+and J,J is the same, and if the sub-style allows for mixing, then the
+coefficients for I,J can be mixed. This means you do not have to
+specify a pair_coeff command for I,J since the I,J type pair will be
+assigned automatically to the sub-style defined for both I,I and J,J
+and its coefficients generated by the mixing rule used by that
+sub-style. For the <I>hybrid/overlay</I> style, there is an additional
+requirement that both the I,I and J,J pairs are assigned to a single
+sub-style. See the "pair_modify" command for details of mixing rules.
+See the See the doc page for the sub-style to see if allows for
+mixing.
+</P>
+<P>The hybrid pair styles supports the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options for an I,J pair interaction, if the
+associated sub-style supports it.
+</P>
+<P>For the hybrid pair styles, the list of sub-styles and their
+respective settings are written to <A HREF = "restart.html">binary restart
+files</A>, so a <A HREF = "pair_style.html">pair_style</A> command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file. Thus, pair_coeff commands need to be re-specified in the
+restart input script.
+</P>
+<P>These pair styles support the use of the <I>inner</I>, <I>middle</I>, and
+<I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A> command, if
+their sub-styles do.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>When using a long-range Coulombic solver (via the
+<A HREF = "kspace_style.html">kspace_style</A> command) with a hybrid pair_style,
+one or more sub-styles will be of the "long" variety,
+e.g. <I>lj/cut/coul/long</I> or <I>buck/coul/long</I>. You must insure that the
+short-range Coulombic cutoff used by each of these long pair styles is
+the same or else LAMMPS will generate an error.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_kim.html b/doc/doc2/pair_kim.html
new file mode 100644
index 000000000..7ff025a96
--- /dev/null
+++ b/doc/doc2/pair_kim.html
@@ -0,0 +1,123 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style kim command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style kim virialmode model printflag
+</PRE>
+<UL><LI>virialmode = KIMvirial or LAMMPSvirial
+<LI>model = name of KIM model (potential)
+<LI>printflag = 1/0 do or do not print KIM descriptor file, optional
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style kim KIMvirial model_Ar_P_Morse
+pair_coeff * * Ar Ar
+</PRE>
+<PRE>pair_style kim KIMvirial model_Ar_P_Morse 1
+pair_coeff * * Ar Ar
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This pair style is a wrapper on the <A HREF = "https://openkim.org">Knowledge Base for Interatomic
+Models (KIM)</A> repository of interatomic potentials,
+so that they can be used by LAMMPS scripts.
+</P>
+<P>In KIM lingo, a potential is a "model" and a model contains both the
+analytic formulas that define the potential as well as the parameters
+needed to run it for one or more materials, including coefficients and
+cutoffs.
+</P>
+<P>The argument <I>virialmode</I> determines how the global virial is
+calculated. If <I>KIMvirial</I> is specified, the KIM model performs the
+global virial calculation (if it knows how). If <I>LAMMPSvirial</I> is
+specified, LAMMPS computes the global virial using its fdotr mechanism.
+</P>
+<P>The argument <I>model</I> is the name of the KIM model for a specific
+potential as KIM defines it. In principle, LAMMPS can invoke any KIM
+model. You should get an error or warning message from either LAMMPS
+or KIM if there is an incompatibility.
+</P>
+<P>The argument <I>printflag</I> is optional. If it is set to a non-zero
+value then a KIM dsecriptor file is printed when KIM is invoked. This
+can be useful for debugging. The default is to not print this file.
+</P>
+<P>Only a single pair_coeff command is used with the <I>kim</I> style which
+specifies the mapping of LAMMPS atom types to KIM elements. This is
+done by specifying N additional arguments after the * * in the
+pair_coeff command, where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>N element names = mapping of KIM elements to atom types
+</UL>
+<P>As an example, imagine the KIM model supports Si and C atoms. If your
+LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
+and the 4th to be C, you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
+defined within KIM. The final C argument maps LAMMPS atom type 4 to C
+as defined within KIM. If a mapping value is specified as NULL, the
+mapping is not performed. This can only be used when a <I>kim</I>
+potential is used as part of the <I>hybrid</I> pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+</P>
+<HR>
+
+<P>In addition to the usual LAMMPS error messages, the KIM library itself
+may generate errors, which should be printed to the screen. In this
+case it is also useful to check the kim.log file for additional error
+information. This file kim.log should be generated in the same
+directory where LAMMPS is running.
+</P>
+<P>To download, build, and install the KIM library on your system, see
+the lib/kim/README file. Once you have done this and built LAMMPS
+with the KIM package installed you can run the example input scripts
+in examples/kim.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since KIM stores the potential parameters.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the KIM package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This current version of pair_style kim is compatible with the
+kim-api package version 1.6.0 and higher.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lcbop.html b/doc/doc2/pair_lcbop.html
new file mode 100644
index 000000000..8b407d672
--- /dev/null
+++ b/doc/doc2/pair_lcbop.html
@@ -0,0 +1,103 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lcbop command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lcbop
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lcbop
+pair_coeff * * ../potentials/C.lcbop C
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lcbop</I> pair style computes the long-range bond-order potential
+for carbon (LCBOP) of <A HREF = "#Los">(Los and Fasolino)</A>. See section II in
+that paper for the analytic equations associated with the potential.
+</P>
+<P>Only a single pair_coeff command is used with the <I>lcbop</I> style which
+specifies an LCBOP potential file with parameters for specific
+elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of LCBOP elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * C.lcbop C C C NULL
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first C argument maps LAMMPS atom type 1 to the C element in the
+LCBOP file. If a mapping value is specified as NULL, the mapping is
+not performed. This can be used when a <I>lcbop</I> potential is used as
+part of the <I>hybrid</I> pair style. The NULL values are placeholders for
+atom types that will be used with other potentials.
+</P>
+<P>The parameters/coefficients for the LCBOP potential as applied to C
+are listed in the C.lcbop file to agree with the original <A HREF = "#Los">(Los and
+Fasolino)</A> paper. Thus the parameters are specific to this
+potential and the way it was fit, so modifying the file should be done
+carefully.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair styles is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair potential requires the <A HREF = "newton.html">newton</A> setting to be
+"on" for pair interactions.
+</P>
+<P>The C.lcbop potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal <A HREF = "units.html">units</A>. You can use
+the LCBOP potential with any LAMMPS units, but you would need to
+create your own LCBOP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_airebo.html">pair_airebo</A>, <A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Los"></A>
+
+<P><B>(Los and Fasolino)</B> J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107
+(2003).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_line_lj.html b/doc/doc2/pair_line_lj.html
new file mode 100644
index 000000000..26b801f80
--- /dev/null
+++ b/doc/doc2/pair_line_lj.html
@@ -0,0 +1,142 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style line/lj command
+</H3>
+<H3>pair_style line/lj/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style line/lj cutoff
+</PRE>
+<P>cutoff = global cutoff for interactions (distance units)
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style line/lj 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>line/lj</I> treats particles which are line segments as a set of
+small spherical particles that tile the line segment length as
+explained below. Interactions between two line segments, each with N1
+and N2 spherical particles, are calculated as the pairwise sum of
+N1*N2 Lennard-Jones interactions. Interactions between a line segment
+with N spherical particles and a point particle are treated as the
+pairwise sum of N Lennard-Jones interactions. See the <A HREF = "pair_lj.html">pair_style
+lj/cut</A> doc page for the definition of Lennard-Jones
+interactions.
+</P>
+<P>The cutoff distance for an interaction between 2 line segments, or
+between a line segment and a point particle, is calculated from the
+position of the line segment (its center), not between pairs of
+individual spheres comprising the line segment. Thus an interaction
+is either calculated in its entirety or not at all.
+</P>
+<P>The set of non-overlapping spherical particles that represent a line
+segment, for purposes of this pair style, are generated in the
+following manner. Their size is a function of the line segment length
+and the specified sigma for that particle type. If a line segment has
+a length L and is of type I, then the number of spheres N that
+represent the segment is calculated as N = L/sigma_II, rounded up to
+an integer value. Thus if L is not evenly divisibly by sigam_II, N is
+incremented to include one extra sphere. In this case, the spheres
+must be slightly smaller than sigma_II so as not to overlap, so a new
+sigma-prime is chosen as the sphere diameter, such that L/N =
+sigma-prime. Thus the line segment interacts with other segments or
+point particles as a collection of N spheres of diameter sigma-prime,
+evenly spaced along the line segment, so as to exactly cover its
+length.
+</P>
+<P>The LJ interaction between 2 spheres on different line segments of
+types I,J is computed with an arithmetic mixing of the sigma values of
+the 2 spheres and using the specified epsilon value for I,J atom
+types. Note that because the sigma values for line segment spheres is
+computed using only sigma_II values, specific to the line segment's
+type, this means that any specified sigma_IJ values (for I != J) are
+effectively ignored.
+</P>
+<P>For style <I>line/lj</I>, the following coefficients must be defined for
+each pair of atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command
+as in the examples above, or in the data file or restart files read by
+the <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of this pair style can be mixed. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the ASPHERE package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Defining particles to be line segments so they participate in
+line/line or line/particle interactions requires the use the
+<A HREF = "atom_style.html">atom_style line</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_tri_lj.html">pair_style tri/lj</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_list.html b/doc/doc2/pair_list.html
new file mode 100644
index 000000000..b0981813f
--- /dev/null
+++ b/doc/doc2/pair_list.html
@@ -0,0 +1,154 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style list command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style list listfile cutoff keyword
+</PRE>
+<UL><LI>listfile = name of file with list of pairwise interactions
+<LI>cutoff = global cutoff (distance units)
+<LI>keyword = optional flag <I>nocheck</I> or <I>check</I> (default is <I>check</I>)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style list restraints.txt 200.0
+pair_coeff * *
+</PRE>
+<PRE>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 3* 3* list
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>list</I> computes interactions between explicitly listed pairs of
+atoms with the option to select functional form and parameters for
+each individual pair. Because the parameters are set in the list
+file, the pair_coeff command has no parameters (but still needs to be
+provided). The <I>check</I> and <I>nocheck</I> keywords enable/disable a test
+that checks whether all listed bonds were present and computed.
+</P>
+<P>This pair style can be thought of as a hybrid between bonded,
+non-bonded, and restraint interactions. It will typically be used as
+an additional interaction within the <I>hybrid/overlay</I> pair style. It
+currently supports three interaction styles: a 12-6 Lennard-Jones, a
+Morse and a harmonic potential.
+</P>
+<P>The format of the list file is as follows:
+</P>
+<UL><LI>one line per pair of atoms
+
+<LI>empty lines will be ignored
+
+<LI>comment text starts with a '#' character
+
+<LI>line syntax: <I>ID1 ID2 style coeffs cutoff</I>
+
+<PRE> ID1 = atom ID of first atom
+ ID2 = atom ID of second atom
+ style = style of interaction
+ coeffs = list of coeffs
+ cutoff = cutoff for interaction (optional)
+</PRE>
+
+</UL>
+<P>The cutoff parameter is optional. If not specified, the global cutoff
+is used.
+</P>
+<P>Here is an example file:
+</P>
+<PRE># this is a comment
+</PRE>
+<PRE>15 259 lj126 1.0 1.0 50.0
+15 603 morse 10.0 1.2 2.0 10.0 # and another comment
+18 470 harmonic 50.0 1.2 5.0
+</PRE>
+<P>The style <I>lj126</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+</UL>
+<P>The style <I>morse</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>D0 (energy units)
+<LI>alpha (1/distance units)
+<LI>r0 (distance units)
+</UL>
+<P>The style <I>harmonic</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>K (energy units)
+<LI>r0 (distance units)
+</UL>
+<P>Note that the usual 1/2 factor is included in K.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support mixing since all parameters are
+explicit for each pair.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is supported by this
+pair style.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for this pair style.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style does not use a neighbor list and instead identifies
+atoms by their IDs. This has two consequences: 1) The cutoff has to be
+chosen sufficiently large, so that the second atom of a pair has to be
+a ghost atom on the same node on which the first atom is local;
+otherwise the interaction will be skipped. You can use the <I>check</I>
+option to detect, if interactions are missing. 2) Unlike other pair
+styles in LAMMPS, an atom I will not interact with multiple images of
+atom J (assuming the images are within the cutoff distance), but only
+with the nearest image.
+</P>
+<P>This style is part of the USER-MISC package. It is only enabled if
+LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>,
+<A HREF = "pair_lj.html">pair_style lj/cut</A>,
+<A HREF = "pair_morse.html">pair_style morse</A>,
+<A HREF = "bond_harmonic.html">bond_style harmonic</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj.html b/doc/doc2/pair_lj.html
new file mode 100644
index 000000000..1a8c57f73
--- /dev/null
+++ b/doc/doc2/pair_lj.html
@@ -0,0 +1,357 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/cut command
+</H3>
+<H3>pair_style lj/cut/cuda command
+</H3>
+<H3>pair_style lj/cut/gpu command
+</H3>
+<H3>pair_style lj/cut/intel command
+</H3>
+<H3>pair_style lj/cut/kk command
+</H3>
+<H3>pair_style lj/cut/opt command
+</H3>
+<H3>pair_style lj/cut/omp command
+</H3>
+<H3>pair_style lj/cut/coul/cut command
+</H3>
+<H3>pair_style lj/cut/coul/cut/cuda command
+</H3>
+<H3>pair_style lj/cut/coul/cut/gpu command
+</H3>
+<H3>pair_style lj/cut/coul/cut/omp command
+</H3>
+<H3>pair_style lj/cut/coul/debye command
+</H3>
+<H3>pair_style lj/cut/coul/debye/cuda command
+</H3>
+<H3>pair_style lj/cut/coul/debye/gpu command
+</H3>
+<H3>pair_style lj/cut/coul/debye/kk command
+</H3>
+<H3>pair_style lj/cut/coul/debye/omp command
+</H3>
+<H3>pair_style lj/cut/coul/dsf command
+</H3>
+<H3>pair_style lj/cut/coul/dsf/gpu command
+</H3>
+<H3>pair_style lj/cut/coul/dsf/kk command
+</H3>
+<H3>pair_style lj/cut/coul/dsf/omp command
+</H3>
+<H3>pair_style lj/cut/coul/long command
+</H3>
+<H3>pair_style lj/cut/coul/long/cuda command
+</H3>
+<H3>pair_style lj/cut/coul/long/gpu command
+</H3>
+<H3>pair_style lj/cut/coul/long/intel command
+</H3>
+<H3>pair_style lj/cut/coul/long/opt command
+</H3>
+<H3>pair_style lj/cut/coul/long/omp command
+</H3>
+<H3>pair_style lj/cut/coul/msm command
+</H3>
+<H3>pair_style lj/cut/coul/msm/gpu command
+</H3>
+<H3>pair_style lj/cut/coul/msm/omp command
+</H3>
+<H3>pair_style lj/cut/tip4p/cut command
+</H3>
+<H3>pair_style lj/cut/tip4p/cut/omp command
+</H3>
+<H3>pair_style lj/cut/tip4p/long command
+</H3>
+<H3>pair_style lj/cut/tip4p/long/omp command
+</H3>
+<H3>pair_style lj/cut/tip4p/long/opt command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/dsf</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/msm</I> or <I>lj/cut/tip4p/long</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/cut</I> args = cutoff
+ cutoff = global cutoff for Lennard Jones interactions (distance units)
+ <I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
+ kappa = inverse of the Debye length (inverse distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/coul/dsf</I> args = alpha cutoff (cutoff2)
+ alpha = damping parameter (inverse distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (distance units)
+ <I>lj/cut/coul/long</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/coul/msm</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/tip4p/cut</I> args = otype htype btype atype qdist cutoff (cutoff2)
+ otype,htype = atom types for TIP4P O and H
+ btype,atype = bond and angle types for TIP4P waters
+ qdist = distance from O atom to massless charge (distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/tip4p/long</I> args = otype htype btype atype qdist cutoff (cutoff2)
+ otype,htype = atom types for TIP4P O and H
+ btype,atype = bond and angle types for TIP4P waters
+ qdist = distance from O atom to massless charge (distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cut 2.5
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8
+</PRE>
+<PRE>pair_style lj/cut/coul/cut 10.0
+pair_style lj/cut/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+</PRE>
+<PRE>pair_style lj/cut/coul/debye 1.5 3.0
+pair_style lj/cut/coul/debye 1.5 2.5 5.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+pair_coeff 1 1 1.0 1.5 2.5 5.0
+</PRE>
+<PRE>pair_style lj/cut/coul/dsf 0.05 2.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 2.5
+</PRE>
+<PRE>pair_style lj/cut/coul/long 10.0
+pair_style lj/cut/coul/long 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<PRE>pair_style lj/cut/coul/msm 10.0
+pair_style lj/cut/coul/msm 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<PRE>pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<PRE>pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/cut</I> styles compute the standard 12/6 Lennard-Jones potential,
+given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
+</CENTER>
+<P>where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
+specified in the pair_style command, it is used for both the LJ and
+Coulombic terms. If two cutoffs are specified, they are used as
+cutoffs for the LJ and Coulombic terms respectively.
+</P>
+<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
+to the Coulombic term, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
+</CENTER>
+<P>where kappa is the inverse of the Debye length. This potential is
+another way to mimic the screening effect of a polar solvent.
+</P>
+<P>Style <I>lj/cut/coul/dsf</I> computes the Coulombic term via the damped
+shifted force model described in <A HREF = "#Fennell">Fennell</A>, given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coul_dsf.jpg">
+</CENTER>
+<P>where <I>alpha</I> is the damping parameter and erfc() is the complementary
+error-function. This potential is essentially a short-range,
+spherically-truncated, charge-neutralized, shifted, pairwise <I>1/r</I>
+summation. The potential is based on Wolf summation, proposed as an
+alternative to Ewald summation for condensed phase systems where
+charge screening causes electrostatic interactions to become
+effectively short-ranged. In order for the electrostatic sum to be
+absolutely convergent, charge neutralization within the cutoff radius
+is enforced by shifting the potential through placement of image
+charges on the cutoff sphere. Convergence can often be improved by
+setting <I>alpha</I> to a small non-zero value.
+</P>
+<P>Styles <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> compute the same
+Coulombic interactions as style <I>lj/cut/coul/cut</I> except that an
+additional damping factor is applied to the Coulombic term so it can
+be used in conjunction with the <A HREF = "kspace_style.html">kspace_style</A>
+command and its <I>ewald</I> or <I>pppm</I> option. The Coulombic cutoff
+specified for this style means that pairwise interactions within this
+distance are computed directly; interactions outside that distance are
+computed in reciprocal space.
+</P>
+<P>Styles <I>lj/cut/tip4p/cut</I> and <I>lj/cut/tip4p/long</I> implement the TIP4P
+water model of <A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless
+site located a short distance away from the oxygen atom along the
+bisector of the HOH angle. The atomic types of the oxygen and
+hydrogen atoms, the bond and angle types for OH and HOH interactions,
+and the distance to the massless charge site are specified as
+pair_style arguments. Style <I>lj/cut/tip4p/cut</I> uses a cutoff for
+Coulomb interactions; style <I>lj/cut/tip4p/long</I> is for use with a
+long-range Coulombic solver (Ewald or PPPM).
+</P>
+<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
+IDs for the O and 2 H atoms must be consecutive, with the O atom
+first. This is to enable LAMMPS to "find" the 2 H atoms associated
+with each O atom. For example, if the atom ID of an O atom in a TIP4P
+water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+</P>
+<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
+information on how to use the TIP4P pair styles and lists of
+parameters to set. Note that the neighobr list cutoff for Coulomb
+interactions is effectively extended by a distance 2*qdist when using
+the TIP4P pair style, to account for the offset distance of the
+fictitious charges on O atoms in water molecules. Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
+to slightly larger cost for the long-range calculation, so you can
+test the trade-off for your model.
+</P>
+<P>For all of the <I>lj/cut</I> pair styles, the following coefficients must
+be defined for each pair of atoms types via the
+<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
+the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands, or by mixing as
+described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2^(1/6)
+sigma.
+</P>
+<P>The latter 2 coefficients are optional. If not specified, the global
+LJ and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair. You cannot specify 2 cutoffs for style <I>lj/cut</I>, since it
+has no Coulombic terms.
+</P>
+<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/cut</I>
+and <I>lj/cut/tip4p/long</I> only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>All of the <I>lj/cut</I> pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+</P>
+<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/tip4p/long</I> pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+</P>
+<P>All of the <I>lj/cut</I> pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
+tail correction to the energy and pressure for the Lennard-Jones
+portion of the pair interaction.
+</P>
+<P>All of the <I>lj/cut</I> pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>The <I>lj/cut</I> and <I>lj/cut/coul/long</I> pair styles support the use of the
+<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
+respa</A> command, meaning the pairwise forces can be
+partitioned by distance at different levels of the rRESPA hierarchy.
+The other styles only support the <I>pair</I> keyword of run_style respa.
+See the <A HREF = "run_style.html">run_style</A> command for details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/tip4p/long</I> styles are part of the
+KSPACE package. The <I>lj/cut/tip4p/cut</I> style is part of the MOLECULE
+package. These styles are only enabled if LAMMPS was built with those
+packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info. Note that the KSPACE and MOLECULE packages are
+installed by default.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Jorgensen"></A>
+
+<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+</P>
+<A NAME = "Fennell"></A>
+
+<P><B>(Fennell)</B> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
+234104 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj96.html b/doc/doc2/pair_lj96.html
new file mode 100644
index 000000000..768c8fc3f
--- /dev/null
+++ b/doc/doc2/pair_lj96.html
@@ -0,0 +1,116 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj96/cut command
+</H3>
+<H3>pair_style lj96/cut/cuda command
+</H3>
+<H3>pair_style lj96/cut/gpu command
+</H3>
+<H3>pair_style lj96/cut/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj96/cut cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for lj96/cut interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj96/cut 2.5
+pair_coeff * * 1.0 1.0 4.0
+pair_coeff 1 1 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj96/cut</I> style compute a 9/6 Lennard-Jones potential, instead
+of the standard 12/6 potential, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj96.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global LJ
+cutoff specified in the pair_style command is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
+keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
+details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_cubic.html b/doc/doc2/pair_lj_cubic.html
new file mode 100644
index 000000000..386a41988
--- /dev/null
+++ b/doc/doc2/pair_lj_cubic.html
@@ -0,0 +1,137 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/cubic command
+</H3>
+<H3>pair_style lj/cubic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/cubic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/cubic</I> style computes a truncated LJ interaction potential whose
+energy and force are continuous everywhere.
+Inside the inflection point the interaction is identical to the
+standard 12/6 <A HREF = "pair_lj.html">Lennard-Jones</A> potential.
+The LJ function outside the inflection point is replaced
+with a cubic function of distance. The energy, force, and second
+derivative are continuous at the inflection point.
+The cubic coefficient A3 is chosen so
+that both energy and force go to zero at the cutoff distance.
+Outside the cutoff distance the energy and force are zero.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_cubic.jpg">
+</CENTER>
+<P>The location of the inflection point rs is defined
+by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance
+is defined by rc/rs = 67/48 or rc/sigma = 1.737....
+The analytic expression for the
+the cubic coefficient
+A3*rmin^3/epsilon = 27.93... is given in the paper by
+Holian and Ravelo <A HREF = "#Holian">(Holian)</A>.
+</P>
+<P>This potential is commonly used to study the shock mechanics
+of FCC solids, as in Ravelo et al. <A HREF = "#Ravelo">(Ravelo)</A>.
+</P>
+<P>The following coefficients must be defined for each pair of atom
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum, which
+is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987,
+so rmin = 1.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>The lj/cubic pair style does not support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option,
+since pair interaction is already smoothed to 0.0 at the
+cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>The lj/cubic pair style does not support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
+corrections to energy and pressure, since there are no corrections for
+a potential that goes to 0.0 at the cutoff.
+</P>
+<P>The lj/cubic pair style writes its information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>The lj/cubic pair style can only be used via the <I>pair</I>
+keyword of the <A HREF = "run_style.html">run_style respa</A> command. It does not
+support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Holian"></A>
+
+<A NAME = "Ravelo"></A><B>(Holian)</B> Holian and Ravelo, Phys Rev B, 51, 11275 (1995).
+
+
+<P><B>(Ravelo)</B> Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_cut_smooth.html b/doc/doc2/pair_lj_cut_smooth.html
new file mode 100644
index 000000000..1430313a8
--- /dev/null
+++ b/doc/doc2/pair_lj_cut_smooth.html
@@ -0,0 +1,111 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/cut/smooth command
+</H3>
+<H3>pair_style lj/cut/smooth/cuda command
+</H3>
+<H3>pair_style lj/cut/smooth/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/cut/smooth Rc
+</PRE>
+<UL><LI>Rc = cutoff for lj/cut/smooth interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cut/smooth 5.456108274435118
+pair_coeff * * 0.7242785984051078 2.598146797350056
+pair_coeff 1 1 20.0 1.3 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/cut/smooth</I> computes a LJ interaction that combines the standard
+12/6 Lennard-Jones function and subtracts a linear term that includes a
+cutoff distance Rc.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
+</CENTER>
+<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>If not specified, the global value for Rc is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
+the same as the corresponding style without the suffix. They have
+been optimized to run faster, depending on your available hardware, as
+discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
+manual. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
+packages, respectively. They are only enabled if LAMMPS was built with
+those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients and
+cutoff distance can be mixed. The default mix value is geometric.
+See the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_expand.html b/doc/doc2/pair_lj_expand.html
new file mode 100644
index 000000000..4dc314a37
--- /dev/null
+++ b/doc/doc2/pair_lj_expand.html
@@ -0,0 +1,120 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/expand command
+</H3>
+<H3>pair_style lj/expand/cuda command
+</H3>
+<H3>pair_style lj/expand/gpu command
+</H3>
+<H3>pair_style lj/expand/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/expand cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for lj/expand interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/expand 2.5
+pair_coeff * * 1.0 1.0 0.5
+pair_coeff 1 1 1.0 1.0 -0.2 2.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/expand</I> computes a LJ interaction with a distance shifted by
+delta which can be useful when particles are of different sizes, since
+it is different that using different sigma values in a standard LJ
+formula:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_expand.jpg">
+</CENTER>
+<P>Rc is the cutoff which does not include the delta distance. I.e. the
+actual force cutoff is the sum of cutoff + delta.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>delta (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The delta values can be positive or negative. The last coefficient is
+optional. If not specified, the global LJ cutoff is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon, sigma, and shift
+coefficients and cutoff distance for this pair style can be mixed.
+Shift is always mixed via an <I>arithmetic</I> rule. The other
+coefficients are mixed according to the pair_modify mix value. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_long.html b/doc/doc2/pair_lj_long.html
new file mode 100644
index 000000000..5b7455771
--- /dev/null
+++ b/doc/doc2/pair_lj_long.html
@@ -0,0 +1,235 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/long/coul/long command
+</H3>
+<H3>pair_style lj/long/coul/long/omp command
+</H3>
+<H3>pair_style lj/long/coul/long/opt command
+</H3>
+<H3>pair_style lj/long/tip4p/long command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/long/coul/long</I> or <I>lj/long/tip4p/long</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/long/coul/long</I> args = flag_lj flag_coul cutoff (cutoff2)
+ flag_lj = <I>long</I> or <I>cut</I> or <I>off</I>
+ <I>long</I> = use Kspace long-range summation for dispersion 1/r^6 term
+ <I>cut</I> = use a cutoff on dispersion 1/r^6 term
+ <I>off</I> = omit disperion 1/r^6 term entirely
+ flag_coul = <I>long</I> or <I>off</I>
+ <I>long</I> = use Kspace long-range summation for Coulombic 1/r term
+ <I>off</I> = omit Coulombic term
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/long/tip4p/long</I> args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
+ flag_lj = <I>long</I> or <I>cut</I>
+ <I>long</I> = use Kspace long-range summation for dispersion 1/r^6 term
+ <I>cut</I> = use a cutoff
+ flag_coul = <I>long</I> or <I>off</I>
+ <I>long</I> = use Kspace long-range summation for Coulombic 1/r term
+ <I>off</I> = omit Coulombic term
+ otype,htype = atom types for TIP4P O and H
+ btype,atype = bond and angle types for TIP4P waters
+ qdist = distance from O atom to massless charge (distance units)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/long/coul/long cut off 2.5
+pair_style lj/long/coul/long cut long 2.5 4.0
+pair_style lj/long/coul/long long long 2.5 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+</PRE>
+<PRE>pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
+pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/long/coul/long</I> computes the standard 12/6 Lennard-Jones and
+Coulombic potentials, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
+</CENTER>
+<P>where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, epsilon is the dielectric constant which can be set by
+the <A HREF = "dielectric.html">dielectric</A> command, and Rc is the cutoff. If
+one cutoff is specified in the pair_style command, it is used for both
+the LJ and Coulombic terms. If two cutoffs are specified, they are
+used as cutoffs for the LJ and Coulombic terms respectively.
+</P>
+<P>The purpose of this pair style is to capture long-range interactions
+resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
+interactions. This is done by use of the <I>flag_lj</I> and <I>flag_coul</I>
+settings. The <A HREF = "#Veld">In 't Veld</A> paper has more details on when it is
+appropriate to include long-range 1/r^6 interactions, using this
+potential.
+</P>
+<P>Style <I>lj/long/tip4p/long</I> implements the TIP4P water model of
+<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
+short distance away from the oxygen atom along the bisector of the HOH
+angle. The atomic types of the oxygen and hydrogen atoms, the bond
+and angle types for OH and HOH interactions, and the distance to the
+massless charge site are specified as pair_style arguments.
+</P>
+<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
+IDs for the O and 2 H atoms must be consecutive, with the O atom
+first. This is to enable LAMMPS to "find" the 2 H atoms associated
+with each O atom. For example, if the atom ID of an O atom in a TIP4P
+water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+</P>
+<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
+information on how to use the TIP4P pair style. Note that the
+neighobr list cutoff for Coulomb interactions is effectively extended
+by a distance 2*qdist when using the TIP4P pair style, to account for
+the offset distance of the fictitious charges on O atoms in water
+molecules. Thus it is typically best in an efficiency sense to use a
+LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
+neighbor list. This leads to slightly larger cost for the long-range
+calculation, so you can test the trade-off for your model.
+</P>
+<P>If <I>flag_lj</I> is set to <I>long</I>, no cutoff is used on the LJ 1/r^6
+dispersion term. The long-range portion can be calculated by using
+the <A HREF = "kspace_style.html">kspace_style ewald/disp or pppm/disp</A> commands.
+The specified LJ cutoff then determines which portion of the LJ
+interactions are computed directly by the pair potential versus which
+part is computed in reciprocal space via the Kspace style. If
+<I>flag_lj</I> is set to <I>cut</I>, the LJ interactions are simply cutoff, as
+with <A HREF = "pair_lj.html">pair_style lj/cut</A>.
+</P>
+<P>If <I>flag_coul</I> is set to <I>long</I>, no cutoff is used on the Coulombic
+interactions. The long-range portion can calculated by using any of
+several <A HREF = "kspace_style.html">kspace_style</A> command options such as
+<I>pppm</I> or <I>ewald</I>. Note that if <I>flag_lj</I> is also set to long, then
+the <I>ewald/disp</I> or <I>pppm/disp</I> Kspace style needs to be used to
+perform the long-range calculations for both the LJ and Coulombic
+interactions. If <I>flag_coul</I> is set to <I>off</I>, Coulombic interactions
+are not computed.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum at 2^(1/6)
+sigma.
+</P>
+<P>The latter 2 coefficients are optional. If not specified, the global
+LJ and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+</P>
+<P>Note that if you are using <I>flag_lj</I> set to <I>long</I>, you
+cannot specify a LJ cutoff for an atom type pair, since only one
+global LJ cutoff is allowed. Similarly, if you are using <I>flag_coul</I>
+set to <I>long</I>, you cannot specify a Coulombic cutoff for an atom type
+pair, since only one global Coulombic cutoff is allowed.
+</P>
+<P>For <I>lj/long/tip4p/long</I> only the LJ cutoff can be specified
+since a Coulombic cutoff cannot be specified for an individual I,J
+type pair. All type pairs use the same global Coulombic cutoff
+specified in the pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/long pair styles can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, assuming <I>flag_lj</I> is <I>cut</I>.
+</P>
+<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> table and
+table/disp options since they can tabulate the short-range portion of
+the long-range Coulombic and dispersion interactions.
+</P>
+<P>Thes pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding a long-range tail correction to the
+Lennard-Jones portion of the energy and pressure.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>The pair lj/long/coul/long styles support the use of the <I>inner</I>,
+<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
+command, meaning the pairwise forces can be partitioned by distance at
+different levels of the rRESPA hierarchy. See the
+<A HREF = "run_style.html">run_style</A> command for details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These styles are part of the KSPACE package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info. Note that
+the KSPACE package is installed by default.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Veld"></A>
+
+<P><B>(In 't Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_sf.html b/doc/doc2/pair_lj_sf.html
new file mode 100644
index 000000000..582c4604e
--- /dev/null
+++ b/doc/doc2/pair_lj_sf.html
@@ -0,0 +1,121 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/sf command
+</H3>
+<H3>pair_style lj/sf/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/sf cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for Lennard-Jones interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/sf 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 3.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/sf</I> computes a truncated and force-shifted LJ interaction
+(Shifted Force Lennard-Jones), so that both the potential and the
+force go continuously to zero at the cutoff <A HREF = "#Toxvaerd">(Toxvaerd)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_sf.jpg">
+</CENTER>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global
+LJ cutoff specified in the pair_style command is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma
+coefficients and cutoff distance for this pair style can be mixed.
+Rin is a cutoff value and is mixed like the cutoff. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant for
+this pair style, since the pair interaction goes to 0.0 at the cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Toxvaerd"></A>
+
+<P><B>(Toxvaerd)</B> Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_smooth.html b/doc/doc2/pair_lj_smooth.html
new file mode 100644
index 000000000..f5d381fe3
--- /dev/null
+++ b/doc/doc2/pair_lj_smooth.html
@@ -0,0 +1,130 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/smooth command
+</H3>
+<H3>pair_style lj/smooth/cuda command
+</H3>
+<H3>pair_style lj/smooth/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/smooth Rin Rc
+</PRE>
+<UL><LI>Rin = inner cutoff beyond which force smoothing will be applied (distance units)
+<LI>Rc = outer cutoff for lj/smooth interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/smooth 8.0 10.0
+pair_coeff * * 10.0 1.5
+pair_coeff 1 1 20.0 1.3 7.0 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/smooth</I> computes a LJ interaction with a force smoothing
+applied between the inner and outer cutoff.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_smooth.jpg">
+</CENTER>
+<P>The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
+cause the force to vary smoothly from the inner cutoff Rin to the
+outer cutoff Rc.
+</P>
+<P>At the inner cutoff the force and its 1st derivative
+will match the unsmoothed LJ formula. At the outer cutoff the force
+and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0.
+</P>
+<P>IMPORTANT NOTE: this force smoothing causes the energy to be
+discontinuous both in its values and 1st derivative. This can lead to
+poor energy conservation and may require the use of a thermostat.
+Plot the energy and force resulting from this formula via the
+<A HREF = "pair_write.html">pair_write</A> command to see the effect.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>innner (distance units)
+<LI>outer (distance units)
+</UL>
+<P>The last 2 coefficients are optional inner and outer cutoffs. If not
+specified, the global values for Rin and Rc are used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon, sigma, Rin
+coefficients and the cutoff distance for this pair style can be mixed.
+Rin is a cutoff value and is mixed like the cutoff. The other
+coefficients are mixed according to the pair_modify mix option. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lj_smooth_linear.html">pair
+lj/smooth/linear</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_smooth_linear.html b/doc/doc2/pair_lj_smooth_linear.html
new file mode 100644
index 000000000..43f35bbba
--- /dev/null
+++ b/doc/doc2/pair_lj_smooth_linear.html
@@ -0,0 +1,111 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/smooth/linear command
+</H3>
+<H3>pair_style lj/smooth/linear/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lj/smooth/linear Rc
+</PRE>
+<UL><LI>Rc = cutoff for lj/smooth/linear interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/smooth/linear 5.456108274435118
+pair_coeff * * 0.7242785984051078 2.598146797350056
+pair_coeff 1 1 20.0 1.3 9.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>lj/smooth/linear</I> computes a LJ interaction that combines the
+standard 12/6 Lennard-Jones function and subtracts a linear term that
+includes the cutoff distance Rc, as in this formula:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_smooth_linear.jpg">
+</CENTER>
+<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global value
+for Rc is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance can be mixed. The default mix value is geometric.
+See the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
+this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lj_smooth.html">pair lj/smooth</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lj_soft.html b/doc/doc2/pair_lj_soft.html
new file mode 100644
index 000000000..9b49d3a3a
--- /dev/null
+++ b/doc/doc2/pair_lj_soft.html
@@ -0,0 +1,299 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/cut/soft command
+</H3>
+<H3>pair_style lj/cut/soft/omp command
+</H3>
+<H3>pair_style lj/cut/coul/cut/soft command
+</H3>
+<H3>pair_style lj/cut/coul/cut/soft/omp command
+</H3>
+<H3>pair_style lj/cut/coul/long/soft command
+</H3>
+<H3>pair_style lj/cut/coul/long/soft/omp command
+</H3>
+<H3>pair_style lj/cut/tip4p/long/soft command
+</H3>
+<H3>pair_style lj/cut/tip4p/long/soft/omp command
+</H3>
+<H3>pair_style lj/charmm/coul/long/soft command
+</H3>
+<H3>pair_style lj/charmm/coul/long/soft/omp command
+</H3>
+<H3>pair_style coul/cut/soft command
+</H3>
+<H3>pair_style coul/cut/soft/omp command
+</H3>
+<H3>pair_style coul/long/soft command
+</H3>
+<H3>pair_style coul/long/soft/omp command
+</H3>
+<H3>pair_style tip4p/long/soft command
+</H3>
+<H3>pair_style tip4p/long/soft/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/cut/soft</I> or <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> or <I>lj/cut/tip4p/long/soft</I> or <I>lj/charmm/coul/long/soft</I> or <I>coul/cut/soft</I> or <I>coul/long/soft</I> or <I>tip4p/long/soft</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/cut/soft</I> args = n alpha_lj cutoff
+ n, alpha_LJ = parameters of soft-core potential
+ cutoff = global cutoff for Lennard-Jones interactions (distance units)
+ <I>lj/cut/coul/cut/soft</I> args = n alpha_LJ alpha_C cutoff (cutoff2)
+ n, alpha_LJ, alpha_C = parameters of soft-core potential
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/coul/long/soft</I> args = n alpha_LJ alpha_C cutoff
+ n, alpha_LJ, alpha_C = parameters of the soft-core potential
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/cut/tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
+ otype,htype = atom types for TIP4P O and H
+ btype,atype = bond and angle types for TIP4P waters
+ qdist = distance from O atom to massless charge (distance units)
+ n, alpha_LJ, alpha_C = parameters of the soft-core potential
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>lj/charmm/coul/long/soft</I> args = n alpha_LJ alpha_C inner outer (cutoff)
+ n, alpha_LJ, alpha_C = parameters of the soft-core potential
+ inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
+ cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
+ <I>coul/cut/soft</I> args = n alpha_C cutoff
+ n, alpha_C = parameters of the soft-core potential
+ cutoff = global cutoff for Coulomb interactions (distance units)
+ <I>coul/long/soft</I> args = n alpha_C cutoff
+ n, alpha_C = parameters of the soft-core potential
+ cutoff = global cutoff for Coulomb interactions (distance units)
+ <I>tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_C cutoff
+ otype,htype = atom types for TIP4P O and H
+ btype,atype = bond and angle types for TIP4P waters
+ qdist = distance from O atom to massless charge (distance units)
+ n, alpha_C = parameters of the soft-core potential
+ cutoff = global cutoff for Coulomb interactions (distance units)
+
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cut/soft 2.0 0.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 9.5
+</PRE>
+<PRE>pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
+</PRE>
+<PRE>pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
+</PRE>
+<PRE>pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
+pair_coeff * * 0.155 3.1536 1.0
+pair_coeff 1 1 0.155 3.1536 1.0 9.5
+</PRE>
+<PRE>pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
+pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
+</PRE>
+<PRE>pair_style coul/long/soft 1.0 10.0 9.5
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+</PRE>
+<PRE>pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/cut/soft</I> style and substyles compute the 12/6 Lennard-Jones
+and Coulomb potential modified by a soft core, in order to avoid
+singularities during free energy calculations when sites are created
+or anihilated <A HREF = "#Beutler">(Beutler)</A>,
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj_soft.jpg">
+</CENTER>
+<P>Coulomb interactions are also damped with a soft core at short
+distance,
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coul_soft.jpg">
+</CENTER>
+<P>In the Coulomb part C is an energy-conversion constant, q_i and q_j
+are the charges on the 2 atoms, and epsilon is the dielectric constant
+which can be set by the <A HREF = "dielectric.html">dielectric</A> command.
+</P>
+<P>The coefficient lambda is an activation parameter. When lambda = 1 the
+pair potentiel is identical to a Lennard-Jones term or a Coulomb term
+or a combination of both. When lambda = 0 the interactions are
+deactivated. The transition between these two extrema is smoothed by a
+soft repulsive core in order to avoid singularities in potential
+energy and forces when sites are created or anihilated and can overlap
+<A HREF = "#Beutler">(Beutler)</A>.
+</P>
+<P>The paratemers n, alpha_LJ and alpha_C are set in the
+<A HREF = "pair_style.html">pair_style</A> command, before the cutoffs. Usual
+choices for the exponent are n = 2 or n = 1. For the remaining
+coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
+appropriate choices. Plots of the LJ and Coulomb terms are shown
+below, for lambda ranging from 1 to 0 every 0.1.
+</P>
+<CENTER><IMG SRC = "JPG/lj_soft.jpg"><IMG SRC = "JPG/coul_soft.jpg">
+</CENTER>
+<P>For the <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> pair styles,
+the following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>lambda (activation parameter between 0 and 1)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The latter two coefficients are optional. If not specified, the global
+LJ and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair. You cannot specify 2 cutoffs for style <I>lj/cut/soft</I>,
+since it has no Coulombic terms. For the <I>coul/cut/soft</I> and
+<I>coul/long/soft</I> only lambda and the optional cutoff2 are to be
+specified.
+</P>
+<P>Style <I>lj/cut/tip4p/long/soft</I> implements a soft-core version of the
+TIP4P water model. The usage of this pair style is documented in the
+<A HREF = "pair_lj.html">pair_lj</A> styles. The soft-core version introduces the
+lambda parameter to the list of arguments, after epsilon and sigma in
+the <A HREF = "pair_coeff.html">pair_coeff</A> command. The paratemers n, alpha_LJ
+and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A> command,
+before the cutoffs.
+</P>
+<P>Style <I>lj/charmm/coul/long/soft</I> implements a soft-core version of the
+CHARMM version of LJ interactions with an additional switching
+function S(r) that ramps the energy and force smoothly to zero between
+an inner and outer cutoff. The usage of this pair style is documented
+in the <A HREF = "pair_charmm.html">pair_charmm</A> styles. The soft-core version
+introduces the lambda parameter to the list of arguments, after
+epsilon and sigma in the <A HREF = "pair_coeff.html">pair_coeff</A> command (and
+before the optional eps14 and sigma14). The paratemers n,
+alpha_LJ and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A>
+command, before the cutoffs.
+</P>
+<P>The <I>coul/cut/soft</I>, <I>coul/long/soft</I> and <I>tip4p/long/soft</I> substyles
+are designed to be combined with other pair potentials via the
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command. This is because
+they have no repulsive core. Hence, if used by themselves, there will
+be no repulsion to keep two oppositely charged particles from
+overlapping each other. In this case, if lambda = 1, a singularity may
+occur. These substyles are suitable to represent charges embedded in
+the Lennard-Jones radius of another site (for example hydrogen atoms
+in several water models).
+</P>
+<P>IMPORTANT NOTES: When using the core-softed Coulomb potentials with
+long-range solvers (<I>coul/long/soft</I>, <I>lj/cut/coul/long/soft</I>, etc.)
+in a free energy calculation in which sites holding electrostatic
+charges are being created or anihilated (using
+<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A> and <A HREF = "compute_fep.html">compute_fep</A>)
+it is important to adapt both the lambda activation parameter (from 0
+to 1, or the reverse) and the value of the charge (from 0 to its final
+value, or the reverse). This ensures that long-range electrostatic
+terms (kspace) are correct. It is not necessary to use core-softed
+Coulomb potentials if the van der Waals site is present during the
+free-energy route, thus avoiding overlap of the charges. Examples are
+provided in the LAMMPS source directory tree, under examples/USER/fep.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, tail correction, restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed.
+The default mix value is <I>geometric</I>. See the "pair_modify" command
+for details.
+</P>
+<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction.
+</P>
+<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> tail
+option for adding a long-range tail correction to the energy and
+pressure for the Lennard-Jones portion of the pair interaction.
+</P>
+<P>These pair styles write information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To avoid division by zero do not set sigma = 0; use the lambda
+parameter instead to activate/deactivate interactions, or use
+epsilon = 0 and sigma = 1. Alternatively, when sites do not
+interact though the Lennard-Jones term the <I>coul/long/soft</I> or
+similar substyle can be used via the
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command.
+</P>
+<HR>
+
+<P>All of the plain <I>soft</I> pair styles are part of the USER-FEP package.
+The <I>long</I> styles also requires the KSPACE package to be installed.
+They are only enabled if LAMMPS was built with those packages. See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_adapt.html">fix_adapt</A>,
+<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A>, <A HREF = "compute_fep.html">compute_fep</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Beutler"></A>
+
+<P><B>(Beutler)</B> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
+Phys Lett, 222, 529 (1994).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lubricate.html b/doc/doc2/pair_lubricate.html
new file mode 100644
index 000000000..cdef2a104
--- /dev/null
+++ b/doc/doc2/pair_lubricate.html
@@ -0,0 +1,239 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lubricate command
+</H3>
+<H3>pair_style lubricate/omp command
+</H3>
+<H3>pair_style lubricate/poly command
+</H3>
+<H3>pair_style lubricate/poly/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
+</PRE>
+<UL><LI>style = <I>lubricate</I> or <I>lubricate/poly</I>
+<LI>mu = dynamic viscosity (dynamic viscosity units)
+<LI>flaglog = 0/1 to exclude/include log terms in the lubrication approximation
+<LI>flagfld = 0/1 to exclude/include Fast Lubrication Dynamics (FLD) effects
+<LI>cutinner = inner cutoff distance (distance units)
+<LI>cutoff = outer cutoff for interactions (distance units)
+<LI>flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
+<LI>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
+</UL>
+<P><B>Examples:</B> (all assume radius = 1)
+</P>
+<PRE>pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</PRE>
+<PRE>pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff * *
+variable mu equal ramp(1,2)
+fix 1 all adapt 1 pair lubricate mu * * v_mu
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Styles <I>lubricate</I> and <I>lubricate/poly</I> compute hydrodynamic
+interactions between mono-disperse spherical particles in a pairwise
+fashion. The interactions have 2 components. The first is
+Ball-Melrose lubrication terms via the formulas in <A HREF = "#Ball">(Ball and
+Melrose)</A>
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lubricate.jpg">
+</CENTER>
+<P>which represents the dissipation W between two nearby particles due to
+their relative velocities in the presence of a background solvent with
+viscosity <I>mu</I>. Note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity.
+</P>
+<P>The Asq (squeeze) term is the strongest and is included if <I>flagHI</I> is
+set to 1 (default). It scales as 1/gap where gap is the separation
+between the surfaces of the 2 particles. The Ash (shear) and Apu
+(pump) terms are only included if <I>flaglog</I> is set to 1. They are the
+next strongest interactions, and the only other singular interaction,
+and scale as log(gap). Note that <I>flaglog</I> = 1 and <I>flagHI</I> = 0 is
+invalid, and will result in a warning message, after which <I>flagHI</I> will
+be set to 1. The Atw (twist) term is currently not included. It is
+typically a very small contribution to the lubrication forces.
+</P>
+<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
+used, or both must be defined.
+</P>
+<P><I>Cutinner</I> sets the minimum center-to-center separation that will be
+used in calculations irrespective of the actual separation. <I>Cutoff</I>
+is the maximum center-to-center separation at which an interaction is
+computed. Using a <I>cutoff</I> less than 3 radii is recommended if
+<I>flaglog</I> is set to 1.
+</P>
+<P>The other component is due to the Fast Lubrication Dynamics (FLD)
+approximation, described in <A HREF = "#Kumar">(Kumar)</A>, which can be
+represented by the following equation
+</P>
+<CENTER><IMG SRC = "Eqs/fld.jpg">
+</CENTER>
+<P>where U represents the velocities and angular velocities of the
+particles, U^<I>infty</I> represents the velocity and the angular velocity
+of the undisturbed fluid, and E^<I>infty</I> represents the rate of strain
+tensor of the undisturbed fluid with viscosity <I>mu</I>. Again, note that
+this is dynamic viscosity which has units of mass/distance/time, not
+kinematic viscosity. Volume fraction corrections to R_FU are included
+as long as <I>flagVF</I> is set to 1 (default).
+</P>
+<P>IMPORTANT NOTE: When using the FLD terms, these pair styles are
+designed to be used with explicit time integration and a
+correspondingly small timestep. Thus either <A HREF = "fix_nve_sphere.html">fix
+nve/sphere</A> or <A HREF = "fix_nve_asphere.html">fix
+nve/asphere</A> should be used for time integration.
+To perform implicit FLD, see the <A HREF = "pair_lubricateU.html">pair_style
+lubricateU</A> command.
+</P>
+<P>Style <I>lubricate</I> requires monodisperse spherical particles; style
+<I>lubricate/poly</I> allows for polydisperse spherical particles.
+</P>
+<P>The viscosity <I>mu</I> can be varied in a time-dependent manner over the
+course of a simluation, in which case in which case the pair_style
+setting for <I>mu</I> will be overridden. See the <A HREF = "fix_adapt.html">fix adapt</A>
+command for details.
+</P>
+<P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A>
+command then the pair style uses the shear rate to adjust the
+hydrodynamic interactions accordingly. Volume changes due to fix
+deform are accounted for when computing the volume fraction
+corrections to R_FU.
+</P>
+<P>When computing the volume fraction corrections to R_FU, the presence
+of walls (whether moving or stationary) will affect the volume
+fraction available to colloidal particles. This is currently accounted
+for with the following types of walls: <A HREF = "fix_wall.html">wall/lj93</A>,
+<A HREF = "fix_wall.html">wall/lj126</A>, <A HREF = "fix_wall.html">wall/colloid</A>, and
+<A HREF = "fix_wall.html">wall/harmonic</A>. For these wall styles, the correct
+volume fraction will be used when walls do not coincide with the box
+boundary, as well as when walls move and thereby cause a change in the
+volume fraction. Other wall styles will still work, but they will
+result in the volume fraction being computed based on the box
+boundaries.
+</P>
+<P>Since lubrication forces are dissipative, it is usually desirable to
+thermostat the system at a constant temperature. If Brownian motion
+(at a constant temperature) is desired, it can be set using the
+<A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles
+and the brownian style should use consistent parameters for <I>mu</I>,
+<I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, <I>cutoff</I>, <I>flagHI</I> and <I>flagVF</I>.
+</P>
+<HR>
+
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutinner (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The two coefficients are optional. If neither is specified, the two
+cutoffs specified in the pair_style command are used. Otherwise both
+must be specified.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">this section</A> of
+the manual. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
+instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed. The default mix value is <I>geometric</I>. See
+the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These styles are part of the FLD package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Only spherical monodisperse particles are allowed for pair_style
+lubricate.
+</P>
+<P>Only spherical particles are allowed for pair_style lubricate/poly.
+</P>
+<P>These pair styles will not restart exactly when using the
+<A HREF = "read_restart.html">read_restart</A> command, though they should provide
+statistically similar results. This is because the forces they
+compute depend on atom velocities. See the
+<A HREF = "read_restart.html">read_restart</A> command for more details.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricateU.html">pair_style
+lubricateU</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+</P>
+<HR>
+
+<A NAME = "Ball"></A>
+
+<P><B>(Ball)</B> Ball and Melrose, Physica A, 247, 444-472 (1997).
+</P>
+<A NAME = "Kumar"></A>
+
+<P><B>(Kumar)</B> Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also
+his thesis for more details: A. Kumar, "Microscale Dynamics in
+Suspensions of Non-spherical Particles", Thesis, University of
+Illinois Urbana-Champaign,
+(2010). (<A HREF = "https://www.ideals.illinois.edu/handle/2142/16032">https://www.ideals.illinois.edu/handle/2142/16032</A>)
+</P>
+</HTML>
diff --git a/doc/doc2/pair_lubricateU.html b/doc/doc2/pair_lubricateU.html
new file mode 100644
index 000000000..42a596c70
--- /dev/null
+++ b/doc/doc2/pair_lubricateU.html
@@ -0,0 +1,225 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lubricateU command
+</H3>
+<H3>pair_style lubricateU/poly command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
+</PRE>
+<UL><LI>style = <I>lubricateU</I> or <I>lubricateU/poly</I>
+<LI>mu = dynamic viscosity (dynamic viscosity units)
+<LI>flaglog = 0/1 to exclude/include log terms in the lubrication approximation
+<LI>cutinner = inner cut off distance (distance units)
+<LI>cutoff = outer cutoff for interactions (distance units)
+<LI>gdot = shear rate (1/time units)
+<LI>flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
+<LI>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
+</UL>
+<P><B>Examples:</B> (all assume radius = 1)
+</P>
+<PRE>pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Styles <I>lubricateU</I> and <I>lubricateU/poly</I> compute velocities and
+angular velocities such that the hydrodynamic interaction balances the
+force and torque due to all other types of interactions.
+</P>
+<P>The interactions have 2 components. The first is
+Ball-Melrose lubrication terms via the formulas in <A HREF = "#Ball">(Ball and
+Melrose)</A>
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lubricate.jpg">
+</CENTER>
+<P>which represents the dissipation W between two nearby particles due to
+their relative velocities in the presence of a background solvent with
+viscosity <I>mu</I>. Note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity.
+</P>
+<P>The Asq (squeeze) term is the strongest and is included as long as
+<I>flagHI</I> is set to 1 (default). It scales as 1/gap where gap is the
+separation between the surfaces of the 2 particles. The Ash (shear)
+and Apu (pump) terms are only included if <I>flaglog</I> is set to 1. They
+are the next strongest interactions, and the only other singular
+interaction, and scale as log(gap). Note that <I>flaglog</I> = 1 and
+<I>flagHI</I> = 0 is invalid, and will result in a warning message, after
+which <I>flagHI</I> will be set to 1. The Atw (twist) term is currently not
+included. It is typically a very small contribution to the lubrication
+forces.
+</P>
+<P>The <I>flagHI</I> and <I>flagVF</I> settings are optional. Neither should be
+used, or both must be defined.
+</P>
+<P><I>Cutinner</I> sets the minimum center-to-center separation that will be
+used in calculations irrespective of the actual separation. <I>Cutoff</I>
+is the maximum center-to-center separation at which an interaction is
+computed. Using a <I>cutoff</I> less than 3 radii is recommended if
+<I>flaglog</I> is set to 1.
+</P>
+<P>The other component is due to the Fast Lubrication Dynamics (FLD)
+approximation, described in <A HREF = "#Kumar">(Kumar)</A>. The equation being
+solved to balance the forces and torques is
+</P>
+<CENTER><IMG SRC = "Eqs/fld2.jpg">
+</CENTER>
+<P>where U represents the velocities and angular velocities of the
+particles, U^<I>infty</I> represents the velocities and the angular
+velocities of the undisturbed fluid, and E^<I>infty</I> represents the rate
+of strain tensor of the undisturbed fluid flow with viscosity
+<I>mu</I>. Again, note that this is dynamic viscosity which has units of
+mass/distance/time, not kinematic viscosity. Volume fraction
+corrections to R_FU are included if <I>flagVF</I> is set to 1 (default).
+</P>
+<P>F<I>rest</I> represents the forces and torques due to all other types of
+interactions, e.g. Brownian, electrostatic etc. Note that this
+algorithm neglects the inertial terms, thereby removing the
+restriction of resolving the small interial time scale, which may not
+be of interest for colloidal particles. This pair style solves for
+the velocity such that the hydrodynamic force balances all other types
+of forces, thereby resulting in a net zero force (zero inertia limit).
+When defining this pair style, it must be defined last so that when
+this style is invoked all other types of forces have already been
+computed. For the same reason, it won't work if additional non-pair
+styles are defined (such as bond or Kspace forces) as they are
+calculated in LAMMPS after the pairwise interactions have been
+computed.
+</P>
+<P>IMPORTANT NOTE: When using these styles, the these pair styles are
+designed to be used with implicit time integration and a
+correspondingly larger timestep. Thus either <A HREF = "fix_nve_noforce.html">fix
+nve/noforce</A> should be used for spherical
+particles defined via <A HREF = "atom_style.html">atom_style sphere</A> or <A HREF = "fix_nve_asphere_noforce.html">fix
+nve/asphere/noforce</A> should be used for
+spherical particles defined via <A HREF = "atom_style.html">atom_style
+ellipsoid</A>. This is because the velocity and angular
+momentum of each particle is set by the pair style, and should not be
+reset by the time integration fix.
+</P>
+<P>Style <I>lubricateU</I> requires monodisperse spherical particles; style
+<I>lubricateU/poly</I> allows for polydisperse spherical particles.
+</P>
+<P>If the suspension is sheared via the <A HREF = "fix_deform.html">fix deform</A>
+command then the pair style uses the shear rate to adjust the
+hydrodynamic interactions accordingly. Volume changes due to fix
+deform are accounted for when computing the volume fraction
+corrections to R_FU.
+</P>
+<P>When computing the volume fraction corrections to R_FU, the presence
+of walls (whether moving or stationary) will affect the volume
+fraction available to colloidal particles. This is currently accounted
+for with the following types of walls: <A HREF = "fix_wall.html">wall/lj93</A>,
+<A HREF = "fix_wall.html">wall/lj126</A>, <A HREF = "fix_wall.html">wall/colloid</A>, and
+"wall/harmonic_fix_wall.html". For these wall styles, the correct
+volume fraction will be used when walls do not coincide with the box
+boundary, as well as when walls move and thereby cause a change in the
+volume fraction. To use these wall styles with pair_style <I>lubricateU</I>
+or <I>lubricateU/poly</I>, the <I>fld yes</I> option must be specified in the
+fix wall command.
+</P>
+<P>Since lubrication forces are dissipative, it is usually desirable to
+thermostat the system at a constant temperature. If Brownian motion
+(at a constant temperature) is desired, it can be set using the
+<A HREF = "pair_brownian.html">pair_style brownian</A> command. These pair styles
+and the brownian style should use consistent parameters for <I>mu</I>,
+<I>flaglog</I>, <I>flagfld</I>, <I>cutinner</I>, <I>cutoff</I>, <I>flagHI</I> and <I>flagVF</I>.
+</P>
+<HR>
+
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cutinner (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The two coefficients are optional. If neither is specified, the two
+cutoffs specified in the pair_style command are used. Otherwise both
+must be specified.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the two cutoff distances for this
+pair style can be mixed. The default mix value is <I>geometric</I>. See
+the "pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>These styles are part of the FLD package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Currently, these pair styles assume that all other types of
+forces/torques on the particles have been already been computed when
+it is invoked. This requires this style to be defined as the last of
+the pair styles, and that no fixes apply additional constraint forces.
+One exception is the <A HREF = "fix_wall.html">fix wall/colloid</A> commands, which
+has an "fld" option to apply their wall forces correctly.
+</P>
+<P>Only spherical monodisperse particles are allowed for pair_style
+lubricateU.
+</P>
+<P>Only spherical particles are allowed for pair_style lubricateU/poly.
+</P>
+<P>For sheared suspensions, it is assumed that the shearing is done in
+the xy plane, with x being the velocity direction and y being the
+velocity-gradient direction. In this case, one must use <A HREF = "fix_deform.html">fix
+deform</A> with the same rate of shear (erate).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lubricate.html">pair_style
+lubricate</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default settings for the optional args are flagHI = 1 and flagVF =
+1.
+</P>
+<HR>
+
+<A NAME = "Ball"></A>
+
+<P><B>(Ball)</B> Ball and Melrose, Physica A, 247, 444-472 (1997).
+</P>
+<A NAME = "Kumar"></A>
+
+<P><B>(Kumar)</B> Kumar and Higdon, Phys Rev E, 82, 051401 (2010).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_meam.html b/doc/doc2/pair_meam.html
new file mode 100644
index 000000000..3a8f578f4
--- /dev/null
+++ b/doc/doc2/pair_meam.html
@@ -0,0 +1,383 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style meam command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style meam
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style meam
+pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
+pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>NOTE: The behavior of the MEAM potential for alloy systems has changed
+as of November 2010; see description below of the mixture_ref_t
+parameter
+</P>
+<P>Style <I>meam</I> computes pairwise interactions for a variety of materials
+using modified embedded-atom method (MEAM) potentials
+<A HREF = "#Baskes">(Baskes)</A>. Conceptually, it is an extension to the original
+<A HREF = "pair_eam.html">EAM potentials</A> which adds angular forces. It is
+thus suitable for modeling metals and alloys with fcc, bcc, hcp and
+diamond cubic structures, as well as covalently bonded materials like
+silicon and carbon.
+</P>
+<P>In the MEAM formulation, the total energy E of a system of atoms is
+given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_meam.jpg">
+</CENTER>
+<P>where F is the embedding energy which is a function of the atomic
+electron density rho, and phi is a pair potential interaction. The
+pair interaction is summed over all neighbors J of atom I within the
+cutoff distance. As with EAM, the multi-body nature of the MEAM
+potential is a result of the embedding energy term. Details of the
+computation of the embedding and pair energies, as implemented in
+LAMMPS, are given in <A HREF = "#Gullet">(Gullet)</A> and references therein.
+</P>
+<P>The various parameters in the MEAM formulas are listed in two files
+which are specified by the <A HREF = "pair_coeff.html">pair_coeff</A> command.
+These are ASCII text files in a format consistent with other MD codes
+that implement MEAM potentials, such as the serial DYNAMO code and
+Warp. Several MEAM potential files with parameters for different
+materials are included in the "potentials" directory of the LAMMPS
+distribution with a ".meam" suffix. All of these are parameterized in
+terms of LAMMPS <A HREF = "units.html">metal units</A>.
+</P>
+<P>Note that unlike for other potentials, cutoffs for MEAM potentials are
+not set in the pair_style or pair_coeff command; they are specified in
+the MEAM potential files themselves.
+</P>
+<P>Only a single pair_coeff command is used with the <I>meam</I> style which
+specifies two MEAM files and the element(s) to extract information
+for. The MEAM elements are mapped to LAMMPS atom types by specifying
+N additional arguments after the 2nd filename in the pair_coeff
+command, where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>MEAM library file
+<LI>Elem1, Elem2, ...
+<LI>MEAM parameter file
+<LI>N element names = mapping of MEAM elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential files.
+</P>
+<P>As an example, the potentials/library.meam file has generic MEAM
+settings for a variety of elements. The potentials/sic.meam file has
+specific parameter settings for a Si and C alloy system. If your
+LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
+and the 4th to be C, you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * library.meam Si C sic.meam Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The two filenames are for the library and parameter file respectively.
+The Si and C arguments (between the file names) are the two elements
+for which info will be extracted from the library file. The first
+three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
+element. The final C argument maps LAMMPS atom type 4 to the MEAM C
+element.
+</P>
+<P>If the 2nd filename is specified as NULL, no parameter file is read,
+which simply means the generic parameters in the library file are
+used. Use of the NULL specification for the parameter file is
+discouraged for systems with more than a single element type
+(e.g. alloys), since the parameter file is expected to set element
+interaction terms that are not captured by the information in the
+library file.
+</P>
+<P>If a mapping value is specified as NULL, the mapping is not performed.
+This can be used when a <I>meam</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P>The MEAM library file provided with LAMMPS has the name
+potentials/library.meam. It is the "meamf" file used by other MD
+codes. Aside from blank and comment lines (start with #) which can
+appear anywhere, it is formatted as a series of entries, each of which
+has 19 parameters and can span multiple lines:
+</P>
+<P>elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
+t0, t1, t2, t3, rozero, ibar
+</P>
+<P>The "elt" and "lat" parameters are text strings, such as elt = Si or
+Cu and lat = dia or fcc. Because the library file is used by Fortran
+MD codes, these strings may be enclosed in single quotes, but this is
+not required. The other numeric parameters match values in the
+formulas above. The value of the "elt" string is what is used in the
+pair_coeff command to identify which settings from the library file
+you wish to read in. There can be multiple entries in the library
+file with the same "elt" value; LAMMPS reads the 1st matching entry it
+finds and ignores the rest.
+</P>
+<P>Other parameters in the MEAM library file correspond to single-element
+potential parameters:
+</P>
+<PRE>lat = lattice structure of reference configuration
+z = number of nearest neighbors in the reference structure
+ielement = atomic number
+atwt = atomic weight
+alat = lattice constant of reference structure
+esub = energy per atom (eV) in the reference structure at equilibrium
+asub = "A" parameter for MEAM (see e.g. <A HREF = "#Baskes">(Baskes)</A>)
+</PRE>
+<P>The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
+standard MEAM parameters in the literature <A HREF = "#Baskes">(Baskes)</A> (the b
+parameters are the standard beta parameters). The rozero parameter is
+an element-dependent density scaling that weights the reference
+background density (see e.g. equation 4.5 in <A HREF = "#Gullet">(Gullet)</A>) and
+is typically 1.0 for single-element systems. The ibar parameter
+selects the form of the function G(Gamma) used to compute the electron
+density; options are
+</P>
+<PRE> 0 => G = sqrt(1+Gamma)
+ 1 => G = exp(Gamma/2)
+ 2 => not implemented
+ 3 => G = 2/(1+exp(-Gamma))
+ 4 => G = sqrt(1+Gamma)
+ -5 => G = +-sqrt(abs(1+Gamma))
+</PRE>
+<P>If used, the MEAM parameter file contains settings that override or
+complement the library file settings. Examples of such parameter
+files are in the potentials directory with a ".meam" suffix. Their
+format is the same as is read by other Fortran MD codes. Aside from
+blank and comment lines (start with #) which can appear anywhere, each
+line has one of the following forms. Each line can also have a
+trailing comment (starting with #) which is ignored.
+</P>
+<PRE>keyword = value
+keyword(I) = value
+keyword(I,J) = value
+keyword(I,J,K) = value
+</PRE>
+<P>The recognized keywords are as follows:
+</P>
+<P>Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
+augt1, gsmooth_factor, re
+</P>
+<P>where
+</P>
+<PRE>rc = cutoff radius for cutoff function; default = 4.0
+delr = length of smoothing distance for cutoff function; default = 0.1
+rho0(I) = relative density for element I (overwrites value
+ read from meamf file)
+Ec(I,J) = cohesive energy of reference structure for I-J mixture
+delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
+ zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
+alpha(I,J) = alpha parameter for pair potential between I and J (can
+ be computed from bulk modulus of reference structure
+re(I,J) = equilibrium distance between I and J in the reference
+ structure
+Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
+ by K (I<=J); default = 2.8
+Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
+ by K (I<=J); default = 2.0
+lattce(I,J) = lattice structure of I-J reference structure:
+ dia = diamond (interlaced fcc for alloy)
+ fcc = face centered cubic
+ bcc = body centered cubic
+ dim = dimer
+ b1 = rock salt (NaCl structure)
+ hcp = hexagonal close-packed
+ c11 = MoSi2 structure
+ l12 = Cu3Au structure (lower case L, followed by 12)
+ b2 = CsCl structure (interpenetrating simple cubic)
+nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
+ I-J pair (see for example <A HREF = "#Lee">(Lee)</A>).
+ 0 = second-nearest neighbor formulation off
+ 1 = second-nearest neighbor formulation on
+ default = 0
+attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
+ default = 0
+repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
+ default = 0
+zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
+ atom separations <A HREF = "#ZBL">(ZBL)</A>
+ default = 1
+gsmooth_factor = factor determining the length of the G-function smoothing
+ region; only significant for ibar=0 or ibar=4.
+ 99.0 = short smoothing region, sharp step
+ 0.5 = long smoothing region, smooth step
+ default = 99.0
+augt1 = integer flag for whether to augment t1 parameter by
+ 3/5*t3 to account for old vs. new meam formulations;
+ 0 = don't augment t1
+ 1 = augment t1
+ default = 1
+ialloy = integer flag to use alternative averaging rule for t parameters,
+ for comparison with the DYNAMO MEAM code
+ 0 = standard averaging (matches ialloy=0 in DYNAMO)
+ 1 = alternative averaging (matches ialloy=1 in DYNAMO)
+ 2 = no averaging of t (use single-element values)
+ default = 0
+mixture_ref_t = integer flag to use mixture average of t to compute the background
+ reference density for alloys, instead of the single-element values
+ (see description and warning elsewhere in this doc page)
+ 0 = do not use mixture averaging for t in the reference density
+ 1 = use mixture averaging for t in the reference density
+ default = 0
+erose_form = integer value to select the form of the Rose energy function
+ (see description below).
+ default = 0
+emb_lin_neg = integer value to select embedding function for negative densities
+ 0 = F(rho)=0
+ 1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
+ default = 0
+bkgd_dyn = integer value to select background density formula
+ 0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
+ 1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
+ default = 0
+</PRE>
+<P>Rc, delr, re are in distance units (Angstroms in the case of metal
+units). Ec and delta are in energy units (eV in the case of metal
+units).
+</P>
+<P>Each keyword represents a quantity which is either a scalar, vector,
+2d array, or 3d array and must be specified with the correct
+corresponding array syntax. The indices I,J,K each run from 1 to N
+where N is the number of MEAM elements being used.
+</P>
+<P>Thus these lines
+</P>
+<PRE>rho0(2) = 2.25
+alpha(1,2) = 4.37
+</PRE>
+<P>set rho0 for the 2nd element to the value 2.25 and set alpha for the
+alloy interaction between elements 1 and 2 to 4.37.
+</P>
+<P>The augt1 parameter is related to modifications in the MEAM
+formulation of the partial electron density function. In recent
+literature, an extra term is included in the expression for the
+third-order density in order to make the densities orthogonal (see for
+example <A HREF = "#Wang">(Wang)</A>, equation 3d); this term is included in the
+MEAM implementation in lammps. However, in earlier published work
+this term was not included when deriving parameters, including most of
+those provided in the library.meam file included with lammps, and to
+account for this difference the parameter t1 must be augmented by
+3/5*t3. If augt1=1, the default, this augmentation is done
+automatically. When parameter values are fit using the modified
+density function, as in more recent literature, augt1 should be set to
+0.
+</P>
+<P>The mixture_ref_t parameter is available to match results with those
+of previous versions of lammps (before January 2011). Newer versions
+of lammps, by default, use the single-element values of the t
+parameters to compute the background reference density. This is the
+proper way to compute these parameters. Earlier versions of lammps
+used an alloy mixture averaged value of t to compute the background
+reference density. Setting mixture_ref_t=1 gives the old behavior.
+WARNING: using mixture_ref_t=1 will give results that are demonstrably
+incorrect for second-neighbor MEAM, and non-standard for
+first-neighbor MEAM; this option is included only for matching with
+previous versions of lammps and should be avoided if possible.
+</P>
+<P>The parameters attrac and repuls, along with the integer selection
+parameter erose_form, can be used to modify the Rose energy function
+used to compute the pair potential. This function gives the energy of
+the reference state as a function of interatomic spacing. The form of
+this function is:
+</P>
+<PRE>astar = alpha * (r/re - 1.d0)
+if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
+if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
+if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
+a3 = repuls, astar < 0
+a3 = attrac, astar >= 0
+</PRE>
+<P>Most published MEAM parameter sets use the default values attrac=repulse=0.
+Setting repuls=attrac=delta corresponds to the form used in several
+recent published MEAM parameter sets, such as <A HREF = "#Vallone">(Vallone)</A>
+</P>
+<P>NOTE: The default form of the erose expression in LAMMPS was corrected
+in March 2009. The current version is correct, but may show different
+behavior compared with earlier versions of lammps with the attrac
+and/or repuls parameters are non-zero. To obtain the previous default
+form, use erose_form = 1 (this form does not seem to appear in the
+literature). An alternative form (see e.g. <A HREF = "#Lee2">(Lee2)</A>) is
+available using erose_form = 2.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above. You never need to
+specify a pair_coeff command with I != J arguments for this style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the MEAM package. It is only enabled if LAMMPS
+was built with that package, which also requires the MEAM library be
+built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_eam.html">pair_style eam</A>,
+<A HREF = "pair_meam_spline.html">pair_style meam/spline</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Baskes"></A>
+
+<P><B>(Baskes)</B> Baskes, Phys Rev B, 46, 2727-2742 (1992).
+</P>
+<A NAME = "Gullet"></A>
+
+<P><B>(Gullet)</B> Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
+This report may be accessed on-line via <A HREF = "http://infoserve.sandia.gov/sand_doc/2003/038782.pdf">this link</A>.
+</P>
+
+
+<A NAME = "Lee"></A>
+
+<P><B>(Lee)</B> Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
+</P>
+<A NAME = "Lee2"></A>
+
+<P><B>(Lee2)</B> Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
+</P>
+<A NAME = "Valone"></A>
+
+<P><B>(Valone)</B> Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
+</P>
+<A NAME = "Wang"></A>
+
+<P><B>(Wang)</B> Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
+</P>
+<A NAME = "ZBL"></A>
+
+<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
+of Ions in Matter", Vol 1, 1985, Pergamon Press.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_meam_spline.html b/doc/doc2/pair_meam_spline.html
new file mode 100644
index 000000000..e1a17d7b5
--- /dev/null
+++ b/doc/doc2/pair_meam_spline.html
@@ -0,0 +1,152 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style meam/spline
+</H3>
+<H3>pair_style meam/spline/omp
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style meam/spline
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style meam/spline
+pair_coeff * * Ti.meam.spline Ti
+pair_coeff * * Ti.meam.spline Ti Ti Ti
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>meam/spline</I> style computes pairwise interactions for metals
+using a variant of modified embedded-atom method (MEAM) potentials
+<A HREF = "#Lenosky">(Lenosky)</A>. The total energy E is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_meam_spline.jpg">
+</CENTER>
+<P>where rho_i is the density at atom I, theta_jik is the angle between
+atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
+f, and g are represented by cubic splines.
+</P>
+<P>The cutoffs and the coefficients for these spline functions are listed
+in a parameter file which is specified by the
+<A HREF = "pair_coeff.html">pair_coeff</A> command. Parameter files for different
+elements are included in the "potentials" directory of the LAMMPS
+distribution and have a ".meam.spline" file suffix. All of these
+files are parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
+</P>
+<P>Note that unlike for other potentials, cutoffs for spline-based MEAM
+potentials are not set in the pair_style or pair_coeff command; they
+are specified in the potential files themselves.
+</P>
+<P>Unlike the EAM pair style, which retrieves the atomic mass from the
+potential file, the spline-based MEAM potentials do not include mass
+information; thus you need to use the <A HREF = "mass.html">mass</A> command to
+specify it.
+</P>
+<P>Only a single pair_coeff command is used with the <I>meam/spline</I> style
+which specifies a potential file with parameters for all needed
+elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of spline-based MEAM elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine the Ti.meam.spline file has values for Ti. If
+your LAMMPS simulation has 3 atoms types and they are all to be
+treated with this potentials, you would use the following pair_coeff
+command:
+</P>
+<PRE>pair_coeff * * Ti.meam.spline Ti Ti Ti
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
+in the potential file. If a mapping value is specified as NULL, the
+mapping is not performed. This can be used when a <I>meam/spline</I>
+potential is used as part of the <I>hybrid</I> pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+</P>
+<P>IMPORTANT NOTE: The <I>meam/spline</I> style currently supports only
+single-element MEAM potentials. It may be extended for alloy systems
+in the future.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>The current version of this pair style does not support multiple
+element types or mixing. It has been designed for pure elements only.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>The <I>meam/spline</I> pair style does not write its information to <A HREF = "restart.html">binary
+restart files</A>, since it is stored in an external
+potential parameter file. Thus, you need to re-specify the pair_style
+and pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>The <I>meam/spline</I> pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>This pair style is only enabled if LAMMPS was built with the USER-MISC
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_meam.html">pair_style meam</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Lenosky"></A>
+
+<P><B>(Lenosky)</B> Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
+Kress, Modelling Simulation Materials Science Enginerring, 8, 825
+(2000).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_meam_sw_spline.html b/doc/doc2/pair_meam_sw_spline.html
new file mode 100644
index 000000000..391a28686
--- /dev/null
+++ b/doc/doc2/pair_meam_sw_spline.html
@@ -0,0 +1,146 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style meam/sw/spline
+</H3>
+<H3>pair_style meam/sw/spline/omp
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style meam/sw/spline
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style meam/sw/spline
+pair_coeff * * Ti.meam.sw.spline Ti
+pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>meam/sw/spline</I> style computes pairwise interactions for metals
+using a variant of modified embedded-atom method (MEAM) potentials
+<A HREF = "#Lenosky">(Lenosky)</A> with an additional Stillinger-Weber (SW) term
+<A HREF = "#Stillinger">(Stillinger)</A> in the energy. This form of the potential
+was first proposed by Nicklas, Fellinger, and Park
+<A HREF = "#Nicklas">(Nicklas)</A>. We refer to it as MEAM+SW. The total energy E
+is given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_meam_sw_spline.jpg">
+</CENTER>
+<P>where rho_I is the density at atom I, theta_JIK is the angle between
+atoms J, I, and K centered on atom I. The seven functions
+Phi, F, G, U, rho, f, and g are represented by cubic splines.
+</P>
+<P>The cutoffs and the coefficients for these spline functions are listed
+in a parameter file which is specified by the
+<A HREF = "pair_coeff.html">pair_coeff</A> command. Parameter files for different
+elements are included in the "potentials" directory of the LAMMPS
+distribution and have a ".meam.sw.spline" file suffix. All of these
+files are parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
+</P>
+<P>Note that unlike for other potentials, cutoffs for spline-based
+MEAM+SW potentials are not set in the pair_style or pair_coeff
+command; they are specified in the potential files themselves.
+</P>
+<P>Unlike the EAM pair style, which retrieves the atomic mass from the
+potential file, the spline-based MEAM+SW potentials do not include
+mass information; thus you need to use the <A HREF = "mass.html">mass</A> command to
+specify it.
+</P>
+<P>Only a single pair_coeff command is used with the meam/sw/spline style
+which specifies a potential file with parameters for all needed
+elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of spline-based MEAM+SW elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine the Ti.meam.sw.spline file has values for Ti.
+If your LAMMPS simulation has 3 atoms types and they are all to be
+treated with this potential, you would use the following pair_coeff
+command:
+</P>
+<P>pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
+</P>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
+in the potential file. If a mapping value is specified as NULL, the
+mapping is not performed. This can be used when a <I>meam/sw/spline</I>
+potential is used as part of the hybrid pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+</P>
+<P>IMPORTANT NOTE: The <I>meam/sw/spline</I> style currently supports only
+single-element MEAM+SW potentials. It may be extended for alloy
+systems in the future.
+</P>
+<P>Example input scripts that use this pair style are provided
+in the examples/USER/misc/meam_sw_spline directory.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>The pair style does not support multiple element types or mixing.
+It has been designed for pure elements only.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>The <I>meam/sw/spline</I> pair style does not write its information to
+<A HREF = "restart.html">binary restart files</A>, since it is stored in an external
+potential parameter file. Thus, you need to re-specify the pair_style
+and pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>The <I>meam/sw/spline</I> pair style can only be used via the <I>pair</I>
+keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
+support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>This pair style is only enabled if LAMMPS was built with the USER-MISC package.
+See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_meam.html">pair_style meam</A>,
+<A HREF = "pair_meam_spline.html">pair_style meam/spline</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Lenosky"></A>
+
+<P><B>(Lenosky)</B> Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
+Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000).
+</P>
+<A NAME = "Stillinger"></A>
+
+<P><B>(Stillinger)</B> Stillinger, Weber, Phys. Rev. B 31, 5262 (1985).
+</P>
+<A NAME = "Nicklas"></A>
+
+<P><B>(Nicklas)</B>
+The spline-based MEAM+SW format was first devised and used to develop
+potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
+and Hyoungki Park at The Ohio State University.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_mie.html b/doc/doc2/pair_mie.html
new file mode 100644
index 000000000..e5207cb23
--- /dev/null
+++ b/doc/doc2/pair_mie.html
@@ -0,0 +1,107 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style mie/cut command
+</H3>
+<H3>pair_style mie/cut/gpu command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style mie/cut cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for mie/cut interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style mie/cut 10.0
+pair_coeff 1 1 0.72 3.40 23.00 6.66
+pair_coeff 2 2 0.30 3.55 12.65 6.00
+pair_coeff 1 2 0.46 3.32 16.90 6.31
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>mie/cut</I> style computes the Mie potential, given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_mie.jpg">
+</CENTER>
+<P>Rc is the cutoff and C is a function that depends on the repulsive and
+attractive exponents, given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_mie2.jpg">
+</CENTER>
+<P>Note that for 12/6 exponents, C is equal to 4 and the formula is the
+same as the standard Lennard-Jones potential.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>gammaR
+<LI>gammaA
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global
+cutoff specified in the pair_style command is used.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the mie/cut pair styles can be mixed.
+If not explicity defined, both the repulsive and attractive gamma
+exponents for different atoms will be calculated following the same
+mixing rule defined for distances. The default mix value is
+<I>geometric</I>. See the "pair_modify" command for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
+keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
+pairwise forces can be partitioned by distance at different levels of
+the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
+details.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mie"></A>
+
+<P><B>(Mie)</B> G. Mie, Ann Phys, 316, 657 (1903).
+</P>
+<A NAME = "Avendano"></A>
+
+<P><B>(Avendano)</B> C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman,
+G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_modify.html b/doc/doc2/pair_modify.html
new file mode 100644
index 000000000..f6013a430
--- /dev/null
+++ b/doc/doc2/pair_modify.html
@@ -0,0 +1,280 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_modify keyword values ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be listed
+
+<LI>keyword = <I>pair</I> or <I>special</I> or <I>shift</I> or <I>mix</I> or <I>table</I> or <I>table/disp</I> or <I>tabinner</I> or <I>tabinner/disp</I> or <I>tail</I> or <I>compute</I>
+
+<PRE> <I>pair</I> values = sub-style N special which w1 wt2 wt3
+ sub-style = sub-style of <A HREF = "pair_hybrid.html">pair hybrid</A>
+ N = which instance of sub-style (only if sub-style is used multiple times)
+ <I>special</I> values = flavor w1 w2 w3
+ flavor = <I>lj/coul</I> or <I>lj</I> or <I>coul</I>
+ w1,w2,w3 = weights from 0.0 to 1.0 inclusive
+ <I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
+ <I>shift</I> value = <I>yes</I> or <I>no</I>
+ <I>table</I> value = N
+ 2^N = # of values in table
+ <I>table/disp</I> value = N
+ 2^N = # of values in table
+ <I>tabinner</I> value = cutoff
+ cutoff = inner cutoff at which to begin table (distance units)
+ <I>tabinner/disp</I> value = cutoff
+ cutoff = inner cutoff at which to begin table (distance units)
+ <I>tail</I> value = <I>yes</I> or <I>no</I>
+ <I>compute</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_modify shift yes mix geometric
+pair_modify tail yes
+pair_modify table 12
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Modify the parameters of the currently defined pair style. Not all
+parameters are relevant to all pair styles.
+</P>
+<P>If used, the <I>pair</I> keyword must appear first in the list of keywords.
+It can only be used with the <A HREF = "pair_hybrid.html">hybrid and
+hybrid/overlay</A> pair styles. It means that all the
+following parameters will only be modified for the specified
+sub-style. If the sub-style is defined multiple times, then an
+additional numeric argument <I>N</I> must also be specified, which is a
+number from 1 to M where M is the number of times the sub-style was
+listed in the <A HREF = "pair_hybrid.html">pair_style hybrid</A> command. The extra
+number indicates which instance of the sub-style the remaining
+keywords will be applied to. Note that if the <I>pair</I> keyword is not
+used, and the pair style is <I>hybrid</I> or <I>hybrid/overlay</I>, then all the
+specified keywords will be applied to all sub-styles.
+</P>
+<P>If used, the <I>special</I> keyword must appear second in the list of
+keywords, and must follow the <I>pair</I> keyword. Like the <I>pair</I>
+keyword, it also can only be used with the <A HREF = "pair_hybrid.html">hybrid and
+hybrid/overlay</A> pair styles. Its parameters are
+similar to the <A HREF = "special_bonds.html">special_bonds</A> command, and it
+overrides the special_bond settings for the specified sub-style. More
+details are given below.
+</P>
+<P>The <I>mix</I> keyword affects pair coefficients for interactions between
+atoms of type I and J, when I != J and the coefficients are not
+explicitly set in the input script. Note that coefficients for I = J
+must be set explicitly, either in the input script via the
+"pair_coeff" command or in the "Pair Coeffs" section of the <A HREF = "read_data.html">data
+file</A>. For some pair styles it is not necessary to
+specify coefficients when I != J, since a "mixing" rule will create
+them from the I,I and J,J settings. The pair_modify <I>mix</I> value
+determines what formulas are used to compute the mixed coefficients.
+In each case, the cutoff distance is mixed the same way as sigma.
+</P>
+<P>Note that not all pair styles support mixing. Also, some mix options
+are not available for certain pair styles. See the doc page for
+individual pair styles for those restrictions. Note also that the
+<A HREF = "pair_coeff.html">pair_coeff</A> command also can be to directly set
+coefficients for a specific I != J pairing, in which case no mixing is
+performed.
+</P>
+<P>mix <I>geometric</I>
+</P>
+<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = sqrt(sigma_i * sigma_j)
+</PRE>
+<P>mix <I>arithmetic</I>
+</P>
+<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = (sigma_i + sigma_j) / 2
+</PRE>
+<P>mix <I>sixthpower</I>
+</P>
+<PRE>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
+ (sigma_i^6 + sigma_j^6)
+sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+</PRE>
+<P>The <I>shift</I> keyword determines whether a Lennard-Jones potential is
+shifted at its cutoff to 0.0. If so, this adds an energy term to each
+pairwise interaction which will be included in the thermodynamic
+output, but does not affect pair forces or atom trajectories. See the
+doc page for individual pair styles to see which ones support this
+option.
+</P>
+<P>The <I>table</I> and <I>table/disp</I> keywords apply to pair styles with a
+long-range Coulombic term or long-range dispersion term respectively;
+see the doc page for individual styles to see which potentials support
+these options. If N is non-zero, a table of length 2^N is
+pre-computed for forces and energies, which can shrink their
+computational cost by up to a factor of 2. The table is indexed via a
+bit-mapping technique <A HREF = "#Wolff">(Wolff)</A> and a linear interpolation is
+performed between adjacent table values. In our experiments with
+different table styles (lookup, linear, spline), this method typically
+gave the best performance in terms of speed and accuracy.
+</P>
+<P>The choice of table length is a tradeoff in accuracy versus speed. A
+larger N yields more accurate force computations, but requires more
+memory which can slow down the computation due to cache misses. A
+reasonable value of N is between 8 and 16. The default value of 12
+(table of length 4096) gives approximately the same accuracy as the
+no-table (N = 0) option. For N = 0, forces and energies are computed
+directly, using a polynomial fit for the needed erfc() function
+evaluation, which is what earlier versions of LAMMPS did. Values
+greater than 16 typically slow down the simulation and will not
+improve accuracy; values from 1 to 8 give unreliable results.
+</P>
+<P>The <I>tabinner</I> and <I>tabinner/disp</I> keywords set an inner cutoff above
+which the pairwise computation is done by table lookup (if tables are
+invoked), for the corresponding Coulombic and dispersion tables
+discussed with the <I>table</I> and <I>table/disp</I> keywords. The smaller the
+cutoff is set, the less accurate the table becomes (for a given number
+of table values), which can require use of larger tables. The default
+cutoff value is sqrt(2.0) distance units which means nearly all
+pairwise interactions are computed via table lookup for simulations
+with "real" units, but some close pairs may be computed directly
+(non-table) for simulations with "lj" units.
+</P>
+<P>When the <I>tail</I> keyword is set to <I>yes</I>, certain pair styles will add
+a long-range VanderWaals tail "correction" to the energy and pressure.
+These corrections are bookkeeping terms which do not affect dynamics,
+unless a constant-pressure simulation is being performed. See the doc
+page for individual styles to see which support this option. These
+corrections are included in the calculation and printing of
+thermodynamic quantities (see the <A HREF = "thermo_style.html">thermo_style</A>
+command). Their effect will also be included in constant NPT or NPH
+simulations where the pressure influences the simulation box
+dimensions (e.g. the <A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_nh.html">fix nph</A>
+commands). The formulas used for the long-range corrections come from
+equation 5 of <A HREF = "#Sun">(Sun)</A>.
+</P>
+<P>IMPORTANT NOTE: The tail correction terms are computed at the
+beginning of each run, using the current atom counts of each atom
+type. If atoms are deleted (or lost) or created during a simulation,
+e.g. via the <A HREF = "fix_gcmc.html">fix gcmc</A> command, the correction factors
+are not re-computed. If you expect the counts to change dramatically,
+you can break a run into a series of shorter runs so that the
+correction factors are re-computed more frequently.
+</P>
+<P>Several additional assumptions are inherent in using tail corrections,
+including the following:
+</P>
+<UL><LI>The simulated system is a 3d bulk homogeneous liquid. This option
+should not be used for systems that are non-liquid, 2d, have a slab
+geometry (only 2d periodic), or inhomogeneous.
+
+<LI>G(r), the radial distribution function (rdf), is unity beyond the
+cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
+LJ fluid), and it is probably a good idea to verify this assumption by
+checking the rdf. The rdf is not exactly unity beyond the cutoff for
+each pair of interaction types, so the tail correction is necessarily
+an approximation.
+
+<P>The tail corrections are computed at the beginning of each simulation
+run. If the number of atoms changes during the run, e.g. due to atoms
+leaving the simulation domain, or use of the <A HREF = "fix_gcmc.html">fix gcmc</A>
+command, then the corrections are not updates to relect the changed
+atom count. If this is a large effect in your simulation, you should
+break the long run into several short runs, so that the correction
+factors are re-computed multiple times.
+</P>
+<LI>Thermophysical properties obtained from calculations with this option
+enabled will not be thermodynamically consistent with the truncated
+force-field that was used. In other words, atoms do not feel any LJ
+pair interactions beyond the cutoff, but the energy and pressure
+reported by the simulation include an estimated contribution from
+those interactions.
+</UL>
+<P>The <I>compute</I> keyword allows pairwise computations to be turned off,
+even though a <A HREF = "pair_style.html">pair_style</A> is defined. This is not
+useful for running a real simulation, but can be useful for debugging
+purposes or for performing a <A HREF = "rerun.html">rerun</A> simulation, when you
+only wish to compute partial forces that do not include the pairwise
+contribution.
+</P>
+<P>Two examples are as follows. First, this option allows you to perform
+a simulation with <A HREF = "pair_hybrid.html">pair_style hybrid</A> with only a
+subset of the hybrid sub-styles enabled. Second, this option allows
+you to perform a simulation with only long-range interactions but no
+short-range pairwise interactions. Doing this by simply not defining
+a pair style will not work, because the
+<A HREF = "kspace_style.html">kspace_style</A> command requires a Kspace-compatible
+pair style be defined.
+</P>
+<HR>
+
+<H5>Use of <I>special</I> keyword
+</H5>
+<P>The <I>special</I> keyword requires 4 values similar to those specified
+with the <A HREF = "special_bonds.html">special_bonds</A> command, <I>flavor</I> and
+w1,w2,w3. The <I>flavor</I> argument can be <I>lj</I> to change the
+Lennard-Jones settings, <I>coul</I> to change the Coulombic settings, or
+<I>lj/coul</I> to change both to the same set of 3 values. The w1,w2,w3
+values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
+1-3, and 1-4 bond topology neighbors. For example, these commands
+</P>
+<PRE>special_bonds lj/coul 0.0 0.0 0.1
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333
+</PRE>
+<P>show how to use both the CHARMM and AMBER force fields in a single
+simulation. The first pair modify command sets the special bonds to
+CHARMM values (all 0.0). The last 2 pair modify commands set the
+standard AMBER values for LJ and Coulombic weights.
+</P>
+<P>IMPORTANT NOTE: The global settings specified by the
+<A HREF = "special_bonds.html">special_bonds</A> command affect the construction of
+neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
+exclude those pairs from the neighbor list entirely. Weights of 1.0
+store the neighbor with no weighting applied. The format of the
+neighbor list cannot be changed by setting a sub-style weight to a
+non-zero or non-one value. Thus an error is generated if the new
+sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
+1.0). Note that as in the example above, the global factor can simply
+be set a value other than 0.0 or 1.0, then overridden by any of the
+sub-styles with a value that is 0.0 or 1.0.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
+conflicting options. You cannot use <I>tail</I> yes with 2d simulations.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "thermo_style.html">thermo_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are mix = geometric, shift = no, table = 12,
+tabinner = sqrt(2.0), tail = no, and compute = yes.
+</P>
+<P>Note that some pair styles perform mixing, but only a certain style of
+mixing. See the doc pages for individual pair styles for details.
+</P>
+<HR>
+
+<A NAME = "Wolff"></A>
+
+<P><B>(Wolff)</B> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
+</P>
+<A NAME = "Sun"></A>
+
+<P><B>(Sun)</B> Sun, J Phys Chem B, 102, 7338-7364 (1998).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_morse.html b/doc/doc2/pair_morse.html
new file mode 100644
index 000000000..58beb18f7
--- /dev/null
+++ b/doc/doc2/pair_morse.html
@@ -0,0 +1,114 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style morse command
+</H3>
+<H3>pair_style morse/cuda command
+</H3>
+<H3>pair_style morse/gpu command
+</H3>
+<H3>pair_style morse/omp command
+</H3>
+<H3>pair_style morse/opt command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style morse cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for Morse interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style morse 2.5
+pair_coeff * * 100.0 2.0 1.5
+pair_coeff 1 1 100.0 2.0 1.5 3.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>morse</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>D0 (energy units)
+<LI>alpha (1/distance units)
+<LI>r0 (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global morse
+cutoff is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>None of these pair styles support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>All of these pair styles support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table options is not relevant for
+the Morse pair styles.
+</P>
+<P>None of these pair styles support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>All of these pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_nb3b_harmonic.html b/doc/doc2/pair_nb3b_harmonic.html
new file mode 100644
index 000000000..6d258736e
--- /dev/null
+++ b/doc/doc2/pair_nb3b_harmonic.html
@@ -0,0 +1,129 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style nb3b/harmonic command
+</H3>
+<H3>pair_style nb3b/harmonic/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style nb3b/harmonic
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style nb3b/harmonic
+pair_coeff * * MgOH.nb3bharmonic Mg O H
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This pair style computes a nonbonded 3-body harmonic potential for the
+energy E of a system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_nb3b_harmonic.jpg">
+</CENTER>
+<P>where <I>theta_0</I> is the equilibrium value of the angle and <I>K</I> is a
+prefactor. Note that the usual 1/2 factor is included in <I>K</I>. The form
+of the potential is identical to that used in angle_style <I>harmonic</I>,
+but in this case, the atoms do not need to be explicitly bonded.
+</P>
+<P>Only a single pair_coeff command is used with this style which
+specifies a potential file with parameters for specified elements.
+These are mapped to LAMMPS atom types by specifying N additional
+arguments after the filename in the pair_coeff command, where N is the
+number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine a file SiC.nb3b.harmonic has potential values
+for Si and C. If your LAMMPS simulation has 4 atoms types and you
+want the 1st 3 to be Si, and the 4th to be C, you would use the
+following pair_coeff command:
+</P>
+<PRE>pair_coeff * * SiC.nb3b.harmonic Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the potential file. The final C argument maps LAMMPS atom
+type 4 to the C element in the potential file. If a mapping value is
+specified as NULL, the mapping is not performed. This can be used
+when the potential is used as part of the <I>hybrid</I> pair style. The
+NULL values are placeholders for atom types that will be used with
+other potentials. An example of a pair_coeff command for use with the
+<I>hybrid</I> pair style is:
+</P>
+<P>pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H
+</P>
+<P>Three-body nonbonded harmonic files in the <I>potentials</I> directory of
+the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that
+are not blank or comments (starting with #) define parameters for a
+triplet of elements.
+</P>
+<P>Each entry has six arguments. The first three are atom types as
+referenced in the LAMMPS input file. The first argument specifies the
+central atom. The fourth argument indicates the <I>K</I> parameter. The
+fifth argument indicates <I>theta_0</I>. The sixth argument indicates a
+separation cutoff in Angstroms.
+</P>
+<P>For a given entry, if the second and third arguments are identical,
+then the entry is for a cutoff for the distance between types 1 and 2
+(values for <I>K</I> and <I>theta_0</I> are irrelevant in this case).
+</P>
+<P>For a given entry, if the first three arguments are all different,
+then the entry is for the <I>K</I> and <I>theta_0</I> parameters (the cutoff in
+this case is irrelevant).
+</P>
+<P>It is <I>not</I> required that the potential file contain entries for all
+of the elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style can only be used if LAMMPS was built with the MANYBODY
+package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_nm.html b/doc/doc2/pair_nm.html
new file mode 100644
index 000000000..809bdb3bd
--- /dev/null
+++ b/doc/doc2/pair_nm.html
@@ -0,0 +1,183 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style nm/cut command
+</H3>
+<H3>pair_style nm/cut/coul/cut command
+</H3>
+<H3>pair_style nm/cut/coul/long command
+</H3>
+<H3>pair_style nm/cut/omp command
+</H3>
+<H3>pair_style nm/cut/coul/cut/omp command
+</H3>
+<H3>pair_style nm/cut/coul/long/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>nm/cut</I> or <I>nm/cut/coul/cut</I> or <I>nm/cut/coul/long</I>
+
+<LI>args = list of arguments for a particular style
+
+<PRE> <I>nm/cut</I> args = cutoff
+ cutoff = global cutoff for Pair interactions (distance units)
+ <I>nm/cut/coul/cut</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ <I>nm/cut/coul/long</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style nm/cut 12.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</PRE>
+<PRE>pair_style nm/cut/coul/cut 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</PRE>
+<PRE>pair_style nm/cut/coul/long 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>nm</I> computes site-site interactions based on the N-M potential
+by <A HREF = "#Clarke">Clarke</A>, mainly used for ionic liquids. A site can
+represent a single atom or a united-atom site. The energy of an
+interaction has the following form:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_nm.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>Style <I>nm/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
+</CENTER>
+<P>where C is an energy-conversion constant, Qi and Qj are the charges on
+the 2 atoms, and epsilon is the dielectric constant which can be set
+by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
+specified in the pair_style command, it is used for both the NM and
+Coulombic terms. If two cutoffs are specified, they are used as
+cutoffs for the NM and Coulombic terms respectively.
+</P>
+<P>Styles <I>nm/cut/coul/long</I> compute the same
+Coulombic interactions as style <I>nm/cut/coul/cut</I> except that an
+additional damping factor is applied to the Coulombic term so it can
+be used in conjunction with the <A HREF = "kspace_style.html">kspace_style</A>
+command and its <I>ewald</I> or <I>pppm</I> option. The Coulombic cutoff
+specified for this style means that pairwise interactions within this
+distance are computed directly; interactions outside that distance are
+computed in reciprocal space.
+</P>
+<P>For all of the <I>nm</I> pair styles, the following coefficients must
+be defined for each pair of atoms types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the
+examples above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<UL><LI>E0 (energy units)
+<LI>r0 (distance units)
+<LI>n (unitless)
+<LI>m (unitless)
+<LI>cutoff1 (distance units)
+<LI>cutoff2 (distance units)
+</UL>
+<P>The latter 2 coefficients are optional. If not specified, the global
+NM and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both NM
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the NM and Coulombic cutoffs for this
+type pair. You cannot specify 2 cutoffs for style <I>nm</I>, since it
+has no Coulombic terms.
+</P>
+<P>For <I>nm/cut/coul/long</I> only the NM cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>All of the <I>nm</I> pair styles supports the
+<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the pair
+interaction.
+</P>
+<P>The <I>nm/cut/coul/long</I> pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+</P>
+<P>All of the <I>nm</I> pair styles support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding a long-range tail correction to the energy and
+pressure for the NM portion of the pair interaction.
+</P>
+<P>All of the <I>nm</I> pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>All of the <I>nm</I> pair styles can only be used via the <I>pair</I> keyword of
+the <A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Clarke"></A>
+
+<P><B>(Clarke)</B> Clarke and Smith, J Chem Phys, 84, 2290 (1986).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_none.html b/doc/doc2/pair_none.html
new file mode 100644
index 000000000..d6d1fedea
--- /dev/null
+++ b/doc/doc2/pair_none.html
@@ -0,0 +1,45 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style none command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style none
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Using a pair style of none means pair forces are not computed.
+</P>
+<P>With this choice, the force cutoff is 0.0, which means that only atoms
+within the neighbor skin distance (see the <A HREF = "neighbor.html">neighbor</A>
+command) are communicated between processors. You must insure the
+skin distance is large enough to acquire atoms needed for computing
+bonds, angles, etc.
+</P>
+<P>A pair style of <I>none</I> will also prevent pairwise neighbor lists from
+being built. However if the <A HREF = "neighbor.html">neighbor</A> style is <I>bin</I>,
+data structures for binning are still allocated. If the neighbor skin
+distance is small, then these data structures can consume a large
+amount of memory. So you should either set the neighbor style to
+<I>nsq</I> or set the skin distance to a larger value.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_peri.html b/doc/doc2/pair_peri.html
new file mode 100644
index 000000000..a505847a6
--- /dev/null
+++ b/doc/doc2/pair_peri.html
@@ -0,0 +1,231 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style peri/pmb command
+</H3>
+<H3>pair_style peri/pmb/omp command
+</H3>
+<H3>pair_style peri/lps command
+</H3>
+<H3>pair_style peri/lps/omp command
+</H3>
+<H3>pair_style peri/ves command
+</H3>
+<H3>pair_style peri/eps command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style
+</PRE>
+<P>style = <I>peri/pmb</I> or <I>peri/lps</I> or <I>peri/ves</I> or <I>peri/eps</I>:ul
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+</PRE>
+<PRE>pair_style peri/lps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
+</PRE>
+<PRE>pair_style peri/ves
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
+</PRE>
+<PRE>pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The peridynamic pair styles implement material models that can be used
+at the mescscopic and macroscopic scales. See <A HREF = "PDF/PDLammps_overview.pdf">this
+document</A> for an overview of LAMMPS commands
+for Peridynamics modeling.
+</P>
+<P>Style <I>peri/pmb</I> implements the Peridynamic bond-based prototype
+microelastic brittle (PMB) model.
+</P>
+<P>Style <I>peri/lps</I> implements the Peridynamic state-based linear
+peridynamic solid (LPS) model.
+</P>
+<P>Style <I>peri/ves</I> implements the Peridynamic state-based linear
+peridynamic viscoelastic solid (VES) model.
+</P>
+<P>Style <I>peri/eps</I> implements the Peridynamic state-based elastic-plastic
+solid (EPS) model.
+</P>
+<P>The canonical papers on Peridynamics are <A HREF = "#Silling2000">(Silling 2000)</A>
+and <A HREF = "#Silling2007">(Silling 2007)</A>. The implementation of Peridynamics
+in LAMMPS is described in <A HREF = "#Parks">(Parks)</A>. Also see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS
+user guide</A> for
+more details about its implementation.
+</P>
+<P>The peridynamic VES and EPS models in PDLAMMPS were implemented by
+R. Rahman and J. T. Foster at University of Texas at San Antonio. The
+original VES formulation is described in "(Mitchell2011)" and the
+original EPS formulation is in "(Mitchell2011a)". Additional PDF docs
+that describe the VES and EPS implementations are include in the
+LAMMPS distro in <A HREF = "PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</A> and
+<A HREF = "PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</A>. For questions
+regarding the VES and EPS models in LAMMPS you can contact R. Rahman
+(rezwanur.rahman at utsa.edu).
+</P>
+<P>The following coefficients must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below.
+</P>
+<P>For the <I>peri/pmb</I> style:
+</P>
+<UL><LI>c (energy/distance/volume^2 units)
+<LI>horizon (distance units)
+<LI>s00 (unitless)
+<LI>alpha (unitless)
+</UL>
+<P>C is the effectively a spring constant for Peridynamic bonds, the
+horizon is a cutoff distance for truncating interactions, and s00 and
+alpha are used as a bond breaking criteria. The units of c are such
+that c/distance = stiffness/volume^2, where stiffness is
+energy/distance^2 and volume is distance^3. See the users guide for
+more details.
+</P>
+<P>For the <I>peri/lps</I> style:
+</P>
+<UL><LI>K (force/area units)
+<LI>G (force/area units)
+<LI>horizon (distance units)
+<LI>s00 (unitless)
+<LI>alpha (unitless)
+</UL>
+<P>K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. See the users guide for more
+details.
+</P>
+<P>For the <I>peri/ves</I> style:
+</P>
+<UL><LI>K (force/area units)
+<LI>G (force/area units)
+<LI>horizon (distance units)
+<LI>s00 (unitless)
+<LI>alpha (unitless)
+<LI>m_lambdai (unitless)
+<LI>m_taubi (unitless)
+</UL>
+<P>K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. m_lambdai and m_taubi are the
+viscoelastic relaxation parameter and time constant,
+respectively. m_lambdai varies within zero to one. For very small
+values of m_lambdai the viscoelsatic model responds very similar to a
+linear elastic model. For details please see the description in
+"(Mtchell2011)".
+</P>
+<P>For the <I>peri/eps</I> style:
+</P>
+<P>K (force/area units)
+G (force/area units)
+horizon (distance units)
+s00 (unitless)
+alpha (unitless)
+m_yield_stress (force/area units)
+</P>
+<P>K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance and s00 and alpha are used as a bond breaking
+criteria. m_yield_stress is the yield stress of the material. For
+details please see the description in "(Mtchell2011a)".
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>These pair styles do not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for these pair styles.
+</P>
+<P>These pair styles write their information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>These pair styles can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. They do not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>All of these styles are part of the PERI package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Parks"></A>
+
+<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11),
+777-783 (2008).
+</P>
+<A NAME = "Silling2000"></A>
+
+<P><B>(Silling 2000)</B> Silling, J Mech Phys Solids, 48, 175-209 (2000).
+</P>
+<A NAME = "Silling2007"></A>
+
+<P><B>(Silling 2007)</B> Silling, Epton, Weckner, Xu, Askari, J Elasticity,
+88, 151-184 (2007).
+</P>
+<A NAME = "Mitchell2011"></A>
+
+<P><B>(Mitchell2011)</B> Mitchell. A non-local, ordinary-state-based
+viscoelasticity model for peridynamics. Sandia National Lab Report,
+8064:1-28 (2011).
+</P>
+<A NAME = "Mitchell2011a"></A>
+
+<P><B>(Mitchell2011a)</B> Mitchell. A Nonlocal, Ordinary, State-Based
+Plasticity Model for Peridynamics. Sandia National Lab Report,
+3166:1-34 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_polymorphic.html b/doc/doc2/pair_polymorphic.html
new file mode 100644
index 000000000..6cfd6bf3c
--- /dev/null
+++ b/doc/doc2/pair_polymorphic.html
@@ -0,0 +1,245 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style polymorphic command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style polymorphic
+</PRE>
+<P>style = <I>polymorphic</I>
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style polymorphic
+pair_coeff * * TlBr_msw.polymorphic Tl Br
+pair_coeff * * AlCu_eam.polymorphic Al Cu
+pair_coeff * * GaN_tersoff.polymorphic Ga N
+pair_coeff * * GaN_sw.polymorphic GaN
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>polymorphic</I> pair style computes a 3-body free-form potential
+(<A HREF = "#Zhou">Zhou</A>) for the energy E of a system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/polymorphic1.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/polymorphic2.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/polymorphic2.jpg">
+</CENTER>
+<P>where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N
+represents a list of i's neighbors, delta_ij is a Direc constant
+(i.e., delta_ij = 1 when i = j, and delta_ij = 0 otherwise), eta_ij is
+similar constant that can be set either to eta_ij = delta_ij or eta_ij
+= 1 - delta_ij depending on the potential type, U_IJ(r_ij),
+V_IJ(r_ij), W_IK(r_ik) are pair functions, G_JIK(cos(theta)) is an
+angular function, P_IK(delta r_jik) is a function of atomic spacing
+differential delta r_jik = r_ij - xi_IJ*r_ik with xi_IJ being a
+pair-dependent parameter, and F_IJ(X_ij) is a function of the local
+environment variable X_ij. This generic potential is fully defined
+once the constants eta_ij and xi_IJ, and the six functions U_IJ(r_ij),
+V_IJ(r_ij), W_IK(r_ik), G_JIK(cos(theta)), P_IK(delta r_jik), and
+F_IJ(X_ij) are given. Note that these six functions are all one
+dimensional, and hence can be provided in an analytic or tabular
+form. This allows users to design different potentials solely based on
+a manipulation of these functions. For instance, the potential reduces
+to Stillinger-Weber potential (<A HREF = "#SW">SW</A>) if we set
+</P>
+<CENTER><IMG SRC = "Eqs/polymorphic4.jpg">
+</CENTER>
+<P>The potential reduces to Tersoff types of potential
+(<A HREF = "#Tersoff">Tersoff</A> or <A HREF = "#Albe">Albe</A>) if we set
+</P>
+<CENTER><IMG SRC = "Eqs/polymorphic5.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/polymorphic6.jpg">
+</CENTER>
+<P>The potential reduces to Rockett-Tersoff (<A HREF = "#Wang">Wang</A>) type if we set
+</P>
+<CENTER><IMG SRC = "Eqs/polymorphic7.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/polymorphic6.jpg">
+</CENTER>
+<CENTER><IMG SRC = "Eqs/polymorphic8.jpg">
+</CENTER>
+<P>The potential becomes embedded atom method (<A HREF = "#Daw">Daw</A>) if we set
+</P>
+<CENTER><IMG SRC = "Eqs/polymorphic9.jpg">
+</CENTER>
+<P>In the embedded atom method case, phi_IJ(r_ij) is the pair energy,
+F_I(X) is the embedding energy, X is the local electron density, and
+f_K(r) is the atomic electron density function.
+</P>
+<P>If the tabulated functions are created using the parameters of sw,
+tersoff, and eam potentials, the polymorphic pair style will produce
+the same global properties (energies and stresses) and the same forces
+as the sw, tersoff, and eam pair styles. The polymorphic pair style
+also produces the same atom properties (energies and stresses) as the
+corresponding tersoff and eam pair styles. However, due to a different
+partition of global properties to atom properties, the polymorphic
+pair style will produce different atom properties (energies and
+stresses) as the sw pair style. This does not mean that polymorphic
+pair style is different from the sw pair style in this case. It just
+means that the definitions of the atom energies and atom stresses are
+different.
+</P>
+<P>Only a single pair_coeff command is used with the polymorphic style
+which specifies an potential file for all needed elements. These are
+mapped to LAMMPS atom types by specifying N additional arguments after
+the filename in the pair_coeff command, where N is the number of
+LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of Tersoff elements to atom types
+</UL>
+<P>See the pair_coeff doc page for alternate ways to specify the path for
+the potential file. Several files for polymorphic potentials are
+included in the potentials dir of the LAMMPS distro. They have a
+"poly" suffix.
+</P>
+<P>As an example, imagine the SiC_tersoff.polymorphic file has tabulated
+functions for Si-C tersoff potential. If your LAMMPS simulation has 4
+atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
+would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * SiC_tersoff.polymorphic Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom
+types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
+Si element in the polymorphic file. The final C argument maps LAMMPS
+atom type 4 to the C element in the polymorphic file. If a mapping
+value is specified as NULL, the mapping is not performed. This can be
+used when an polymorphic potential is used as part of the hybrid pair
+style. The NULL values are placeholders for atom types that will be
+used with other potentials.
+</P>
+<P>Potential files in the potentials directory of the LAMMPS distribution
+have a ".poly" suffix. At the beginning of the files, an unlimited
+number of lines starting with '#' are used to describe the potential
+and are ignored by LAMMPS. The next line lists two numbers:
+</P>
+<PRE>ntypes eta
+</PRE>
+<P>Here ntypes represent total number of species defined in the potential
+file, and eta = 0 or 1. The number ntypes must equal the total number
+of different species defined in the pair_coeff command. When eta = 1,
+eta_ij defined in the potential functions above is set to 1 -
+delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines
+each lists two numbers and a character string representing atomic
+number, atomic mass, and name of the species of the ntypes elements:
+</P>
+<PRE>atomic_number atomic-mass element (1)
+atomic_number atomic-mass element (2)
+...
+atomic_number atomic-mass element (ntypes)
+</PRE>
+<P>The next ntypes*(ntypes+1)/2 lines contain two numbers:
+</P>
+<PRE>cut xi (1)
+cut xi (2)
+...
+cut xi (ntypes*(ntypes+1)/2)
+</PRE>
+<P>Here cut means the cutoff distance of the pair functions, xi is the
+same as defined in the potential functions above. The
+ntypes*(ntypes+1)/2 lines are related to the pairs according to the
+sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then
+then ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ...,
+ntypes (i.e., the sequence of the ij pairs follows 11, 22, ..., 12,
+13, 14, ..., 23, 24, ...).
+</P>
+<P>The final blocks of the potential file are the U, V, W, P, G, and F
+functions are listed sequentially. First, U functions are given for
+each of the ntypes*(ntypes+1)/2 pairs according to the sequence
+described above. For each of the pairs, nr values are listed. Next,
+similar arrays are given for V, W, and P functions. Then G functions
+are given for all the ntypes*ntypes*ntypes ijk triplets in a natural
+sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to
+ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212,
+...). Each of the ijk functions contains ng values. Finally, the F
+functions are listed for all ntypes*(ntypes+1)/2 pairs, each
+containing nx values. Either analytic or tabulated functions can be
+specified. Currently, constant, exponential, sine and cosine analytic
+functions are available which are specified with: constant c1 , where
+f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2*x) sine c1 c2 ,
+where f(x) = c1 sin(c2*x) cos c1 c2 , where f(x) = c1 cos(c2*x)
+Tabulated functions are specified by spline n x1 x2, where n=number of
+point, (x1,x2)=range and then followed by n values evaluated uniformly
+over these argument ranges. The valid argument ranges of the
+functions are between 0 <= r <= cut for the U(r), V(r), W(r)
+functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions,
+-1 <= costheta <= 1 for the G(costheta) functions, and 0 <= X <= maxX
+for the F(X) functions.
+</P>
+<P><B>Mixing, shift, table tail correction, restart</B>:
+</P>
+<P>This pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write their information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>If using create_atoms command, atomic masses must be defined in the
+input script. If using read_data, atomic masses must be defined in the
+atomic structure data file.
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled if
+LAMMPS was built with that package (which it is by default). See the
+<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair potential requires the <A HREF = "newton.html">newtion</A> setting to be
+"on" for pair interactions.
+</P>
+<P>The potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal <A HREF = "units.html">units</A>. You can use
+any LAMMPS units, but you would need to create your own potential
+files.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<HR>
+
+<A NAME = "Zhou"></A>
+
+<P><B>(Zhou)</B> X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and
+F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
+</P>
+<A NAME = "SW"></A>
+
+<P><B>(SW)</B> F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).
+</P>
+<A NAME = "Tersoff"></A>
+
+<P><B>(Tersoff)</B> J. Tersoff, Phys. Rev. B, 39, 5566 (1989).
+</P>
+<A NAME = "Albe"></A>
+
+<P><B>(Albe)</B> K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
+66, 035205 (2002).
+</P>
+<A NAME = "Wang"></A>
+
+<P><B>(Wang)</B> J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).
+</P>
+<A NAME = "Daw"></A>
+
+<P><B>(Daw)</B> M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_quip.html b/doc/doc2/pair_quip.html
new file mode 100644
index 000000000..93096fca1
--- /dev/null
+++ b/doc/doc2/pair_quip.html
@@ -0,0 +1,102 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style quip command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style quip
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style quip
+pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
+pair_coeff * * sw_example.xml "IP SW" 14
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>quip</I> provides an interface for calling potential routines from
+the QUIP package. QUIP is built separately, and then linked to
+LAMMPS. The most recent version of the QUIP package can be downloaded
+from GitHub:
+<A HREF = "https://github.com/libAtoms/QUIP">https://github.com/libAtoms/QUIP</A>. The
+interface is chiefly intended to be used to run Gaussian Approximation
+Potentials (GAP), which are described in the following publications:
+<A HREF = "#Bartok_2010">(Bartok et al)</A> and <A HREF = "#Bartok_PhD">(PhD thesis of
+Bartok)</A>.
+</P>
+<P>Only a single pair_coeff command is used with the <I>quip</I> style that
+specifies a QUIP potential file containing the parameters of the
+potential for all needed elements in XML format. This is followed by a
+QUIP initialization string. Finally, the QUIP elements are mapped to
+LAMMPS atom types by specifying N atomic numbers, where N is the
+number of LAMMPS atom types:
+</P>
+<UL><LI>QUIP filename
+<LI>QUIP initialization string
+<LI>N atomic numbers = mapping of QUIP elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>A QUIP potential is fully specified by the filename which contains the
+parameters of the potential in XML format, the initialisation string,
+and the map of atomic numbers.
+</P>
+<P>GAP potentials can be obtained from the Data repository section of
+<A HREF = "http://www.libatoms.org">http://www.libatoms.org</A>, where the
+appropriate initialisation strings are also advised. The list of
+atomic numbers must be matched to the LAMMPS atom types specified in
+the LAMMPS data file or elsewhere.
+</P>
+<P>Two examples input scripts are provided in the examples/USER/quip
+directory.
+</P>
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-QUIP package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>QUIP potentials are parametrized in electron-volts and Angstroms and
+therefore should be used with LAMMPS metal <A HREF = "units.html">units</A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<HR>
+
+<A NAME = "Bartok_2010"></A>
+
+<P><B>(Bartok_2010)</B> AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
+Review Letters 104, 136403 (2010).
+</P>
+<A NAME = "Bartok_PhD"></A>
+
+<P><B>(Bartok_PhD)</B> A Bartok-Partay, PhD Thesis, University of Cambridge,
+(2010).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_reax.html b/doc/doc2/pair_reax.html
new file mode 100644
index 000000000..bbd554e1b
--- /dev/null
+++ b/doc/doc2/pair_reax.html
@@ -0,0 +1,216 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style reax command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style reax hbcut hbnewflag tripflag precision
+</PRE>
+<UL><LI>hbcut = hydrogen-bond cutoff (optional) (distance units)
+<LI>hbnewflag = use old or new hbond function style (0 or 1) (optional)
+<LI>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
+<LI>precision = precision for charge equilibration (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style reax
+pair_style reax 10.0 0 1 1.0e-5
+pair_coeff * * ffield.reax 3 1 2 2
+pair_coeff * * ffield.reax 3 NULL NULL 3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>reax</I> computes the ReaxFF potential of van Duin, Goddard and
+co-workers. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. There is more than one version of ReaxFF. The version
+implemented in LAMMPS uses the functional forms documented in the
+supplemental information of the following paper:
+<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
+the most up-to-date version of ReaxFF as of summer 2010.
+</P>
+<P>The <I>reax</I> style differs from the <A HREF = "pair_reax_c.html">pair_style reax/c</A>
+command in the lo-level implementation details. The <I>reax</I> style is a
+Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
+implemented as stand-alone C code and is now integrated into LAMMPS as
+a package.
+</P>
+<P>LAMMPS requires that a file called ffield.reax be provided, containing
+the ReaxFF parameters for each atom type, bond type, etc. The format
+is identical to the ffield file used by van Duin and co-workers. The
+filename is required as an argument in the pair_coeff command. Any
+value other than "ffield.reax" will be rejected (see below).
+</P>
+<P>LAMMPS provides several different versions of ffield.reax in its
+potentials dir, each called potentials/ffield.reax.label. These are
+documented in potentials/README.reax. The default ffield.reax
+contains parameterizations for the following elements: C, H, O, N, S.
+</P>
+<P>IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force
+field files with LAMMPS. Adri van Duin's group at PSU is the central
+repository for this kind of data as they are continuously deriving and
+updating parameterizations for different classes of materials. You
+can visit their WWW site at
+<A HREF = "http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</A>, register
+as a "new user", and then submit a request to their group describing
+material(s) you are interested in modeling with ReaxFF. They can tell
+you what is currently available or what it would take to create a
+suitable ReaxFF parameterization.
+</P>
+<P>The format of these files is identical to that used originally by van
+Duin. We have tested the accuracy of <I>pair_style reax</I> potential
+against the original ReaxFF code for the systems mentioned above. You
+can use other ffield files for specific chemical systems that may be
+available elsewhere (but note that their accuracy may not have been
+tested).
+</P>
+<P>The <I>hbcut</I>, <I>hbnewflag</I>, <I>tripflag</I>, and <I>precision</I> settings are
+optional arguments. If none are provided, default settings are used:
+<I>hbcut</I> = 6 (which is Angstroms in real units), <I>hbnewflag</I> = 1 (use
+new hbond function style), <I>tripflag</I> = 1 (apply stabilization to all
+triple bonds), and <I>precision</I> = 1.0e-6 (one part in 10^6). If you
+wish to override any of these defaults, then all of the settings must
+be specified.
+</P>
+<P>Two examples using <I>pair_style reax</I> are provided in the examples/reax
+sub-directory, along with corresponding examples for
+<A HREF = "pair_reax_c.html">pair_style reax/c</A>.
+</P>
+<P>Use of this pair style requires that a charge be defined for every
+atom since the <I>reax</I> pair style performs a charge equilibration (QEq)
+calculation. See the <A HREF = "atom_style.html">atom_style</A> and
+<A HREF = "read_data.html">read_data</A> commands for details on how to specify
+charges.
+</P>
+<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
+energy contributions, with the exception of the Coulombic and charge
+equilibration contributions which are stored in the thermo variable
+<I>ecoul</I>. The output of these quantities is controlled by the
+<A HREF = "thermo.html">thermo</A> command.
+</P>
+<P>This pair style tallies a breakdown of the total ReaxFF potential
+energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
+pair</A> command as a vector of values of length 14.
+The 14 values correspond to the following sub-categories (the variable
+names in italics match those used in the ReaxFF FORTRAN library):
+</P>
+<OL><LI><I>eb</I> = bond energy
+<LI><I>ea</I> = atom energy
+<LI><I>elp</I> = lone-pair energy
+<LI><I>emol</I> = molecule energy (always 0.0)
+<LI><I>ev</I> = valence angle energy
+<LI><I>epen</I> = double-bond valence angle penalty
+<LI><I>ecoa</I> = valence angle conjugation energy
+<LI><I>ehb</I> = hydrogen bond energy
+<LI><I>et</I> = torsion energy
+<LI><I>eco</I> = conjugation energy
+<LI><I>ew</I> = van der Waals energy
+<LI><I>ep</I> = Coulomb energy
+<LI><I>efi</I> = electric field energy (always 0.0)
+<LI><I>eqeq</I> = charge equilibration energy
+</OL>
+<P>To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+</P>
+<PRE>compute reax all pair reax
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+...
+variable eqeq equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+</PRE>
+<P>Only a single pair_coeff command is used with the <I>reax</I> style which
+specifies a ReaxFF potential file with parameters for all needed
+elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N indices = mapping of ReaxFF elements to atom types
+</UL>
+<P>The specification of the filename and the mapping of LAMMPS atom types
+recognized by the ReaxFF is done differently than for other LAMMPS
+potentials, due to the non-portable difficulty of passing character
+strings (e.g. filename, element names) between C++ and Fortran.
+</P>
+<P>The filename has to be "ffield.reax" and it has to exist in the
+directory you are running LAMMPS in. This means you cannot prepend a
+path to the file in the potentials dir. Rather, you should copy that
+file into the directory you are running from. If you wish to use
+another ReaxFF potential file, then name it "ffield.reax" and put it
+in the directory you run from.
+</P>
+<P>In the ReaxFF potential file, near the top, after the general
+parameters, is the atomic parameters section that contains element
+names, each with a couple dozen numeric parameters. If there are M
+elements specified in the <I>ffield</I> file, think of these as numbered 1
+to M. Each of the N indices you specify for the N atom types of LAMMPS
+atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
+be mapped to whatever element you specify as the first index value,
+etc. If a mapping value is specified as NULL, the mapping is not
+performed. This can be used when a ReaxFF potential is used as part
+of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
+types that will be used with other potentials.
+</P>
+<P>IMPORTANT NOTE: Currently the reax pair style cannot be used as part
+of the <I>hybrid</I> pair style. Some additional changes still need to be
+made to enable this.
+</P>
+<P>As an example, say your LAMMPS simulation has 4 atom types and the
+elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
+the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
+H, you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * ffield.reax 1 1 4 2
+</PRE>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>The ReaxFF potential files provided with LAMMPS in the potentials
+directory are parameterized for real <A HREF = "units.html">units</A>. You can use
+the ReaxFF potential with any LAMMPS units, but you would need to
+create your own potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "real" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
+<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are <I>hbcut</I> = 6, <I>hbnewflag</I> = 1, <I>tripflag</I> = 1,
+<I>precision</I> = 1.0e-6.
+</P>
+<HR>
+
+<A NAME = "Chenoweth_2008"></A>
+
+<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
+Journal of Physical Chemistry A, 112, 1040-1053 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_reax_c.html b/doc/doc2/pair_reax_c.html
new file mode 100644
index 000000000..49e0e59e1
--- /dev/null
+++ b/doc/doc2/pair_reax_c.html
@@ -0,0 +1,323 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style reax/c command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style reax/c cfile keyword value
+</PRE>
+<UL><LI>cfile = NULL or name of a control file
+
+<LI>zero or more keyword/value pairs may be appended
+
+<PRE>keyword = <I>checkqeq</I> or <I>lgvdw</I> or <I>safezone</I> or <I>mincap</I>
+ <I>checkqeq</I> value = <I>yes</I> or <I>no</I> = whether or not to require qeq/reax fix
+ <I>lgvdw</I> value = <I>yes</I> or <I>no</I> = whether or not to use a low gradient vdW correction
+ <I>safezone</I> = factor used for array allocation
+ <I>mincap</I> = minimum size for array allocation
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style reax/c NULL
+pair_style reax/c controlfile checkqeq no
+pair_style reax/c NULL lgvdw yes
+pair_style reax/c NULL safezone 1.6 mincap 100
+pair_coeff * * ffield.reax C H O N
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>reax/c</I> computes the ReaxFF potential of van Duin, Goddard and
+co-workers. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. There is more than one version of ReaxFF. The version
+implemented in LAMMPS uses the functional forms documented in the
+supplemental information of the following paper: <A HREF = "#Chenoweth_2008">(Chenoweth et al.,
+2008)</A>. The version integrated into LAMMPS matches
+the most up-to-date version of ReaxFF as of summer 2010. For more
+technical details about the pair reax/c implementation of ReaxFF, see
+the <A HREF = "#Aktulga">(Aktulga)</A> paper.
+</P>
+<P>The <I>reax/c</I> style differs from the <A HREF = "pair_reax.html">pair_style reax</A>
+command in the lo-level implementation details. The <I>reax</I> style is a
+Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
+implemented as stand-alone C code and is now integrated into LAMMPS as
+a package.
+</P>
+<P>LAMMPS provides several different versions of ffield.reax in its
+potentials dir, each called potentials/ffield.reax.label. These are
+documented in potentials/README.reax. The default ffield.reax
+contains parameterizations for the following elements: C, H, O, N, S.
+</P>
+<P>The format of these files is identical to that used originally by van
+Duin. We have tested the accuracy of <I>pair_style reax/c</I> potential
+against the original ReaxFF code for the systems mentioned above. You
+can use other ffield files for specific chemical systems that may be
+available elsewhere (but note that their accuracy may not have been
+tested).
+</P>
+<P>IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force
+field files with LAMMPS. Adri van Duin's group at PSU is the central
+repository for this kind of data as they are continuously deriving and
+updating parameterizations for different classes of materials. You
+can visit their WWW site at
+<A HREF = "http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</A>, register
+as a "new user", and then submit a request to their group describing
+material(s) you are interested in modeling with ReaxFF. They can tell
+you what is currently available or what it would take to create a
+suitable ReaxFF parameterization.
+</P>
+<P>The <I>cfile</I> setting can be specified as NULL, in which case default
+settings are used. A control file can be specified which defines
+values of control variables. Some control variables are
+global parameters for the ReaxFF potential. Others define certain
+performance and output settings.
+Each line in the control file specifies the value for
+a control variable. The format of the control file is described
+below.
+</P>
+<P>IMPORTANT NOTE: The LAMMPS default values for the ReaxFF global parameters
+correspond to those used by
+Adri van Duin's stand-alone serial code. If these are changed by
+setting control variables in the control file, the results from
+LAMMPS and the serial code will not agree.
+</P>
+<P>Two examples using <I>pair_style reax/c</I> are provided in the examples/reax
+sub-directory, along with corresponding examples for
+<A HREF = "pair_reax.html">pair_style reax</A>.
+</P>
+<P>Use of this pair style requires that a charge be defined for every
+atom. See the <A HREF = "atom_style.html">atom_style</A> and
+<A HREF = "read_data.html">read_data</A> commands for details on how to specify
+charges.
+</P>
+<P>The ReaxFF parameter files provided were created using a charge
+equilibration (QEq) model for handling the electrostatic interactions.
+Therefore, by default, LAMMPS requires that the <A HREF = "fix_qeq_reax.html">fix
+qeq/reax</A> command be used with <I>pair_style reax/c</I>
+when simulating a ReaxFF model, to equilibrate charge each timestep.
+Using the keyword <I>checkqeq</I> with the value <I>no</I>
+turns off the check for <I>fix qeq/reax</I>,
+allowing a simulation to be run without charge equilibration.
+In this case, the static charges you
+assign to each atom will be used for computing the electrostatic
+interactions in the system.
+See the <A HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for details.
+</P>
+<P>Using the optional keyword <I>lgvdw</I> with the value <I>yes</I> turns on
+the low-gradient correction of the ReaxFF/C for long-range
+London Dispersion, as described in the <A HREF = "#Liu_2011">(Liu)</A> paper. Force field
+file <I>ffield.reax.lg</I> is designed for this correction, and is trained
+for several energetic materials (see "Liu"). When using lg-correction,
+recommended value for parameter <I>thb</I> is 0.01, which can be set in the
+control file. Note: Force field files are different for the original
+or lg corrected pair styles, using wrong ffield file generates an error message.
+</P>
+<P>Optional keywords <I>safezone</I> and <I>mincap</I> are used for allocating
+reax/c arrays. Increase these values can avoid memory problems, such
+as segmentation faults and bondchk failed errors, that could occur under
+certain conditions.
+</P>
+<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
+energy contributions, with the exception of the Coulombic and charge
+equilibration contributions which are stored in the thermo variable
+<I>ecoul</I>. The output of these quantities is controlled by the
+<A HREF = "thermo.html">thermo</A> command.
+</P>
+<P>This pair style tallies a breakdown of the total ReaxFF potential
+energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
+pair</A> command as a vector of values of length 14.
+The 14 values correspond to the following sub-categories (the variable
+names in italics match those used in the original FORTRAN ReaxFF code):
+</P>
+<OL><LI><I>eb</I> = bond energy
+<LI><I>ea</I> = atom energy
+<LI><I>elp</I> = lone-pair energy
+<LI><I>emol</I> = molecule energy (always 0.0)
+<LI><I>ev</I> = valence angle energy
+<LI><I>epen</I> = double-bond valence angle penalty
+<LI><I>ecoa</I> = valence angle conjugation energy
+<LI><I>ehb</I> = hydrogen bond energy
+<LI><I>et</I> = torsion energy
+<LI><I>eco</I> = conjugation energy
+<LI><I>ew</I> = van der Waals energy
+<LI><I>ep</I> = Coulomb energy
+<LI><I>efi</I> = electric field energy (always 0.0)
+<LI><I>eqeq</I> = charge equilibration energy
+</OL>
+<P>To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+</P>
+<PRE>compute reax all pair reax/c
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+...
+variable eqeq equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+</PRE>
+<P>Only a single pair_coeff command is used with the <I>reax/c</I> style which
+specifies a ReaxFF potential file with parameters for all needed
+elements. These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N indices = ReaxFF elements
+</UL>
+<P>The filename is the ReaxFF potential file. Unlike for the <I>reax</I>
+pair style, any filename can be used.
+</P>
+<P>In the ReaxFF potential file, near the top, after the general
+parameters, is the atomic parameters section that contains element
+names, each with a couple dozen numeric parameters. If there are M
+elements specified in the <I>ffield</I> file, think of these as numbered 1
+to M. Each of the N indices you specify for the N atom types of LAMMPS
+atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
+be mapped to whatever element you specify as the first index value,
+etc. If a mapping value is specified as NULL, the mapping is not
+performed. This can be used when the <I>reax/c</I> style is used as part
+of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
+types that will be used with other potentials.
+</P>
+<P>As an example, say your LAMMPS simulation has 4 atom types and the
+elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
+the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
+H, you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * ffield.reax C C N H
+</PRE>
+<HR>
+
+<P>The format of a line in the control file is as follows:
+</P>
+<PRE>variable_name value
+</PRE>
+<P>and it may be followed by an "!" character and a trailing comment.
+</P>
+<P>If the value of a control variable is not specified, then default
+values are used. What follows is the list of variables along with a
+brief description of their use and default values.
+</P>
+<P>simulation_name: Output files produced by <I>pair_style reax/c</I> carry
+this name + extensions specific to their contents. Partial energies
+are reported with a ".pot" extension, while the trajectory file has
+".trj" extension.
+</P>
+<P>tabulate_long_range: To improve performance, long range interactions
+can optionally be tabulated (0 means no tabulation). Value of this
+variable denotes the size of the long range interaction table. The
+range from 0 to long range cutoff (defined in the <I>ffield</I> file) is
+divided into <I>tabulate_long_range</I> points. Then at the start of
+simulation, we fill in the entries of the long range interaction table
+by computing the energies and forces resulting from van der Waals and
+Coulomb interactions between every possible atom type pairs present in
+the input system. During the simulation we consult to the long range
+interaction table to estimate the energy and forces between a pair of
+atoms. Linear interpolation is used for estimation. (default value =
+0)
+</P>
+<P>energy_update_freq: Denotes the frequency (in number of steps) of
+writes into the partial energies file. (default value = 0)
+</P>
+<P>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
+regarding the bonded interactions. (default value = 5.0)
+</P>
+<P>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
+bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen
+ bonds)
+</P>
+<P>bond_graph_cutoff: is the threshold used in determining what is a
+physical bond, what is not. Bonds and angles reported in the
+trajectory file rely on this cutoff. (default value = 0.3)
+</P>
+<P>thb_cutoff: cutoff value for the strength of bonds to be considered in
+three body interactions. (default value = 0.001)
+</P>
+<P>thb_cutoff_sq: cutoff value for the strength of bond order products
+to be considered in three body interactions. (default value = 0.00001)
+</P>
+<P>write_freq: Frequency of writes into the trajectory file. (default
+value = 0)
+</P>
+<P>traj_title: Title of the trajectory - not the name of the trajectory
+file.
+</P>
+<P>atom_info: 1 means print only atomic positions + charge (default = 0)
+</P>
+<P>atom_forces: 1 adds net forces to atom lines in the trajectory file
+(default = 0)
+</P>
+<P>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)
+</P>
+<P>bond_info: 1 prints bonds in the trajectory file (default = 0)
+</P>
+<P>angle_info: 1 prints angles in the trajectory file (default = 0)
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-REAXC package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>The ReaxFF potential files provided with LAMMPS in the potentials
+directory are parameterized for real <A HREF = "units.html">units</A>. You can use
+the ReaxFF potential with any LAMMPS units, but you would need to
+create your own potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "real" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_qeq_reax.html">fix qeq/reax</A>, <A HREF = "fix_reax_bonds.html">fix
+reax/c/bonds</A>, <A HREF = "fix_reaxc_species.html">fix
+reax/c/species</A>, <A HREF = "pair_reax.html">pair_style
+reax</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
+mincap = 50.
+</P>
+<HR>
+
+<A NAME = "Chenoweth_2008"></A>
+
+<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
+Journal of Physical Chemistry A, 112, 1040-1053 (2008).
+</P>
+<A NAME = "Aktulga"></A>
+
+<P>(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+245-259 (2012).
+</P>
+<A NAME = "Liu_2011"></A>
+
+<P><B>(Liu)</B> L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
+of Physical Chemistry A, 115, 11016-11022 (2011).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_resquared.html b/doc/doc2/pair_resquared.html
new file mode 100644
index 000000000..e391abdbc
--- /dev/null
+++ b/doc/doc2/pair_resquared.html
@@ -0,0 +1,244 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style resquared command
+</H3>
+<H3>pair_style resquared/gpu command
+</H3>
+<H3>pair_style resquared/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style resquared cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style resquared 10.0
+pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>resquared</I> computes the RE-squared anisotropic interaction
+<A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
+ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
+interactions, the potential considers the ellipsoid as being comprised
+of small spheres of size sigma. LJ particles are a single sphere of
+size sigma. The distinction is made to allow the pair style to make
+efficient calculations of ellipsoid/solvent interactions.
+</P>
+<P>Details for the equations used are given in the references below and
+in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
+</P>
+<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
+<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
+order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
+ellipsoid</A> should be used since it defines the
+rotational state and the size and shape of each ellipsoidal particle.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>A12 = Energy Prefactor/Hamaker constant (energy units)
+<LI>sigma = atomic interaction diameter (distance units)
+<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
+<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
+<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
+<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
+<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
+<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
+<LI>cutoff (distance units)
+</UL>
+<P>The parameters used depend on the type of the interacting particles,
+i.e. ellipsoids or LJ spheres. The type of a particle is determined
+by the diameters specified for its 3 shape paramters. If all 3 shape
+parameters = 0.0, then the particle is treated as an LJ sphere. The
+epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
+the 3 shape paraemters are > 0.0, then the particle is treated as an
+ellipsoid (even if the 3 parameters are equal to each other).
+</P>
+<P>A12 specifies the energy prefactor which depends on the types of the
+two interacting particles.
+</P>
+<P>For ellipsoid/ellipsoid interactions, the interaction is computed by
+the formulas in the supplementary docuement referenced above. A12 is
+the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
+units:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_resquared.jpg">
+</CENTER>
+<P>where rho gives the number density of the spherical particles
+composing the ellipsoids and epsilon_LJ determines the interaction
+strength of the spherical particles.
+</P>
+<P>For ellipsoid/LJ sphere interactions, the interaction is also computed
+by the formulas in the supplementary docuement referenced above. A12
+has a modifed form (see <A HREF = "PDF/pair_resquared_extra.pdf">here</A> for
+details):
+</P>
+<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
+</CENTER>
+<P>For ellipsoid/LJ sphere interactions, a correction to the distance-
+of-closest approach equation has been implemented to reduce the error
+from two particles of disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary
+document</A>.
+</P>
+<P>For LJ sphere/LJ sphere interactions, the interaction is computed
+using the standard Lennard-Jones formula, which is much cheaper to
+compute than the ellipsoidal formulas. A12 is used as epsilon in the
+standard LJ formula:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
+</CENTER>
+<P>and the specified <I>sigma</I> is used as the sigma in the standard LJ
+formula.
+</P>
+<P>When one of both of the interacting particles are ellipsoids, then
+<I>sigma</I> specifies the diameter of the continuous distribution of
+constituent particles within each ellipsoid used to model the
+RE-squared potential. Note that this is a different meaning for
+<I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_style gayberne</A> potential
+uses.
+</P>
+<P>The epsilon_i and epsilon_j coefficients are defined for atom types,
+not for pairs of atom types. Thus, in a series of pair_coeff
+commands, they only need to be specified once for each atom type.
+</P>
+<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
+non-zero, the three values are assigned to atom type I. If all the
+epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
+epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
+to atom type J. If all three epsilon_i values are zero, they are
+ignored. Thus the typical way to define the epsilon_i and epsilon_j
+coefficients is to list their values in "pair_coeff I J" commands when
+I = J, but set them to 0.0 when I != J. If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair_coeff commands.
+</P>
+<P>Note that if this potential is being used as a sub-style of
+<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
+setting made for RE-squared for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type in a "pair_coeff I J" command.
+</P>
+<P>For large uniform molecules it has been shown that the epsilon_*_*
+energy parameters are approximately representable in terms of local
+contact curvatures <A HREF = "#Everaers">(Everaers)</A>:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_resquared4.jpg">
+</CENTER>
+<P>where a, b, and c give the particle diameters.
+</P>
+<P>The last coefficient is optional. If not specified, the global cutoff
+specified in the pair_style command is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance can be mixed, but only for sphere pairs. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details. Other type pairs cannot be mixed, due to the different
+meanings of the energy prefactors used to calculate the interactions
+and the implicit dependence of the ellipsoid-sphere interaction on the
+equation for the Hamaker constant presented here. Mixing of sigma and
+epsilon followed by calculation of the energy prefactors using the
+equations above is recommended.
+</P>
+<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions. There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
+command</A>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the ASPHERE package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires that atoms be ellipsoids as defined by the
+<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
+</P>
+<P>Particles acted on by the potential can be finite-size aspherical or
+spherical particles, or point particles. Spherical particles have all
+3 of their shape parameters equal to each other. Point particles have
+all 3 of their shape parameters equal to 0.0.
+</P>
+<P>The distance-of-closest-approach approximation used by LAMMPS becomes
+less accurate when high-aspect ratio ellipsoids are used.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
+<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_gayberne.html">pair_style
+gayberne</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Everaers"></A>
+
+<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
+</P>
+<A NAME = "Babadi"></A>
+
+<P><B>(Berardi)</B> Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sdk.html b/doc/doc2/pair_sdk.html
new file mode 100644
index 000000000..edfb1d220
--- /dev/null
+++ b/doc/doc2/pair_sdk.html
@@ -0,0 +1,169 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style lj/sdk command
+</H3>
+<H3>pair_style lj/sdk/gpu command
+</H3>
+<H3>pair_style lj/sdk/kk command
+</H3>
+<H3>pair_style lj/sdk/omp command
+</H3>
+<H3>pair_style lj/sdk/coul/long command
+</H3>
+<H3>pair_style lj/sdk/coul/long/gpu command
+</H3>
+<H3>pair_style lj/sdk/coul/long/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = <I>lj/sdk</I> or <I>lj/sdk/coul/long</I>
+<LI>args = list of arguments for a particular style
+</UL>
+<PRE> <I>lj/sdk</I> args = cutoff
+ cutoff = global cutoff for Lennard Jones interactions (distance units)
+ <I>lj/sdk/coul/long</I> args = cutoff (cutoff2)
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/sdk 2.5
+pair_coeff 1 1 lj12_6 1 1.1 2.8
+</PRE>
+<PRE>pair_style lj/sdk/coul/long 10.0
+pair_style lj/sdk/coul/long 10.0 12.0
+pair_coeff 1 1 lj9_6 100.0 3.5 12.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lj/sdk</I> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
+given by
+</P>
+<CENTER><IMG SRC = "Eqs/pair_cmm.jpg">
+</CENTER>
+<P>as required for the SDK Coarse-grained MD parametrization discussed in
+<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
+</P>
+<P>Style <I>lj/sdk/coul/long</I> computes the adds Coulombic interactions
+with an additional damping factor applied so it can be used in
+conjunction with the <A HREF = "kspace_style.html">kspace_style</A> command and
+its <I>ewald</I> or <I>pppm</I> or <I>pppm/cg</I> option. The Coulombic cutoff
+specified for this style means that pairwise interactions within
+this distance are computed directly; interactions outside that
+distance are computed in reciprocal space.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>cg_type (lj9_6, lj12_4, or lj12_6)
+<LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff1 (distance units)
+</UL>
+<P>Note that sigma is defined in the LJ formula as the zero-crossing
+distance for the potential, not as the energy minimum. The prefactors
+are chosen so that the potential minimum is at -epsilon.
+</P>
+<P>The latter 2 coefficients are optional. If not specified, the global
+LJ and Coulombic cutoffs specified in the pair_style command are used.
+If only one cutoff is specified, it is used as the cutoff for both LJ
+and Coulombic interactions for this type pair. If both coefficients
+are specified, they are used as the LJ and Coulombic cutoffs for this
+type pair.
+</P>
+<P>For <I>lj/sdk/coul/long</I> only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I> or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP, and OPT packages respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, and rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/sdk pair styles <I>cannot</I> be mixed,
+since different pairs may have different exponents. So all parameters
+for all pairs have to be specified explicitly through the "pair_coeff"
+command. Defining then in a data file is also not supported, due to
+limitations of that file format.
+</P>
+<P>All of the lj/sdk pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+</P>
+<P>The <I>lj/sdk/coul/long</I> pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
+the short-range portion of the long-range Coulombic interaction.
+</P>
+<P>All of the lj/sdk pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<P>The lj/sdk and lj/cut/coul/long pair styles do not support
+the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
+respa</A> command.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
+The <I>lj/sdk/coul/long</I> style also requires the KSPACE package to be
+built (which is enabled by default). They are only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "angle_sdk.html">angle_style sdk</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Shinoda"></A>
+
+<P><B>(Shinoda)</B> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
+</P>
+<A NAME = "DeVane"></A>
+
+<P><B>(DeVane)</B> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_snap.html b/doc/doc2/pair_snap.html
new file mode 100644
index 000000000..c5fb036e4
--- /dev/null
+++ b/doc/doc2/pair_snap.html
@@ -0,0 +1,201 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style snap command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style snap
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style snap
+pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>snap</I> computes interactions
+using the spectral neighbor analysis potential (SNAP)
+<A HREF = "#Thompson2014">(Thompson)</A>. Like the GAP framework of Bartok et al.
+<A HREF = "#Bartok2010">(Bartok2010)</A>, <A HREF = "#Bartok2013">(Bartok2013)</A>
+it uses bispectrum components
+to characterize the local neighborhood of each atom
+in a very general way. The mathematical definition of the
+bispectrum calculation used by SNAP is identical
+to that used of <A HREF = "compute_sna_atom.html">compute sna/atom</A>.
+In SNAP, the total energy is decomposed into a sum over
+atom energies. The energy of atom <I>i</I> is
+expressed as a weighted sum over bispectrum components.
+</P>
+<CENTER><IMG SRC = "Eqs/pair_snap.jpg">
+</CENTER>
+<P>where <I>B_k^i</I> is the <I>k</I>-th bispectrum component of atom <I>i</I>,
+and <I>beta_k^alpha_i</I> is the corresponding linear coefficient
+that depends on <I>alpha_i</I>, the SNAP element of atom <I>i</I>. The
+number of bispectrum components used and their definitions
+depend on the values of <I>twojmax</I> and <I>diagonalstyle</I>
+defined in the SNAP parameter file described below.
+The bispectrum calculation is described in more detail
+in <A HREF = "compute_sna_atom.html">compute sna/atom</A>.
+</P>
+<P>Note that unlike for other potentials, cutoffs for SNAP potentials are
+not set in the pair_style or pair_coeff command; they are specified in
+the SNAP potential files themselves.
+</P>
+<P>Only a single pair_coeff command is used with the <I>snap</I> style which
+specifies two SNAP files and the list SNAP element(s) to be
+extracted.
+The SNAP elements are mapped to LAMMPS atom types by specifying
+N additional arguments after the 2nd filename in the pair_coeff
+command, where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>SNAP element file
+<LI>Elem1, Elem2, ...
+<LI>SNAP parameter file
+<LI>N element names = mapping of SNAP elements to atom types
+</UL>
+<P>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
+types, with the first two being indium and the 3rd and 4th being
+phophorous, the pair_coeff command would look like this:
+</P>
+<PRE>pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The two filenames are for the element and parameter files, respectively.
+The 'In' and 'P' arguments (between the file names) are the two elements
+which will be extracted from the element file. The
+two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
+SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
+3 and 4 to the SNAP 'P' element.
+</P>
+<P>If a SNAP mapping value is
+specified as NULL, the mapping is not performed.
+This can be used when a <I>snap</I> potential is used as part of the
+<I>hybrid</I> pair style. The NULL values are placeholders for atom types
+that will be used with other potentials.
+</P>
+<P>The name of the SNAP element file usually ends in the
+".snapcoeff" extension. It may contain coefficients
+for many SNAP elements.
+Only those elements listed in the pair_coeff command are extracted.
+The name of the SNAP parameter file usually ends in the ".snapparam"
+extension. It contains a small number
+of parameters that define the overall form of the SNAP potential.
+See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for these files.
+</P>
+<P>Quite commonly,
+SNAP potentials are combined with one or more other LAMMPS pair styles
+using the <I>hybrid/overlay</I> pair style. As an example, the SNAP
+tantalum potential provided in the LAMMPS potentials directory
+combines the <I>snap</I> and <I>zbl</I> pair styles. It is invoked
+by the following commands:
+</P>
+<PRE> variable zblcutinner equal 4
+ variable zblcutouter equal 4.8
+ variable zblz equal 73
+ pair_style hybrid/overlay &
+ zbl ${zblcutinner} ${zblcutouter} snap
+ pair_coeff * * zbl 0.0
+ pair_coeff 1 1 zbl ${zblz}
+ pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+ ../potentials/Ta06A.snapparam Ta
+</PRE>
+<P>It is convenient to keep these commands in a separate file that can
+be inserted in any LAMMPS input script using the <A HREF = "include.html">include</A>
+command.
+</P>
+<P>The top of the SNAP element file can contain any number of blank and comment
+lines (start with #), but follows a strict
+format after that. The first non-blank non-comment
+line must contain two integers:
+</P>
+<UL><LI>nelem = Number of elements
+<LI>ncoeff = Number of coefficients
+</UL>
+<P>This is followed by one block for each of the <I>nelem</I> elements.
+The first line of each block contains three entries:
+</P>
+<UL><LI>Element symbol (text string)
+<LI>R = Element radius (distance units)
+<LI>w = Element weight (dimensionless)
+</UL>
+<P>This line is followed by <I>ncoeff</I> coefficients, one per line.
+</P>
+<P>The SNAP parameter file can contain blank and comment lines (start
+with #) anywhere. Each non-blank non-comment line must contain one
+keyword/value pair. The required keywords are <I>rcutfac</I> and
+<I>twojmax</I>. Optional keywords are <I>rfac0</I>, <I>rmin0</I>, <I>diagonalstyle</I>,
+and <I>switchflag</I>.
+</P>
+<P>The default values for these keywords are
+</P>
+<UL><LI><I>rfac0</I> = 0.99363
+<LI><I>rmin0</I> = 0.0
+<LI><I>diagonalstyle</I> = 3
+<LI><I>switchflag</I> = 0
+</UL>
+<P>Detailed definitions of these keywords are given on the <A HREF = "compute_sna_atom.html">compute
+sna/atom</A> doc page.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above. You never need to
+specify a pair_coeff command with I != J arguments for this style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the SNAP package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_sna_atom.html">compute sna/atom</A>,
+<A HREF = "compute_sna_atom.html">compute snad/atom</A>,
+<A HREF = "compute_sna_atom.html">compute snav/atom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Thompson2014"></A>
+
+<P><B>(Thompson)</B> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
+available at <A HREF = "http://arxiv.org/abs/1409.3880">arXiv:1409.3880</A>
+</P>
+<A NAME = "Bartok2010"></A>
+
+<P><B>(Bartok2010)</B> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
+</P>
+<A NAME = "Bartok2013"></A>
+
+<P><B>(Bartok2013)</B> Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_soft.html b/doc/doc2/pair_soft.html
new file mode 100644
index 000000000..e99ddacd6
--- /dev/null
+++ b/doc/doc2/pair_soft.html
@@ -0,0 +1,143 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style soft command
+</H3>
+<H3>pair_style soft/gpu command
+</H3>
+<H3>pair_style soft/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style soft cutoff
+</PRE>
+<UL><LI>cutoff = global cutoff for soft interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style soft 2.5
+pair_coeff * * 10.0
+pair_coeff 1 1 10.0 3.0
+</PRE>
+<PRE>pair_style soft 2.5
+pair_coeff * * 0.0
+variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>soft</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_soft.jpg">
+</CENTER>
+<P>It is useful for pushing apart overlapping atoms, since it does not
+blow up as r goes to 0. A is a pre-factor that can be made to vary in
+time from the start to the end of the run (see discussion below),
+e.g. to start with a very soft potential and slowly harden the
+interactions over time. Rc is the cutoff. See the <A HREF = "fix_nve_limit.html">fix
+nve/limit</A> command for another way to push apart
+overlapping atoms.
+</P>
+<P>The following coefficients must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
+or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>A (energy units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global soft
+cutoff is used.
+</P>
+<P>IMPORTANT NOTE: The syntax for <A HREF = "pair_coeff.html">pair_coeff</A> with a
+single A coeff is different in the current version of LAMMPS than in
+older versions which took two values, Astart and Astop, to ramp
+between them. This functionality is now available in a more general
+form through the <A HREF = "fix_adapt.html">fix adapt</A> command, as explained
+below. Note that if you use an old input script and specify Astart
+and Astop without a cutoff, then LAMMPS will interpret that as A and a
+cutoff, which is probabably not what you want.
+</P>
+<P>The <A HREF = "fix_adapt.html">fix adapt</A> command can be used to vary A for one
+or more pair types over the course of a simulation, in which case
+pair_coeff settings for A must still be specified, but will be
+overridden. For example these commands will vary the prefactor A for
+all pairwise interactions from 0.0 at the beginning to 30.0 at the end
+of a run:
+</P>
+<PRE>variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</PRE>
+<P>Note that a formula defined by an <A HREF = "variable.html">equal-style variable</A>
+can use the current timestep, elapsed time in the current run, elapsed
+time since the beginning of a series of runs, as well as access other
+variables.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed. A is always mixed via a
+<I>geometric</I> rule. The cutoff is mixed according to the pair_modify
+mix value. The default mix value is <I>geometric</I>. See the
+"pair_modify" command for details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option, since the pair interaction goes to 0.0 at the cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for this pair style.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_limit.html">fix nve/limit</A>, <A HREF = "fix_adapt.html">fix
+adapt</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_heatconduction.html b/doc/doc2/pair_sph_heatconduction.html
new file mode 100644
index 000000000..570a324b8
--- /dev/null
+++ b/doc/doc2/pair_sph_heatconduction.html
@@ -0,0 +1,68 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/heatconduction command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/heatconduction
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/heatconduction
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/heatconduction style computes heat transport between SPH particles.
+The transport model is the diffusion euqation for the internal energy.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>D diffusion coefficient (length^2/time units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_idealgas.html b/doc/doc2/pair_sph_idealgas.html
new file mode 100644
index 000000000..4d45b2959
--- /dev/null
+++ b/doc/doc2/pair_sph_idealgas.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/idealgas command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/idealgas
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/idealgas
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/idealgas style computes pressure forces between particles
+according to the ideal gas equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_ideal.jpg">
+</CENTER>
+<P>where gamma = 1.4 is the heat capacity ratio, rho is the local
+density, and e is the internal energy per unit mass. This pair style
+also computes Monaghan's artificial viscosity to prevent particles
+from interpentrating <A HREF = "#Monoghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_lj.html b/doc/doc2/pair_sph_lj.html
new file mode 100644
index 000000000..60cbdc67c
--- /dev/null
+++ b/doc/doc2/pair_sph_lj.html
@@ -0,0 +1,86 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/lj command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/lj
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/lj
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/lj style computes pressure forces between particles according
+to the Lennard-Jones equation of state, which is computed according to
+Ree's 1980 polynomial fit <A HREF = "#Ree">(Ree)</A>. The Lennard-Jones parameters
+epsilon and sigma are set to unity. This pair style also computes
+Monaghan's artificial viscosity to prevent particles from
+interpentrating <A HREF = "#Monoghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>As noted above, the Lennard-Jones parameters epsilon and sigma are set
+to unity.
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ree"></A>
+
+<P><B>(Ree)</B> Ree, Journal of Chemical Physics, 73, 5401 (1980).
+</P>
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_rhosum.html b/doc/doc2/pair_sph_rhosum.html
new file mode 100644
index 000000000..7e3f38a91
--- /dev/null
+++ b/doc/doc2/pair_sph_rhosum.html
@@ -0,0 +1,69 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/rhosum command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/rhosum Nstep
+</PRE>
+<UL><LI>Nstep = timestep interval
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/rhosum 10
+pair_coeff * * 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/rhosum style computes the local particle mass density rho for
+SPH particles by kernel function interpolation, every Nstep timesteps.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>h (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/taitwater
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_taitwater.html b/doc/doc2/pair_sph_taitwater.html
new file mode 100644
index 000000000..7c350f2f3
--- /dev/null
+++ b/doc/doc2/pair_sph_taitwater.html
@@ -0,0 +1,85 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/taitwater command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/taitwater
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/taitwater
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/taitwater style computes pressure forces between SPH particles
+according to Tait's equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_tait.jpg">
+</CENTER>
+<P>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+</P>
+<P>This pair style also computes Monaghan's artificial viscosity to
+prevent particles from interpentrating <A HREF = "#Monaghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>rho0 reference density (mass/volume units)
+<LI>c0 reference soundspeed (distance/time units)
+<LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_sph_taitwater_morris.html b/doc/doc2/pair_sph_taitwater_morris.html
new file mode 100644
index 000000000..4a2568ff7
--- /dev/null
+++ b/doc/doc2/pair_sph_taitwater_morris.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/taitwater/morris command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/taitwater/morris
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/taitwater/morris
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/taitwater/morris style computes pressure forces between SPH
+particles according to Tait's equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_tait.jpg">
+</CENTER>
+<P>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+</P>
+<P>This pair style also computes laminar viscosity <A HREF = "#Morris">(Morris)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>rho0 reference density (mass/volume units)
+<LI>c0 reference soundspeed (distance/time units)
+<LI>nu dynamic viscosity (mass*distance/time units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Morris"></A>
+
+<P><B>(Morris)</B> Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_srp.html b/doc/doc2/pair_srp.html
new file mode 100644
index 000000000..df195432b
--- /dev/null
+++ b/doc/doc2/pair_srp.html
@@ -0,0 +1,172 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style srp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<P>pair_style srp cutoff bond_type dist keyword value ...
+</P>
+<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
+
+<LI>bond_type = bond type to apply SRP interactions
+
+<LI>distance = <I>min</I> or <I>mid</I>
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>exclude</I>
+
+<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
+pair_coeff 1 1 dpd 60.0 4.5 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+</PRE>
+<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
+pair_coeff 1 1 dpd 60.0 50 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 40.0
+</PRE>
+<PRE>pair_style hybrid srp 0.8 2 mid
+pair_coeff 1 1 none
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>srp</I> computes a soft segmental repulsive potential (SRP) that
+acts between pairs of bonds. This potential is useful for preventing
+bonds from passing through one another when a soft non-bonded
+potential acts between beads in, for example, DPD polymer chains. An
+example input script that uses this command is provided in
+examples/USER/srp.
+</P>
+<P>Bonds of type <I>btype</I> interact with one another through a
+bond-pairwise potential, such that the force on bond <I>i</I> due to bond
+<I>j</I> is as follows
+</P>
+<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
+</CENTER>
+<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
+bonds. The bondtype can also be specified as an asterisk (*) and then
+this interaction applied to all bonds.
+The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
+distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
+the minimum distance between bonds. The force acting on a bond is
+mapped onto the two bond atoms according to the lever rule,
+</P>
+<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
+</CENTER>
+<P>where <I>L</I> is the normalized distance from the atom to the point of
+closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
+0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
+</P>
+<P>The following coefficients must be defined via the
+<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
+the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
+or <A HREF = "read_restart.html">read_restart</A> commands:
+</P>
+<UL><LI><I>C</I> (force units)
+<LI><I>rc</I> (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+is used.
+</P>
+<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
+a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
+atom type in the system. These "bond particles" are inserted at the
+beginning of the run, and serve as placeholders that define the
+position of the bonds. This allows neighbor lists to be constructed
+and pairwise interactions to be computed in almost the same way as is
+done for point particles. Because bonds interact only with other
+bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
+interactions between atom type <I>bptype</I> and all other types of atoms.
+An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
+not used. Further, only bond particles should be given an atom type
+of <I>bptype</I>; a check is done at the beginning of the run to ensure
+there are no regular atoms of <I>bptype</I>.
+</P>
+<P>The optional <I>exclude</I> keyword determines if forces are computed
+between first neighbor (directly connected) bonds. For a setting of
+<I>no</I>, first neighbor forces are computed; for <I>yes</I> they are not computed. A setting of <I>no</I>
+cannot be used with the <I>min</I> option for distance calculation because the the minimum distance between
+directly connected bonds is zero.
+</P>
+<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
+by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
+no</A> had been issued.
+</P>
+<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
+at the cutoff distance <I>rc</I>.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair styles does not support mixing.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option for the energy of the pair interaction. Note that as
+discussed above, the energy term is already shifted to be 0.0 at the
+cutoff distance <I>rc</I>.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
+this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
+restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
+hybrid</A>, thus the pair_coeff commands need to be
+specified in the input script when reading a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the Making LAMMPS section
+for more info.
+</P>
+<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
+for non-bonded interactions.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "pair_dpd.html">pair dpd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default keyword value is exclude = yes.
+</P>
+<HR>
+
+<A NAME = "Sirk"></A>
+
+<P><B>(Sirk)</B> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
+Chem Phys, 136 (13) 134903, 2012.
+</P>
+</HTML>
diff --git a/doc/doc2/pair_style.html b/doc/doc2/pair_style.html
new file mode 100644
index 000000000..6cfd97335
--- /dev/null
+++ b/doc/doc2/pair_style.html
@@ -0,0 +1,234 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style args
+</PRE>
+<UL><LI>style = one of the styles from the list below
+<LI>args = arguments used by a particular style
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lj/cut 2.5
+pair_style eam/alloy
+pair_style hybrid lj/charmm/coul/long 10.0 eam
+pair_style table linear 1000
+pair_style none
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the formula(s) LAMMPS uses to compute pairwise interactions. In
+LAMMPS, pair potentials are defined between pairs of atoms that are
+within a cutoff distance and the set of active interactions typically
+changes over time. See the <A HREF = "bond_style.html">bond_style</A> command to
+define potentials between pairs of bonded atoms, which typically
+remain in place for the duration of a simulation.
+</P>
+<P>In LAMMPS, pairwise force fields encompass a variety of interactions,
+some of which include many-body effects, e.g. EAM, Stillinger-Weber,
+Tersoff, REBO potentials. They are still classified as "pairwise"
+potentials because the set of interacting atoms changes with time
+(unlike molecular bonds) and thus a neighbor list is used to find
+nearby interacting atoms.
+</P>
+<P>Hybrid models where specified pairs of atom types interact via
+different pair potentials can be setup using the <I>hybrid</I> pair style.
+</P>
+<P>The coefficients associated with a pair style are typically set for
+each pair of atom types, and are specified by the
+<A HREF = "pair_coeff.html">pair_coeff</A> command or read from a file by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> command sets options for mixing of
+type I-J interaction coefficients and adding energy offsets or tail
+corrections to Lennard-Jones potentials. Details on these options as
+they pertain to individual potentials are described on the doc page
+for the potential. Likewise, info on whether the potential
+information is stored in a <A HREF = "write_restart.html">restart file</A> is listed
+on the potential doc page.
+</P>
+<P>In the formulas listed for each pair style, <I>E</I> is the energy of a
+pairwise interaction between two atoms separated by a distance <I>r</I>.
+The force between the atoms is the negative derivative of this
+expression.
+</P>
+<P>If the pair_style command has a cutoff argument, it sets global
+cutoffs for all pairs of atom types. The distance(s) can be smaller
+or larger than the dimensions of the simulation box.
+</P>
+<P>Typically, the global cutoff value can be overridden for a specific
+pair of atom types by the <A HREF = "pair_coeff.html">pair_coeff</A> command. The
+pair style settings (including global cutoffs) can be changed by a
+subsequent pair_style command using the same style. This will reset
+the cutoffs for all atom type pairs, including those previously set
+explicitly by a <A HREF = "pair_coeff.html">pair_coeff</A> command. The exceptions
+to this are that pair_style <I>table</I> and <I>hybrid</I> settings cannot be
+reset. A new pair_style command for these styles will wipe out all
+previously specified pair_coeff values.
+</P>
+<HR>
+
+<P>Here is an alphabetic list of pair styles defined in LAMMPS. They are
+also given in more compact form in the pair section of <A HREF = "Section_commands.html#cmd_5">this
+page</A>.
+</P>
+<P>Click on the style to display the formula it computes, arguments
+specified in the pair_style command, and coefficients specified by the
+associated <A HREF = "pair_coeff.html">pair_coeff</A> command.
+</P>
+<P>There are also additional pair styles (not listed here) submitted by
+users which are included in the LAMMPS distribution. The list of
+these with links to the individual styles are given in the pair
+section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<P>There are also additional accelerated pair styles (not listed here)
+included in the LAMMPS distribution for faster performance on CPUs and
+GPUs. The list of these with links to the individual styles are given
+in the pair section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
+</P>
+<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
+<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - multiple styles of pairwise interactions
+<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
+</UL>
+<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
+<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
+<LI><A HREF = "pair_beck.html">pair_style beck</A> - Beck potential
+<LI><A HREF = "pair_body.html">pair_style body</A> - interactions between body particles
+<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
+<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
+<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
+<LI><A HREF = "pair_born.html">pair_style born/coul/long/cs</A> - Born-Mayer-Huggins with long-range Coulombics and core/shell
+<LI><A HREF = "pair_born.html">pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
+<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
+<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
+<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
+<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
+<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
+<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulombics
+<LI><A HREF = "pair_buck.html">pair_style buck/coul/long/cs</A> - Buckingham with long-range Coulombics and core/shell
+<LI><A HREF = "pair_buck.html">pair_style buck/coul/msm</A> - Buckingham long-range MSM Coulombics
+<LI><A HREF = "pair_buck_long.html">pair_style buck/long/coul/long</A> - long-range Buckingham with long-range Coulombics
+<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
+<LI><A HREF = "pair_comb.html">pair_style comb</A> - charge-optimized many-body (COMB) potential
+<LI><A HREF = "pair_comb.html">pair_style comb3</A> - charge-optimized many-body (COMB3) potential
+<LI><A HREF = "pair_coul.html">pair_style coul/cut</A> - cutoff Coulombic potential
+<LI><A HREF = "pair_coul.html">pair_style coul/debye</A> - cutoff Coulombic potential with Debye screening
+<LI><A HREF = "pair_coul.html">pair_style coul/dsf</A> - Coulombics via damped shifted forces
+<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
+<LI><A HREF = "pair_coul.html">pair_style coul/long/cs</A> - long-range Coulombic potential and core/shell
+<LI><A HREF = "pair_coul.html">pair_style coul/msm</A> - long-range MSM Coulombics
+<LI><A HREF = "pair_coul_streitz.html">pair_style coul/msm</A> - Coulombics via Streitz/Mintmire Slater orbitals
+<LI><A HREF = "pair_coul.html">pair_style coul/wolf</A> - Coulombics via Wolf potential
+<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
+<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A> - DPD thermostatting
+<LI><A HREF = "pair_dsmc.html">pair_style dsmc</A> - Direct Simulation Monte Carlo (DSMC)
+<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
+<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
+<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
+<LI><A HREF = "pair_eim.html">pair_style eim</A> - embedded ion method (EIM)
+<LI><A HREF = "pair_gauss.html">pair_style gauss</A> - Gaussian potential
+<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
+<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
+<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
+<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
+<LI><A HREF = "pair_kim.html">pair_style kim</A> - interface to potentials provided by KIM project
+<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
+<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
+<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
+<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
+<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
+<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/msm</A> - CHARMM with long-range MSM Coulombics
+<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
+<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
+<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
+<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/dsf</A> - LJ with Coulombics via damped shifted forces
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulombics
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/msm</A> - LJ with long-range MSM Coulombics
+<LI><A HREF = "pair_dipole.html">pair_style lj/cut/dipole/cut</A> - point dipoles with cutoff
+<LI><A HREF = "pair_dipole.html">pair_style lj/cut/dipole/long</A> - point dipoles with long-range Ewald
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A> - LJ with cutoff Coulomb for TIP4P water
+<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A> - LJ with long-range Coulomb for TIP4P water
+<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
+<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
+<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
+<LI><A HREF = "pair_lj_long.html">pair_style lj/long/coul/long</A> - long-range LJ and long-range Coulombics
+<LI><A HREF = "pair_dipole.html">pair_style lj/long/dipole/long</A> - long-range LJ and long-range point dipoles
+<LI><A HREF = "pair_lj_long.html">pair_style lj/long/tip4p/long</A> - long-range LJ and long-range Coulomb for TIP4P water
+<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
+<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
+<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
+<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
+<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity
+<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics
+<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU/poly</A> - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
+<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
+<LI><A HREF = "pair_mie.html">pair_style mie/cut</A> - Mie potential
+<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
+<LI><A HREF = "pair_nb3b_harmonic.html">pair_style nb3b/harmonic</A> - nonbonded 3-body harmonic potential
+<LI><A HREF = "pair_nm.html">pair_style nm/cut</A> - N-M potential
+<LI><A HREF = "pair_nm.html">pair_style nm/cut/coul/cut</A> - N-M potential with cutoff Coulomb
+<LI><A HREF = "pair_nm.html">pair_style nm/cut/coul/long</A> - N-M potential with long-range Coulombics
+<LI><A HREF = "pair_peri.html">pair_style peri/eps</A> - peridynamic EPS potential
+<LI><A HREF = "pair_peri.html">pair_style peri/lps</A> - peridynamic LPS potential
+<LI><A HREF = "pair_peri.html">pair_style peri/pmb</A> - peridynamic PMB potential
+<LI><A HREF = "pair_peri.html">pair_style peri/ves</A> - peridynamic VES potential
+<LI><A HREF = "pair_polymorphic.html">pair_style polymorphic</A> - polymorphic 3-body potential
+<LI><A HREF = "pair_reax.html">pair_style reax</A> - ReaxFF potential
+<LI><A HREF = "pair_airebo.html">pair_style rebo</A> - 2nd generation REBO potential of Brenner
+<LI><A HREF = "pair_resquared.html">pair_style resquared</A> - Everaers RE-Squared ellipsoidal potential
+<LI><A HREF = "pair_snap.html">pair_style snap</A> - SNAP quantum-accurate potential
+<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential
+<LI><A HREF = "pair_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
+<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
+<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
+<LI><A HREF = "pair_tersoff_mod.html">pair_style tersoff/mod</A> - modified Tersoff 3-body potential
+<LI><A HREF = "pair_tersoff_zbl.html">pair_style tersoff/zbl</A> - Tersoff/ZBL 3-body potential
+<LI><A HREF = "pair_coul.html">pair_style tip4p/cut</A> - Coulomb for TIP4P water w/out LJ
+<LI><A HREF = "pair_coul.html">pair_style tip4p/long</A> - long-range Coulombics for TIP4P water w/out LJ
+<LI><A HREF = "pair_tri_lj.html">pair_style tri/lj</A> - LJ potential between triangles
+<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
+<LI><A HREF = "pair_yukawa_colloid.html">pair_style yukawa/colloid</A> - screened Yukawa potential for finite-size particles
+<LI><A HREF = "pair_zbl.html">pair_style zbl</A> - Ziegler-Biersack-Littmark potential
+</UL>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must be used before any coefficients are set by the
+<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "read_data.html">read_data</A>, or
+<A HREF = "read_restart.html">read_restart</A> commands.
+</P>
+<P>Some pair styles are part of specific packages. They are only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info on packages.
+The doc pages for individual pair potentials tell if it is part of a
+package.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "read_data.html">read_data</A>,
+<A HREF = "pair_modify.html">pair_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
+<A HREF = "dielectric.html">dielectric</A>, <A HREF = "pair_write.html">pair_write</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>pair_style none
+</PRE>
+</HTML>
diff --git a/doc/doc2/pair_sw.html b/doc/doc2/pair_sw.html
new file mode 100644
index 000000000..8a9164f90
--- /dev/null
+++ b/doc/doc2/pair_sw.html
@@ -0,0 +1,228 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sw command
+</H3>
+<H3>pair_style sw/cuda command
+</H3>
+<H3>pair_style sw/gpu command
+</H3>
+<H3>pair_style sw/intel command
+</H3>
+<H3>pair_style sw/kk command
+</H3>
+<H3>pair_style sw/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sw
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sw
+pair_coeff * * si.sw Si
+pair_coeff * * GaN.sw Ga N Ga
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>sw</I> style computes a 3-body <A HREF = "#Stillinger">Stillinger-Weber</A>
+potential for the energy E of a system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sw.jpg">
+</CENTER>
+<P>where phi2 is a two-body term and phi3 is a three-body term. The
+summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = a*sigma.
+</P>
+<P>Only a single pair_coeff command is used with the <I>sw</I> style which
+specifies a Stillinger-Weber potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of SW elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine a file SiC.sw has Stillinger-Weber values for
+Si and C. If your LAMMPS simulation has 4 atoms types and you want
+the 1st 3 to be Si, and the 4th to be C, you would use the following
+pair_coeff command:
+</P>
+<PRE>pair_coeff * * SiC.sw Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the SW file. The final C argument maps LAMMPS atom type 4
+to the C element in the SW file. If a mapping value is specified as
+NULL, the mapping is not performed. This can be used when a <I>sw</I>
+potential is used as part of the <I>hybrid</I> pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+</P>
+<P>Stillinger-Weber files in the <I>potentials</I> directory of the LAMMPS
+distribution have a ".sw" suffix. Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements. The parameters in a single entry correspond to the two-body
+and three-body coefficients in the formula above:
+</P>
+<UL><LI>element 1 (the center atom in a 3-body interaction)
+<LI>element 2
+<LI>element 3
+<LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>a
+<LI>lambda
+<LI>gamma
+<LI>costheta0
+<LI>A
+<LI>B
+<LI>p
+<LI>q
+<LI>tol
+</UL>
+<P>The A, B, p, and q parameters are used only for two-body
+interactions. The lambda and costheta0 parameters are used only for
+three-body interactions. The epsilon, sigma and a parameters are used
+for both two-body and three-body interactions. gamma is used only in the
+three-body interactions, but is defined for pairs of atoms.
+The non-annotated parameters are unitless.
+</P>
+<P>LAMMPS introduces an additional performance-optimization parameter tol
+that is used for both two-body and three-body interactions. In the
+Stillinger-Weber potential, the interaction energies become negligibly
+small at atomic separations substantially less than the theoretical
+cutoff distances. LAMMPS therefore defines a virtual cutoff distance
+based on a user defined tolerance tol. The use of the virtual cutoff
+distance in constructing atom neighbor lists can significantly reduce
+the neighbor list sizes and therefore the computational cost. LAMMPS
+provides a <I>tol</I> value for each of the three-body entries so that they
+can be separately controlled. If tol = 0.0, then the standard
+Stillinger-Weber cutoff is used.
+</P>
+<P>The Stillinger-Weber potential file must contain entries for all the
+elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify SW parameters for all permutations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 27
+entries would be required, etc.
+</P>
+<P>As annotated above, the first element in the entry is the center atom
+in a three-body interaction. Thus an entry for SiCC means a Si atom
+with 2 C atoms as neighbors. The parameter values used for the
+two-body interaction come from the entry where the 2nd and 3rd
+elements are the same. Thus the two-body parameters for Si
+interacting with C, comes from the SiCC entry. The three-body
+parameters can in principle be specific to the three elements of the
+configuration. In the literature, however, the three-body parameters
+are usually defined by simple formulas involving two sets of pair-wise
+parameters, corresponding to the ij and ik pairs, where i is the
+center atom. The user must ensure that the correct combining rule is
+used to calculate the values of the threebody parameters for
+alloys. Note also that the function phi3 contains two exponential
+screening factors with parameter values from the ij pair and ik
+pairs. So phi3 for a C atom bonded to a Si atom and a second C atom
+will depend on the three-body parameters for the CSiC entry, and also
+on the two-body parameters for the CCC and CSiSi entries. Since the
+order of the two neighbors is arbitrary, the threebody parameters for
+entries CSiC and CCSi should be the same. Similarly, the two-body
+parameters for entries SiCC and CSiSi should also be the same. The
+parameters used only for two-body interactions (A, B, p, and q) in
+entries whose 2nd and 3rd element are different (e.g. SiCSi) are not
+used for anything and can be set to 0.0 if desired.
+This is also true for the parameters in phi3 that are
+taken from the ij and ik pairs (sigma, a, gamma)
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>When using the USER-INTEL package with this style, there is an
+additional 5 to 10 percent performance improvement when the
+Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
+These parameters are common for modeling silicon and water.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The Stillinger-Weber potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
+You can use the SW potential with any LAMMPS units, but you would need
+to create your own SW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Stillinger"></A>
+
+<P><B>(Stillinger)</B> Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_table.html b/doc/doc2/pair_table.html
new file mode 100644
index 000000000..ea976ba19
--- /dev/null
+++ b/doc/doc2/pair_table.html
@@ -0,0 +1,263 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style table command
+</H3>
+<H3>pair_style table/gpu command
+</H3>
+<H3>pair_style table/kk command
+</H3>
+<H3>pair_style table/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style table style N keyword ...
+</PRE>
+<UL><LI>style = <I>lookup</I> or <I>linear</I> or <I>spline</I> or <I>bitmap</I> = method of interpolation
+<LI>N = use N values in <I>lookup</I>, <I>linear</I>, <I>spline</I> tables
+<LI>N = use 2^N values in <I>bitmap</I> tables
+<LI>zero or more keywords may be appended
+<LI>keyword = <I>ewald</I> or <I>pppm</I> or <I>msm</I> or <I>dispersion</I> or <I>tip4p</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style table linear 1000
+pair_style table linear 1000 pppm
+pair_style table bitmap 12
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff * 3 morse.table ENTRY1 7.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from pair
+potential and force values listed in a file(s) as a function of
+distance. The files are read by the <A HREF = "pair_coeff.html">pair_coeff</A>
+command.
+</P>
+<P>The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and force values at each of <I>N</I>
+distances. During a simulation, these tables are used to interpolate
+energy and force values as needed. The interpolation is done in one
+of 4 styles: <I>lookup</I>, <I>linear</I>, <I>spline</I>, or <I>bitmap</I>.
+</P>
+<P>For the <I>lookup</I> style, the distance between 2 atoms is used to find
+the nearest table entry, which is the energy or force.
+</P>
+<P>For the <I>linear</I> style, the pair distance is used to find 2
+surrounding table values from which an energy or force is computed by
+linear interpolation.
+</P>
+<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
+stored at each of the <I>N</I> values in the table. The pair distance is
+used to find the appropriate set of coefficients which are used to
+evaluate a cubic polynomial which computes the energy or force.
+</P>
+<P>For the <I>bitmap</I> style, the N means to create interpolation tables
+that are 2^N in length. The pair distance is used to index into the
+table via a fast bit-mapping technique due to <A HREF = "#Wolff">(Wolff)</A>, and a
+linear interpolation is performed between adjacent table values.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>filename
+<LI>keyword
+<LI>cutoff (distance units)
+</UL>
+<P>The filename specifies a file containing tabulated energy and force
+values. The keyword specifies a section of the file. The cutoff is
+an optional coefficient. If not specified, the outer cutoff in the
+table itself (see below) will be used to build an interpolation table
+that extend to the largest tabulated distance. If specified, only
+file values up to the cutoff are used to create the interpolation
+table. The format of this file is described below.
+</P>
+<P>If your tabulated potential(s) are designed to be used as the
+short-range part of one of the long-range solvers specified by the
+<A HREF = "kspace_style.html">kspace_style</A> command, then you must use one or
+more of the optional keywords listed above for the pair_style command.
+These are <I>ewald</I> or <I>pppm</I> or <I>msm</I> or <I>dispersion</I> or <I>tip4p</I>. This
+is so LAMMPS can insure the short-range potential and long-range
+solver are compatible with each other, as it does for other
+short-range pair styles, such as <A HREF = "pair_lj.html">pair_style
+lj/cut/coul/long</A>. Note that it is up to you to insure
+the tabulated values for each pair of atom types has the correct
+functional form to be compatible with the matching long-range solver.
+</P>
+<HR>
+
+<P>Here are some guidelines for using the pair_style table command to
+best effect:
+</P>
+<UL><LI>Vary the number of table points; you may need to use more than you think
+to get good resolution.
+
+<LI>Always use the <A HREF = "pair_write.html">pair_write</A> command to produce a plot
+of what the final interpolated potential looks like. This can show up
+interpolation "features" you may not like.
+
+<LI>Start with the linear style; it's the style least likely to have problems.
+
+<LI>Use <I>N</I> in the pair_style command equal to the "N" in the tabulation
+file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation
+is not needed. See discussion below.
+
+<LI>Make sure that your tabulated forces and tabulated energies are consistent
+(dE/dr = -F) along the entire range of r values.
+
+<LI>Use as large an inner cutoff as possible. This avoids fitting splines
+to very steep parts of the potential.
+</UL>
+<HR>
+
+<P>The format of a tabulated file is a series of one or more sections,
+defined as follows (without the parenthesized comments):
+</P>
+<PRE># Morse potential for Fe (one or more comment or blank lines)
+</PRE>
+<PRE>MORSE_FE (keyword is first text on line)
+N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters)
+ (blank)
+1 1.0 25.5 102.34 (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+</PRE>
+<P>A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the pair_coeff
+command. The next line lists (in any order) one or more parameters
+for the table. Each parameter is a keyword followed by one or more
+numeric values.
+</P>
+<P>The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the <I>N</I>
+specified in the <A HREF = "pair_style.html">pair_style table</A> command. Let
+Ntable = <I>N</I> in the pair_style command, and Nfile = "N" in the
+tabulated file. What LAMMPS does is a preliminary interpolation by
+creating splines using the Nfile tabulated values as nodal points. It
+uses these to interpolate as needed to generate energy and force
+values at Ntable different points. The resulting tables of length
+Ntable are then used as described above, when computing energy and
+force for individual pair distances. This means that if you want the
+interpolation tables of length Ntable to match exactly what is in the
+tabulated file (with effectively no preliminary interpolation), you
+should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter.
+The internal table abscissa is RSQ (separation distance squared).
+</P>
+<P>All other parameters are optional. If "R" or "RSQ" or "BITMAP" does
+not appear, then the distances in each line of the table are used
+as-is to perform spline interpolation. In this case, the table values
+can be spaced in <I>r</I> uniformly or however you wish to position table
+values in regions of large gradients.
+</P>
+<P>If used, the parameters "R" or "RSQ" are followed by 2 values <I>rlo</I>
+and <I>rhi</I>. If specified, the distance associated with each energy and
+force value is computed from these 2 values (at high accuracy), rather
+than using the (low-accuracy) value listed in each line of the table.
+The distance values in the table file are ignored in this case.
+For "R", distances uniformly spaced between <I>rlo</I> and <I>rhi</I> are
+computed; for "RSQ", squared distances uniformly spaced between
+<I>rlo*rlo</I> and <I>rhi*rhi</I> are computed.
+</P>
+<P>If used, the parameter "BITMAP" is also followed by 2 values <I>rlo</I> and
+<I>rhi</I>. These values, along with the "N" value determine the ordering
+of the N lines that follow and what distance is associated with each.
+This ordering is complex, so it is not documented here, since this
+file is typically produced by the <A HREF = "pair_write.html">pair_write</A> command
+with its <I>bitmap</I> option. When the table is in BITMAP format, the "N"
+parameter in the file must be equal to 2^M where M is the value
+specified in the pair_style command. Also, a cutoff parameter cannot
+be used as an optional 3rd argument in the pair_coeff command; the
+entire table extent as specified in the file must be used.
+</P>
+<P>If used, the parameter "FPRIME" is followed by 2 values <I>fplo</I> and
+<I>fphi</I> which are the derivative of the force at the innermost and
+outermost distances listed in the table. These values are needed by
+the spline construction routines. If not specified by the "FPRIME"
+parameter, they are estimated (less accurately) by the first 2 and
+last 2 force values in the table. This parameter is not used by
+BITMAP tables.
+</P>
+<P>Following a blank line, the next N lines list the tabulated values.
+On each line, the 1st value is the index from 1 to N, the 2nd value is
+r (in distance units), the 3rd value is the energy (in energy units),
+and the 4th is the force (in force units). The r values must increase
+from one line to the next (unless the BITMAP parameter is specified).
+</P>
+<P>Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds
+one that matches the specified keyword.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift, table, and tail options are
+not relevant for this pair style.
+</P>
+<P>This pair style writes the settings for the "pair_style table" command
+to <A HREF = "restart.html">binary restart files</A>, so a pair_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files. Thus, pair_coeff
+commands do need to be specified in the restart input script.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Wolff"></A>
+
+<P><B>(Wolff)</B> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_tersoff.html b/doc/doc2/pair_tersoff.html
new file mode 100644
index 000000000..1d17fc697
--- /dev/null
+++ b/doc/doc2/pair_tersoff.html
@@ -0,0 +1,265 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style tersoff command
+</H3>
+<H3>pair_style tersoff/table command
+</H3>
+<H3>pair_style tersoff/cuda
+</H3>
+<H3>pair_style tersoff/kk
+</H3>
+<H3>pair_style tersoff/omp
+</H3>
+<H3>pair_style tersoff/table/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style style
+</PRE>
+<P>style = <I>tersoff</I> or <I>tersoff/table</I> or <I>tersoff/cuda</I> or <I>tersoff/omp</I> or <I>tersoff/table/omp</I>
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style tersoff
+pair_coeff * * Si.tersoff Si
+pair_coeff * * SiC.tersoff Si C Si
+</PRE>
+<PRE>pair_style tersoff/table
+pair_coeff * * SiCGe.tersoff Si(D)
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>tersoff</I> style computes a 3-body Tersoff potential
+<A HREF = "#Tersoff_1">(Tersoff_1)</A> for the energy E of a system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_tersoff_1.jpg">
+</CENTER>
+<P>where f_R is a two-body term and f_A includes three-body interactions.
+The summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = R + D.
+</P>
+<P>The <I>tersoff/table</I> style uses tabulated forms for the two-body,
+environment and angular functions. Linear interpolation is performed
+between adjacent table entries. The table length is chosen to be
+accurate within 10^-6 with respect to the <I>tersoff</I> style energy.
+The <I>tersoff/table</I> should give better performance in terms of speed.
+</P>
+<P>Only a single pair_coeff command is used with the <I>tersoff</I> style
+which specifies a Tersoff potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of Tersoff elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine the SiC.tersoff file has Tersoff values for Si
+and C. If your LAMMPS simulation has 4 atoms types and you want the
+1st 3 to be Si, and the 4th to be C, you would use the following
+pair_coeff command:
+</P>
+<PRE>pair_coeff * * SiC.tersoff Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the Tersoff file. The final C argument maps LAMMPS atom
+type 4 to the C element in the Tersoff file. If a mapping value is
+specified as NULL, the mapping is not performed. This can be used
+when a <I>tersoff</I> potential is used as part of the <I>hybrid</I> pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
+</P>
+<P>Tersoff files in the <I>potentials</I> directory of the LAMMPS distribution
+have a ".tersoff" suffix. Lines that are not blank or comments
+(starting with #) define parameters for a triplet of elements. The
+parameters in a single entry correspond to coefficients in the formula
+above:
+</P>
+<UL><LI>element 1 (the center atom in a 3-body interaction)
+<LI>element 2 (the atom bonded to the center atom)
+<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+<LI>m
+<LI>gamma
+<LI>lambda3 (1/distance units)
+<LI>c
+<LI>d
+<LI>costheta0 (can be a value < -1 or > 1)
+<LI>n
+<LI>beta
+<LI>lambda2 (1/distance units)
+<LI>B (energy units)
+<LI>R (distance units)
+<LI>D (distance units)
+<LI>lambda1 (1/distance units)
+<LI>A (energy units)
+</UL>
+<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions. The m, gamma, lambda3, c, d, and costheta0
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions. The
+non-annotated parameters are unitless. The value of m must be 3 or 1.
+</P>
+<P>The Tersoff potential file must contain entries for all the elements
+listed in the pair_coeff command. It can also contain entries for
+additional elements not being used in a particular simulation; LAMMPS
+ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify Tersoff parameters for all permutations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 27
+entries would be required, etc.
+</P>
+<P>As annotated above, the first element in the entry is the center atom
+in a three-body interaction and it is bonded to the 2nd atom and the
+bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
+bonded to a C with another C atom influencing the bond. Thus
+three-body parameters for SiCSi and SiSiC entries will not, in
+general, be the same. The parameters used for the two-body
+interaction come from the entry where the 2nd element is repeated.
+Thus the two-body parameters for Si interacting with C, comes from the
+SiCC entry.
+</P>
+<P>The parameters used for a particular
+three-body interaction come from the entry with the corresponding
+three elements. The parameters used only for two-body interactions
+(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
+</P>
+<P>Note that the twobody parameters in entries such as SiCC and CSiSi
+are often the same, due to the common use of symmetric mixing rules,
+but this is not always the case. For example, the beta and n parameters in
+Tersoff_2 <A HREF = "#Tersoff_2">(Tersoff_2)</A> are not symmetric.
+</P>
+<P>We chose the above form so as to enable users to define all commonly
+used variants of the Tersoff potential. In particular, our form
+reduces to the original Tersoff form when m = 3 and gamma = 1, while
+it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1 and m = 1.
+Note that in the current Tersoff implementation in LAMMPS, m must be
+specified as either 3 or 1. Tersoff used a slightly different but
+equivalent form for alloys, which we will refer to as Tersoff_2
+potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>. The <I>tersoff/table</I> style implements
+Tersoff_2 parameterization only.
+</P>
+<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
+gamma_ijk = omega_ik, lambda3 = 0 and the value of
+m has no effect. The parameters for species i and j can be calculated
+using the Tersoff_2 mixing rules:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
+</CENTER>
+<P>Tersoff_2 parameters R and S must be converted to the LAMMPS
+parameters R and D (R is different in both forms), using the following
+relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
+Tersoff_2 parameters.
+</P>
+<P>In the potentials directory, the file SiCGe.tersoff provides the
+LAMMPS parameters for Tersoff's various versions of Si, as well as his
+alloy parameters for Si, C, and Ge. This file can be used for pure Si,
+(three different versions), pure C, pure Ge, binary SiC, and binary
+SiGe. LAMMPS will generate an error if this file is used with any
+combination involving C and Ge, since there are no entries for the GeC
+interactions (Tersoff did not publish parameters for this
+cross-interaction.) Tersoff files are also provided for the SiC alloy
+(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
+</P>
+<P>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
+for helping clarify how Tersoff parameters for alloys have been
+defined in various papers.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The Tersoff potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal <A HREF = "units.html">units</A>. You can
+use the Tersoff potential with any LAMMPS units, but you would need to
+create your own Tersoff potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Tersoff_1"></A>
+
+<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
+</P>
+<A NAME = "Albe"></A>
+
+<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.:
+Condens. Matter, 15, 5649(2003).
+</P>
+<A NAME = "Tersoff_2"></A>
+
+<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
+</P>
+</HTML>
diff --git a/doc/doc2/pair_tersoff_mod.html b/doc/doc2/pair_tersoff_mod.html
new file mode 100644
index 000000000..2e6a5a366
--- /dev/null
+++ b/doc/doc2/pair_tersoff_mod.html
@@ -0,0 +1,204 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style tersoff/mod command
+</H3>
+<H3>pair_style tersoff/mod/kk command
+</H3>
+<H3>pair_style tersoff/mod/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style tersoff/mod
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style tersoff/mod
+pair_coeff * * Si.tersoff.mod Si Si
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>tersoff/mod</I> style computes a bond-order type interatomic
+potential <A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential
+<A HREF = "#Tersoff_1">(Tersoff_1)</A>, <A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified
+cutoff function and angular-dependent term, giving the energy E of a
+system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_tersoff_mod.jpg">
+</CENTER>
+<P>where f_R is a two-body term and f_A includes three-body interactions.
+The summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance = R + D.
+</P>
+<P>The modified cutoff function f_C proposed by <A HREF = "#Murty">(Murty)</A> and
+having a continuous second-order differential is employed. The
+angular-dependent term g(theta) was modified to increase the
+flexibility of the potential.
+</P>
+<P>The <I>tersoff/mod</I> potential is fitted to both the elastic constants
+and melting point by employing the modified Tersoff potential function
+form in which the angular-dependent term is improved. The model
+performs extremely well in describing the crystalline, liquid, and
+amorphous phases <A HREF = "#Schelling">(Schelling)</A>.
+</P>
+<P>Only a single pair_coeff command is used with the <I>tersoff/mod</I> style
+which specifies a Tersoff/MOD potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of Tersoff/MOD elements to atom types
+</UL>
+<P>As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
+If your LAMMPS simulation has 3 Si atoms types, you would use the following
+pair_coeff command:
+</P>
+<PRE>pair_coeff * * Si.tersoff_mod Si Si Si
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
+in the Tersoff/MOD file. If a mapping value is specified as NULL, the
+mapping is not performed. This can be used when a <I>tersoff/mod</I>
+potential is used as part of the <I>hybrid</I> pair style. The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+</P>
+<P>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS
+distribution have a ".tersoff.mod" suffix. Lines that are not blank
+or comments (starting with #) define parameters for a triplet of
+elements. The parameters in a single entry correspond to coefficients
+in the formula above:
+</P>
+<UL><LI>element 1 (the center atom in a 3-body interaction)
+<LI>element 2 (the atom bonded to the center atom)
+<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+<LI>beta
+<LI>alpha
+<LI>h
+<LI>eta
+<LI>beta_ters = 1 (dummy parameter)
+<LI>lambda2 (1/distance units)
+<LI>B (energy units)
+<LI>R (distance units)
+<LI>D (distance units)
+<LI>lambda1 (1/distance units)
+<LI>A (energy units)
+<LI>n
+<LI>c1
+<LI>c2
+<LI>c3
+<LI>c4
+<LI>c5
+</UL>
+<P>The n, eta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions. The
+non-annotated parameters are unitless.
+</P>
+<P>The Tersoff/MOD potential file must contain entries for all the elements
+listed in the pair_coeff command. It can also contain entries for
+additional elements not being used in a particular simulation; LAMMPS
+ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). As annotated above, the first element in the entry is
+the center atom in a three-body interaction and it is bonded to the
+2nd atom and the bond is influenced by the 3rd atom. Thus an entry
+for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The Tersoff/MOD potential files provided with LAMMPS (see the potentials
+directory) are parameterized for metal <A HREF = "units.html">units</A>. You can
+use the Tersoff/MOD potential with any LAMMPS units, but you would need to
+create your own Tersoff/MOD potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Kumagai"></A>
+
+<P><B>(Kumagai)</B> T. Kumagai, S. Izumi, S. Hara, S. Sakai,
+Comp. Mat. Science, 39, 457 (2007).
+</P>
+<A NAME = "Tersoff_1"></A>
+
+<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
+</P>
+<A NAME = "Tersoff_2"></A>
+
+<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 38, 9902 (1988).
+</P>
+<A NAME = "Murty"></A>
+
+<P><B>(Murty)</B> M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).
+</P>
+<A NAME = "Schelling"></A>
+
+<P><B>(Schelling)</B> Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_tersoff_zbl.html b/doc/doc2/pair_tersoff_zbl.html
new file mode 100644
index 000000000..3374f8914
--- /dev/null
+++ b/doc/doc2/pair_tersoff_zbl.html
@@ -0,0 +1,278 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style tersoff/zbl command
+</H3>
+<H3>pair_style tersoff/zbl/kk command
+</H3>
+<H3>pair_style tersoff/zbl/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style tersoff/zbl
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style tersoff/zbl
+pair_coeff * * SiC.tersoff.zbl Si C Si
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>tersoff/zbl</I> style computes a 3-body Tersoff potential
+<A HREF = "#Tersoff_1">(Tersoff_1)</A> with a close-separation pairwise modification
+based on a Coulomb potential and the Ziegler-Biersack-Littmark
+universal screening function <A HREF = "#ZBL">(ZBL)</A>, giving the energy E of a
+system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_tersoff_zbl.jpg">
+</CENTER>
+<P>The f_F term is a fermi-like function used to smoothly connect the ZBL
+repulsive potential with the Tersoff potential. There are 2
+parameters used to adjust it: A_F and r_C. A_F controls how "sharp"
+the transition is between the two, and r_C is essentially the cutoff
+for the ZBL potential.
+</P>
+<P>For the ZBL portion, there are two terms. The first is the Coulomb
+repulsive term, with Z1, Z2 as the number of protons in each nucleus,
+e as the electron charge (1 for metal and real units) and epsilon0 as
+the permittivity of vacuum. The second part is the ZBL universal
+screening function, with a0 being the Bohr radius (typically 0.529
+Angstroms), and the remainder of the coefficients provided by the
+original paper. This screening function should be applicable to most
+systems. However, it is only accurate for small separations
+(i.e. less than 1 Angstrom).
+</P>
+<P>For the Tersoff portion, f_R is a two-body term and f_A includes
+three-body interactions. The summations in the formula are over all
+neighbors J and K of atom I within a cutoff distance = R + D.
+</P>
+<P>Only a single pair_coeff command is used with the <I>tersoff/zbl</I> style
+which specifies a Tersoff/ZBL potential file with parameters for all
+needed elements. These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of Tersoff/ZBL elements to atom types
+</UL>
+<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
+to specify the path for the potential file.
+</P>
+<P>As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
+for Si and C. If your LAMMPS simulation has 4 atoms types and you
+want the 1st 3 to be Si, and the 4th to be C, you would use the
+following pair_coeff command:
+</P>
+<PRE>pair_coeff * * SiC.tersoff Si Si Si C
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the Tersoff/ZBL file. The final C argument maps LAMMPS
+atom type 4 to the C element in the Tersoff/ZBL file. If a mapping
+value is specified as NULL, the mapping is not performed. This can be
+used when a <I>tersoff/zbl</I> potential is used as part of the <I>hybrid</I>
+pair style. The NULL values are placeholders for atom types that will
+be used with other potentials.
+</P>
+<P>Tersoff/ZBL files in the <I>potentials</I> directory of the LAMMPS
+distribution have a ".tersoff.zbl" suffix. Lines that are not blank
+or comments (starting with #) define parameters for a triplet of
+elements. The parameters in a single entry correspond to coefficients
+in the formula above:
+</P>
+<UL><LI>element 1 (the center atom in a 3-body interaction)
+<LI>element 2 (the atom bonded to the center atom)
+<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
+<LI>m
+<LI>gamma
+<LI>lambda3 (1/distance units)
+<LI>c
+<LI>d
+<LI>costheta0 (can be a value < -1 or > 1)
+<LI>n
+<LI>beta
+<LI>lambda2 (1/distance units)
+<LI>B (energy units)
+<LI>R (distance units)
+<LI>D (distance units)
+<LI>lambda1 (1/distance units)
+<LI>A (energy units)
+<LI>Z_i
+<LI>Z_j
+<LI>ZBLcut (distance units)
+<LI>ZBLexpscale (1/distance units)
+</UL>
+<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
+two-body interactions. The m, gamma, lambda3, c, d, and costheta0
+parameters are only used for three-body interactions. The R and D
+parameters are used for both two-body and three-body interactions. The
+Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
+portion of the potential and in the Fermi-like function. The
+non-annotated parameters are unitless. The value of m must be 3 or 1.
+</P>
+<P>The Tersoff/ZBL potential file must contain entries for all the
+elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. SiSiSi). For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify Tersoff parameters for all permutations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 27
+entries would be required, etc.
+</P>
+<P>As annotated above, the first element in the entry is the center atom
+in a three-body interaction and it is bonded to the 2nd atom and the
+bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
+bonded to a C with another C atom influencing the bond. Thus
+three-body parameters for SiCSi and SiSiC entries will not, in
+general, be the same. The parameters used for the two-body
+interaction come from the entry where the 2nd element is repeated.
+Thus the two-body parameters for Si interacting with C, comes from the
+SiCC entry.
+</P>
+<P>The parameters used for a particular
+three-body interaction come from the entry with the corresponding
+three elements. The parameters used only for two-body interactions
+(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
+</P>
+<P>Note that the twobody parameters in entries such as SiCC and CSiSi
+are often the same, due to the common use of symmetric mixing rules,
+but this is not always the case. For example, the beta and n parameters in
+Tersoff_2 <A HREF = "#Tersoff_2">(Tersoff_2)</A> are not symmetric.
+</P>
+<P>We chose the above form so as to enable users to define all commonly
+used variants of the Tersoff portion of the potential. In particular,
+our form reduces to the original Tersoff form when m = 3 and gamma =
+1, while it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1
+and m = 1. Note that in the current Tersoff implementation in LAMMPS,
+m must be specified as either 3 or 1. Tersoff used a slightly
+different but equivalent form for alloys, which we will refer to as
+Tersoff_2 potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
+</P>
+<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
+gamma = omega_ijk, lambda3 = 0 and the value of
+m has no effect. The parameters for species i and j can be calculated
+using the Tersoff_2 mixing rules:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
+</CENTER>
+<P>Tersoff_2 parameters R and S must be converted to the LAMMPS
+parameters R and D (R is different in both forms), using the following
+relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
+Tersoff_2 parameters.
+</P>
+<P>In the potentials directory, the file SiCGe.tersoff provides the
+LAMMPS parameters for Tersoff's various versions of Si, as well as his
+alloy parameters for Si, C, and Ge. This file can be used for pure Si,
+(three different versions), pure C, pure Ge, binary SiC, and binary
+SiGe. LAMMPS will generate an error if this file is used with any
+combination involving C and Ge, since there are no entries for the GeC
+interactions (Tersoff did not publish parameters for this
+cross-interaction.) Tersoff files are also provided for the SiC alloy
+(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
+</P>
+<P>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
+for helping clarify how Tersoff parameters for alloys have been
+defined in various papers. Also thanks to Ram Devanathan for
+providing the base ZBL implementation.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files. Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package (which it is by default). See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
+</P>
+<P>The Tersoff/ZBL potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
+You can use the Tersoff potential with any LAMMPS units, but you would
+need to create your own Tersoff potential file with coefficients
+listed in the appropriate units if your simulation doesn't use "metal"
+units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Tersoff_1"></A>
+
+<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
+</P>
+<A NAME = "ZBL"></A>
+
+<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
+of Ions in Matter' Vol 1, 1985, Pergamon Press.
+</P>
+<A NAME = "Albe"></A>
+
+<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
+Condens. Matter, 15, 5649(2003).
+</P>
+<A NAME = "Tersoff_2"></A>
+
+<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
+</P>
+</HTML>
diff --git a/doc/doc2/pair_thole.html b/doc/doc2/pair_thole.html
new file mode 100644
index 000000000..2fa01d9e8
--- /dev/null
+++ b/doc/doc2/pair_thole.html
@@ -0,0 +1,133 @@
+<HTML>
+<script type="text/javascript"
+ src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style thole command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style thole damp cutoff
+</PRE>
+<UL><LI>thole = style name
+<LI>damp = global damping parameter
+<LI>cutoff = global cutoff
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style hybrid/overlay ... thole 2.6 12.0
+pair_coeff 1 1 thole 1.0
+pair_coeff 1 2 thole 1.0 2.6 10.0
+pair_coeff * 2 thole 1.0 2.6
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>thole</I> pair style is meant to be used with force fields that
+include explicit polarization through Drude dipoles. This link
+describes how to use the <A HREF = "tutorial_drude.html">thermalized Drude oscillator
+model</A> in LAMMPS and polarizable models in LAMMPS
+are discussed in <A HREF = "Section_howto.html#howto_25">this Section</A>.
+</P>
+<P>The <I>thole</I> pair style should be used as a sub-style within in the
+<A HREF = "pair_hybrid.html">pair_hybrid/overlay</A> command, in conjunction with a
+main pair style including Coulomb interactions, i.e. any pair style
+containing <I>coul/cut</I> or <I>coul/long</I> in its style name.
+</P>
+<P>The <I>thole</I> pair style computes the Coulomb interaction damped at
+short distances by a function
+</P>
+<P>\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
+\frac{s_{ij} r_{ij} }{2} \right)
+\exp \left( - s_{ij} r_{ij} \right) \end{equation}
+</P>
+<P>This function results from an adaptation to point charges
+<A HREF = "#Noskov">(Noskov)</A> of the dipole screening scheme originally proposed
+by <A HREF = "#Thole">Thole</A>. The scaling coefficient \(s_{ij} \) is determined
+by the polarizability of the atoms, \( \alpha_i \), and by a Thole
+damping parameter \( a \). This Thole damping parameter usually takes
+a value of 2.6, but in certain force fields the value can depend upon
+the atom types. The mixing rule for Thole damping parameters is the
+arithmetic average, and for polarizabilities the geometric average
+between the atom-specific values.
+</P>
+<P>\begin{equation} s_{ij} = \frac{ a_{ij} }{
+(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
+[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}
+</P>
+<P>The damping function is only applied to the interactions between the
+point charges representing the induced dipoles on polarizable sites,
+that is, charges on Drude particles, \( q_{D,i} \), and opposite
+charges, \( -q_{D,i} \), located on the respective core particles
+(to which each Drude particle is bonded). Therefore, Thole screening
+is not applied to the full charge of the core particle \( q_i \), but
+only to the \( -q_{D,i} \) part of it.
+</P>
+<P>The interactions between core charges are subject to the weighting
+factors set by the <A HREF = "special_bonds.html">special_bonds</A> command. The
+interactions between Drude particles and core charges or
+non-polarizable atoms are also subject to these weighting factors. The
+Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
+their respective cores.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example
+above.
+</P>
+<UL><LI>alpha (distance units^3)
+<LI>damp
+<LI>cutoff (distance units)
+</UL>
+<P>The last two coefficients are optional. If not specified the global
+Thole damping parameter or global cutoff specified in the pair_style
+command are used. In order to specify a cutoff (third argument) a damp
+parameter (second argument) must also be specified.
+</P>
+<P><B>Mixing</B>:
+</P>
+<P>The <I>thole</I> pair style does not support mixing. Thus, coefficients
+for all I,J pairs must be specified explicitly.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>These pair styles are part of the USER-DRUDE package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This pair_style should currently not be used with the <A HREF = "dihedral_charmm.html">charmm dihedral
+style</A> if the latter non-zero 1-4 weighting
+factors. This is because the <I>thole</I> pair style does not know which
+pairs are 1-4 partners of which dihedrals.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_drude.html">fix drude</A>, <A HREF = "fix_langevin_drude.html">fix
+langevin/drude</A>, <A HREF = "fix_drude_transform.html">fix
+drude/transform</A>, <A HREF = "compute_temp_drude.html">compute
+temp/drude</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Noskov"></A>
+
+<P><B>(Noskov)</B> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
+</P>
+<A NAME = "Thole"></A>
+
+<P><B>(Thole)</B> Chem Phys, 59, 341 (1981).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_tri_lj.html b/doc/doc2/pair_tri_lj.html
new file mode 100644
index 000000000..98a230c73
--- /dev/null
+++ b/doc/doc2/pair_tri_lj.html
@@ -0,0 +1,145 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style tri/lj command
+</H3>
+<H3>pair_style tri/lj/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style tri/lj cutoff
+</PRE>
+<P>cutoff = global cutoff for interactions (distance units)
+</P>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style tri/lj 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>tri/lj</I> treats particles which are triangles as a set of small
+spherical particles that tile the triangle surface as explained below.
+Interactions between two triangles, each with N1 and N2 spherical
+particles, are calculated as the pairwise sum of N1*N2 Lennard-Jones
+interactions. Interactions between a triangle with N spherical
+particles and a point particle are treated as the pairwise sum of N
+Lennard-Jones interactions. See the <A HREF = "pair_lj.html">pair_style lj/cut</A>
+doc page for the definition of Lennard-Jones interactions.
+</P>
+<P>The cutoff distance for an interaction between 2 triangles, or between
+a triangle and a point particle, is calculated from the position of
+the triangle (its centroid), not between pairs of individual spheres
+comprising the triangle. Thus an interaction is either calculated in
+its entirety or not at all.
+</P>
+<P>The set of non-overlapping spherical particles that represent a
+triangle, for purposes of this pair style, are generated in the
+following manner. Assume the triangle is of type I, and sigma_II has
+been specified. We want a set of spheres with centers in the plane of
+the triangle, none of them larger in diameter than sigma_II, which
+completely cover the triangle's area, but with minimial overlap and a
+minimal total number of spheres. This is done in a recursive manner.
+Place a sphere at the centroid of the original triangle. Calculate
+what diameter it must have to just cover all 3 corner points of the
+triangle. If that diameter is equal to or smaller than sigma_II, then
+include a sphere of the calculated diameter in the set of covering
+spheres. It the diameter is larger than sigma_II, then split the
+triangle into 2 triangles by bisecting its longest side. Repeat the
+process on each sub-triangle, recursing as far as needed to generate a
+set of covering spheres. When finished, the original criteria are
+met, and the set of covering spheres shoule be near minimal in number
+and overlap, at least for input triangles with a reasonable
+aspect-ratio.
+</P>
+<P>The LJ interaction between 2 spheres on different triangles of types
+I,J is computed with an arithmetic mixing of the sigma values of the 2
+spheres and using the specified epsilon value for I,J atom types.
+Note that because the sigma values for triangles spheres is computed
+using only sigma_II values, specific to the triangles's type, this
+means that any specified sigma_IJ values (for I != J) are effectively
+ignored.
+</P>
+<P>For style <I>tri/lj</I>, the following coefficients must be defined for
+each pair of atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command
+as in the examples above, or in the data file or restart files read by
+the <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global cutoff
+is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of this pair style can be mixed. The
+default mix value is <I>geometric</I>. See the "pair_modify" command for
+details.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the ASPHERE package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Defining particles to be triangles so they participate in tri/tri or
+tri/particle interactions requires the use the <A HREF = "atom_style.html">atom_style
+tri</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_line_lj.html">pair_style line/lj</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_write.html b/doc/doc2/pair_write.html
new file mode 100644
index 000000000..f39244441
--- /dev/null
+++ b/doc/doc2/pair_write.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_write command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_write itype jtype N style inner outer file keyword Qi Qj
+</PRE>
+<UL><LI>itype,jtype = 2 atom types
+<LI>N = # of values
+<LI>style = <I>r</I> or <I>rsq</I> or <I>bitmap</I>
+<LI>inner,outer = inner and outer cutoff (distance units)
+<LI>file = name of file to write values to
+<LI>keyword = section name in file for this set of tabulated values
+<LI>Qi,Qj = 2 atom charges (charge units) (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_write 1 3 500 r 1.0 10.0 table.txt LJ
+pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write energy and force values to a file as a function of distance for
+the currently defined pair potential. This is useful for plotting the
+potential function or otherwise debugging its values. If the file
+already exists, the table of values is appended to the end of the file
+to allow multiple tables of energy and force to be included in one
+file.
+</P>
+<P>The energy and force values are computed at distances from inner to
+outer for 2 interacting atoms of type itype and jtype, using the
+appropriate <A HREF = "pair_coeff.html">pair_coeff</A> coefficients. If the style
+is <I>r</I>, then N distances are used, evenly spaced in r; if the style is
+<I>rsq</I>, N distances are used, evenly spaced in r^2.
+</P>
+<P>For example, for N = 7, style = <I>r</I>, inner = 1.0, and outer = 4.0,
+values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
+</P>
+<P>If the style is <I>bitmap</I>, then 2^N values are written to the file in a
+format and order consistent with how they are read in by the
+<A HREF = "pair_coeff.html">pair_coeff</A> command for pair style <I>table</I>. For
+reasonable accuracy in a bitmapped table, choose N >= 12, an <I>inner</I>
+value that is smaller than the distance of closest approach of 2
+atoms, and an <I>outer</I> value <= cutoff of the potential.
+</P>
+<P>If the pair potential is computed between charged atoms, the charges
+of the pair of interacting atoms can optionally be specified. If not
+specified, values of Qi = Qj = 1.0 are used.
+</P>
+<P>The file is written in the format used as input for the
+<A HREF = "pair_style.html">pair_style</A> <I>table</I> option with <I>keyword</I> as the
+section name. Each line written to the file lists an index number
+(1-N), a distance (in distance units), an energy (in energy units),
+and a force (in force units).
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>All force field coefficients for pair and other kinds of interactions
+must be set before this command can be invoked.
+</P>
+<P>Due to how the pairwise force is computed, an inner value > 0.0 must
+be specified even if the potential has a finite value at r = 0.0.
+</P>
+<P>For EAM potentials, the pair_write command only tabulates the
+pairwise portion of the potential, not the embedding portion.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_yukawa.html b/doc/doc2/pair_yukawa.html
new file mode 100644
index 000000000..d4c78f82d
--- /dev/null
+++ b/doc/doc2/pair_yukawa.html
@@ -0,0 +1,111 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style yukawa command
+</H3>
+<H3>pair_style yukawa/gpu command
+</H3>
+<H3>pair_style yukawa/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style yukawa kappa cutoff
+</PRE>
+<UL><LI>kappa = screening length (inverse distance units)
+<LI>cutoff = global cutoff for Yukawa interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style yukawa 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>yukawa</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_yukawa.jpg">
+</CENTER>
+<P>Rc is the cutoff.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>A (energy*distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global yukawa
+cutoff is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed. A is an energy value mixed
+like a LJ epsilon. The default mix value is <I>geometric</I>. See the
+"pair_modify" command for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/pair_yukawa_colloid.html b/doc/doc2/pair_yukawa_colloid.html
new file mode 100644
index 000000000..595e76135
--- /dev/null
+++ b/doc/doc2/pair_yukawa_colloid.html
@@ -0,0 +1,163 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style yukawa/colloid command
+</H3>
+<H3>pair_style yukawa/colloid/gpu command
+</H3>
+<H3>pair_style yukawa/colloid/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style yukawa/colloid kappa cutoff
+</PRE>
+<UL><LI>kappa = screening length (inverse distance units)
+<LI>cutoff = global cutoff for colloidal Yukawa interactions (distance units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style yukawa/colloid 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>yukawa/colloid</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_yukawa_colloid.jpg">
+</CENTER>
+<P>where Ri and Rj are the radii of the two particles and Rc is the
+cutoff.
+</P>
+<P>In contrast to <A HREF = "pair_yukawa.html">pair_style yukawa</A>, this functional
+form arises from the Coulombic interaction between two colloid
+particles, screened due to the presence of an electrolyte, see the
+book by <A HREF = "#Safran">Safran</A> for a derivation in the context of DVLO
+theory. <A HREF = "pair_yukawa.html">Pair_style yukawa</A> is a screened Coulombic
+potential between two point-charges and uses no such approximation.
+</P>
+<P>This potential applies to nearby particle pairs for which the Derjagin
+approximation holds, meaning h << Ri + Rj, where h is the
+surface-to-surface separation of the two particles.
+</P>
+<P>When used in combination with <A HREF = "pair_colloid.html">pair_style colloid</A>,
+the two terms become the so-called DLVO potential, which combines
+electrostatic repulsion and van der Waals attraction.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above, or in the data file or restart files read by the
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands, or by mixing as described below:
+</P>
+<UL><LI>A (energy/distance units)
+<LI>cutoff (distance units)
+</UL>
+<P>The prefactor A is determined from the relationship between surface
+charge and surface potential due to the presence of electrolyte. Note
+that the A for this potential style has different units than the A
+used in <A HREF = "pair_yukawa.html">pair_style yukawa</A>. For low surface
+potentials, i.e. less than about 25 mV, A can be written as:
+</P>
+<PRE>A = 2 * PI * R*eps*eps0 * kappa * psi^2
+</PRE>
+<P>where
+</P>
+<UL><LI>R = colloid radius (distance units)
+<LI>eps0 = permittivity of free space (charge^2/energy/distance units)
+<LI>eps = relative permittivity of fluid medium (dimensionless)
+<LI>kappa = inverse screening length (1/distance units)
+<LI>psi = surface potential (energy/charge units)
+</UL>
+<P>The last coefficient is optional. If not specified, the global
+yukawa/colloid cutoff is used.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed. A is an energy value mixed
+like a LJ epsilon. The default mix value is <I>geometric</I>. See the
+"pair_modify" command for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the COLLOID package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires that atoms be finite-size spheres with a
+diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
+command.
+</P>
+<P>Per-particle polydispersity is not yet supported by this pair style;
+per-type polydispersity is allowed. This means all particles of the
+same type must have the same diameter. Each type can have a different
+diameter.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Safran"></A>
+
+<P><B>(Safran)</B> Safran, Statistical Thermodynamics of Surfaces, Interfaces,
+And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
+</P>
+</HTML>
diff --git a/doc/doc2/pair_zbl.html b/doc/doc2/pair_zbl.html
new file mode 100644
index 000000000..ad0b94557
--- /dev/null
+++ b/doc/doc2/pair_zbl.html
@@ -0,0 +1,134 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style zbl command
+</H3>
+<H3>pair_style zbl/omp command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style zbl inner outer
+</PRE>
+<UL><LI>inner = distance where switching function begins
+<LI>outer = global cutoff for ZBL interaction
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style zbl 3.0 4.0
+pair_coeff * * 73.0
+pair_coeff 1 1 14.0
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>zbl</I> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
+repulsion for describing high-energy collisions between atoms.
+<A HREF = "#Ziegler">(Ziegler)</A>. It includes an additional switching function
+that ramps the energy, force, and curvature smoothly to zero
+between an inner and outer cutoff. The potential
+energy due to a pair of atoms at a distance r_ij is given by:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_zbl.jpg">
+</CENTER>
+<P>where e is the electron charge, epsilon_0 is the electrical
+permittivity of vacuum, and Z_i and Z_j are the nuclear charges of the
+two atoms. The switching function S(r) is identical to that used by
+<A HREF = "pair_gromacs.html">pair_style lj/gromacs</A>. Here, the inner and outer
+cutoff are the same for all pairs of atom types.
+</P>
+<P>The following coefficient must be defined for each pair of atom types
+via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
+or in the LAMMPS data file. Z can not be specified for two different
+atoms types. Therefore the lists of atom types I and atom types J
+must match.
+</P>
+<UL><LI>Z (multiples of proton charge, e.g. 13.0 for aluminum)
+</UL>
+<P>Although Z must be defined for all atom type pairs I,J, it is only
+stored for individual atom types, i.e. when I = J. Z is normally equal
+to the atomic number of the atom type.
+</P>
+<P>IMPORTANT NOTE: The numerical values of the exponential decay
+constants in the screening function depend on the unit of distance. In
+the above equation they are given for units of angstroms. LAMMPS will
+automatically convert these values to the distance unit of the
+specified LAMMPS <A HREF = "units.html">units</A> setting. The values of Z should
+always be given as multiples of a proton's charge, e.g. 29.0 for
+copper.
+</P>
+<HR>
+
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>Mixing is not relevant for this pair style, since as explained above,
+Z values are stored on a per-type basis, and both Zi and Zj are used
+explicitly in the ZBL formula.
+</P>
+<P>The ZBL pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option, since the ZBL interaction is already smoothed to 0.0 at
+the cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
+this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since there are no corrections for a potential that goes to
+0.0 at the cutoff.
+</P>
+<P>This pair style does not write information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands must be
+specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ziegler"></A>
+
+<P><B>(Ziegler)</B> J.F. Ziegler, J. P. Biersack and U. Littmark, "The
+Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
+</P>
+</HTML>
diff --git a/doc/doc2/partition.html b/doc/doc2/partition.html
new file mode 100644
index 000000000..483282333
--- /dev/null
+++ b/doc/doc2/partition.html
@@ -0,0 +1,78 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>partition command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>partition style N command ...
+</PRE>
+<UL><LI>style = <I>yes</I> or <I>no</I>
+<LI>N = partition number (see asterisk form below)
+<LI>command = any LAMMPS command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>partition yes 1 processors 4 10 6
+partition no 5 print "Active partition"
+partition yes *5 fix all nve
+partition yes 6* fix all nvt temp 1.0 1.0 0.1
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command invokes the specified command on a subset of the
+partitions of processors you have defined via the -partition
+command-line switch. See <A HREF = "Section_start.html#start_7">Section_start 6</A>
+for an explanation of the switch.
+</P>
+<P>Normally, every input script command in your script is invoked by
+every partition. This behavior can be modified by defining world- or
+universe-style <A HREF = "variable.html">variables</A> that have different values
+for each partition. This mechanism can be used to cause your script
+to jump to different input script files on different partitions, if
+such a variable is used in a <A HREF = "jump.html">jump</A> command.
+</P>
+<P>The "partition" command is another mechanism for having as input
+script operate differently on different partitions. It is basically a
+prefix on any LAMMPS command. The commmand will only be invoked on
+the partition(s) specified by the <I>style</I> and <I>N</I> arguments.
+</P>
+<P>If the <I>style</I> is <I>yes</I>, the command will be invoked on any partition
+which matches the <I>N</I> argument. If the <I>style</I> is <I>no</I> the command
+will be invoked on all the partitions which do not match the Np
+argument.
+</P>
+<P>Partitions are numbered from 1 to Np, where Np is the number of
+partitions specified by the <A HREF = "Section_start.html#start_7">-partition command-line
+switch</A>.
+</P>
+<P><I>N</I> can be specified in one of two ways. An explicit numeric value
+can be used, as in the 1st example above. Or a wild-card asterisk can
+be used to span a range of partition numbers. This takes the form "*"
+or "*n" or "n*" or "m*n". An asterisk with no numeric values means
+all partitions from 1 to Np. A leading asterisk means all partitions
+from 1 to n (inclusive). A trailing asterisk means all partitions
+from n to Np (inclusive). A middle asterisk means all partitions from
+m to n (inclusive).
+</P>
+<P>This command can be useful for the "run_style verlet/split" command
+which imposed requirements on how the <A HREF = "processors.html">processors</A>
+command lays out a 3d grid of processors in each of 2 partitions.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "run_style.html">run_style verlet/split</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/prd.html b/doc/doc2/prd.html
new file mode 100644
index 000000000..dbd74f8d3
--- /dev/null
+++ b/doc/doc2/prd.html
@@ -0,0 +1,339 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>prd command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
+</PRE>
+<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
+
+<LI>t_event = timestep interval between event checks
+
+<LI>n_dephase = number of velocity randomizations to perform in each dephase run
+
+<LI>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase
+
+<LI>t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated
+
+<LI>compute-ID = ID of the compute used for event detection
+
+<LI>random_seed = random # seed (positive integer)
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>min</I> or <I>temp</I> or <I>vel</I>
+
+<PRE> <I>min</I> values = etol ftol maxiter maxeval
+ etol = stopping tolerance for energy, used in quenching
+ ftol = stopping tolerance for force, used in quenching
+ maxiter = max iterations of minimize, used in quenching
+ maxeval = max number of force/energy evaluations, used in quenching
+ <I>temp</I> value = Tdephase
+ Tdephase = target temperature for velocity randomization, used in dephasing
+ <I>vel</I> values = loop dist
+ loop = <I>all</I> or <I>local</I> or <I>geom</I>, used in dephasing
+ dist = <I>uniform</I> or <I>gaussian</I>, used in dephasing
+ <I>time</I> value = <I>step</I> or <I>clock</I>
+ <I>step</I> = simulation runs for N timesteps on each replica (default)
+ <I>clock</I> = simulation runs for N timesteps across all replicas
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>prd 5000 100 10 10 100 1 54982
+prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Run a parallel replica dynamics (PRD) simulation using multiple
+replicas of a system. One or more replicas can be used. The total
+number of steps <I>N</I> to run can be interpreted in one of two ways; see
+discussion of the <I>time</I> keyword below.
+</P>
+<P>PRD is described in <A HREF = "#Voter">this paper</A> by Art Voter. It is a method
+for performing accelerated dynamics that is suitable for
+infrequent-event systems that obey first-order kinetics. A good
+overview of accelerated dynamics methods for such systems in given in
+<A HREF = "#Voter2">this review paper</A> from the same group. To quote from the
+paper: "The dynamical evolution is characterized by vibrational
+excursions within a potential basin, punctuated by occasional
+transitions between basins." The transition probability is
+characterized by p(t) = k*exp(-kt) where k is the rate constant.
+Running multiple replicas gives an effective enhancement in the
+timescale spanned by the multiple simulations, while waiting for an
+event to occur.
+</P>
+<P>Each replica runs on a partition of one or more processors. Processor
+partitions are defined at run-time using the -partition command-line
+switch; see <A HREF = "Section_start.html#start_7">Section_start 6</A> of the
+manual. Note that if you have MPI installed, you can run a
+multi-replica simulation with more replicas (partitions) than you have
+physical processors, e.g you can run a 10-replica simulation on one or
+two processors. For PRD, this makes little sense, since this offers
+no effective parallel speed-up in searching for infrequent events. See
+<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual for further
+discussion.
+</P>
+<P>When a PRD simulation is performed, it is assumed that each replica is
+running the same model, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of atoms, the interaction
+potentials, etc should be the same for every replica.
+</P>
+<P>A PRD run has several stages, which are repeated each time an "event"
+occurs in one of the replicas, as defined below. The logic for a PRD
+run is as follows:
+</P>
+<PRE>while (time remains):
+ dephase for n_dephase*t_dephase steps
+ until (event occurs on some replica):
+ run dynamics for t_event steps
+ quench
+ check for uncorrelated event on any replica
+ until (no correlated event occurs):
+ run dynamics for t_correlate steps
+ quench
+ check for correlated event on this replica
+ event replica shares state with all replicas
+</PRE>
+<P>Before this loop begins, the state of the system on replica 0 is
+shared with all replicas, so that all replicas begin from the same
+initial state. The first potential energy basin is identified by
+quenching (an energy minimization, see below) the initial state and
+storing the resulting coordinates for reference.
+</P>
+<P>In the first stage, dephasing is performed by each replica
+independently to eliminate correlations between replicas. This is
+done by choosing a random set of velocities, based on the
+<I>random_seed</I> that is specified, and running <I>t_dephase</I> timesteps of
+dynamics. This is repeated <I>n_dephase</I> times. At each of the
+<I>n_dephase</I> stages, if an event occurs during the <I>t_dephase</I> steps of
+dynamics for a particular replica, the replica repeats the stage until
+no event occurs.
+</P>
+<P>If the <I>temp</I> keyword is not specified, the target temperature for
+velocity randomization for each replica is the current temperature of
+that replica. Otherwise, it is the specified <I>Tdephase</I> temperature.
+The style of velocity randomization is controlled using the keyword
+<I>vel</I> with arguments that have the same meaning as their counterparts
+in the <A HREF = "velocity.html">velocity</A> command.
+</P>
+<P>In the second stage, each replica runs dynamics continuously, stopping
+every <I>t_event</I> steps to check if a transition event has occurred.
+This check is performed by quenching the system and comparing the
+resulting atom coordinates to the coordinates from the previous basin.
+The first time through the PRD loop, the "previous basin" is the set
+of quenched coordinates from the initial state of the system.
+</P>
+<P>A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the <A HREF = "min_style.html">min_style</A> command.
+Minimization parameters may be set via the
+<A HREF = "min_modify.html">min_modify</A> command and by the <I>min</I> keyword of the
+PRD command. The latter are the settings that would be used with the
+<A HREF = "minimize.html">minimize</A> command. Note that typically, you do not
+need to perform a highly-converged minimization to detect a transition
+event.
+</P>
+<P>The event check is performed by a compute with the specified
+<I>compute-ID</I>. Currently there is only one compute that works with the
+PRD commmand, which is the <A HREF = "compute_event_displace.html">compute
+event/displace</A> command. Other
+event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
+event/displace</A> checks whether any atom in
+the compute group has moved further than a specified threshold
+distance. If so, an "event" has occurred.
+</P>
+<P>In the third stage, the replica on which the event occurred (event
+replica) continues to run dynamics to search for correlated events.
+This is done by running dynamics for <I>t_correlate</I> steps, quenching
+every <I>t_event</I> steps, and checking if another event has occurred.
+</P>
+<P>The first time no correlated event occurs, the final state of the
+event replica is shared with all replicas, the new basin reference
+coordinates are updated with the quenched state, and the outer loop
+begins again. While the replica event is searching for correlated
+events, all the other replicas also run dynamics and event checking
+with the same schedule, but the final states are always overwritten by
+the state of the event replica.
+</P>
+<P>The outer loop of the pseudo-code above continues until <I>N</I> steps of
+dynamics have been performed. Note that <I>N</I> only includes the
+dynamics of stages 2 and 3, not the steps taken during dephasing or
+the minimization iterations of quenching. The specified <I>N</I> is
+interpreted in one of two ways, depending on the <I>time</I> keyword. If
+the <I>time</I> value is <I>step</I>, which is the default, then each replica
+runs for <I>N</I> timesteps. If the <I>time</I> value is <I>clock</I>, then the
+simulation runs until <I>N</I> aggregate timesteps across all replicas have
+elapsed. This aggregate time is the "clock" time defined below, which
+typically advances nearly M times faster than the timestepping on a
+single replica.
+</P>
+<HR>
+
+<P>Four kinds of output can be generated during a PRD run: event
+statistics, thermodynamic output by each replica, dump files, and
+restart files.
+</P>
+<P>When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file is
+limited to event statistics. Note that if a PRD run is performed on
+only a single replica then the event statistics will be intermixed
+with the usual thermodynamic output discussed below.
+</P>
+<P>The quantities printed each time an event occurs are the timestep, CPU
+time, clock, event number, a correlation flag, the number of
+coincident events, and the replica number of the chosen event.
+</P>
+<P>The timestep is the usual LAMMPS timestep, except that time does not
+advance during dephasing or quenches, but only during dynamics. Note
+that are two kinds of dynamics in the PRD loop listed above. The
+first is when all replicas are performing independent dynamics,
+waiting for an event to occur. The second is when correlated events
+are being searched for and only one replica is running dynamics.
+</P>
+<P>The CPU time is the total processor time since the start of the PRD
+run.
+</P>
+<P>The clock is the same as the timestep except that it advances by M
+steps every timestep during the first kind of dynamics when the M
+replicas are running independently. The clock advances by only 1 step
+per timestep during the second kind of dynamics, since only a single
+replica is checking for a correlated event. Thus "clock" time
+represents the aggregate time (in steps) that effectively elapses
+during a PRD simulation on M replicas. If most of the PRD run is
+spent in the second stage of the loop above, searching for infrequent
+events, then the clock will advance nearly M times faster than it
+would if a single replica was running. Note the clock time between
+events will be drawn from p(t).
+</P>
+<P>The event number is a counter that increments with each event, whether
+it is uncorrelated or correlated.
+</P>
+<P>The correlation flag will be 0 when an uncorrelated event occurs
+during the second stage of the loop listed above, i.e. when all
+replicas are running independently. The correlation flag will be 1
+when a correlated event occurs during the third stage of the loop
+listed above, i.e. when only one replica is running dynamics.
+</P>
+<P>When more than one replica detects an event at the end of the second
+stage, then one of them is chosen at random. The number of coincident
+events is the number of replicas that detected an event. Normally, we
+expect this value to be 1. If it is often greater than 1, then either
+the number of replicas is too large, or <I>t_event</I> is too large.
+</P>
+<P>The replica number is the ID of the replica (from 0 to M-1) that
+found the event.
+</P>
+<HR>
+
+<P>When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
+the PRD command, these contain the thermodynamic output for each
+replica. You will see short runs and minimizations corresponding to
+the dynamics and quench operations of the loop listed above. The
+timestep will be reset aprpopriately depending on whether the
+operation advances time or not.
+</P>
+<P>After the PRD command completes, timing statistics for the PRD run are
+printed in each replica's log file, giving a breakdown of how much CPU
+time was spent in each stage (dephasing, dynamics, quenching, etc).
+</P>
+<HR>
+
+<P>Any <A HREF = "dump.html">dump files</A> defined in the input script, will be
+written to during a PRD run at timesteps corresponding to both
+uncorrelated and correlated events. This means the the requested dump
+frequency in the <A HREF = "dump.html">dump</A> command is ignored. There will be
+one dump file (per dump command) created for all partitions.
+</P>
+<P>The atom coordinates of the dump snapshot are those of the minimum
+energy configuration resulting from quenching following a transition
+event. The timesteps written into the dump files correspond to the
+timestep at which the event occurred and NOT the clock. A dump
+snapshot corresponding to the initial minimum state used for event
+detection is written to the dump file at the beginning of each PRD
+run.
+</P>
+<HR>
+
+<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
+for all the partitions is generated, which allows a PRD run to be
+continued by a new input script in the usual manner.
+</P>
+<P>The restart file is generated at the end of the loop listed above. If
+no correlated events are found, this means it contains a snapshot of
+the system at time T + <I>t_correlate</I>, where T is the time at which the
+uncorrelated event occurred. If correlated events were found, then it
+contains a snapshot of the system at time T + <I>t_correlate</I>, where T
+is the time of the last correlated event.
+</P>
+<P>The restart frequency specified in the <A HREF = "restart.html">restart</A> command
+is interpreted differently when performing a PRD run. It does not
+mean the timestep interval between restart files. Instead it means an
+event interval for uncorrelated events. Thus a frequency of 1 means
+write a restart file every time an uncorrelated event occurs. A
+frequency of 10 means write a restart file every 10th uncorrelated
+event.
+</P>
+<P>When an input script reads a restart file from a previous PRD run, the
+new script can be run on a different number of replicas or processors.
+However, it is assumed that <I>t_correlate</I> in the new PRD command is
+the same as it was previously. If not, the calculation of the "clock"
+value for the first event in the new run will be slightly off.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><I>N</I> and <I>t_correlate</I> settings must be integer multiples of
+<I>t_event</I>.
+</P>
+<P>Runs restarted from restart file written during a PRD run will not
+produce identical results due to changes in the random numbers used
+for dephasing.
+</P>
+<P>This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform time-dependent operations. Examples
+include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
+dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
+<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
+<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
+<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
+<A HREF = "tad.html">tad</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
+geom gaussian, and time = step.
+</P>
+<HR>
+
+<A NAME = "Voter"></A>
+
+<P><B>(Voter)</B> Voter, Phys Rev B, 57, 13985 (1998).
+</P>
+<A NAME = "Voter2"></A>
+
+<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).
+</P>
+</HTML>
diff --git a/doc/doc2/print.html b/doc/doc2/print.html
new file mode 100644
index 000000000..e97b5e218
--- /dev/null
+++ b/doc/doc2/print.html
@@ -0,0 +1,86 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>print command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>print string keyword value
+</PRE>
+<UL><LI>string = text string to print, which may contain variables
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>file</I> or <I>append</I> or <I>screen</I>
+
+<PRE> <I>file</I> value = filename
+ <I>append</I> value = filename
+ <I>screen</I> value = <I>yes</I> or <I>no</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>print "Done with equilibration" file info.dat
+print Vol=$v append info.dat screen no
+print "The system volume is now $v"
+print 'The system volume is now $v'
+print """
+System volume = $v
+System temperature = $t
+"""
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Print a text string to the screen and logfile. The text string must
+be a single argument, so if it is one line but more than one word, it
+should be enclosed in single or double quotes. To generate multiple
+lines of output, the string can be enclosed in triple quotes, as in
+the last example above. If the text string contains variables, they
+will be evaluated and their current values printed.
+</P>
+<P>If the <I>file</I> or <I>append</I> keyword is used, a filename is specified to
+which the output will be written. If <I>file</I> is used, then the
+filename is overwritten if it already exists. If <I>append</I> is used,
+then the filename is appended to if it already exists, or created if
+it does not exist.
+</P>
+<P>If the <I>screen</I> keyword is used, output to the screen and logfile can
+be turned on or off as desired.
+</P>
+<P>If you want the print command to be executed multiple times (with
+changing variable values), there are 3 options. First, consider using
+the <A HREF = "fix_print.html">fix print</A> command, which will print a string
+periodically during a simulation. Second, the print command can be
+used as an argument to the <I>every</I> option of the <A HREF = "run.html">run</A>
+command. Third, the print command could appear in a section of the
+input script that is looped over (see the <A HREF = "jump.html">jump</A> and
+<A HREF = "next.html">next</A> commands).
+</P>
+<P>See the <A HREF = "variable.html">variable</A> command for a description of <I>equal</I>
+style variables which are typically the most useful ones to use with
+the print command. Equal-style variables can calculate formulas
+involving mathematical operations, atom properties, group properties,
+thermodynamic properties, global values calculated by a
+<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>, or references to other
+<A HREF = "variable.html">variables</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_print.html">fix print</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are no file output and screen = yes.
+</P>
+</HTML>
diff --git a/doc/doc2/processors.html b/doc/doc2/processors.html
new file mode 100644
index 000000000..d819aa4fb
--- /dev/null
+++ b/doc/doc2/processors.html
@@ -0,0 +1,351 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>processors command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>processors Px Py Pz keyword args ...
+</PRE>
+<UL><LI>Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain
+
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>grid</I> or <I>map</I> or <I>part</I> or <I>file</I>
+
+<PRE> <I>grid</I> arg = gstyle params ...
+ gstyle = <I>onelevel</I> or <I>twolevel</I> or <I>numa</I> or <I>custom</I>
+ onelevel params = none
+ twolevel params = Nc Cx Cy Cz
+ Nc = number of cores per node
+ Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
+ numa params = none
+ custom params = infile
+ infile = file containing grid layout
+ <I>map</I> arg = <I>cart</I> or <I>cart/reorder</I> or <I>xyz</I> or <I>xzy</I> or <I>yxz</I> or <I>yzx</I> or <I>zxy</I> or <I>zyx</I>
+ cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
+ cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
+ xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
+ <I>numa</I> arg = none
+ <I>part</I> args = Psend Precv cstyle
+ Psend = partition # (1 to Np) which will send its processor layout
+ Precv = partition # (1 to Np) which will recv the processor layout
+ cstyle = <I>multiple</I>
+ <I>multiple</I> = Psend grid will be multiple of Precv grid in each dimension
+ <I>file</I> arg = outfile
+ outfile = name of file to write 3d grid of processors to
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>processors * * 5
+processors 2 4 4
+processors * * 8 map xyz
+processors * * * grid numa
+processors * * * grid twolevel 4 * * 1
+processors 4 8 16 grid custom myfile
+processors * * * part 1 2 multiple
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Specify how processors are mapped as a regular 3d grid to the global
+simulation box. The mapping involves 2 steps. First if there are P
+processors it means choosing a factorization P = Px by Py by Pz so
+that there are Px processors in the x dimension, and similarly for the
+y and z dimensions. Second, the P processors are mapped to the
+regular 3d grid. The arguments to this command control each of these
+2 steps.
+</P>
+<P>The Px, Py, Pz parameters affect the factorization. Any of the 3
+parameters can be specified with an asterisk "*", which means LAMMPS
+will choose the number of processors in that dimension of the grid.
+It will do this based on the size and shape of the global simulation
+box so as to minimize the surface-to-volume ratio of each processor's
+sub-domain.
+</P>
+<P>Choosing explicit values for Px or Py or Pz can be used to override
+the default manner in which LAMMPS will create the regular 3d grid of
+processors, if it is known to be sub-optimal for a particular problem.
+E.g. a problem where the extent of atoms will change dramatically in a
+particular dimension over the course of the simulation.
+</P>
+<P>The product of Px, Py, Pz must equal P, the total # of processors
+LAMMPS is running on. For a <A HREF = "dimension.html">2d simulation</A>, Pz must
+equal 1.
+</P>
+<P>Note that if you run on a prime number of processors P, then a grid
+such as 1 x P x 1 will be required, which may incur extra
+communication costs due to the high surface area of each processor's
+sub-domain.
+</P>
+<P>Also note that if multiple partitions are being used then P is the
+number of processors in this partition; see <A HREF = "Section_start.html#start_7">this
+section</A> for an explanation of the
+-partition command-line switch. Also note that you can prefix the
+processors command with the <A HREF = "partition.html">partition</A> command to
+easily specify different Px,Py,Pz values for different partitions.
+</P>
+<P>You can use the <A HREF = "partition.html">partition</A> command to specify
+different processor grids for different partitions, e.g.
+</P>
+<PRE>partition yes 1 processors 4 4 4
+partition yes 2 processors 2 3 2
+</PRE>
+<P>IMPORTANT NOTE: This command only affects the initial regular 3d grid
+created when the simulation box is first specified via a
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> command. Or if the simulation box is
+re-created via the <A HREF = "replicate.html">replicate</A> command. The same
+regular grid is initially created, regardless of which
+<A HREF = "comm_style.html">comm_style</A> command is in effect.
+</P>
+<P>If load-balancing is never invoked via the <A HREF = "balance.html">balance</A> or
+<A HREF = "fix_balance.html">fix balance</A> commands, then the initial regular grid
+will persist for all simulations. If balancing is performed, some of
+the methods invoked by those commands retain the logical toplogy of
+the initial 3d grid, and the mapping of processors to the grid
+specified by the processors command. However the grid spacings in
+different dimensions may change, so that processors own sub-domains of
+different sizes. If the <A HREF = "comm_style.html">comm_style tiled</A> command is
+used, methods invoked by the balancing commands may discard the 3d
+grid of processors and tile the simulation domain with sub-domains of
+different sizes and shapes which no longer have a logical 3d
+connectivity. If that occurs, all the information specified by the
+processors command is ignored.
+</P>
+<HR>
+
+<P>The <I>grid</I> keyword affects the factorization of P into Px,Py,Pz and it
+can also affect how the P processor IDs are mapped to the 3d grid of
+processors.
+</P>
+<P>The <I>onelevel</I> style creates a 3d grid that is compatible with the
+Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of
+each processor's sub-domain, as described above. The mapping of
+processors to the grid is determined by the <I>map</I> keyword setting.
+</P>
+<P>The <I>twolevel</I> style can be used on machines with multicore nodes to
+minimize off-node communication. It insures that contiguous
+sub-sections of the 3d grid are assigned to all the cores of a node.
+For example if <I>Nc</I> is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of
+the 3d grid will correspond to the cores of each node. This affects
+both the factorization and mapping steps.
+</P>
+<P>The <I>Cx</I>, <I>Cy</I>, <I>Cz</I> settings are similar to the <I>Px</I>, <I>Py</I>, <I>Pz</I>
+settings, only their product should equal <I>Nc</I>. Any of the 3
+parameters can be specified with an asterisk "*", which means LAMMPS
+will choose the number of cores in that dimension of the node's
+sub-grid. As with Px,Py,Pz, it will do this based on the size and
+shape of the global simulation box so as to minimize the
+surface-to-volume ratio of each processor's sub-domain.
+</P>
+<P>IMPORTANT NOTE: For the <I>twolevel</I> style to work correctly, it
+assumes the MPI ranks of processors LAMMPS is running on are ordered
+by core and then by node. E.g. if you are running on 2 quad-core
+nodes, for a total of 8 processors, then it assumes processors 0,1,2,3
+are on node 1, and processors 4,5,6,7 are on node 2. This is the
+default rank ordering for most MPI implementations, but some MPIs
+provide options for this ordering, e.g. via environment variable
+settings.
+</P>
+<P>The <I>numa</I> style operates similar to the <I>twolevel</I> keyword except
+that it auto-detects which cores are running on which nodes.
+Currently, it does this in only 2 levels, but it may be extended in
+the future to account for socket topology and other non-uniform memory
+access (NUMA) costs. It also uses a different algorithm than the
+<I>twolevel</I> keyword for doing the two-level factorization of the
+simulation box into a 3d processor grid to minimize off-node
+communication, and it does its own MPI-based mapping of nodes and
+cores to the regular 3d grid. Thus it may produce a different layout
+of the processors than the <I>twolevel</I> options.
+</P>
+<P>The <I>numa</I> style will give an error if the number of MPI processes is
+not divisible by the number of cores used per node, or any of the Px
+or Py of Pz values is greater than 1.
+</P>
+<P>IMPORTANT NOTE: Unlike the <I>twolevel</I> style, the <I>numa</I> style does not
+require any particular ordering of MPI ranks i norder to work
+correctly. This is because it auto-detects which processes are
+running on which nodes.
+</P>
+<P>The <I>custom</I> style uses the file <I>infile</I> to define both the 3d
+factorization and the mapping of processors to the grid.
+</P>
+<P>The file should have the following format. Any number of initial
+blank or comment lines (starting with a "#" character) can be present.
+The first non-blank, non-comment line should have
+3 values:
+</P>
+<PRE>Px Py Py
+</PRE>
+<P>These must be compatible with the total number of processors
+and the Px, Py, Pz settings of the processors commmand.
+</P>
+<P>This line should be immediately followed by
+P = Px*Py*Pz lines of the form:
+</P>
+<PRE>ID I J K
+</PRE>
+<P>where ID is a processor ID (from 0 to P-1) and I,J,K are the
+processors location in the 3d grid. I must be a number from 1 to Px
+(inclusive) and similarly for J and K. The P lines can be listed in
+any order, but no processor ID should appear more than once.
+</P>
+<HR>
+
+<P>The <I>map</I> keyword affects how the P processor IDs (from 0 to P-1) are
+mapped to the 3d grid of processors. It is only used by the
+<I>onelevel</I> and <I>twolevel</I> grid settings.
+</P>
+<P>The <I>cart</I> style uses the family of MPI Cartesian functions to perform
+the mapping, namely MPI_Cart_create(), MPI_Cart_get(),
+MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the
+MPI_Cart_create() function with its reorder flag = 0, so that MPI is
+not free to reorder the processors.
+</P>
+<P>The <I>cart/reorder</I> style does the same thing as the <I>cart</I> style
+except it sets the reorder flag to 1, so that MPI can reorder
+processors if it desires.
+</P>
+<P>The <I>xyz</I>, <I>xzy</I>, <I>yxz</I>, <I>yzx</I>, <I>zxy</I>, and <I>zyx</I> styles are all
+similar. If the style is IJK, then it maps the P processors to the
+grid so that the processor ID in the I direction varies fastest, the
+processor ID in the J direction varies next fastest, and the processor
+ID in the K direction varies slowest. For example, if you select
+style <I>xyz</I> and you have a 2x2x2 grid of 8 processors, the assignments
+of the 8 octants of the simulation domain will be:
+</P>
+<PRE>proc 0 = lo x, lo y, lo z octant
+proc 1 = hi x, lo y, lo z octant
+proc 2 = lo x, hi y, lo z octant
+proc 3 = hi x, hi y, lo z octant
+proc 4 = lo x, lo y, hi z octant
+proc 5 = hi x, lo y, hi z octant
+proc 6 = lo x, hi y, hi z octant
+proc 7 = hi x, hi y, hi z octant
+</PRE>
+<P>Note that, in principle, an MPI implementation on a particular machine
+should be aware of both the machine's network topology and the
+specific subset of processors and nodes that were assigned to your
+simulation. Thus its MPI_Cart calls can optimize the assignment of
+MPI processes to the 3d grid to minimize communication costs. In
+practice, however, few if any MPI implementations actually do this.
+So it is likely that the <I>cart</I> and <I>cart/reorder</I> styles simply give
+the same result as one of the IJK styles.
+</P>
+<P>Also note, that for the <I>twolevel</I> grid style, the <I>map</I> setting is
+used to first map the nodes to the 3d grid, then again to the cores
+within each node. For the latter step, the <I>cart</I> and <I>cart/reorder</I>
+styles are not supported, so an <I>xyz</I> style is used in their place.
+</P>
+<HR>
+
+<P>The <I>part</I> keyword affects the factorization of P into Px,Py,Pz.
+</P>
+<P>It can be useful when running in multi-partition mode, e.g. with the
+<A HREF = "run_style.html">run_style verlet/split</A> command. It specifies a
+dependency bewteen a sending partition <I>Psend</I> and a receiving
+partition <I>Precv</I> which is enforced when each is setting up their own
+mapping of their processors to the simulation box. Each of <I>Psend</I>
+and <I>Precv</I> must be integers from 1 to Np, where Np is the number of
+partitions you have defined via the <A HREF = "Section_start.html#start_7">-partition command-line
+switch</A>.
+</P>
+<P>A "dependency" means that the sending partition will create its
+regular 3d grid as Px by Py by Pz and after it has done this, it will
+send the Px,Py,Pz values to the receiving partition. The receiving
+partition will wait to receive these values before creating its own
+regular 3d grid and will use the sender's Px,Py,Pz values as a
+constraint. The nature of the constraint is determined by the
+<I>cstyle</I> argument.
+</P>
+<P>For a <I>cstyle</I> of <I>multiple</I>, each dimension of the sender's processor
+grid is required to be an integer multiple of the corresponding
+dimension in the receiver's processor grid. This is a requirement of
+the <A HREF = "run_style.html">run_style verlet/split</A> command.
+</P>
+<P>For example, assume the sending partition creates a 4x6x10 grid = 240
+processor grid. If the receiving partition is running on 80
+processors, it could create a 4x2x10 grid, but it will not create a
+2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of
+4.
+</P>
+<P>IMPORTANT NOTE: If you use the <A HREF = "partition.html">partition</A> command to
+invoke different "processsors" commands on different partitions, and
+you also use the <I>part</I> keyword, then you must insure that both the
+sending and receiving partitions invoke the "processors" command that
+connects the 2 partitions via the <I>part</I> keyword. LAMMPS cannot
+easily check for this, but your simulation will likely hang in its
+setup phase if this error has been made.
+</P>
+<HR>
+
+<P>The <I>file</I> keyword writes the mapping of the factorization of P
+processors and their mapping to the 3d grid to the specified file
+<I>outfile</I>. This is useful to check that you assigned physical
+processors in the manner you desired, which can be tricky to figure
+out, especially when running on multiple partitions or on, a multicore
+machine or when the processor ranks were reordered by use of the
+<A HREF = "Section_start.html#start_7">-reorder command-line switch</A> or due to
+use of MPI-specific launch options such as a config file.
+</P>
+<P>If you have multiple partitions you should insure that each one writes
+to a different file, e.g. using a <A HREF = "variable.html">world-style variable</A>
+for the filename. The file has a self-explanatory header, followed by
+one-line per processor in this format:
+</P>
+<P>world-ID universe-ID original-ID: I J K: name
+</P>
+<P>The IDs are the processor's rank in this simulation (the world), the
+universe (of multiple simulations), and the original MPI communicator
+used to instantiate LAMMPS, respectively. The world and universe IDs
+will only be different if you are running on more than one partition;
+see the <A HREF = "Section_start.html#start_7">-partition command-line switch</A>.
+The universe and original IDs will only be different if you used the
+<A HREF = "Section_start.html#start_7">-reorder command-line switch</A> to reorder
+the processors differently than their rank in the original
+communicator LAMMPS was instantiated with.
+</P>
+<P>I,J,K are the indices of the processor in the regular 3d grid, each
+from 1 to Nd, where Nd is the number of processors in that dimension
+of the grid.
+</P>
+<P>The <I>name</I> is what is returned by a call to MPI_Get_processor_name()
+and should represent an identifier relevant to the physical processors
+in your machine. Note that depending on the MPI implementation,
+multiple cores can have the same <I>name</I>.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
+It can be used before a restart file is read to change the 3d
+processor grid from what is specified in the restart file.
+</P>
+<P>The <I>grid numa</I> keyword only currently works with the <I>map cart</I>
+option.
+</P>
+<P>The <I>part</I> keyword (for the receiving partition) only works with the
+<I>grid onelevel</I> or <I>grid twolevel</I> options.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "partition.html">partition</A>, <A HREF = "Section_start.html#start_7">-reorder command-line switch</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
+cart.
+</P>
+</HTML>
diff --git a/doc/doc2/python.html b/doc/doc2/python.html
new file mode 100644
index 000000000..02193dd77
--- /dev/null
+++ b/doc/doc2/python.html
@@ -0,0 +1,490 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>python command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>python func keyword args ...
+</PRE>
+<UL><LI>func = name of Python function
+
+<LI>one or more keyword/args pairs must be appended
+
+<PRE>keyword = <I>invoke</I> or <I>input</I> or <I>return</I> or <I>format</I> or <I>file</I> or <I>here</I> or <I>exists</I>
+ <I>invoke</I> arg = none = invoke the previously defined Python function
+ <I>input</I> args = N i1 i2 ... iN
+ N = # of inputs to function
+ i1,...,iN = value, SELF, or LAMMPS variable name
+ value = integer number, floating point number, or string
+ SELF = reference to LAMMPS itself which can be accessed by Python function
+ variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
+ <I>return</I> arg = varReturn
+ varReturn = v_name = LAMMPS variable name which return value of function will be assigned to
+ <I>format</I> arg = fstring with M characters
+ M = N if no return value, where N = # of inputs
+ M = N+1 if there is a return value
+ fstring = each character (i,f,s,p) corresponds in order to an input or return value
+ 'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+ <I>file</I> arg = filename
+ filename = file of Python code, which defines func
+ <I>here</I> arg = inline
+ inline = one or more lines of Python code which defines func
+ must be a single argument, typically enclosed between triple quotes
+ <I>exists</I> arg = none = Python code has been loaded by previous python command
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>python pForce input 2 v_x 20.0 return v_f format fff file force.py
+python pForce invoke
+</PRE>
+<PRE>python factorial input 1 myN return v_fac format ii here """
+def factorial(n):
+ if n == 1: return n
+ return n * factorial(n-1)
+ """
+</PRE>
+<PRE>python loop input 1 SELF return v_value format -f here """
+def loop(lmpptr,N,cut0):
+ from lammps import lammps
+ lmp = lammps(ptr=lmpptr)
+</PRE>
+<PRE> # loop N times, increasing cutoff each time
+</PRE>
+<PRE> for i in range(N):
+ cut = cut0 + i*0.1
+ lmp.set_variable("cut",cut) # set a variable in LAMMPS
+ lmp.command("pair_style lj/cut $<I>cut</I>") # LAMMPS commands
+ lmp.command("pair_coeff * * 1.0 1.0")
+ lmp.command("run 100")
+ """
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>IMPORTANT NOTE: It is not currently possible to use the
+<A HREF = "python.html">python</A> command described in this section with Python 3,
+only with Python 2. The C API changed from Python 2 to 3 and the
+LAMMPS code is not compatible with both.
+</P>
+<P>Define a Python function or execute a previously defined function.
+Arguments, including LAMMPS variables, can be passed to the function
+from the LAMMPS input script and a value returned by the Python
+function to a LAMMPS variable. The Python code for the function can
+be included directly in the input script or in a separate Python file.
+The function can be standard Python code or it can make "callbacks" to
+LAMMPS through its library interface to query or set internal values
+within LAMMPS. This is a powerful mechanism for performing complex
+operations in a LAMMPS input script that are not possible with the
+simple input script and variable syntax which LAMMPS defines. Thus
+your input script can operate more like a true programming language.
+</P>
+<P>Use of this command requires building LAMMPS with the PYTHON package
+which links to the Python library so that the Python interpreter is
+embedded in LAMMPS. More details about this process are given below.
+</P>
+<P>There are two ways to invoke a Python function once it has been
+defined. One is using the <I>invoke</I> keyword. The other is to assign
+the function to a <A HREF = "variable.html">python-style variable</A> defined in
+your input script. Whenever the variable is evaluated, it will
+execute the Python function to assign a value to the variable. Note
+that variables can be evaluated in many different ways within LAMMPS.
+They can be substituted for directly in an input script. Or they can
+be passed to various commands as arguments, so that the variable is
+evaluated during a simulation run.
+</P>
+<P>A broader overview of how Python can be used with LAMMPS is
+given in <A HREF = "Section_python.html">Section python</A>. There is an
+examples/python directory which illustrates use of the python
+command.
+</P>
+<HR>
+
+<P>The <I>func</I> setting specifies the name of the Python function. The
+code for the function is defined using the <I>file</I> or <I>here</I> keywords
+as explained below.
+</P>
+<P>If the <I>invoke</I> keyword is used, no other keywords can be used, and a
+previous python command must have defined the Python function
+referenced by this command. This invokes the Python function with the
+previously defined arguments and return value processed as explained
+below. You can invoke the function as many times as you wish in your
+input script.
+</P>
+<P>The <I>input</I> keyword defines how many arguments <I>N</I> the Python function
+expects. If it takes no arguments, then the <I>input</I> keyword should
+not be used. Each argument can be specified directly as a value,
+e.g. 6 or 3.14159 or abc (a string of characters). The type of each
+argument is specified by the <I>format</I> keyword as explained below, so
+that Python will know how to interpret the value. If the word SELF is
+used for an argument it has a special meaning. A pointer is passed to
+the Python function which it converts into a reference to LAMMPS
+itself. This enables the function to call back to LAMMPS through its
+library interface as explained below. This allows the Python function
+to query or set values internal to LAMMPS which can affect the
+subsequent execution of the input script. A LAMMPS variable can also
+be used as an argument, specified as v_name, where "name" is the name
+of the variable. Any style of LAMMPS variable can be used, as defined
+by the <A HREF = "variable.html">variable</A> command. Each time the Python
+function is invoked, the LAMMPS variable is evaluated and its value is
+passed to the Python function.
+</P>
+<P>The <I>return</I> keyword is only needed if the Python function returns a
+value. The specified <I>varReturn</I> must be of the form v_name, where
+"name" is the name of a python-style LAMMPS variable, defined by the
+<A HREF = "variable.html">variable</A> command. The Python function can return a
+numeric or string value, as specified by the <I>format</I> keyword.
+</P>
+<P>As explained on the <A HREF = "variable.html">variable</A> doc page, the definition
+of a python-style variable associates a Python function name with the
+variable. This must match the <I>func</I> setting for this command. For
+exampe these two commands would be self-consistent:
+</P>
+<PRE>variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+</PRE>
+<P>The two commands can appear in either order in the input script so
+long as both are specified before the Python function is invoked for
+the first time.
+</P>
+<P>The <I>format</I> keyword must be used if the <I>input</I> or <I>return</I> keyword
+is used. It defines an <I>fstring</I> with M characters, where M = sum of
+number of inputs and outputs. The order of characters corresponds to
+the N inputs, followed by the return value (if it exists). Each
+character must be one of the following: "i" for integer, "f" for
+floating point, "s" for string, or "p" for SELF. Each character
+defines the type of the corresponding input or output value of the
+Python function and affects the type conversion that is performed
+internally as data is passed back and forth between LAMMPS and Python.
+Note that it is permissible to use a <A HREF = "variable.html">python-style
+variable</A> in a LAMMPS command that allows for an
+equal-style variable as an argument, but only if the output of the
+Python function is flagged as a numeric value ("i" or "f") via the
+<I>format</I> keyword.
+</P>
+<P>Either the <I>file</I>, <I>here</I>, or <I>exists</I> keyword must be used, but only
+one of them. These keywords specify what Python code to load into the
+Python interpreter. The <I>file</I> keyword gives the name of a file,
+which should end with a ".py" suffix, which contains Python code. The
+code will be immediately loaded into and run in the "main" module of
+the Python interpreter. Note that Python code which contains a
+function definition does not "execute" the function when it is run; it
+simply defines the function so that it can be invoked later.
+</P>
+<P>The <I>here</I> keyword does the same thing, except that the Python code
+follows as a single argument to the <I>here</I> keyword. This can be done
+using triple quotes as delimiters, as in the examples above. This
+allows Python code to be listed verbatim in your input script, with
+proper indentation, blank lines, and comments, as desired. See
+<A HREF = "Section_commands.html#cmd_2">Section 3.2</A>, for an explanation of how
+triple quotes can be used as part of input script syntax.
+</P>
+<P>The <I>exists</I> keyword takes no argument. It means that Python code
+containing the required Python function defined by the <I>func</I> setting,
+is assumed to have been previously loaded by another python command.
+</P>
+<P>Note that the Python code that is loaded and run must contain a
+function with the specified <I>func</I> name. To operate properly when
+later invoked, the the function code must match the <I>input</I> and
+<I>return</I> and <I>format</I> keywords specified by the python command.
+Otherwise Python will generate an error.
+</P>
+<HR>
+
+<P>This section describes how Python code can be written to work with
+LAMMPS.
+</P>
+<P>Whether you load Python code from a file or directly from your input
+script, via the <I>file</I> and <I>here</I> keywords, the code can be identical.
+It must be indented properly as Python requires. It can contain
+comments or blank lines. If the code is in your input script, it
+cannot however contain triple-quoted Python strings, since that will
+conflict with the triple-quote parsing that the LAMMPS input script
+performs.
+</P>
+<P>All the Python code you specify via one or more python commands is
+loaded into the Python "main" module, i.e. __main__. The code can
+define global variables or statements that are outside of function
+definitions. It can contain multiple functions, only one of which
+matches the <I>func</I> setting in the python command. This means you can
+use the <I>file</I> keyword once to load several functions, and the
+<I>exists</I> keyword thereafter in subsequent python commands to access
+the other functions previously loaded.
+</P>
+<P>A Python function you define (or more generally, the code you load)
+can import other Python modules or classes, it can make calls to other
+system functions or functions you define, and it can access or modify
+global variables (in the "main" module) which will persist between
+successive function calls. The latter can be useful, for example, to
+prevent a function from being invoke multiple times per timestep by
+different commands in a LAMMPS input script that access the returned
+python-style variable associated with the function. For example,
+consider this function loaded with two global variables defined
+outside the function:
+</P>
+<PRE>nsteplast = -1
+nvaluelast = 0
+</PRE>
+<PRE>def expensive(nstep):
+ global nsteplast,nvaluelast
+ if nstep == nsteplast: return nvaluelast
+ nsteplast = nstep
+ # perform complicated calculation
+ nvalue = ...
+ nvaluelast = nvalue
+ return nvalue
+</PRE>
+<P>Nsteplast stores the previous timestep the function was invoked
+(passed as an argument to the function). Nvaluelast stores the return
+value computed on the last function invocation. If the function is
+invoked again on the same timestep, the previous value is simply
+returned, without re-computing it. The "global" statement inside the
+Python function allows it to overwrite the global variables.
+</P>
+<P>Note that if you load Python code multiple times (via multiple python
+commands), you can overwrite previously loaded variables and functions
+if you are not careful. E.g. if the code above were loaded twice, the
+global variables would be re-initialized, which might not be what you
+want. Likewise, if a function with the same name exists in two chunks
+of Python code you load, the function loaded second will override the
+function loaded first.
+</P>
+<P>It's important to realize that if you are running LAMMPS in parallel,
+each MPI task will load the Python interpreter and execute a local
+copy of the Python function(s) you define. There is no connection
+between the Python interpreters running on different processors.
+This implies three important things.
+</P>
+<P>First, if you put a print statement in your Python function, you will
+see P copies of the output, when running on P processors. If the
+prints occur at (nearly) the same time, the P copies of the output may
+be mixed together. Welcome to the world of parallel programming and
+debugging.
+</P>
+<P>Second, if your Python code loads modules that are not pre-loaded by
+the Python library, then it will load the module from disk. This may
+be a bottleneck if 1000s of processors try to load a module at the
+same time. On some large supercomputers, loading of modules from disk
+by Python may be disabled. In this case you would need to pre-build a
+Python library that has the required modules pre-loaded and link
+LAMMPS with that library.
+</P>
+<P>Third, if your Python code calls back to LAMMPS (discussed in the
+next section) and causes LAMMPS to perform an MPI operation requires
+global communication (e.g. via MPI_Allreduce), such as computing the
+global temperature of the system, then you must insure all your Python
+functions (running independently on different processors) call back to
+LAMMPS. Otherwise the code may hang.
+</P>
+<HR>
+
+<P>Your Python function can "call back" to LAMMPS through its
+library interface, if you use the SELF input to pass Python
+a pointer to LAMMPS. The mechanism for doing this in your
+Python function is as follows:
+</P>
+<PRE>def foo(lmpptr,...):
+ from lammps import lammps
+ lmp = lammps(ptr=lmpptr)
+ lmp.command('print "Hello from inside Python"')
+ ...
+</PRE>
+<P>The function definition must include a variable (lmpptr in this case)
+which corresponds to SELF in the python command. The first line of
+the function imports the Python module lammps.py in the python dir of
+the distribution. The second line creates a Python object "lmp" which
+wraps the instance of LAMMPS that called the function. The
+"ptr=lmpptr" argument is what makes that happen. The thrid line
+invokes the command() function in the LAMMPS library interface. It
+takes a single string argument which is a LAMMPS input script command
+for LAMMPS to execute, the same as if it appeared in your input
+script. In this case, LAMMPS should output
+</P>
+<PRE>Hello from inside Python
+</PRE>
+<P>to the screen and log file. Note that since the LAMMPS print command
+itself takes a string in quotes as its argument, the Python string
+must be delimited with a different style of quotes.
+</P>
+<P><A HREF = "Section_python.html#py_7">Section 11.7</A> describes the syntax for how
+Python wraps the various functions included in the LAMMPS library
+interface.
+</P>
+<P>A more interesting example is in the examples/python/in.python script
+which loads and runs the following function from examples/python/funcs.py:
+</P>
+<PRE>def loop(N,cut0,thresh,lmpptr):
+ print "LOOP ARGS",N,cut0,thresh,lmpptr
+ from lammps import lammps
+ lmp = lammps(ptr=lmpptr)
+ natoms = lmp.get_natoms()
+</PRE>
+<PRE> for i in range(N):
+ cut = cut0 + i*0.1
+</PRE>
+<PRE> lmp.set_variable("cut",cut) # set a variable in LAMMPS
+ lmp.command("pair_style lj/cut $<I>cut</I>") # LAMMPS command
+ #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
+</PRE>
+<PRE> lmp.command("pair_coeff * * 1.0 1.0") # ditto
+ lmp.command("run 10") # ditto
+ pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
+ print "PE",pe/natoms,thresh
+ if pe/natoms < thresh: return
+</PRE>
+<P>with these input script commands:
+</P>
+<PRE>python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
+python loop invoke
+</PRE>
+<P>This has the effect of looping over a series of 10 short runs (10
+timesteps each) where the pair style cutoff is increased from a value
+of 1.0 in distance units, in increments of 0.1. The looping stops
+when the per-atom potential energy falls below a threshhold of -4.0 in
+energy units. More generally, Python can be used to implement a loop
+with complex logic, much more so than can be created using the LAMMPS
+<A HREF = "jump.html">jump</A> and <A HREF = "if.html">if</A> commands.
+</P>
+<P>Several LAMMPS library functions are called from the loop function.
+Get_natoms() returns the number of atoms in the simulation, so that it
+can be used to normalize the potential energy that is returned by
+extract_compute() for the "thermo_pe" compute that is defined by
+default for LAMMPS thermodynamic output. Set_variable() sets the
+value of a string variable defined in LAMMPS. This library function
+is a useful way for a Python function to return multiple values to
+LAMMPS, more than the single value that can be passed back via a
+return statement. This cutoff value in the "cut" variable is then
+substituted (by LAMMPS) in the pair_style command that is executed
+next. Alternatively, the "LAMMPS command option" line could be used
+in place of the 2 preceeding lines, to have Python insert the value
+into the LAMMPS command string.
+</P>
+<P>IMPORTANT NOTE: When using the callback mechanism just described,
+recognize that there are some operations you should not attempt
+because LAMMPS cannot execute them correctly. If the Python function
+is invoked between runs in the LAMMPS input script, then it should be
+OK to invoke any LAMMPS input script command via the library interface
+command() or file() functions, so long as the command would work if it
+were executed in the LAMMPS input script directly at the same point.
+</P>
+<P>However, a Python function can also be invoked during a run, whenever
+an associated LAMMPS variable it is assigned to is evaluted. If the
+variable is an input argument to another LAMMPS command (e.g. <A HREF = "fix_setforce.html">fix
+setforce</A>), then the Python function will be invoked
+inside the class for that command, in one of its methods that is
+invoked in the middle of a timestep. You cannot execute arbitrary
+input script commands from the Python function (again, via the
+command() or file() functions) at that point in the run and expect it
+to work. Other library functions such as those that invoke computes
+or other variables may have hidden side effects as well. In these
+cases, LAMMPS has no simple way to check that something illogical is
+being attempted.
+</P>
+<HR>
+
+<P>If you run Python code directly on your workstation, either
+interactively or by using Python to launch a Python script stored in a
+file, and your code has an error, you will typically see informative
+error messages. That is not the case when you run Python code from
+LAMMPS using an embedded Python interpreter. The code will typically
+fail silently. LAMMPS will catch some errors but cannot tell you
+where in the Python code the problem occurred. For example, if the
+Python code cannot be loaded and run because it has syntax or other
+logic errors, you may get an error from Python pointing to the
+offending line, or you may get one of these generic errors from
+LAMMPS:
+</P>
+<PRE>Could not process Python file
+Could not process Python string
+</PRE>
+<P>When the Python function is invoked, if it does not return properly,
+you will typically get this generic error from LAMMPS:
+</P>
+<PRE>Python function evaluation failed
+</PRE>
+<P>Here are three suggestions for debugging your Python code while
+running it under LAMMPS.
+</P>
+<P>First, don't run it under LAMMPS, at least to start with! Debug it
+using plain Python. Load and invoke your function, pass it arguments,
+check return values, etc.
+</P>
+<P>Second, add Python print statements to the function to check how far
+it gets and intermediate values it calculates. See the discussion
+above about printing from Python when running in parallel.
+</P>
+<P>Third, use Python exception handling. For example, say this statement
+in your Python function is failing, because you have not initialized the
+variable foo:
+</P>
+<PRE>foo += 1
+</PRE>
+<P>If you put one (or more) statements inside a "try" statement,
+like this:
+</P>
+<PRE>import exceptions
+print "Inside simple function"
+try:
+ foo += 1 # one or more statements here
+except Exception, e:
+ print "FOO error:",e
+</PRE>
+<P>then you will get this message printed to the screen:
+</P>
+<PRE>FOO error: local variable 'foo' referenced before assignment
+</PRE>
+<P>If there is no error in the try statements, then nothing is printed.
+Either way the function continues on (unless you put a return or
+sys.exit() in the except clause).
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command is part of the PYTHON package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>Building LAMMPS with the PYTHON package will link LAMMPS with the
+Python library on your system. Settings to enable this are in the
+lib/python/Makefile.lammps file. See the lib/python/README file for
+information on those settings.
+</P>
+<P>If you use Python code which calls back to LAMMPS, via the SELF input
+argument explained above, there is an extra step required when
+building LAMMPS. LAMMPS must also be built as a shared library and
+your Python function must be able to to load the Python module in
+python/lammps.py that wraps the LAMMPS library interface. These are
+the same steps required to use Python by itself to wrap LAMMPS.
+Details on these steps are explained in <A HREF = "Section.python.html">Section
+python</A>. Note that it is important that the
+stand-alone LAMMPS executable and the LAMMPS shared library be
+consistent (built from the same source code files) in order for this
+to work. If the two have been built at different times using
+different source files, problems may occur.
+</P>
+<P>As described above, you can use the python command to invoke a Python
+function which calls back to LAMMPS through its Python-wrapped library
+interface. However you cannot do the opposite. I.e. you cannot call
+LAMMPS from Python and invoke the python command to "callback" to
+Python and execute a Python function. LAMMPS will generate an error
+if you try to do that. Note that we think there actually should be a
+way to do that, but haven't yet been able to figure out how to do it
+successfully.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/quit.html b/doc/doc2/quit.html
new file mode 100644
index 000000000..38aadaed6
--- /dev/null
+++ b/doc/doc2/quit.html
@@ -0,0 +1,42 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>quit command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>quit
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>quit
+if "$n > 10000" then quit
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command causes LAMMPS to exit, after shutting down all
+output cleanly.
+</P>
+<P>It can be used as a debug statement in an input script, to terminate
+the script at some intermediate point.
+</P>
+<P>It can also be used as an invoked command inside the
+"then" or "else" portion of an <A HREF = "if.html">if</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "if.html">if</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/read_data.html b/doc/doc2/read_data.html
new file mode 100644
index 000000000..cf535e366
--- /dev/null
+++ b/doc/doc2/read_data.html
@@ -0,0 +1,1231 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>read_data command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>read_data file keyword args ...
+</PRE>
+<UL><LI>file = name of data file to read in
+
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>add</I> or <I>offset</I> or <I>shift</I> or <I>extra/atom/types</I> or <I>extra/bond/types</I> or <I>extra/angle/types</I> or <I>extra/dihedral/types</I> or <I>extra/improper/types</I> or <I>group</I> or <I>fix</I>
+
+<PRE> <I>add</I> arg = <I>append</I> or <I>Nstart</I> or <I>merge</I>
+ append = add new atoms with IDs appended to current IDs
+ Nstart = add new atoms with IDs starting with Nstart
+ merge = add new atoms with their IDs unchanged
+ <I>offset</I> args = toff boff aoff doff ioff
+ toff = offset to add to atom types
+ boff = offset to add to bond types
+ aoff = offset to add to angle types
+ doff = offset to add to dihedral types
+ ioff = offset to add to improper types
+ <I>shift</I> args = Sx Sy Sz
+ Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
+ <I>extra/atom/types</I> arg = # of extra atom types
+ <I>extra/bond/types</I> arg = # of extra bond types
+ <I>extra/angle/types</I> arg = # of extra angle types
+ <I>extra/dihedral/types</I> arg = # of extra dihedral types
+ <I>extra/improper/types</I> arg = # of extra improper types
+ <I>group</I> args = groupID
+ groupID = add atoms in data file to this group
+ <I>fix</I> args = fix-ID header-string section-string
+ fix-ID = ID of fix to process header lines and sections of data file
+ header-string = header lines containing this string will be passed to fix
+ section-string = section names with this string will be passed to fix
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>read_data data.lj
+read_data ../run7/data.polymer.gz
+read_data data.protein fix mycmap crossterm CMAP
+read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
+read_data data.water add merge 1 group solvent
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Read in a data file containing information LAMMPS needs to run a
+simulation. The file can be ASCII text or a gzipped text file
+(detected by a .gz suffix). This is one of 3 ways to specify initial
+atom coordinates; see the <A HREF = "read_restart.html">read_restart</A> and
+<A HREF = "create_atoms.html">create_atoms</A> commands for alternative methods.
+Also see the explanation of the <A HREF = "Section_start.html#start_7">-restart command-line
+switch</A> which can convert a restart file to
+a data file.
+</P>
+<P>This command can be used multiple times to add new atoms and their
+properties to an existing system by using the <I>add</I>, <I>offset</I>, and
+<I>shift</I> keywords. See more details below, which includes the use case
+for the <I>extra</I> keywords.
+</P>
+<P>The <I>group</I> keyword adds all the atoms in the data file to the
+specified group-ID. The group will be created if it does not already
+exist. This is useful if you are reading multiple data files and wish
+to put sets of atoms into different groups so they can be operated on
+later. E.g. a group of added atoms can be moved to new positions via
+the <A HREF = "displace_atoms.html">displace_atoms</A> command. Note that atoms
+read from the data file are also always added to the "all" group. The
+<A HREF = "group.html">group</A> command discusses atom groups, as used in LAMMPS.
+</P>
+<P>The use of the <I>fix</I> keyword is discussed below.
+</P>
+<HR>
+
+<P><B>Reading multiple data files</B>
+</P>
+<P>The read_data command can be used multiple times with the same or
+different data files to build up a complex system from components
+contained in individual data files. For example one data file could
+contain fluid in a confined domain; a second could contain wall atoms,
+and the second file could be read a third time to create a wall on the
+other side of the fluid. The third set of atoms could be rotated to
+an opposing direction using the <A HREF = "displace_atoms.html">displace_atoms</A>
+command, after the third read_data command is used.
+</P>
+<P>The <I>add</I>, <I>offset</I>, <I>shift</I>, <I>extra</I>, and <I>group</I> keywords are
+useful in this context.
+</P>
+<P>If a simulation box does not yet exist, the <I>add</I> keyword
+cannot be used; the read_data command is being used for the first
+time. If a simulation box does exist, due to using the
+<A HREF = "create_box.html">create_box</A> command, or a previous read_data command,
+then the <I>add</I> keyword must be used.
+</P>
+<P>IMPORTANT NOTE: The simulation box size (xlo to xhi, ylo to yhi, zlo
+to zhi) in the new data file will be merged with the existing
+simulation box to create a large enough box in each dimension to
+contain both the existing and new atoms. Each box dimension never
+shrinks due to this merge operation, it only stays the same or
+grows. Care must be used if you are growing the existing simulation
+box in a periodic dimension. If there are existing atoms with bonds
+that straddle that periodic boundary, then the atoms may become far
+apart if the box size grows. This will separate the atoms in the
+bond, which can lead to "lost" bond atoms or bad dynamics.
+</P>
+<P>The three choices for the <I>add</I> argument affect how the IDs of atoms
+in the data file are treated. If <I>append</I> is specified, atoms in the
+data file are added to the current system, with their atom IDs reset
+so that an atomID = M in the data file becomes atomID = N+M, where N
+is the largest atom ID in the current system. This rule is applied to
+all occurrences of atom IDs in the data file, e.g. in the Velocity or
+Bonds section. If <I>Nstart</I> is specified, then <I>Nstart</I> is a numeric
+value is given, e.g. 1000, so that an atomID = M in the data file
+becomes atomID = 1000+M. If <I>merge</I> is specified, the data file atoms
+are added to the current system without changing their IDs. They are
+assumed to merge (without duplication) with the currently defined
+atoms. It is up to you to insure there are no multiply defined atom
+IDs, as LAMMPS only performs an incomplete check that this is the case
+by insuring the resulting max atomID >= the number of atoms.
+</P>
+<P>The <I>offset</I> and <I>shift</I> keywords can only be used if the <I>add</I>
+keyword is also specified.
+</P>
+<P>The <I>offset</I> keyword adds the specified offset values to the atom
+types, bond types, angle types, dihedral types, and improper types as
+they are read from the data file. E.g. if <I>toff</I> = 2, and the file
+uses atom types 1,2,3, then the added atoms will have atom types
+3,4,5. These offsets apply to all occurrences of types in the data
+file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
+sections. This makes it easy to use atoms and molecules and their
+attributes from a data file in different simulations, where you want
+their types (atom, bond, angle, etc) to be different depending on what
+other types already exist. All five offset values must be specified,
+but individual values will be ignored if the data file does not use
+that attribute (e.g. no bonds).
+</P>
+<P>The <I>shift</I> keyword can be used to specify an (Sx, Sy, Sz)
+displacement applied to the coordinates of each atom. Sz must be 0.0
+for a 2d simulation. This is a mechanism for adding structured
+collections of atoms at different locations within the simulation box,
+to build up a complex geometry. It is up to you to insure atoms do
+not end up overlapping unphysically which would lead to bad dynamics.
+Note that the <A HREF = "displace_atoms.html">displace_atoms</A> command can be used
+to move a subset of atoms after they have been read from a data file.
+Likewise, the <A HREF = "delete_atoms.html">delete_atoms</A> command can be used to
+remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
+also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
+zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
+Sx, xhi_new = xhi + Sx.
+</P>
+<P>The <I>extra</I> keywords can only be used the first time the read_data
+command is used. They are useful if you intend to add new atom, bond,
+angle, etc types later with additional read_data commands. This is
+because the maximum number of allowed atom, bond, angle, etc types is
+set by LAMMPS when the system is first initialized. If you do not use
+the <I>extra</I> keywords, then the number of these types will be limited
+to what appears in the first data file you read. For example, if the
+first data file is a solid substrate of Si, it will likely specify a
+single atom type. If you read a second data file with a different
+material (water molecules) that sit on top of the substrate, you will
+want to use different atom types for those atoms. You can only do
+this if you set the <I>extra/atom/types</I> keyword to a sufficiently large
+value when reading the substrate data file. Note that use of the
+<I>extra</I> keywords also allows each data file to contain sections like
+Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
+the number of types in that data file. If the <I>offset</I> keyword is
+used appropriately when each data file is read, the values in those
+sections will be stored correctly in the larger data structures
+allocated by the use of the <I>extra</I> keywords. E.g. the substrate file
+can list mass and pair coefficients for type 1 silicon atoms. The
+water file can list mass and pair coeffcients for type 1 and type 2
+hydrogen and oxygen atoms. Use of the <I>extra</I> and <I>offset</I> keywords
+will store those mass and pair coefficient values appropriately in
+data structures that allow for 3 atom types (Si, H, O). Of course,
+you would still need to specify coefficients for H/Si and O/Si
+interactions in your input script to have a complete pairwise
+interaction model.
+</P>
+<P>An alternative to using the <I>extra</I> keywords with the read_data
+command, is to use the <A HREF = "create_box.html">create_box</A> command to
+initialize the simulation box and all the various type limits you need
+via its <I>extra</I> keywords. Then use the read_data command one or more
+times to populate the system with atoms, bonds, angles, etc, using the
+<I>offset</I> keyword if desired to alter types used in the various data
+files you read.
+</P>
+<HR>
+
+<P><B>Format of a data file</B>
+</P>
+<P>The structure of the data file is important, though many settings and
+sections are optional or can come in any order. See the examples
+directory for sample data files for different problems.
+</P>
+<P>A data file has a header and a body. The header appears first. The
+first line of the header is always skipped; it typically contains a
+description of the file. Then lines are read one at a time. Lines
+can have a trailing comment starting with '#' that is ignored. If the
+line is blank (only whitespace after comment is deleted), it is
+skipped. If the line contains a header keyword, the corresponding
+value(s) is read from the line. If it doesn't contain a header
+keyword, the line begins the body of the file.
+</P>
+<P>The body of the file contains zero or more sections. The first line
+of a section has only a keyword. This line can have a trailing
+comment starting with '#' that is either ignored or can be used to
+check for a style match, as described below. The next line is
+skipped. The remaining lines of the section contain values. The
+number of lines depends on the section keyword as described below.
+Zero or more blank lines can be used between sections. Sections can
+appear in any order, with a few exceptions as noted below.
+</P>
+<P>The keyword <I>fix</I> can be used one or more times. Each usage specifies
+a fix that will be used to process a specific portion of the data
+file. Any header line containing <I>header-string</I> and any section with
+a name containing <I>section-string</I> will be passed to the specified
+fix. See the <A HREF = "fix_property_atom.html">fix property/atom</A> command for
+an example of a fix that operates in this manner. The doc page for
+the fix defines the syntax of the header line(s) and section(s) that
+it reads from the data file. Note that the <I>header-string</I> can be
+specified as NULL, in which case no header lines are passed to the
+fix. This means that it can infer the length of its Section from
+standard header settings, such as the number of atoms.
+</P>
+<P>The formatting of individual lines in the data file (indentation,
+spacing between words and numbers) is not important except that header
+and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
+be capitalized as shown and can't have extra white space between their
+words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or
+the 2 words in "Bond Coeffs", is not valid.
+</P>
+<HR>
+
+<P><B>Format of the header of a data file</B>
+</P>
+<P>These are the recognized header keywords. Header lines can come in
+any order. The value(s) are read from the beginning of the line.
+Thus the keyword <I>atoms</I> should be in a line like "1000 atoms"; the
+keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
+keyword <I>xy xz yz</I> should be in a line like "0.0 5.0 6.0 xy xz yz".
+All these settings have a default value of 0, except the lo/hi box
+size defaults are -0.5 and 0.5. A line need only appear if the value
+is different than the default.
+</P>
+<UL><LI><I>atoms</I> = # of atoms in system
+<LI><I>bonds</I> = # of bonds in system
+<LI><I>angles</I> = # of angles in system
+<LI><I>dihedrals</I> = # of dihedrals in system
+<LI><I>impropers</I> = # of impropers in system
+<LI><I>atom types</I> = # of atom types in system
+<LI><I>bond types</I> = # of bond types in system
+<LI><I>angle types</I> = # of angle types in system
+<LI><I>dihedral types</I> = # of dihedral types in system
+<LI><I>improper types</I> = # of improper types in system
+<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
+<LI><I>extra angle per atom</I> = leave space for this many new angles per atom
+<LI><I>extra dihedral per atom</I> = leave space for this many new dihedrals per atom
+<LI><I>extra improper per atom</I> = leave space for this many new impropers per atom
+<LI><I>extra special per atom</I> = leave space for this many new special bonds per atom
+<LI><I>ellipsoids</I> = # of ellipsoids in system
+<LI><I>lines</I> = # of line segments in system
+<LI><I>triangles</I> = # of triangles in system
+<LI><I>bodies</I> = # of bodies in system
+<LI><I>xlo xhi</I> = simulation box boundaries in x dimension
+<LI><I>ylo yhi</I> = simulation box boundaries in y dimension
+<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
+<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic system
+</UL>
+<P>The initial simulation box size is determined by the lo/hi settings.
+In any dimension, the system may be periodic or non-periodic; see the
+<A HREF = "boundary.html">boundary</A> command. When the simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the <A HREF = "processors.html">processors</A> command. The
+partitioning can later be changed by the <A HREF = "balance.html">balance</A> or
+<A HREF = "fix_balance.html">fix balance</A> commands.
+</P>
+<P>If the <I>xy xz yz</I> line does not appear, LAMMPS will set up an
+axis-aligned (orthogonal) simulation box. If the line does appear,
+LAMMPS creates a non-orthogonal simulation domain shaped as a
+parallelepiped with triclinic symmetry. The parallelepiped has its
+"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
+from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
+(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped.
+</P>
+<P>By default, the tilt factors (xy,xz,yz) can not skew the box more than
+half the distance of the corresponding parallel box length. For
+example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
+xy tilt factor must be between -5 and 5. Similarly, both xz and yz
+must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not
+a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are all geometrically equivalent. If you wish to define a box
+with tilt factors that exceed these limits, you can use the <A HREF = "box.html">box
+tilt</A> command, with a setting of <I>large</I>; a setting of
+<I>small</I> is the default.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+</P>
+<P>When a triclinic system is used, the simulation domain should normally
+be periodic in the dimension that the tilt is applied to, which is
+given by the second dimension of the tilt factor (e.g. y for xy tilt).
+This is so that pairs of atoms interacting across that boundary will
+have one of them shifted by the tilt factor. Periodicity is set by
+the <A HREF = "boundary.html">boundary</A> command. For example, if the xy tilt
+factor is non-zero, then the y dimension should be periodic.
+Similarly, the z dimension should be periodic if xz or yz is non-zero.
+LAMMPS does not require this periodicity, but you may lose atoms if
+this is not the case.
+</P>
+<P>Also note that if your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
+deform</A> command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0. You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the <A HREF = "change_box.html">change box</A> command with its <I>ortho</I> and
+<I>triclinic</I> options.
+</P>
+<P>For 2d simulations, the <I>zlo zhi</I> values should be set to bound the z
+coords for atoms that appear in the file; the default of -0.5 0.5 is
+valid if all z coords are 0.0. For 2d triclinic simulations, the xz
+and yz tilt factors must be 0.0.
+</P>
+<P>If the system is periodic (in a dimension), then atom coordinates can
+be outside the bounds (in that dimension); they will be remapped (in a
+periodic sense) back inside the box. Note that if the <I>add</I> option is
+being used to add atoms to a simulation box that already exists, this
+periodic remapping will be performed using simulation box bounds that
+are the union of the existing box and the box boundaries in the new
+data file.
+</P>
+<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
+all atoms in the data file must have coordinates (in that dimension)
+that are "greater than or equal to" the lo value and "less than or
+equal to" the hi value. If the non-periodic dimension is of style
+"fixed" (see the <A HREF = "boundary.html">boundary</A> command), then the atom
+coords must be strictly "less than" the hi value, due to the way
+LAMMPS assign atoms to processors. Note that you should not make the
+lo/hi values radically smaller/larger than the extent of the atoms.
+For example, if your atoms extend from 0 to 50, you should not specify
+the box bounds as -10000 and 10000. This is because LAMMPS uses the
+specified box size to layout the 3d grid of processors. A huge
+(mostly empty) box will be sub-optimal for performance when using
+"fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
+command). When using "shrink-wrap" boundary conditions (see the
+<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
+a parallel simulation to lose atoms when LAMMPS shrink-wraps the box
+around the atoms. The read_data command will generate an error
+in this case.
+</P>
+<P>The "extra bond per atom" setting (angle, dihedral, improper) is only
+needed if new bonds (angles, dihedrals, impropers) will be added to
+the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
+bond/create</A> command. This will pre-allocate
+space in LAMMPS data structures for storing the new bonds (angles,
+dihedrals, impropers).
+</P>
+<P>The "extra special per atom" setting is typically only needed if new
+bonds/angles/etc will be added to the system, e.g. by using the <A HREF = "fix_bond_create.html">fix
+bond/create</A> command. Or if entire new molecules
+will be added to the system, e.g. by using the <A HREF = "fix_deposit.html">fix
+deposit</A> or <A HREF = "fix_pour.html">fix pour</A> commands, which
+will have more special 1-2,1-3,1-4 neighbors than any other molecules
+defined in the data file. Using this setting will pre-allocate space
+in the LAMMPS data structures for storing these neighbors. See the
+<A HREF = "special_bonds.html">special_bonds</A> and <A HREF = "molecule.html">molecule</A> doc
+pages for more discussion of 1-2,1-3,1-4 neighbors.
+</P>
+<P>IMPORTANT NOTE: All of the "extra" settings are only used if they
+appear in the first data file read; see the description of the <I>add</I>
+keyword above for reading multiple data files. If they appear in
+later data files, they are ignored.
+</P>
+<P>The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
+only used with <A HREF = "atom_style.html">atom_style ellipsoid or line or tri or
+body</A> and specify how many of the atoms are
+finite-size ellipsoids or lines or triangles or bodies; the remainder
+are point particles. See the discussion of ellipsoidflag and the
+<I>Ellipsoids</I> section below. See the discussion of lineflag and the
+<I>Lines</I> section below. See the discussion of triangleflag and the
+<I>Triangles</I> section below. See the discussion of bodyflag and the
+<I>Bodies</I> section below.
+</P>
+<P>IMPORTANT NOTE: For <A HREF = "atom_style.html">atom_style template</A>, the
+molecular topology (bonds,angles,etc) is contained in the molecule
+templates read-in by the <A HREF = "molecule.html">molecule</A> command. This means
+you cannot set the <I>bonds</I>, <I>angles</I>, etc header keywords in the data
+file, nor can you define <I>Bonds</I>, <I>Angles</I>, etc sections as discussed
+below. You can set the <I>bond types</I>, <I>angle types</I>, etc header
+keywords, though it is not necessary. If specified, they must match
+the maximum values defined in any of the template molecules.
+</P>
+<HR>
+
+<P><B>Format of the body of a data file</B>
+</P>
+<P>These are the section keywords for the body of the file.
+</P>
+<UL><LI><I>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</I> = atom-property sections
+<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
+<LI><I>Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
+<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
+</UL>
+<P>These keywords will check an appended comment for a match with the
+currently defined style:
+</P>
+<UL><LI><I>Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I>
+</UL>
+<P>For example, these lines:
+</P>
+<PRE>Atoms # sphere
+Pair Coeffs # lj/cut
+</PRE>
+<P>will check if the currently-defined <A HREF = "atom_style.html">atom_style</A> is
+<I>sphere</I>, and the current <A HREF = "pair_style">pair_style</A> is <I>lj/cut</I>. If
+not, LAMMPS will issue a warning to indicate that the data file
+section likely does not contain the correct number or type of
+parameters expected for the currently-defined style.
+</P>
+<P>Each section is listed below in alphabetic order. The format of each
+section is described including the number of lines it must contain and
+rules (if any) for where it can appear in the data file.
+</P>
+<P>Any individual line in the various sections can have a trailing
+comment starting with "#" for annotation purposes. E.g. in the
+Atoms section:
+</P>
+<PRE>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
+</PRE>
+<HR>
+
+<P><I>Angle Coeffs</I> section:
+</P>
+<UL><LI>one line per angle type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = angle type (1-N)
+ coeffs = list of coeffs
+</PRE>
+<LI>example:
+
+<PRE> 6 70 108.5 0 0
+</PRE>
+
+</UL>
+<P>The number and meaning of the coefficients are specific to the defined
+angle style. See the <A HREF = "angle_style.html">angle_style</A> and
+<A HREF = "angle_coeff.html">angle_coeff</A> commands for details. Coefficients can
+also be set via the <A HREF = "angle_coeff.html">angle_coeff</A> command in the
+input script.
+</P>
+<HR>
+
+<P><I>AngleAngle Coeffs</I> section:
+</P>
+<UL><LI>one line per improper type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = improper type (1-N)
+ coeffs = list of coeffs (see <A HREF = "improper_coeff.html">improper_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>AngleAngleTorsion Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>Angles</I> section:
+</P>
+<UL><LI>one line per angle
+
+<LI>line syntax: ID type atom1 atom2 atom3
+
+<PRE> ID = number of angle (1-Nangles)
+ type = angle type (1-Nangletype)
+ atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
+</PRE>
+example:
+<BR>
+<PRE> 2 2 17 29 430
+</PRE>
+
+</UL>
+<P>The 3 atoms are ordered linearly within the angle. Thus the central
+atom (around which the angle is computed) is the atom2 in the list.
+E.g. H,O,H for a water molecule. The <I>Angles</I> section must appear
+after the <I>Atoms</I> section. All values in this section must be
+integers (1, not 1.0).
+</P>
+<HR>
+
+<P><I>AngleTorsion Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>Atoms</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: depends on atom style
+</UL>
+<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
+header section. The atoms can be listed in any order. These are the
+line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS. As
+discussed below, each line can optionally have 3 flags (nx,ny,nz)
+appended to it, which indicate which image of a periodic simulation
+box the atom is in. These may be important to include for some kinds
+of analysis.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
+<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
+<TR><TD >body</TD><TD > atom-ID atom-type bodyflag mass x y z</TD></TR>
+<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
+<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
+<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
+<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
+<TR><TD >ellipsoid</TD><TD > atom-ID atom-type ellipsoidflag density x y z</TD></TR>
+<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
+<TR><TD >line</TD><TD > atom-ID molecule-ID atom-type lineflag density x y z</TD></TR>
+<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
+<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
+<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
+<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
+<TR><TD >template</TD><TD > atom-ID molecule-ID template-index template-atom atom-type x y z</TD></TR>
+<TR><TD >tri</TD><TD > atom-ID molecule-ID atom-type triangleflag density x y z</TD></TR>
+<TR><TD >wavepacket</TD><TD > atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</TD></TR>
+<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
+</TD></TR></TABLE></DIV>
+
+<P>The keywords have these meanings:
+</P>
+<UL><LI>atom-ID = integer ID of atom
+<LI>molecule-ID = integer ID of molecule the atom belongs to
+<LI>atom-type = type of atom (1-Ntype)
+<LI>q = charge on atom (charge units)
+<LI>diameter = diameter of spherical atom (distance units)
+<LI>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
+<LI>lineflag = 1 for line segment particles, 0 for point particles
+<LI>triangleflag = 1 for triangular particles, 0 for point particles
+<LI>bodyflag = 1 for body particles, 0 for point particles
+<LI>template-index = which molecule within the molecule template the atom is part of
+<LI>template-atom = which atom within a template molecule the atom is
+<LI>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
+<LI>mass = mass of particle (mass units)
+<LI>volume = volume of particle (distance^3 units)
+<LI>x,y,z = coordinates of atom
+<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
+<LI>rho = density (need units) for SPH particles
+<LI>e = energy (need units) for SPH particles
+<LI>cv = heat capacity (need units) for SPH particles
+<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
+<LI>eradius = electron radius (or fixed-core radius)
+<LI>etag = integer ID of electron that each wavepacket belongs to
+<LI>cs_re,cs_im = real/imaginary parts of wavepacket coefficients
+</UL>
+<P>The units for these quantities depend on the unit style; see the
+<A HREF = "units.html">units</A> command for details.
+</P>
+<P>For 2d simulations specify z as 0.0, or a value within the <I>zlo zhi</I>
+setting in the data file header.
+</P>
+<P>The atom-ID is used to identify the atom throughout the simulation and
+in dump files. Normally, it is a unique value from 1 to Natoms for
+each atom. Unique values larger than Natoms can be used, but they
+will cause extra memory to be allocated on each processor, if an atom
+map array is used, but not if an atom map hash is used; see the
+<A HREF = "atom_modify.html">atom_modify</A> command for details. If an atom map is
+not used (e.g. an atomic system with no bonds), and you don't care if
+unique atom IDs appear in dump files, then the atom-IDs can all be set
+to 0.
+</P>
+<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
+is a number from 1 to N, identifying which molecule the atom belongs
+to. It can be 0 if it is an unbonded atom or if you don't care to
+keep track of molecule assignments.
+</P>
+<P>The diameter specifies the size of a finite-size spherical particle.
+It can be set to 0.0, which means that atom is a point particle.
+</P>
+<P>The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
+whether the particle is a finite-size ellipsoid or line or triangle or
+body of finite size, or whether the particle is a point particle.
+Additional attributes must be defined for each ellipsoid, line,
+triangle, or body in the corresponding <I>Ellipsoids</I>, <I>Lines</I>,
+<I>Triangles</I>, or <I>Bodies</I> section.
+</P>
+<P>The <I>template-index</I> and <I>template-atom</I> are only defined used by
+<A HREF = "atom_style.html">atom_style template</A>. In this case the
+<A HREF = "molecule.html">molecule</A> command is used to define a molecule template
+which contains one or more molecules. If an atom belongs to one of
+those molecules, its <I>template-index</I> and <I>template-atom</I> are both set
+to positive integers; if not the values are both 0. The
+<I>template-index</I> is which molecule (1 to Nmols) the atom belongs to.
+The <I>template-atom</I> is which atom (1 to Natoms) within the molecule
+the atom is.
+</P>
+<P>Some pair styles and fixes and computes that operate on finite-size
+particles allow for a mixture of finite-size and point particles. See
+the doc pages of individual commands for details.
+</P>
+<P>For finite-size particles, the density is used in conjunction with the
+particle volume to set the mass of each particle as mass = density *
+volume. In this context, volume can be a 3d quantity (for spheres or
+ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
+segments). If the volume is 0.0, meaning a point particle, then the
+density value is used as the mass. One exception is for the body atom
+style, in which case the mass of each particle (body or point
+particle) is specified explicitly. This is because the volume of the
+body is unknown.
+</P>
+<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
+specific values for each sub-style must be listed. The order of the
+sub-styles is the same as they were listed in the
+<A HREF = "atom_style.html">atom_style</A> command. The sub-style specific values
+are those that are not the 5 standard ones (ID,type,x,y,z). For
+example, for the "charge" sub-style, a "q" value would appear. For
+the "full" sub-style, a "molecule-ID" and "q" would appear. These are
+listed in the same order they appear as listed above. Thus if
+</P>
+<PRE>atom_style hybrid charge sphere
+</PRE>
+<P>were used in the input script, each atom line would have these fields:
+</P>
+<PRE>atom-ID atom-type x y z q diameter density
+</PRE>
+<P>Note that if a non-standard value is defined by multiple sub-styles,
+it must appear mutliple times in the atom line. E.g. the atom line
+for atom_style hybrid dipole full would list "q" twice:
+</P>
+<PRE>atom-ID atom-type x y z q mux muy myz molecule-ID q
+</PRE>
+<P>Atom lines specify the (x,y,z) coordinates of atoms. These can be
+inside or outside the simulation box. When the data file is read,
+LAMMPS wraps coordinates outside the box back into the box for
+dimensions that are periodic. As discussed above, if an atom is
+outside the box in a non-periodic dimension, it will be lost.
+</P>
+<P>LAMMPS always stores atom coordinates as values which are inside the
+simulation box. It also stores 3 flags which indicate which image of
+the simulation box (in each dimension) the atom would be in if its
+coordinates were unwrapped across periodic boundaries. An image flag
+of 0 means the atom is still inside the box when unwrapped. A value
+of 2 means add 2 box lengths to get the unwrapped coordinate. A value
+of -1 means subtract 1 box length to get the unwrapped coordinate.
+LAMMPS updates these flags as atoms cross periodic boundaries during
+the simulation. The <A HREF = "dump.html">dump</A> command can output atom atom
+coordinates in wrapped or unwrapped form, as well as the 3 image
+flags.
+</P>
+<P>In the data file, atom lines (all lines or none of them) can
+optionally list 3 trailing integer values (nx,ny,nz), which are used
+to initialize the atom's image flags. If nx,ny,nz values are not
+listed in the data file, LAMMPS initializes them to 0. Note that the
+image flags are immediately updated if an atom's coordinates need to
+wrapped back into the simulation box.
+</P>
+<P>It is only important to set image flags correctly in a data file if a
+simulation model relies on unwrapped coordinates for some calculation;
+otherwise they can be left unspecified. Examples of LAMMPS commands
+that use unwrapped coordinates internally are as follows:
+</P>
+<UL><LI>Atoms in a rigid body (see <A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_rigid.html">fix
+rigid/small</A>) must have consistent image flags, so that
+when the atoms are unwrapped, they are near each other, i.e. as a
+single body.
+
+<LI>If the <A HREF = "replicate.html">replicate</A> command is used to generate a larger
+system, image flags must be consistent for bonded atoms when the bond
+crosses a periodic boundary. I.e. the values of the image flags
+should be different by 1 (in the appropriate dimension) for the two
+atoms in such a bond.
+
+<LI>If you plan to <A HREF = "dump.html">dump</A> image flags and perform post-analysis
+that will unwrap atom coordinates, it may be important that a
+continued run (restarted from a data file) begins with image flags
+that are consistent with the previous run.
+</UL>
+<P>Atom velocities and other atom quantities not defined above are set to
+0.0 when the <I>Atoms</I> section is read. Velocities can be set later by
+a <I>Velocities</I> section in the data file or by a
+<A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A> command in the input
+script.
+</P>
+<HR>
+
+<P><I>Bodies</I> section:
+</P>
+<UL><LI>one or more lines per body
+
+<LI>first line syntax: atom-ID ninteger ndouble
+
+<PRE> ninteger = # of integer quantities for this particle
+ ndouble = # of floating-point quantities for this particle
+</PRE>
+<LI>0 or more integer lines: one line for every 10 integer quantities
+
+<LI>0 or more double lines: one line for every 10 double quantities
+
+<LI>example:
+
+<PRE> 12 3 6
+ 2 3 2
+ 1.0 2.0 3.0 1.0 2.0 4.0
+</PRE>
+<LI>example:
+
+<PRE> 12 0 14
+ 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
+ 2.0 4.0 4.0 2.0
+</PRE>
+
+</UL>
+<P>The <I>Bodies</I> section must appear if <A HREF = "atom_style.html">atom_style body</A>
+is used and any atoms listed in the <I>Atoms</I> section have a bodyflag =
+1. The number of bodies should be specified in the header section via
+the "bodies" keyword.
+</P>
+<P>Each body can have a variable number of integer and/or floating-point
+values. The number and meaning of the values is defined by the body
+style, as described in the <A HREF = "body.html">body</A> doc page. The body style
+is given as an argument to the <A HREF = "atom_style.html">atom_style body</A>
+command.
+</P>
+<P>The ninteger and ndouble values determine how many integer and
+floating-point values are specified for this particle. Ninteger and
+ndouble can be as large as needed and can be different for every body.
+Integer values are then listed on subsequent lines, 10 values per
+line. Floating-point values follow on subsequent lines, again 10 per
+line. If the number of lines is not evenly divisible by 10, the last
+line in that group contains the remaining values, e.g. 4 values out of
+14 in the last example above, for floating-point values. If there are
+no values of a particular type, no lines appear for that type,
+e.g. there are no integer lines in the last example above.
+</P>
+<P>The <I>Bodies</I> section must appear after the <I>Atoms</I> section.
+</P>
+<HR>
+
+<P><I>Bond Coeffs</I> section:
+</P>
+<UL><LI>one line per bond type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = bond type (1-N)
+ coeffs = list of coeffs
+</PRE>
+<LI>example:
+
+<PRE> 4 250 1.49
+</PRE>
+
+</UL>
+<P>The number and meaning of the coefficients are specific to the defined
+bond style. See the <A HREF = "bond_style.html">bond_style</A> and
+<A HREF = "bond_coeff.html">bond_coeff</A> commands for details. Coefficients can
+also be set via the <A HREF = "bond_coeff.html">bond_coeff</A> command in the input
+script.
+</P>
+<HR>
+
+<P><I>BondAngle Coeffs</I> section:
+</P>
+<UL><LI>one line per angle type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = angle type (1-N)
+ coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>BondBond Coeffs</I> section:
+</P>
+<UL><LI>one line per angle type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = angle type (1-N)
+ coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>BondBond13 Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>Bonds</I> section:
+</P>
+<UL><LI>one line per bond
+
+<LI>line syntax: ID type atom1 atom2
+
+<PRE> ID = bond number (1-Nbonds)
+ type = bond type (1-Nbondtype)
+ atom1,atom2 = IDs of 1st,2nd atoms in bond
+</PRE>
+<LI>example:
+
+<PRE> 12 3 17 29
+</PRE>
+
+</UL>
+<P>The <I>Bonds</I> section must appear after the <I>Atoms</I> section. All values
+in this section must be integers (1, not 1.0).
+</P>
+<HR>
+
+<P><I>Dihedral Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs
+</PRE>
+<LI>example:
+
+<PRE> 3 0.6 1 0 1
+</PRE>
+
+</UL>
+<P>The number and meaning of the coefficients are specific to the defined
+dihedral style. See the <A HREF = "dihedral_style.html">dihedral_style</A> and
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands for details.
+Coefficients can also be set via the
+<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script.
+</P>
+<HR>
+
+<P><I>Dihedrals</I> section:
+</P>
+<UL><LI>one line per dihedral
+
+<LI>line syntax: ID type atom1 atom2 atom3 atom4
+
+<PRE> ID = number of dihedral (1-Ndihedrals)
+ type = dihedral type (1-Ndihedraltype)
+ atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
+</PRE>
+<LI>example:
+
+<PRE> 12 4 17 29 30 21
+</PRE>
+
+</UL>
+<P>The 4 atoms are ordered linearly within the dihedral. The <I>Dihedrals</I>
+section must appear after the <I>Atoms</I> section. All values in this
+section must be integers (1, not 1.0).
+</P>
+<HR>
+
+<P><I>Ellipsoids</I> section:
+</P>
+<UL><LI>one line per ellipsoid
+
+<LI>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
+
+<PRE> atom-ID = ID of atom which is an ellipsoid
+ shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
+ quatw,quati,quatj,quatk = quaternion components for orientation of atom
+</PRE>
+<LI>example:
+
+<PRE> 12 1 2 1 1 0 0 0
+</PRE>
+
+</UL>
+<P>The <I>Ellipsoids</I> section must appear if <A HREF = "atom_style.html">atom_style
+ellipsoid</A> is used and any atoms are listed in the
+<I>Atoms</I> section with an ellipsoidflag = 1. The number of ellipsoids
+should be specified in the header section via the "ellipsoids"
+keyword.
+</P>
+<P>The 3 shape values specify the 3 diameters or aspect ratios of a
+finite-size ellipsoidal particle, when it is oriented along the 3
+coordinate axes. They must all be non-zero values.
+</P>
+<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
+of the atom as a quaternion (4-vector). Note that the shape
+attributes specify the aspect ratios of an ellipsoidal particle, which
+is oriented by default with its x-axis along the simulation box's
+x-axis, and similarly for y and z. If this body is rotated (via the
+right-hand rule) by an angle theta around a unit vector (a,b,c), then
+the quaternion that represents its new orientation is given by
+(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
+4 components are quatw, quati, quatj, and quatk as specified above.
+LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
+specified as a unit vector.
+</P>
+<P>The <I>Ellipsoids</I> section must appear after the <I>Atoms</I> section.
+</P>
+<HR>
+
+<P><I>EndBondTorsion Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>Improper Coeffs</I> section:
+</P>
+<UL><LI>one line per improper type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = improper type (1-N)
+ coeffs = list of coeffs
+</PRE>
+<LI>example:
+
+<PRE> 2 20 0.0548311
+</PRE>
+
+</UL>
+<P>The number and meaning of the coefficients are specific to the defined
+improper style. See the <A HREF = "improper_style.html">improper_style</A> and
+<A HREF = "improper_coeff.html">improper_coeff</A> commands for details.
+Coefficients can also be set via the
+<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script.
+</P>
+<HR>
+
+<P><I>Impropers</I> section:
+</P>
+<UL><LI>one line per improper
+
+<LI>line syntax: ID type atom1 atom2 atom3 atom4
+
+<PRE> ID = number of improper (1-Nimpropers)
+ type = improper type (1-Nimpropertype)
+ atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
+</PRE>
+<LI>example:
+
+<PRE> 12 3 17 29 13 100
+</PRE>
+
+</UL>
+<P>The ordering of the 4 atoms determines the definition of the improper
+angle used in the formula for each <A HREF = "improper_style.html">improper
+style</A>. See the doc pages for individual styles
+for details.
+</P>
+<P>The <I>Impropers</I> section must appear after the <I>Atoms</I> section. All
+values in this section must be integers (1, not 1.0).
+</P>
+<HR>
+
+<P><I>Lines</I> section:
+</P>
+<UL><LI>one line per line segment
+
+<LI>line syntax: atom-ID x1 y1 x2 y2
+
+<PRE> atom-ID = ID of atom which is a line segment
+ x1,y1 = 1st end point
+ x2,y2 = 2nd end point
+</PRE>
+<LI>example:
+
+<PRE> 12 1.0 0.0 2.0 0.0
+</PRE>
+
+</UL>
+<P>The <I>Lines</I> section must appear if <A HREF = "atom_style.html">atom_style line</A>
+is used and any atoms are listed in the <I>Atoms</I> section with a
+lineflag = 1. The number of lines should be specified in the header
+section via the "lines" keyword.
+</P>
+<P>The 2 end points are the end points of the line segment. The ordering
+of the 2 points should be such that using a right-hand rule to cross
+the line segment with a unit vector in the +z direction, gives an
+"outward" normal vector perpendicular to the line segment.
+I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
+for defining some interactions.
+</P>
+<P>The <I>Lines</I> section must appear after the <I>Atoms</I> section.
+</P>
+<HR>
+
+<P><I>Masses</I> section:
+</P>
+<UL><LI>one line per atom type
+
+<LI>line syntax: ID mass
+
+<PRE> ID = atom type (1-N)
+ mass = mass value
+</PRE>
+<LI>example:
+
+<PRE> 3 1.01
+</PRE>
+
+</UL>
+<P>This defines the mass of each atom type. This can also be set via the
+<A HREF = "mass.html">mass</A> command in the input script. This section cannot be
+used for atom styles that define a mass for individual atoms -
+e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
+</P>
+<HR>
+
+<P><I>MiddleBondTorsion Coeffs</I> section:
+</P>
+<UL><LI>one line per dihedral type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = dihedral type (1-N)
+ coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
+</PRE>
+
+</UL>
+<HR>
+
+<P><I>Pair Coeffs</I> section:
+</P>
+<UL><LI>one line per atom type
+
+<LI>line syntax: ID coeffs
+
+<PRE> ID = atom type (1-N)
+ coeffs = list of coeffs
+</PRE>
+<LI>example:
+
+<PRE> 3 0.022 2.35197 0.022 2.35197
+</PRE>
+
+</UL>
+<P>The number and meaning of the coefficients are specific to the defined
+pair style. See the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Since pair
+coefficients for types I != J are not specified, these will be
+generated automatically by the pair style's mixing rule. See the
+individual pair_style doc pages and the <A HREF = "pair_modify.html">pair_modify
+mix</A> command for details. Pair coefficients can also
+be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
+script.
+</P>
+<HR>
+
+<P><I>PairIJ Coeffs</I> section:
+</P>
+<UL><LI>one line per pair of atom types for all I,J with I <= J
+
+<LI>line syntax: ID1 ID2 coeffs
+
+<PRE> ID1 = atom type I = 1-N
+ ID2 = atom type J = I-N, with I <= J
+ coeffs = list of coeffs
+</PRE>
+<LI>examples:
+
+<PRE> 3 3 0.022 2.35197 0.022 2.35197
+ 3 5 0.022 2.35197 0.022 2.35197
+</PRE>
+
+</UL>
+<P>This section must have N*(N+1)/2 lines where N = # of atom types. The
+number and meaning of the coefficients are specific to the defined
+pair style. See the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Since pair
+coefficients for types I != J are all specified, these values will
+turn off the default mixing rule defined by the pair style. See the
+individual pair_style doc pages and the <A HREF = "pair_modify.html">pair_modify
+mix</A> command for details. Pair coefficients can also
+be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
+script.
+</P>
+<HR>
+
+<P><I>Triangles</I> section:
+</P>
+<UL><LI>one line per triangle
+
+<LI>line syntax: atom-ID x1 y1 x2 y2
+
+<PRE> atom-ID = ID of atom which is a line segment
+ x1,y1,z1 = 1st corner point
+ x2,y2,z2 = 2nd corner point
+ x3,y3,z3 = 3rd corner point
+</PRE>
+<LI>example:
+
+<PRE> 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
+</PRE>
+
+</UL>
+<P>The <I>Triangles</I> section must appear if <A HREF = "atom_style.html">atom_style
+tri</A> is used and any atoms are listed in the <I>Atoms</I>
+section with a triangleflag = 1. The number of lines should be
+specified in the header section via the "triangles" keyword.
+</P>
+<P>The 3 corner points are the corner points of the triangle. The
+ordering of the 3 points should be such that using a right-hand rule
+to go from point1 to point2 to point3 gives an "outward" normal vector
+to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
+orientation may be important for defining some interactions.
+</P>
+<P>The <I>Triangles</I> section must appear after the <I>Atoms</I> section.
+</P>
+<HR>
+
+<P><I>Velocities</I> section:
+</P>
+<UL><LI>one line per atom
+<LI>line syntax: depends on atom style
+</UL>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
+<TR><TD >electron</TD><TD > atom-ID vx vy vz ervel</TD></TR>
+<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
+<TR><TD >sphere</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
+<TR><TD >hybrid</TD><TD > atom-ID vx vy vz sub-style1 sub-style2 ...
+</TD></TR></TABLE></DIV>
+
+<P>where the keywords have these meanings:
+</P>
+<P>vx,vy,vz = translational velocity of atom
+lx,ly,lz = angular momentum of aspherical atom
+wx,wy,wz = angular velocity of spherical atom
+ervel = electron radial velocity (0 for fixed-core):ul
+</P>
+<P>The velocity lines can appear in any order. This section can only be
+used after an <I>Atoms</I> section. This is because the <I>Atoms</I> section
+must have assigned a unique atom ID to each atom so that velocities
+can be assigned to them.
+</P>
+<P>Vx, vy, vz, and ervel are in <A HREF = "units.html">units</A> of velocity. Lx, ly,
+lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
+Wz are in units of angular velocity (radians/time).
+</P>
+<P>For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
+specific values for each sub-style must be listed. The order of the
+sub-styles is the same as they were listed in the
+<A HREF = "atom_style.html">atom_style</A> command. The sub-style specific values
+are those that are not the 5 standard ones (ID,vx,vy,vz). For
+example, for the "sphere" sub-style, "wx", "wy", "wz" values would
+appear. These are listed in the same order they appear as listed
+above. Thus if
+</P>
+<PRE>atom_style hybrid electron sphere
+</PRE>
+<P>were used in the input script, each velocity line would have these
+fields:
+</P>
+<PRE>atom-ID vx vy vz ervel wx wy wz
+</PRE>
+<P>Translational velocities can also be set by the
+<A HREF = "velocity.html">velocity</A> command in the input script.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To read gzipped data files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
+LAMMPS</A> section of the documentation.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "write_data.html">write_data</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The default for all the <I>extra</I> keywords is 0.
+</P>
+</HTML>
diff --git a/doc/doc2/read_dump.html b/doc/doc2/read_dump.html
new file mode 100644
index 000000000..3f1a8b124
--- /dev/null
+++ b/doc/doc2/read_dump.html
@@ -0,0 +1,336 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>read_dump command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>read_dump file Nstep field1 field2 ... keyword values ...
+</PRE>
+<UL><LI>file = name of dump file to read
+
+<LI>Nstep = snapshot timestep to read from file
+
+<LI>one or more fields may be appended
+
+<PRE>field = <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>q</I> or <I>ix</I> or <I>iy</I> or <I>iz</I>
+ <I>x</I>,<I>y</I>,<I>z</I> = atom coordinates
+ <I>vx</I>,<I>vy</I>,<I>vz</I> = velocity components
+ <I>q</I> = charge
+ <I>ix</I>,<I>iy</I>,<I>iz</I> = image flags in each dimension
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>box</I> or <I>replace</I> or <I>purge</I> or <I>trim</I> or <I>add</I> or <I>label</I> or <I>scaled</I> or <I>wrapped</I> or <I>format</I>
+
+<PRE> <I>box</I> value = <I>yes</I> or <I>no</I> = replace simulation box with dump box
+ <I>replace</I> value = <I>yes</I> or <I>no</I> = overwrite atoms with dump atoms
+ <I>purge</I> value = <I>yes</I> or <I>no</I> = delete all atoms before adding dump atoms
+ <I>trim</I> value = <I>yes</I> or <I>no</I> = trim atoms not in dump snapshot
+ <I>add</I> value = <I>yes</I> or <I>no</I> = add new dump atoms to system
+ <I>label</I> value = field column
+ field = one of the listed fields or <I>id</I> or <I>type</I>
+ column = label on corresponding column in dump file
+ <I>scaled</I> value = <I>yes</I> or <I>no</I> = coords in dump file are scaled/unscaled
+ <I>wrapped</I> value = <I>yes</I> or <I>no</I> = coords in dump file are wrapped/unwrapped
+ <I>format</I> values = format of dump file, must be last keyword if used
+ <I>native</I> = native LAMMPS dump file
+ <I>xyz</I> = XYZ file
+ <I>molfile</I> style path = VMD molfile plugin interface
+ style = <I>dcd</I> or <I>xyz</I> or others supported by molfile plugins
+ path = optional path for location of molfile plugins
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>read_dump dump.file 5000 x y z
+read_dump dump.xyz 5 x y z box no format xyz
+read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
+read_dump dump.dcd 0 x y z box yes format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+read_dump dump.file 5000 x y vx vy trim yes
+read_dump ../run7/dump.file.gz 10000 x y z box yes
+read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
+read_dump dump.dcd 0 x y z format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Read atom information from a dump file to overwrite the current atom
+coordinates, and optionally the atom velocities and image flags and
+the simluation box dimensions. This is useful for restarting a run
+from a particular snapshot in a dump file. See the
+<A HREF = "read_restart.html">read_restart</A> and <A HREF = "read_data.html">read_data</A>
+commands for alternative methods to do this. Also see the
+<A HREF = "rerun.html">rerun</A> command for a means of reading multiple snapshots
+from a dump file.
+</P>
+<P>Note that a simulation box must already be defined before using the
+read_dump command. This can be done by the
+<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
+<A HREF = "read_restart.html">read_restart</A> commands. The read_dump command can
+reset the simulation box dimensions, as explained below.
+</P>
+<P>Also note that reading per-atom information from a dump snapshot is
+limited to the atom coordinates, velocities and image flags, as
+explained below. Other atom properties, which may be necessary to run
+a valid simulation, such as atom charge, or bond topology information
+for a molecular system, are not read from (or even contained in) dump
+files. Thus this auxiliary information should be defined in the usual
+way, e.g. in a data file read in by a <A HREF = "read_data.html">read_data</A>
+command, before using the read_dump command, or by the <A HREF = "set.html">set</A>
+command, after the dump snapshot is read.
+</P>
+<HR>
+
+<P>If the dump filename specified as <I>file</I> ends with ".gz", the dump
+file is read in gzipped format. You cannot (yet) read a dump file
+that was written in binary format with a ".bin" suffix, or to multiple
+files via the "%" option in the dump file name. See the
+<A HREF = "dump.html">dump</A> command for details.
+</P>
+<P>The format of the dump file is selected through the <I>format</I> keyword.
+If specified, it must be the last keyword used, since all remaining
+arguments are passed on to the dump reader. The <I>native</I> format is
+for native LAMMPS dump files, written with a <A HREF = "dump.html">dump atom</A> or
+<A HREF = "dump.html">dump custom</A> command. The <I>xyz</I> format is for generic XYZ
+formatted dump files. These formats take no additional values.
+</P>
+<P>The <I>molfile</I> format supports reading data through using the <A HREF = "vmd">VMD</A>
+molfile plugin interface. This dump reader format is only available,
+if the USER-MOLFILE package has been installed when compiling
+LAMMPS.
+</P>
+<P>The <I>molfile</I> format takes one or two additional values. The <I>style</I>
+value determines the file format to be used and can be any format that
+the molfile plugins support, such as DCD or XYZ. Note that DCD dump
+files can be written by LAMMPS via the <A HREF = "dump.html">dump dcd</A> command.
+The <I>path</I> value specifies a list of directories which LAMMPS will
+search for the molfile plugins appropriate to the specified <I>style</I>.
+The syntax of the <I>path</I> value is like other search paths: it can
+contain multiple directories separated by a colon (or semi-colon on
+windows). The <I>path</I> keyword is optional and defaults to ".",
+i.e. the current directory.
+</P>
+<P>Support for other dump format readers may be added in the future.
+</P>
+<HR>
+
+<P>Global information is first read from the dump file, namely timestep
+and box information.
+</P>
+<P>The dump file is scanned for a snapshot with a time stamp that matches
+the specified <I>Nstep</I>. This means the LAMMPS timestep the dump file
+snapshot was written on for the <I>native</I> format. Note that the <I>xyz</I>
+and <I>molfile</I> formats do not store the timestep. For these formats,
+timesteps are numbered logically, in a sequential manner, starting
+from 0. Thus to access the 10th snapshot in an <I>xyz</I> or <I>mofile</I>
+formatted dump file, use <I>Nstep</I> = 9.
+</P>
+<P>The dimensions of the simulation box for the selected snapshot are
+also read; see the <I>box</I> keyword discussion below. For the <I>native</I>
+format, an error is generated if the snapshot is for a triclinic box
+and the current simulation box is orthogonal or vice versa. A warning
+will be generated if the snapshot box boundary conditions (periodic,
+shrink-wrapped, etc) do not match the current simulation boundary
+conditions, but the boundary condition information in the snapshot is
+otherwise ignored. See the "boundary" command for more details.
+</P>
+<P>For the <I>xyz</I> format, no information about the box is available, so
+you must set the <I>box</I> flag to <I>no</I>. See details below.
+</P>
+<P>For the <I>molfile</I> format, reading simulation box information is
+typically supported, but the location of the simulation box origin is
+lost and no explicit information about periodicity or
+orthogonal/triclinic box shape is available. The USER-MOLFILE package
+makes a best effort to guess based on heuristics, but this may not
+always work perfectly.
+</P>
+<HR>
+
+<P>Per-atom information from the dump file snapshot is then read from the
+dump file snapshot. This corresponds to the specified <I>fields</I> listed
+in the read_dump command. It is an error to specify a z-dimension
+field, namely <I>z</I>, <I>vz</I>, or <I>iz</I>, for a 2d simulation.
+</P>
+<P>For dump files in <I>native</I> format, each column of per-atom data has a
+text label listed in the file. A matching label for each field must
+appear, e.g. the label "vy" for the field <I>vy</I>. For the <I>x</I>, <I>y</I>, <I>z</I>
+fields any of the following labels are considered a match:
+</P>
+<PRE>x, xs, xu, xsu for field <I>x</I>
+y, ys, yu, ysu for field <I>y</I>
+z, zs, zu, zsu for field <I>z</I>
+</PRE>
+<P>The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
+unwrapped) is explained on the <A HREF = "dump.html">dump</A> command doc page.
+These labels are searched for in the list of column labels in the dump
+file, in order, until a match is found.
+</P>
+<P>The dump file must also contain atom IDs, with a column label of "id".
+</P>
+<P>If the <I>add</I> keyword is specified with a value of <I>yes</I>, as discussed
+below, the dump file must contain atom types, with a column label of
+"type".
+</P>
+<P>If a column label you want to read from the dump file is not a match
+to a specified field, the <I>label</I> keyword can be used to specify the
+specific column label from the dump file to associate with that field.
+An example is if a time-averaged coordinate is written to the dump
+file via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command. The column
+will then have a label corresponding to the fix-ID rather than "x" or
+"xs". The <I>label</I> keyword can also be used to specify new column
+labels for fields <I>id</I> and <I>type</I>.
+</P>
+<P>For dump files in <I>xyz</I> format, only the <I>x</I>, <I>y</I>, and <I>z</I> fields are
+supported. The dump file does not store atom IDs, so these are
+assigned consecutively to the atoms as they appear in the dump file,
+starting from 1. Thus you should insure that order of atoms is
+consistent from snapshot to snapshot in the the XYZ dump file. See
+the <A HREF = "dump_modify.html">dump_modify sort</A> command if the XYZ dump file
+was written by LAMMPS.
+</P>
+<P>For dump files in <I>molfile</I> format, the <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, and
+<I>vz</I> fields can be specified. However, not all molfile formats store
+velocities, or their respective plugins may not support reading of
+velocities. The molfile dump files do not store atom IDs, so these
+are assigned consecutively to the atoms as they appear in the dump
+file, starting from 1. Thus you should insure that order of atoms are
+consistent from snapshot to snapshot in the the molfile dump file.
+See the <A HREF = "dump_modify.html">dump_modify sort</A> command if the dump file
+was written by LAMMPS.
+</P>
+<HR>
+
+<P>Information from the dump file snapshot is used to overwrite or
+replace properties of the current system. There are various options
+for how this is done, determined by the specified fields and optional
+keywords.
+</P>
+<P>The timestep of the snapshot becomes the current timestep for the
+simulation. See the <A HREF = "reset_timestep.html">reset_timestep</A> command if
+you wish to change this after the dump snapshot is read.
+</P>
+<P>If the <I>box</I> keyword is specified with a <I>yes</I> value, then the current
+simulation box dimensions are replaced by the dump snapshot box
+dimensions. If the <I>box</I> keyword is specified with a <I>no</I> value, the
+current simulatoin box is unchanged.
+</P>
+<P>If the <I>purge</I> keyword is specified with a <I>yes</I> value, then all
+current atoms in the system are deleted before any of the operations
+invoked by the <I>replace</I>, <I>trim</I>, or <I>add</I> keywords take place.
+</P>
+<P>If the <I>replace</I> keyword is specified with a <I>yes</I> value, then atoms
+with IDs that are in both the current system and the dump snapshot
+have their properties overwritten by field values. If the <I>replace</I>
+keyword is specified with a <I>no</I> value, atoms with IDs that are in
+both the current system and the dump snapshot are not modified.
+</P>
+<P>If the <I>trim</I> keyword is specified with a <I>yes</I> value, then atoms with
+IDs that are in the current system but not in the dump snapshot are
+deleted. These atoms are unaffected if the <I>trim</I> keyword is
+specified with a <I>no</I> value.
+</P>
+<P>If the <I>add</I> keyword is specified with a <I>yes</I> value, then atoms with
+IDs that are in the dump snapshot, but not in the current system are
+added to the system. These dump atoms are ignored if the <I>add</I>
+keyword is specified with a <I>no</I> value.
+</P>
+<P>Note that atoms added via the <I>add</I> keyword will have only the
+attributes read from the dump file due to the <I>field</I> arguments. If
+<I>x</I> or <I>y</I> or <I>z</I> is not specified as a field, a value of 0.0 is used
+for added atoms. Added atoms must have an atom type, so this value
+must appear in the dump file.
+</P>
+<P>Any other attributes (e.g. charge or particle diameter for spherical
+particles) will be set to default values, the same as if the
+<A HREF = "create_atoms.html">create_atoms</A> command were used.
+</P>
+<P>Note that atom IDs are not preserved for new dump snapshot atoms added
+via the <I>add</I> keyword. The procedure for assigning new atom IDS to
+added atoms is the same as is described for the
+<A HREF = "create_atoms.html">create_atoms</A> command.
+</P>
+<HR>
+
+<P>Atom coordinates read from the dump file are first converted into
+unscaled coordinates, relative to the box dimensions of the snapshot.
+These coordinates are then be assigned to an existing or new atom in
+the current simulation. The coordinates will then be remapped to the
+simulation box, whether it is the original box or the dump snapshot
+box. If periodic boundary conditions apply, this means the atom will
+be remapped back into the simulation box if necessary. If shrink-wrap
+boundary conditions apply, the new coordinates may change the
+simulation box dimensions. If fixed boundary conditions apply, the
+atom will be lost if it is outside the simulation box.
+</P>
+<P>For <I>native</I> format dump files, the 3 xyz image flags for an atom in
+the dump file are set to the corresponding values appearing in the
+dump file if the <I>ix</I>, <I>iy</I>, <I>iz</I> fields are specified. If not
+specified, the image flags for replaced atoms are not changed and
+image flags for new atoms are set to default values. If coordinates
+read from the dump file are in unwrapped format (e.g. <I>xu</I>) then the
+image flags for read-in atoms are also set to default values. The
+remapping procedure described in the previous paragraph will then
+change images flags for all atoms (old and new) if periodic boundary
+conditions are applied to remap an atom back into the simulation box.
+</P>
+<P>IMPORTANT NOTE: If you get a warning about inconsistent image flags
+after reading in a dump snapshot, it means one or more pairs of bonded
+atoms now have inconsistent image flags. As discussed in <A HREF = "Section_errors.html">Section
+errors</A> this may or may not cause problems for
+subsequent simulations, One way this can happen is if you read image
+flag fields from the dump file but do not also use the dump file box
+parameters.
+</P>
+<P>LAMMPS knows how to compute unscaled and remapped coordinates for the
+snapshot column labels discussed above, e.g. <I>x</I>, <I>xs</I>, <I>xu</I>, <I>xsu</I>.
+If another column label is assigned to the <I>x</I> or <I>y</I> or <I>z</I> field via
+the <I>label</I> keyword, e.g. for coordinates output by the <A HREF = "fix_ave_atom.html">fix
+ave/atom</A> command, then LAMMPS needs to know whether
+the coordinate information in the dump file is scaled and/or wrapped.
+This can be set via the <I>scaled</I> and <I>wrapped</I> keywords. Note that
+the value of the <I>scaled</I> and <I>wrapped</I> keywords is ignored for fields
+<I>x</I> or <I>y</I> or <I>z</I> if the <I>label</I> keyword is not used to assign a
+column label to that field.
+</P>
+<P>The scaled/unscaled and wrapped/unwrapped setting must be identical
+for any of the <I>x</I>, <I>y</I>, <I>z</I> fields that are specified. Thus you
+cannot read <I>xs</I> and <I>yu</I> from the dump file. Also, if the dump file
+coordinates are scaled and the simulation box is triclinic, then all 3
+of the <I>x</I>, <I>y</I>, <I>z</I> fields must be specified, since they are all
+needed to generate absolute, unscaled coordinates.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To read gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
+LAMMPS</A> section of the documentation.
+</P>
+<P>The <I>molfile</I> dump file formats are part of the USER-MOLFILE package.
+They are only enabled if LAMMPS was built with that packages. See the
+<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_molfile.html">dump molfile</A>,
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "rerun.html">rerun</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are box = yes, replace = yes, purge = no, trim =
+no, add = no, scaled = no, wrapped = yes, and format = native.
+</P>
+</HTML>
diff --git a/doc/doc2/read_restart.html b/doc/doc2/read_restart.html
new file mode 100644
index 000000000..66afe6a1b
--- /dev/null
+++ b/doc/doc2/read_restart.html
@@ -0,0 +1,223 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>read_restart command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>read_restart file flag
+</PRE>
+<UL><LI>file = name of binary restart file to read in
+<LI>flag = remap (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>read_restart save.10000
+read_restart save.10000 remap
+read_restart restart.*
+read_restart restart.*.mpiio
+read_restart poly.*.% remap
+</PRE>
+<PRE>
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Read in a previously saved system configuration from a restart file.
+This allows continuation of a previous run. Details about what
+information is stored (and not stored) in a restart file is given
+below. Basically this operation will re-create the simulation box
+with all its atoms and their attributes as well as some related global
+settings, at the point in time it was written to the restart file by a
+previous simluation. The simulation box will be partitioned into a
+regular 3d grid of rectangular bricks, one per processor, based on the
+number of processors in the current simulation and the settings of the
+<A HREF = "processors.html">processors</A> command. The partitioning can later be
+changed by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
+balance</A> commands.
+</P>
+<P>IMPORTANT NOTE: Normally, restart files are written by the
+<A HREF = "restart.html">restart</A> or <A HREF = "write_restart.html">write_restart</A> commands
+so that all atoms in the restart file are inside the simulation box.
+If this is not the case, the read_restart command will print an error
+that atoms were "lost" when the file is read. This error should be
+reported to the LAMMPS developers so the invalid writing of the
+restart file can be fixed. If you still wish to use the restart file,
+the optional <I>remap</I> flag can be appended to the read_restart command.
+This should avoid the error, by explicitly remapping each atom back into
+the simulation box, updating image flags for the atom appropriately.
+</P>
+<P>Restart files are saved in binary format to enable exact restarts,
+meaning that the trajectories of a restarted run will precisely match
+those produced by the original run had it continued on.
+</P>
+<P>Several things can prevent exact restarts due to round-off effects, in
+which case the trajectories in the 2 runs will slowly diverge. These
+include running on a different number of processors or changing
+certain settings such as those set by the <A HREF = "newton.html">newton</A> or
+<A HREF = "processors.html">processors</A> commands. LAMMPS will issue a warning in
+these cases.
+</P>
+<P>Certain fixes will not restart exactly, though they should provide
+statistically similar results. These include <A HREF = "fix_shake.html">fix
+shake</A> and <A HREF = "fix_langevin.html">fix langevin</A>.
+</P>
+<P>Certain pair styles will not restart exactly, though they should
+provide statistically similar results. This is because the forces
+they compute depend on atom velocities, which are used at half-step
+values every timestep when forces are computed. When a run restarts,
+forces are initially evaluated with a full-step velocity, which is
+different than if the run had continued. These pair styles include
+<A HREF = "pair_gran.html">granular pair styles</A>, <A HREF = "pair_dpd.html">pair dpd</A>, and
+<A HREF = "pair_lubricate.html">pair lubricate</A>.
+</P>
+<P>If a restarted run is immediately different than the run which
+produced the restart file, it could be a LAMMPS bug, so consider
+<A HREF = "Section_errors.html#err_2">reporting it</A> if you think the behavior is
+wrong.
+</P>
+<P>Because restart files are binary, they may not be portable to other
+machines. In this case, you can use the <A HREF = "Section_start.html#start_7">-restart command-line
+switch</A> to convert a restart file to a data
+file.
+</P>
+<P>Similar to how restart files are written (see the
+<A HREF = "write_restart.html">write_restart</A> and <A HREF = "restart.html">restart</A>
+commands), the restart filename can contain two wild-card characters.
+If a "*" appears in the filename, the directory is searched for all
+filenames that match the pattern where "*" is replaced with a timestep
+value. The file with the largest timestep value is read in. Thus,
+this effectively means, read the latest restart file. It's useful if
+you want your script to continue a run from where it left off. See
+the <A HREF = "run.html">run</A> command and its "upto" option for how to specify
+the run command so it doesn't need to be changed either.
+</P>
+<P>If a "%" character appears in the restart filename, LAMMPS expects a
+set of multiple files to exist. The <A HREF = "restart.html">restart</A> and
+<A HREF = "write_restart.html">write_restart</A> commands explain how such sets are
+created. Read_restart will first read a filename where "%" is
+replaced by "base". This file tells LAMMPS how many processors
+created the set and how many files are in it. Read_restart then reads
+the additional files. For example, if the restart file was specified
+as save.% when it was written, then read_restart reads the files
+save.base, save.0, save.1, ... save.P-1, where P is the number of
+processors that created the restart file.
+</P>
+<P>Note that P could be the total number of processors in the previous
+simulation, or some subset of those processors, if the <I>fileper</I> or
+<I>nfile</I> options were used when the restart file was written; see the
+<A HREF = "restart.html">restart</A> and <A HREF = "write_restart.html">write_restart</A> commands
+for details. The processors in the current LAMMPS simulation share
+the work of reading these files; each reads a roughly equal subset of
+the files. The number of processors which created the set can be
+different the number of processors in the current LAMMPS simulation.
+This can be a fast mode of input on parallel machines that support
+parallel I/O.
+</P>
+<P>A restart file can also be read in parallel as one large binary file
+via the MPI-IO library, assuming it was also written with MPI-IO.
+MPI-IO is part of the MPI standard for versions 2.0 and above. Using
+MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
+installed, e.g.
+</P>
+<PRE>make yes-mpiio # installs the MPIIO package
+make g++ # build LAMMPS for your platform
+</PRE>
+<P>Second, use a restart filename which contains ".mpiio". Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+</P>
+<HR>
+
+<P>A restart file stores the following information about a simulation:
+units, atom style and atom style related settings (<I>id</I>, <I>map</I>,
+<I>sort</I>), communication settings (<I>mode</I>, <I>cutoff</I>, <I>vel</I>), timestep,
+simulation box size and shape and boundary settings, group
+definitions, per-type atom settings such as mass, per-atom attributes
+including their group assignments and molecular topology attributes,
+force field styles and - in most cases - force field coefficients, and
+<A HREF = "special_bonds.html">special_bonds</A> settings. This means that commands
+for these quantities do not need to be re-specified in the input
+script that reads the restart file, though you can redefine settings
+after the restart file is read.
+</P>
+<P>One exception is that some force styles (pair, bond, angle, etc) do
+not store their coefficient info in restart files. Typically these
+are many-body or tabulated potentials which read their parameters from
+separate files; you may need to re-specify the <A HREF = "pair_style.html">pair
+style</A> and <A HREF = "pair_coeff.html">pair coeff</A> commands in
+your restart input script. The doc pages for individual pair styles
+mention if this is the case. This is also true of bond_style hybrid
+(and angle_style, dihedral_style, improper_style hybrid).
+</P>
+<P>All settings made by the <A HREF = "pair_modify.html">pair_modify</A> command, such
+as the shift and tail settings, are stored in the restart file with
+the pair style. The one exception is the <A HREF = "pair_modify.html">pair_modify
+compute</A> setting is not stored, since it is typically
+only used for debugging purposes.
+</P>
+<P>Information about <A HREF = "kspace_style.html">kspace_style</A> settings are not
+stored in the restart file. Hence if you wish to use an Ewald or PPPM
+solver, these commands must be re-issued after the restart file is
+read.
+</P>
+<P>The list of <A HREF = "fix.html">fixes</A> used for a simulation is not stored in
+the restart file. This means the new input script should specify all
+fixes it will use. Note that some fixes store an internal "state"
+which is written to the restart file. This allows the fix to continue
+on with its calculations in a restarted simulation. To re-enable such
+a fix, the fix command in the new input script must use the same
+fix-ID and group-ID as was used in the input script that wrote the
+restart file. If a match is found, LAMMPS prints a message indicating
+that the fix is being re-enabled. If no match is found before the
+first run or minimization is performed by the new script, the "state"
+information for the saved fix is discarded. See the doc pages for
+individual fixes for info on which ones can be restarted in this
+manner.
+</P>
+<P>Bond interactions (angle, etc) that have been turned off by the <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> command will
+be written to a restart file as if they are turned on. This means
+they will need to be turned off again in a new run after the restart
+file is read.
+</P>
+<P>Bonds that are broken (e.g. by a bond-breaking potential) are written
+to the restart file as broken bonds with a type of 0. Thus these
+bonds will still be broken when the restart file is read.
+</P>
+<P>Bonds that have been broken by the <A HREF = "fix_bond_break.html">fix
+bond/break</A> command have disappeared from the
+system. No information about these bonds is written to the restart
+file.
+</P>
+<P>IMPORTANT NOTE: No other information is stored in the restart file.
+This means that an input script that reads a restart file should
+specify settings for quantities like <A HREF = "timestep.html">timestep size</A>,
+<A HREF = "thermo_style.html">thermodynamic</A>, <A HREF = "neighbor.html">neighbor list</A>
+criteria including settings made via the
+<A HREF = "neigh_modify.html">neigh_modify</A> comand, <A HREF = "dump.html">dump</A> file
+output, <A HREF = "region.html">geometric regions</A>, etc.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "read_dump.html">read_dump</A>,
+<A HREF = "write_restart.html">write_restart</A>, <A HREF = "restart.html">restart</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/region.html b/doc/doc2/region.html
new file mode 100644
index 000000000..a1a454856
--- /dev/null
+++ b/doc/doc2/region.html
@@ -0,0 +1,327 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>region command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>region ID style args keyword arg ...
+</PRE>
+<UL><LI>ID = user-assigned name for the region
+
+<LI>style = <I>delete</I> or <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>plane</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I>
+
+<PRE> <I>delete</I> = no args
+ <I>block</I> args = xlo xhi ylo yhi zlo zhi
+ xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
+ <I>cone</I> args = dim c1 c2 radlo radhi lo hi
+ dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cone
+ c1,c2 = coords of cone axis in other 2 dimensions (distance units)
+ radlo,radhi = cone radii at lo and hi end (distance units)
+ lo,hi = bounds of cone in dim (distance units)
+ <I>cylinder</I> args = dim c1 c2 radius lo hi
+ dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
+ c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+ radius = cylinder radius (distance units)
+ radius can be a variable (see below)
+ lo,hi = bounds of cylinder in dim (distance units)
+ <I>plane</I> args = px py pz nx ny nz
+ px,py,pz = point on the plane (distance units)
+ nx,ny,nz = direction normal to plane (distance units)
+ <I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
+ xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
+ xy = distance to tilt y in x direction (distance units)
+ xz = distance to tilt z in x direction (distance units)
+ yz = distance to tilt z in y direction (distance units)
+ <I>sphere</I> args = x y z radius
+ x,y,z = center of sphere (distance units)
+ radius = radius of sphere (distance units)
+ radius can be a variable (see below)
+ <I>union</I> args = N reg-ID1 reg-ID2 ...
+ N = # of regions to follow, must be 2 or greater
+ reg-ID1,reg-ID2, ... = IDs of regions to join together
+ <I>intersect</I> args = N reg-ID1 reg-ID2 ...
+ N = # of regions to follow, must be 2 or greater
+ reg-ID1,reg-ID2, ... = IDs of regions to intersect
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>side</I> or <I>units</I> or <I>move</I> or <I>rotate</I>
+
+<PRE> <I>side</I> value = <I>in</I> or <I>out</I>
+ <I>in</I> = the region is inside the specified geometry
+ <I>out</I> = the region is outside the specified geometry
+ <I>units</I> value = <I>lattice</I> or <I>box</I>
+ <I>lattice</I> = the geometry is defined in lattice units
+ <I>box</I> = the geometry is defined in simulation box units
+ <I>move</I> args = v_x v_y v_z
+ v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
+ <I>rotate</I> args = v_theta Px Py Pz Rx Ry Rz
+ v_theta = equal-style variable for rotaton of region over time (in radians)
+ Px,Py,Pz = origin for axis of rotation (distance units)
+ Rx,Ry,Rz = axis of rotation vector
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>region 1 block -3.0 5.0 INF 10.0 INF INF
+region 2 sphere 0.0 0.0 0.0 5 side out
+region void cylinder y 2 3 5 -5.0 EDGE units box
+region 1 prism 0 10 0 10 0 10 2 0 0
+region outside union 4 side1 side2 side3 side4
+region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command defines a geometric region of space. Various other
+commands use regions. For example, the region can be filled with
+atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or a bounding
+box around the region, can be used to define the simulation box via
+the <A HREF = "create_box.html">create_box</A> command. Or the atoms in the region
+can be identified as a group via the <A HREF = "group.html">group</A> command, or
+deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command. Or the
+surface of the region can be used as a boundary wall via the <A HREF = "fix_wall_region.html">fix
+wall/region</A> command.
+</P>
+<P>Commands which use regions typically test whether an atom's position
+is contained in the region or not. For this purpose, coordinates
+exactly on the region boundary are considered to be interior to the
+region. This means, for example, for a spherical region, an atom on
+the sphere surface would be part of the region if the sphere were
+defined with the <I>side in</I> keyword, but would not be part of the
+region if it were defined using the <I>side out</I> keyword. See more
+details on the <I>side</I> keyword below.
+</P>
+<P>Normally, regions in LAMMPS are "static", meaning their geometric
+extent does not change with time. If the <I>move</I> or <I>rotate</I> keyword
+is used, as described below, the region becomes "dynamic", meaning
+it's location or orientation changes with time. This may be useful,
+for example, when thermostatting a region, via the compute temp/region
+command, or when the fix wall/region command uses a region surface as
+a bounding wall on particle motion, i.e. a rotating container.
+</P>
+<P>The <I>delete</I> style removes the named region. Since there is little
+overhead to defining extra regions, there is normally no need to do
+this, unless you are defining and discarding large numbers of regions
+in your input script.
+</P>
+<P>The lo/hi values for <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>prism</I> styles
+can be specified as EDGE or INF. EDGE means they extend all the way
+to the global simulation box boundary. Note that this is the current
+box boundary; if the box changes size during a simulation, the region
+does not. INF means a large negative or positive number (1.0e20), so
+it should encompass the simulation box even if it changes size. If a
+region is defined before the simulation box has been created (via
+<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
+<A HREF = "read_restart.html">read_restart</A> commands), then an EDGE or INF
+parameter cannot be used. For a <I>prism</I> region, a non-zero tilt
+factor in any pair of dimensions cannot be used if both the lo/hi
+values in either of those dimensions are INF. E.g. if the xy tilt is
+non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi.
+</P>
+<P>IMPORTANT NOTE: Regions in LAMMPS do not get wrapped across periodic
+boundaries, as specified by the <A HREF = "boundary.html">boundary</A> command. For
+example, a spherical region that is defined so that it overlaps a
+periodic boundary is not treated as 2 half-spheres, one on either side
+of the simulation box.
+</P>
+<P>IMPORTANT NOTE: Regions in LAMMPS are always 3d geometric objects,
+regardless of whether the <A HREF = "dimension.html">dimension</A> of a simulation
+is 2d or 3d. Thus when using regions in a 2d simulation, you should
+be careful to define the region so that its intersection with the 2d
+x-y plane of the simulation has the 2d geometric extent you want.
+</P>
+<P>For style <I>cone</I>, an axis-aligned cone is defined which is like a
+<I>cylinder</I> except that two different radii (one at each end) can be
+defined. Either of the radii (but not both) can be 0.0.
+</P>
+<P>For style <I>cone</I> and <I>cylinder</I>, the c1,c2 params are coordinates in
+the 2 other dimensions besides the cylinder axis dimension. For dim =
+x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y.
+Thus the third example above specifies a cylinder with its axis in the
+y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
+extending in the y-direction from -5.0 to the upper box boundary.
+</P>
+<P>For style <I>plane</I>, a plane is defined which contain the point
+(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does
+not have to be of unit length. The "inside" of the plane is the
+half-space in the direction of the normal vector; see the discussion
+of the <I>side</I> option below.
+</P>
+<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
+parallelepiped in an input script!). The parallelepiped has its
+"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
+from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
+(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped.
+</P>
+<P>A prism region that will be used with the <A HREF = "create_box.html">create_box</A>
+command to define a triclinic simulation box must have tilt factors
+(xy,xz,yz) that do not skew the box more than half the distance of
+corresponding the parallel box length. For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
+between -5 and 5. Similarly, both xz and yz must be between
+-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
+since if the maximum tilt factor is 5 (as in this example), then
+configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
+geometrically equivalent.
+</P>
+<P>The <I>radius</I> value for style <I>sphere</I> and <I>cylinder</I> can be specified
+as an equal-style <A HREF = "variable.html">variable</A>. If the value is a
+variable, it should be specified as v_name, where name is the variable
+name. In this case, the variable will be evaluated each timestep, and
+its value used to determine the radius of the region.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. Thus it is easy to specify a time-dependent radius.
+</P>
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
+for a geometric description of triclinic boxes, as defined by LAMMPS,
+and how to transform these parameters to and from other commonly used
+triclinic representations.
+</P>
+<P>The <I>union</I> style creates a region consisting of the volume of all the
+listed regions combined. The <I>intersect</I> style creates a region
+consisting of the volume that is common to all the listed regions.
+</P>
+<P>IMPORTANT NOTE: The <I>union</I> and <I>intersect</I> regions operate by
+invoking methods from their list of sub-regions. Thus you cannot
+delete the sub-regions after defining the <I>union</I> or <I>intersection</I>
+region.
+</P>
+<HR>
+
+<P>The <I>side</I> keyword determines whether the region is considered to be
+inside or outside of the specified geometry. Using this keyword in
+conjunction with <I>union</I> and <I>intersect</I> regions, complex geometries
+can be built up. For example, if the interior of two spheres were
+each defined as regions, and a <I>union</I> style with <I>side</I> = out was
+constructed listing the region-IDs of the 2 spheres, the resulting
+region would be all the volume in the simulation box that was outside
+both of the spheres.
+</P>
+<P>The <I>units</I> keyword determines the meaning of the distance units used
+to define the region for any argument above listed as having distance
+units. It also affects the scaling of the velocity vector specfied
+with the <I>vel</I> keyword, the amplitude vector specified with the
+<I>wiggle</I> keyword, and the rotation point specified with the <I>rotate</I>
+keyword, since they each involve a distance metric.
+</P>
+<P>A <I>box</I> value selects standard distance units as defined by the
+<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
+A <I>lattice</I> value means the distance units are in lattice spacings.
+The <A HREF = "lattice.html">lattice</A> command must have been previously used to
+define the lattice spacings which are used as follows:
+</P>
+<UL><LI>For style <I>block</I>, the lattice spacing in dimension x is applied to
+xlo and xhi, similarly the spacings in dimensions y,z are applied to
+ylo/yhi and zlo/zhi.
+
+<LI>For style <I>cone</I>, the lattice spacing in argument <I>dim</I> is applied to
+lo and hi. The spacings in the two radial dimensions are applied to
+c1 and c2. The two cone radii are scaled by the lattice
+spacing in the dimension corresponding to c1.
+
+<LI>For style <I>cylinder</I>, the lattice spacing in argument <I>dim</I> is applied
+to lo and hi. The spacings in the two radial dimensions are applied
+to c1 and c2. The cylinder radius is scaled by the lattice
+spacing in the dimension corresponding to c1.
+
+<LI>For style <I>plane</I>, the lattice spacing in dimension x is applied to
+px and nx, similarly the spacings in dimensions y,z are applied to
+py/ny and pz/nz.
+
+<LI>For style <I>prism</I>, the lattice spacing in dimension x is applied to
+xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing
+in dimension x is applied to xy and xz, and the spacing in dimension y
+to yz.
+
+<LI>For style <I>sphere</I>, the lattice spacing in dimensions x,y,z are
+applied to the sphere center x,y,z. The spacing in dimension x is
+applied to the sphere radius.
+</UL>
+<HR>
+
+<P>If the <I>move</I> or <I>rotate</I> keywords are used, the region is "dynamic",
+meaning its location or orientation changes with time. These keywords
+cannot be used with a <I>union</I> or <I>intersect</I> style region. Instead,
+the keywords should be used to make the individual sub-regions of the
+<I>union</I> or <I>intersect</I> region dynamic. Normally, each sub-region
+should be "dynamic" in the same manner (e.g. rotate around the same
+point), though this is not a requirement.
+</P>
+<P>The <I>move</I> keyword allows one or more <A HREF = "variable.html">equal-style
+variables</A> to be used to specify the x,y,z displacement
+of the region, typically as a function of time. A variable is
+specified as v_name, where name is the variable name. Any of the
+three variables can be specified as NULL, in which case no
+displacement is calculated in that dimension.
+</P>
+<P>Note that equal-style variables can specify formulas with various
+mathematical functions, and include <A HREF = "thermo_style.html">thermo_style</A>
+command keywords for the simulation box parameters and timestep and
+elapsed time. Thus it is easy to specify a region displacement that
+change as a function of time or spans consecutive runs in a continuous
+fashion. For the latter, see the <I>start</I> and <I>stop</I> keywords of the
+<A HREF = "run.html">run</A> command and the <I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style
+custom</A> for details.
+</P>
+<P>For example, these commands would displace a region from its initial
+position, in the positive x direction, effectively at a constant
+velocity:
+</P>
+<PRE>variable dx equal ramp(0,10)
+region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
+</PRE>
+<P>Note that the initial displacemet is 0.0, though that is not required.
+</P>
+<P>Either of these varaibles would "wiggle" the region back and forth in
+the y direction:
+</P>
+<PRE>variable dy equal swiggle(0,5,100)
+variable dysame equal 5*sin(2*PI*elaplong*dt/100)
+region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
+</PRE>
+<P>The <I>rotate</I> keyword rotates the region around a rotation axis <I>R</I> =
+(Rx,Ry,Rz) that goes thru a point <I>P</I> = (Px,Py,Pz). The rotation
+angle is calculated, presumably as a function of time, by a variable
+specified as v_theta, where theta is the variable name. The variable
+should generate its result in radians. The direction of rotation for
+the region around the rotation axis is consistent with the right-hand
+rule: if your right-hand thumb points along <I>R</I>, then your fingers
+wrap around the axis in the direction of rotation.
+</P>
+<P>The <I>move</I> and <I>rotate</I> keywords can be used together. In this case,
+the displacement specified by the <I>move</I> keyword is applied to the <I>P</I>
+point of the <I>rotate</I> keyword.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
+thickness for 2d simulations. For 2d simulations, the xz and yz
+parameters must be 0.0.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "lattice.html">lattice</A>, <A HREF = "create_atoms.html">create_atoms</A>,
+<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "group.html">group</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are side = in, units = lattice, and no move or
+rotation.
+</P>
+</HTML>
diff --git a/doc/doc2/replicate.html b/doc/doc2/replicate.html
new file mode 100644
index 000000000..6b1bac382
--- /dev/null
+++ b/doc/doc2/replicate.html
@@ -0,0 +1,100 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>replicate command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>replicate nx ny nz
+</PRE>
+<UL><LI>nx,ny,nz = replication factors in each dimension
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>replicate 2 3 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Replicate the current simulation one or more times in each dimension.
+For example, replication factors of 2,2,2 will create a simulation
+with 8x as many atoms by doubling the simulation domain in each
+dimension. A replication factor of 1 in a dimension leaves the
+simulation domain unchanged. When the new simulation box is created
+it is also partitioned into a regular 3d grid of rectangular bricks,
+one per processor, based on the number of processors being used and
+the settings of the <A HREF = "processors.html">processors</A> command. The
+partitioning can later be changed by the <A HREF = "balance.html">balance</A> or
+<A HREF = "fix_balance.html">fix balance</A> commands.
+</P>
+<P>All properties of the atoms are replicated, including their
+velocities, which may or may not be desirable. New atom IDs are
+assigned to new atoms, as are molecule IDs. Bonds and other topology
+interactions are created between pairs of new atoms as well as between
+old and new atoms. This is done by using the image flag for each atom
+to "unwrap" it out of the periodic box before replicating it.
+</P>
+<P>This means that any molecular bond you specify in the original data
+file that crosses a periodic boundary should be between two atoms with
+image flags that differ by 1. This will allow the bond to be
+unwrapped appropriately.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>A 2d simulation cannot be replicated in the z dimension.
+</P>
+<P>If a simulation is non-periodic in a dimension, care should be used
+when replicating it in that dimension, as it may put atoms nearly on
+top of each other.
+</P>
+<P>IMPORTANT NOTE: You cannot use the replicate command on a system which
+has a molecule that spans the box and is bonded to itself across a
+periodic boundary, so that the molecule is efffectively a loop. A
+simple example would be a linear polymer chain that spans the
+simulation box and bonds back to itself across the periodic boundary.
+More realistic examples would be a CNT (meant to be an infinitely long
+CNT) or a graphene sheet or a bulk periodic crystal where there are
+explicit bonds specified between near neighbors. (Note that this only
+applies to systems that have permanent bonds as specified in the data
+file. A CNT that is just atoms modeled with the <A HREF = "pair_airebo.html">AIREBO
+potential</A> has no such permanent bonds, so it can be
+replicated.) The reason replication does not work with those systems
+is that the image flag settings described above cannot be made
+consistent. I.e. it is not possible to define images flags so that
+when every pair of bonded atoms is unwrapped (using the image flags),
+they will be close to each other. The only way the replicate command
+could work in this scenario is for it to break a bond, insert more
+atoms, and re-connect the loop for the larger simulation box. But it
+is not clever enough to do this. So you will have to construct a
+larger version of your molecule as a pre-processing step and input a
+new data file to LAMMPS.
+</P>
+<P>If the current simulation was read in from a restart file (before a
+run is performed), there can have been no fix information stored in
+the file for individual atoms. Similarly, no fixes can be defined at
+the time the replicate command is used that require vectors of atom
+information to be stored. This is because the replicate command does
+not know how to replicate that information for new atoms it creates.
+</P>
+<P>Replicating a system that has rigid bodies (defined via the <A HREF = "fix_rigid.html">fix
+rigid</A> command), either currently defined or that
+created the restart file which was read in before replicating, can
+cause problems if there is a bond between a pair of rigid bodies that
+straddle a periodic boundary. This is because the periodic image
+information for particles in the rigid bodies are set differently than
+for a non-rigid system and can result in a new bond being created that
+spans the periodic box. Thus you cannot use the replicate command in
+this scenario.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/rerun.html b/doc/doc2/rerun.html
new file mode 100644
index 000000000..8bb6b2951
--- /dev/null
+++ b/doc/doc2/rerun.html
@@ -0,0 +1,210 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>rerun command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>rerun file1 file2 ... keyword args ...
+</PRE>
+<UL><LI>file1,file2,... = dump file(s) to read
+
+<LI>one or more keywords may be appended, keyword <I>dump</I> must appear and be last
+
+<PRE>keyword = <I>first</I> or <I>last</I> or <I>every</I> or <I>skip</I> or <I>start</I> or <I>stop</I> or <I>dump</I>
+ <I>first</I> args = Nfirts
+ Nfirst = dump timestep to start on
+ <I>last</I> args = Nlast
+ Nlast = dumptimestep to stop on
+ <I>every</I> args = Nevery
+ Nevery = read snapshots matching every this many timesteps
+ <I>skip</I> args = Nskip
+ Nskip = read one out of every Nskip snapshots
+ <I>start</I> args = Nstart
+ Nstart = timestep on which pseudo run will start
+ <I>stop</I> args = Nstop
+ Nstop = timestep to which pseudo run will end
+ <I>dump</I> args = same as <A HREF = "read_dump.html">read_dump</A> command starting with its field arguments
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>rerun dump.file dump x y z vx vy vz
+rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
+rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj
+rerun dump.dcd dump x y z box no format molfile dcd
+rerun ../run7/dump.file.gz skip 2 dump x y z box yes
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Perform a psuedo simulation run where atom information is read one
+snapshot at a time from a dump file(s), and energies and forces are
+computed on the shapshot to produce thermodynamic or other output.
+</P>
+<P>This can be useful in the following kinds of scenarios, after an
+initial simulation produced the dump file:
+</P>
+<UL><LI>Compute the energy and forces of snaphots using a different potential.
+
+
+<LI>Calculate one or more diagnostic quantities on the snapshots that
+weren't computed in the initial run. These can also be computed with
+settings not used in the initial run, e.g. computing an RDF via the
+<A HREF = "compute.rdf.html">compute rdf</A> command with a longer cutoff than was
+used initially.
+
+<LI>Calculate the portion of per-atom forces resulting from a subset of
+the potential. E.g. compute only Coulombic forces. This can be done
+by only defining only a Coulombic pair style in the rerun script.
+Doing this in the original script would result in different (bad)
+dynamics.
+</UL>
+<P>Conceptually, using the rerun command is like running an input script
+that has a loop in it (see the <A HREF = "next.html">next</A> and <A HREF = "jump.html">jump</A>
+commands). Each iteration of the loop reads one snapshot from the
+dump file via the <A HREF = "read_dump.html">read_dump</A> command, sets the
+timestep to the appropriate value, and then invokes a <A HREF = "run.html">run</A>
+command for zero timesteps to simply compute energy and forces, and
+any other <A HREF = "thermo_style.html">thermodynamic output</A> or diagnostic info
+you have defined. This computation also invokes any fixes you have
+defined that apply constraints to the system, such as <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "fix_indent.html">fix indent</A>.
+</P>
+<P>Note that a simulation box must already be defined before using the
+rerun command. This can be done by the <A HREF = "create_box.html">create_box</A>,
+<A HREF = "read_data.html">read_data</A>, or <A HREF = "read_restart.html">read_restart</A>
+commands.
+</P>
+<P>Also note that reading per-atom information from dump snapshots is
+limited to the atom coordinates, velocities and image flags as
+explained in the <A HREF = "read_dump.html">read_dump</A> command. Other atom
+properties, which may be necessary to compute energies and forces,
+such as atom charge, or bond topology information for a molecular
+system, are not read from (or even contained in) dump files. Thus
+this auxiliary information should be defined in the usual way, e.g. in
+a data file read in by a <A HREF = "read_data.html">read_data</A> command, before
+using the rerun command.
+</P>
+<HR>
+
+<P>If more than one dump file is specified, the dump files are read one
+after the other. It is assumed that snapshot timesteps will be in
+ascending order. If a snapshot is encountered that is not in
+ascending order, it will cause the rerun command to complete.
+</P>
+<P>The <I>first</I>, <I>last</I>, <I>every</I>, <I>skip</I> keywords determine which
+snapshots are read from the dump file(s). Snapshots are skipped until
+they have a timestamp >= <I>Nfirst</I>. When a snapshot with a timestamp >
+<I>Nlast</I> is encountered, the rerun command finishes. Note below that
+the defaults for <I>first</I> and <I>last</I> are to read all snapshots. If the
+<I>every</I> keyword is set to a value > 0, then only snapshots with
+timestamps that are a multiple of <I>Nevery</I> are read (the first
+snapshot is always read). If <I>Nevery</I> = 0, then this criterion is
+ignored, i.e. every snapshot is read that meets the other criteria.
+If the <I>skip</I> keyword is used, then after the first snapshot is read,
+every Nth snapshot is read, where N = <I>Nskip</I>. E.g. if <I>Nskip</I> = 3,
+then only 1 out of every 3 snapshots is read, assuming the snapshot
+timestamp is also consistent with the other criteria.
+</P>
+<P>The <I>start</I> and <I>stop</I> keywords do not affect which snapshots are read
+from the dump file(s). Rather, they have the same meaning that they
+do for the <A HREF = "run.html">run</A> command. They only need to be defined if
+(a) you are using a <A HREF = "fix.html">fix</A> command that changes some value
+over time, and (b) you want the reference point for elapsed time (from
+start to stop) to be different than the <I>first</I> and <I>last</I> settings.
+See the doc page for individual fixes to see which ones can be used
+with the <I>start/stop</I> keywords. Note that if you define neither of
+the <I>start</I>/<I>stop</I> or <I>first</I>/<I>last</I> keywords, then LAMMPS treats the
+pseudo run as going from 0 to a huge value (effectively infinity).
+This means that any quantity that a fix scales as a fraction of
+elapsed time in the run, will essentially remain at its intiial value.
+Also note that an error will occur if you read a snapshot from the
+dump file with a timestep value larger than the <I>stop</I> setting you
+have specified.
+</P>
+<P>The <I>dump</I> keyword is required and must be the last keyword specified.
+Its arguments are passed internally to the <A HREF = "read_dump.html">read_dump</A>
+command. The first argument following the <I>dump</I> keyword should be
+the <I>field1</I> argument of the <A HREF = "read_dump.html">read_dump</A> command. See
+the <A HREF = "read_dump.html">read_dump</A> doc page for details on the various
+options it allows for extracting information from the dump file
+snapshots, and for using that information to alter the LAMMPS
+simulation.
+</P>
+<HR>
+
+<P>In general, a LAMMPS input script that uses a rerun command can
+include and perform all the usual operations of an input script that
+uses the <A HREF = "run.html">run</A> command. There are a few exceptions and
+points to consider, as discussed here.
+</P>
+<P>Fixes that perform time integration, such as <A HREF = "fix_nve.html">fix nve</A> or
+<A HREF = "fix_nh.html">fix npt</A> are not invoked, since no time integration is
+performed. Fixes that perturb or constrain the forces on atoms will
+be invoked, just as they would during a normal run. Examples are <A HREF = "fix_indent.html">fix
+indent</A> and <A HREF = "fix_langevin.html">fix langevin</A>. So you
+should think carefully as to whether that makes sense for the manner
+in which you are reprocessing the dump snapshots.
+</P>
+<P>If you only want the rerun script to perform analyses that do not
+involve pair interactions, such as use compute msd to calculated
+displacements over time, you do not need to define a <A HREF = "pair_style.html">pair
+style</A>, which may also mean neighbor lists will not
+need to be calculated which saves time. The <A HREF = "comm_modify.html">comm_modify
+cutoff</A> command can also be used to insure ghost
+atoms are acquired from far enough away for operations like bond and
+angle evaluations, if no pair style is being used.
+</P>
+<P>Every time a snapshot is read, the timestep for the simulation is
+reset, as if the <A HREF = "reset_timestep.html">reset_timestep</A> command were
+used. This command has some restrictions as to what fixes can be
+defined. See its doc page for details. For example, the <A HREF = "fix_deposit.html">fix
+deposit</A> and <A HREF = "fix_dt_reset.html">fix dt/reset</A> fixes
+are in this category. They also make no sense to use with a rerun
+command.
+</P>
+<P>If time-averaging fixes like <A HREF = "fix_ave_time.html">fix ave/time</A> are
+used, they are invoked on timesteps that are a function of their
+<I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> settings. As an example, see the
+<A HREF = "fix_ave_time.html">fix ave/time</A> doc page for details. You must
+insure those settings are consistent with the snapshot timestamps that
+are read from the dump file(s). If an averaging fix is not invoked on
+a timestep it expects to be, LAMMPS will flag an error.
+</P>
+<P>The various forms of LAMMPS output, as defined by the
+<A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "thermo.html">thermo</A>,
+<A HREF = "dump.html">dump</A>, and <A HREF = "restart.html">restart</A> commands occur on
+specific timesteps. If successvive dump snapshots skip those
+timesteps, then no output will be produced. E.g. if you request
+thermodynamic output every 100 steps, but the dump file snapshots are
+every 1000 steps, then you will only see thermodynamic output every
+1000 steps.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To read gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
+LAMMPS</A> section of the documentation.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_dump.html">read_dump</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are first = 0, last = a huge value (effectively
+infinity), start = same as first, stop = same as last, every = 0, skip
+= 1;
+</P>
+</HTML>
diff --git a/doc/doc2/reset_timestep.html b/doc/doc2/reset_timestep.html
new file mode 100644
index 000000000..5e678cb59
--- /dev/null
+++ b/doc/doc2/reset_timestep.html
@@ -0,0 +1,66 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>reset_timestep command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>reset_timestep N
+</PRE>
+<UL><LI>N = timestep number
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>reset_timestep 0
+reset_timestep 4000000
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the timestep counter to the specified value. This command
+normally comes after the timestep has been set by reading a restart
+file via the <A HREF = "read_restart.html">read_restart</A> command, or a previous
+simulation advanced the timestep.
+</P>
+<P>The <A HREF = "read_data.html">read_data</A> and <A HREF = "create_box.html">create_box</A>
+commands set the timestep to 0; the <A HREF = "read_restart.html">read_restart</A>
+command sets the timestep to the value it had when the restart file
+was written.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P>This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform certain kinds of time-dependent operations.
+Examples are the <A HREF = "fix_deposit.html">fix deposit</A> and <A HREF = "fix_dt_reset.html">fix
+dt/reset</A> commands. The former adds atoms on
+specific timesteps. The latter keeps track of accumulated time.
+</P>
+<P>Various fixes use the current timestep to calculate related
+quantities. If the timestep is reset, this may produce unexpected
+behavior, but LAMMPS allows the fixes to be defined even if the
+timestep is reset. For example, commands which thermostat the system,
+e.g. <A HREF = "fix_nh.html">fix nvt</A>, allow you to specify a target temperature
+which ramps from Tstart to Tstop which may persist over several runs.
+If you change the timestep, you may induce an instantaneous change in
+the target temperature.
+</P>
+<P>Resetting the timestep clears flags for <A HREF = "compute.html">computes</A> that
+may have calculated some quantity from a previous run. This means
+these quantity cannot be accessed by a variable in between runs until
+a new run is performed. See the <A HREF = "variable.html">variable</A> command for
+more details.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "rerun.html">rerun</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/restart.html b/doc/doc2/restart.html
new file mode 100644
index 000000000..083e74e02
--- /dev/null
+++ b/doc/doc2/restart.html
@@ -0,0 +1,187 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>restart command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>restart 0
+restart N root keyword value ...
+restart N file1 file2 keyword value ...
+</PRE>
+<UL><LI>N = write a restart file every this many timesteps
+
+<LI>N can be a variable (see below)
+
+<LI>root = filename to which timestep # is appended
+
+<LI>file1,file2 = two full filenames, toggle between them when writing file
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>fileper</I> or <I>nfile</I>
+
+<PRE> <I>fileper</I> arg = Np
+ Np = write one file for every this many processors
+ <I>nfile</I> arg = Nf
+ Nf = write this many files, one from each of Nf processors
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>restart 0
+restart 1000 poly.restart
+restart 1000 poly.restart.mpiio
+restart 1000 restart.*.equil
+restart 10000 poly.%.1 poly.%.2 nfile 10
+restart v_mystep poly.restart
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write out a binary restart file with the current state of the
+simulation every so many timesteps, in either or both of two modes, as
+a run proceeds. A value of 0 means do not write out any restart
+files. The two modes are as follows. If one filename is specified, a
+series of filenames will be created which include the timestep in the
+filename. If two filenames are specified, only 2 restart files will
+be created, with those names. LAMMPS will toggle between the 2 names
+as it writes successive restart files.
+</P>
+<P>Note that you can specify the restart command twice, once with a
+single filename and once with two filenames. This would allow you,
+for example, to write out archival restart files every 100000 steps
+using a single filenname, and more frequent temporary restart files
+every 1000 steps, using two filenames. Using restart 0 will turn off
+both modes of output.
+</P>
+<P>Similar to <A HREF = "dump.html">dump</A> files, the restart filename(s) can contain
+two wild-card characters.
+</P>
+<P>If a "*" appears in the single filename, it is replaced with the
+current timestep value. This is only recognized when a single
+filename is used (not when toggling back and forth). Thus, the 3rd
+example above creates restart files as follows: restart.1000.equil,
+restart.2000.equil, etc. If a single filename is used with no "*",
+then the timestep value is appended. E.g. the 2nd example above
+creates restart files as follows: poly.restart.1000,
+poly.restart.2000, etc.
+</P>
+<P>If a "%" character appears in the restart filename(s), then one file
+is written for each processor and the "%" character is replaced with
+the processor ID from 0 to P-1. An additional file with the "%"
+replaced by "base" is also written, which contains global information.
+For example, the files written on step 1000 for filename restart.%
+would be restart.base.1000, restart.0.1000, restart.1.1000, ...,
+restart.P-1.1000. This creates smaller files and can be a fast mode
+of output and subsequent input on parallel machines that support
+parallel I/O. The optional <I>fileper</I> and <I>nfile</I> keywords discussed
+below can alter the number of files written.
+</P>
+<P>The restart file can also be written in parallel as one large binary
+file via the MPI-IO library, which is part of the MPI standard for
+versions 2.0 and above. Using MPI-IO requires two steps. First,
+build LAMMPS with its MPIIO package installed, e.g.
+</P>
+<PRE>make yes-mpiio # installs the MPIIO package
+make g++ # build LAMMPS for your platform
+</PRE>
+<P>Second, use a restart filename which contains ".mpiio". Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+</P>
+<P>Restart files are written on timesteps that are a multiple of N but
+not on the first timestep of a run or minimization. You can use the
+<A HREF = "write_restart.html">write_restart</A> command to write a restart file
+before a run begins. A restart file is not written on the last
+timestep of a run unless it is a multiple of N. A restart file is
+written on the last timestep of a minimization if N > 0 and the
+minimization converges.
+</P>
+<P>Instead of a numeric value, N can be specifed as an <A HREF = "variable.html">equal-style
+variable</A>, which should be specified as v_name, where
+name is the variable name. In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which a
+restart file will be written out. On that timestep, the variable will
+be evaluated again to determine the next timestep, etc. Thus the
+variable should return timestep values. See the stagger() and
+logfreq() and stride() math functions for <A HREF = "variable.html">equal-style
+variables</A>, as examples of useful functions to use in
+this context. Other similar math functions could easily be added as
+options for <A HREF = "variable.html">equal-style variables</A>.
+</P>
+<P>For example, the following commands will write restart files
+every step from 1100 to 1200, and could be useful for debugging
+a simulation where something goes wrong at step 1163:
+</P>
+<PRE>variable s equal stride(1100,1200,1)
+restart v_s tmp.restart
+</PRE>
+<HR>
+
+<P>See the <A HREF = "read_restart.html">read_restart</A> command for information about
+what is stored in a restart file.
+</P>
+<P>Restart files can be read by a <A HREF = "read_restart.html">read_restart</A>
+command to restart a simulation from a particular state. Because the
+file is binary (to enable exact restarts), it may not be readable on
+another machine. In this case, you can use the <A HREF = "Section_start.html#start_7">-r command-line
+switch</A> to convert a restart file to a data
+file.
+</P>
+<P>IMPORTANT NOTE: Although the purpose of restart files is to enable
+restarting a simulation from where it left off, not all information
+about a simulation is stored in the file. For example, the list of
+fixes that were specified during the initial run is not stored, which
+means the new input script must specify any fixes you want to use.
+Even when restart information is stored in the file, as it is for some
+fixes, commands may need to be re-specified in the new input script,
+in order to re-use that information. See the
+<A HREF = "read_restart.html">read_restart</A> command for information about what is
+stored in a restart file.
+</P>
+<HR>
+
+<P>The optional <I>nfile</I> or <I>fileper</I> keywords can be used in conjunction
+with the "%" wildcard character in the specified restart file name(s).
+As explained above, the "%" character causes the restart file to be
+written in pieces, one piece for each of P processors. By default P =
+the number of processors the simulation is running on. The <I>nfile</I> or
+<I>fileper</I> keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+</P>
+<P>The <I>nfile</I> keyword sets P to the specified Nf value. For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75. Each will collect information
+from itself and the next 24 processors and write it to a restart file.
+</P>
+<P>For the <I>fileper</I> keyword, the specified value of Np means write one
+file for every Np processors. For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "write_restart.html">write_restart</A>, <A HREF = "read_restart.html">read_restart</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>restart 0
+</PRE>
+</HTML>
diff --git a/doc/doc2/run.html b/doc/doc2/run.html
new file mode 100644
index 000000000..3ccb7bb70
--- /dev/null
+++ b/doc/doc2/run.html
@@ -0,0 +1,215 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>run command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>run N keyword values ...
+</PRE>
+<UL><LI>N = # of timesteps
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>upto</I> or <I>start</I> or <I>stop</I> or <I>pre</I> or <I>post</I> or <I>every</I>
+
+<PRE> <I>upto</I> value = none
+ <I>start</I> value = N1
+ N1 = timestep at which 1st run started
+ <I>stop</I> value = N2
+ N2 = timestep at which last run will end
+ <I>pre</I> value = <I>no</I> or <I>yes</I>
+ <I>post</I> value = <I>no</I> or <I>yes</I>
+ <I>every</I> values = M c1 c2 ...
+ M = break the run into M-timestep segments and invoke one or more commands between each segment
+ c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
+ c1 = NULL means no command will be invoked
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>run 10000
+run 1000000 upto
+run 100 start 0 stop 1000
+run 1000 pre no post yes
+run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
+run 100000 every 1000 NULL
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Run or continue dynamics for a specified number of timesteps.
+</P>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, N refers to outer
+loop (largest) timesteps.
+</P>
+<P>A value of N = 0 is acceptable; only the thermodynamics of the system
+are computed and printed without taking a timestep.
+</P>
+<P>The <I>upto</I> keyword means to perform a run starting at the current
+timestep up to the specified timestep. E.g. if the current timestep
+is 10,000 and "run 100000 upto" is used, then an additional 90,000
+timesteps will be run. This can be useful for very long runs on a
+machine that allocates chunks of time and terminate your job when time
+is exceeded. If you need to restart your script multiple times
+(reading in the last restart file), you can keep restarting your
+script with the same run command until the simulation finally
+completes.
+</P>
+<P>The <I>start</I> or <I>stop</I> keywords can be used if multiple runs are being
+performed and you want a <A HREF = "fix.html">fix</A> command that changes some
+value over time (e.g. temperature) to make the change across the
+entire set of runs and not just a single run. See the doc page for
+individual fixes to see which ones can be used with the <I>start/stop</I>
+keywords.
+</P>
+<P>For example, consider this fix followed by 10 run commands:
+</P>
+<PRE>fix 1 all nvt 200.0 300.0 1.0
+run 1000 start 0 stop 10000
+run 1000 start 0 stop 10000
+...
+run 1000 start 0 stop 10000
+</PRE>
+<P>The NVT fix ramps the target temperature from 200.0 to 300.0 during a
+run. If the run commands did not have the start/stop keywords (just
+"run 1000"), then the temperature would ramp from 200.0 to 300.0
+during the 1000 steps of each run. With the start/stop keywords, the
+ramping takes place over the 10000 steps of all runs together.
+</P>
+<P>The <I>pre</I> and <I>post</I> keywords can be used to streamline the setup,
+clean-up, and associated output to the screen that happens before and
+after a run. This can be useful if you wish to do many short runs in
+succession (e.g. LAMMPS is being called as a library which is doing
+other computations between successive short LAMMPS runs).
+</P>
+<P>By default (pre and post = yes), LAMMPS creates neighbor lists,
+computes forces, and imposes fix constraints before every run. And
+after every run it gathers and prints timings statistics. If a run is
+just a continuation of a previous run (i.e. no settings are changed),
+the initial computation is not necessary; the old neighbor list is
+still valid as are the forces. So if <I>pre</I> is specified as "no" then
+the initial setup is skipped, except for printing thermodynamic info.
+Note that if <I>pre</I> is set to "no" for the very 1st run LAMMPS
+performs, then it is overridden, since the initial setup computations
+must be done.
+</P>
+<P>IMPORTANT NOTE: If your input script changes the system between 2
+runs, then the initial setup must be performed to insure the change is
+recognized by all parts of the code that are affected. Examples are
+adding a <A HREF = "fix.html">fix</A> or <A HREF = "dump.html">dump</A> or <A HREF = "compute.html">compute</A>,
+changing a <A HREF = "neigh_modify.html">neighbor</A> list parameter, or writing
+restart file which can migrate atoms between processors. LAMMPS has
+no easy way to check if this has happened, but it is an error to use
+the <I>pre no</I> option in this case.
+</P>
+<P>If <I>post</I> is specified as "no", the full timing summary is skipped;
+only a one-line summary timing is printed.
+</P>
+<P>The <I>every</I> keyword provides a means of breaking a LAMMPS run into a
+series of shorter runs. Optionally, one or more LAMMPS commands (c1,
+c2, ..., cN) will be executed in between the short runs. If used, the
+<I>every</I> keyword must be the last keyword, since it has a variable
+number of arguments. Each of the trailing arguments is a single
+LAMMPS command, and each command should be enclosed in quotes, so that
+the entire command will be treated as a single argument. This will
+also prevent any variables in the command from being evaluated until
+it is executed multiple times during the run. Note that if a command
+itself needs one of its arguments quoted (e.g. the <A HREF = "print.html">print</A>
+command), then you can use a combination of single and double quotes,
+as in the example above or below.
+</P>
+<P>The <I>every</I> keyword is a means to avoid listing a long series of runs
+and interleaving commands in your input script. For example, a
+<A HREF = "print.html">print</A> command could be invoked or a <A HREF = "fix.html">fix</A> could
+be redefined, e.g. to reset a thermostat temperature. Or this could
+be useful for invoking a command you have added to LAMMPS that wraps
+some other code (e.g. as a library) to perform a computation
+periodically during a long LAMMPS run. See <A HREF = "Section_modify.html">this
+section</A> of the documentation for info about how
+to add new commands to LAMMPS. See <A HREF = "Section_howto.html#howto_10">this
+section</A> of the documentation for ideas
+about how to couple LAMMPS to other codes.
+</P>
+<P>With the <I>every</I> option, N total steps are simulated, in shorter runs
+of M steps each. After each M-length run, the specified commands are
+invoked. If only a single command is specified as NULL, then no
+command is invoked. Thus these lines:
+</P>
+<PRE>variable q equal x[100]
+run 6000 every 2000 "print 'Coord = $q'"
+</PRE>
+<P>are the equivalent of:
+</P>
+<PRE>variable q equal x[100]
+run 2000
+print "Coord = $q"
+run 2000
+print "Coord = $q"
+run 2000
+print "Coord = $q"
+</PRE>
+<P>which does 3 runs of 2000 steps and prints the x-coordinate of a
+particular atom between runs. Note that the variable "$q" will
+be evaluated afresh each time the print command is executed.
+</P>
+<P>Note that by using the line continuation character "&", the run every
+command can be spread across many lines, though it is still a single
+command:
+</P>
+<PRE>run 100000 every 1000 &
+ "print 'Minimum value = $a'" &
+ "print 'Maximum value = $b'" &
+ "print 'Temp = $c'" &
+ "print 'Press = $d'"
+</PRE>
+<P>If the <I>pre</I> and <I>post</I> options are set to "no" when used with the
+<I>every</I> keyword, then the 1st run will do the full setup and the last
+run will print the full timing summary, but these operations will be
+skipped for intermediate runs.
+</P>
+<P>IMPORTANT NOTE: You might hope to specify a command that exits the run
+by jumping out of the loop, e.g.
+</P>
+<PRE>variable t equal temp
+run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"
+</PRE>
+<P>Unfortunately this will not currently work. The run command simply
+executes each command one at a time each time it pauses, then
+continues the run. You can replace the jump command with a simple
+<A HREF = "quit.html">quit</A> command and cause LAMMPS to exit during the
+middle of a run when the condition is met.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>When not using the <I>upto</I> keyword, the number of specified timesteps N
+must fit in a signed 32-bit integer, so you are limited to slightly
+more than 2 billion steps (2^31) in a single run. When using <I>upto</I>,
+N can be larger than a signed 32-bit integer, however the difference
+between N and the current timestep must still be no larger than
+2^31 steps.
+</P>
+<P>However, with or without the <I>upto</I> keyword, you can perform
+successive runs to run a simulation for any number of steps (ok, up to
+2^63 total steps). I.e. the timestep counter within LAMMPS is a
+64-bit signed integer.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "minimize.html">minimize</A>, <A HREF = "run_style.html">run_style</A>,
+<A HREF = "temper.html">temper</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are start = the current timestep, stop = current
+timestep + N, pre = yes, and post = yes.
+</P>
+</HTML>
diff --git a/doc/doc2/run_style.html b/doc/doc2/run_style.html
new file mode 100644
index 000000000..2e12bbac8
--- /dev/null
+++ b/doc/doc2/run_style.html
@@ -0,0 +1,298 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>run_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>run_style style args
+</PRE>
+<UL><LI>style = <I>verlet</I> or <I>verlet/split</I> or <I>respa</I> or <I>respa/omp</I>
+
+<PRE> <I>verlet</I> args = none
+ <I>verlet/split</I> args = none
+ <I>respa</I> args = N n1 n2 ... keyword values ...
+ N = # of levels of rRESPA
+ n1, n2, ... = loop factor between rRESPA levels (N-1 values)
+ zero or more keyword/value pairings may be appended to the loop factors
+ keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
+ <I>pair</I> or <I>inner</I> or <I>middle</I> or <I>outer</I> or <I>hybrid</I> or <I>kspace</I>
+ <I>bond</I> value = M
+ M = which level (1-N) to compute bond forces in
+ <I>angle</I> value = M
+ M = which level (1-N) to compute angle forces in
+ <I>dihedral</I> value = M
+ M = which level (1-N) to compute dihedral forces in
+ <I>improper</I> value = M
+ M = which level (1-N) to compute improper forces in
+ <I>pair</I> value = M
+ M = which level (1-N) to compute pair forces in
+ <I>inner</I> values = M cut1 cut2
+ M = which level (1-N) to compute pair inner forces in
+ cut1 = inner cutoff between pair inner and
+ pair middle or outer (distance units)
+ cut2 = outer cutoff between pair inner and
+ pair middle or outer (distance units)
+ <I>middle</I> values = M cut1 cut2
+ M = which level (1-N) to compute pair middle forces in
+ cut1 = inner cutoff between pair middle and pair outer (distance units)
+ cut2 = outer cutoff between pair middle and pair outer (distance units)
+ <I>outer</I> value = M
+ M = which level (1-N) to compute pair outer forces in
+ <I>hybrid</I> values = M1 [M2 ...] (as many values as there are hybrid sub-styles
+ M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
+ M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
+ ...
+ <I>kspace</I> value = M
+ M = which level (1-N) to compute kspace forces in
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>run_style verlet
+run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
+</PRE>
+<PRE>run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Choose the style of time integrator used for molecular dynamics
+simulations performed by LAMMPS.
+</P>
+<P>The <I>verlet</I> style is a standard velocity-Verlet integrator.
+</P>
+<HR>
+
+<P>The <I>verlet/split</I> style is also a velocity-Verlet integrator, but it
+splits the force calculation within each timestep over 2 partitions of
+processors. See <A HREF = "Section_start.html#start_7">Section_start 6</A> for an
+explanation of the -partition command-line switch.
+</P>
+<P>Specifically, this style performs all computation except the
+<A HREF = "kspace_style.html">kspace_style</A> portion of the force field on the 1st
+partition. This include the <A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond
+style</A>, <A HREF = "neighbor.html">neighbor list building</A>,
+<A HREF = "fix.html">fixes</A> including time intergration, and output. The
+<A HREF = "kspace_style.html">kspace_style</A> portion of the calculation is
+performed on the 2nd partition.
+</P>
+<P>This is most useful for the PPPM kspace_style when its performance on
+a large number of processors degrades due to the cost of communication
+in its 3d FFTs. In this scenario, splitting your P total processors
+into 2 subsets of processors, P1 in the 1st partition and P2 in the
+2nd partition, can enable your simulation to run faster. This is
+because the long-range forces in PPPM can be calculated at the same
+time as pair-wise and bonded forces are being calculated, and the FFTs
+can actually speed up when running on fewer processors.
+</P>
+<P>To use this style, you must define 2 partitions where P1 is a multiple
+of P2. Typically having P1 be 3x larger than P2 is a good choice.
+The 3d processor layouts in each partition must overlay in the
+following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by
+Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
+for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
+</P>
+<P>Typically the best way to do this is to let the 1st partition choose
+its onn optimal layout, then require the 2nd partition's layout to
+match the integer multiple constraint. See the
+<A HREF = "processors.html">processors</A> command with its <I>part</I> keyword for a way
+to control this, e.g.
+</P>
+<PRE>procssors * * * part 1 2 multiple
+</PRE>
+<P>You can also use the <A HREF = "partition.html">partition</A> command to explicitly
+specity the processor layout on each partition. E.g. for 2 partitions
+of 60 and 15 processors each:
+</P>
+<PRE>partition yes 1 processors 3 4 5
+partition yes 2 processors 3 1 5
+</PRE>
+<P>When you run in 2-partition mode with the <I>verlet/split</I> style, the
+thermodyanmic data for the entire simulation will be output to the log
+and screen file of the 1st partition, which are log.lammps.0 and
+screen.0 by default; see the "-plog and -pscreen command-line
+switches"Section_start.html#start_7 to change this. The log and
+screen file for the 2nd partition will not contain thermodynamic
+output beyone the 1st timestep of the run.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+performance details of the speed-up offered by the <I>verlet/split</I>
+style. One important performance consideration is the assignemnt of
+logical processors in the 2 partitions to the physical cores of a
+parallel machine. The <A HREF = "processors.html">processors</A> command has
+options to support this, and strategies are discussed in
+<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual.
+</P>
+<HR>
+
+<P>The <I>respa</I> style implements the rRESPA multi-timescale integrator
+<A HREF = "#Tuckerman">(Tuckerman)</A> with N hierarchical levels, where level 1 is
+the innermost loop (shortest timestep) and level N is the outermost
+loop (largest timestep). The loop factor arguments specify what the
+looping factor is between levels. N1 specifies the number of
+iterations of level 1 for a single iteration of level 2, N2 is the
+iterations of level 2 per iteration of level 3, etc. N-1 looping
+parameters must be specified.
+</P>
+<P>The <A HREF = "timestep.html">timestep</A> command sets the timestep for the
+outermost rRESPA level. Thus if the example command above for a
+4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
+would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that
+specify number of timesteps (e.g. <A HREF = "neigh_modify.html">neigh_modify</A>
+parameters, <A HREF = "dump.html">dump</A> every N timesteps, etc) refer to the
+outermost timesteps.
+</P>
+<P>The rRESPA keywords enable you to specify at what level of the
+hierarchy various forces will be computed. If not specified, the
+defaults are that bond forces are computed at level 1 (innermost
+loop), angle forces are computed where bond forces are, dihedral
+forces are computed where angle forces are, improper forces are
+computed where dihedral forces are, pair forces are computed at the
+outermost level, and kspace forces are computed where pair forces are.
+The inner, middle, outer forces have no defaults.
+</P>
+<P>The <I>inner</I> and <I>middle</I> keywords take additional arguments for
+cutoffs that are used by the pairwise force computations. If the 2
+cutoffs for <I>inner</I> are 5.0 and 6.0, this means that all pairs up to
+6.0 apart are computed by the inner force. Those between 5.0 and 6.0
+have their force go ramped to 0.0 so the overlap with the next regime
+(middle or outer) is smooth. The next regime (middle or outer) will
+compute forces for all pairs from 5.0 outward, with those from 5.0 to
+6.0 having their value ramped in an inverse manner.
+</P>
+<P>Only some pair potentials support the use of the <I>inner</I> and <I>middle</I>
+and <I>outer</I> keywords. If not, only the <I>pair</I> keyword can be used
+with that pair style, meaning all pairwise forces are computed at the
+same rRESPA level. See the doc pages for individual pair styles for
+details.i
+</P>
+<P>Another variant to use pair potentials in rRESPA is with the <I>hybrid</I>
+keyword, which requires the use of a <A HREF = "pair_hybrid.html">hybrid pair_style</A>
+In this scenario, different sub-styles of the hybrid pair style are
+evaluated at different rRESPA levels. Thus the hybrid keyword requires
+as many level assignments as there are hybrid substyles which designate
+the respective sub-styles to the rRESPA level according to their order
+of definition in the pair_style command. Since the <I>hybrid</I> designates
+pair force computations, it is mututally exclusive with either the <I>pair</I>
+or the <I>inner</I>/<I>middle</I>/<I>outer</I> keywords.
+</P>
+<P>When using rRESPA (or for any MD simulation) care must be taken to
+choose a timestep size(s) that insures the Hamiltonian for the chosen
+ensemble is conserved. For the constant NVE ensemble, total energy
+must be conserved. Unfortunately, it is difficult to know <I>a priori</I>
+how well energy will be conserved, and a fairly long test simulation
+(~10 ps) is usually necessary in order to verify that no long-term
+drift in energy occurs with the trial set of parameters.
+</P>
+<P>With that caveat, a few rules-of-thumb may be useful in selecting
+<I>respa</I> settings. The following applies mostly to biomolecular
+simulations using the CHARMM or a similar all-atom force field, but
+the concepts are adaptable to other problems. Without SHAKE, bonds
+involving hydrogen atoms exhibit high-frequency vibrations and require
+a timestep on the order of 0.5 fmsec in order to conserve energy. The
+relatively inexpensive force computations for the bonds, angles,
+impropers, and dihedrals can be computed on this innermost 0.5 fmsec
+step. The outermost timestep cannot be greater than 4.0 fmsec without
+risking energy drift. Smooth switching of forces between the levels
+of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
+angstrom "healing distance" (the distance between the outer and inner
+cutoffs) works reasonably well. We thus recommend the following
+settings for use of the <I>respa</I> style without SHAKE in biomolecular
+simulations:
+</P>
+<PRE>timestep 4.0
+run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
+</PRE>
+<P>With these settings, users can expect good energy conservation and
+roughly a 2.5 fold speedup over the <I>verlet</I> style with a 0.5 fmsec
+timestep.
+</P>
+<P>If SHAKE is used with the <I>respa</I> style, time reversibility is lost,
+but substantially longer time steps can be achieved. For biomolecular
+simulations using the CHARMM or similar all-atom force field, bonds
+involving hydrogen atoms exhibit high frequency vibrations and require
+a time step on the order of 0.5 fmsec in order to conserve energy.
+These high frequency modes also limit the outer time step sizes since
+the modes are coupled. It is therefore desirable to use SHAKE with
+respa in order to freeze out these high frequency motions and increase
+the size of the time steps in the respa hierarchy. The following
+settings can be used for biomolecular simulations with SHAKE and
+rRESPA:
+</P>
+<PRE>fix 2 all shake 0.000001 500 0 m 1.0 a 1
+timestep 4.0
+run_style respa 2 2 inner 1 4.0 5.0 outer 2
+</PRE>
+<P>With these settings, users can expect good energy conservation and
+roughly a 1.5 fold speedup over the <I>verlet</I> style with SHAKE and a
+2.0 fmsec timestep.
+</P>
+<P>For non-biomolecular simulations, the <I>respa</I> style can be
+advantageous if there is a clear separation of time scales - fast and
+slow modes in the simulation. Even a LJ system can benefit from
+rRESPA if the interactions are divided by the inner, middle and outer
+keywords. A 2-fold or more speedup can be obtained while maintaining
+good energy conservation. In real units, for a pure LJ fluid at
+liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
+Kcal/mol, the following settings seem to work well:
+</P>
+<PRE>timestep 36.0
+run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
+</PRE>
+<HR>
+
+<P>The <I>respa/omp</I> styles is a variant of <I>respa</I> adapted for use with
+pair, bond, angle, dihedral, improper, or kspace styles with an <I>omp</I>
+suffix. It is functionally equivalent to <I>respa</I> but performs additional
+operations required for managing <I>omp</I> styles. For more on <I>omp</I> styles
+see the <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual.
+Accelerated styles take the same arguments and should produce the same
+results, except for round-off and precision issues.
+</P>
+<P>You can specify <I>respa/omp</I> explicitly in your input script, or
+you can use the <A HREF = "Section_start.html#start_7">-suffix command-line switch</A>
+when you invoke LAMMPS, or you can use the <A HREF = "suffix.html">suffix</A>
+command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>The <I>verlet/split</I> style can only be used if LAMMPS was built with the
+REPLICA package. Correspondingly the <I>respa/omp</I> style is available only
+if the USER-OMP package was included. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
+</P>
+<P>Whenever using rRESPA, the user should experiment with trade-offs in
+speed and accuracy for their system, and verify that they are
+conserving energy to adequate precision.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "timestep.html">timestep</A>, <A HREF = "run.html">run</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>run_style verlet
+</PRE>
+<HR>
+
+<A NAME = "Tuckerman"></A>
+
+<P><B>(Tuckerman)</B> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
+(1992).
+</P>
+</HTML>
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+ <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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diff --git a/doc/doc2/set.html b/doc/doc2/set.html
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--- /dev/null
+++ b/doc/doc2/set.html
@@ -0,0 +1,392 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>set command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>set style ID keyword values ...
+</PRE>
+<UL><LI>style = <I>atom</I> or <I>type</I> or <I>mol</I> or <I>group</I> or <I>region</I>
+
+<LI>ID = atom ID range or type range or mol ID range or group ID or region ID
+
+<LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>diameter</I> or <I>shape</I> or <I>length</I> or <I>tri</I> or <I>theta</I> or <I>angmom</I> or <I>mass</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
+ <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
+ <I>meso_e</I> or <I>meso_cv</I> or <I>meso_rho</I> or <I>i_name</I> or <I>d_name</I>
+
+<PRE> <I>type</I> value = atom type
+ value can be an atom-style variable (see below)
+ <I>type/fraction</I> values = type fraction seed
+ type = new atom type
+ fraction = fraction of selected atoms to set to new atom type
+ seed = random # seed (positive integer)
+ <I>mol</I> value = molecule ID
+ value can be an atom-style variable (see below)
+ <I>x</I>,<I>y</I>,<I>z</I> value = atom coordinate (distance units)
+ value can be an atom-style variable (see below)
+ <I>charge</I> value = atomic charge (charge units)
+ value can be an atom-style variable (see below)
+ <I>dipole</I> values = x y z
+ x,y,z = orientation of dipole moment vector
+ any of x,y,z can be an atom-style variable (see below)
+ <I>dipole/random</I> value = seed Dlen
+ seed = random # seed (positive integer) for dipole moment orientations
+ Dlen = magnitude of dipole moment (dipole units)
+ <I>quat</I> values = a b c theta
+ a,b,c = unit vector to rotate particle around via right-hand rule
+ theta = rotation angle (degrees)
+ any of a,b,c,theta can be an atom-style variable (see below)
+ <I>quat/random</I> value = seed
+ seed = random # seed (positive integer) for quaternion orientations
+ <I>diameter</I> value = diameter of spherical particle (distance units)
+ value can be an atom-style variable (see below)
+ <I>shape</I> value = Sx Sy Sz
+ Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
+ <I>length</I> value = len
+ len = length of line segment (distance units)
+ len can be an atom-style variable (see below)
+ <I>tri</I> value = side
+ side = side length of equilateral triangle (distance units)
+ side can be an atom-style variable (see below)
+ <I>theta</I> value = angle (degrees)
+ angle = orientation of line segment with respect to x-axis
+ angle can be an atom-style variable (see below)
+ <I>angmom</I> values = Lx Ly Lz
+ Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
+ any of Lx,Ly,Lz can be an atom-style variable (see below)
+ <I>mass</I> value = per-atom mass (mass units)
+ value can be an atom-style variable (see below)
+ <I>density</I> value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
+ value can be an atom-style variable (see below)
+ <I>volume</I> value = particle volume for Peridynamic particle (distance^3 units)
+ value can be an atom-style variable (see below)
+ <I>image</I> nx ny nz
+ nx,ny,nz = which periodic image of the simulation box the atom is in
+ <I>bond</I> value = bond type for all bonds between selected atoms
+ <I>angle</I> value = angle type for all angles between selected atoms
+ <I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
+ <I>improper</I> value = improper type for all impropers between selected atoms
+ <I>meso_e</I> value = energy of SPH particles (need units)
+ value can be an atom-style variable (see below)
+ <I>meso_cv</I> value = heat capacity of SPH particles (need units)
+ value can be an atom-style variable (see below)
+ <I>meso_rho</I> value = density of SPH particles (need units)
+ value can be an atom-style variable (see below)
+ <I>i_name</I> value = value for custom integer vector with name
+ value can be an atom-style variable (see below)
+ <I>d_name</I> value = value for custom floating-point vector with name
+ value can be an atom-style variable (see below)
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>set group solvent type 2
+set group solvent type/fraction 2 0.5 12393
+set group edge bond 4
+set region half charge 0.5
+set type 3 charge 0.5
+set type 1*3 charge 0.5
+set atom * charge v_atomfile
+set atom 100*200 x 0.5 y 1.0
+set atom 1492 type 3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set one or more properties of one or more atoms. Since atom
+properties are initially assigned by the <A HREF = "read_data.html">read_data</A>,
+<A HREF = "read_restart.html">read_restart</A> or <A HREF = "create_atoms.html">create_atoms</A>
+commands, this command changes those assignments. This can be useful
+for overriding the default values assigned by the
+<A HREF = "create_atoms.html">create_atoms</A> command (e.g. charge = 0.0). It can
+be useful for altering pairwise and molecular force interactions,
+since force-field coefficients are defined in terms of types. It can
+be used to change the labeling of atoms by atom type or molecule ID
+when they are output in <A HREF = "dump.html">dump</A> files. It can also be useful
+for debugging purposes; i.e. positioning an atom at a precise location
+to compute subsequent forces or energy.
+</P>
+<P>Note that the <I>style</I> and <I>ID</I> arguments determine which atoms have
+their properties reset. The remaining keywords specify which
+properties to reset and what the new values are. Some strings like
+<I>type</I> or <I>mol</I> can be used as a style and/or a keyword.
+</P>
+<HR>
+
+<P>This section describes how to select which atoms to change
+the properties of, via the <I>style</I> and <I>ID</I> arguments.
+</P>
+<P>The style <I>atom</I> selects all the atoms in a range of atom IDs. The
+style <I>type</I> selects all the atoms in a range of types. The style
+<I>mol</I> selects all the atoms in a range of molecule IDs.
+</P>
+<P>In each of the range cases, the range can be specified as a single
+numeric value, or a wildcard asterisk can be used to specify a range
+of values. This takes the form "*" or "*n" or "n*" or "m*n". For
+example, for the style <I>type</I>, if N = the number of atom types, then
+an asterisk with no numeric values means all types from 1 to N. A
+leading asterisk means all types from 1 to n (inclusive). A trailing
+asterisk means all types from n to N (inclusive). A middle asterisk
+means all types from m to n (inclusive). For all the styles except
+<I>mol</I>, the lowest value for the wildcard is 1; for <I>mol</I> it is 0.
+</P>
+<P>The style <I>group</I> selects all the atoms in the specified group. The
+style <I>region</I> selects all the atoms in the specified geometric
+region. See the <A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands
+for details of how to specify a group or region.
+</P>
+<HR>
+
+<P>This section describes the keyword options for which properties to
+change, for the selected atoms.
+</P>
+<P>Note that except where explicitly prohibited below, all of the
+keywords allow an <A HREF = "variable.html">atom-style or atomfile-style
+variable</A> to be used as the specified value(s). If the
+value is a variable, it should be specified as v_name, where name is
+the variable name. In this case, the variable will be evaluated, and
+its resulting per-atom value used to determine the value assigned to
+each selected atom. Note that the per-atom value from the variable
+will be ignored for atoms that are not selected via the <I>style</I> and
+<I>ID</I> settings explained above. A simple way to use per-atom values
+from the variable to reset a property for all atoms is to use style
+<I>atom</I> with <I>ID</I> = "*"; this selects all atom IDs.
+</P>
+<P>Atom-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters and timestep and elapsed
+time. They can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a time-dependent or
+spatially-dependent set of per-atom values. As explained on the
+<A HREF = "variable.html">variable</A> doc page, atomfile-style variables can be
+used in place of atom-style variables, and thus as arguments to the
+set command. Atomfile-style variables read their per-atoms values
+from a file.
+</P>
+<P>IMPORTANT NOTE: Atom-style and atomfile-style variables return
+floating point per-atom values. If the values are assigned to an
+integer variable, such as the molecule ID, then the floating point
+value is truncated to its integer portion, e.g. a value of 2.6 would
+become 2.
+</P>
+<P>Keyword <I>type</I> sets the atom type for all selected atoms. The
+specified value must be from 1 to ntypes, where ntypes was set by the
+<A HREF = "create_box.html">create_box</A> command or the <I>atom types</I> field in the
+header of the data file read by the <A HREF = "read_data.html">read_data</A>
+command.
+</P>
+<P>Keyword <I>type/fraction</I> sets the atom type for a fraction of the
+selected atoms. The actual number of atoms changed is not guaranteed
+to be exactly the requested fraction, but should be statistically
+close. Random numbers are used in such a way that a particular atom
+is changed or not changed, regardless of how many processors are being
+used. This keyword does not allow use of an atom-style variable.
+</P>
+<P>Keyword <I>mol</I> sets the molecule ID for all selected atoms. The <A HREF = "atom_style.html">atom
+style</A> being used must support the use of molecule
+IDs.
+</P>
+<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, and <I>charge</I> set the coordinates or charge of
+all selected atoms. For <I>charge</I>, the <A HREF = "atom_style.html">atom style</A>
+being used must support the use of atomic charge.
+</P>
+<P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a
+vector to set as the orientation of the dipole moment vectors of the
+selected atoms. The magnitude of the dipole moment is set
+by the length of this orientation vector.
+</P>
+<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
+moment vectors of the selected atoms and sets the magnitude of each to
+the specified <I>Dlen</I> value. For 2d systems, the z component of the
+orientation is set to 0.0. Random numbers are used in such a way that
+the orientation of a particular atom is the same, regardless of how
+many processors are being used. This keyword does not allow use of an
+atom-style variable.
+</P>
+<P>Keyword <I>quat</I> uses the specified values to create a quaternion
+(4-vector) that represents the orientation of the selected atoms. The
+particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
+ellipsoid</A> command or triangles as defined by the
+<A HREF = "atom_style.html">atom_style tri</A> command. Note that particles defined
+by <A HREF = "atom_style.html">atom_style ellipsoid</A> have 3 shape parameters.
+The 3 values must be non-zero for each particle set by this command.
+They are used to specify the aspect ratios of an ellipsoidal particle,
+which is oriented by default with its x-axis along the simulation
+box's x-axis, and similarly for y and z. If this body is rotated (via
+the right-hand rule) by an angle theta around a unit rotation vector
+(a,b,c), then the quaternion that represents its new orientation is
+given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
+c*sin(theta/2)). The theta and a,b,c values are the arguments to the
+<I>quat</I> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
+not specified as a unit vector. For 2d systems, the a,b,c values are
+ignored, since a rotation vector of (0,0,1) is the only valid choice.
+</P>
+<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
+the selected atoms. The particles must be ellipsoids as defined by
+the <A HREF = "atom_style.html">atom_style ellipsoid</A> command or triangles as
+defined by the <A HREF = "atom_style.html">atom_style tri</A> command. Random
+numbers are used in such a way that the orientation of a particular
+atom is the same, regardless of how many processors are being used.
+For 2d systems, only orientations in the xy plane are generated. As
+with keyword <I>quat</I>, for ellipsoidal particles, the 3 shape values
+must be non-zero for each particle set by this command. This keyword
+does not allow use of an atom-style variable.
+</P>
+<P>Keyword <I>diameter</I> sets the size of the selected atoms. The particles
+must be finite-size spheres as defined by the <A HREF = "atom_style.html">atom_style
+sphere</A> command. The diameter of a particle can be
+set to 0.0, which means they will be treated as point particles. Note
+that this command does not adjust the particle mass, even if it was
+defined with a density, e.g. via the <A HREF = "read_data.html">read_data</A>
+command.
+</P>
+<P>Keyword <I>shape</I> sets the size and shape of the selected atoms. The
+particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
+ellipsoid</A> command. The <I>Sx</I>, <I>Sy</I>, <I>Sz</I> settings are
+the 3 diameters of the ellipsoid in each direction. All 3 can be set
+to the same value, which means the ellipsoid is effectively a sphere.
+They can also all be set to 0.0 which means the particle will be
+treated as a point particle. Note that this command does not adjust
+the particle mass, even if it was defined with a density, e.g. via the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Keyword <I>length</I> sets the length of selected atoms. The particles
+must be line segments as defined by the <A HREF = "atom_style.html">atom_style
+line</A> command. If the specified value is non-zero the
+line segment is (re)set to a length = the specified value, centered
+around the particle position, with an orientation along the x-axis.
+If the specified value is 0.0, the particle will become a point
+particle. Note that this command does not adjust the particle mass,
+even if it was defined with a density, e.g. via the
+<A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Keyword <I>tri</I> sets the size of selected atoms. The particles must be
+triangles as defined by the <A HREF = "atom_style.html">atom_style tri</A> command.
+If the specified value is non-zero the triangle is (re)set to be an
+equilateral triangle in the xy plane with side length = the specified
+value, with a centroid at the particle position, with its base
+parallel to the x axis, and the y-axis running from the center of the
+base to the top point of the triangle. If the specified value is 0.0,
+the particle will become a point particle. Note that this command
+does not adjust the particle mass, even if it was defined with a
+density, e.g. via the <A HREF = "read_data.html">read_data</A> command.
+</P>
+<P>Keyword <I>theta</I> sets the orientation of selected atoms. The particles
+must be line segments as defined by the <A HREF = "atom_style.html">atom_style
+line</A> command. The specified value is used to set the
+orientation angle of the line segments with respect to the x axis.
+</P>
+<P>Keyword <I>angmom</I> sets the angular momentum of selected atoms. The
+particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
+ellipsoid</A> command or triangles as defined by the
+<A HREF = "atom_style.html">atom_style tri</A> command. The angular momentum vector
+of the particles is set to the 3 specified components.
+</P>
+<P>Keyword <I>mass</I> sets the mass of all selected particles. The particles
+must have a per-atom mass attribute, as defined by the
+<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
+to set mass values on a per-type basis.
+</P>
+<P>Keyword <I>density</I> also sets the mass of all selected particles, but in
+a different way. The particles must have a per-atom mass attribute,
+as defined by the <A HREF = "atom_style.html">atom_style</A> command. If the atom
+has a radius attribute (see <A HREF = "atom_style.html">atom_style sphere</A>) and
+its radius is non-zero, its mass is set from the density and particle
+volume. If the atom has a shape attribute (see <A HREF = "atom_style.html">atom_style
+ellipsoid</A>) and its 3 shape parameters are non-zero,
+then its mass is set from the density and particle volume. If the
+atom has a length attribute (see <A HREF = "atom_style.html">atom_style line</A>)
+and its length is non-zero, then its mass is set from the density and
+line segment length (the input density is assumed to be in
+mass/distance units). If the atom has an area attribute (see
+<A HREF = "atom_style.html">atom_style tri</A>) and its area is non-zero, then its
+mass is set from the density and triangle area (the input density is
+assumed to be in mass/distance^2 units). If none of these cases are
+valid, then the mass is set to the density value directly (the input
+density is assumed to be in mass units).
+</P>
+<P>Keyword <I>volume</I> sets the volume of all selected particles.
+Currently, only the <A HREF = "atom_style.html">atom_style peri</A> command defines
+particles with a volume attribute. Note that this command does not
+adjust the particle mass.
+</P>
+<P>Keyword <I>image</I> sets which image of the simulation box the atom is
+considered to be in. An image of 0 means it is inside the box as
+defined. A value of 2 means add 2 box lengths to get the true value.
+A value of -1 means subtract 1 box length to get the true value.
+LAMMPS updates these flags as atoms cross periodic boundaries during
+the simulation. The flags can be output with atom snapshots via the
+<A HREF = "dump.html">dump</A> command. If a value of NULL is specified for any of
+nx,ny,nz, then the current image value for that dimension is
+unchanged. For non-periodic dimensions only a value of 0 can be
+specified. This keyword does not allow use of atom-style variables.
+</P>
+<P>This command can be useful after a system has been equilibrated and
+atoms have diffused one or more box lengths in various directions.
+This command can then reset the image values for atoms so that they
+are effectively inside the simulation box, e.g if a diffusion
+coefficient is about to be measured via the <A HREF = "compute_msd.html">compute
+msd</A> command. Care should be taken not to reset the
+image flags of two atoms in a bond to the same value if the bond
+straddles a periodic boundary (rather they should be different by +/-
+1). This will not affect the dynamics of a simulation, but may mess
+up analysis of the trajectories if a LAMMPS diagnostic or your own
+analysis relies on the image flags to unwrap a molecule which
+straddles the periodic box.
+</P>
+<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, set the bond
+type (angle type, etc) of all bonds (angles, etc) of selected atoms to
+the specified value from 1 to nbondtypes (nangletypes, etc). All
+atoms in a particular bond (angle, etc) must be selected atoms in
+order for the change to be made. The value of nbondtype (nangletypes,
+etc) was set by the <I>bond types</I> (<I>angle types</I>, etc) field in the
+header of the data file read by the <A HREF = "read_data.html">read_data</A>
+command. These keywords do not allow use of an atom-style variable.
+</P>
+<P>Keywords <I>meso_e</I>, <I>meso_cv</I>, and <I>meso_rho</I> set the energy, heat
+capacity, and density of smmothed particle hydrodynamics (SPH)
+particles. See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to
+using SPH in LAMMPS.
+</P>
+<P>Keywords <I>i_name</I> and <I>d_name</I> refer to custom integer and
+floating-point properties that have been added to each atom via the
+<A HREF = "fix_property_atom.html">fix property/atom</A> command. When that command
+is used specific names are given to each attribute which are what is
+specified as the "name" portion of <I>i_name</I> or <I>d_name</I>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I> or <I>volume</I>) if
+the <A HREF = "atom_style.html">atom_style</A> does not have that attribute.
+</P>
+<P>This command requires inter-processor communication to coordinate the
+setting of bond types (angle types, etc). This means that your system
+must be ready to perform a simulation before using one of these
+keywords (force fields set, atom mass set, etc). This is not
+necessary for other keywords.
+</P>
+<P>Using the <I>region</I> style with the bond (angle, etc) keywords can give
+unpredictable results if there are bonds (angles, etc) that straddle
+periodic boundaries. This is because the region may only extend up to
+the boundary and partner atoms in the bond (angle, etc) may have
+coordinates outside the simulation box if they are ghost atoms.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>,
+<A HREF = "read_data.html">read_data</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/shell.html b/doc/doc2/shell.html
new file mode 100644
index 000000000..0bb8b3b6d
--- /dev/null
+++ b/doc/doc2/shell.html
@@ -0,0 +1,114 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>shell command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>shell cmd args
+</PRE>
+<UL><LI>cmd = <I>cd</I> or <I>mkdir</I> or <I>mv</I> or <I>rm</I> or <I>rmdir</I> or <I>putenv</I> or arbitrary command
+
+<PRE> <I>cd</I> arg = dir
+ dir = directory to change to
+ <I>mkdir</I> args = dir1 dir2 ...
+ dir1,dir2 = one or more directories to create
+ <I>mv</I> args = old new
+ old = old filename
+ new = new filename
+ <I>rm</I> args = file1 file2 ...
+ file1,file2 = one or more filenames to delete
+ <I>rmdir</I> args = dir1 dir2 ...
+ dir1,dir2 = one or more directories to delete
+ <I>putenv</I> args = var1=value1 var2=value2
+ var=value = one of more definitions of environment variables
+ anything else is passed as a command to the shell for direct execution
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>shell cd sub1
+shell cd ..
+shell mkdir tmp1 tmp2 tmp3
+shell rmdir tmp1
+shell mv log.lammps hold/log.1
+shell rm TMP/file1 TMP/file2
+shell putenv LAMMPS_POTENTIALS=../../potentials
+shell my_setup file1 10 file2
+shell my_post_process 100 dump.out
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Execute a shell command. A few simple file-based shell commands are
+supported directly, in Unix-style syntax. Any command not listed
+above is passed as-is to the C-library system() call, which invokes
+the command in a shell.
+</P>
+<P>This is means to invoke other commands from your input script. For
+example, you can move files around in preparation for the next section
+of the input script. Or you can run a program that pre-processes data
+for input into LAMMPS. Or you can run a program that post-processes
+LAMMPS output data.
+</P>
+<P>With the exception of <I>cd</I>, all commands, including ones invoked via a
+system() call, are executed by only a single processor, so that
+files/directories are not being manipulated by multiple processors.
+</P>
+<P>The <I>cd</I> cmd executes the Unix "cd" command to change the working
+directory. All subsequent LAMMPS commands that read/write files will
+use the new directory. All processors execute this command.
+</P>
+<P>The <I>mkdir</I> cmd executes the Unix "mkdir" command to create one or
+more directories.
+</P>
+<P>The <I>mv</I> cmd executes the Unix "mv" command to rename a file and/or
+move it to a new directory.
+</P>
+<P>The <I>rm</I> cmd executes the Unix "rm" command to remove one or more
+files.
+</P>
+<P>The <I>rmdir</I> cmd executes the Unix "rmdir" command to remove one or
+more directories. A directory must be empty to be successfully
+removed.
+</P>
+<P>The <I>putenv</I> cmd defines or updates an environment variable directly.
+Since this command does not pass through the shell, no shell variable
+expansion or globbing is performed, only the usual substitution for
+LAMMPS variables defined with the <A HREF = "variable.html">variable</A> command is
+performed. The resulting string is then used literally.
+</P>
+<P>Any other cmd is passed as-is to the shell along with its arguments as
+one string, invoked by the C-library system() call. For example,
+these lines in your input script:
+</P>
+<PRE>variable n equal 10
+variable foo string file2
+shell my_setup file1 $n ${foo}
+</PRE>
+<P>would be the same as invoking
+</P>
+<PRE>% my_setup file1 10 file2
+</PRE>
+<P>from a command-line prompt. The executable program "my_setup" is run
+with 3 arguments: file1 10 file2.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>LAMMPS does not detect errors or print warnings when any of these
+commands execute. E.g. if the specified directory does not exist,
+executing the <I>cd</I> command will silently do nothing.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/special_bonds.html b/doc/doc2/special_bonds.html
new file mode 100644
index 000000000..58fa49398
--- /dev/null
+++ b/doc/doc2/special_bonds.html
@@ -0,0 +1,276 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>special_bonds command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>special_bonds keyword values ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be appended
+
+<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>dreiding</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
+
+<PRE> <I>amber</I> values = none
+ <I>charmm</I> values = none
+ <I>dreiding</I> values = none
+ <I>fene</I> values = none
+ <I>lj/coul</I> values = w1,w2,w3
+ w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
+ <I>lj</I> values = w1,w2,w3
+ w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
+ <I>coul</I> values = w1,w2,w3
+ w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
+ <I>angle</I> value = <I>yes</I> or <I>no</I>
+ <I>dihedral</I> value = <I>yes</I> or <I>no</I>
+ <I>extra</I> value = N
+ N = number of extra 1-2,1-3,1-4 interactions to save space for
+</PRE>
+
+</UL>
+<P>Examples:
+</P>
+<PRE>special_bonds amber
+special_bonds charmm
+special_bonds fene dihedral no
+special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
+special_bonds lj/coul 0 1 1 extra 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set weighting coefficients for pairwise energy and force contributions
+between pairs of atoms that are also permanently bonded to each other,
+either directly or via one or two intermediate bonds. These weighting
+factors are used by nearly all <A HREF = "pair_style.html">pair styles</A> in LAMMPS
+that compute simple pairwise interactions. Permanent bonds between
+atoms are specified by defining the bond topology in the data file
+read by the <A HREF = "read_data.html">read_data</A> command. Typically a
+<A HREF = "bond_style.html">bond_style</A> command is also used to define a bond
+potential. The rationale for using these weighting factors is that
+the interaction between a pair of bonded atoms is all (or mostly)
+specified by the bond, angle, dihedral potentials, and thus the
+non-bonded Lennard-Jones or Coulombic interaction between the pair of
+atoms should be excluded (or reduced by a weighting factor).
+</P>
+<P>IMPORTANT NOTE: These weighting factors are NOT used by <A HREF = "pair_style.html">pair
+styles</A> that compute many-body interactions, since the
+"bonds" that result from such interactions are not permanent, but are
+created and broken dynamically as atom conformations change. Examples
+of pair styles in this category are EAM, MEAM, Stillinger-Weber,
+Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
+sense to define permanent bonds between atoms that interact via these
+potentials, though such bonds may exist elsewhere in your system,
+e.g. when using the <A HREF = "pair_hybrid.html">pair_style hybrid</A> command.
+Thus LAMMPS ignores special_bonds settings when manybody potentials
+are calculated.
+</P>
+<P>IMPORTANT NOTE: Unlike some commands in LAMMPS, you cannot use this
+command multiple times in an incremental fashion: e.g. to first set
+the LJ settings and then the Coulombic ones. Each time you use this
+command it sets all the coefficients to default values and only
+overrides the one you specify, so you should set all the options you
+need each time you use it. See more details at the bottom of this
+page.
+</P>
+<P>The Coulomb factors are applied to any Coulomb (charge interaction)
+term that the potential calculates. The LJ factors are applied to the
+remaining terms that the potential calculates, whether they represent
+LJ interactions or not. The weighting factors are a scaling
+pre-factor on the energy and force between the pair of atoms. A value
+of 1.0 means include the full interaction; a value of 0.0 means
+exclude it completely.
+</P>
+<P>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
+factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
+each other. The 2nd coefficient is the weighting factor on 1-3 atom
+pairs which are those separated by 2 bonds (e.g. the two H atoms in a
+water molecule). The 3rd coefficient is the weighting factor on 1-4
+atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
+atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
+to 0.0, then the pairwise interaction is effectively turned off for
+all pairs of atoms bonded to each other. If it is set to 1.0, then
+that interaction will be at full strength.
+</P>
+<P>IMPORTANT NOTE: For purposes of computing weighted pairwise
+interactions, 1-3 and 1-4 interactions are not defined from the list
+of angles or dihedrals used by the simulation. Rather, they are
+inferred topologically from the set of bonds specified when the
+simulation is defined from a data or restart file (see
+<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
+commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
+apply to is the same whether angle and dihedral potentials are
+computed or not, and remains the same even if bonds are constrained,
+or turned off, or removed during a simulation.
+</P>
+<P>The two exceptions to this rule are (a) if the <I>angle</I> or <I>dihedral</I>
+keywords are set to <I>yes</I> (see below), or (b) if the
+<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
+option that recomputes the 1-2,1-3,1-4 topologies after bonds are
+deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
+details.
+</P>
+<P>The <I>amber</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
+interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
+is the default for a commonly used version of the AMBER force field,
+where the last value is really 5/6. See <A HREF = "#Cornell">(Cornell)</A> for a
+description of the AMBER force field.
+</P>
+<P>The <I>charmm</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
+LJ and Coulombic interactions, which is the default for a commonly
+used version of the CHARMM force field. Note that in pair styles
+<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
+are defined explicitly, and these pairwise contributions are computed
+as part of the charmm dihedral style - see the
+<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
+commands for more information. See <A HREF = "#MacKerell">(MacKerell)</A> for a
+description of the CHARMM force field.
+</P>
+<P>The <I>dreiding</I> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
+LJ and Coulombic interactions, which is the default for the Dreiding
+force field, as discussed in <A HREF = "#Mayo">(Mayo)</A>.
+</P>
+<P>The <I>fene</I> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
+LJ and Coulombic interactions, which is consistent with a
+coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>. See
+<A HREF = "#Kremer">(Kremer)</A> for a description of FENE bonds.
+</P>
+<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
+be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
+Coulombic coefficients to the same 3 values. The <I>lj</I> and <I>coul</I>
+keywords only set either the LJ or Coulombic coefficients. Use both
+of them if you wish to set the LJ coefficients to different values
+than the Coulombic coefficients.
+</P>
+<P>The <I>angle</I> keyword allows the 1-3 weighting factor to be ignored for
+individual atom pairs if they are not listed as the first and last
+atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
+any dihedral defined in the simulation. For example, imagine the 1-3
+weighting factor is set to 0.5 and you have a linear molecule with 4
+atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
+as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
+dihedral, then the pairwise interaction between atoms 1 and 3 will
+always be weighted by 0.5, but different force fields use different
+rules for weighting the pairwise interaction between atoms 2 and 4.
+If the <I>angle</I> keyword is specified as <I>yes</I>, then the pairwise
+interaction between atoms 2 and 4 will be unaffected (full weighting
+of 1.0). If the <I>angle</I> keyword is specified as <I>no</I> which is the
+default, then the 2,4 interaction will also be weighted by 0.5.
+</P>
+<P>The <I>dihedral</I> keyword allows the 1-4 weighting factor to be ignored
+for individual atom pairs if they are not listed as the first and last
+atoms in any dihedral defined in the simulation. For example, imagine
+the 1-4 weighting factor is set to 0.5 and you have a linear molecule
+with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
+defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
+dihedral, then the pairwise interaction between atoms 1 and 4 will
+always be weighted by 0.5, but different force fields use different
+rules for weighting the pairwise interaction between atoms 2 and 5.
+If the <I>dihedral</I> keyword is specified as <I>yes</I>, then the pairwise
+interaction between atoms 2 and 5 will be unaffected (full weighting
+of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
+default, then the 2,5 interaction will also be weighted by 0.5.
+</P>
+<P>The <I>extra</I> keyword can be used when additional bonds will be created
+during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
+bond/create</A> command. It can also be used if
+molecules will be added to the system, e.g. via the <A HREF = "fix_deposit.html">fix
+deposit</A>, or <A HREF = "fix_pour.html">fix pour</A> commands, which
+will have atoms with more special neighbors than any atom in the
+current system has.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
+topology of the system). If new bonds are created (or molecules added
+containing atoms with more special neighbors), the size of this list
+needs to grow. Note that adding a single bond always adds a new 1st
+neighbor but may also induce *many* new 2nd and 3rd neighbors,
+depending on the molecular topology of your system. Using the <I>extra</I>
+keyword leaves empty space in the list for this N additional 1st, 2nd,
+or 3rd neighbors to be added. If you do not do this, you may get an
+error when bonds (or molecules) are added.
+</P>
+<HR>
+
+<P>IMPORTANT NOTE: If you reuse this command in an input script, you
+should set all the options you need each time. This command cannot be
+used a 2nd time incrementally, e.g. to add some extra storage
+locations via the <I>extra</I> keyword. E.g. these two commands:
+</P>
+<P>special_bonds lj 0.0 1.0 1.0
+special_bonds coul 0.0 0.0 1.0
+</P>
+<P>are not the same as
+</P>
+<P>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
+</P>
+<P>In the first case you end up with (after the 2nd command):
+</P>
+<P>LJ: 0.0 0.0 0.0
+Coul: coul 0.0 0.0 1.0
+</P>
+<P>because the LJ settings are reset to their default values
+each time the command is issued.
+</P>
+<P>Likewise
+</P>
+<PRE>special_bonds amber
+special_bonds extra 2
+</PRE>
+<P>is not the same as this single command:
+</P>
+<PRE>special_bonds amber extra 2
+</PRE>
+<P>since in the former case, the 2nd command will reset all the LJ and
+Coulombic weights to 0.0 (the default).
+</P>
+<P>One exception to this rule is the <I>extra</I> option itself. It is not
+reset to its default value of 0 each time the special_bonds command is
+invoked. This is because it can also be set by the
+<A HREF = "read_data.html">read_data</A> and <A HREF = "create_box.html">create_box</A> commands,
+so this command will not override those settings unless you explicitly
+use <I>extra</I> as an option.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "fix_bond_create.html">fix bond/create</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
+angle = no, dihedral = no, and extra = 0.
+</P>
+<HR>
+
+<A NAME = "Cornell"></A>
+
+<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+</P>
+<A NAME = "Kremer"></A>
+
+<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
+</P>
+<A NAME = "MacKerell"></A>
+
+<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+</P>
+<A NAME = "Mayo"></A>
+
+<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
+</P>
+</HTML>
diff --git a/doc/doc2/suffix.html b/doc/doc2/suffix.html
new file mode 100644
index 000000000..c1aae192d
--- /dev/null
+++ b/doc/doc2/suffix.html
@@ -0,0 +1,105 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>suffix command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>suffix style
+</PRE>
+<UL><LI>style = <I>off</I> or <I>on</I> or <I>cuda</I> or <I>gpu</I> or <I>intel</I> or <I>kk</I> or <I>omp</I> or <I>opt</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>suffix off
+suffix on
+suffix gpu
+suffix intel
+suffix kk
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command allows you to use variants of various styles if they
+exist. In that respect it operates the same as the <A HREF = "Section_start.html#start_7">-suffix
+command-line switch</A>. It also has options
+to turn off or back on any suffix setting made via the command line.
+</P>
+<P>The specified style can be <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or
+<I>opt</I>. These refer to optional packages that LAMMPS can be built
+with, as described in <A HREF = "Section_start.html#start_3">this section of the
+manual</A>. The "cuda" style corresponds to
+the USER-CUDA package, the "gpu" style to the GPU package, the "intel"
+style to the USER-INTEL package, the "kk" style to the KOKKOS package,
+the "omp" style to the USER-OMP package, and the "opt" style to the
+OPT package,
+</P>
+<P>These are the variants these packages provide:
+</P>
+<UL><LI>USER-CUDA = a collection of atom, pair, fix, compute, and intergrate
+styles, optimized to run on one or more NVIDIA GPUs
+
+<LI>GPU = a handful of pair styles and the PPPM kspace_style, optimized to
+run on one or more GPUs or multicore CPU/GPU nodes
+
+<LI>USER-INTEL = a collection of pair styles and neighbor routines
+optimized to run in single, mixed, or double precision on CPUs and
+Intel(R) Xeon Phi(TM) coprocessors.
+
+<LI>KOKKOS = a collection of atom, pair, and fix styles optimized to run
+using the Kokkos library on various kinds of hardware, including GPUs
+via Cuda and many-core chips via OpenMP or threading.
+
+<LI>USER-OMP = a collection of pair, bond, angle, dihedral, improper,
+kspace, compute, and fix styles with support for OpenMP
+multi-threading
+
+<LI>OPT = a handful of pair styles, cache-optimized for faster CPU
+performance
+</UL>
+<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
+lj/cut</A> variant, with style names lj/cut/opt, lj/cut/omp,
+lj/cut/gpu, lj/cut/intel, lj/cut/cuda, or lj/cut/kk. A variant styles
+can be specified explicitly in your input script, e.g. pair_style
+lj/cut/gpu. If the suffix command is used with the appropriate style,
+you do not need to modify your input script. The specified suffix
+(opt,omp,gpu,intel,cuda,kk) is automatically appended whenever your
+input script command creates a new <A HREF = "atom_style.html">atom</A>,
+<A HREF = "pair_style.html">pair</A>, <A HREF = "bond_style.html">bond</A>,
+<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
+<A HREF = "improper_style.html">improper</A>, <A HREF = "kspace_style.html">kspace</A>,
+<A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style.
+If the variant version does not exist, the standard version is
+created.
+</P>
+<P>When using the intel suffix, LAMMPS will first attempt to use a style
+with the intel suffix. If the USER-OMP package is installed, the the
+omp suffix will be tried as a second choice, if a requested style is
+not available in the USER-INTEL package.
+</P>
+<P>If the specified style is <I>off</I>, then any previously specified suffix
+is temporarily disabled, whether it was specified by a command-line
+switch or a previous suffix command. If the specified style is <I>on</I>,
+a disabled suffix is turned back on. The use of these 2 commands lets
+your input script use a standard LAMMPS style (i.e. a non-accelerated
+variant), which can be useful for testing or benchmarking purposes.
+Of course this is also possible by not using any suffix commands, and
+explictly appending or not appending the suffix to the relevant
+commands in your input script.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "Section_start.html#start_7">Command-line switch -suffix</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/tad.html b/doc/doc2/tad.html
new file mode 100644
index 000000000..b3e098234
--- /dev/null
+++ b/doc/doc2/tad.html
@@ -0,0 +1,327 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>tad command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
+</PRE>
+<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
+
+<LI>t_event = timestep interval between event checks
+
+<LI>T_lo = temperature at which event times are desired
+
+<LI>T_hi = temperature at which MD simulation is performed
+
+<LI>delta = desired confidence level for stopping criterion
+
+<LI>tmax = reciprocal of lowest expected preexponential factor (time units)
+
+<LI>compute-ID = ID of the compute used for event detection
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>min</I> or <I>neb</I> or <I>min_style</I> or <I>neb_style</I> or <I>neb_log</I>
+
+<PRE> <I>min</I> values = etol ftol maxiter maxeval
+ etol = stopping tolerance for energy (energy units)
+ ftol = stopping tolerance for force (force units)
+ maxiter = max iterations of minimize
+ maxeval = max number of force/energy evaluations
+ <I>neb</I> values = ftol N1 N2 Nevery
+ etol = stopping tolerance for energy (energy units)
+ ftol = stopping tolerance for force (force units)
+ N1 = max # of iterations (timesteps) to run initial NEB
+ N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+ Nevery = print NEB statistics every this many timesteps
+ <I>neb_style</I> value = <I>quickmin</I> or <I>fire</I>
+ <I>neb_step</I> value = dtneb
+ dtneb = timestep for NEB damped dynamics minimization
+ <I>neb_log</I> value = file where NEB statistics are printed
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>tad 2000 50 1800 2300 0.01 0.01 event
+tad 2000 50 1800 2300 0.01 0.01 event &
+ min 1e-05 1e-05 100 100 &
+ neb 0.0 0.01 200 200 20 &
+ min_style cg &
+ neb_style fire &
+ neb_log log.neb
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Run a temperature accelerated dynamics (TAD) simulation. This method
+requires two or more partitions to perform NEB transition state
+searches.
+</P>
+<P>TAD is described in <A HREF = "#Voter">this paper</A> by Art Voter. It is a method
+that uses accelerated dynamics at an elevated temperature to generate
+results at a specified lower temperature. A good overview of
+accelerated dynamics methods for such systems is given in <A HREF = "#Voter2">this review
+paper</A> from the same group. In general, these methods assume
+that the long-time dynamics is dominated by infrequent events i.e. the
+system is is confined to low energy basins for long periods,
+punctuated by brief, randomly-occurring transitions to adjacent
+basins. TAD is suitable for infrequent-event systems, where in
+addition, the transition kinetics are well-approximated by harmonic
+transition state theory (hTST). In hTST, the temperature dependence of
+transition rates follows the Arrhenius relation. As a consequence a
+set of event times generated in a high-temperature simulation can be
+mapped to a set of much longer estimated times in the low-temperature
+system. However, because this mapping involves the energy barrier of
+the transition event, which is different for each event, the first
+event at the high temperature may not be the earliest event at the low
+temperature. TAD handles this by first generating a set of possible
+events from the current basin. After each event, the simulation is
+reflected backwards into the current basin. This is repeated until
+the stopping criterion is satisfied, at which point the event with the
+earliest low-temperature occurrence time is selected. The stopping
+criterion is that the confidence measure be greater than
+1-<I>delta</I>. The confidence measure is the probability that no earlier
+low-temperature event will occur at some later time in the
+high-temperature simulation. hTST provides an lower bound for this
+probability, based on the user-specified minimum pre-exponential
+factor (reciprocal of <I>tmax</I>).
+</P>
+<P>In order to estimate the energy barrier for each event, the TAD method
+invokes the <A HREF = "neb.html">NEB</A> method. Each NEB replica runs on a
+partition of processors. The current NEB implementation in LAMMPS
+restricts you to having exactly one processor per replica. For more
+information, see the documentation for the <A HREF = "neb.html">neb</A> command. In
+the current LAMMPS implementation of TAD, all the non-NEB TAD
+operations are performed on the first partition, while the other
+partitions remain idle. See <A HREF = "Section_howto.html#howto_5">Section_howto
+5</A> of the manual for further discussion of
+multi-replica simulations.
+</P>
+<P>A TAD run has several stages, which are repeated each time an event is
+performed. The logic for a TAD run is as follows:
+</P>
+<PRE>while (time remains):
+ while (time < tstop):
+ until (event occurs):
+ run dynamics for t_event steps
+ quench
+ run neb calculation using all replicas
+ compute tlo from energy barrier
+ update earliest event
+ update tstop
+ reflect back into current basin
+ execute earliest event
+</PRE>
+<P>Before this outer loop begins, the initial potential energy basin is
+identified by quenching (an energy minimization, see below) the
+initial state and storing the resulting coordinates for reference.
+</P>
+<P>Inside the inner loop, dynamics is run continuously according to
+whatever integrator has been specified by the user, stopping every
+<I>t_event</I> steps to check if a transition event has occurred. This
+check is performed by quenching the system and comparing the resulting
+atom coordinates to the coordinates from the previous basin.
+</P>
+<P>A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the <A HREF = "min_style.html">min_style</A> command;
+its default is the CG minimizer. The tolerances and limits for each
+quench can be set by the <I>min</I> keyword. Note that typically, you do
+not need to perform a highly-converged minimization to detect a
+transition event.
+</P>
+<P>The event check is performed by a compute with the specified
+<I>compute-ID</I>. Currently there is only one compute that works with the
+TAD commmand, which is the <A HREF = "compute_event_displace.html">compute
+event/displace</A> command. Other
+event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
+event/displace</A> checks whether any atom in
+the compute group has moved further than a specified threshold
+distance. If so, an "event" has occurred.
+</P>
+<P>The NEB calculation is similar to that invoked by the <A HREF = "neb.html">neb</A>
+command, except that the final state is generated internally, instead
+of being read in from a file. The style of minimization performed by
+NEB is determined by the <I>neb_style</I> keyword and must be a damped
+dynamics minimizer. The tolerances and limits for each NEB
+calculation can be set by the <I>neb</I> keyword. As discussed on the
+<A HREF = "neb.html">neb</A>, it is often advantageous to use a larger timestep for
+NEB than for normal dyanmics. Since the size of the timestep set by
+the <A HREF = "timestep.html">timestep</A> command is used by TAD for performing
+dynamics, there is a <I>neb_step</I> keyword which can be used to set a
+larger timestep for each NEB calculation if desired.
+</P>
+<HR>
+
+<P>A key aspect of the TAD method is setting the stopping criterion
+appropriately. If this criterion is too conservative, then many
+events must be generated before one is finally executed. Conversely,
+if this criterion is too aggressive, high-entropy high-barrier events
+will be over-sampled, while low-entropy low-barrier events will be
+under-sampled. If the lowest pre-exponential factor is known fairly
+accurately, then it can be used to estimate <I>tmax</I>, and the value of
+<I>delta</I> can be set to the desired confidence level e.g. <I>delta</I> = 0.05
+corresponds to 95% confidence. However, for systems where the dynamics
+are not well characterized (the most common case), it will be
+necessary to experiment with the values of <I>delta</I> and <I>tmax</I> to get a
+good trade-off between accuracy and performance.
+</P>
+<P>A second key aspect is the choice of <I>t_hi</I>. A larger value greatly
+increases the rate at which new events are generated. However, too
+large a value introduces errors due to anharmonicity (not accounted
+for within hTST). Once again, for any given system, experimentation is
+necessary to determine the best value of <I>t_hi</I>.
+</P>
+<HR>
+
+<P>Five kinds of output can be generated during a TAD run: event
+statistics, NEB statistics, thermodynamic output by each replica, dump
+files, and restart files.
+</P>
+<P>Event statistics are printed to the screen and master log.lammps file
+each time an event is executed. The quantities are the timestep, CPU
+time, global event number <I>N</I>, local event number <I>M</I>, event status,
+energy barrier, time margin, <I>t_lo</I> and <I>delt_lo</I>. The timestep is
+the usual LAMMPS timestep, which corresponds to the high-temperature
+time at which the event was detected, in units of timestep. The CPU
+time is the total processor time since the start of the TAD run. The
+global event number <I>N</I> is a counter that increments with each
+executed event. The local event number <I>M</I> is a counter that resets to
+zero upon entering each new basin. The event status is <I>E</I> when an
+event is executed, and is <I>D</I> for an event that is detected, while
+<I>DF</I> is for a detected event that is also the earliest (first) event
+at the low temperature.
+</P>
+<P>The time margin is the ratio of the high temperature time in the
+current basin to the stopping time. This last number can be used to
+judge whether the stopping time is too short or too long (see above).
+</P>
+<P><I>t_lo</I> is the low-temperature event time when the current basin was
+entered, in units of timestep. del<I>t_lo</I> is the time of each detected
+event, measured relative to <I>t_lo</I>. <I>delt_lo</I> is equal to the
+high-temperature time since entering the current basin, scaled by an
+exponential factor that depends on the hi/lo temperature ratio and the
+energy barrier for that event.
+</P>
+<P>On lines for executed events, with status <I>E</I>, the global event number
+is incremented by one,
+the local event number and time margin are reset to zero,
+while the global event number, energy barrier, and
+<I>delt_lo</I> match the last event with status <I>DF</I>
+in the immediately preceding block of detected events.
+The low-temperature event time <I>t_lo</I> is incremented by <I>delt_lo</I>.
+</P>
+<P>NEB statistics are written to the file specified by the <I>neb_log</I>
+keyword. If the keyword value is "none", then no NEB statistics are
+printed out. The statistics are written every <I>Nevery</I> timesteps. See
+the <A HREF = "neb.html">neb</A> command for a full description of the NEB
+statistics. When invoked from TAD, NEB statistics are never printed to
+the screen.
+</P>
+<P>Because the NEB calculation must run on multiple partitions, LAMMPS
+produces additional screen and log files for each partition,
+e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these
+contain the thermodynamic output of each NEB replica. In addition, the
+log file for the first partition, log.lammps.0, will contain
+thermodynamic output from short runs and minimizations corresponding
+to the dynamics and quench operations, as well as a line for each new
+detected event, as described above.
+</P>
+<P>After the TAD command completes, timing statistics for the TAD run are
+printed in each replica's log file, giving a breakdown of how much CPU
+time was spent in each stage (NEB, dynamics, quenching, etc).
+</P>
+<P>Any <A HREF = "dump.html">dump files</A> defined in the input script will be written
+to during a TAD run at timesteps when an event is executed. This
+means the the requested dump frequency in the <A HREF = "dump.html">dump</A> command
+is ignored. There will be one dump file (per dump command) created
+for all partitions. The atom coordinates of the dump snapshot are
+those of the minimum energy configuration resulting from quenching
+following the executed event. The timesteps written into the dump
+files correspond to the timestep at which the event occurred and NOT
+the clock. A dump snapshot corresponding to the initial minimum state
+used for event detection is written to the dump file at the beginning
+of each TAD run.
+</P>
+<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
+for all the partitions is generated, which allows a TAD run to be
+continued by a new input script in the usual manner. The restart file
+is generated after an event is executed. The restart file contains a
+snapshot of the system in the new quenched state, including the event
+number and the low-temperature time. The restart frequency specified
+in the <A HREF = "restart.html">restart</A> command is interpreted differently when
+performing a TAD run. It does not mean the timestep interval between
+restart files. Instead it means an event interval for executed
+events. Thus a frequency of 1 means write a restart file every time
+an event is executed. A frequency of 10 means write a restart file
+every 10th executed event. When an input script reads a restart file
+from a previous TAD run, the new script can be run on a different
+number of replicas or processors.
+</P>
+<P>Note that within a single state, the dynamics will typically
+temporarily continue beyond the event that is ultimately chosen, until
+the stopping criterionis satisfied. When the event is eventually
+executed, the timestep counter is reset to the value when the event
+was detected. Similarly, after each quench and NEB minimization, the
+timestep counter is reset to the value at the start of the
+minimization. This means that the timesteps listed in the replica log
+files do not always increase monotonically. However, the timestep
+values printed to the master log file, dump files, and restart files
+are always monotonically increasing.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><I>N</I> setting must be integer multiple of <I>t_event</I>.
+</P>
+<P>Runs restarted from restart files written during a TAD run will only
+produce identical results if the user-specified integrator supports
+exact restarts. So <A HREF = "fix_nh.html">fix nvt</A> will produce an exact
+restart, but <A HREF = "fix_langevin.html">fix langevin</A> will not.
+</P>
+<P>This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform time-dependent operations. Examples
+include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
+dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
+<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
+<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
+<A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
+<A HREF = "prd.html">prd</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, <I>neb</I> = 0.01 100 100
+10, <I>neb_style</I> = <I>quickmin</I>, <I>neb_step</I> = the same timestep set by
+the <A HREF = "timestep.html">timestep</A> command, and <I>neb_log</I> = "none".
+</P>
+<HR>
+
+<A NAME = "Voter"></A>
+
+<P><B>(Voter)</B> Sorensen and Voter, J Chem Phys, 112, 9599 (2000)
+</P>
+<A NAME = "Voter2"></A>
+
+<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).
+</P>
+</HTML>
diff --git a/doc/doc2/temper.html b/doc/doc2/temper.html
new file mode 100644
index 000000000..fd5727b88
--- /dev/null
+++ b/doc/doc2/temper.html
@@ -0,0 +1,137 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>temper command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>temper N M temp fix-ID seed1 seed2 index
+</PRE>
+<UL><LI>N = total # of timesteps to run
+<LI>M = attempt a tempering swap every this many steps
+<LI>temp = initial temperature for this ensemble
+<LI>fix-ID = ID of the fix that will control temperature during the run
+<LI>seed1 = random # seed used to decide on adjacent temperature to partner with
+<LI>seed2 = random # seed for Boltzmann factor in Metropolis swap
+<LI>index = which temperature (0 to N-1) I am simulating (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>temper 100000 100 $t tempfix 0 58728
+temper 40000 100 $t tempfix 0 32285 $w
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Run a parallel tempering or replica exchange simulation using multiple
+replicas (ensembles) of a system. Two or more replicas must be used.
+</P>
+<P>Each replica runs on a partition of one or more processors. Processor
+partitions are defined at run-time using the -partition command-line
+switch; see <A HREF = "Section_start.html#start_7">Section_start 6</A> of the
+manual. Note that if you have MPI installed, you can run a
+multi-replica simulation with more replicas (partitions) than you have
+physical processors, e.g you can run a 10-replica simulation on one or
+two processors. You will simply not get the performance speed-up you
+would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
+section</A> of the manual for further
+discussion.
+</P>
+<P>Each replica's temperature is controlled at a different value by a fix
+with <I>fix-ID</I> that controls temperature. Possible fix styles are
+<A HREF = "fix_nh.html">nvt</A>, <A HREF = "fix_nh.html">temp/berendsen</A>,
+<A HREF = "fix_langevin.html">langevin</A> and <A HREF = "fix_temp_rescale.html">temp/rescale</A>.
+The desired temperature is specified by <I>temp</I>, which is typically a
+variable previously set in the input script, so that each partition is
+assigned a different temperature. See the <A HREF = "variable.html">variable</A>
+command for more details. For example:
+</P>
+<PRE>variable t world 300.0 310.0 320.0 330.0
+fix myfix all nvt $t $t 100.0
+temper 100000 100 $t myfix 3847 58382
+</PRE>
+<P>would define 4 temperatures, and assign one of them to the thermostat
+used by each replica, and to the temper command.
+</P>
+<P>As the tempering simulation runs for <I>N</I> timesteps, a temperature swap
+between adjacent ensembles will be attempted every <I>M</I> timesteps. If
+<I>seed1</I> is 0, then the swap attempts will alternate between odd and
+even pairings. If <I>seed1</I> is non-zero then it is used as a seed in a
+random number generator to randomly choose an odd or even pairing each
+time. Each attempted swap of temperatures is either accepted or
+rejected based on a Boltzmann-weighted Metropolis criterion which uses
+<I>seed2</I> in the random number generator.
+</P>
+<P>As a tempering run proceeds, multiple log files and screen output
+files are created, one per replica. By default these files are named
+log.lammps.M and screen.M where M is the replica number from 0 to N-1,
+with N = # of replicas. See the <A HREF = "Section_start.html#start_7">section on command-line
+switches</A> for info on how to change these
+names.
+</P>
+<P>The main screen and log file (log.lammps) will list information about
+which temperature is assigned to each replica at each thermodynamic
+output timestep. E.g. for a simulation with 16 replicas:
+</P>
+<PRE>Running on 16 partitions of processors
+Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
+0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
+1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
+1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
+2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
+2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
+...
+</PRE>
+<P>The column headings T0 to TN-1 mean which temperature is currently
+assigned to the replica 0 to N-1. Thus the columns represent replicas
+and the value in each column is its temperature (also numbered 0 to
+N-1). For example, a 0 in the 4th column (column T3, step 2500) means
+that the 4th replica is assigned temperature 0, i.e. the lowest
+temperature. You can verify this time sequence of temperature
+assignments for the Nth replica by comparing the Nth column of screen
+output to the thermodynamic data in the corresponding log.lammps.N or
+screen.N files as time proceeds.
+</P>
+<P>The last argument <I>index</I> in the temper command is optional and is
+used when restarting a tempering run from a set of restart files (one
+for each replica) which had previously swapped to new temperatures.
+The <I>index</I> value (from 0 to N-1, where N is the # of replicas)
+identifies which temperature the replica was simulating on the
+timestep the restart files were written. Obviously, this argument
+must be a variable so that each partition has the correct value. Set
+the variable to the <I>N</I> values listed in the log file for the previous
+run for the replica temperatures at that timestep. For example if the
+log file listed the following for a simulation with 5 replicas:
+</P>
+<PRE>500000 2 4 0 1 3
+</PRE>
+<P>then a setting of
+</P>
+<PRE>variable w world 2 4 0 1 3
+</PRE>
+<P>would be used to restart the run with a tempering command like the
+example above with $w as the last argument.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command can only be used if LAMMPS was built with the REPLICA
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "variable.html">variable</A>, <A HREF = "prd.html">prd</A>, <A HREF = "neb.html">neb</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/thermo.html b/doc/doc2/thermo.html
new file mode 100644
index 000000000..aa36e9eb5
--- /dev/null
+++ b/doc/doc2/thermo.html
@@ -0,0 +1,64 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>thermo command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>thermo N
+</PRE>
+<UL><LI>N = output thermodynamics every N timesteps
+<LI>N can be a variable (see below)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>thermo 100
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Compute and print thermodynamic info (e.g. temperature, energy,
+pressure) on timesteps that are a multiple of N and at the beginning
+and end of a simulation. A value of 0 will only print thermodynamics
+at the beginning and end.
+</P>
+<P>The content and format of what is printed is controlled by the
+<A HREF = "thermo_style.html">thermo_style</A> and
+<A HREF = "thermo_modify.html">thermo_modify</A> commands.
+</P>
+<P>Instead of a numeric value, N can be specifed as an <A HREF = "variable.html">equal-style
+variable</A>, which should be specified as v_name, where
+name is the variable name. In this case, the variable is evaluated at
+the beginning of a run to determine the next timestep at which
+thermodynamic info will be written out. On that timestep, the
+variable will be evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values. See the stagger()
+and logfreq() and stride() math functions for <A HREF = "variable.html">equal-style
+variables</A>, as examples of useful functions to use in
+this context. Other similar math functions could easily be added as
+options for <A HREF = "variable.html">equal-style variables</A>.
+</P>
+<P>For example, the following commands will output thermodynamic info at
+timesteps 0,10,20,30,100,200,300,1000,2000,etc:
+</P>
+<PRE>variable s equal logfreq(10,3,10)
+thermo v_s
+</PRE>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "thermo_modify.html">thermo_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>thermo 0
+</PRE>
+</HTML>
diff --git a/doc/doc2/thermo_modify.html b/doc/doc2/thermo_modify.html
new file mode 100644
index 000000000..5d2b90f23
--- /dev/null
+++ b/doc/doc2/thermo_modify.html
@@ -0,0 +1,173 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>thermo_modify command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>thermo_modify keyword value ...
+</PRE>
+<UL><LI>one or more keyword/value pairs may be listed
+
+<PRE>keyword = <I>lost</I> or <I>lost/bond</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l
+ <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
+ <I>lost/bond</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
+ <I>norm</I> value = <I>yes</I> or <I>no</I>
+ <I>flush</I> value = <I>yes</I> or <I>no</I>
+ <I>line</I> value = <I>one</I> or <I>multi</I>
+ <I>format</I> values = <I>int</I> string or <I>float</I> string or M string
+ M = integer from 1 to N, where N = # of quantities being printed
+ string = C-style format string
+ <I>temp</I> value = compute ID that calculates a temperature
+ <I>press</I> value = compute ID that calculates a pressure
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>thermo_modify lost ignore flush yes
+thermo_modify temp myTemp format 3 %15.8g
+thermo_modify line multi format float %g
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set options for how thermodynamic information is computed and printed
+by LAMMPS.
+</P>
+<P>IMPORTANT NOTE: These options apply to the currently defined thermo
+style. When you specify a <A HREF = "thermo_style.html">thermo_style</A> command,
+all thermodynamic settings are restored to their default values,
+including those previously reset by a thermo_modify command. Thus if
+your input script specifies a thermo_style command, you should use the
+thermo_modify command after it.
+</P>
+<P>The <I>lost</I> keyword determines whether LAMMPS checks for lost atoms
+each time it computes thermodynamics and what it does if atoms are
+lost. An atom can be "lost" if it moves across a non-periodic
+simulation box <A HREF = "boundary.html">boundary</A> or if it moves more than a box
+length outside the simulation domain (or more than a processor
+sub-domain length) before reneighboring occurs. The latter case is
+typically due to bad dynamics, e.g. too large a timestep or huge
+forces and velocities. If the value is <I>ignore</I>, LAMMPS does not
+check for lost atoms. If the value is <I>error</I> or <I>warn</I>, LAMMPS
+checks and either issues an error or warning. The code will exit with
+an error and continue with a warning. A warning will only be issued
+once, the first time an atom is lost. This can be a useful debugging
+option.
+</P>
+<P>The <I>lost/bond</I> keyword determines whether LAMMPS throws an error or
+not if an atom in a bonded interaction (bond, angle, etc) cannot be
+found when it creates bonded neighbor lists. By default this is a
+fatal error. However in some scenarios it may be desirable to only
+issue a warning or ignore it and skip the computation of the missing
+bond, angle, etc. An example would be when gas molecules in a vapor
+are drifting out of the box through a fixed boundary condition (see
+the <A HREF = "boundary.html">boundary</A> command). In this case one atom may be
+deleted before the rest of the molecule is, on a later timestep.
+</P>
+<P>The <I>norm</I> keyword determines whether various thermodynamic output
+values are normalized by the number of atoms or not, depending on
+whether it is set to <I>yes</I> or <I>no</I>. Different unit styles have
+different defaults for this setting (see below). Even if <I>norm</I> is
+set to <I>yes</I>, a value is only normalized if it is an "extensive"
+quantity, meaning that it scales with the number of atoms in the
+system. For the thermo keywords described by the doc page for the
+<A HREF = "thermo_style.html">thermo_style</A> command, all energy-related keywords
+are extensive, such as <I>pe</I> or <I>ebond</I> or <I>enthalpy</I>. Other keywords
+such as <I>temp</I> or <I>press</I> are "intensive" meaning their value is
+independent (in a statistical sense) of the number of atoms in the
+system and thus are never normalized. For thermodynamic output values
+extracted from fixes and computes in a <A HREF = "thermo_style.html">thermo_style
+custom</A> command, the doc page for the individual
+<A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> lists whether the value is
+"extensive" or "intensive" and thus whether it is normalized.
+Thermodynamic output values calculated by a variable formula are
+assumed to be "intensive" and thus are never normalized. You can
+always include a divide by the number of atoms in the variable formula
+if this is not the case.
+</P>
+<P>The <I>flush</I> keyword invokes a flush operation after thermodynamic info
+is written to the log file. This insures the output in that file is
+current (no buffering by the OS), even if LAMMPS halts before the
+simulation completes.
+</P>
+<P>The <I>line</I> keyword determines whether thermodynamics will be printed
+as a series of numeric values on one line or in a multi-line format
+with 3 quantities with text strings per line and a dashed-line header
+containing the timestep and CPU time. This modify option overrides
+the <I>one</I> and <I>multi</I> thermo_style settings.
+</P>
+<P>The <I>format</I> keyword sets the numeric format of individual printed
+quantities. The <I>int</I> and <I>float</I> keywords set the format for all
+integer or floating-point quantities printed. The setting with a
+numeric value M (e.g. format 5 %10.4g) sets the format of the Mth
+value printed in each output line, e.g. the 5th column of output in
+this case. If the format for a specific column has been set, it will
+take precedent over the <I>int</I> or <I>float</I> setting.
+</P>
+<P>IMPORTANT NOTE: The thermo output values <I>step</I> and <I>atoms</I> are stored
+internally as 8-byte signed integers, rather than the usual 4-byte
+signed integers. When specifying the "format int" keyword you can use
+a "%d"-style format identifier in the format string and LAMMPS will
+convert this to the corresponding "%lu" form when it is applied to
+those keywords. However, when specifying the "format M string"
+keyword for <I>step</I> and <I>natoms</I>, you should specify a string
+appropriate for an 8-byte signed integer, e.g. one with "%ld".
+</P>
+<P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
+is calculated, which is used by all thermo quantities that require a
+temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
+The specified compute ID must have been previously defined by the user
+via the <A HREF = "compute.html">compute</A> command and it must be a style of
+compute that calculates a temperature. As described in the
+<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
+compute for temperature with ID = <I>thermo_temp</I>. This option allows
+the user to override the default.
+</P>
+<P>The <I>press</I> keyword is used to determine how thermodynamic pressure is
+calculated, which is used by all thermo quantities that require a
+pressure ("press", "enthalpy", "pxx", etc). The specified compute ID
+must have been previously defined by the user via the
+<A HREF = "compute.html">compute</A> command and it must be a style of compute that
+calculates a pressure. As described in the
+<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
+compute for pressure with ID = <I>thermo_press</I>. This option allows the
+user to override the default.
+</P>
+<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
+single thermo_modify command (or in two separate commands), then the
+order in which the keywords are specified is important. Note that a
+<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
+compute as an argument when it is specified. The <I>temp</I> keyword will
+override this (for the pressure compute being used by thermodynamics),
+but only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If
+the <I>temp</I> keyword comes before the <I>press</I> keyword, then the new
+pressure compute specified by the <I>press</I> keyword will be unaffected
+by the <I>temp</I> setting.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are lost = error, norm = yes for unit style of
+<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
+and temp/press = compute IDs defined by thermo_style.
+</P>
+<P>The defaults for the line and format options depend on the thermo
+style. For styles "one" and "custom", the line and format defaults
+are "one", "%8d", and "%12.8g". For style "multi", the line and
+format defaults are "multi", "%8d", and "%14.4f".
+</P>
+</HTML>
diff --git a/doc/doc2/thermo_style.html b/doc/doc2/thermo_style.html
new file mode 100644
index 000000000..593ba371f
--- /dev/null
+++ b/doc/doc2/thermo_style.html
@@ -0,0 +1,371 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>thermo_style command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>thermo_style style args
+</PRE>
+<UL><LI>style = <I>one</I> or <I>multi</I> or <I>custom</I>
+
+<LI>args = list of arguments for a particular style
+
+<PRE> <I>one</I> args = none
+ <I>multi</I> args = none
+ <I>custom</I> args = list of keywords
+ possible keywords = step, elapsed, elaplong, dt, time,
+ cpu, tpcpu, spcpu, cpuremain, part,
+ atoms, temp, press, pe, ke, etotal, enthalpy,
+ evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
+ emol, elong, etail,
+ vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
+ xy, xz, yz, xlat, ylat, zlat,
+ bonds, angles, dihedrals, impropers,
+ pxx, pyy, pzz, pxy, pxz, pyz,
+ fmax, fnorm, nbuild, ndanger,
+ cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+ c_ID, c_ID[I], c_ID[I][J],
+ f_ID, f_ID[I], f_ID[I][J],
+ v_name
+ step = timestep
+ elapsed = timesteps since start of this run
+ elaplong = timesteps since start of initial run in a series of runs
+ dt = timestep size
+ time = simulation time
+ cpu = elapsed CPU time in seconds
+ tpcpu = time per CPU second
+ spcpu = timesteps per CPU second
+ cpuremain = estimated CPU time remaining in run
+ part = which partition (0 to Npartition-1) this is
+ atoms = # of atoms
+ temp = temperature
+ press = pressure
+ pe = total potential energy
+ ke = kinetic energy
+ etotal = total energy (pe + ke)
+ enthalpy = enthalpy (etotal + press*vol)
+ evdwl = VanderWaal pairwise energy
+ ecoul = Coulombic pairwise energy
+ epair = pairwise energy (evdwl + ecoul + elong + etail)
+ ebond = bond energy
+ eangle = angle energy
+ edihed = dihedral energy
+ eimp = improper energy
+ emol = molecular energy (ebond + eangle + edihed + eimp)
+ elong = long-range kspace energy
+ etail = VanderWaal energy long-range tail correction
+ vol = volume
+ density = mass density of system
+ lx,ly,lz = box lengths in x,y,z
+ xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
+ xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
+ xlat,ylat,zlat = lattice spacings as calculated by <A HREF = "lattice.html">lattice</A> command
+ bonds,angles,dihedrals,impropers = # of these interactions defined
+ pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
+ fmax = max component of force on any atom in any dimension
+ fnorm = length of force vector for all atoms
+ nbuild = # of neighbor list builds
+ ndanger = # of dangerous neighbor list builds
+ cella,cellb,cellc = periodic cell lattice constants a,b,c
+ cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
+ c_ID = global scalar value calculated by a compute with ID
+ c_ID[I] = Ith component of global vector calculated by a compute with ID
+ c_ID[I][J] = I,J component of global array calculated by a compute with ID
+ f_ID = global scalar value calculated by a fix with ID
+ f_ID[I] = Ith component of global vector calculated by a fix with ID
+ f_ID[I][J] = I,J component of global array calculated by a fix with ID
+ v_name = scalar value calculated by an equal-style variable with name
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>thermo_style multi
+thermo_style custom step temp pe etotal press vol
+thermo_style custom step temp etotal c_myTemp v_abc
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the style and content for printing thermodynamic data to the
+screen and log file.
+</P>
+<P>Style <I>one</I> prints a one-line summary of thermodynamic info that is
+the equivalent of "thermo_style custom step temp epair emol etotal
+press". The line contains only numeric values.
+</P>
+<P>Style <I>multi</I> prints a multiple-line listing of thermodynamic info
+that is the equivalent of "thermo_style custom etotal ke temp pe ebond
+eangle edihed eimp evdwl ecoul elong press". The listing contains
+numeric values and a string ID for each quantity.
+</P>
+<P>Style <I>custom</I> is the most general setting and allows you to specify
+which of the keywords listed above you want printed on each
+thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
+references to <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
+equal-style <A HREF = "variable.html"">variables</A> that have been defined
+elsewhere in the input script or can even be new styles which users
+have added to LAMMPS (see the <A HREF = "Section_modify.html">Section_modify</A>
+section of the documentation). Thus the <I>custom</I> style provides a
+flexible means of outputting essentially any desired quantity as a
+simulation proceeds.
+</P>
+<P>All styles except <I>custom</I> have <I>vol</I> appended to their list of
+outputs if the simulation box volume changes during the simulation.
+</P>
+<P>The values printed by the various keywords are instantaneous values,
+calculated on the current timestep. Time-averaged quantities, which
+include values from previous timesteps, can be output by using the
+f_ID keyword and accessing a fix that does time-averaging such as the
+<A HREF = "fix_ave_time.html">fix ave/time</A> command.
+</P>
+<P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
+be used to set the one- or multi-line format of the print-out, the
+normalization of thermodynamic output (total values versus per-atom
+values for extensive quantities (ones which scale with the number of
+atoms in the system), and the numeric precision of each printed value.
+</P>
+<P>IMPORTANT NOTE: When you use a "thermo_style" command, all
+thermodynamic settings are restored to their default values, including
+those previously set by a <A HREF = "thermo_modify.html">thermo_modify</A> command.
+Thus if your input script specifies a thermo_style command, you should
+use the thermo_modify command after it.
+</P>
+<HR>
+
+<P>Several of the thermodynamic quantities require a temperature to be
+computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By
+default this is done by using a <I>temperature</I> compute which is created
+when LAMMPS starts up, as if this command had been issued:
+</P>
+<PRE>compute thermo_temp all temp
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
+that the ID of this compute is <I>thermo_temp</I> and the group is <I>all</I>.
+You can change the attributes of this temperature (e.g. its
+degrees-of-freedom) via the <A HREF = "compute_modify.html">compute_modify</A>
+command. Alternatively, you can directly assign a new compute (that
+calculates temperature) which you have defined, to be used for
+calculating any thermodynamic quantity that requires a temperature.
+This is done via the <A HREF = "thermo_modify.html">thermo_modify</A> command.
+</P>
+<P>Several of the thermodynamic quantities require a pressure to be
+computed: "press", "enthalpy", "pxx", etc. By default this is done by
+using a <I>pressure</I> compute which is created when LAMMPS starts up, as
+if this command had been issued:
+</P>
+<PRE>compute thermo_press all pressure thermo_temp
+</PRE>
+<P>See the <A HREF = "compute_pressure.html">compute pressure</A> command for details.
+Note that the ID of this compute is <I>thermo_press</I> and the group is
+<I>all</I>. You can change the attributes of this pressure via the
+<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
+directly assign a new compute (that calculates pressure) which you
+have defined, to be used for calculating any thermodynamic quantity
+that requires a pressure. This is done via the
+<A HREF = "thermo_modify.html">thermo_modify</A> command.
+</P>
+<P>Several of the thermodynamic quantities require a potential energy to
+be computed: "pe", "etotal", "ebond", etc. This is done by using a
+<I>pe</I> compute which is created when LAMMPS starts up, as if this
+command had been issued:
+</P>
+<PRE>compute thermo_pe all pe
+</PRE>
+<P>See the <A HREF = "compute_pe.html">compute pe</A> command for details. Note that
+the ID of this compute is <I>thermo_pe</I> and the group is <I>all</I>. You can
+change the attributes of this potential energy via the
+<A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<HR>
+
+<P>The kinetic energy of the system <I>ke</I> is inferred from the temperature
+of the system with 1/2 Kb T of energy for each degree of freedom.
+Thus, using different <A HREF = "compute.html">compute commands</A> for calculating
+temperature, via the <A HREF = "thermo_modify.html">thermo_modify temp</A> command,
+may yield different kinetic energies, since different computes that
+calculate temperature can subtract out different non-thermal
+components of velocity and/or include different degrees of freedom
+(translational, rotational, etc).
+</P>
+<P>The potential energy of the system <I>pe</I> will include contributions
+from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
+for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall.html">fix
+wall/lj93</A> fix calculates the energy of atoms
+interacting with the wall. See the doc pages for "individual fixes"
+to see which ones contribute.
+</P>
+<P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
+energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify
+tail</A> option is turned on. The <I>etail</I> contribution
+is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding tail
+correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
+etc.
+</P>
+<HR>
+
+<P>The <I>step</I>, <I>elapsed</I>, and <I>elaplong</I> keywords refer to timestep
+count. <I>Step</I> is the current timestep, or iteration count when a
+<A HREF = "minimize.html">minimization</A> is being performed. <I>Elapsed</I> is the
+number of timesteps elapsed since the beginning of this run.
+<I>Elaplong</I> is the number of timesteps elapsed since the beginning of
+an initial run in a series of runs. See the <I>start</I> and <I>stop</I>
+keywords for the <A HREF = "run.html">run</A> for info on how to invoke a series of
+runs that keep track of an initial starting time. If these keywords
+are not used, then <I>elapsed</I> and <I>elaplong</I> are the same value.
+</P>
+<P>The <I>dt</I> keyword is the current timestep size in time
+<A HREF = "units.html">units</A>. The <I>time</I> keyword is the current elapsed
+simulation time, also in time <A HREF = "units.html">units</A>, which is simply
+(step*dt) if the timestep size has not changed and the timestep has
+not been reset. If the timestep has changed (e.g. via <A HREF = "fix_dt_reset.html">fix
+dt/reset</A>) or the timestep has been reset (e.g. via
+the "reset_timestep" command), then the simulation time is effectively
+a cummulative value up to the current point.
+</P>
+<P>The <I>cpu</I> keyword is elapsed CPU seconds since the beginning of this
+run. The <I>tpcpu</I> and <I>spcpu</I> keywords are measures of how fast your
+simulation is currently running. The <I>tpcpu</I> keyword is simulation
+time per CPU second, where simulation time is in time
+<A HREF = "units.html">units</A>. E.g. for metal units, the <I>tpcpu</I> value would be
+picoseconds per CPU second. The <I>spcpu</I> keyword is the number of
+timesteps per CPU second. Both quantities are on-the-fly metrics,
+measured relative to the last time they were invoked. Thus if you are
+printing out thermodyamic output every 100 timesteps, the two keywords
+will continually output the time and timestep rate for the last 100
+steps. The <I>tpcpu</I> keyword does not attempt to track any changes in
+timestep size, e.g. due to using the <A HREF = "fix_dt_reset.html">fix dt/reset</A>
+command.
+</P>
+<P>The <I>cpuremain</I> keyword estimates the CPU time remaining in the
+current run, based on the time elapsed thus far. It will only be a
+good estimate if the CPU time/timestep for the rest of the run is
+similar to the preceding timesteps. On the initial timestep the value
+will be 0.0 since there is no history to estimate from. For a
+minimization run performed by the "minimize" command, the estimate is
+based on the <I>maxiter</I> parameter, assuming the minimization will
+proceed for the maximum number of allowed iterations.
+</P>
+<P>The <I>part</I> keyword is useful for multi-replica or multi-partition
+simulations to indicate which partition this output and this file
+corresponds to, or for use in a <A HREF = "variable.html">variable</A> to append to
+a filename for output specific to this partition. See <A HREF = "Section_start.html#start_7">Section_start
+7</A> of the manual for details on running in
+multi-partition mode.
+</P>
+<P>The <I>fmax</I> and <I>fnorm</I> keywords are useful for monitoring the progress
+of an <A HREF = "minimize.html">energy minimization</A>. The <I>fmax</I> keyword
+calculates the maximum force in any dimension on any atom in the
+system, or the infinity-norm of the force vector for the system. The
+<I>fnorm</I> keyword calculates the 2-norm or length of the force vector.
+</P>
+<P>The <I>nbuild</I> and <I>ndanger</I> keywords are useful for monitoring neighbor
+list builds during a run. Note that both these values are also
+printed with the end-of-run statistics. The <I>nbuild</I> keyword is the
+number of re-builds during the current run. The <I>ndanger</I> keyword is
+the number of re-builds that LAMMPS considered potentially
+"dangerous". If atom movement triggered neighbor list rebuilding (see
+the <A HREF = "neigh_modify.html">neigh_modify</A> command), then dangerous
+reneighborings are those that were triggered on the first timestep
+atom movement was checked for. If this count is non-zero you may wish
+to reduce the delay factor to insure no force interactions are missed
+by atoms moving beyond the neighbor skin distance before a rebuild
+takes place.
+</P>
+<P>The keywords <I>cella</I>, <I>cellb</I>, <I>cellc</I>, <I>cellalpha</I>, <I>cellbeta</I>,
+<I>cellgamma</I>, correspond to the usual crystallographic quantities that
+define the periodic unit cell of a crystal. See <A HREF = "Section_howto.html#howto_12">this
+section</A> of the doc pages for a geometric
+description of triclinic periodic cells, including a precise defintion
+of these quantities in terms of the internal LAMMPS cell dimensions
+<I>lx</I>, <I>ly</I>, <I>lz</I>, <I>yz</I>, <I>xz</I>, <I>xy</I>.
+</P>
+<HR>
+
+<P>The <I>c_ID</I> and <I>c_ID[I]</I> and <I>c_ID[I][J]</I> keywords allow global
+values calculated by a compute to be output. As discussed on the
+<A HREF = "compute.html">compute</A> doc page, computes can calculate global,
+per-atom, or local values. Only global values can be referenced by
+this command. However, per-atom compute values can be referenced in a
+<A HREF = "variable.html">variable</A> and the variable referenced by thermo_style
+custom, as discussed below.
+</P>
+<P>The ID in the keyword should be replaced by the actual ID of a compute
+that has been defined elsewhere in the input script. See the
+<A HREF = "compute.html">compute</A> command for details. If the compute calculates
+a global scalar, vector, or array, then the keyword formats with 0, 1,
+or 2 brackets will reference a scalar value from the compute.
+</P>
+<P>Note that some computes calculate "intensive" global quantities like
+temperature; others calculate "extensive" global quantities like
+kinetic energy that are summed over all atoms in the compute group.
+Intensive quantities are printed directly without normalization by
+thermo_style custom. Extensive quantities may be normalized by the
+total number of atoms in the simulation (NOT the number of atoms in
+the compute group) when output, depending on the <A HREF = "thermo_modify.html">thermo_modify
+norm</A> option being used.
+</P>
+<P>The <I>f_ID</I> and <I>f_ID[I]</I> and <I>f_ID[I][J]</I> keywords allow global
+values calculated by a fix to be output. As discussed on the
+<A HREF = "fix.html">fix</A> doc page, fixes can calculate global, per-atom, or
+local values. Only global values can be referenced by this command.
+However, per-atom fix values can be referenced in a
+<A HREF = "variable.html">variable</A> and the variable referenced by thermo_style
+custom, as discussed below.
+</P>
+<P>The ID in the keyword should be replaced by the actual ID of a fix
+that has been defined elsewhere in the input script. See the
+<A HREF = "fix.html">fix</A> command for details. If the fix calculates a global
+scalar, vector, or array, then the keyword formats with 0, 1, or 2
+brackets will reference a scalar value from the fix.
+</P>
+<P>Note that some fixes calculate "intensive" global quantities like
+timestep size; others calculate "extensive" global quantities like
+energy that are summed over all atoms in the fix group. Intensive
+quantities are printed directly without normalization by thermo_style
+custom. Extensive quantities may be normalized by the total number of
+atoms in the simulation (NOT the number of atoms in the fix group)
+when output, depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A>
+option being used.
+</P>
+<P>The <I>v_name</I> keyword allow the current value of a variable to be
+output. The name in the keyword should be replaced by the variable
+name that has been defined elsewhere in the input script. Only
+equal-style variables can be referenced. See the
+<A HREF = "variable.html">variable</A> command for details. Variables of style
+<I>equal</I> can reference per-atom properties or thermodynamic keywords,
+or they can invoke other computes, fixes, or variables when evaluated,
+so this is a very general means of creating thermodynamic output.
+</P>
+<P>Note that equal-style variables are assumed to be "intensive" global
+quantities, which are thus printed as-is, without normalization by
+thermo_style custom. You can include a division by "natoms" in the
+variable formula if this is not the case.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command must come after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
+<A HREF = "create_box.html">create_box</A> command.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_modify.html">thermo_modify</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
+<A HREF = "compute_pressure.html">compute pressure</A>
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>thermo_style one
+</PRE>
+</HTML>
diff --git a/doc/doc2/timestep.html b/doc/doc2/timestep.html
new file mode 100644
index 000000000..b12cc15c9
--- /dev/null
+++ b/doc/doc2/timestep.html
@@ -0,0 +1,49 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>timestep command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>timestep dt
+</PRE>
+<UL><LI>dt = timestep size (time units)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>timestep 2.0
+timestep 0.003
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set the timestep size for subsequent molecular dynamics simulations.
+See the <A HREF = "units.html">units</A> command for a discussion of time units.
+The default value for the timestep also depends on the choice of units
+for the simulation; see the default values below.
+</P>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, dt is the timestep for
+the outer loop (largest) timestep.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_dt_reset.html">fix dt/reset</A>, <A HREF = "run.html">run</A>,
+<A HREF = "run_style.html">run_style</A> respa, <A HREF = "units.html">units</A>
+</P>
+<P><B>Default:</B>
+</P>
+timestep = 0.005 tau for units = lj<BR>
+timestep = 1.0 fmsec for units = real<BR>
+timestep = 0.001 psec for units = metal<BR>
+timestep = 1.0e-8 sec (10 nsec) for units = si or cgs <BR>
+
+</HTML>
diff --git a/doc/doc2/tutorial_drude.html b/doc/doc2/tutorial_drude.html
new file mode 100644
index 000000000..b90044029
--- /dev/null
+++ b/doc/doc2/tutorial_drude.html
@@ -0,0 +1,467 @@
+<HTML>
+<script type="text/javascript"
+ src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+<H3>Tutorial for Thermalized Drude oscillators in LAMMPS
+</H3>
+<P>This tutorial explains how to use Drude oscillators in LAMMPS to
+simulate polarizable systems using the USER-DRUDE package. As an
+illustration, the input files for a simulation of 250 phenol molecules
+are documented. First of all, LAMMPS has to be compiled with the
+USER-DRUDE package activated. Then, the data file and input scripts
+have to be modified to include the Drude dipoles and how to handle
+them.
+</P>
+<HR>
+
+<P><B>Overview of Drude induced dipoles</B>
+</P>
+<P>Polarizable atoms acquire an induced electric dipole moment under the
+action of an external electric field, for example the electric field
+created by the surrounding particles. Drude oscillators represent
+these dipoles by two fixed charges: the core (DC) and the Drude
+particle (DP) bound by a harmonic potential. The Drude particle can be
+thought of as the electron cloud whose center can be displaced from
+the position of the the corresponding nucleus.
+</P>
+<P>The sum of the masses of a core-Drude pair should be the mass of the
+initial (unsplit) atom, \(m_C + m_D = m\). The sum of their charges
+should be the charge of the initial (unsplit) atom, \(q_C + q_D = q\).
+A harmonic potential between the core and Drude partners should be
+present, with force constant \(k_D\) and an equilibrium distance of
+zero. The (half-)stiffness of the <A HREF = "bond_harmonic.html">harmonic bond</A>
+\(K_D = k_D/2\) and the Drude charge \(q_D\) are related to the atom
+polarizability \(\alpha\) by
+</P>
+<P>\begin{equation} K_D = \frac 1 2\, \frac {q_D^2} \alpha
+\end{equation}
+</P>
+<P>Ideally, the mass of the Drude particle should be small, and the
+stiffness of the harmonic bond should be large, so that the Drude
+particle remains close ot the core. The values of Drude mass, Drude
+charge, and force constant can be chosen following different
+strategies, as in the following examples of polarizable force
+fields.
+</P>
+<UL><LI><A HREF = "#Lamoureux">Lamoureux and Roux</A> suggest adopting a global
+half-stiffness, \(K_D\) = 500 kcal/(mol &Aring;<sup>2</sup>) &mdash;
+which corresponds to a force constant \(k_D\) = 4184 kJ/(mol
+&Aring;<sup>2</sup>) &mdash; for all types of core-Drude bond, a
+global mass \(m_D\) = 0.4 g/mol (or u) for all types of Drude
+particle, and to calculate the Drude charges for individual atom types
+from the atom polarizabilities using equation (1). This choice is
+followed in the polarizable CHARMM force field.
+
+<LI><A HREF = "#Schroeder">Schroeder and Steinhauser</A> suggest adopting a global
+charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u)
+for all Drude particles, and to calculate the force constant for each
+type of core-Drude bond from equation (1). The timesteps used by these
+authors are between 0.5 and 2 fs, with the degrees of freedom of the
+Drude oscillators kept cold at 1 K. In both these force fields
+hydrogen atoms are treated as non-polarizable.
+</UL>
+<P>The motion of of the Drude particles can be calculated by minimizing
+the energy of the induced dipoles at each timestep, by an interative,
+self-consistent procedure. The Drude particles can be massless and
+therefore do not contribute to the kinetic energy. However, the
+relaxed method is computationall slow. An extended-lagrangian method
+can be used to calculate the positions of the Drude particles, but
+this requires them to have mass. It is important in this case to
+decouple the degrees of freedom associated with the Drude oscillators
+from those of the normal atoms. Thermalizing the Drude dipoles at
+temperatures comparable to the rest of the simulation leads to several
+problems (kinetic energy transfer, very short timestep, etc.), which
+can be remediated by the "cold Drude" technique (<A HREF = "#Lamoureux">Lamoureux and
+Roux</A>).
+</P>
+<P>Two closely related models are used to represent polarization through
+"charges on a spring": the core-shell model and the Drude
+model. Although the basic idea is the same, the core-shell model is
+normally used for ionic/crystalline materials, whereas the Drude model
+is normally used for molecular systems and fluid states. In ionic
+crystals the symmetry around each ion and the distance between them
+are such that the core-shell model is sufficiently stable. But to be
+applicable to molecular/covalent systems the Drude model includes two
+important features:
+</P>
+<OL><LI>The possibility to thermostat the additional degrees of freedom
+associated with the induced dipoles at very low temperature, in terms
+of the reduced coordinates of the Drude particles with respect to
+their cores. This makes the trajectory close to that of relaxed
+induced dipoles.
+
+<LI>The Drude dipoles on covalently bonded atoms interact too strongly
+due to the short distances, so an atom may capture the Drude particle
+(shell) of a neighbor, or the induced dipoles within the same molecule
+may align too much. To avoid this, damping at short of the
+interactions between the point charges composing the induced dipole
+can be done by <A HREF = "#Thole">Thole</A> functions.
+</OL>
+<HR>
+
+<P><B>Preparation of the data file</B>
+</P>
+<P>The data file is similar to a standard LAMMPS data file for
+<I>atom_style full</I>. The DPs and the <I>harmonic bonds</I> connecting them
+to their DC should appear in the data file as normal atoms and bonds.
+</P>
+<P>You can use the <I>polarizer</I> tool (Python script distributed with the
+USER-DRUDE package) to convert a non-polarizable data file (here
+<I>data.102494.lmp</I>) to a polarizable data file (<I>data-p.lmp</I>)
+</P>
+<PRE>polarizer -q -f phenol.dff data.102494.lmp data-p.lmp
+</PRE>
+<P>This will automatically insert the new atoms and bonds.
+The masses and charges of DCs and DPs are computed
+from <I>phenol.dff</I>, as well as the DC-DP bond constants. The file
+<I>phenol.dff</I> contains the polarizabilities of the atom types
+and the mass of the Drude particles, for instance:
+</P>
+<PRE># units: kJ/mol, A, deg
+# kforce is in the form k/2 r_D^2
+# type m_D/u q_D/e k_D alpha/A3 thole
+OH 0.4 -1.0 4184.0 0.63 0.67
+CA 0.4 -1.0 4184.0 1.36 2.51
+CAI 0.4 -1.0 4184.0 1.09 2.51
+</PRE>
+<P>The hydrogen atoms are absent from this file, so they will be treated
+as non-polarizable atoms. In the non-polarizable data file
+<I>data.102494.lmp</I>, atom names corresponding to the atom type numbers
+have to be specified as comments at the end of lines of the <I>Masses</I>
+section. You probably need to edit it to add these names. It should
+look like
+</P>
+<PRE>Masses
+</PRE>
+<PRE>1 12.011 # CAI
+2 12.011 # CA
+3 15.999 # OH
+4 1.008 # HA
+5 1.008 # HO
+</PRE>
+<HR>
+
+<P><B>Basic input file</B>
+</P>
+<P>The atom style should be set to (or derive from) <I>full</I>, so that you
+can define atomic charges and molecular bonds, angles, dihedrals...
+</P>
+<P>The <I>polarizer</I> tool also outputs certain lines related to the input
+script (the use of these lines will be explained below). In order for
+LAMMPS to recognize that you are using Drude oscillators, you should
+use the fix <I>drude</I>. The command is
+</P>
+<PRE>fix DRUDE all drude C C C N N D D D
+</PRE>
+<P>The N, C, D following the <I>drude</I> keyword have the following meaning:
+There is one tag for each atom type. This tag is C for DCs, D for DPs
+and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O
+atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
+the atom types 6 to 8 are the newly created DPs.
+</P>
+<P>By recognizing the fix <I>drude</I>, LAMMPS will find and store matching
+DC-DP pairs and will treat DP as equivalent to their DC in the
+<I>special bonds</I> relations. It may be necessary to extend the space
+for storing such special relations. In this case extra space should
+be reserved by using the <I>extra</I> keyword of the <I>special_bonds</I>
+command. With our phenol, there is 1 more special neighbor for which
+space is required. Otherwise LAMMPS crashes and gives the required
+value.
+</P>
+<PRE>special_bonds lj/coul 0.0 0.0 0.5 extra 1
+</PRE>
+<P>Let us assume we want to run a simple NVT simulation at 300 K. Note
+that Drude oscillators need to be thermalized at a low temperature in
+order to approximate a self-consistent field (SCF), therefore it is not
+possible to simulate an NVE ensemble with this package. Since dipoles
+are approximated by a charged DC-DP pair, the <I>pair_style</I> must
+include Coulomb interactions, for instance <I>lj/cut/coul/long</I> with
+<I>kspace_style pppm</I>. For example, with a cutoff of 10. and a precision
+1.e-4:
+</P>
+<PRE>pair_style lj/cut/coul/long 10.0
+kspace_style pppm 1.0e-4
+</PRE>
+<P>As compared to the non-polarizable input file, <I>pair_coeff</I> lines need
+to be added for the DPs. Since the DPs have no Lennard-Jones
+interactions, their <I>epsilon</I> is 0. so the only <I>pair_coeff</I> line
+that needs to be added is
+</P>
+<PRE>pair_coeff * 6* 0.0 0.0 # All-DPs
+</PRE>
+<P>Now for the thermalization, the simplest choice is to use the <A HREF = "fix_langevin_drude.html">fix
+langevin/drude</A>.
+</P>
+<PRE>fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+</PRE>
+<P>This applies a Langevin thermostat at temperature 300. to the centers
+of mass of the DC-DP pairs, with relaxation time 100 and with random
+seed 12345. This fix applies also a Langevin thermostat at temperature
+1. to the relative motion of the DPs around their DCs, with relaxation
+time 20 and random seed 13977. Only the DCs and non-polarizable
+atoms need to be in this fix's group. LAMMPS will thermostate the DPs
+together with their DC. For this, ghost atoms need to know their
+velocities. Thus you need to add the following command:
+</P>
+<PRE>comm_modify vel yes
+</PRE>
+<P>In order to avoid that the center of mass of the whole system
+drifts due to the random forces of the Langevin thermostat on DCs, you
+can add the <I>zero yes</I> option at the end of the fix line.
+</P>
+<P>If the fix <I>shake</I> is used to constrain the C-H bonds, it should be
+invoked after the fix <I>langevin/drude</I> for more accuracy.
+</P>
+<PRE>fix SHAKE ATOMS shake 0.0001 20 0 t 4 5
+</PRE>
+<P>IMPORTANT NOTE: The group of the fix <I>shake</I> must not include the DPs.
+If the group <I>ATOMS</I> is defined by non-DPs atom types, you could use
+</P>
+<P>Since the fix <I>langevin/drude</I> does not perform time integration (just
+modification of forces but no position/velocity updates), the fix
+<I>nve</I> should be used in conjunction.
+</P>
+<PRE>fix NVE all nve
+</PRE>
+<P>Finally, do not forget to update the atom type elements if you use
+them in a <I>dump_modify ... element ...</I> command, by adding the element
+type of the DPs. Here for instance
+</P>
+<PRE>dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
+dump_modify DUMP element C C O H H D D D
+</PRE>
+<P>The input file should now be ready for use!
+</P>
+<P>You will notice that the global temperature <I>thermo_temp</I> computed by
+LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as
+standard atoms in his default compute. If you want to output the
+temperatures of the DC-DP pair centers of mass and of the DPs relative
+to their DCs, you should use the <A HREF = "compute_temp_drude.html">compute
+temp_drude</A>
+</P>
+<PRE>compute TDRUDE all temp/drude
+</PRE>
+<P>And then output the correct temperatures of the Drude oscillators
+using <I>thermo_style custom</I> with respectively <I>c_TDRUDE[1]</I> and
+<I>c_TDRUDE[2]</I>. These should be close to 300.0 and 1.0 on average.
+</P>
+<PRE>thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
+</PRE>
+<HR>
+
+<P><B>Thole screening</B>
+</P>
+<P>Dipolar interactions represented by point charges on springs may not
+be stable, for example if the atomic polarizability is too high for
+instance, a DP can escape from its DC and be captured by another DC,
+which makes the force and energy diverge and the simulation
+crash. Even without reaching this extreme case, the correlation
+between nearby dipoles on the same molecule may be exagerated. Often,
+special bond relations prevent bonded neighboring atoms to see the
+charge of each other's DP, so that the problem does not always appear.
+It is possible to use screened dipole dipole interactions by using the
+<A HREF = "pair_thole.html"><I>pair_style thole</I></A>. This is implemented as a
+correction to the Coulomb pair_styles, which dampens at short distance
+the interactions between the charges representing the induced dipoles.
+It is to be used as <I>hybrid/overlay</I> with any standard <I>coul</I> pair
+style. In our example, we would use
+</P>
+<PRE>pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
+</PRE>
+<P>This tells LAMMPS that we are using two pair_styles. The first one is
+as above (<I>lj/cut/coul/long 10.0</I>). The second one is a <I>thole</I>
+pair_style with default screening factor 2.6 (<A HREF = "#Noskov">Noskov</A>) and
+cutoff 10.0.
+</P>
+<P>Since <I>hybrid/overlay</I> does not support mixing rules, the interaction
+coefficients of all the pairs of atom types with i < j should be
+explicitly defined. The output of the <I>polarizer</I> script can be used
+to complete the <I>pair_coeff</I> section of the input file. In our
+example, this will look like:
+</P>
+<PRE>pair_coeff 1 1 lj/cut/coul/long 0.0700 3.550
+pair_coeff 1 2 lj/cut/coul/long 0.0700 3.550
+pair_coeff 1 3 lj/cut/coul/long 0.1091 3.310
+pair_coeff 1 4 lj/cut/coul/long 0.0458 2.985
+pair_coeff 2 2 lj/cut/coul/long 0.0700 3.550
+pair_coeff 2 3 lj/cut/coul/long 0.1091 3.310
+pair_coeff 2 4 lj/cut/coul/long 0.0458 2.985
+pair_coeff 3 3 lj/cut/coul/long 0.1700 3.070
+pair_coeff 3 4 lj/cut/coul/long 0.0714 2.745
+pair_coeff 4 4 lj/cut/coul/long 0.0300 2.420
+pair_coeff * 5 lj/cut/coul/long 0.0000 0.000
+pair_coeff * 6* lj/cut/coul/long 0.0000 0.000
+pair_coeff 1 1 thole 1.090 2.510
+pair_coeff 1 2 thole 1.218 2.510
+pair_coeff 1 3 thole 0.829 1.590
+pair_coeff 1 6 thole 1.090 2.510
+pair_coeff 1 7 thole 1.218 2.510
+pair_coeff 1 8 thole 0.829 1.590
+pair_coeff 2 2 thole 1.360 2.510
+pair_coeff 2 3 thole 0.926 1.590
+pair_coeff 2 6 thole 1.218 2.510
+pair_coeff 2 7 thole 1.360 2.510
+pair_coeff 2 8 thole 0.926 1.590
+pair_coeff 3 3 thole 0.630 0.670
+pair_coeff 3 6 thole 0.829 1.590
+pair_coeff 3 7 thole 0.926 1.590
+pair_coeff 3 8 thole 0.630 0.670
+pair_coeff 6 6 thole 1.090 2.510
+pair_coeff 6 7 thole 1.218 2.510
+pair_coeff 6 8 thole 0.829 1.590
+pair_coeff 7 7 thole 1.360 2.510
+pair_coeff 7 8 thole 0.926 1.590
+pair_coeff 8 8 thole 0.630 0.670
+</PRE>
+<P>For the <I>thole</I> pair style the coefficients are
+</P>
+<OL><LI>the atom polarizability in units of cubic length
+
+<LI>the screening factor of the Thole function (optional, default value
+specified by the pair_style command)
+
+<LI>the cutoff (optional, default value defined by the pair_style command)
+
+</OL>
+<P>The special neighbors have charge-charge and charge-dipole
+interactions screened by the <I>coul</I> factors of the <I>special_bonds</I>
+command (0.0, 0.0, and 0.5 in the example above). Without using the
+pair_style <I>thole</I>, dipole-dipole interactions are screened by the
+same factor. By using the pair_style <I>thole</I>, dipole-dipole
+interactions are screened by Thole's function, whatever their special
+relationship (except within each DC-DP pair of course). Consider for
+example 1-2 neighbors: using the pair_style <I>thole</I>, their dipoles
+will see each other (despite the <I>coul</I> factor being 0.) and the
+interactions between these dipoles will be damped by Thole's function.
+</P>
+<HR>
+
+<P><B>Thermostats and barostats</B>
+</P>
+<P>Using a Nose-Hoover barostat with the <I>langevin/drude</I> thermostat is
+straightforward using fix <I>nph</I> instead of <I>nve</I>. For example:
+</P>
+<PRE>fix NPH all nph iso 1. 1. 500
+</PRE>
+<P>It is also possible to use a Nose-Hoover instead of a Langevin
+thermostat. This requires to use <A HREF = "fix_drude_transform.html"><I>fix
+drude/transform</I></A> just before and after the
+time intergation fixes. The <I>fix drude/transform/direct</I> converts the
+atomic masses, positions, velocities and forces into a reduced
+representation, where the DCs transform into the centers of mass of
+the DC-DP pairs and the DPs transform into their relative position
+with respect to their DC. The <I>fix drude/transform/inverse</I> performs
+the reverse transformation. For a NVT simulation, with the DCs and
+atoms at 300 K and the DPs at 1 K relative to their DC one would use
+</P>
+<PRE>fix DIRECT all drude/transform/direct
+fix NVT1 ATOMS nvt temp 300. 300. 100
+fix NVT2 DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</PRE>
+<P>For our phenol example, the groups would be defined as
+</P>
+<PRE>group ATOMS type 1 2 3 4 5 # DCs and non-polarizable atoms
+group CORES type 1 2 3 # DCs
+group DRUDES type 6 7 8 # DPs
+</PRE>
+<P>Note that with the fixes <I>drude/transform</I>, it is not required to
+specify <I>comm_modify vel yes</I> because the fixes do it anyway (several
+times and for the forces also). To avoid the flying ice cube artifact
+<A HREF = "#Lamoureux">(Lamoureux)</A>, where the atoms progressively freeze and the
+center of mass of the whole system drifts faster and faster, the <I>fix
+momentum</I> can be used. For instance:
+</P>
+<PRE>fix MOMENTUM all momentum 100 linear 1 1 1
+</PRE>
+<P>It is a bit more tricky to run a NPT simulation with Nose-Hoover
+barostat and thermostat. First, the volume should be integrated only
+once. So the fix for DCs and atoms should be <I>npt</I> while the fix for
+DPs should be <I>nvt</I> (or vice versa). Second, the <I>fix npt</I> computes a
+global pressure and thus a global temperature whatever the fix group.
+We do want the pressure to correspond to the whole system, but we want
+the temperature to correspond to the fix group only. We must then use
+the <I>fix_modify</I> command for this. In the end, the block of
+instructions for thermostating and barostating will look like
+</P>
+<PRE>compute TATOMS ATOMS temp
+fix DIRECT all drude/transform/direct
+fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
+fix_modify NPT temp TATOMS press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</PRE>
+<HR>
+
+<P><B>Rigid bodies</B>
+</P>
+<P>You may want to simulate molecules as rigid bodies (but polarizable).
+Common cases are water models such as <A HREF = "#SWM4-NDP">SWM4-NDP</A>, which is a
+kind of polarizable TIP4P water. The rigid bodies and the DPs should
+be integrated separately, even with the Langevin thermostat. Let us
+review the different thermostats and ensemble combinations.
+</P>
+<P>NVT ensemble using Langevin thermostat:
+</P>
+<PRE>comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nve/small molecule
+fix NVE DRUDES nve
+</PRE>
+<P>NVT ensemble using Nose-Hoover thermostat:
+</P>
+<PRE>fix DIRECT all drude/transform/direct
+fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</PRE>
+<P>NPT ensemble with Langevin thermostat:
+</P>
+<PRE>comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
+fix NVE DRUDES nve
+</PRE>
+<P>NPT ensemble using Nose-Hoover thermostat:
+</P>
+<PRE>compute TATOM ATOMS temp
+fix DIRECT all drude/transform/direct
+fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
+fix_modify RIGID temp TATOM press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</PRE>
+<HR>
+
+<A NAME = "Lamoureux"></A>
+
+<P><B>(Lamoureux)</B> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
+</P>
+<A NAME = "Schroeder"></A>
+
+<P><B>(Schroeder)</B> Schr&ouml;der and Steinhauser, J Chem Phys, 133,
+154511 (2010).
+</P>
+<A NAME = "Jiang"></A>
+
+<P><B>(Jiang)</B> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
+ J Phys Chem Lett, 2, 87-92 (2011).
+</P>
+<A NAME = "Thole"></A>
+
+<P><B>(Thole)</B> Chem Phys, 59, 341 (1981).
+</P>
+<A NAME = "Noskov"></A>
+
+<P><B>(Noskov)</B> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
+</P>
+<A NAME = "SWM4-NDP"></A>
+
+<P><B>(SWM4-NDP)</B> Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
+Let, 418, 245-249 (2006)
+</P>
+</HTML>
diff --git a/doc/doc2/uncompute.html b/doc/doc2/uncompute.html
new file mode 100644
index 000000000..8487f4aac
--- /dev/null
+++ b/doc/doc2/uncompute.html
@@ -0,0 +1,39 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>uncompute command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>uncompute compute-ID
+</PRE>
+<UL><LI>compute-ID = ID of a previously defined compute
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>uncompute 2
+uncompute lower-boundary
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Delete a compute that was previously defined with a <A HREF = "compute.html">compute</A>
+command. This also wipes out any additional changes made to the compute
+via the <A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/undump.html b/doc/doc2/undump.html
new file mode 100644
index 000000000..246fe0375
--- /dev/null
+++ b/doc/doc2/undump.html
@@ -0,0 +1,38 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>undump command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>undump dump-ID
+</PRE>
+<UL><LI>dump-ID = ID of previously defined dump
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>undump mine
+undump 2
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Turn off a previously defined dump so that it is no longer active.
+This closes the file associated with the dump.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/unfix.html b/doc/doc2/unfix.html
new file mode 100644
index 000000000..2ae948c2c
--- /dev/null
+++ b/doc/doc2/unfix.html
@@ -0,0 +1,39 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>unfix command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>unfix fix-ID
+</PRE>
+<UL><LI>fix-ID = ID of a previously defined fix
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>unfix 2
+unfix lower-boundary
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Delete a fix that was previously defined with a <A HREF = "fix.html">fix</A>
+command. This also wipes out any additional changes made to the fix
+via the <A HREF = "fix_modify.html">fix_modify</A> command.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix.html">fix</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/units.html b/doc/doc2/units.html
new file mode 100644
index 000000000..d532b2ae3
--- /dev/null
+++ b/doc/doc2/units.html
@@ -0,0 +1,223 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>units command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>units style
+</PRE>
+<UL><LI>style = <I>lj</I> or <I>real</I> or <I>metal</I> or <I>si</I> or <I>cgs</I> or <I>electron</I> or <I>micro</I> or <I>nano</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>units metal
+units lj
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command sets the style of units used for a simulation. It
+determines the units of all quantities specified in the input script
+and data file, as well as quantities output to the screen, log file,
+and dump files. Typically, this command is used at the very beginning
+of an input script.
+</P>
+<P>For all units except <I>lj</I>, LAMMPS uses physical constants from
+www.physics.nist.gov. For the definition of Kcal in real units,
+LAMMPS uses the thermochemical calorie = 4.184 J.
+</P>
+<P>The choice you make for units simply sets some internal conversion
+factors within LAMMPS. This means that any simulation you perform for
+one choice of units can be duplicated with any other unit setting
+LAMMPS supports. In this context "duplicate" means the particles will
+have identical trajectories and all output generated by the simulation
+will be identical. This will be the case for some number of timesteps
+until round-off effects accumulate, since the conversion factors for
+two different unit systems are not identical to infinite precision.
+</P>
+<P>To perform the same simulation in a different set of units you must
+change all the unit-based input parameters in your input script and
+other input files (data file, potential files, etc) correctly to the
+new units. And you must correctly convert all output from the new
+units to the old units when comparing to the original results. That
+is often not simple to do.
+</P>
+<HR>
+
+<P>For style <I>lj</I>, all quantities are unitless. Without loss of
+generality, LAMMPS sets the fundamental quantities mass, sigma,
+epsilon, and the Boltzmann constant = 1. The masses, distances,
+energies you specify are multiples of these fundamental values. The
+formulas relating the reduced or unitless quantity (with an asterisk)
+to the same quantity with units is also given. Thus you can use the
+mass & sigma & epsilon values for a specific material and convert the
+results from a unitless LJ simulation into physical quantities.
+</P>
+<UL><LI>mass = mass or m
+<LI>distance = sigma, where x* = x / sigma
+<LI>time = tau, where t* = t (epsilon / m / sigma^2)^1/2
+<LI>energy = epsilon, where E* = E / epsilon
+<LI>velocity = sigma/tau, where v* = v tau / sigma
+<LI>force = epsilon/sigma, where f* = f sigma / epsilon
+<LI>torque = epsilon, where t* = t / epsilon
+<LI>temperature = reduced LJ temperature, where T* = T Kb / epsilon
+<LI>pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
+<LI>dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
+<LI>charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2
+<LI>dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
+<LI>electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
+<LI>density = mass/volume, where rho* = rho sigma^dim
+</UL>
+<P>Note that for LJ units, the default mode of thermodyamic output via
+the <A HREF = "thermo_style.html">thermo_style</A> command is to normalize energies
+by the number of atoms, i.e. energy/atom. This can be changed via the
+<A HREF = "thermo_modify.html">thermo_modify norm</A> command.
+</P>
+<P>For style <I>real</I>, these are the units:
+</P>
+<UL><LI>mass = grams/mole
+<LI>distance = Angstroms
+<LI>time = femtoseconds
+<LI>energy = Kcal/mole
+<LI>velocity = Angstroms/femtosecond
+<LI>force = Kcal/mole-Angstrom
+<LI>torque = Kcal/mole
+<LI>temperature = Kelvin
+<LI>pressure = atmospheres
+<LI>dynamic viscosity = Poise
+<LI>charge = multiple of electron charge (1.0 is a proton)
+<LI>dipole = charge*Angstroms
+<LI>electric field = volts/Angstrom
+<LI>density = gram/cm^dim
+</UL>
+<P>For style <I>metal</I>, these are the units:
+</P>
+<UL><LI>mass = grams/mole
+<LI>distance = Angstroms
+<LI>time = picoseconds
+<LI>energy = eV
+<LI>velocity = Angstroms/picosecond
+<LI>force = eV/Angstrom
+<LI>torque = eV
+<LI>temperature = Kelvin
+<LI>pressure = bars
+<LI>dynamic viscosity = Poise
+<LI>charge = multiple of electron charge (1.0 is a proton)
+<LI>dipole = charge*Angstroms
+<LI>electric field = volts/Angstrom
+<LI>density = gram/cm^dim
+</UL>
+<P>For style <I>si</I>, these are the units:
+</P>
+<UL><LI>mass = kilograms
+<LI>distance = meters
+<LI>time = seconds
+<LI>energy = Joules
+<LI>velocity = meters/second
+<LI>force = Newtons
+<LI>torque = Newton-meters
+<LI>temperature = Kelvin
+<LI>pressure = Pascals
+<LI>dynamic viscosity = Pascal*second
+<LI>charge = Coulombs (1.6021765e-19 is a proton)
+<LI>dipole = Coulombs*meters
+<LI>electric field = volts/meter
+<LI>density = kilograms/meter^dim
+</UL>
+<P>For style <I>cgs</I>, these are the units:
+</P>
+<UL><LI>mass = grams
+<LI>distance = centimeters
+<LI>time = seconds
+<LI>energy = ergs
+<LI>velocity = centimeters/second
+<LI>force = dynes
+<LI>torque = dyne-centimeters
+<LI>temperature = Kelvin
+<LI>pressure = dyne/cm^2 or barye = 1.0e-6 bars
+<LI>dynamic viscosity = Poise
+<LI>charge = statcoulombs or esu (4.8032044e-10 is a proton)
+<LI>dipole = statcoul-cm = 10^18 debye
+<LI>electric field = statvolt/cm or dyne/esu
+<LI>density = grams/cm^dim
+</UL>
+<P>For style <I>electron</I>, these are the units:
+</P>
+<UL><LI>mass = atomic mass units
+<LI>distance = Bohr
+<LI>time = femtoseconds
+<LI>energy = Hartrees
+<LI>velocity = Bohr/atomic time units [1.03275e-15 seconds]
+<LI>force = Hartrees/Bohr
+<LI>temperature = Kelvin
+<LI>pressure = Pascals
+<LI>charge = multiple of electron charge (1.0 is a proton)
+<LI>dipole moment = Debye
+<LI>electric field = volts/cm
+</UL>
+<P>For style <I>micro</I>, these are the units:
+</P>
+<UL><LI>mass = picograms
+<LI>distance = micrometers
+<LI>time = microseconds
+<LI>energy = picogram-micrometer^2/microsecond^2
+<LI>velocity = micrometers/microsecond
+<LI>force = picogram-micrometer/microsecond^2
+<LI>torque = picogram-micrometer^2/microsecond^2
+<LI>temperature = Kelvin
+<LI>pressure = picogram/(micrometer-microsecond^2)
+<LI>dynamic viscosity = picogram/(micrometer-microsecond)
+<LI>charge = picocoulombs (1.6021765e-7 is a proton)
+<LI>dipole = picocoulomb-micrometer
+<LI>electric field = volt/micrometer
+<LI>density = picograms/micrometer^dim
+</UL>
+<P>For style <I>nano</I>, these are the units:
+</P>
+<UL><LI>mass = attograms
+<LI>distance = nanometers
+<LI>time = nanoseconds
+<LI>energy = attogram-nanometer^2/nanosecond^2
+<LI>velocity = nanometers/nanosecond
+<LI>force = attogram-nanometer/nanosecond^2
+<LI>torque = attogram-nanometer^2/nanosecond^2
+<LI>temperature = Kelvin
+<LI>pressure = attogram/(nanometer-nanosecond^2)
+<LI>dynamic viscosity = attogram/(nanometer-nanosecond)
+<LI>charge = multiple of electron charge (1.0 is a proton)
+<LI>dipole = charge-nanometer
+<LI>electric field = volt/nanometer
+<LI>density = attograms/nanometer^dim
+</UL>
+<P>The units command also sets the timestep size and neighbor skin
+distance to default values for each style:
+</P>
+<UL><LI>For style <I>lj</I> these are dt = 0.005 tau and skin = 0.3 sigma.
+<LI>For style <I>real</I> these are dt = 1.0 fmsec and skin = 2.0 Angstroms.
+<LI>For style <I>metal</I> these are dt = 0.001 psec and skin = 2.0 Angstroms.
+<LI>For style <I>si</I> these are dt = 1.0e-8 sec and skin = 0.001 meters.
+<LI>For style <I>cgs</I> these are dt = 1.0e-8 sec and skin = 0.1 cm.
+<LI>For style <I>electron</I> these are dt = 0.001 fmsec and skin = 2.0 Bohr.
+<LI>For style <I>micro</I> these are dt = 2.0 microsec and skin = 0.1 micrometers.
+<LI>For style <I>nano</I> these are dt = 0.00045 nanosec and skin = 0.1 nanometers.
+</UL>
+<P><B>Restrictions:</B>
+</P>
+<P>This command cannot be used after the simulation box is defined by a
+<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B>
+</P>
+<PRE>units lj
+</PRE>
+</HTML>
diff --git a/doc/doc2/variable.html b/doc/doc2/variable.html
new file mode 100644
index 000000000..9d10201bf
--- /dev/null
+++ b/doc/doc2/variable.html
@@ -0,0 +1,1146 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>variable command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>variable name style args ...
+</PRE>
+<UL><LI>name = name of variable to define
+
+<LI>style = <I>delete</I> or <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or
+<I>uloop</I> or <I>string</I> or <I>format</I> or <I>getenv</I> or <I>file</I> or <I>atomfile</I> or <I>python</I> or <I>equal</I> or <I>atom</I>
+
+<PRE> <I>delete</I> = no args
+ <I>index</I> args = one or more strings
+ <I>loop</I> args = N
+ N = integer size of loop, loop from 1 to N inclusive
+ <I>loop</I> args = N pad
+ N = integer size of loop, loop from 1 to N inclusive
+ pad = all values will be same length, e.g. 001, 002, ..., 100
+ <I>loop</I> args = N1 N2
+ N1,N2 = loop from N1 to N2 inclusive
+ <I>loop</I> args = N1 N2 pad
+ N1,N2 = loop from N1 to N2 inclusive
+ pad = all values will be same length, e.g. 050, 051, ..., 100
+ <I>world</I> args = one string for each partition of processors
+ <I>universe</I> args = one or more strings
+ <I>uloop</I> args = N
+ N = integer size of loop
+ <I>uloop</I> args = N pad
+ N = integer size of loop
+ pad = all values will be same length, e.g. 001, 002, ..., 100
+ <I>string</I> arg = one string
+ <I>format</I> args = vname fstr
+ vname = name of equal-style variable to evaluate
+ fstr = C-style format string
+ <I>getenv</I> arg = one string
+ <I>file</I> arg = filename
+ <I>atomfile</I> arg = filename
+ <I>python</I> arg = function
+ <I>equal</I> or <I>atom</I> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
+ numbers = 0.0, 100, -5.4, 2.8e-4, etc
+ constants = PI
+ thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
+ math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
+ x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
+ math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
+ sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
+ random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
+ ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
+ stride(x,y,z), stride2(x,y,z,a,b,c),
+ vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+ group functions = count(group), mass(group), charge(group),
+ xcm(group,dim), vcm(group,dim), fcm(group,dim),
+ bound(group,dir), gyration(group), ke(group),
+ angmom(group,dim), torque(group,dim),
+ inertia(group,dimdim), omega(group,dim)
+ region functions = count(group,region), mass(group,region), charge(group,region),
+ xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
+ bound(group,dir,region), gyration(group,region), ke(group,reigon),
+ angmom(group,dim,region), torque(group,dim,region),
+ inertia(group,dimdim,region), omega(group,dim,region)
+ special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
+ atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
+ atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
+ compute references = c_ID, c_ID[i], c_ID[i][j]
+ fix references = f_ID, f_ID[i], f_ID[i][j]
+ variable references = v_name, v_name[i]
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>variable x index run1 run2 run3 run4 run5 run6 run7 run8
+variable LoopVar loop $n
+variable beta equal temp/3.0
+variable b1 equal x[234]+0.5*vol
+variable b1 equal "x[234] + 0.5*vol"
+variable b equal xcm(mol1,x)/2.0
+variable b equal c_myTemp
+variable b atom x*y/vol
+variable foo string myfile
+variable myPy python increase
+variable f file values.txt
+variable temp world 300.0 310.0 320.0 ${Tfinal}
+variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+variable x uloop 15 pad
+variable str format x %.6g
+variable x delete
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This command assigns one or more strings to a variable name for
+evaluation later in the input script or during a simulation.
+</P>
+<P>Variables can thus be useful in several contexts. A variable can be
+defined and then referenced elsewhere in an input script to become
+part of a new input command. For variable styles that store multiple
+strings, the <A HREF = "next.html">next</A> command can be used to increment which
+string is assigned to the variable. Variables of style <I>equal</I> store
+a formula which when evaluated produces a single numeric value which
+can be output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
+print</A>, and <A HREF = "run.html">run every</A> commands) or as part
+of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
+command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command). Variables of style <I>atom</I> store
+a formula which when evaluated produces one numeric value per atom
+which can be output to a dump file (see the <A HREF = "dump.html">dump custom</A>
+command) or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
+commands). Variables of style <I>atomfile</I> can be used anywhere in an
+input script that atom-style variables are used; they get their
+per-atom values from a file rather than from a formula. Variables can
+be hooked to Python functions using code you provide, so that the
+variable gets its value from the evaluation of the Python code.
+</P>
+<P>IMPORTANT NOTE: As discussed in <A HREF = "Section_commands.html#cmd_2">Section 3.2</A>
+of the manual, an input script can use "immediate" variables, specified
+as $(formula) with parenthesis, where the formula has the same syntax
+as equal-style variables described on this page. This is a convenient
+way to evaluate a formula immediately without using the variable command
+to define a named variable and then evaluate that variable. See below
+for a more detailed discussion of this feature.
+</P>
+<P>In the discussion that follows, the "name" of the variable is the
+arbitrary string that is the 1st argument in the variable command.
+This name can only contain alphanumeric characters and underscores.
+The "string" is one or more of the subsequent arguments. The "string"
+can be simple text as in the 1st example above, it can contain other
+variables as in the 2nd example, or it can be a formula as in the 3rd
+example. The "value" is the numeric quantity resulting from
+evaluation of the string. Note that the same string can generate
+different values when it is evaluated at different times during a
+simulation.
+</P>
+<P>IMPORTANT NOTE: When the input script line is encountered that defines
+a variable of style <I>equal</I> or <I>atom</I> or <I>python</I> that contains a
+formula or Python code, the formula is NOT immediately evaluated.
+It will be evaluated every time when the variable is <B>used</B> instead.
+If you simply want to evaluate a formula in place you can use as
+so-called. See the section below about "Immediate Evaluation
+of Variables" for more details on the topic. This is also true of
+a <I>format</I> style variable since it evaluates another variable when
+it is invoked.
+</P>
+<P>IMPORTANT NOTE: Variables of style <I>equal</I> and <I>atom</I> can be used as
+inputs to various other LAMMPS commands which evaluate their formulas
+as needed, e.g. at different timesteps during a <A HREF = "run.html">run</A>.
+Variables of style <I>python</I> can be used in place of an equal-style
+variable so long as the associated Python function, as defined by the
+<A HREF = "python.html">python</A> command, returns a numeric value. Thus any
+command that states it can use an equal-style variable as an argument,
+can also use such a python-style variable. This means that when the
+LAMMPS command evaluates the variable, the Python function will be
+executed.
+</P>
+<P>IMPORTANT NOTE: When a variable command is encountered in the input
+script and the variable name has already been specified, the command
+is ignored. This means variables can NOT be re-defined in an input
+script (with two exceptions, read further). This is to allow an input
+script to be processed multiple times without resetting the variables;
+see the <A HREF = "jump.html">jump</A> or <A HREF = "include.html">include</A> commands. It also
+means that using the <A HREF = "Section_start.html#start_7">command-line switch</A>
+-var will override a corresponding index variable setting in the input
+script.
+</P>
+<P>There are two exceptions to this rule. First, variables of style
+<I>string</I>, <I>getenv</I>, <I>equal</I>, <I>atom</I>, and <I>python</I> ARE redefined each
+time the command is encountered. This allows these style of variables
+to be redefined multiple times in an input script. In a loop, this
+means the formula associated with an <I>equal</I> or <I>atom</I> style variable
+can change if it contains a substitution for another variable, e.g. $x
+or v_x.
+</P>
+<P>Second, as described below, if a variable is iterated on to the end of
+its list of strings via the <A HREF = "next.html">next</A> command, it is removed
+from the list of active variables, and is thus available to be
+re-defined in a subsequent variable command. The <I>delete</I> style does
+the same thing.
+</P>
+<HR>
+
+<P><A HREF = "Section_commands.html#cmd_2">This section</A> of the manual explains how
+occurrences of a variable name in an input script line are replaced by
+the variable's string. The variable name can be referenced as $x if
+the name "x" is a single character, or as ${LoopVar} if the name
+"LoopVar" is one or more characters.
+</P>
+<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>file</I>,
+<I>universe</I>, and <I>uloop</I>, which string is assigned to a variable can be
+incremented via the <A HREF = "next.html">next</A> command. When there are no more
+strings to assign, the variable is exhausted and a flag is set that
+causes the next <A HREF = "jump.html">jump</A> command encountered in the input
+script to be skipped. This enables the construction of simple loops
+in the input script that are iterated over and then exited from.
+</P>
+<P>As explained above, an exhausted variable can be re-used in an input
+script. The <I>delete</I> style also removes the variable, the same as if
+it were exhausted, allowing it to be redefined later in the input
+script or when the input script is looped over. This can be useful
+when breaking out of a loop via the <A HREF = "if.html">if</A> and <A HREF = "jump.html">jump</A>
+commands before the variable would become exhausted. For example,
+</P>
+<PRE>label loop
+variable a loop 5
+print "A = $a"
+if "$a > 2" then "jump in.script break"
+next a
+jump in.script loop
+label break
+variable a delete
+</PRE>
+<HR>
+
+<P>This section describes how all the various variable styles are defined
+and what they store. Except for the <I>equal</I> and <I>atom</I> styles,
+which are explaine in the next section.
+</P>
+<P>Many of the styles store one or more strings. Note that a single
+string can contain spaces (multiple words), if it is enclosed in
+quotes in the variable command. When the variable is substituted for
+in another input script command, its returned string will then be
+interpreted as multiple arguments in the expanded command.
+</P>
+<P>For the <I>index</I> style, one or more strings are specified. Initially,
+the 1st string is assigned to the variable. Each time a
+<A HREF = "next.html">next</A> command is used with the variable name, the next
+string is assigned. All processors assign the same string to the
+variable.
+</P>
+<P><I>Index</I> style variables with a single string value can also be set by
+using the command-line switch -var; see <A HREF = "Section_start.html#start_7">this
+section</A> for details.
+</P>
+<P>The <I>loop</I> style is identical to the <I>index</I> style except that the
+strings are the integers from 1 to N inclusive, if only one argument N
+is specified. This allows generation of a long list of runs
+(e.g. 1000) without having to list N strings in the input script.
+Initially, the string "1" is assigned to the variable. Each time a
+<A HREF = "next.html">next</A> command is used with the variable name, the next
+string ("2", "3", etc) is assigned. All processors assign the same
+string to the variable. The <I>loop</I> style can also be specified with
+two arguments N1 and N2. In this case the loop runs from N1 to N2
+inclusive, and the string N1 is initially assigned to the variable.
+N1 <= N2 and N2 >= 0 is required.
+</P>
+<P>For the <I>world</I> style, one or more strings are specified. There must
+be one string for each processor partition or "world". See <A HREF = "Section_start.html#start_7">this
+section</A> of the manual for information on
+running LAMMPS with multiple partitions via the "-partition"
+command-line switch. This variable command assigns one string to each
+world. All processors in the world are assigned the same string. The
+next command cannot be used with <I>equal</I> style variables, since there
+is only one value per world. This style of variable is useful when
+you wish to run different simulations on different partitions, or when
+performing a parallel tempering simulation (see the
+<A HREF = "temper.html">temper</A> command), to assign different temperatures to
+different partitions.
+</P>
+<P>For the <I>universe</I> style, one or more strings are specified. There
+must be at least as many strings as there are processor partitions or
+"worlds". See <A HREF = "Section_start.html#start_7">this page</A> for information
+on running LAMMPS with multiple partitions via the "-partition"
+command-line switch. This variable command initially assigns one
+string to each world. When a <A HREF = "next.html">next</A> command is encountered
+using this variable, the first processor partition to encounter it, is
+assigned the next available string. This continues until all the
+variable strings are consumed. Thus, this command can be used to run
+50 simulations on 8 processor partitions. The simulations will be run
+one after the other on whatever partition becomes available, until
+they are all finished. <I>Universe</I> style variables are incremented
+using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
+which you will see in your directory during such a LAMMPS run.
+</P>
+<P>The <I>uloop</I> style is identical to the <I>universe</I> style except that the
+strings are the integers from 1 to N. This allows generation of long
+list of runs (e.g. 1000) without having to list N strings in the input
+script.
+</P>
+<P>For the <I>string</I> style, a single string is assigned to the variable.
+The only difference between this and using the <I>index</I> style with a
+single string is that a variable with <I>string</I> style can be redefined.
+E.g. by another command later in the input script, or if the script is
+read again in a loop.
+</P>
+<P>For the <I>format</I> style, an equal-style variable is specified along
+with a C-style format string, e.g. "%f" or "%.10g", which must be
+appropriate for formatting a double-precision floating-point value.
+This allows an equal-style variable to be formatted specifically for
+output as a string, e.g. by the <A HREF = "print.html">print</A> command, if the
+default format "%.15g" has too much precision.
+</P>
+<P>For the <I>getenv</I> style, a single string is assigned to the variable
+which should be the name of an environment variable. When the
+variable is evaluated, it returns the value of the environment
+variable, or an empty string if it not defined. This style of
+variable can be used to adapt the behavior of LAMMPS input scripts via
+environment variable settings, or to retrieve information that has
+been previously stored with the <A HREF = "shell.html">shell putenv</A> command.
+Note that because environment variable settings are stored by the
+operating systems, they persist beyond a <A HREF = "clear.html">clear</A> command.
+</P>
+<P>For the <I>file</I> style, a filename is provided which contains a list of
+strings to assign to the variable, one per line. The strings can be
+numeric values if desired. See the discussion of the next() function
+below for equal-style variables, which will convert the string of a
+file-style variable into a numeric value in a formula.
+</P>
+<P>When a file-style variable is defined, the file is opened and the
+string on the first line is read and stored with the variable. This
+means the variable can then be evaluated as many times as desired and
+will return that string. There are two ways to cause the next string
+from the file to be read: use the <A HREF = "next.html">next</A> command or the
+next() function in an equal- or atom-style variable, as discussed
+below.
+</P>
+<P>The rules for formatting the file are as follows. A comment character
+"#" can be used anywhere on a line; text starting with the comment
+character is stripped. Blank lines are skipped. The first "word" of
+a non-blank line, delimited by white space, is the "string" assigned
+to the variable.
+</P>
+<P>For the <I>atomfile</I> style, a filename is provided which contains one or
+more sets of values, to assign on a per-atom basis to the variable.
+The format of the file is described below.
+</P>
+<P>When an atomfile-style variable is defined, the file is opened and the
+first set of per-atom values are read and stored with the variable.
+This means the variable can then be evaluated as many times as desired
+and will return those values. There are two ways to cause the next
+set of per-atom values from the file to be read: use the
+<A HREF = "next.html">next</A> command or the next() function in an atom-style
+variable, as discussed below.
+</P>
+<P>The rules for formatting the file are as follows. Each time a set of
+per-atom values is read, a non-blank line is searched for in the file.
+A comment character "#" can be used anywhere on a line; text starting
+with the comment character is stripped. Blank lines are skipped. The
+first "word" of a non-blank line, delimited by white space, is read as
+the count N of per-atom lines to immediately follow. N can be be the
+total number of atoms in the system, or only a subset. The next N
+lines have the following format
+</P>
+<PRE>ID value
+</PRE>
+<P>where ID is an atom ID and value is the per-atom numeric value that
+will be assigned to that atom. IDs can be listed in any order.
+</P>
+<P>IMPORTANT NOTE: Every time a set of per-atom lines is read, the value
+for all atoms is first set to 0.0. Thus values for atoms whose ID
+does not appear in the set, will remain 0.0.
+</P>
+<P>For the <I>python</I> style a Python function name is provided. This needs
+to match a function name specified in a <A HREF = "python.html">python</A> command
+which returns a value to this variable as defined by its <I>return</I>
+keyword. For exampe these two commands would be self-consistent:
+</P>
+<PRE>variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+</PRE>
+<P>The two commands can appear in either order so long as both are
+specified before the Python function is invoked for the first time.
+</P>
+<P>Each time the variable is evaluated, the associated Python function is
+invoked, and the value it returns is also returned by the variable.
+Since the Python function can use other LAMMPS variables as input, or
+query interal LAMMPS quantities to perform its computation, this means
+the variable can return a different value each time it is evaluated.
+</P>
+<P>The type of value stored in the variable is determined by the <I>format</I>
+keyword of the <A HREF = "python.html">python</A> command. It can be an integer
+(i), floating point (f), or string (s) value. As mentioned above, if
+it is a numeric value (integer or floating point), then the
+python-style variable can be used in place of an equal-style variable
+anywhere in an input script, e.g. as an argument to another command
+that allows for equal-style variables.
+</P>
+<HR>
+
+<P>For the <I>equal</I> and <I>atom</I> styles, a single string is specified which
+represents a formula that will be evaluated afresh each time the
+variable is used. If you want spaces in the string, enclose it in
+double quotes so the parser will treat it as a single argument. For
+<I>equal</I> style variables the formula computes a scalar quantity, which
+becomes the value of the variable whenever it is evaluated. For
+<I>atom</I> style variables the formula computes one quantity for each
+atom whenever it is evaluated.
+</P>
+<P>Note that <I>equal</I> and <I>atom</I> variables can produce different values at
+different stages of the input script or at different times during a
+run. For example, if an <I>equal</I> variable is used in a <A HREF = "fix_print.html">fix
+print</A> command, different values could be printed each
+timestep it was invoked. If you want a variable to be evaluated
+immediately, so that the result is stored by the variable instead of
+the string, see the section below on "Immediate Evaluation of
+Variables".
+</P>
+<P>The next command cannot be used with <I>equal</I> or <I>atom</I> style
+variables, since there is only one string.
+</P>
+<P>The formula for an <I>equal</I> or <I>atom</I> variable can contain a variety
+of quantities. The syntax for each kind of quantity is simple, but
+multiple quantities can be nested and combined in various ways to
+build up formulas of arbitrary complexity. For example, this is a
+valid (though strange) variable formula:
+</P>
+<PRE>variable x equal "pe + c_MyTemp / vol^(1/3)"
+</PRE>
+<P>Specifically, an formula can contain numbers, thermo keywords, math
+operators, math functions, group functions, region functions, atom
+values, atom vectors, compute references, fix references, and
+references to other variables.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >Number</TD><TD > 0.2, 100, 1.0e20, -15.4, etc</TD></TR>
+<TR><TD >Constant</TD><TD > PI</TD></TR>
+<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
+<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x%y, </TD></TR>
+<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x</TD></TR>
+<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)</TD></TR>
+<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)</TD></TR>
+<TR><TD >Region functions</TD><TD > count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</TD></TR>
+<TR><TD >Special functions</TD><TD > sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)</TD></TR>
+<TR><TD >Atom values</TD><TD > id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]</TD></TR>
+<TR><TD >Atom vectors</TD><TD > id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q</TD></TR>
+<TR><TD >Compute references</TD><TD > c_ID, c_ID[i], c_ID[i][j]</TD></TR>
+<TR><TD >Fix references</TD><TD > f_ID, f_ID[i], f_ID[i][j]</TD></TR>
+<TR><TD >Other variables</TD><TD > v_name, v_name[i]
+</TD></TR></TABLE></DIV>
+
+<HR>
+
+<P>Most of the formula elements produce a scalar value. A few produce a
+per-atom vector of values. These are the atom vectors, compute
+references that represent a per-atom vector, fix references that
+represent a per-atom vector, and variables that are atom-style
+variables. Math functions that operate on scalar values produce a
+scalar value; math function that operate on per-atom vectors do so
+element-by-element and produce a per-atom vector.
+</P>
+<P>A formula for equal-style variables cannot use any formula element
+that produces a per-atom vector. A formula for an atom-style variable
+can use formula elements that produce either a scalar value or a
+per-atom vector. Atom-style variables are evaluated by other commands
+that define a <A HREF = "group.html">group</A> on which they operate, e.g. a
+<A HREF = "dump.html">dump</A> or <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> command.
+When they invoke the atom-style variable, only atoms in the group are
+inlcuded in the formula evaluation. The variable evaluates to 0.0 for
+atoms not in the group.
+</P>
+<P>The thermo keywords allowed in a formula are those defined by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command. Thermo keywords that
+require a <A HREF = "compute.html">compute</A> to calculate their values such as
+"temp" or "press", use computes stored and invoked by the
+<A HREF = "thermo_style.html">thermo_style</A> command. This means that you can
+only use those keywords in a variable if the style you are using with
+the thermo_style command (and the thermo keywords associated with that
+style) also define and use the needed compute. Note that some thermo
+keywords use a compute indirectly to calculate their value (e.g. the
+enthalpy keyword uses temp, pe, and pressure). If a variable is
+evaluated directly in an input script (not during a run), then the
+values accessed by the thermo keyword must be current. See the
+discussion below about "Variable Accuracy".
+</P>
+<HR>
+
+<H4>Math Operators
+</H4>
+<P>Math operators are written in the usual way, where the "x" and "y" in
+the examples can themselves be arbitrarily complex formulas, as in the
+examples above. In this syntax, "x" and "y" can be scalar values or
+per-atom vectors. For example, "ke/natoms" is the division of two
+scalars, where "vy+vz" is the element-by-element sum of two per-atom
+vectors of y and z velocities.
+</P>
+<P>Operators are evaluated left to right and have the usual C-style
+precedence: unary minus and unary logical NOT operator "!" have the
+highest precedence, exponentiation "^" is next; multiplication and
+division and the modulo operator "%" are next; addition and
+subtraction are next; the 4 relational operators "<", "<=", ">", and
+">=" are next; the two remaining relational operators "==" and "!="
+are next; then the logical AND operator "&&"; and finally the logical
+OR operator "||" has the lowest precedence. Parenthesis can be used
+to group one or more portions of a formula and/or enforce a different
+order of evaluation than what would occur with the default precedence.
+</P>
+<P>IMPORTANT NOTE: Because a unary minus is higher precedence than
+exponentiation, the formula "-2^2" will evaluate to 4, not -4. This
+convention is compatible with some programming languages, but not
+others. As mentioned, this behavior can be easily overridden with
+parenthesis; the formula "-(2^2)" will evaluate to -4.
+</P>
+<P>The 6 relational operators return either a 1.0 or 0.0 depending on
+whether the relationship between x and y is TRUE or FALSE. For
+example the expression x<10.0 in an atom-style variable formula will
+return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0
+for the others. The logical AND operator will return 1.0 if both its
+arguments are non-zero, else it returns 0.0. The logical OR operator
+will return 1.0 if either of its arguments is non-zero, else it
+returns 0.0. The logical NOT operator returns 1.0 if its argument is
+0.0, else it returns 0.0.
+</P>
+<P>These relational and logical operators can be used as a masking or
+selection operation in a formula. For example, the number of atoms
+whose properties satifsy one or more criteria could be calculated by
+taking the returned per-atom vector of ones and zeroes and passing it
+to the <A HREF = "compute_reduce.html">compute reduce</A> command.
+</P>
+<HR>
+
+<H4>Math Functions
+</H4>
+<P>Math functions are specified as keywords followed by one or more
+parenthesized arguments "x", "y", "z", each of which can themselves be
+arbitrarily complex formulas. In this syntax, the arguments can
+represent scalar values or per-atom vectors. In the latter case, the
+math operation is performed on each element of the vector. For
+example, "sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)"
+yields a per-atom vector with each element being the sqrt() of the
+product of one atom's y and z coordinates.
+</P>
+<P>Most of the math functions perform obvious operations. The ln() is
+the natural log; log() is the base 10 log.
+</P>
+<P>The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z =
+seed. It generates a uniform random number between lo and hi. The
+normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and
+z = seed. It generates a Gaussian variate centered on mu with
+variance sigma^2. In both cases the seed is used the first time the
+internal random number generator is invoked, to initialize it. For
+equal-style variables, every processor uses the same seed so that they
+each generate the same sequence of random numbers. For atom-style
+variables, a unique seed is created for each processor, based on the
+specified seed. This effectively generates a different random number
+for each atom being looped over in the atom-style variable.
+</P>
+<P>IMPORTANT NOTE: Internally, there is just one random number generator
+for all equal-style variables and one for all atom-style variables.
+If you define multiple variables (of each style) which use the
+random() or normal() math functions, then the internal random number
+generators will only be initialized once, which means only one of the
+specified seeds will determine the sequence of generated random
+numbers.
+</P>
+<P>The ceil(), floor(), and round() functions are those in the C math
+library. Ceil() is the smallest integer not less than its argument.
+Floor() if the largest integer not greater than its argument. Round()
+is the nearest integer to its argument.
+</P>
+<P>The ramp(x,y) function uses the current timestep to generate a value
+linearly intepolated between the specified x,y values over the course
+of a run, according to this formula:
+</P>
+<PRE>value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
+</PRE>
+<P>The run begins on startstep and ends on stopstep. Startstep and
+stopstep can span multiple runs, using the <I>start</I> and <I>stop</I> keywords
+of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for
+details of how to do this.
+</P>
+<P>The stagger(x,y) function uses the current timestep to generate a new
+timestep. X,y > 0 and x > y are required. The generated timesteps
+increase in a staggered fashion, as the sequence
+x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
+timestep in the sequence is returned. Thus if stagger(1000,100) is
+used in a variable by the <A HREF = "dump_modify.html">dump_modify every</A>
+command, it will generate the sequence of output timesteps:
+</P>
+<PRE>100,1000,1100,2000,2100,3000,etc
+</PRE>
+<P>The logfreq(x,y,z) function uses the current timestep to generate a
+new timestep. X,y,z > 0 and y < z are required. The generated
+timesteps are on a base-z logarithmic scale, starting with x, and the
+y value is how many of the z-1 possible timesteps within one
+logarithmic interval are generated. I.e. the timesteps follow the
+sequence x,2x,3x,...y*x,x*z,2x*z,3x*z,...y*x*z,x*z^2,2x*z^2,etc. For
+any current timestep, the next timestep in the sequence is returned.
+Thus if logfreq(100,4,10) is used in a variable by the <A HREF = "dump_modify.html">dump_modify
+every</A> command, it will generate this sequence of
+output timesteps:
+</P>
+<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
+</PRE>
+<P>The logfreq2(x,y,z) function is similar to logfreq, except a single
+logarithmic interval is divided into y equally-spaced timesteps and
+all of them are output. Y < z is not required. Thus, if
+logfreq2(100,18,10) is used in a variable by the <A HREF = "dump_modify.html">dump_modify
+every</A> command, then the interval between 100 and
+1000 is divided as 900/18 = 50 steps, and it will generate the
+sequence of output timesteps:
+</P>
+<PRE>100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc
+</PRE>
+<P>The stride(x,y,z) function uses the current timestep to generate a new
+timestep. X,y >= 0 and z > 0 and x <= y are required. The generated
+timesteps increase in increments of z, from x to y, i.e. it generates
+the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then
+similar to the way a for loop operates, the last value will be one
+that does not exceed y. For any current timestep, the next timestep
+in the sequence is returned. Thus if stride(1000,2000,100) is used
+in a variable by the <A HREF = "dump_modify.html">dump_modify every</A> command, it
+will generate the sequence of output timesteps:
+</P>
+<PRE>1000,1100,1200, ... ,1900,2000
+</PRE>
+<P>The stride2(x,y,z,a,b,c) function is similar to the stride() function
+except it generates two sets of strided timesteps, one at a coarser
+level and one at a finer level. Thus it is useful for debugging,
+e.g. to produce output every timestep at the point in simulation when
+a problem occurs. X,y >= 0 and z > 0 and x <= y are required, as are
+a,b >= 0 and c > 0 and a < b. Also, a >= x and b <= y are required so
+that the second stride is inside the first. The generated timesteps
+increase in increments of z, starting at x, until a is reached. At
+that point the timestep increases in increments of c, from a to b,
+then after b, increments by z are resumed until y is reached. For any
+current timestep, the next timestep in the sequence is returned. Thus
+if stride(1000,2000,100,1350,1360,1) is used in a variable by the
+<A HREF = "dump_modify.html">dump_modify every</A> command, it will generate the
+sequence of output timesteps:
+</P>
+<PRE>1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000
+</PRE>
+<P>The vdisplace(x,y) function takes 2 arguments: x = value0 and y =
+velocity, and uses the elapsed time to change the value by a linear
+displacement due to the applied velocity over the course of a run,
+according to this formula:
+</P>
+<PRE>value = value0 + velocity*(timestep-startstep)*dt
+</PRE>
+<P>where dt = the timestep size.
+</P>
+<P>The run begins on startstep. Startstep can span multiple runs, using
+the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this. Note that the
+<A HREF = "thermo_style.html">thermo_style</A> keyword elaplong =
+timestep-startstep.
+</P>
+<P>The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
+x = value0, y = amplitude, z = period. They use the elapsed time to
+oscillate the value by a sin() or cos() function over the course of a
+run, according to one of these formulas, where omega = 2 PI / period:
+</P>
+<PRE>value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
+value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
+</PRE>
+<P>where dt = the timestep size.
+</P>
+<P>The run begins on startstep. Startstep can span multiple runs, using
+the <I>start</I> keyword of the <A HREF = "run.html">run</A> command. See the
+<A HREF = "run.html">run</A> command for details of how to do this. Note that the
+<A HREF = "thermo_style.html">thermo_style</A> keyword elaplong =
+timestep-startstep.
+</P>
+<HR>
+
+<H4>Group and Region Functions
+</H4>
+<P>Group functions are specified as keywords followed by one or two
+parenthesized arguments. The first argument <I>ID</I> is the group-ID.
+The <I>dim</I> argument, if it exists, is <I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I>
+argument, if it exists, is <I>xmin</I>, <I>xmax</I>, <I>ymin</I>, <I>ymax</I>, <I>zmin</I>, or
+<I>zmax</I>. The <I>dimdim</I> argument, if it exists, is <I>xx</I> or <I>yy</I> or <I>zz</I>
+or <I>xy</I> or <I>yz</I> or <I>xz</I>.
+</P>
+<P>The group function count() is the number of atoms in the group. The
+group functions mass() and charge() are the total mass and charge of
+the group. Xcm() and vcm() return components of the position and
+velocity of the center of mass of the group. Fcm() returns a
+component of the total force on the group of atoms. Bound() returns
+the min/max of a particular coordinate for all atoms in the group.
+Gyration() computes the radius-of-gyration of the group of atoms. See
+the <A HREF = "compute_gyration.html">compute gyration</A> command for a definition
+of the formula. Angmom() returns components of the angular momentum
+of the group of atoms around its center of mass. Torque() returns
+components of the torque on the group of atoms around its center of
+mass, based on current forces on the atoms. Inertia() returns one of
+6 components of the symmetric inertia tensor of the group of atoms
+around its center of mass, ordered as Ixx,Iyy,Izz,Ixy,Iyz,Ixz.
+Omega() returns components of the angular velocity of the group of
+atoms around its center of mass.
+</P>
+<P>Region functions are specified exactly the same way as group functions
+except they take an extra final argument <I>IDR</I> which is the region ID.
+The function is computed for all atoms that are in both the group and
+the region. If the group is "all", then the only criteria for atom
+inclusion is that it be in the region.
+</P>
+<HR>
+
+<H4>Special Functions
+</H4>
+<P>Special functions take specific kinds of arguments, meaning their
+arguments cannot be formulas themselves.
+</P>
+<P>The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
+each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
+"f_ID" or "f_ID[N]". The first two are computes and the second two
+are fixes; the ID in the reference should be replaced by the ID of a
+compute or fix defined elsewhere in the input script. The compute or
+fix must produce either a global vector or array. If it produces a
+global vector, then the notation without "[N]" should be used. If
+it produces a global array, then the notation with "[N]" should be
+used, when N is an integer, to specify which column of the global
+array is being referenced.
+</P>
+<P>These functions operate on the global vector of inputs and reduce it
+to a single scalar value. This is analagous to the operation of the
+<A HREF = "compute_reduce.html">compute reduce</A> command, which invokes the same
+functions on per-atom and local vectors.
+</P>
+<P>The sum() function calculates the sum of all the vector elements. The
+min() and max() functions find the minimum and maximum element
+respectively. The ave() function is the same as sum() except that it
+divides the result by the length of the vector.
+</P>
+<P>The trap() function is the same as sum() except the first and last
+elements are multiplied by a weighting factor of 1/2 when performing
+the sum. This effectively implements an integration via the
+trapezoidal rule on the global vector of data. I.e. consider a set of
+points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
+..., (N,VN), where the Vi are the values in the global vector of
+length N. The integral from 1 to N of these points is trap(). When
+appropriately normalized by the timestep size, this function is useful
+for calculating integrals of time-series data, like that generated by
+the <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command.
+</P>
+<P>The slope() function uses linear regression to fit a line to the set
+of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
+..., (N,VN), where the Vi are the values in the global vector of
+length N. The returned value is the slope of the line. If the line
+has a single point or is vertical, it returns 1.0e20.
+</P>
+<P>The gmask(x) function takes 1 argument which is a group ID. It
+can only be used in atom-style variables. It returns a 1 for
+atoms that are in the group, and a 0 for atoms that are not.
+</P>
+<P>The rmask(x) function takes 1 argument which is a region ID. It can
+only be used in atom-style variables. It returns a 1 for atoms that
+are in the geometric region, and a 0 for atoms that are not.
+</P>
+<P>The grmask(x,y) function takes 2 arguments. The first is a group ID,
+and the second is a region ID. It can only be used in atom-style
+variables. It returns a 1 for atoms that are in both the group and
+region, and a 0 for atoms that are not in both.
+</P>
+<P>The next(x) function takes 1 argument which is a variable ID (not
+"v_foo", just "foo"). It must be for a file-style or atomfile-style
+variable. Each time the next() function is invoked (i.e. each time
+the equal-style or atom-style variable is evaluated), the following
+steps occur.
+</P>
+<P>For file-style variables, the current string value stored by the
+file-style variable is converted to a numeric value and returned by
+the function. And the next string value in the file is read and
+stored. Note that if the line previously read from the file was not a
+numeric string, then it will typically evaluate to 0.0, which is
+likely not what you want.
+</P>
+<P>For atomfile-style variables, the current per-atom values stored by
+the atomfile-style variable are returned by the function. And the
+next set of per-atom values in the file is read and stored.
+</P>
+<P>Since file-style and atomfile-style variables read and store the first
+line of the file or first set of per-atoms values when they are
+defined in the input script, these are the value(s) that will be
+returned the first time the next() function is invoked. If next() is
+invoked more times than there are lines or sets of lines in the file,
+the variable is deleted, similar to how the <A HREF = "next.html">next</A> command
+operates.
+</P>
+<HR>
+
+<H4>Atom Values and Vectors
+</H4>
+<P>Atom values take an integer argument I from 1 to N, where I is the
+atom-ID, e.g. x[243], which means use the x coordinate of the atom
+with ID = 243. Or they can take a variable name, specified as v_name,
+where name is the name of the variable, like x[v_myIndex]. The
+variable can be of any style except atom or atom-file variables. The
+variable is evaluated and the result is expected to be numeric and is
+cast to an integer (i.e. 3.4 becomes 3), to use an an index, which
+must be a value from 1 to N. Note that a "formula" cannot be used as
+the argument between the brackets, e.g. x[243+10] or
+x[v_myIndex+1] are not allowed. To do this a single variable can be
+defined that contains the needed formula.
+</P>
+<P>Note that the 0 < atom-ID <= N, where N is the largest atom ID
+in the system. If an ID is specified for an atom that does not
+currently exist, then the generated value is 0.0.
+</P>
+<P>Atom vectors generate one value per atom, so that a reference like
+"vx" means the x-component of each atom's velocity will be used when
+evaluating the variable.
+</P>
+<P>The meaning of the different atom values and vectors is mostly
+self-explanatory. Mol refers to the molecule ID of an atom, and is
+only defined if an <A HREF = "atom_style.html">atom_style</A> is being used that
+defines molecule IDs.
+</P>
+<P>Note that many other atom attributes can be used as inputs to a
+variable by using the <A HREF = "compute_property_atom.html">compute
+property/atom</A> command and then specifying
+a quantity from that compute.
+</P>
+<HR>
+
+<H4>Compute References
+</H4>
+<P>Compute references access quantities calculated by a
+<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
+the ID of a compute defined elsewhere in the input script. As
+discussed in the doc page for the <A HREF = "compute.html">compute</A> command,
+computes can produce global, per-atom, or local values. Only global
+and per-atom values can be used in a variable. Computes can also
+produce a scalar, vector, or array. An equal-style variable can only
+use scalar values, which means a global scalar, or an element of a
+global or per-atom vector or array. Atom-style variables can use the
+same scalar values. They can also use per-atom vector values. A
+vector value can be a per-atom vector itself, or a column of an
+per-atom array. See the doc pages for individual computes to see what
+kind of values they produce.
+</P>
+<P>Examples of different kinds of compute references are as follows.
+There is no ambiguity as to what a reference means, since computes
+only produce global or per-atom quantities, never both.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >c_ID</TD><TD > global scalar, or per-atom vector</TD></TR>
+<TR><TD >c_ID[I]</TD><TD > Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array</TD></TR>
+<TR><TD >c_ID[I][J]</TD><TD > I,J element of global array, or atom I's Jth value in per-atom array
+</TD></TR></TABLE></DIV>
+
+<P>For I and J, integers can be specified or a variable name, specified
+as v_name, where name is the name of the variable. The rules for this
+syntax are the same as for the "Atom Values and Vectors" discussion
+above.
+</P>
+<P>If a variable containing a compute is evaluated directly in an input
+script (not during a run), then the values accessed by the compute
+must be current. See the discussion below about "Variable Accuracy".
+</P>
+<HR>
+
+<H4>Fix References
+</H4>
+<P>Fix references access quantities calculated by a <A HREF = "compute.html">fix</A>.
+The ID in the reference should be replaced by the ID of a fix defined
+elsewhere in the input script. As discussed in the doc page for the
+<A HREF = "fix.html">fix</A> command, fixes can produce global, per-atom, or local
+values. Only global and per-atom values can be used in a variable.
+Fixes can also produce a scalar, vector, or array. An equal-style
+variable can only use scalar values, which means a global scalar, or
+an element of a global or per-atom vector or array. Atom-style
+variables can use the same scalar values. They can also use per-atom
+vector values. A vector value can be a per-atom vector itself, or a
+column of an per-atom array. See the doc pages for individual fixes
+to see what kind of values they produce.
+</P>
+<P>The different kinds of fix references are exactly the same as the
+compute references listed in the above table, where "c_" is replaced
+by "f_". Again, there is no ambiguity as to what a reference means,
+since fixes only produce global or per-atom quantities, never both.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >f_ID</TD><TD > global scalar, or per-atom vector</TD></TR>
+<TR><TD >f_ID[I]</TD><TD > Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array</TD></TR>
+<TR><TD >f_ID[I][J]</TD><TD > I,J element of global array, or atom I's Jth value in per-atom array
+</TD></TR></TABLE></DIV>
+
+<P>For I and J, integers can be specified or a variable name, specified
+as v_name, where name is the name of the variable. The rules for this
+syntax are the same as for the "Atom Values and Vectors" discussion
+above.
+</P>
+<P>If a variable containing a fix is evaluated directly in an input
+script (not during a run), then the values accessed by the fix should
+be current. See the discussion below about "Variable Accuracy".
+</P>
+<P>Note that some fixes only generate quantities on certain timesteps.
+If a variable attempts to access the fix on non-allowed timesteps, an
+error is generated. For example, the <A HREF = "fix_ave_time.html">fix ave/time</A>
+command may only generate averaged quantities every 100 steps. See
+the doc pages for individual fix commands for details.
+</P>
+<HR>
+
+<H4>Variable References
+</H4>
+<P>Variable references access quantities stored or calculated by other
+variables, which will cause those variables to be evaluated. The name
+in the reference should be replaced by the name of a variable defined
+elsewhere in the input script.
+</P>
+<P>As discussed on this doc page, equal-style variables generate a global
+scalar numeric value; atom-style and atomfile-style variables generate
+a per-atom vector of numeric values; all other variables store a
+string. The formula for an equal-style variable can use any style of
+variable except an atom-style or atomfile-style (unless only a single
+value from the variable is accessed via a subscript). If a
+string-storing variable is used, the string is converted to a numeric
+value. Note that this will typically produce a 0.0 if the string is
+not a numeric string, which is likely not what you want. The formula
+for an atom-style variable can use any style of variable, including
+other atom-style or atomfile-style variables.
+</P>
+<P>Examples of different kinds of variable references are as follows.
+There is no ambiguity as to what a reference means, since variables
+produce only a global scalar or a per-atom vector, never both.
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >v_name</TD><TD > scalar, or per-atom vector</TD></TR>
+<TR><TD >v_name[I]</TD><TD > atom I's value in per-atom vector
+</TD></TR></TABLE></DIV>
+
+<P>For I, an integer can be specified or a variable name, specified as
+v_name, where name is the name of the variable. The rules for this
+syntax are the same as for the "Atom Values and Vectors" discussion
+above.
+</P>
+<HR>
+
+<P><B>Immediate Evaluation of Variables:</B>
+</P>
+<P>If you want an equal-style variable to be evaluated immediately, it
+may be the case that you do not need to define a variable at all. See
+<A HREF = "Section_commands.html#cmd_2">Section 3.2</A> of the manual, which
+describes the use of "immediate" variables in an input script,
+specified as $(formula) with parenthesis, where the formula has the
+same syntax as equal-style variables described on this page. This
+effectively evaluates a formula immediately without using the variable
+command to define a named variable.
+</P>
+<P>More generally, there is a difference between referencing a variable
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v_"
+(e.g. v_x or v_abc). The former can be used in any input script
+command, including a variable command. The input script parser
+evaluates the reference variable immediately and substitutes its value
+into the command. As explained in <A HREF = "Section_commands.html#3_2">Section commands
+3.2</A> for "Parsing rules", you can also use
+un-named "immediate" variables for this purpose. For example, a
+string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
+command evaluates the string between the parenthesis as an equal-style
+variable formula.
+</P>
+<P>Referencing a variable with a leading "v_" is an optional or required
+kind of argument for some commands (e.g. the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A> or <A HREF = "dump.html">dump custom</A> or
+<A HREF = "thermo_style.html">thermo_style</A> commands) if you wish it to evaluate
+a variable periodically during a run. It can also be used in a
+variable formula if you wish to reference a second variable. The
+second variable will be evaluated whenever the first variable is
+evaluated.
+</P>
+<P>As an example, suppose you use this command in your input script to
+define the variable "v" as
+</P>
+<PRE>variable v equal vol
+</PRE>
+<P>before a run where the simulation box size changes. You might think
+this will assign the initial volume to the variable "v". That is not
+the case. Rather it assigns a formula which evaluates the volume
+(using the thermo_style keyword "vol") to the variable "v". If you
+use the variable "v" in some other command like <A HREF = "fix_ave_time.html">fix
+ave/time</A> then the current volume of the box will be
+evaluated continuously during the run.
+</P>
+<P>If you want to store the initial volume of the system, you can do it
+this way:
+</P>
+<PRE>variable v equal vol
+variable v0 equal $v
+</PRE>
+<P>The second command will force "v" to be evaluated (yielding the
+initial volume) and assign that value to the variable "v0". Thus the
+command
+</P>
+<PRE>thermo_style custom step v_v v_v0
+</PRE>
+<P>would print out both the current and initial volume periodically
+during the run.
+</P>
+<P>Note that it is a mistake to enclose a variable formula in double
+quotes if it contains variables preceeded by $ signs. For example,
+</P>
+<PRE>variable vratio equal "${vfinal}/${v0}"
+</PRE>
+<P>This is because the quotes prevent variable substitution (see <A HREF = "Section_commands.html#cmd_2">this
+section</A> on parsing input script
+commands), and thus an error will occur when the formula for "vratio"
+is evaluated later.
+</P>
+<HR>
+
+<P><B>Variable Accuracy:</B>
+</P>
+<P>Obviously, LAMMPS attempts to evaluate variables containing formulas
+(<I>equal</I> and <I>atom</I> style variables) accurately whenever the
+evaluation is performed. Depending on what is included in the
+formula, this may require invoking a <A HREF = "compute.html">compute</A>, either
+directly or indirectly via a thermo keyword, or accessing a value
+previously calculated by a compute, or accessing a value calculated
+and stored by a <A HREF = "fix.html">fix</A>. If the compute is one that calculates
+the pressure or energy of the system, then these quantities need to be
+tallied during the evaluation of the interatomic potentials (pair,
+bond, etc) on timesteps that the variable will need the values.
+</P>
+<P>LAMMPS keeps track of all of this during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
+minimization</A>. An error will be generated if you
+attempt to evaluate a variable on timesteps when it cannot produce
+accurate values. For example, if a <A HREF = "thermo_style.html">thermo_style
+custom</A> command prints a variable which accesses
+values stored by a <A HREF = "fix_ave_time.html">fix ave/time</A> command and the
+timesteps on which thermo output is generated are not multiples of the
+averaging frequency used in the fix command, then an error will occur.
+</P>
+<P>An input script can also request variables be evaluated before or
+after or in between runs, e.g. by including them in a
+<A HREF = "print.html">print</A> command. In this case, if a compute is needed to
+evaluate a variable (either directly or indirectly), LAMMPS will not
+invoke the compute, but it will use a value previously calculated by
+the compute, and can do this only if it was invoked on the current
+timestep. Fixes will always provide a quantity needed by a variable,
+but the quantity may or may not be current. This leads to one of
+three kinds of behavior:
+</P>
+<P>(1) The variable may be evaluated accurately. If it contains
+references to a compute or fix, and these values were calculated on
+the last timestep of a preceeding run, then they will be accessed and
+used by the variable and the result will be accurate.
+</P>
+<P>(2) LAMMPS may not be able to evaluate the variable and will generate
+an error message stating so. For example, if the variable requires a
+quantity from a <A HREF = "compute.html">compute</A> that has not been invoked on
+the current timestep, LAMMPS will generate an error. This means, for
+example, that such a variable cannot be evaluated before the first run
+has occurred. Likewise, in between runs, a variable containing a
+compute cannot be evaluated unless the compute was invoked on the last
+timestep of the preceding run, e.g. by thermodynamic output.
+</P>
+<P>One way to get around this problem is to perform a 0-timestep run
+before using the variable. For example, these commands
+</P>
+<PRE>variable t equal temp
+print "Initial temperature = $t"
+run 1000
+</PRE>
+<P>will generate an error if the run is the first run specified in the
+input script, because generating a value for the "t" variable requires
+a compute for calculating the temperature to be invoked.
+</P>
+<P>However, this sequence of commands would be fine:
+</P>
+<PRE>run 0
+variable t equal temp
+print "Initial temperature = $t"
+run 1000
+</PRE>
+<P>The 0-timestep run initializes and invokes various computes, including
+the one for temperature, so that the value it stores is current and
+can be accessed by the variable "t" after the run has completed. Note
+that a 0-timestep run does not alter the state of the system, so it
+does not change the input state for the 1000-timestep run that
+follows. Also note that the 0-timestep run must actually use and
+invoke the compute in question (e.g. via <A HREF = "thermo_style.html">thermo</A> or
+<A HREF = "dump.html">dump</A> output) in order for it to enable the compute to be
+used in a variable after the run. Thus if you are trying to print a
+variable that uses a compute you have defined, you can insure it is
+invoked on the last timestep of the preceding run by including it in
+thermodynamic output.
+</P>
+<P>Unlike computes, <A HREF = "fix.html">fixes</A> will never generate an error if
+their values are accessed by a variable in between runs. They always
+return some value to the variable. However, the value may not be what
+you expect if the fix has not yet calculated the quantity of interest
+or it is not current. For example, the <A HREF = "fix_indent.html">fix indent</A>
+command stores the force on the indenter. But this is not computed
+until a run is performed. Thus if a variable attempts to print this
+value before the first run, zeroes will be output. Again, performing
+a 0-timestep run before printing the variable has the desired effect.
+</P>
+<P>(3) The variable may be evaluated incorrectly and LAMMPS may have no
+way to detect this has occurred. Consider the following sequence of
+commands:
+</P>
+<PRE>pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+variable e equal pe
+print "Final potential energy = $e"
+</PRE>
+<P>The first run is performed using one setting for the pairwise
+potential defined by the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands. The potential energy is
+evaluated on the final timestep and stored by the <A HREF = "compute_pe.html">compute
+pe</A> compute (this is done by the
+<A HREF = "thermo_style.html">thermo_style</A> command). Then a pair coefficient is
+changed, altering the potential energy of the system. When the
+potential energy is printed via the "e" variable, LAMMPS will use the
+potential energy value stored by the <A HREF = "compute_pe.html">compute pe</A>
+compute, thinking it is current. There are many other commands which
+could alter the state of the system between runs, causing a variable
+to evaluate incorrectly.
+</P>
+<P>The solution to this issue is the same as for case (2) above, namely
+perform a 0-timestep run before the variable is evaluated to insure
+the system is up-to-date. For example, this sequence of commands
+would print a potential energy that reflected the changed pairwise
+coefficient:
+</P>
+<PRE>pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+run 0
+variable e equal pe
+print "Final potential energy = $e"
+</PRE>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Indexing any formula element by global atom ID, such as an atom value,
+requires the atom style to use a global mapping in order to look up
+the vector indices. By default, only atom styles with molecular
+information create global maps. The <A HREF = "atom_modify.html">atom_modify
+map</A> command can override the default.
+</P>
+<P>All <I>universe</I>- and <I>uloop</I>-style variables defined in an input script
+must have the same number of values.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "next.html">next</A>, <A HREF = "jump.html">jump</A>, <A HREF = "include.html">include</A>,
+<A HREF = "temper.html">temper</A>, <A HREF = "fix_print.html">fix print</A>, <A HREF = "print.html">print</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/doc2/velocity.html b/doc/doc2/velocity.html
new file mode 100644
index 000000000..5e06774da
--- /dev/null
+++ b/doc/doc2/velocity.html
@@ -0,0 +1,270 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>velocity command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>velocity group-ID style args keyword value ...
+</PRE>
+<UL><LI>group-ID = ID of group of atoms whose velocity will be changed
+
+<LI>style = <I>create</I> or <I>set</I> or <I>scale</I> or <I>ramp</I> or <I>zero</I>
+
+<PRE> <I>create</I> args = temp seed
+ temp = temperature value (temperature units)
+ seed = random # seed (positive integer)
+ <I>set</I> args = vx vy vz
+ vx,vy,vz = velocity value or NULL (velocity units)
+ any of vx,vy,vz van be a variable (see below)
+ <I>scale</I> arg = temp
+ temp = temperature value (temperature units)
+ <I>ramp</I> args = vdim vlo vhi dim clo chi
+ vdim = <I>vx</I> or <I>vy</I> or <I>vz</I>
+ vlo,vhi = lower and upper velocity value (velocity units)
+ dim = <I>x</I> or <I>y</I> or <I>z</I>
+ clo,chi = lower and upper coordinate bound (distance units)
+ <I>zero</I> arg = <I>linear</I> or <I>angular</I>
+ <I>linear</I> = zero the linear momentum
+ <I>angular</I> = zero the angular momentum
+</PRE>
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>dist</I> or <I>sum</I> or <I>mom</I> or <I>rot</I> or <I>temp</I> or <I>bias</I> or <I>loop</I> or <I>units</I>
+
+<PRE> <I>dist</I> value = <I>uniform</I> or <I>gaussian</I>
+ <I>sum</I> value = <I>no</I> or <I>yes</I>
+ <I>mom</I> value = <I>no</I> or <I>yes</I>
+ <I>rot</I> value = <I>no</I> or <I>yes</I>
+ <I>temp</I> value = temperature compute ID
+ <I>bias</I> value = <I>no</I> or <I>yes</I>
+ <I>loop</I> value = <I>all</I> or <I>local</I> or <I>geom</I>
+ <I>rigid</I> value = fix-ID
+ fix-ID = ID of rigid body fix
+ <I>units</I> value = <I>box</I> or <I>lattice</I>
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>velocity all create 300.0 4928459 rot yes dist gaussian
+velocity border set NULL 4.0 v_vz sum yes units box
+velocity flow scale 300.0
+velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
+velocity all zero linear
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Set or change the velocities of a group of atoms in one of several
+styles. For each style, there are required arguments and optional
+keyword/value parameters. Not all options are used by each style.
+Each option has a default as listed below.
+</P>
+<P>The <I>create</I> style generates an ensemble of velocities using a random
+number generator with the specified seed as the specified temperature.
+</P>
+<P>The <I>set</I> style sets the velocities of all atoms in the group to the
+specified values. If any component is specified as NULL, then it is
+not set. Any of the vx,vy,vz velocity components can be specified as
+an equal-style or atom-style <A HREF = "variable.html">variable</A>. If the value
+is a variable, it should be specified as v_name, where name is the
+variable name. In this case, the variable will be evaluated, and its
+value used to determine the velocity component. Note that if a
+variable is used, the velocity it calculates must be in box units, not
+lattice units; see the discussion of the <I>units</I> keyword below.
+</P>
+<P>Equal-style variables can specify formulas with various mathematical
+functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
+keywords for the simulation box parameters or other parameters.
+</P>
+<P>Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent
+velocity field.
+</P>
+<P>The <I>scale</I> style computes the current temperature of the group of
+atoms and then rescales the velocities to the specified temperature.
+</P>
+<P>The <I>ramp</I> style is similar to that used by the <A HREF = "compute_temp_ramp.html">compute
+temp/ramp</A> command. Velocities ramped
+uniformly from vlo to vhi are applied to dimension vx, or vy, or vz.
+The value assigned to a particular atom depends on its relative
+coordinate value (in dim) from clo to chi. For the example above, an
+atom with y-coordinate of 10 (1/4 of the way from 5 to 25), would be
+assigned a x-velocity of 1.25 (1/4 of the way from 0.0 to 5.0). Atoms
+outside the coordinate bounds (less than 5 or greater than 25 in this
+case), are assigned velocities equal to vlo or vhi (0.0 or 5.0 in this
+case).
+</P>
+<P>The <I>zero</I> style adjusts the velocities of the group of atoms so that
+the aggregate linear or angular momentum is zero. No other changes
+are made to the velocities of the atoms. If the <I>rigid</I> option is
+specified (see below), then the zeroing is performed on individual
+rigid bodies, as defined by the <A HREF = "fix_rigid.html">fix rigid or fix
+rigid/small</A> commands. In other words, zero linear
+will set the linear momentum of each rigid body to zero, and zero
+angular will set the angular momentum of each rigid body to zero.
+This is done by adjusting the velocities of the atoms in each rigid
+body.
+</P>
+<P>All temperatures specified in the velocity command are in temperature
+units; see the <A HREF = "units.html">units</A> command. The units of velocities and
+coordinates depend on whether the <I>units</I> keyword is set to <I>box</I> or
+<I>lattice</I>, as discussed below.
+</P>
+<P>For all styles, no atoms are assigned z-component velocities if the
+simulation is 2d; see the <A HREF = "dimension.html">dimension</A> command.
+</P>
+<HR>
+
+<P>The keyword/value options are used in the following ways by the
+various styles.
+</P>
+<P>The <I>dist</I> keyword is used by <I>create</I>. The ensemble of generated
+velocities can be a <I>uniform</I> distribution from some minimum to
+maximum value, scaled to produce the requested temperature. Or it can
+be a <I>gaussian</I> distribution with a mean of 0.0 and a sigma scaled to
+produce the requested temperature.
+</P>
+<P>The <I>sum</I> keyword is used by all styles, except <I>zero</I>. The new
+velocities will be added to the existing ones if sum = yes, or will
+replace them if sum = no.
+</P>
+<P>The <I>mom</I> and <I>rot</I> keywords are used by <I>create</I>. If mom = yes, the
+linear momentum of the newly created ensemble of velocities is zeroed;
+if rot = yes, the angular momentum is zeroed.
+</P>
+<P>*line
+</P>
+<P>If specified, the <I>temp</I> keyword is used by <I>create</I> and <I>scale</I> to
+specify a <A HREF = "compute.html">compute</A> that calculates temperature in a
+desired way, e.g. by first subtracting out a velocity bias, as
+discussed in <A HREF = "Section_howto.html#howto_15">Section howto 16</A> of the doc
+pages. If this keyword is not specified, <I>create</I> and <I>scale</I>
+calculate temperature using a compute that is defined internally as
+follows:
+</P>
+<PRE>compute velocity_temp group-ID temp
+</PRE>
+<P>where group-ID is the same ID used in the velocity command. i.e. the
+group of atoms whose velocity is being altered. This compute is
+deleted when the velocity command is finished. See the <A HREF = "compute_temp.html">compute
+temp</A> command for details. If the calculated
+temperature should have degrees-of-freedom removed due to fix
+constraints (e.g. SHAKE or rigid-body constraints), then the
+appropriate fix command must be specified before the velocity command
+is issued.
+</P>
+<P>The <I>bias</I> keyword with a <I>yes</I> setting is used by <I>create</I> and
+<I>scale</I>, but only if the <I>temp</I> keyword is also used to specify a
+<A HREF = "compute.html">compute</A> that calculates temperature in a desired way.
+If the temperature compute also calculates a velocity bias, the the
+bias is subtracted from atom velocities before the <I>create</I> and
+<I>scale</I> operations are performed. After the operations, the bias is
+added back to the atom velocities. See <A HREF = "Section_howto.html#howto_15">Section howto
+16</A> of the doc pages for more discussion
+of temperature computes with biases. Note that the velocity bias is
+only applied to atoms in the temperature compute specified with the
+<I>temp</I> keyword.
+</P>
+<P>As an example, assume atoms are currently streaming in a flow
+direction (which could be separately initialized with the <I>ramp</I>
+style), and you wish to initialize their thermal velocity to a desired
+temperature. In this context thermal velocity means the per-particle
+velocity that remains when the streaming velocity is subtracted. This
+can be done using the <I>create</I> style with the <I>temp</I> keyword
+specifying the ID of a <A HREF = "compute_temp_ramp.html">compute temp/ramp</A> or
+<A HREF = "compute_temp_profile.html">compute temp/profile</A> command, and the
+<I>bias</I> keyword set to a <I>yes</I> value.
+</P>
+<HR>
+
+<P>The <I>loop</I> keyword is used by <I>create</I> in the following ways.
+</P>
+<P>If loop = all, then each processor loops over all atoms in the
+simulation to create velocities, but only stores velocities for atoms
+it owns. This can be a slow loop for a large simulation. If atoms
+were read from a data file, the velocity assigned to a particular atom
+will be the same, independent of how many processors are being used.
+This will not be the case if atoms were created using the
+<A HREF = "create_atoms.html">create_atoms</A> command, since atom IDs will likely
+be assigned to atoms differently.
+</P>
+<P>If loop = local, then each processor loops over only its atoms to
+produce velocities. The random number seed is adjusted to give a
+different set of velocities on each processor. This is a fast loop,
+but the velocity assigned to a particular atom will depend on which
+processor owns it. Thus the results will always be different when a
+simulation is run on a different number of processors.
+</P>
+<P>If loop = geom, then each processor loops over only its atoms. For
+each atom a unique random number seed is created, based on the atom's
+xyz coordinates. A velocity is generated using that seed. This is a
+fast loop and the velocity assigned to a particular atom will be the
+same, independent of how many processors are used. However, the set
+of generated velocities may be more correlated than if the <I>all</I> or
+<I>local</I> keywords are used.
+</P>
+<P>Note that the <I>loop geom</I> keyword will not necessarily assign
+identical velocities for two simulations run on different machines.
+This is because the computations based on xyz coordinates are
+sensitive to tiny differences in the double-precision value for a
+coordinate as stored on a particular machine.
+</P>
+<HR>
+
+<P>The <I>rigid</I> keyword only has meaning when used with the <I>zero</I> style.
+It allows specification of a fix-ID for one of the <A HREF = "fix_rigid.html">rigid-body
+fix</A> variants which defines a set of rigid bodies. The
+zeroing of linear or angular momentum is then performed for each rigid
+body defined by the fix, as described above.
+</P>
+<P>The <I>units</I> keyword is used by <I>set</I> and <I>ramp</I>. If units = box,
+the velocities and coordinates specified in the velocity command are
+in the standard units described by the <A HREF = "units.html">units</A> command
+(e.g. Angstroms/fmsec for real units). If units = lattice, velocities
+are in units of lattice spacings per time (e.g. spacings/fmsec) and
+coordinates are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
+command must have been previously used to define the lattice spacing.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>Assigning a temperature via the <I>create</I> style to a system with <A HREF = "fix_rigid.html">rigid
+bodies</A> or <A HREF = "fix_shake.html">SHAKE constraints</A> may not
+have the desired outcome for two reasons. First, the velocity command
+can be invoked before all of the relevant fixes are created and
+initialized and the number of adjusted degrees of freedom (DOFs) is
+known. Thus it is not possible to compute the target temperature
+correctly. Second, the assigned velocities may be partially canceled
+when constraints are first enforced, leading to a different
+temperature than desired. A workaround for this is to perform a <A HREF = "run.html">run
+0</A> command, which insures all DOFs are accounted for
+properly, and then rescale the temperature to the desired value before
+performing a simulation. For example:
+</P>
+<PRE>velocity all create 300.0 12345
+run 0 # temperature may not be 300K
+velocity all scale 300.0 # now it should be
+</PRE>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_shake.html">fix shake</A>,
+<A HREF = "lattice.html">lattice</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The keyword defaults are dist = uniform, sum = no, mom = yes, rot =
+no, bias = no, loop = all, and units = lattice. The temp and rigid
+keywords are not defined by default.
+</P>
+</HTML>
diff --git a/doc/doc2/write_data.html b/doc/doc2/write_data.html
new file mode 100644
index 000000000..426b0a206
--- /dev/null
+++ b/doc/doc2/write_data.html
@@ -0,0 +1,131 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>write_data command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>write_data file keyword value ...
+</PRE>
+<UL><LI>file = name of data file to write out
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>pair</I> or <I>nocoeff</I>
+
+<PRE> <I>nocoeff</I> = do not write out force field info
+ <I>pair</I> value = <I>ii</I> or <I>ij</I>
+ <I>ii</I> = write one line of pair coefficient info per atom type
+ <I>ij</I> = write one line of pair coefficient info per IJ atom type pair
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>write_data data.polymer
+write_data data.*
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write a data file in text format of the current state of the
+simulation. Data files can be read by the <A HREF = "read_data.html">read data</A>
+command to begin a simulation. The <A HREF = "read_data.html">read_data</A> command
+also describes their format.
+</P>
+<P>Similar to <A HREF = "dump.html">dump</A> files, the data filename can contain a "*"
+wild-card character. The "*" is replaced with the current timestep
+value.
+</P>
+<P>IMPORTANT NOTE: The write-data command is not yet fully implemented in
+two respects. First, most pair styles do not yet write their
+coefficient information into the data file. This means you will need
+to specify that information in your input script that reads the data
+file, via the <A HREF = "pair_coeff.html">pair_coeff</A> command. Second, a few of
+the <A HREF = "atom_style.html">atom styles</A> (body, ellipsoid, line, tri) that
+store auxiliary "bonus" information about aspherical particles, do not
+yet write the bonus info into the data file. Both these
+functionalities will be added to the write_data command later.
+</P>
+<P>Because a data file is in text format, if you use a data file written
+out by this command to restart a simulation, the initial state of the
+new run will be slightly different than the final state of the old run
+(when the file was written) which was represented internally by LAMMPS
+in binary format. A new simulation which reads the data file will
+thus typically diverge from a simulation that continued in the
+original input script.
+</P>
+<P>If you want to do more exact restarts, using binary files, see the
+<A HREF = "restart.html">restart</A>, <A HREF = "write_restart.html">write_restart</A>, and
+<A HREF = "read_restart.html">read_restart</A> commands. You can also convert
+binary restart files to text data files, after a simulation has run,
+using the <A HREF = "Section_start.html#start_7">-r command-line switch</A>.
+</P>
+<P>IMPORTANT NOTE: Only limited information about a simulation is stored
+in a data file. For example, no information about atom
+<A HREF = "group.html">groups</A> and <A HREF = "fix.html">fixes</A> are stored. <A HREF = "read_restart.html">Binary restart
+files</A> store more information.
+</P>
+<P>Bond interactions (angle, etc) that have been turned off by the <A HREF = "fix_shake.html">fix
+shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> command will
+be written to a data file as if they are turned on. This means they
+will need to be turned off again in a new run after the data file is
+read.
+</P>
+<P>Bonds that are broken (e.g. by a bond-breaking potential) are not
+written to the data file. Thus these bonds will not exist when the
+data file is read.
+</P>
+<HR>
+
+<P>The <I>nocoeff</I> keyword requests that no force field parameters should
+be written to the data file. This can be very helpful, if one wants
+to make significant changes to the force field or if the parameters
+are read in separately anyway, e.g. from an include file.
+</P>
+<P>The <I>pair</I> keyword lets you specify in what format the pair
+coefficient information is written into the data file. If the value
+is specified as <I>ii</I>, then one line per atom type is written, to
+specify the coefficients for each of the I=J interactions. This means
+that no cross-interactions for I != J will be specified in the data
+file and the pair style will apply its mixing rule, as documented on
+individual <A HREF = "pair_style.html">pair_style</A> doc pages. Of course this
+behavior can be overridden in the input script after reading the data
+file, by specifying additional <A HREF = "pair_coeff.html">pair_coeff</A> commands
+for any desired I,J pairs.
+</P>
+<P>If the value is specified as <I>ij</I>, then one line of coefficients is
+written for all I,J pairs where I <= J. These coefficients will
+include any specific settings made in the input script up to that
+point. The presence of these I != J coefficients in the data file
+will effectively turn off the default mixing rule for the pair style.
+Again, the coefficient values in the data file can can be overridden
+in the input script after reading the data file, by specifying
+additional <A HREF = "pair_coeff.html">pair_coeff</A> commands for any desired I,J
+pairs.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command requires inter-processor communication to migrate atoms
+before the data file is written. This means that your system must be
+ready to perform a simulation before using this command (force fields
+setup, atom masses initialized, etc).
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "read_data.html">read_data</A>, <A HREF = "write_restart.html">write_restart</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The option defaults are pair = ii.
+</P>
+</HTML>
diff --git a/doc/doc2/write_dump.html b/doc/doc2/write_dump.html
new file mode 100644
index 000000000..79dc858e5
--- /dev/null
+++ b/doc/doc2/write_dump.html
@@ -0,0 +1,101 @@
+<HTML>
+<CENTER> <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>write_dump command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>write_dump group-ID style file dump-args modify dump_modify-args
+</PRE>
+<UL><LI>group-ID = ID of the group of atoms to be dumped
+
+<LI>style = any of the supported <A HREF = "dump.html">dump styles</A>
+
+<LI>file = name of file to write dump info to
+
+<LI>dump-args = any additional args needed for a particular <A HREF = "dump.html">dump style</A>
+
+<LI>modify = all args after this keyword are passed to <A HREF = "dump_modify.html">dump_modify</A> (optional)
+
+<LI>dump-modify-args = args for <A HREF = "dump_modify.html">dump_modify</A> (optional)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>write_dump all atom dump.atom
+write_dump subgroup atom dump.run.bin
+write_dump all custom dump.myforce.* id type x y vx fx
+write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
+write_dump all xyz system.xyz modify sort id elements O H
+write_dump all image snap*.jpg type type size 960 960 modify backcolor white
+write_dump all image snap*.jpg element element &
+ bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600 &
+ modify backcolor white element C C O H N C C C O H H S O H
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Dump a single snapshot of atom quantities to one or more files for the
+current state of the system. This is a one-time immediate operation,
+in contrast to the <A HREF = "dump.html">dump</A> command which will will set up a
+dump style to write out snapshots periodically during a running
+simulation.
+</P>
+<P>The syntax for this command is mostly identical to that of the
+<A HREF = "dump.html">dump</A> and <A HREF = "dump_modify.html">dump_modify</A> commands as if
+they were concatenated together, with the following exceptions: There
+is no need for a dump ID or dump frequency and the keyword <I>modify</I> is
+added. The latter is so that the full range of
+<A HREF = "dump_modify.html">dump_modify</A> options can be specified for the single
+snapshot, just as they can be for multiple snapshots. The <I>modify</I>
+keyword separates the arguments that would normally be passed to the
+<I>dump</I> command from those that would be given the <I>dump_modify</I>. Both
+support optional arguments and thus LAMMPS needs to be able to cleanly
+separate the two sets of args.
+</P>
+<P>Note that if the specified filename uses wildcard characters "*" or
+"%", as supported by the <A HREF = "dump.html">dump</A> commmand, they will operate
+in the same fashion to create the new filename(s). Normally, <A HREF = "dump_image.html">dump
+image</A> files require a filename with a "*" character
+for the timestep. That is not the case for the write_dump command; no
+wildcard "*" character is necessary.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>All restrictions for the <A HREF = "dump.html">dump</A> and
+<A HREF = "dump_modify.html">dump_modify</A> commands apply to this command as well,
+with the exception of the <A HREF = "dump_image.html">dump image</A> filename not
+requiring a wildcard "*" character, as noted above.
+</P>
+<P>Since dumps are normally written during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
+minimization</A>, the simulation has to be ready to run
+before this command can be used. Similarly, if the dump requires
+information from a compute, fix, or variable, the information needs to
+have been calculated for the current timestep (e.g. by a prior run),
+else LAMMPS will generate an error message.
+</P>
+<P>For example, it is not possible to dump per-atom energy with this
+command before a run has been performed, since no energies and forces
+have yet been calculated. See the <A HREF = "variable.html">variable</A> doc page
+sectinn on Variable Accuracy for more information on this topic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
+<A HREF = "dump_modify.html">dump_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The defaults are listed on the doc pages for the <A HREF = "dump.html">dump</A> and
+<A HREF = "dump_image.html">dump image</A> and <A HREF = "dump_modify.html">dump_modify</A>
+commands.
+</P>
+</HTML>
diff --git a/doc/doc2/write_restart.html b/doc/doc2/write_restart.html
new file mode 100644
index 000000000..8da34fb33
--- /dev/null
+++ b/doc/doc2/write_restart.html
@@ -0,0 +1,130 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>write_restart command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>write_restart file keyword value ...
+</PRE>
+<UL><LI>file = name of file to write restart information to
+
+<LI>zero or more keyword/value pairs may be appended
+
+<LI>keyword = <I>fileper</I> or <I>nfile</I>
+
+<PRE> <I>fileper</I> arg = Np
+ Np = write one file for every this many processors
+ <I>nfile</I> arg = Nf
+ Nf = write this many files, one from each of Nf processors
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>write_restart restart.equil
+write_restart restart.equil.mpiio
+write_restart poly.%.* nfile 10
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Write a binary restart file of the current state of the simulation.
+</P>
+<P>During a long simulation, the <A HREF = "restart.html">restart</A> command is
+typically used to output restart files periodically. The
+write_restart command is useful after a minimization or whenever you
+wish to write out a single current restart file.
+</P>
+<P>Similar to <A HREF = "dump.html">dump</A> files, the restart filename can contain
+two wild-card characters. If a "*" appears in the filename, it is
+replaced with the current timestep value. If a "%" character appears
+in the filename, then one file is written by each processor and the
+"%" character is replaced with the processor ID from 0 to P-1. An
+additional file with the "%" replaced by "base" is also written, which
+contains global information. For example, the files written for
+filename restart.% would be restart.base, restart.0, restart.1, ...
+restart.P-1. This creates smaller files and can be a fast mode of
+output and subsequent input on parallel machines that support parallel
+I/O. The optional <I>fileper</I> and <I>nfile</I> keywords discussed below can
+alter the number of files written.
+</P>
+<P>The restart file can also be written in parallel as one large binary
+file via the MPI-IO library, which is part of the MPI standard for
+versions 2.0 and above. Using MPI-IO requires two steps. First,
+build LAMMPS with its MPIIO package installed, e.g.
+</P>
+<PRE>make yes-mpiio # installs the MPIIO package
+make g++ # build LAMMPS for your platform
+</PRE>
+<P>Second, use a restart filename which contains ".mpiio". Note that it
+does not have to end in ".mpiio", just contain those characters.
+Unlike MPI-IO dump files, a particular restart file must be both
+written and read using MPI-IO.
+</P>
+<P>Restart files can be read by a <A HREF = "read_restart.html">read_restart</A>
+command to restart a simulation from a particular state. Because the
+file is binary (to enable exact restarts), it may not be readable on
+another machine. In this case, you can use the <A HREF = "Section_start.html#start_7">-r command-line
+switch</A> to convert a restart file to a data
+file.
+</P>
+<P>IMPORTANT NOTE: Although the purpose of restart files is to enable
+restarting a simulation from where it left off, not all information
+about a simulation is stored in the file. For example, the list of
+fixes that were specified during the initial run is not stored, which
+means the new input script must specify any fixes you want to use.
+Even when restart information is stored in the file, as it is for some
+fixes, commands may need to be re-specified in the new input script,
+in order to re-use that information. Details are usually given in
+the documentation of the respective command. Also, see the
+<A HREF = "read_restart.html">read_restart</A> command for general information
+about what is stored in a restart file.
+</P>
+<HR>
+
+<P>The optional <I>nfile</I> or <I>fileper</I> keywords can be used in conjunction
+with the "%" wildcard character in the specified restart file name.
+As explained above, the "%" character causes the restart file to be
+written in pieces, one piece for each of P processors. By default P =
+the number of processors the simulation is running on. The <I>nfile</I> or
+<I>fileper</I> keyword can be used to set P to a smaller value, which can
+be more efficient when running on a large number of processors.
+</P>
+<P>The <I>nfile</I> keyword sets P to the specified Nf value. For example, if
+Nf = 4, and the simulation is running on 100 processors, 4 files will
+be written, by processors 0,25,50,75. Each will collect information
+from itself and the next 24 processors and write it to a restart file.
+</P>
+<P>For the <I>fileper</I> keyword, the specified value of Np means write one
+file for every Np processors. For example, if Np = 4, every 4th
+processor (0,4,8,12,etc) will collect information from itself and the
+next 3 processors and write it to a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This command requires inter-processor communication to migrate atoms
+before the restart file is written. This means that your system must
+be ready to perform a simulation before using this command (force
+fields setup, atom masses initialized, etc).
+</P>
+<P>To write and read restart files in parallel with MPI-IO, the MPIIO
+package must be installed.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "restart.html">restart</A>, <A HREF = "read_restart.html">read_restart</A>,
+<A HREF = "write_data.html">write_data</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>

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