<LI>If you find a bug, <A HREF = "Section_errors.html#9_2">this section</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">this section</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 = "1_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 papers describe the parallel algorithms used in LAMMPS.
</P>
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
</P>
<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov).
</P>
<P>If you send is information about your publication, we'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs. They
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
</P>
<P>Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)</TD></TR>
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson and Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >region prism </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (Sandia)</TD></TR>
+<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#2_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.
+fix ID group-ID style_name keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style_name = {nvt/eff} or {npt/eff} or {nph/eff} :l
+one or more keyword value pairs may be appended
+keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
+ {temp} values = Tstart Tstop Tdamp
+ Tstart,Tstop = external temperature at start/end of run
+ Tdamp = temperature damping parameter (time units)
+ {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
+ Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
+ Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+ Pdamp = stress damping parameter (time units)
+ {couple} = {none} or {xyz} or {xy} or {yz} or {xz}
+ {tchain} value = length of thermostat chain (1 = single thermostat)
+ {pchain} values = length of thermostat chain on barostat (0 = no thermostat)
+ {mtk} value = {yes} or {no} = add in MTK adjustment term or not
+ {tloop} value = number of sub-cycles to perform on thermostat
+ {ploop} value = number of sub-cycles to perform on barostat thermostat
+ {nreset} value = reset reference cell every this many timesteps
+ {drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
+ {dilate} value = {all} or {partial} :pre
+:ule
+
+[Examples:]
+
+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
+
+[Description:]
+
+These commands perform time integration on Nose-Hoover style
+non-Hamiltonian equations of motion for nuclei and electrons in the
+group for the "electron force field"_pair_eff.html 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 {xy},
+{xz} and {yz} 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.
+
+The operation of these fixes is exactly like that described by the
+"fix nvt, npt, and nph"_fix_nh.html 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 "fix nvt, npt, and nph"_fix_nh.html
+doc page), are performed with computes that include the eFF contribution
+to the temperature or kinetic energy from the electron radial velocity.
+
+IMPORTANT NOTE: there are two different pressures that can be reported
+for eFF when defining the pair_style (see "pair
+eff/cut"_pair_eff_cut.html 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).
+
+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 "velocity"_velocity.html
+command, so the the user must allow for these degrees of freedom to
+equilibrate (i.e. equi-partitioning of energy) through time
+integration.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands
+for details.
+
+[Restrictions:]
+
+This fix is part of the "user-eff" package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
+
+Other restriction discussed on the doc page for the "fix nvt, npt, and
+nph"_fix_nh.html commands also apply.
+
+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.
-This example is just for illustration purposes, and should not be used to determine the proper dynamics of this system because the cell size is too small (you will not get the correct energies). Note, the impact velocities are introduced in the data file, but the user may choose to override these with the velocity command in LAMMPS.