diff --git a/doc/compute.html b/doc/compute.html
index cab6f21b2..a5e7195fa 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -1,150 +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 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>Create 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. There are two kinds of computes, "global"
computes that calculate one or more values for the entire group of
atoms, and "per-atom" computes that calculate one or more values for
each atom in the group. The latter has the word "atom" in its style
name.
</P>
<P>In LAMMPS, a "compute" can be used in several ways. The results of
global computes 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. The results of computes that
calculate a global temperature or pressure can be used by fixes that
do thermostatting or barostatting and when atom velocities are
created.
</P>
<P>The results of per-atom computes 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 the per-atom values can
be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command and
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> commands. Or the per-atom values
can be referenced in a <A HREF = "variable.html">variable atom</A> command. Note
that the value of per-atom computes will be 0.0 for atoms not in the
specified compute group.
</P>
<P>See this <A HREF = "Section_howto.html#4_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>
<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 depending on the "thermo_modify norm" setting. But if a
compute value is accessed in another way, e.g. by a
<A HREF = "variable.html">variable</A>, you may need to know whether it is an
intensive or extensive value. See the doc page for individual
computes for further info.
</P>
<P>LAMMPS creates its own global computes 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 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>
<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:
</P>
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<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_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_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
<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_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_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
<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_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_dipole.html">temp/dipole</A> - temperature of point dipolar particles
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<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
</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#3_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>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html
index e0c82d434..0477fdef1 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_damage_atom.html
@@ -1,55 +1,55 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.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/peri command
+<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. Please 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>The value of the damage will be 0.0 for atoms 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#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>damage/atom</I> style is part of the "peri" 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 = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt
index cee83108c..15753b137 100644
--- a/doc/compute_damage_atom.txt
+++ b/doc/compute_damage_atom.txt
@@ -1,50 +1,50 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
-compute damage/peri command :h3
+compute damage/atom command :h3
[Syntax:]
compute ID group-ID damage/atom :pre
ID, group-ID are documented in "compute"_compute.html command
damage/atom = style name of this compute command :ul
[Examples:]
compute 1 all damage/atom :pre
[Description:]
Define a computation that calculates the per-atom damage for each atom
in a group. Please see the "PDLAMMPS user
guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
The value of the damage will be 0.0 for atoms not in the specified
compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:]
The {damage/atom} style is part of the "peri" 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.
[Related commands:]
"dump custom"_dump.html
[Default:] none
diff --git a/doc/pair_peri_pmb.html b/doc/pair_peri_pmb.html
index 026ecb71e..3835444a6 100644
--- a/doc/pair_peri_pmb.html
+++ b/doc/pair_peri_pmb.html
@@ -1,57 +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 peri/pmb command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style peri/pmb
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
</PRE>
<P><B>Description:</B>
</P>
-<P>The <I>peri/pmb</I> style implements the peridynamic bond-based prototype
-microelastic brittle (PMB) model. Please see the
-<A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS</A> user guide for more
-details.
+<P>Style <I>peri/pmb</I> style implements the Peridynamic bond-based prototype
+microelastic brittle (PMB) model, which can be used to model materials
+at the mesoscopic or macroscopic scale. 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 this particular potential.
</P>
-<P>The syntax for the pair_coeff command is:
+<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>
-<PRE>pair_coeff type1 type2 c horizon s00 alpha
-</PRE>
-<P>The following coefficients must be defined for each pair of atoms types via
-the pair_coeff command as in the examples above.
-</P>
-<UL><LI>c (peridynamic PMB "spring constant")
-<LI>horizon (peridynamic horizon)
-<LI>s00 (used when calculating if bond should break)
-<LI>alpha (used when calculating if bond should break)
+<UL><LI>K (energy/distance^2 units)
+<LI>horizon (distance units)
+<LI>s00 (?? units)
+<LI>alpha (?? units)
</UL>
+<P>K is the 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. See the users guide for more
+details.
+</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>This pair style does 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 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>
</P>
-<P>The <I>peri/pmb</I> style is part of the "peridynamic" package. It is only
-enabled if LAMMPS was built with that package (which it is not by
-default). See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
-more info.
+<P>The <I>peri/pmb</I> style is part of the "peri" 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>
</P>
<P><B>Default:</B> none
</P>
+<HR>
+
+<A NAME = "Parks"></A>
+
+<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys
+Comm, (2008).
+</P>
</HTML>
diff --git a/doc/pair_peri_pmb.txt b/doc/pair_peri_pmb.txt
index 98b74ebee..d07ea487b 100644
--- a/doc/pair_peri_pmb.txt
+++ b/doc/pair_peri_pmb.txt
@@ -1,52 +1,85 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style peri/pmb command :h3
[Syntax:]
pair_style peri/pmb :pre
[Examples:]
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre
[Description:]
-The {peri/pmb} style implements the peridynamic bond-based prototype
-microelastic brittle (PMB) model. Please see the
-"PDLAMMPS"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf user guide for more
-details.
+Style {peri/pmb} style implements the Peridynamic bond-based prototype
+microelastic brittle (PMB) model, which can be used to model materials
+at the mesoscopic or macroscopic scale. The implementation of
+Peridynamics in LAMMPS is described in "(Parks)"_#Parks. Also see the
+"PDLAMMPS user
+guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for more
+details about this particular potential.
+
+The following coefficients must be defined for each pair of atom
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands, or by mixing as described below:
+
+K (energy/distance^2 units)
+horizon (distance units)
+s00 (?? units)
+alpha (?? units) :ul
+
+K is the 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. See the users guide for more
+details.
-The syntax for the pair_coeff command is:
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift option.
-pair_coeff type1 type2 c horizon s00 alpha :pre
+The "pair_modify"_pair_modify.html table and tail options are not
+relevant for this pair style.
-The following coefficients must be defined for each pair of atoms types via
-the pair_coeff command as in the examples above.
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
-c (peridynamic PMB "spring constant")
-horizon (peridynamic horizon)
-s00 (used when calculating if bond should break)
-alpha (used when calculating if bond should break) :ul
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-The {peri/pmb} style is part of the "peridynamic" package. It is only
-enabled if LAMMPS was built with that package (which it is not by
-default). See the "Making LAMMPS"_Section_start.html#2_3 section for
-more info.
+The {peri/pmb} style is part of the "peri" 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.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
+
+:line
+
+:link(Parks)
+[(Parks)] Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys
+Comm, (2008).