From 3a7d11a81f6af298456f8caba7440d299dbd7aba Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 9 Nov 2009 18:30:55 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3356
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/atom_style.html  | 33 ++++++++++++---------------------
 doc/atom_style.txt   | 33 ++++++++++++---------------------
 doc/communicate.html | 37 ++++++++++++++++++++++++-------------
 doc/communicate.txt  | 35 +++++++++++++++++++++++------------
 doc/read_data.html   |  1 -
 doc/read_data.txt    |  1 -
 6 files changed, 71 insertions(+), 69 deletions(-)

diff --git a/doc/atom_style.html b/doc/atom_style.html
index 92e0c00163..915ca00711 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -15,7 +15,7 @@
 </P>
 <PRE>atom_style style args 
 </PRE>
-<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or         <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or 	<I>peri</I> or <I>hybrid</I> 
+<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or         <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or 	<I>peri</I> or <I>hybrid</I> 
 </UL>
 <PRE>  args = none for any style except <I>hybrid</I>
   <I>hybrid</I> args = list of one or more sub-styles 
@@ -59,7 +59,6 @@ quantities.
 <TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
 <TR><TD ><I>colloid</I> </TD><TD > angular velocity </TD><TD > extended spherical particles </TD></TR>
 <TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > atomic system with dipoles </TD></TR>
-<TR><TD ><I>dpd</I> </TD><TD > default values, also communicates velocities </TD><TD > DPD models </TD></TR>
 <TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
 <TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
 <TR><TD ><I>granular</I> </TD><TD > diameter, density, angular velocity </TD><TD > granular models </TD></TR>
@@ -68,7 +67,7 @@ quantities.
 </TD></TR></TABLE></DIV>
 
 <P>All of the styles define point particles, except the <I>colloid</I>,
-<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles.  These define
+<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles, which define
 finite-size particles.  For <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I>
 systems, the <A HREF = "shape.html">shape</A> command is used to specify the size
 and shape of particles on a per-type basis, which is spherical for
@@ -85,13 +84,6 @@ the specified diameter and density are used to calculate each
 particle's mass.  For <I>peri</I> systems, the speficied volume and density
 are used to calculate each particle's mass.
 </P>
-<P>Only the <I>colloid</I>, <I>dpd</I>, and <I>granular</I> styles communicate
-velocities and angular velocities (if defined) with ghost atoms; the
-others do not.  This is because the pairwise interactions calculated
-by the pair styles that typically use these atom styles
-(e.g. <A HREF = "pair_dpd.html">pair_style dpd</A> and <A HREF = "pair_gran.html">pair_style
-granular</A>) require velocities of both particles.
-</P>
 <HR>
 
 <P>Typically, simulations require only a single (non-hybrid) atom style.
@@ -103,10 +95,10 @@ 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 charged DPD particles, you would need to use
-"atom_style hybrid dpd charge".  When a hybrid style is used, atoms
-store and communicate the union of all quantities implied by the
-individual styles.
+example, if you want colloidal particles with charge, you would need
+to use "atom_style hybrid colloid charge".  When a hybrid style is
+used, atoms store and communicate the union of all quantities implied
+by the individual styles.
 </P>
 <P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
 section</A>.
@@ -118,13 +110,12 @@ section</A>.
 </P>
 <P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
 "molecular" package.  The <I>granular</I> style is part of the "granular"
-package.  The <I>dpd</I> style is part of the "dpd" package.  The <I>colloid</I>
-style is part of the "colloid" package.  The <I>dipole</I> style is part of
-the "dipole" package.  The <I>ellipsoid</I> style is part of the "asphere"
-package.  The <I>peri</I> style is part of the "peri" package for
-Peridynamics.  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.
+package.  The <I>colloid</I> style is part of the "colloid" package.  The
+<I>dipole</I> style is part of the "dipole" package.  The <I>ellipsoid</I> style
+is part of the "asphere" package.  The <I>peri</I> style is part of the
+"peri" package for Peridynamics.  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><B>Related commands:</B>
 </P>
diff --git a/doc/atom_style.txt b/doc/atom_style.txt
index b172896f51..f8e44046b6 100644
--- a/doc/atom_style.txt
+++ b/doc/atom_style.txt
@@ -13,7 +13,7 @@ atom_style command :h3
 atom_style style args :pre
 
 style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
-        {dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \
+        {ellipsoid} or {full} or {granular} or {molecular} or \
 	{peri} or {hybrid} :ul
   args = none for any style except {hybrid}
   {hybrid} args = list of one or more sub-styles :pre
@@ -56,7 +56,6 @@ quantities.
 {charge} | charge | atomic system with charges |
 {colloid} | angular velocity | extended spherical particles |
 {dipole} | charge and dipole moment | atomic system with dipoles |
-{dpd} | default values, also communicates velocities | DPD models |
 {ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles |
 {full} | molecular + charge | bio-molecules |
 {granular} | diameter, density, angular velocity | granular models |
@@ -64,7 +63,7 @@ quantities.
 {peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|)
 
 All of the styles define point particles, except the {colloid},
-{dipole}, {ellipsoid}, {granular}, and {peri} styles.  These define
+{dipole}, {ellipsoid}, {granular}, and {peri} styles, which define
 finite-size particles.  For {colloid}, {dipole}, and {ellipsoid}
 systems, the "shape"_shape.html command is used to specify the size
 and shape of particles on a per-type basis, which is spherical for
@@ -81,13 +80,6 @@ the specified diameter and density are used to calculate each
 particle's mass.  For {peri} systems, the speficied volume and density
 are used to calculate each particle's mass.
 
-Only the {colloid}, {dpd}, and {granular} styles communicate
-velocities and angular velocities (if defined) with ghost atoms; the
-others do not.  This is because the pairwise interactions calculated
-by the pair styles that typically use these atom styles
-(e.g. "pair_style dpd"_pair_dpd.html and "pair_style
-granular"_pair_gran.html) require velocities of both particles.
-
 :line
 
 Typically, simulations require only a single (non-hybrid) atom style.
@@ -99,10 +91,10 @@ If some atoms have bonds, but others do not, use the {bond} style.
 
 The only scenario where the {hybrid} style is needed is if there is no
 single style which defines all needed properties of all atoms.  For
-example, if you want charged DPD particles, you would need to use
-"atom_style hybrid dpd charge".  When a hybrid style is used, atoms
-store and communicate the union of all quantities implied by the
-individual styles.
+example, if you want colloidal particles with charge, you would need
+to use "atom_style hybrid colloid charge".  When a hybrid style is
+used, atoms store and communicate the union of all quantities implied
+by the individual styles.
 
 LAMMPS can be extended with new atom styles; see "this
 section"_Section_modify.html.
@@ -114,13 +106,12 @@ This command cannot be used after the simulation box is defined by a
 
 The {angle}, {bond}, {full}, and {molecular} styles are part of the
 "molecular" package.  The {granular} style is part of the "granular"
-package.  The {dpd} style is part of the "dpd" package.  The {colloid}
-style is part of the "colloid" package.  The {dipole} style is part of
-the "dipole" package.  The {ellipsoid} style is part of the "asphere"
-package.  The {peri} style is part of the "peri" package for
-Peridynamics.  They are only enabled if LAMMPS was built with that
-package.  See the "Making LAMMPS"_Section_start.html#2_3 section for
-more info.
+package.  The {colloid} style is part of the "colloid" package.  The
+{dipole} style is part of the "dipole" package.  The {ellipsoid} style
+is part of the "asphere" package.  The {peri} style is part of the
+"peri" package for Peridynamics.  They are only enabled if LAMMPS was
+built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/communicate.html b/doc/communicate.html
index 8914e83247..3d691b24f5 100644
--- a/doc/communicate.html
+++ b/doc/communicate.html
@@ -19,10 +19,11 @@
 
 <LI>zero or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>group</I> or <I>cutoff</I> 
+<LI>keyword = <I>cutoff</I> or <I>group</I> or <I>vel</I> 
 
-<PRE>  <I>group</I> value = group-ID = only communicate atoms in the group
-  <I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away 
+<PRE>  <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>
@@ -30,7 +31,8 @@
 </P>
 <PRE>communicate multi
 communicate multi group solvent
-communicate single cutoff 5.0 
+communicate single ghost yes
+communicate single cutoff 5.0 ghost yes 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -52,13 +54,6 @@ communicated.  See the <A HREF = "neighbor.html">neighbor multi</A> command for
 neighbor list construction option that may also be beneficial for
 simulations of this kind.
 </P>
-<P>The <I>group</I> option 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>cutoff</I> option 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
@@ -98,6 +93,22 @@ 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>The <I>group</I> option 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> option 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><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
@@ -106,8 +117,8 @@ find the needed atoms.
 </P>
 <P><B>Default:</B>
 </P>
-<P>The default settings are style = single, group = all, cutoff = 0.0.
-The cutoff default of 0.0 means that effectively ghost cutoff =
+<P>The default settings are style = single, group = all, cutoff = 0.0,
+ghost = no.  The cutoff default of 0.0 means that ghost cutoff =
 neighbor cutoff = pairwise force cutoff + neighbor skin.
 </P>
 </HTML>
diff --git a/doc/communicate.txt b/doc/communicate.txt
index 5fb23aa91d..51169fe99d 100644
--- a/doc/communicate.txt
+++ b/doc/communicate.txt
@@ -14,16 +14,18 @@ communicate style keyword value ... :pre
 
 style = {single} or {multi} :ulb,l
 zero or more keyword/value pairs may be appended :l
-keyword = {group} or {cutoff} :l
+keyword = {cutoff} or {group} or {vel} :l
+  {cutoff} value = Rcut (distance units) = communicate atoms from this far away
   {group} value = group-ID = only communicate atoms in the group
-  {cutoff} value = Rcut (distance units) = communicate atoms from this far away :pre
+  {vel} value = {yes} or {no} = do or do not communicate velocity info with ghost atoms :pre
 :ule
 
 [Examples:]
 
 communicate multi
 communicate multi group solvent
-communicate single cutoff 5.0 :pre
+communicate single ghost yes
+communicate single cutoff 5.0 ghost yes :pre
 
 [Description:]
 
@@ -45,13 +47,6 @@ communicated.  See the "neighbor multi"_neighbor.html command for a
 neighbor list construction option that may also be beneficial for
 simulations of this kind.
 
-The {group} option 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
-"atom_modify first"_atom_modify.html command.
-
 The {cutoff} option 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
@@ -91,6 +86,22 @@ 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.
 
+The {group} option 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
+"atom_modify first"_atom_modify.html command.
+
+The {vel} option enables velocity information to be communicated with
+ghost particles.  Depending on the "atom_style"_atom_style.html,
+velocity info includes the translational velocity, angular velocity,
+and angular momentum of a particle.  If the {vel} option is set to
+{yes}, then ghost atoms store these quantities; if {no} then they do
+not.  The {yes} 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.
+
 [Restrictions:] none
 
 [Related commands:]
@@ -99,6 +110,6 @@ find the needed atoms.
 
 [Default:]
 
-The default settings are style = single, group = all, cutoff = 0.0.
-The cutoff default of 0.0 means that effectively ghost cutoff =
+The default settings are style = single, group = all, cutoff = 0.0,
+ghost = no.  The cutoff default of 0.0 means that ghost cutoff =
 neighbor cutoff = pairwise force cutoff + neighbor skin.
diff --git a/doc/read_data.html b/doc/read_data.html
index e5859f2769..69c5600518 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -272,7 +272,6 @@ of analysis.
 <TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
 <TR><TD >colloid</TD><TD > atom-ID atom-type 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 >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
 <TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
 <TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
 <TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
diff --git a/doc/read_data.txt b/doc/read_data.txt
index f7fd07ea6d..47d9085f65 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -252,7 +252,6 @@ bond: atom-ID molecule-ID atom-type x y z
 charge: atom-ID atom-type q x y z
 colloid: atom-ID atom-type x y z
 dipole: atom-ID atom-type q x y z mux muy muz
-dpd: atom-ID atom-type x y z
 ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
 full: atom-ID molecule-ID atom-type q x y z
 granular: atom-ID atom-type diameter density x y z