From dec203161aadcab6b97d837c7c78d34d541e5a56 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 17 Mar 2009 15:41:12 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2657
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/group.html        | 26 +++++++++++++++++++-------
 doc/group.txt         | 24 ++++++++++++++++++------
 doc/neigh_modify.html |  5 ++---
 doc/neigh_modify.txt  |  2 +-
 doc/thermo_style.html |  4 +++-
 doc/thermo_style.txt  |  4 +++-
 doc/variable.html     |  4 ++--
 doc/variable.txt      |  4 ++--
 8 files changed, 50 insertions(+), 23 deletions(-)

diff --git a/doc/group.html b/doc/group.html
index bfa1a1bfa3..8c6d43189a 100644
--- a/doc/group.html
+++ b/doc/group.html
@@ -17,9 +17,10 @@
 </PRE>
 <UL><LI>ID = user-defined name of the group 
 
-<LI>style = <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>subtract</I> or         <I>union</I> or <I>intersect</I> 
+<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>subtract</I> or         <I>union</I> or <I>intersect</I> 
 
-<PRE>  <I>region</I> args = region-ID
+<PRE>  <I>delete</I> = no args
+  <I>region</I> args = region-ID
   <I>type</I> or <I>id</I> or <I>molecule</I>
     args = one or more atom types, atom IDs, or molecule IDs
     args = logical value
@@ -43,17 +44,27 @@ group sub id <= 150
 group polyA molecule <> 50 250
 group boundary subtract all a2 a3
 group boundary union lower upper
-group boundary intersect upper flow 
+group boundary intersect upper flow
+group boundary delete 
 </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 fix, velocity, dump, or
-temperature to act on the atoms together.
+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>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>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
@@ -85,11 +96,12 @@ as arguments.  Atoms that belong to every one of the listed groups are
 added to the specified group.
 </P>
 <P>A group with the ID <I>all</I> is predefined.  All atoms belong to this
-group.
+group.  This group cannot be deleted.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>There can be no more than 32 defined groups, including "all".
+<P>There can be no more than 32 groups defined at one time, including
+"all".
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/group.txt b/doc/group.txt
index a17ca4a2fb..9e7dcab6cc 100644
--- a/doc/group.txt
+++ b/doc/group.txt
@@ -13,8 +13,9 @@ group command :h3
 group ID style args :pre
 
 ID = user-defined name of the group :ulb,l
-style = {region} or {type} or {id} or {molecule} or {subtract} or \
+style = {delete} or {region} or {type} or {id} or {molecule} or {subtract} or \
         {union} or {intersect} :l
+  {delete} = no args
   {region} args = region-ID
   {type} or {id} or {molecule}
     args = one or more atom types, atom IDs, or molecule IDs
@@ -38,17 +39,27 @@ group sub id <= 150
 group polyA molecule <> 50 250
 group boundary subtract all a2 a3
 group boundary union lower upper
-group boundary intersect upper flow :pre
+group boundary intersect upper flow
+group boundary delete :pre
 
 [Description:]
 
 Identify a collection of atoms as belonging to a group.  The group ID
-can then be used in other commands such as fix, velocity, dump, or
-temperature to act on the atoms together.
+can then be used in other commands such as "fix"_fix.html,
+"compute"_compute.html, "dump"_dump.html, or "velocity"_velocity.html
+to act on those atoms together.
 
 If the group ID already exists, the group command adds the specified
 atoms to the group.
 
+The {delete} 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
+{delete} 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 "fix"_fix.html or "compute"_compute.html
+or "dump"_dump.html.
+
 The {region} 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
@@ -80,11 +91,12 @@ as arguments.  Atoms that belong to every one of the listed groups are
 added to the specified group.
 
 A group with the ID {all} is predefined.  All atoms belong to this
-group.
+group.  This group cannot be deleted.
 
 [Restrictions:]
 
-There can be no more than 32 defined groups, including "all".
+There can be no more than 32 groups defined at one time, including
+"all".
 
 [Related commands:]
 
diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html
index ecf6a0312d..a59e2e4e0c 100644
--- a/doc/neigh_modify.html
+++ b/doc/neigh_modify.html
@@ -42,9 +42,8 @@
   <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 
-</PRE>
-<PRE>  <I>binsize</I> value = size
+    N = max number of neighbors of one atom
+  <I>binsize</I> value = size
     size = bin size for neighbor list construction (distance units) 
 </PRE>
 
diff --git a/doc/neigh_modify.txt b/doc/neigh_modify.txt
index 6fa5ca012a..3fff0f65c4 100644
--- a/doc/neigh_modify.txt
+++ b/doc/neigh_modify.txt
@@ -38,7 +38,7 @@ keyword = {delay} or {every} or {check} or {once} or {include} or {exclude} or {
   {page} value = N
     N = number of pairs stored in a single neighbor page
   {one} value = N
-    N = max number of neighbors of one atom :pre
+    N = max number of neighbors of one atom
   {binsize} value = size
     size = bin size for neighbor list construction (distance units) :pre
 :ule
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 684550e1a8..2c29dc3fa5 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -27,7 +27,8 @@
                           evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                           emol, elong, etail,
                           vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-			  pxx, pyy, pzz, pxy, pxz, pyz
+			  xy, xz, yz,
+			  pxx, pyy, pzz, pxy, pxz, pyz,
 			  c_ID, c_ID[n], f_ID, f_ID[n], v_name
       step = timestep
       atoms = # of atoms
@@ -51,6 +52,7 @@
       vol = volume
       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
       pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
       c_ID = global scalar value calculated by a compute with ID
       c_ID[N] = Nth component of global vector calculated by a compute with ID
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index 54dc3fad7d..cc14b1ae11 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -22,7 +22,8 @@ args = list of arguments for a particular style :l
                           evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                           emol, elong, etail,
                           vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-			  pxx, pyy, pzz, pxy, pxz, pyz
+			  xy, xz, yz,
+			  pxx, pyy, pzz, pxy, pxz, pyz,
 			  c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
       step = timestep
       atoms = # of atoms
@@ -46,6 +47,7 @@ args = list of arguments for a particular style :l
       vol = volume
       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
       pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
       c_ID = global scalar value calculated by a compute with ID
       c_ID\[N\] = Nth component of global vector calculated by a compute with ID
diff --git a/doc/variable.html b/doc/variable.html
index 3edaed46dd..f8cdcb104e 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -118,7 +118,7 @@ for example, in a loop.
 <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> option does
+re-defined in a subsequent variable command.  The <I>delete</I> style does
 the same thing.
 </P>
 <HR>
@@ -138,7 +138,7 @@ 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> option also removes the variable, the same as if
+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>
diff --git a/doc/variable.txt b/doc/variable.txt
index c41d9f2d21..e769b9638d 100644
--- a/doc/variable.txt
+++ b/doc/variable.txt
@@ -112,7 +112,7 @@ for example, in a loop.
 Second, as described below, if a variable is iterated on to the end of
 its list of strings via the "next"_next.html command, it is removed
 from the list of active variables, and is thus available to be
-re-defined in a subsequent variable command.  The {delete} option does
+re-defined in a subsequent variable command.  The {delete} style does
 the same thing.
 
 :line
@@ -132,7 +132,7 @@ skipped.  This enables the construction of simple loops in the input
 script that are iterated over and then exited from.
 
 As explained above, an exhausted variable can be re-used in an input
-script.  The {delete} option also removes the variable, the same as if
+script.  The {delete} 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 "if"_if.html and "jump"_jump.html