From 48cb4ac2af9e35bc0ce2c281b4db8c73103e0949 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 4 Aug 2010 15:10:06 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4434
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/special_bonds.html | 25 ++++++++++++++++++++-----
 doc/special_bonds.txt  | 25 ++++++++++++++++++++-----
 2 files changed, 40 insertions(+), 10 deletions(-)

diff --git a/doc/special_bonds.html b/doc/special_bonds.html
index 73026d8d36..b8b4a6ad37 100644
--- a/doc/special_bonds.html
+++ b/doc/special_bonds.html
@@ -17,7 +17,7 @@
 </PRE>
 <UL><LI>one or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>dihedral</I> or <I>extra</I> 
+<LI>keyword = <I>amber</I> or <I>charmm</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
@@ -28,6 +28,7 @@
     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 
@@ -39,7 +40,7 @@
 <PRE>special_bonds amber
 special_bonds charmm
 special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
+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>
@@ -69,8 +70,8 @@ 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>dihedral</I> keyword is
-set to <I>yes</I> (see below), or (b) if the
+<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
@@ -101,6 +102,20 @@ 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.  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, 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
@@ -132,6 +147,6 @@ you do not do this, you may get an error when bonds are added.
 <P><B>Default:</B>
 </P>
 <P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
-dihedral = no, and extra = 0.
+angle = no, dihedral = no, and extra = 0.
 </P>
 </HTML>
diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt
index 7d33897e16..3eedd32bc8 100644
--- a/doc/special_bonds.txt
+++ b/doc/special_bonds.txt
@@ -13,7 +13,7 @@ special_bonds command :h3
 special_bonds keyword values ... :pre
 
 one or more keyword/value pairs may be appended :ulb,l
-keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihedral} or {extra} :l
+keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
   {amber} values = none
   {charmm} values = none
   {fene} values = none
@@ -23,6 +23,7 @@ keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihed
     w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
   {coul} values = w1,w2,w3
     w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
+  {angle} value = {yes} or {no}
   {dihedral} value = {yes} or {no}
   {extra} value = N
     N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
@@ -33,7 +34,7 @@ Examples:
 special_bonds amber
 special_bonds charmm
 special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
+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
 
@@ -63,8 +64,8 @@ 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.
 
-The two exceptions to this rule are (a) if the {dihedral} keyword is
-set to {yes} (see below), or (b) if the
+The two exceptions to this rule are (a) if the {angle} or {dihedral}
+keywords are set to {yes} (see below), or (b) if the
 "delete_bonds"_delete_bonds.html command is used with the {special}
 option that recomputes the 1-2,1-3,1-4 topologies after bonds are
 deleted; see the "delete_bonds"_delete_bonds.html command for more
@@ -95,6 +96,20 @@ 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.
 
+The {angle} 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.  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, 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 {angle} keyword is
+specified as {yes}, then the pairwise interaction between atoms 2 and
+4 will be unaffected (full weighting of 1.0).  If the {angle} keyword
+is specified as {no} which is the default, then the 2,4 interaction
+will also be weighted by 0.5.
+
 The {dihedral} 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
@@ -126,4 +141,4 @@ you do not do this, you may get an error when bonds are added.
 [Default:]
 
 All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
-dihedral = no, and extra = 0.
+angle = no, dihedral = no, and extra = 0.