git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9535 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/delete_bonds.html

@@ -51,13 +51,16 @@ off via the <A HREF = "neigh_modify.html">neigh_modify exclude</A> command.  The
 <A HREF = "fix_shake.html">fix shake</A> command also effectively turns off certain
 bond and angle interactions.
 </P>
-<P>For all styles, an interaction is only turned off (or on) if all the
+<P>For all styles, by default, an interaction is only turned off (or on)
-atoms involved are in the specified group.  For style <I>multi</I> this is
+if all the atoms involved are in the specified group.  See the <I>any</I>
-the only criterion applied - all types of bonds, angles, dihedrals,
+keyword to change the behavior.
-impropers in the group turned off.
 </P>
-<P>For style <I>atom</I>, one or more of the atoms involved must also be of
+<P>For style <I>multi</I> all bond, angle, dihedral, and improper interactions
-the specified type.
+of any type, involving atoms in the group, are turned off.
+</P>
+<P>Style <I>atom</I> is the same as style <I>multi</I> except that in addition, one
+or more of the atoms involved in the bond, angle, dihedral, or
+improper interaction must also be of the specified atom type.
 </P>
 <P>For style <I>bond</I>, only bonds are candidates for turn-off, and the bond
 must also be of the specified type.  Styles <I>angle</I>, <I>dihedral</I>, and
@@ -84,13 +87,13 @@ force and energy calculations.  This means that pairwise computations
 will proceed as if the bond (or angle, etc) were still turned on.
 </P>
 <P>Several keywords can be appended to the argument list to alter the
-default behavior.
+default behaviors.
 </P>
 <P>The <I>any</I> keyword changes the requirement that all atoms in the bond
 (angle, etc) must be in the specified group in order to turn-off the
-interaction.  If any of the atoms in the interaction are in the
+interaction.  Instead, if any of the atoms in the interaction are in
-specified group, it will be turned off (or on if the <I>undo</I> keyword is
+the specified group, it will be turned off (or on if the <I>undo</I>
-used).
+keyword is used).
 </P>
 <P>The <I>undo</I> keyword inverts the delete_bonds command so that the
 specified bonds, angles, etc are turned on if they are currently

doc/delete_bonds.txt

@@ -43,13 +43,16 @@ off via the "neigh_modify exclude"_neigh_modify.html command.  The
 "fix shake"_fix_shake.html command also effectively turns off certain
 bond and angle interactions.
 
-For all styles, an interaction is only turned off (or on) if all the
+For all styles, by default, an interaction is only turned off (or on)
-atoms involved are in the specified group.  For style {multi} this is
+if all the atoms involved are in the specified group.  See the {any}
-the only criterion applied - all types of bonds, angles, dihedrals,
+keyword to change the behavior.
-impropers in the group turned off.
 
-For style {atom}, one or more of the atoms involved must also be of
+For style {multi} all bond, angle, dihedral, and improper interactions
-the specified type.
+of any type, involving atoms in the group, are turned off.
+
+Style {atom} is the same as style {multi} except that in addition, one
+or more of the atoms involved in the bond, angle, dihedral, or
+improper interaction must also be of the specified atom type.
 
 For style {bond}, only bonds are candidates for turn-off, and the bond
 must also be of the specified type.  Styles {angle}, {dihedral}, and
@@ -76,13 +79,13 @@ force and energy calculations.  This means that pairwise computations
 will proceed as if the bond (or angle, etc) were still turned on.
 
 Several keywords can be appended to the argument list to alter the
-default behavior.
+default behaviors.
 
 The {any} keyword changes the requirement that all atoms in the bond
 (angle, etc) must be in the specified group in order to turn-off the
-interaction.  If any of the atoms in the interaction are in the
+interaction.  Instead, if any of the atoms in the interaction are in
-specified group, it will be turned off (or on if the {undo} keyword is
+the specified group, it will be turned off (or on if the {undo}
-used).
+keyword is used).
 
 The {undo} keyword inverts the delete_bonds command so that the
 specified bonds, angles, etc are turned on if they are currently

doc/fix_rigid.html

@@ -135,13 +135,17 @@ numbers of rigid bodies are simulated.
 number of small rigid bodies.  Each body is assigned to the atom
 closest to the geometrical center of the body.  The fix operates using
 local lists of rigid bodies owned by each processor and information is
-summed and exchanged via local communication between neighboring
+exchanged and summed via local communication between neighboring
-processors when ghost atom info is accumlated.  This means that the
+processors when ghost atom info is accumlated.
-ghost atom cutoff be large enough to cover the distance between the
+</P>
-atom that owns the body and every other atom in the body.  If the
+<P>IMPORTANT NOTE: To use <I>rigid/small</I> the ghost atom cutoff must be
-<A HREF = "pair_style.html">pair_style</A> cutoff is not of sufficient extent to
+large enough to span the distance between the atom that owns the body
-insure this, then the <A HREF = "communicate.html">communicate cutoff</A> command
+and every other atom in the body.  This distance value is printed out
-can be used.
+when the rigid bodies are defined.  If the
+<A HREF = "pair_style.html">pair_style</A> cutoff plus neighbor skin does not span
+this distance, then you should use the <A HREF = "communicate.html">communicate
+cutoff</A> command with a setting epsilon larger than
+the distance.
 </P>
 <P>Which of the two variants is faster for a particular problem is hard
 to predict.  The best way to decide is to perform a short test run.

doc/fix_rigid.txt

@@ -121,13 +121,17 @@ The {rigid/small} variant is typically best for a system with a large
 number of small rigid bodies.  Each body is assigned to the atom
 closest to the geometrical center of the body.  The fix operates using
 local lists of rigid bodies owned by each processor and information is
-summed and exchanged via local communication between neighboring
+exchanged and summed via local communication between neighboring
-processors when ghost atom info is accumlated.  This means that the
+processors when ghost atom info is accumlated.
-ghost atom cutoff be large enough to cover the distance between the
+
-atom that owns the body and every other atom in the body.  If the
+IMPORTANT NOTE: To use {rigid/small} the ghost atom cutoff must be
-"pair_style"_pair_style.html cutoff is not of sufficient extent to
+large enough to span the distance between the atom that owns the body
-insure this, then the "communicate cutoff"_communicate.html command
+and every other atom in the body.  This distance value is printed out
-can be used.
+when the rigid bodies are defined.  If the
+"pair_style"_pair_style.html cutoff plus neighbor skin does not span
+this distance, then you should use the "communicate
+cutoff"_communicate.html command with a setting epsilon larger than
+the distance.
 
 Which of the two variants is faster for a particular problem is hard
 to predict.  The best way to decide is to perform a short test run.