From 782e51d0895e54ef5a62148c7fb4de6912dca3de Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 6 May 2010 17:32:58 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4093
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/fix_evaporate.html | 62 ++++++++++++++++++++++++++++++++----------
 doc/fix_evaporate.txt  | 55 ++++++++++++++++++++++++++-----------
 2 files changed, 86 insertions(+), 31 deletions(-)

diff --git a/doc/fix_evaporate.html b/doc/fix_evaporate.html
index 210b51fc0a..ff23f194bd 100644
--- a/doc/fix_evaporate.html
+++ b/doc/fix_evaporate.html
@@ -15,29 +15,59 @@
 </P>
 <PRE>fix ID group-ID evaporate N M region-ID seed 
 </PRE>
-<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
-<LI>evaporate = style name of this fix command
-<LI>N = delete atoms every this many timesteps
-<LI>M = number of atoms to delete each time
-<LI>region-ID = ID of region within which to perform deletions
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
+
+<LI>evaporate = style name of this fix command 
+
+<LI>N = delete atoms every this many timesteps 
+
+<LI>M = number of atoms to delete each time 
+
+<LI>region-ID = ID of region within which to perform deletions 
+
 <LI>seed = random number seed to use for choosing atoms to delete 
+
+<LI>zero or more keyword/value pairs may be appended 
+
+<UL><LI>keyword = <I>molecule</I> 
+</UL>
+<PRE>  <I>molecule</I> value = <I>no</I> or <I>yes</I> 
+</PRE>
+
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>fix 1 solvent evaporate 1000 10 surface 49892 
+<PRE>fix 1 solvent evaporate 1000 10 surface 49892
+fix 1 solvent evaporate 1000 10 surface 38277 molecule yes 
 </PRE>
 <P><B>Description:</B>
 </P>
 <P>Remove M atoms from the simulation every N steps.  This can be used,
-for example, to model evaporation of solvent particles (i.e. drying)
-of a system.  Every N steps, the number of atoms in the fix group and
-within the specifed region are counted.  M of these are chosen at
-random and deleted.  If there are less than M eligible particles, then
-all of them are deleted.
+for example, to model evaporation of solvent particles or moleclues
+(i.e. drying) of a system.  Every N steps, the number of atoms in the
+fix group and within the specifed region are counted.  M of these are
+chosen at random and deleted.  If there are less than M eligible
+particles, then all of them are deleted.
 </P>
-<P>Note that you cannot currently delete solvent molecules with this
-command, only individual atoms.  If you delete only one atom in a
-molecule, an error will result.
+<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
+atoms are deleted.  In this case, you should insure you do not delete
+only a portion of a molecule (only some of its atoms), or LAMMPS will
+soon generate an error when it tries to find those atoms.  LAMMPS will
+warn you if any of the atoms eligible for deletion have a non-zero
+molecule ID, but does not check for this at the time of deletion.
+</P>
+<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, then when an atom
+is chosen for deletion, the entire molecule it is part of is deleted.
+The count of deleted atoms is incremented by the number of atoms in
+the molecule.  If the molecule ID of the chosen atom is 0, then it is
+assumed to not be part of a molecule, and just the single atom is
+deleted.
+</P>
+<P>As an example, if you wish to delete 10 water molecules every <I>N</I>
+steps, you should set <I>M</I> to 30.  If only the water's oxygen atoms
+were in the fix group, then two hydrogen atoms would be deleted when
+an oxygen atom is selected for deletion, whether the hydrogens are
+inside the evaporation region or not.
 </P>
 <P>Note that neighbor lists are re-built on timesteps that atoms are
 removed.  Thus you should not remove atoms too frequently or you will
@@ -64,6 +94,8 @@ minimization</A>.
 </P>
 <P><A HREF = "fix_deposit.html">fix deposit</A>
 </P>
-<P><B>Default:</B> none
+<P><B>Default:</B>
+</P>
+<P>The option defaults are molecule = no.
 </P>
 </HTML>
diff --git a/doc/fix_evaporate.txt b/doc/fix_evaporate.txt
index 800c222a13..58d20d50ae 100644
--- a/doc/fix_evaporate.txt
+++ b/doc/fix_evaporate.txt
@@ -12,29 +12,50 @@ fix evaporate command :h3
 
 fix ID group-ID evaporate N M region-ID seed :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-evaporate = style name of this fix command
-N = delete atoms every this many timesteps
-M = number of atoms to delete each time
-region-ID = ID of region within which to perform deletions
-seed = random number seed to use for choosing atoms to delete :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+evaporate = style name of this fix command :l
+N = delete atoms every this many timesteps :l
+M = number of atoms to delete each time :l
+region-ID = ID of region within which to perform deletions :l
+seed = random number seed to use for choosing atoms to delete :l
+zero or more keyword/value pairs may be appended :l
+keyword = {molecule} :ul
+  {molecule} value = {no} or {yes} :pre
+:ule
 
 [Examples:]
 
-fix 1 solvent evaporate 1000 10 surface 49892 :pre
+fix 1 solvent evaporate 1000 10 surface 49892
+fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
 
 [Description:]
 
 Remove M atoms from the simulation every N steps.  This can be used,
-for example, to model evaporation of solvent particles (i.e. drying)
-of a system.  Every N steps, the number of atoms in the fix group and
-within the specifed region are counted.  M of these are chosen at
-random and deleted.  If there are less than M eligible particles, then
-all of them are deleted.
+for example, to model evaporation of solvent particles or moleclues
+(i.e. drying) of a system.  Every N steps, the number of atoms in the
+fix group and within the specifed region are counted.  M of these are
+chosen at random and deleted.  If there are less than M eligible
+particles, then all of them are deleted.
 
-Note that you cannot currently delete solvent molecules with this
-command, only individual atoms.  If you delete only one atom in a
-molecule, an error will result.
+If the setting for the {molecule} keyword is {no}, then only single
+atoms are deleted.  In this case, you should insure you do not delete
+only a portion of a molecule (only some of its atoms), or LAMMPS will
+soon generate an error when it tries to find those atoms.  LAMMPS will
+warn you if any of the atoms eligible for deletion have a non-zero
+molecule ID, but does not check for this at the time of deletion.
+
+If the setting for the {molecule} keyword is {yes}, then when an atom
+is chosen for deletion, the entire molecule it is part of is deleted.
+The count of deleted atoms is incremented by the number of atoms in
+the molecule.  If the molecule ID of the chosen atom is 0, then it is
+assumed to not be part of a molecule, and just the single atom is
+deleted.
+
+As an example, if you wish to delete 10 water molecules every {N}
+steps, you should set {M} to 30.  If only the water's oxygen atoms
+were in the fix group, then two hydrogen atoms would be deleted when
+an oxygen atom is selected for deletion, whether the hydrogens are
+inside the evaporation region or not.
 
 Note that neighbor lists are re-built on timesteps that atoms are
 removed.  Thus you should not remove atoms too frequently or you will
@@ -61,4 +82,6 @@ minimization"_minimize.html.
 
 "fix deposit"_fix_deposit.html
 
-[Default:] none
+[Default:]
+
+The option defaults are molecule = no.