From f939beaf31cb8afac5ef4bb79cccbf95a7166695 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 27 Jun 2014 23:41:00 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12158 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/group.html | 29 +++++++++++++++++++++++++++++ doc/group.txt | 29 +++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/doc/group.html b/doc/group.html index 981539c2ff..c100bd70b1 100644 --- a/doc/group.html +++ b/doc/group.html @@ -20,6 +20,7 @@
  • style = delete or region or type or id or molecule or variable or subtract or union or intersect or dynamic or static 
      delete = no args
+  clear = no args
   region args = region-ID
   type or id or molecule
     args = list of one or more atom types, atom IDs, or molecule IDs
@@ -33,6 +34,8 @@
       logical = "<>"
       value1,value2 = atom types or atom IDs or molecule IDs (depending on style)
   variable args = variable-name
+  include args = molecule
+    molecule = add atoms to group with same molecule ID as atoms already in group
   subtract args = two or more group IDs
   union args = one or more group IDs
   intersect args = two or more group IDs
@@ -56,6 +59,7 @@ group sub id 100:10000:10
 group sub id <= 150
 group polyA molecule <> 50 250
 group hienergy variable eng
+group hienergy include molecule
 group boundary subtract all a2 a3
 group boundary union lower upper
 group boundary intersect upper flow
@@ -92,6 +96,12 @@ so that more can be specified.  You cannot delete a group if it has
 been used to define a current fix or compute
 or dump.
 
    
+
    The clear style un-assigns all atoms that were assigned to that
+group.  This may be dangerous to do during a simulation run,
+e.g. using the run every command if a fix or compute or
+other operation expects the atoms in the group to remain constant, but
+LAMMPS does not check for this.
+
    
 
    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
@@ -164,6 +174,25 @@ them to the screen.  See the "Variable Accuracy" section of the
 variable doc page for more details on insuring that
 variables are current when they are evaluated between runs.
 
    
+
    The include style with its arg molecule adds atoms to a group that
+have the same molecule ID as atoms already in the group.  The molecule
+ID = 0 is ignored in this operation, since it assumed to represent
+atoms that are not part of molecules.  An example of where this
+operation is useful is if the region style has been used previously
+to add atoms to a group that are within a geometric region.  If
+molecules straddle the region boundary, then atoms outside the region
+that are part of molecules with atoms inside the region will not be in
+the group.  Using the group command a 2nd time with include molecule
+will add those atoms that are outside the region to the group.
+
    
+
    IMPORTANT NOTE: The include molecule operation is relatively
+expensive in a parallel sense.  This is because it requires
+communication of relevant molecule IDs between all the processors and
+each processor to loop over its atoms once per processor, to compare
+its atoms to the list of molecule IDs from every other processor.
+Hence it scales as N, rather than N/P as most of the group operations
+do, where N is the number of atoms, and P is the number of processors.
+
    
 
    The subtract style takes a list of two or more existing group names
 as arguments.  All atoms that belong to the 1st group, but not to any
 of the other groups are added to the specified group.
diff --git a/doc/group.txt b/doc/group.txt
index 5e01836375..8d7d0db0db 100644
--- a/doc/group.txt
+++ b/doc/group.txt
@@ -16,6 +16,7 @@ ID = user-defined name of the group :ulb,l
 style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
       {subtract} or {union} or {intersect} or {dynamic} or {static} :l
   {delete} = no args
+  {clear} = no args
   {region} args = region-ID
   {type} or {id} or {molecule}
     args = list of one or more atom types, atom IDs, or molecule IDs
@@ -29,6 +30,8 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
       logical = "<>"
       value1,value2 = atom types or atom IDs or molecule IDs (depending on {style})
   {variable} args = variable-name
+  {include} args = molecule
+    molecule = add atoms to group with same molecule ID as atoms already in group
   {subtract} args = two or more group IDs
   {union} args = one or more group IDs
   {intersect} args = two or more group IDs
@@ -51,6 +54,7 @@ group sub id 100:10000:10
 group sub id <= 150
 group polyA molecule <> 50 250
 group hienergy variable eng
+group hienergy include molecule
 group boundary subtract all a2 a3
 group boundary union lower upper
 group boundary intersect upper flow
@@ -88,6 +92,12 @@ 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 {clear} style un-assigns all atoms that were assigned to that
+group.  This may be dangerous to do during a simulation run,
+e.g. using the "run every"_run.html command if a fix or compute or
+other operation expects the atoms in the group to remain constant, but
+LAMMPS does not check for this.
+
 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
@@ -160,6 +170,25 @@ them to the screen.  See the "Variable Accuracy" section of the
 "variable"_variable.html doc page for more details on insuring that
 variables are current when they are evaluated between runs.
 
+The {include} style with its arg {molecule} adds atoms to a group that
+have the same molecule ID as atoms already in the group.  The molecule
+ID = 0 is ignored in this operation, since it assumed to represent
+atoms that are not part of molecules.  An example of where this
+operation is useful is if the {region} style has been used previously
+to add atoms to a group that are within a geometric region.  If
+molecules straddle the region boundary, then atoms outside the region
+that are part of molecules with atoms inside the region will not be in
+the group.  Using the group command a 2nd time with {include molecule}
+will add those atoms that are outside the region to the group.
+
+IMPORTANT NOTE: The {include molecule} operation is relatively
+expensive in a parallel sense.  This is because it requires
+communication of relevant molecule IDs between all the processors and
+each processor to loop over its atoms once per processor, to compare
+its atoms to the list of molecule IDs from every other processor.
+Hence it scales as N, rather than N/P as most of the group operations
+do, where N is the number of atoms, and P is the number of processors.
+
 The {subtract} style takes a list of two or more existing group names
 as arguments.  All atoms that belong to the 1st group, but not to any
 of the other groups are added to the specified group.