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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12158 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-06-27 23:41:00 +00:00
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29
doc/group.html
View File

@ -20,6 +20,7 @@
<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>variable</I> or <I>subtract</I> or <I>union</I> or <I>intersect</I> or <I>dynamic</I> or <I>static</I>
<PRE> <I>delete</I> = no args
<I>clear</I> = no args
<I>region</I> args = region-ID
<I>type</I> or <I>id</I> or <I>molecule</I>
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 <I>style</I>)
<I>variable</I> args = variable-name
<I>include</I> args = molecule
molecule = add atoms to group with same molecule ID as atoms already in group
<I>subtract</I> args = two or more group IDs
<I>union</I> args = one or more group IDs
<I>intersect</I> 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 <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A>
or <A HREF = "dump.html">dump</A>.
</P>
<P>The <I>clear</I> 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 <A HREF = "run.html">run every</A> 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.
</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
@ -164,6 +174,25 @@ them to the screen. See the "Variable Accuracy" section of the
<A HREF = "variable.html">variable</A> doc page for more details on insuring that
variables are current when they are evaluated between runs.
</P>
<P>The <I>include</I> style with its arg <I>molecule</I> 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 <I>region</I> 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 <I>include molecule</I>
will add those atoms that are outside the region to the group.
</P>
<P>IMPORTANT NOTE: The <I>include molecule</I> 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.
</P>
<P>The <I>subtract</I> 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.

29
doc/group.txt
View File

@ -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.