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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1516 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2008-02-15 19:09:18 +00:00
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33
doc/atom_modify.html
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@ -17,15 +17,17 @@
</PRE>
<UL><LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>map</I>
<LI>keyword = <I>map</I> or <I>first</I>
<PRE> <I>map</I> value = <I>array</I> or <I>hash</I>
<PRE> <I>map</I> value = <I>array</I> or <I>hash</I>
<I>first</I> value = group-ID = group whose atoms will appear first in internal atom lists
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>atom_modify map hash
<PRE>atom_modify map hash
atom_modify first colloid
</PRE>
<P><B>Description:</B>
</P>
@ -43,6 +45,26 @@ slightly slower than the <I>array</I> method, but its memory cost is
proportional to N/P on each processor, where P is the total number of
processors running the simulation.
</P>
<P>The <I>first</I> keyword allows a <A HREF = "group.html">group</A> to be specified whose
atoms will be maintained as the first atoms in each processor's list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The <A HREF = "neigh_modify.html">neigh_modify
include</A> and <A HREF = "communicate.html">communicate group</A>
commands are two examples of commands that require this setting to
work efficiently. Several <A HREF = "fix.html">fixes</A>, most notably time
integration fixes like <A HREF = "fix_nve.html">fix nve</A>, also take advantage of
this setting if the group they operate on is the group specified by
this command.
</P>
<P>Note that because the atom_modify command must be used in an input
script before a simulation is setup and groups are defined, this means
the <I>first</I> keyword will specify a group that is not yet defined.
This is OK; LAMMPS will check that the group exists before the first
simulation is performed.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command must be used before the simulation box is defined by a
@ -52,7 +74,8 @@ processors running the simulation.
</P>
<P><B>Default:</B>
</P>
<P>By default, atomic (non-molecular) problems do not allocate maps.
For molecular problems, the option default is map = array.
<P>By default, atomic (non-molecular) problems do not allocate maps. For
molecular problems, the option default is map = array. By default,
first = all.
</P>
</HTML>

33
doc/atom_modify.txt
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@ -13,13 +13,15 @@ atom_modify command :h3
atom_modify keyword value ... :pre
one or more keyword/value pairs may be appended :ulb,l
keyword = {map} :l
{map} value = {array} or {hash} :pre
keyword = {map} or {first} :l
{map} value = {array} or {hash}
{first} value = group-ID = group whose atoms will appear first in internal atom lists :pre
:ule
[Examples:]
atom_modify map hash :pre
atom_modify map hash
atom_modify first colloid :pre
[Description:]
@ -37,6 +39,26 @@ slightly slower than the {array} method, but its memory cost is
proportional to N/P on each processor, where P is the total number of
processors running the simulation.
The {first} keyword allows a "group"_group.html to be specified whose
atoms will be maintained as the first atoms in each processor's list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The "neigh_modify
include"_neigh_modify.html and "communicate group"_communicate.html
commands are two examples of commands that require this setting to
work efficiently. Several "fixes"_fix.html, most notably time
integration fixes like "fix nve"_fix_nve.html, also take advantage of
this setting if the group they operate on is the group specified by
this command.
Note that because the atom_modify command must be used in an input
script before a simulation is setup and groups are defined, this means
the {first} keyword will specify a group that is not yet defined.
This is OK; LAMMPS will check that the group exists before the first
simulation is performed.
[Restrictions:]
This command must be used before the simulation box is defined by a
@ -46,5 +68,6 @@ This command must be used before the simulation box is defined by a
[Default:]
By default, atomic (non-molecular) problems do not allocate maps.
For molecular problems, the option default is map = array.
By default, atomic (non-molecular) problems do not allocate maps. For
molecular problems, the option default is map = array. By default,
first = all.

11
doc/communicate.html
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@ -34,7 +34,8 @@ communicate multi group solvent
</P>
<P>This command sets the style of inter-processor communication that
occurs each timestep as atom coordinates and other properties are
exchanged between neighboring processors.
exchanged between neighboring processors and stored as properties of
ghost atoms.
</P>
<P>The default style is <I>single</I> which means each processor acquires
information for ghost atoms that are within a single distance from its
@ -50,9 +51,11 @@ neighbor list construction option that may also be beneficial for
simulations of this kind.
</P>
<P>The <I>group</I> option will limit communication to atoms in the specified
group. This can be useful for certain models where no ghost copies
are needed for some kinds of particles. The particles not in the
specified group will still migrate to new processors as they move.
group. This can be useful for models where no ghost atoms are needed
for some kinds of particles. All atoms (not just those in the
specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
"atom_modify first" command.
</P>
<P><B>Restrictions:</B> none
</P>

11
doc/communicate.txt
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@ -27,7 +27,8 @@ communicate multi group solvent :pre
This command sets the style of inter-processor communication that
occurs each timestep as atom coordinates and other properties are
exchanged between neighboring processors.
exchanged between neighboring processors and stored as properties of
ghost atoms.
The default style is {single} which means each processor acquires
information for ghost atoms that are within a single distance from its
@ -43,9 +44,11 @@ neighbor list construction option that may also be beneficial for
simulations of this kind.
The {group} option will limit communication to atoms in the specified
group. This can be useful for certain models where no ghost copies
are needed for some kinds of particles. The particles not in the
specified group will still migrate to new processors as they move.
group. This can be useful for models where no ghost atoms are needed
for some kinds of particles. All atoms (not just those in the
specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
"atom_modify first" command.
[Restrictions:] none

12
doc/neigh_modify.html
View File

@ -72,6 +72,13 @@ some atom has moved more than half the skin distance (specified in the
command), the <I>every</I> and <I>delay</I> parameters refer to the longest
(outermost) timestep.
</P>
<P>The <I>include</I> option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
other particles or with each other via pairwise interactions. The
group specified with this option must also be specified via the
"atom_modify first" command.
</P>
<P>The <I>exclude</I> option turns off pairwise interactions between certain
pairs of atoms, by not including them in the neighbor list. These are
sample scenarios where this is useful:
@ -88,11 +95,6 @@ to freeze a wall or portion of a bio-molecule.
body can be turned off to save needless computation. See the <A HREF = "fix_rigid.html">fix
rigid</A> command for more details.
</UL>
<P>The <I>include</I> option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful if a large portion
of the simulation is particles that do not interact with the remainder
of the simulation or with each other via pairwise interactions.
</P>
<P>The <I>exclude type</I> option turns off the pairwise interaction if one
atom is of type M and the other of type N. M can equal N. The
<I>exclude group</I> option turns off the interaction if one atom is in the

12
doc/neigh_modify.txt
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@ -66,6 +66,13 @@ When the rRESPA integrator is used (see the "run_style"_run_style.html
command), the {every} and {delay} parameters refer to the longest
(outermost) timestep.
The {include} option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
other particles or with each other via pairwise interactions. The
group specified with this option must also be specified via the
"atom_modify first" command.
The {exclude} option turns off pairwise interactions between certain
pairs of atoms, by not including them in the neighbor list. These are
sample scenarios where this is useful:
@ -82,11 +89,6 @@ When one or more rigid bodies are specified, interactions within each
body can be turned off to save needless computation. See the "fix
rigid"_fix_rigid.html command for more details. :l,ule
The {include} option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful if a large portion
of the simulation is particles that do not interact with the remainder
of the simulation or with each other via pairwise interactions.
The {exclude type} option turns off the pairwise interaction if one
atom is of type M and the other of type N. M can equal N. The
{exclude group} option turns off the interaction if one atom is in the