Commit 9897ee73 authored by sjplimp's avatar sjplimp
Browse files

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2089 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 1bb9bf1e
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@@ -19,9 +19,10 @@

<LI>zero or more keyword/value pairs may be appended 

<LI>keyword = <I>group</I> 
<LI>keyword = <I>group</I> or <I>cutoff</I> 

<PRE>  <I>group</I> value = group-ID = only communicate atoms in the group
  <I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away 
</PRE>

</UL>
@@ -29,6 +30,7 @@
</P>
<PRE>communicate multi
communicate multi group solvent
communicate single cutoff 5.0 
</PRE>
<P><B>Description:</B>
</P>
@@ -57,6 +59,45 @@ specified group) will still migrate to new processors as they move.
The group specified with this option must also be specified via the
<A HREF = "atom_modify.html">atom_modify first</A> command.
</P>
<P>The <I>cutoff</I> option allows you to set a ghost cutoff distance which is
the distance from the borders of a processor's sub-domain at which
ghost atoms are acquired from other processors.  By default the ghost
cutoff = the neighbor cutoff = the pairwise force cutoff + the
neighbor skin.  See the <A HREF = "neighbor.html">neighbor</A> command for more
information about the skin distance.  If the specified Rcut is greater
than the neighbor cutoff, then extra ghost atoms will be acquired.  If
it is smaller, the ghost cutoff is set to the neighbor cutoff.
</P>
<P>These are simulation scenarios in which it may be useful to set a
ghost cutoff > neighbor cutoff:
</P>
<UL><LI>a single polymer chain with bond interactions, but no pairwise interactions
<LI>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
<LI>ghost atoms beyond the pairwise cutoff are needed for some computation 
</UL>
<P>In the first scenario, a pairwise potential may not be defined.  Thus
the pairwise neighbor cutoff will be 0.0.  But ghost atoms are still
needed for computing bond, angle, etc interactions between atoms on
different processors.  The appropriate ghost cutoff depends on the
<A HREF = "newton.html">newton bond</A> setting.  For newton bond <I>off</I>, the
distance needs to be the furthest distance between any two atoms in
the bond, angle, etc.  E.g. the distance between 1-4 atoms in a
dihedral.  For newton bond <I>on</I>, the distance between the central atom
in the bond, angle, etc and any other atom is sufficient.  E.g. the
distance between 2-4 atoms in a dihedral.
</P>
<P>In the second scenario, a pairwise potential is defined, but its
neighbor cutoff is not sufficiently long enough to enable bond, angle,
etc terms to be computed.  As in the previous scenario, an appropriate
ghost cutoff should be set.
</P>
<P>In the last scenario, a <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> or
<A HREF = "pair_style.html">pairwise potential</A> needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential).  Setting the ghost cutoff appropriately can insure it will
find the needed atoms.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@@ -65,6 +106,6 @@ The group specified with this option must also be specified via the
</P>
<P><B>Default:</B>
</P>
<P>The default settings are style = single and group = all.
<P>The default settings are style = single, group = all, cutoff = 0.0.
</P>
</HTML>
+45 −4
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@@ -14,14 +14,16 @@ communicate style keyword value ... :pre

style = {single} or {multi} :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {group} :l
  {group} value = group-ID = only communicate atoms in the group :pre
keyword = {group} or {cutoff} :l
  {group} value = group-ID = only communicate atoms in the group
  {cutoff} value = Rcut (distance units) = communicate atoms from this far away :pre
:ule

[Examples:]

communicate multi
communicate multi group solvent :pre
communicate multi group solvent
communicate single cutoff 5.0 :pre

[Description:]

@@ -50,6 +52,45 @@ 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"_atom_modify.html command.

The {cutoff} option allows you to set a ghost cutoff distance which is
the distance from the borders of a processor's sub-domain at which
ghost atoms are acquired from other processors.  By default the ghost
cutoff = the neighbor cutoff = the pairwise force cutoff + the
neighbor skin.  See the "neighbor"_neighbor.html command for more
information about the skin distance.  If the specified Rcut is greater
than the neighbor cutoff, then extra ghost atoms will be acquired.  If
it is smaller, the ghost cutoff is set to the neighbor cutoff.

These are simulation scenarios in which it may be useful to set a
ghost cutoff > neighbor cutoff:

a single polymer chain with bond interactions, but no pairwise interactions
bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
ghost atoms beyond the pairwise cutoff are needed for some computation :ul

In the first scenario, a pairwise potential may not be defined.  Thus
the pairwise neighbor cutoff will be 0.0.  But ghost atoms are still
needed for computing bond, angle, etc interactions between atoms on
different processors.  The appropriate ghost cutoff depends on the
"newton bond"_newton.html setting.  For newton bond {off}, the
distance needs to be the furthest distance between any two atoms in
the bond, angle, etc.  E.g. the distance between 1-4 atoms in a
dihedral.  For newton bond {on}, the distance between the central atom
in the bond, angle, etc and any other atom is sufficient.  E.g. the
distance between 2-4 atoms in a dihedral.

In the second scenario, a pairwise potential is defined, but its
neighbor cutoff is not sufficiently long enough to enable bond, angle,
etc terms to be computed.  As in the previous scenario, an appropriate
ghost cutoff should be set.

In the last scenario, a "fix"_fix.html or "compute"_compute.html or
"pairwise potential"_pair_style.html needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential).  Setting the ghost cutoff appropriately can insure it will
find the needed atoms.

[Restrictions:] none

[Related commands:]
@@ -58,4 +99,4 @@ The group specified with this option must also be specified via the

[Default:]

The default settings are style = single and group = all.
The default settings are style = single, group = all, cutoff = 0.0.
+5 −1
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@@ -71,7 +71,11 @@ would foul up the bond connectivity that has already been assigned.
<P>The <I>overlap</I> styles requires inter-processor communication to acquire
ghost atoms and build a neighbor list.  This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc).
fields setup, atom masses set, etc).  Since a neighbor list is used to
find overlapping atom pairs, it also means that you must define a
<A HREF = "pair_style.html">pair style</A> with force cutoffs greater than or equal
to the desired overlap cutoff between pairs of relevant atom types,
even though the pair potential will not be evaluated.
</P>
<P>If the <A HREF = "special_bonds.html">special_bonds</A> command is used with a
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
+5 −1
Original line number Diff line number Diff line
@@ -66,7 +66,11 @@ would foul up the bond connectivity that has already been assigned.
The {overlap} styles requires inter-processor communication to acquire
ghost atoms and build a neighbor list.  This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc).
fields setup, atom masses set, etc).  Since a neighbor list is used to
find overlapping atom pairs, it also means that you must define a
"pair style"_pair_style.html with force cutoffs greater than or equal
to the desired overlap cutoff between pairs of relevant atom types,
even though the pair potential will not be evaluated.

If the "special_bonds"_special_bonds.html command is used with a
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
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@@ -56,9 +56,10 @@ neigh_modify exclude molecule rigid
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets parameters that affect the pairwise neighbor list.
<P>This command sets parameters that affect the building and use of
pairwise neighbor lists.
</P>
<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often the list is
<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often lists are
built as a simulation runs.  The <I>delay</I> setting means never build a
new list until at least N steps after the previous build.  The <I>every</I>
setting means build the list every M steps (after the delay has
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