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added molecule option to compute group/group command

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This commit is contained in:
Steve Plimpton
2017-02-10 09:25:32 -07:00
parent 02b0e6cc55
commit 0068ef5616
16 changed files with 295 additions and 15 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="26 Jan 2017 version">
<META NAME="docnumber" CONTENT="10 Feb 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
26 Jan 2017 version :c,h4
10 Feb 2016 version :c,h4
Version info: :h4

2
doc/src/Section_commands.txt
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@ -969,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"lubricateU/poly"_pair_lubricateU.html,
"meam"_pair_meam.html,
"mie/cut (o)"_pair_mie.html,
"morse (got)"_pair_morse.html,
"morse (gkot)"_pair_morse.html,
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,

31
doc/src/compute_group_group.txt
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@ -20,6 +20,7 @@ keyword = {pair} or {kspace} or {boundary} :l
{pair} value = {yes} or {no}
{kspace} value = {yes} or {no}
{boundary} value = {yes} or {no} :pre
{molecule} value = {off} or {inter} or {intra} :pre
:ule
[Examples:]
@ -46,6 +47,13 @@ NOTE: The energies computed by the {pair} keyword do not include tail
corrections, even if they are enabled via the
"pair_modify"_pair_modify.html command.
If the {molecule} keyword is set to {inter} or {intra} than an
additional check is made based on the molecule IDs of the two atoms in
each pair before including their pairwise interaction energy and
force. For the {inter} setting, the two atoms must be in different
molecules. For the {intra} setting, the two atoms must be in the same
molecule.
If the {kspace} keyword is set to {yes}, which is not the default, and
if a "kspace_style"_kspace_style.html is defined, then the interaction
energy will include a Kspace component which is the long-range
@ -66,6 +74,10 @@ affect the force calculation and will be zero if one or both of the
groups are charge neutral. This energy correction term is the same as
that included in the regular Ewald and PPPM routines.
NOTE: The {molecule} setting only affects the group/group
contributions calculated by the {pair} keyword. It does not affect
the group/group contributions calculated by the {kspace} keyword.
This compute does not calculate any bond or angle or dihedral or
improper interactions between atoms in the two groups.
@ -78,6 +90,22 @@ work (FFTs, Ewald summation) as computing long-range forces for the
entire system. Thus it can be costly to invoke this compute too
frequently.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
command, and means those pairwise interactions do not appear in the
neighbor list. Because this compute uses a neighbor list, it also
means those pairs will not be included in the group/group interaction.
This does not apply when using long-range coulomb interactions
({coul/long}, {coul/msm}, {coul/wolf} or similar. One way to get
around this would be to set special_bond scaling factors to very tiny
numbers that are not exactly zero (e.g. 1.0e-50). Another workaround
is to write a dump file, and use the "rerun"_rerun.html command to
compute the group/group interactions for snapshots in the dump file.
The rerun script can use a "special_bonds"_special_bonds.html command
that includes all pairs in the neighbor list.
If you desire a breakdown of the interactions into a pairwise and
Kspace component, simply invoke the compute twice with the appropriate
yes/no settings for the {pair} and {kspace} keywords. This is no more
@ -119,7 +147,8 @@ The {ewald} and {pppm} styles do.
[Default:]
The option defaults are pair = yes, kspace = no, and boundary = yes.
The option defaults are pair = yes, kspace = no, boundary = yes,
molecule = off.
:line