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patch 17Mar17

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This commit is contained in:
Steve Plimpton
2017-03-17 11:29:23 -06:00
parent 9f35b764f8
commit 4a90bca7a3
7 changed files with 32 additions and 25 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="10 Mar 2017 version"> <META NAME="docnumber" CONTENT="17 Mar 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
10 Mar 2017 version :c,h4 17 Mar 2017 version :c,h4
Version info: :h4 Version info: :h4

1
doc/src/Section_commands.txt
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@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
"eos/cv"_fix_eos_cv.html, "eos/cv"_fix_eos_cv.html,
"eos/table"_fix_eos_table.html, "eos/table"_fix_eos_table.html,
"eos/table/rx"_fix_eos_table_rx.html, "eos/table/rx"_fix_eos_table_rx.html,
"filter/corotate"_fix_filter_corotate.html,
"flow/gauss"_fix_flow_gauss.html, "flow/gauss"_fix_flow_gauss.html,
"gle"_fix_gle.html, "gle"_fix_gle.html,
"grem"_fix_grem.html, "grem"_fix_grem.html,

37
doc/src/fix_filter_corotate.txt
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@ -31,26 +31,29 @@ fix cor all filter/corotate b 4 19 a 3 5 2 :pre
[Description:] [Description:]
This fix implements a corotational filter for a mollified impulse method. In This fix implements a corotational filter for a mollified impulse
biomolecular simulations, it allows the usage of larger timesteps for method. In biomolecular simulations, it allows the usage of larger
long-range electrostatic interactions. For details, see "(Fath)"_#Fath2017. timesteps for long-range electrostatic interactions. For details, see
"(Fath)"_#Fath2017.
When using "run_style respa"_run_style.html for a biomolecular simulation with high-frequency covalent When using "run_style respa"_run_style.html for a biomolecular
bonds, the outer time-step is restricted to below ~ 4fs due to resonance simulation with high-frequency covalent bonds, the outer time-step is
problems. This fix filters the outer stage of the respa and thus a larger restricted to below ~ 4fs due to resonance problems. This fix filters
(outer) time-step can be used. Since in large biomolecular simulations the the outer stage of the respa and thus a larger (outer) time-step can
computation of the long-range electrostatic contributions poses a major be used. Since in large biomolecular simulations the computation of
bottleneck, this can significantly accelerate the simulation. the long-range electrostatic contributions poses a major bottleneck,
this can significantly accelerate the simulation.
The filter computes a cluster decomposition of the molecular structure following The filter computes a cluster decomposition of the molecular structure
the criteria indicated by the options a, b, t and m. This process is similar to following the criteria indicated by the options a, b, t and m. This
the approach in "fix shake"_fix_shake.html, however, the clusters are not kept process is similar to the approach in "fix shake"_fix_shake.html,
contrained. Instead, the position is slightly modified only for the computation however, the clusters are not kept contrained. Instead, the position
of long-range forces. A good cluster decomposition constitutes in building is slightly modified only for the computation of long-range forces. A
clusters which contain the fastest covalent bonds inside clusters. good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
If the clusters are chosen suitably, the "run_style respa"_run_style.html is stable for outer If the clusters are chosen suitably, the "run_style
time-steps of at least 8fs. respa"_run_style.html is stable for outer time-steps of at least 8fs.
:line :line

1
src/RIGID/fix_shake.cpp
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@ -66,6 +66,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
virial_flag = 1; virial_flag = 1;
create_attribute = 1; create_attribute = 1;
dof_flag = 1; dof_flag = 1;
// error check // error check
molecular = atom->molecular; molecular = atom->molecular;

9
src/fix_store_state.cpp
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@ -38,7 +38,8 @@ enum{KEYWORD,COMPUTE,FIX,VARIABLE,DNAME,INAME};
FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), Fix(lmp, narg, arg),
nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), values(NULL), nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
ids(NULL), values(NULL),
vbuf(NULL), pack_choice(NULL) vbuf(NULL), pack_choice(NULL)
{ {
if (narg < 5) error->all(FLERR,"Illegal fix store/state command"); if (narg < 5) error->all(FLERR,"Illegal fix store/state command");
@ -1046,7 +1047,8 @@ void FixStoreState::pack_ysu(int n)
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) if (mask[i] & groupbit)
vbuf[n] = (x[i][1]-boxylo)*invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX; vbuf[n] = (x[i][1]-boxylo)*invyprd +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0; else vbuf[n] = 0.0;
n += nvalues; n += nvalues;
} }
@ -1158,7 +1160,8 @@ void FixStoreState::pack_iy(int n)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; if (mask[i] & groupbit)
vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0; else vbuf[n] = 0.0;
n += nvalues; n += nvalues;
} }

1
src/rcb.cpp
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@ -1176,7 +1176,6 @@ void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
void RCB::invert(int sortflag) void RCB::invert(int sortflag)
{ {
// only create Irregular if not previously created // only create Irregular if not previously created
// allows Irregular to persist for multiple RCB calls by fix balance // allows Irregular to persist for multiple RCB calls by fix balance

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "10 Mar 2017" #define LAMMPS_VERSION "17 Mar 2017"