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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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# Conflicts:
#	doc/Manual.html
#	doc/Manual.txt
#	python/install.py
#	python/lammps.py
#	src/read_restart.cpp
#	src/write_restart.cpp
This commit is contained in:
Axel Kohlmeyer
2015-07-03 07:37:10 -04:00
parent 90664ccd41 8db4d80726
commit 0449d00dca
9 changed files with 33 additions and 11 deletions
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4
doc/Manual.html
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@ -1,7 +1,7 @@
<HTML> <HTML>
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="1 Jul 2015 version"> <META NAME="docnumber" CONTENT="2 Jul 2015 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>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation <CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER> </H3></CENTER>
<CENTER><H4>1 Jul 2015 version <CENTER><H4>2 Jul 2015 version
</H4></CENTER> </H4></CENTER>
<H4>Version info: <H4>Version info:
</H4> </H4>

4
doc/Manual.txt
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@ -1,6 +1,6 @@
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="1 Jul 2015 version"> <META NAME="docnumber" CONTENT="2 Jul 2015 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>
@ -18,7 +18,7 @@
<H1></H1> <H1></H1>
LAMMPS-ICMS Documentation :c,h3 LAMMPS-ICMS Documentation :c,h3
1 Jul 2015 version :c,h4 2 Jul 2015 version :c,h4
Version info: :h4 Version info: :h4

3
python/install.py
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@ -4,7 +4,8 @@
instructions = """ instructions = """
Syntax: python install.py [-h] [pydir] Syntax: python install.py [-h] [pydir]
pydir = target dir for lammps.py and liblammps.so, default = Python site-packages dir pydir = target dir for lammps.py and liblammps.so
default = Python site-packages dir
""" """
import sys,os,commands import sys,os,commands

3
python/lammps.py
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@ -16,12 +16,13 @@
import sys,traceback,types import sys,traceback,types
from ctypes import * from ctypes import *
from os.path import dirname,abspath,join from os.path import dirname,abspath,join
from inspect import getsourcefile
class lammps: class lammps:
def __init__(self,name="",cmdargs=None,ptr=None): def __init__(self,name="",cmdargs=None,ptr=None):
# determine module location # determine module location
modpath = dirname(abspath(__file__)) modpath = dirname(abspath(getsourcefile(lambda:0)))
# load liblammps.so by default # load liblammps.so by default
# if name = "g++", load liblammps_g++.so # if name = "g++", load liblammps_g++.so

4
src/domain.cpp
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@ -72,6 +72,10 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
boundary[1][0] = boundary[1][1] = 0; boundary[1][0] = boundary[1][1] = 0;
boundary[2][0] = boundary[2][1] = 0; boundary[2][0] = boundary[2][1] = 0;
minxlo = minxhi = 0.0;
minylo = minyhi = 0.0;
minzlo = minzhi = 0.0;
triclinic = 0; triclinic = 0;
tiltsmall = 1; tiltsmall = 1;

10
src/read_restart.cpp
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@ -60,7 +60,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
SPECIAL_LJ,SPECIAL_COUL, SPECIAL_LJ,SPECIAL_COUL,
MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER, MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER,
MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
IMAGEINT,TIMESTEP, IMAGEINT,BOUNDMIN,TIMESTEP,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL}; COMM_MODE,COMM_CUTOFF,COMM_VEL};
@ -796,6 +796,14 @@ void ReadRestart::header(int incompatible)
domain->nonperiodic = 2; domain->nonperiodic = 2;
} }
} else if (flag == BOUNDMIN) {
double minbound[6];
read_int();
read_double_vec(6,minbound);
domain->minxlo = minbound[0]; domain->minxhi = minbound[1];
domain->minylo = minbound[2]; domain->minyhi = minbound[3];
domain->minzlo = minbound[4]; domain->minzhi = minbound[5];
// create new AtomVec class using any stored args // create new AtomVec class using any stored args
} else if (flag == ATOM_STYLE) { } else if (flag == ATOM_STYLE) {

4
src/update.cpp
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@ -141,7 +141,7 @@ void Update::set_units(const char *style)
force->hplanck = 95.306976368; force->hplanck = 95.306976368;
force->mvv2e = 48.88821291 * 48.88821291; force->mvv2e = 48.88821291 * 48.88821291;
force->ftm2v = 1.0 / 48.88821291 / 48.88821291; force->ftm2v = 1.0 / 48.88821291 / 48.88821291;
force->mv2d = 1.0 / 0.602214179; force->mv2d = 1.0 / 0.602214129;
force->nktv2p = 68568.415; force->nktv2p = 68568.415;
force->qqr2e = 332.06371; force->qqr2e = 332.06371;
force->qe2f = 23.060549; force->qe2f = 23.060549;
@ -162,7 +162,7 @@ void Update::set_units(const char *style)
force->hplanck = 4.135667403e-3; force->hplanck = 4.135667403e-3;
force->mvv2e = 1.0364269e-4; force->mvv2e = 1.0364269e-4;
force->ftm2v = 1.0 / 1.0364269e-4; force->ftm2v = 1.0 / 1.0364269e-4;
force->mv2d = 1.0 / 0.602214179; force->mv2d = 1.0 / 0.602214129;
force->nktv2p = 1.6021765e6; force->nktv2p = 1.6021765e6;
force->qqr2e = 14.399645; force->qqr2e = 14.399645;
force->qe2f = 1.0; force->qe2f = 1.0;

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "1 Jul 2015" #define LAMMPS_VERSION "2 Jul 2015"

10
src/write_restart.cpp
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@ -59,7 +59,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
SPECIAL_LJ,SPECIAL_COUL, SPECIAL_LJ,SPECIAL_COUL,
MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER, MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER,
MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
IMAGEINT,TIMESTEP, IMAGEINT,BOUNDMIN,TIMESTEP,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL}; COMM_MODE,COMM_CUTOFF,COMM_VEL};
@ -456,6 +456,14 @@ void WriteRestart::header()
write_int(ZPERIODIC,domain->zperiodic); write_int(ZPERIODIC,domain->zperiodic);
write_int_vec(BOUNDARY,6,&domain->boundary[0][0]); write_int_vec(BOUNDARY,6,&domain->boundary[0][0]);
// added field for shrink-wrap boundaries with minimum - 2 Jul 2015
double minbound[6];
minbound[0] = domain->minxlo; minbound[1] = domain->minxhi;
minbound[2] = domain->minylo; minbound[3] = domain->minyhi;
minbound[4] = domain->minzlo; minbound[5] = domain->minzhi;
write_double_vec(BOUNDMIN,6,minbound);
// write atom_style and its args // write atom_style and its args
write_string(ATOM_STYLE,atom->atom_style); write_string(ATOM_STYLE,atom->atom_style);