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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11605 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-10 14:24:09 +00:00
parent 88cd9113f0
commit 3f7d79ab82
7 changed files with 2102 additions and 2095 deletions
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6
tools/msi2lmp/src/ReadCarFile.c
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@ -25,9 +25,9 @@ void set_box(double box[3][3], double *h, double *h_inv)
h_inv[1] = 1.0/h[1];
h_inv[2] = 1.0/h[2];
h[3] = box[2][0];
h[3] = box[2][2];
h[4] = box[2][1];
h[5] = box[2][2];
h[5] = box[2][0];
h_inv[3] = -h[3] / (h[1]*h[2]);
h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
h_inv[5] = -h[5] / (h[0]*h[1]);
@ -252,6 +252,8 @@ void ReadCarFile(void)
} else {
if (pflag > 2)
printf(" pbc[0] %f pbc[1] %f pbc[2] %f\n", pbc[0] ,pbc[1] ,pbc[2]);
if (TriclinicFlag == 0) {
for (k=0; k < 3; k++) {
box[0][k] = -0.5*pbc[k] + center[k] + shift[k];

3
tools/msi2lmp/src/WriteDataFile.c
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@ -30,7 +30,8 @@ void WriteDataFile(char *nameroot)
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) total_no_angle_angles = 0;
fprintf(DatF, "LAMMPS data file from msi2lmp v3.8 for %s\n\n", nameroot);
fprintf(DatF, "LAMMPS data file. msi2lmp " MSI2LMP_VERSION
" / CGCMM for %s\n\n", nameroot);
fprintf(DatF, " %6d atoms\n", total_no_atoms);
fprintf(DatF, " %6d bonds\n", total_no_bonds);
fprintf(DatF, " %6d angles\n",total_no_angles);

8
tools/msi2lmp/src/msi2lmp.c
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@ -2,6 +2,10 @@
*
* msi2lmp.exe
*
* v3.9.3 AK- Bugfix for triclinic cells.
*
* v3.9.2 AK- Support for writing out force field style hints
*
* v3.9.1 AK- Bugfix for Class2. Free allocated memory. Print version number.
*
* v3.9 AK - Rudimentary support for OPLS-AA
@ -134,8 +138,6 @@
#include <string.h>
#include <ctype.h>
static const char version[] = "v3.9.1 / 08-Oct-2013";
/* global variables */
char *rootname;
@ -326,7 +328,7 @@ int main (int argc, char *argv[])
if (pflag > 0) {
printf("\nRunning msi2lmp %s ...\n",version);
puts("\nRunning msi2lmp " MSI2LMP_VERSION "\n");
if (forcefield & FF_TYPE_CLASS1) puts(" Forcefield: Class I");
if (forcefield & FF_TYPE_CLASS2) puts(" Forcefield: Class II");
if (forcefield & FF_TYPE_OPLSAA) puts(" Forcefield: OPLS-AA");

4
tools/msi2lmp/src/msi2lmp.h
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@ -27,7 +27,7 @@
* The thrid version was revised in Fall 2011 by
* Stephanie Teich-McGoldrick to add support non-orthogonal cells.
*
* The next revision was done in Summer 2013 by
* The next revision was started in Summer/Fall 2013 by
* Axel Kohlmeyer to improve portability to Windows compilers,
* clean up command line parsing and improve compatibility with
* the then current LAMMPS versions. This revision removes
@ -36,6 +36,8 @@
# include <stdio.h>
#define MSI2LMP_VERSION "v3.9.3 / 07 Mar 2014"
#define PI_180 0.01745329251994329576
#define MAX_LINE_LENGTH 256

1608
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data
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2562
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2
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File diff suppressed because it is too large Load Diff

6
tools/msi2lmp/test/runtests.sh
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@ -29,7 +29,7 @@ counter=0
errors=0
# Class1 tests with cvff
for m in hydrogen water h2-h2o ethane benzene naphthalene crambin nylon phen3_cff97 hap_crystal
for m in hydrogen water h2-h2o ethane benzene naphthalene cnt-hexagonal crambin nylon phen3_cff97 hap_crystal
do \
before=$errors
vglog=${m}-class1.chk
@ -104,7 +104,7 @@ do \
done
# Class2 tests with compass
for m in hydrogen ethane benzene naphthalene
for m in hydrogen ethane benzene naphthalene cnt-hexagonal
do \
before=$errors
vglog=${m}-class2a.chk
@ -129,7 +129,7 @@ do \
done
# Class2 tests with pcff
for m in water h2-h2o ethane benzene naphthalene hap_crystal
for m in water h2-h2o ethane benzene naphthalene cnt-hexagonal hap_crystal
do \
before=$errors
vglog=${m}-class2b.chk