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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10521 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-08-02 15:05:31 +00:00
parent 41bf441838
commit e3300dd7b3
10 changed files with 131 additions and 53 deletions
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5
tools/msi2lmp/README
View File

@ -1,6 +1,11 @@
Stephanie Teich-McGoldrick (Sandai) is the current maintainer
of the msi2lmp tool. She can be contacted at steichm at sandia.gov
02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added rudimentary support for OPLS-AA based on
input provided by jeff greathouse.
18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added support for writing out image flags

10
tools/msi2lmp/src/GetParameters.c
View File

@ -77,7 +77,7 @@ void GetParameters()
printf(" Unable to find vdw data for %s\n",atomtypes[i].potential);
condexit(11);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
if((ff_vdw.data[k].ff_param[0] != 0.0 ) &&
(ff_vdw.data[k].ff_param[1] != 0.0)) {
atomtypes[i].params[0] =
@ -132,7 +132,7 @@ void GetParameters()
potential_types[0],potential_types[1]);
condexit(12);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
bondtypes[i].params[0] = ff_bond.data[k].ff_param[1];
bondtypes[i].params[1] = ff_bond.data[k].ff_param[0];
}
@ -189,7 +189,7 @@ void GetParameters()
potential_types[0],potential_types[1],potential_types[2]);
condexit(13);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
angletypes[i].params[0] = ff_ang.data[k].ff_param[1];
angletypes[i].params[1] = ff_ang.data[k].ff_param[0];
}
@ -341,6 +341,10 @@ void GetParameters()
}
dihedraltypes[i].params[2] = ff_tor.data[k].ff_param[1];
}
if (forcefield & FF_TYPE_OPLSAA) {
for (j=0; j < 4; j++)
dihedraltypes[i].params[j] = ff_tor.data[k].ff_param[j];
}
if (forcefield & FF_TYPE_CLASS2) {
for (j=0; j < 6; j++)
dihedraltypes[i].params[j] = ff_tor.data[k].ff_param[j];

8
tools/msi2lmp/src/InitializeItems.c
View File

@ -31,7 +31,7 @@ void InitializeItems(void)
/* BOND */
ff_bond.number_of_members = 2;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_bond.keyword,"#quadratic_bond");
ff_bond.number_of_parameters = 2;
}
@ -52,7 +52,7 @@ void InitializeItems(void)
/* ANGLE */
ff_ang.number_of_members = 3;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_ang.keyword,"#quadratic_angle");
ff_ang.number_of_parameters = 2;
}
@ -65,7 +65,7 @@ void InitializeItems(void)
/* TORSION */
ff_tor.number_of_members = 4;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_tor.keyword,"#torsion_1");
ff_tor.number_of_parameters = 3;
}
@ -78,7 +78,7 @@ void InitializeItems(void)
/* OOP */
ff_oop.number_of_members = 4;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_oop.keyword,"#out_of_plane");
ff_oop.number_of_parameters = 3;
}

2
tools/msi2lmp/src/ReadCarFile.c
View File

@ -188,7 +188,7 @@ void ReadCarFile(void)
atoms[k].molecule = m;
atoms[k].no = k;
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %f",
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %lf",
atoms[k].name,
&(atoms[k].x[0]),
&(atoms[k].x[1]),

5
tools/msi2lmp/src/ReadFrcFile.c
View File

@ -57,8 +57,9 @@ void ReadFrcFile(void)
ff_vdw.keyword,ff_vdw.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_bond.keyword,ff_bond.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_morse.keyword,ff_morse.entries);
if (forcefield & FF_TYPE_CLASS1)
fprintf(stderr," Item %s has %d entries\n",
ff_morse.keyword,ff_morse.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_ang.keyword,ff_ang.entries);
if (forcefield & FF_TYPE_CLASS2) {

2
tools/msi2lmp/src/SearchAndFill.c
View File

@ -41,7 +41,7 @@ void SearchAndFill(struct FrcFieldItem *item)
while (got_it == 0) {
status = fgets( line, MAX_LINE_LENGTH, FrcF );
if (status == NULL) {
fprintf(stderr," Unable to find forcefield keyword %s\n",item->keyword);
fprintf(stderr," Unable to find keyword '%s'\n",item->keyword);
fprintf(stderr," Check consistency of forcefield name and class \n");
fprintf(stderr," Exiting....\n");
exit(1);

24
tools/msi2lmp/src/WriteDataFile.c
View File

@ -94,6 +94,7 @@ void WriteDataFile(char *nameroot)
if (no_bond_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) m = 4;
fprintf(DatF,"Bond Coeffs\n\n");
@ -109,6 +110,7 @@ void WriteDataFile(char *nameroot)
if (no_angle_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) m = 4;
fprintf(DatF,"Angle Coeffs\n\n");
@ -134,6 +136,17 @@ void WriteDataFile(char *nameroot)
(int) dihedraltypes[i].params[1],
(int) dihedraltypes[i].params[2]);
} else if (forcefield & FF_TYPE_OPLSAA) {
fprintf(DatF,"Dihedral Coeffs\n\n");
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, "%3i",i+1);
for ( j = 0; j < 4; j++)
fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
fprintf(DatF,"Dihedral Coeffs\n\n");
@ -160,6 +173,17 @@ void WriteDataFile(char *nameroot)
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_OPLSAA) {
if (no_oop_types > 0) {
/* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
fprintf(DatF,"Improper Coeffs\n\n");
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
if ((no_oop_types + no_angleangle_types) > 0) {
fprintf(DatF,"Improper Coeffs\n\n");

30
tools/msi2lmp/src/msi2lmp.c
View File

@ -1,6 +1,8 @@
/*
*
* msi2lmp.exe V3.8
* msi2lmp.exe V3.9
*
* v3.9 AK - Rudimentary support for OPLS-AA
*
* v3.6 KLA - Changes to output to either lammps 2001 (F90 version) or to
* lammps 2005 (C++ version)
@ -317,15 +319,23 @@ int main (int argc, char *argv[])
printf(" Forcefield file name: %s\n",FrcFileName);
}
if (((forcefield & FF_TYPE_CLASS1) && (strstr(FrcFileName,"cff") != NULL)) ||
((forcefield & FF_TYPE_CLASS2) &&
! ((strstr(FrcFileName,"cvff") == NULL)
|| (strstr(FrcFileName,"clayff") == NULL)
|| (strstr(FrcFileName,"compass") == NULL))) ||
((forcefield & FF_TYPE_OPLSAA) &&
! (strstr(FrcFileName,"opls") == NULL))) {
fprintf(stderr," WARNING - forcefield name and class appear to\n");
fprintf(stderr," be inconsistent - Errors may result\n\n");
n = 0;
if (forcefield & FF_TYPE_CLASS1) {
if (strstr(FrcFileName,"cvff") != NULL) ++n;
if (strstr(FrcFileName,"clayff") != NULL) ++n;
} else if (forcefield & FF_TYPE_OPLSAA) {
if (strstr(FrcFileName,"oplsaa") != NULL) ++n;
} else if (forcefield & FF_TYPE_CLASS2) {
if (strstr(FrcFileName,"pcff") != NULL) ++n;
if (strstr(FrcFileName,"cff91") != NULL) ++n;
if (strstr(FrcFileName,"compass") != NULL) ++n;
}
if (n == 0) {
if (iflag > 0) fputs(" WARNING",stderr);
else fputs(" Error ",stderr);
fputs("- forcefield name and class appear to be inconsistent\n\n",stderr);
if (iflag == 0) return 7;
}

64
tools/msi2lmp/test/data-compare.pl
View File

@ -826,6 +826,38 @@ sub syscompare {
die "Number of ",$i," types does not match: $a vs $b" unless ($a == $b);
}
topocompare($d1,$d2,'bond',2);
topocompare($d1,$d2,'angle',3);
topocompare($d1,$d2,'dihedral',4);
topocompare($d1,$d2,'improper',4);
coeffcompare($d1,$d2,'pair','atom');
coeffcompare($d1,$d2,'bond','bond');
coeffcompare($d1,$d2,'angle','angle');
coeffcompare($d1,$d2,'bondbond','angle');
coeffcompare($d1,$d2,'bondangle','angle');
coeffcompare($d1,$d2,'dihedral','dihedral');
coeffcompare($d1,$d2,'angleangletorsion','dihedral');
coeffcompare($d1,$d2,'bondbond13','dihedral');
coeffcompare($d1,$d2,'endbondtorsion','dihedral');
coeffcompare($d1,$d2,'middlebondtorsion','dihedral');
coeffcompare($d1,$d2,'improper','improper');
coeffcompare($d1,$d2,'angleangle','improper');
for ($i=0; $i < $d1->{natomtypes}; ++$i) {
$j = $i+1;
if (exists $d1->{mass}[$i]) {
$a = $d1->{mass}[$i];
} else {
die "No mass for atom type $j in data file 1";
}
if (exists $d2->{mass}[$i]) {
$a = $d2->{mass}[$i];
} else {
die "No mass for atom type $j in data file 2";
}
}
# check box information
die "Inconsistent box shape" if ($d1->{triclinic} != $d2->{triclinic});
@ -868,38 +900,6 @@ sub syscompare {
}
}
for ($i=0; $i < $d1->{natomtypes}; ++$i) {
$j = $i+1;
if (exists $d1->{mass}[$i]) {
$a = $d1->{mass}[$i];
} else {
die "No mass for atom type $j in data file 1";
}
if (exists $d2->{mass}[$i]) {
$a = $d2->{mass}[$i];
} else {
die "No mass for atom type $j in data file 2";
}
}
topocompare($d1,$d2,'bond',2);
topocompare($d1,$d2,'angle',3);
topocompare($d1,$d2,'dihedral',4);
topocompare($d1,$d2,'improper',4);
coeffcompare($d1,$d2,'pair','atom');
coeffcompare($d1,$d2,'bond','bond');
coeffcompare($d1,$d2,'angle','angle');
coeffcompare($d1,$d2,'bondbond','angle');
coeffcompare($d1,$d2,'bondangle','angle');
coeffcompare($d1,$d2,'dihedral','dihedral');
coeffcompare($d1,$d2,'angleangletorsion','dihedral');
coeffcompare($d1,$d2,'bondbond13','dihedral');
coeffcompare($d1,$d2,'endbondtorsion','dihedral');
coeffcompare($d1,$d2,'middlebondtorsion','dihedral');
coeffcompare($d1,$d2,'improper','improper');
coeffcompare($d1,$d2,'angleangle','improper');
}
########################################################################

34
tools/msi2lmp/test/runtests.sh
View File

@ -5,6 +5,24 @@ MSI2LMP=../src/msi2lmp.exe
LAMMPS=../../../src/lmp_serial
CHECKDATA=./data-compare.pl
if [ ! -x $MSI2LMP ]
then
echo "No executable $MSI2LMP"
exit 1
fi
if [ ! -d $BIOSYM_LIBRARY ]
then
echo "No directory $BIOSYM_LIBRARY"
exit 1
fi
if [ ! -x $LAMMPS ]
then
echo "No executable $LAMMPS"
exit 1
fi
verbose=1
counter=0
errors=0
@ -41,6 +59,22 @@ do \
counter=$(expr $counter + 4)
done
# OPLS-AA tests
for m in ethane
do \
before=$errors
${MSI2LMP} ${m}-oplsaa -c 0 -p ${verbose} -f oplsaa -n \
|| errors=$(expr $errors + 1)
${LAMMPS} -log none -screen none -in in.${m}-oplsaa \
|| errors=$(expr $errors + 1)
${CHECKDATA} ${m}-oplsaa.data reference/${m}-oplsaa.data \
|| errors=$(expr $errors + 1)
${CHECKDATA} ${m}-oplsaa.data2 reference/${m}-oplsaa.data2 \
|| errors=$(expr $errors + 1)
[ $before -eq $errors ] && rm ${m}-oplsaa.data ${m}-oplsaa.data2 log.${m}-oplsaa
counter=$(expr $counter + 4)
done
# Class2 tests with compass
for m in hydrogen ethane benzene naphthalene
do \