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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-05-30 13:48:37 +00:00
parent 2e521b2a67
commit 4e3bc9d059
5 changed files with 175 additions and 115 deletions
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246
tools/msi2lmp/src/WriteDataFile.c
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@ -30,8 +30,10 @@ void WriteDataFile(char *nameroot)
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) total_no_angle_angles = 0;
fprintf(DatF, "LAMMPS data file. msi2lmp " MSI2LMP_VERSION
" / CGCMM for %s\n\n", nameroot);
if (hintflag) fprintf(DatF, "LAMMPS data file. msi2lmp " MSI2LMP_VERSION
" / CGCMM for %s\n\n", nameroot);
else fprintf(DatF, "LAMMPS data file. msi2lmp " MSI2LMP_VERSION
" 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);
@ -76,8 +78,10 @@ void WriteDataFile(char *nameroot)
/* MASSES */
fprintf(DatF, "\nMasses\n\n");
for(k=0; k < no_atom_types; k++)
fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
for(k=0; k < no_atom_types; k++) {
if (hintflag) fprintf(DatF, " %3d %10.6f # %s\n",k+1,atomtypes[k].mass,atomtypes[k].potential);
else fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
}
fputs("\n",DatF);
@ -85,17 +89,19 @@ void WriteDataFile(char *nameroot)
fputs("Pair Coeffs",DatF);
if (hintflag) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # lj/cut/coul/long\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # lj/class2/coul/long\n\n",DatF);
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # lj/cut/coul/long\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # lj/class2/coul/long\n\n",DatF);
} else fputs("\n\n",DatF);
for (i=0; i < no_atom_types; i++) {
fprintf(DatF, " %3i ", i+1);
for ( j = 0; j < 2; j++)
fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
fputs("\n",DatF);
fprintf(DatF, "%14.10f ",atomtypes[i].params[j]);
if (hintflag) fprintf(DatF, "# %s\n",atomtypes[i].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
@ -107,17 +113,20 @@ void WriteDataFile(char *nameroot)
fputs("Bond Coeffs",DatF);
if (hintflag) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # harmonic\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # class2\n\n",DatF);
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # harmonic\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # class2\n\n",DatF);
} else fputs("\n\n",DatF);
for (i=0; i < no_bond_types; i++) {
fprintf(DatF, "%3i ", i+1);
fprintf(DatF, " %3i", i+1);
for ( j = 0; j < m; j++)
fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
fputs("\n",DatF);
fprintf(DatF, " %10.4f", bondtypes[i].params[j]);
if (hintflag) fprintf(DatF," # %s-%s\n",atomtypes[bondtypes[i].types[0]].potential,
atomtypes[bondtypes[i].types[1]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
}
@ -130,109 +139,151 @@ void WriteDataFile(char *nameroot)
fputs("Angle Coeffs",DatF);
if (hintflag) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # harmonic\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # class2\n\n",DatF);
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
fputs(" # harmonic\n\n",DatF);
else if (forcefield & FF_TYPE_CLASS2)
fputs(" # class2\n\n",DatF);
} else fputs("\n\n",DatF);
for (i=0; i < no_angle_types; i++) {
fprintf(DatF, "%3i ", i+1);
fprintf(DatF, " %3i", i+1);
for ( j = 0; j < m; j++)
fprintf(DatF, " %10.4f", angletypes[i].params[j]);
fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
fputs("\n",DatF);
if (hintflag) fprintf(DatF," # %s-%s-%s\n",
atomtypes[angletypes[i].types[0]].potential,
atomtypes[angletypes[i].types[1]].potential,
atomtypes[angletypes[i].types[2]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
}
if (no_dihedral_types > 0) {
fputs("Dihedral Coeffs",DatF);
if (forcefield & FF_TYPE_CLASS1) {
fputs("Dihedral Coeffs",DatF);
if (forcefield & FF_TYPE_CLASS1) {
if (hintflag) fputs(" # harmonic\n\n",DatF);
else fputs("\n\n",DatF);
if (hintflag) fputs(" # harmonic\n\n",DatF);
else fputs("\n\n",DatF);
for (i=0; i < no_dihedral_types; i++)
fprintf(DatF, "%3i %10.4f %3i %3i\n", i+1,
dihedraltypes[i].params[0],
(int) dihedraltypes[i].params[1],
(int) dihedraltypes[i].params[2]);
} else if (forcefield & FF_TYPE_OPLSAA) {
if (hintflag) fputs(" # opls\n\n",DatF);
else fputs("\n\n",DatF);
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) {
if (hintflag) fputs(" # class2\n\n",DatF);
else fputs("\n\n",DatF);
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, "%3i",i+1);
for ( j = 0; j < 6; j++)
fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
fputs("\n",DatF);
}
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, "%3i %10.4f %3i %3i", i+1,
dihedraltypes[i].params[0],
(int) dihedraltypes[i].params[1],
(int) dihedraltypes[i].params[2]);
if (hintflag) fprintf(DatF," # %s-%s-%s-%s\n",
atomtypes[dihedraltypes[i].types[0]].potential,
atomtypes[dihedraltypes[i].types[1]].potential,
atomtypes[dihedraltypes[i].types[2]].potential,
atomtypes[dihedraltypes[i].types[3]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
} else if (forcefield & FF_TYPE_OPLSAA) {
if (hintflag) fputs(" # opls\n\n",DatF);
else fputs("\n\n",DatF);
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]);
if (hintflag) fprintf(DatF," # %s-%s-%s-%s\n",
atomtypes[dihedraltypes[i].types[0]].potential,
atomtypes[dihedraltypes[i].types[1]].potential,
atomtypes[dihedraltypes[i].types[2]].potential,
atomtypes[dihedraltypes[i].types[3]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
} else if (forcefield & FF_TYPE_CLASS2) {
if (hintflag) fputs(" # class2\n\n",DatF);
else fputs("\n\n",DatF);
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, " %3i",i+1);
for ( j = 0; j < 6; j++)
fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
if (hintflag) fprintf(DatF,"# %s-%s-%s-%s\n",
atomtypes[dihedraltypes[i].types[0]].potential,
atomtypes[dihedraltypes[i].types[1]].potential,
atomtypes[dihedraltypes[i].types[2]].potential,
atomtypes[dihedraltypes[i].types[3]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
}
}
if (forcefield & FF_TYPE_CLASS1) {
if (no_oop_types > 0) {
/* cvff improper coeffs are: type K0 d n */
if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
if (no_oop_types > 0) {
/* cvff improper coeffs are: type K0 d n */
if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
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);
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i ",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
if (hintflag) fprintf(DatF,"# %s-%s-%s-%s\n",
atomtypes[ooptypes[i].types[0]].potential,
atomtypes[ooptypes[i].types[1]].potential,
atomtypes[ooptypes[i].types[2]].potential,
atomtypes[ooptypes[i].types[3]].potential);
else fputs("\n",DatF);
}
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) */
if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
if (no_oop_types > 0) {
/* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
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);
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i ",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
if (hintflag) fprintf(DatF,"# %s-%s-%s-%s\n",
atomtypes[ooptypes[i].types[0]].potential,
atomtypes[ooptypes[i].types[1]].potential,
atomtypes[ooptypes[i].types[2]].potential,
atomtypes[ooptypes[i].types[3]].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
if ((no_oop_types + no_angleangle_types) > 0) {
if (hintflag) fputs("Improper Coeffs # class2\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
if ((no_oop_types + no_angleangle_types) > 0) {
if (hintflag) fputs("Improper Coeffs # class2\n\n",DatF);
else fputs("Improper Coeffs\n\n",DatF);
for (i=0; i < no_oop_types; i++) {
fprintf(DatF, "%3i ", i+1);
for ( j = 0; j < 2; j++)
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
fputs("\n",DatF);
}
for (i=0; i < no_angleangle_types; i++) {
fprintf(DatF, "%3i ", i+no_oop_types+1);
for ( j = 0; j < 2; j++)
fprintf(DatF, "%10.4f ", 0.0);
fputs("\n",DatF);
}
fputs("\n",DatF);
for (i=0; i < no_oop_types; i++) {
fprintf(DatF, "%3i ", i+1);
for ( j = 0; j < 2; j++)
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
if (hintflag) fprintf(DatF,"# %s-%s-%s-%s\n",
atomtypes[ooptypes[i].types[0]].potential,
atomtypes[ooptypes[i].types[1]].potential,
atomtypes[ooptypes[i].types[2]].potential,
atomtypes[ooptypes[i].types[3]].potential);
else fputs("\n",DatF);
}
for (i=0; i < no_angleangle_types; i++) {
fprintf(DatF, "%3i ", i+no_oop_types+1);
for ( j = 0; j < 2; j++)
fprintf(DatF, "%10.4f ", 0.0);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
}
if (forcefield & FF_TYPE_CLASS2) {
@ -338,7 +389,7 @@ void WriteDataFile(char *nameroot)
for(k=0; k < total_no_atoms; k++) {
int typ = atoms[k].type;
fprintf(DatF," %6i %6i %3i %9.6f %15.9f %15.9f %15.9f %3i %3i %3i # %s\n",
fprintf(DatF," %6i %6i %3i %9.6f %15.9f %15.9f %15.9f %3i %3i %3i",
k+1,
atoms[k].molecule,
typ+1,
@ -348,8 +399,9 @@ void WriteDataFile(char *nameroot)
atoms[k].x[2],
atoms[k].image[0],
atoms[k].image[1],
atoms[k].image[2],
atomtypes[typ].potential);
atoms[k].image[2]);
if (hintflag) fprintf(DatF," # %s\n",atomtypes[typ].potential);
else fputs("\n",DatF);
}
fputs("\n",DatF);