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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5949 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-04-15 22:51:43 +00:00
parent 91c348d195
commit 452107d9cb
1 changed files with 10 additions and 3 deletions
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13
src/read_data.cpp
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@ -1006,8 +1006,11 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (atom->natoms > MAXSMALLINT) if (atom->natoms > MAXSMALLINT)
error->all("Molecular data file has too many atoms"); error->all("Molecular data file has too many atoms");
// customize for new sections
int natoms = static_cast<int> (atom->natoms); int natoms = static_cast<int> (atom->natoms);
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0; bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
int ellipsoid_flag = 0;
// customize for new sections // customize for new sections
// allocate topology counting vector // allocate topology counting vector
@ -1027,6 +1030,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
else if (strcmp(keyword,"Ellipsoids") == 0) { else if (strcmp(keyword,"Ellipsoids") == 0) {
if (!avec_ellipsoid) if (!avec_ellipsoid)
error->all("Invalid data file section: Ellipsoids"); error->all("Invalid data file section: Ellipsoids");
ellipsoid_flag = 1;
skip_lines(nellipsoids); skip_lines(nellipsoids);
} else if (strcmp(keyword,"Pair Coeffs") == 0) { } else if (strcmp(keyword,"Pair Coeffs") == 0) {
@ -1108,7 +1112,6 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
skip_lines(atom->nimpropertypes); skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"Bonds") == 0) { } else if (strcmp(keyword,"Bonds") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0; for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond) if (force->newton_bond)
for (i = 0; i < atom->nbonds; i++) { for (i = 0; i < atom->nbonds; i++) {
@ -1133,7 +1136,6 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom); if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
} else if (strcmp(keyword,"Angles") == 0) { } else if (strcmp(keyword,"Angles") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0; for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond) if (force->newton_bond)
for (i = 0; i < atom->nangles; i++) { for (i = 0; i < atom->nangles; i++) {
@ -1160,7 +1162,6 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom); if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
} else if (strcmp(keyword,"Dihedrals") == 0) { } else if (strcmp(keyword,"Dihedrals") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0; for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond) if (force->newton_bond)
for (i = 0; i < atom->ndihedrals; i++) { for (i = 0; i < atom->ndihedrals; i++) {
@ -1246,6 +1247,12 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
(atom->ndihedrals && !dihedral_per_atom) || (atom->ndihedrals && !dihedral_per_atom) ||
(atom->nimpropers && !improper_per_atom)) (atom->nimpropers && !improper_per_atom))
error->one("Needed topology not in data file"); error->one("Needed topology not in data file");
// customize for new sections
// error check that Bonus sections were speficied in file
if (nellipsoids && !ellipsoid_flag)
error->one("Needed Bonus data not in data file");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------