git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8071 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -208,7 +208,7 @@ class Data {
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// atom quantities
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int iatoms,ibonds,iangles,idihedrals,iimpropers;
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bigint iatoms,ibonds,iangles,idihedrals,iimpropers;
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double *mass;
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double *x,*y,*z,*vx,*vy,*vz;
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@ -532,7 +532,7 @@ int main (int narg, char **arg)
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void header(FILE *fp, Data &data)
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{
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const char *version = "6 Feb 2012";
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const char *version = "17 May 2012";
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data.triclinic = 0;
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@ -873,6 +873,7 @@ int atom(double *buf, Data &data)
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// ---------------------------------------------------------------------
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// read one atom's info from buffer
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// one routine per atom style
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// skip broken bonds, angles, etc
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// ---------------------------------------------------------------------
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int atom_angle(double *buf, Data &data, int iatoms)
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@ -897,7 +898,7 @@ int atom_angle(double *buf, Data &data, int iatoms)
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for (int k = 0; k < n; k++) {
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type = static_cast<int> (buf[m++]);
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atom1 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] < atom1 ) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
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data.bond_type[data.ibonds] = type;
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data.bond_atom1[data.ibonds] = data.tag[iatoms];
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data.bond_atom2[data.ibonds] = atom1;
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@ -911,12 +912,12 @@ int atom_angle(double *buf, Data &data, int iatoms)
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atom1 = static_cast<int> (buf[m++]);
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.angle_type[data.iangles] = type;
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data.angle_atom1[data.iangles] = atom1;
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data.angle_atom2[data.iangles] = atom2;
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data.angle_atom3[data.iangles] = atom3;
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data.iangles++;
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data.iangles++;
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}
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}
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@ -962,7 +963,7 @@ int atom_bond(double *buf, Data &data, int iatoms)
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for (int k = 0; k < n; k++) {
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type = static_cast<int> (buf[m++]);
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atom1 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] < atom1) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
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data.bond_type[data.ibonds] = type;
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data.bond_atom1[data.ibonds] = data.tag[iatoms];
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data.bond_atom2[data.ibonds] = atom1;
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@ -1074,7 +1075,7 @@ int atom_full(double *buf, Data &data, int iatoms)
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for (int k = 0; k < n; k++) {
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type = static_cast<int> (buf[m++]);
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atom1 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] < atom1) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
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data.bond_type[data.ibonds] = type;
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data.bond_atom1[data.ibonds] = data.tag[iatoms];
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data.bond_atom2[data.ibonds] = atom1;
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@ -1088,7 +1089,7 @@ int atom_full(double *buf, Data &data, int iatoms)
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atom1 = static_cast<int> (buf[m++]);
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.angle_type[data.iangles] = type;
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data.angle_atom1[data.iangles] = atom1;
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data.angle_atom2[data.iangles] = atom2;
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@ -1104,7 +1105,7 @@ int atom_full(double *buf, Data &data, int iatoms)
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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atom4 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.dihedral_type[data.idihedrals] = type;
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data.dihedral_atom1[data.idihedrals] = atom1;
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data.dihedral_atom2[data.idihedrals] = atom2;
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@ -1121,7 +1122,7 @@ int atom_full(double *buf, Data &data, int iatoms)
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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atom4 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.improper_type[data.iimpropers] = type;
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data.improper_atom1[data.iimpropers] = atom1;
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data.improper_atom2[data.iimpropers] = atom2;
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@ -1168,7 +1169,7 @@ int atom_molecular(double *buf, Data &data, int iatoms)
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for (int k = 0; k < n; k++) {
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type = static_cast<int> (buf[m++]);
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atom1 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] < atom1) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] < atom1))) {
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data.bond_type[data.ibonds] = type;
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data.bond_atom1[data.ibonds] = data.tag[iatoms];
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data.bond_atom2[data.ibonds] = atom1;
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@ -1182,7 +1183,7 @@ int atom_molecular(double *buf, Data &data, int iatoms)
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atom1 = static_cast<int> (buf[m++]);
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.angle_type[data.iangles] = type;
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data.angle_atom1[data.iangles] = atom1;
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data.angle_atom2[data.iangles] = atom2;
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@ -1198,7 +1199,7 @@ int atom_molecular(double *buf, Data &data, int iatoms)
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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atom4 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.dihedral_type[data.idihedrals] = type;
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data.dihedral_atom1[data.idihedrals] = atom1;
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data.dihedral_atom2[data.idihedrals] = atom2;
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@ -1215,7 +1216,7 @@ int atom_molecular(double *buf, Data &data, int iatoms)
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atom2 = static_cast<int> (buf[m++]);
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atom3 = static_cast<int> (buf[m++]);
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atom4 = static_cast<int> (buf[m++]);
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if (data.newton_bond || data.tag[iatoms] == atom2) {
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if ((type != 0) && (data.newton_bond || (data.tag[iatoms] == atom2))) {
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data.improper_type[data.iimpropers] = type;
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data.improper_atom1[data.iimpropers] = atom1;
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data.improper_atom2[data.iimpropers] = atom2;
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@ -1994,6 +1995,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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} else if ((strcmp(style,"lj/charmm/coul/charmm") == 0) ||
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(strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) ||
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(strcmp(style,"lj/charmm/coul/pppm") == 0) ||
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(strcmp(style,"lj/charmm/coul/long") == 0)) {
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if (strcmp(style,"lj/charmm/coul/charmm") == 0) {
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@ -2010,6 +2012,12 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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double cut_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/charmm/coul/pppm") == 0) {
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double cut_lj_inner = read_double(fp);
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double cut_lj = read_double(fp);
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double cut_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/charmm/coul/long") == 0) {
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double cut_lj_inner = read_double(fp);
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double cut_lj = read_double(fp);
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@ -2049,6 +2057,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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} else if ((strcmp(style,"lj/class2") == 0) ||
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(strcmp(style,"lj/class2/coul/cut") == 0) ||
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(strcmp(style,"lj/class2/coul/pppm") == 0) ||
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(strcmp(style,"lj/class2/coul/long") == 0)) {
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if (strcmp(style,"lj/class2") == 0) {
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@ -2062,6 +2071,12 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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double cut_lj_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/class2/coul/pppm") == 0) {
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m = 0;
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double cut_lj_global = read_double(fp);
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double cut_lj_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/class2/coul/long") == 0) {
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m = 0;
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double cut_lj_global = read_double(fp);
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@ -2102,6 +2117,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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(strcmp(style,"lj/cut/coul/cut") == 0) ||
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(strcmp(style,"lj/cut/coul/debye") == 0) ||
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(strcmp(style,"lj/cut/coul/long") == 0) ||
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(strcmp(style,"lj/cut/coul/pppm") == 0) ||
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(strcmp(style,"lj/cut/coul/long/tip4p") == 0) ||
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(strcmp(style,"lj/coul") == 0)) {
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@ -2134,6 +2150,12 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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double cut_lj_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/cut/coul/pppm") == 0) {
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m = 0;
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double cut_lj_global = read_double(fp);
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double cut_lj_coul = read_double(fp);
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int offset_flag = read_int(fp);
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int mix_flag = read_int(fp);
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} else if (strcmp(style,"lj/cut/coul/long/tip4p") == 0) {
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m = 0;
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int typeO = read_int(fp);
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@ -3079,10 +3101,20 @@ void Data::stats()
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if (nellipsoids) printf(" Nellipsoids = " BIGINT_FORMAT "\n",nellipsoids);
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if (nbonds) printf(" Nbonds = " BIGINT_FORMAT "\n",nbonds);
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if (nangles) printf(" Nangles = " BIGINT_FORMAT "\n",nangles);
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if (ndihedrals) printf(" Ndihedrals = " BIGINT_FORMAT "\n",ndihedrals);
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if (nimpropers) printf(" Nimpropers = " BIGINT_FORMAT "\n",nimpropers);
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if (ibonds) printf(" Nbonds = " BIGINT_FORMAT "\n",ibonds);
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if (ibonds != nbonds)
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printf(" Skipping " BIGINT_FORMAT " broken bonds\n",nbonds-ibonds);
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if (iangles) printf(" Nangles = " BIGINT_FORMAT "\n",iangles);
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if (iangles != nangles)
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printf(" Skipping " BIGINT_FORMAT " broken angles\n",nangles-iangles);
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if (idihedrals) printf(" Ndihedrals = " BIGINT_FORMAT "\n",idihedrals);
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if (idihedrals != ndihedrals)
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printf(" Skipping " BIGINT_FORMAT " broken dihedrals\n",
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ndihedrals-idihedrals);
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if (iimpropers) printf(" Nimpropers = " BIGINT_FORMAT "\n",iimpropers);
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if (iimpropers != nimpropers)
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printf(" Skipping " BIGINT_FORMAT " broken impropers\n",
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nimpropers-iimpropers);
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printf(" Unit style = %s\n",unit_style);
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printf(" Atom style = %s\n",atom_style);
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@ -3112,10 +3144,10 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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fprintf(fp,BIGINT_FORMAT " atoms\n",natoms);
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if (nellipsoids) fprintf(fp,BIGINT_FORMAT " ellipsoids\n",nellipsoids);
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if (nbonds) fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
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if (nangles) fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
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if (ndihedrals) fprintf(fp,BIGINT_FORMAT " dihedrals\n",ndihedrals);
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if (nimpropers) fprintf(fp,BIGINT_FORMAT " impropers\n",nimpropers);
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if (ibonds) fprintf(fp,BIGINT_FORMAT " bonds\n",ibonds);
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if (iangles) fprintf(fp,BIGINT_FORMAT " angles\n",iangles);
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if (idihedrals) fprintf(fp,BIGINT_FORMAT " dihedrals\n",idihedrals);
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if (iimpropers) fprintf(fp,BIGINT_FORMAT " impropers\n",iimpropers);
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fprintf(fp,"\n");
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@ -3149,17 +3181,16 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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fprintf(fp2,"\n");
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}
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// mass to either data file or input file
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// mass to both data file and input file for convenience
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if (mass) {
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if (fp2) {
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fprintf(fp2,"\n");
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for (int i = 1; i <= ntypes; i++) fprintf(fp2,"mass %d %g\n",i,mass[i]);
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fprintf(fp2,"\n");
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} else {
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fprintf(fp,"\nMasses\n\n");
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for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
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}
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fprintf(fp,"\nMasses\n\n");
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for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
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}
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// pair coeffs to data file
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@ -3245,6 +3276,7 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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} else if ((strcmp(pair_style,"lj/charmm/coul/charmm") == 0) ||
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(strcmp(pair_style,"lj/charmm/coul/charmm/implicit") == 0) ||
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(strcmp(pair_style,"lj/charmm/coul/pppm") == 0) ||
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(strcmp(pair_style,"lj/charmm/coul/long") == 0)) {
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for (int i = 1; i <= ntypes; i++)
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fprintf(fp,"%d %g %g %g %g\n",i,
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@ -3253,6 +3285,7 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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} else if ((strcmp(pair_style,"lj/class2") == 0) ||
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(strcmp(pair_style,"lj/class2/coul/cut") == 0) ||
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(strcmp(pair_style,"lj/class2/coul/pppm") == 0) ||
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(strcmp(pair_style,"lj/class2/coul/long") == 0)) {
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for (int i = 1; i <= ntypes; i++)
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fprintf(fp,"%d %g %g\n",i,
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@ -3263,6 +3296,7 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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(strcmp(pair_style,"lj/cut/coul/cut") == 0) ||
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(strcmp(pair_style,"lj/cut/coul/debye") == 0) ||
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(strcmp(pair_style,"lj/cut/coul/long") == 0) ||
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(strcmp(pair_style,"lj/cut/coul/pppm") == 0) ||
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(strcmp(pair_style,"lj/cut/coul/long/tip4p") == 0) ||
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(strcmp(pair_style,"lj/coul") == 0)) {
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for (int i = 1; i <= ntypes; i++)
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@ -3314,7 +3348,7 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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}
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// pair coeffs to input file
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// only supported styles = cg/cmm
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// only supported styles = lj/sdk and cg/cmm
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if (write_coeffs && pair_style && fp2) {
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if ((strcmp(pair_style,"lj/sdk") == 0) ||
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@ -3765,31 +3799,31 @@ void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
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}
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}
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if (nbonds) {
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if (ibonds) {
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fprintf(fp,"\nBonds\n\n");
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for (bigint i = 0; i < nbonds; i++)
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for (bigint i = 0; i < ibonds; i++)
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fprintf(fp,BIGINT_FORMAT " %d %d %d\n",
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i+1,bond_type[i],bond_atom1[i],bond_atom2[i]);
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}
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if (nangles) {
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if (iangles) {
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fprintf(fp,"\nAngles\n\n");
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for (bigint i = 0; i < nangles; i++)
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for (bigint i = 0; i < iangles; i++)
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fprintf(fp,BIGINT_FORMAT " %d %d %d %d\n",
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i+1,angle_type[i],angle_atom1[i],angle_atom2[i],angle_atom3[i]);
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}
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if (ndihedrals) {
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if (idihedrals) {
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fprintf(fp,"\nDihedrals\n\n");
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for (bigint i = 0; i < ndihedrals; i++)
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for (bigint i = 0; i < idihedrals; i++)
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fprintf(fp,BIGINT_FORMAT " %d %d %d %d %d\n",
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i+1,dihedral_type[i],dihedral_atom1[i],dihedral_atom2[i],
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dihedral_atom3[i],dihedral_atom4[i]);
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}
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if (nimpropers) {
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if (iimpropers) {
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fprintf(fp,"\nImpropers\n\n");
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for (bigint i = 0; i < nimpropers; i++)
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for (bigint i = 0; i < iimpropers; i++)
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fprintf(fp,BIGINT_FORMAT " %d %d %d %d %d\n",
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i+1,improper_type[i],improper_atom1[i],improper_atom2[i],
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improper_atom3[i],improper_atom4[i]);
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