forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7433 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
0af770b923
commit
edcd54b2eb
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@ -122,6 +122,7 @@ class Data {
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double *pair_gb_epsilon,*pair_gb_sigma;
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double *pair_gb_epsa,*pair_gb_epsb,*pair_gb_epsc;
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double *pair_lj_epsilon,*pair_lj_sigma;
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double *pair_gauss_hgauss,*pair_gauss_rmh,*pair_gauss_sigmah;
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double **pair_cg_epsilon,**pair_cg_sigma;
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int **pair_cg_cmm_type, **pair_setflag;
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double **pair_cut_coul, **pair_cut_lj;
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@ -329,23 +330,19 @@ int main (int narg, char **arg)
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// process command-line args
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int iarg = 1;
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if (strcmp(arg[iarg],"-h") == 0) {
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printf("Syntax: restart2data switch arg ... "
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if (narg < 2 || strcmp(arg[iarg],"-h") == 0) {
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printf("Syntax: restart2data (switch) ... "
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"restart-file data-file (input-file)\n");
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printf(" restart-file and data-file are mandatory");
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printf(" input-file is optional");
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printf(" if specified it will contain LAMMPS input script commands");
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printf(" for mass and force field info");
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printf(" only a few force field styles support this option");
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printf(" 'restart-file' and 'data-file' are mandatory\n");
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printf(" 'input-file' is optional\n");
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printf(" If specified, it will contain LAMMPS input script\n");
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printf(" commands for mass and force field info.\n");
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printf(" Only a few force field styles support this option.\n");
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printf(" 'switch' is optional\n");
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printf(" The only supported switch is '-h' to print this message\n");
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return 0;
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}
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if ((narg-iarg != 2) && (narg-iarg != 3)) {
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printf("Syntax: restart2data switch arg ... "
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"restart-file data-file (input-file)\n");
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return 1;
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}
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char *restartfile = arg[iarg];
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char *datafile = arg[iarg+1];
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char *inputfile = NULL;
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@ -478,7 +475,7 @@ int main (int narg, char **arg)
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void header(FILE *fp, Data &data)
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{
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char *version = "19 Aug 2011";
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const char *version = "5 Jan 2012";
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data.triclinic = 0;
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@ -490,7 +487,8 @@ void header(FILE *fp, Data &data)
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if (flag == VERSION) {
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data.version = read_char(fp);
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if (strcmp(version,data.version) != 0) {
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char *str = "Restart file version does not match restart2data version";
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const char *str =
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"Restart file version does not match restart2data version";
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printf("WARNING %s\n",str);
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printf(" restart2data version = %s\n",version);
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}
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@ -1508,9 +1506,35 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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}
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} else if (strcmp(style,"coul/diel") == 0) {
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m = 1;
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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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if (!flag) return;
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for (i = 1; i <= data.ntypes; i++)
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for (j = i; j <= data.ntypes; j++) {
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itmp = read_int(fp);
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if (i == j && itmp == 0) {
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printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
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exit(1);
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}
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if (itmp) {
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if (i == j) {
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double diel_rme = read_double(fp);
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double diel_sigmae = read_double(fp);
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double cut_coul = read_double(fp);
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} else {
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double diel_rme = read_double(fp);
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double diel_sigmae = read_double(fp);
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double cut_coul = read_double(fp);
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}
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}
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}
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} else if ((strcmp(style,"coul/cut") == 0) ||
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(strcmp(style,"coul/debye") == 0) ||
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(strcmp(style,"coul/long") == 0)) {
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(strcmp(style,"coul/debye") == 0)) {
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if (strcmp(style,"coul/cut") == 0) {
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double cut_coul = read_double(fp);
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@ -1522,10 +1546,6 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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double kappa = 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,"coul/long") == 0) {
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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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}
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if (!flag) return;
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@ -1546,6 +1566,14 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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}
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} else if (strcmp(style,"coul/long") == 0) {
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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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if (!flag) return;
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} else if (strcmp(style,"dipole/cut") == 0) {
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double cut_lj_global = read_double(fp);
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@ -1724,6 +1752,69 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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}
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} else if (strcmp(style,"gauss") == 0) {
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double cut_lj_global = 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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if (!flag) return;
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data.pair_gauss_hgauss = new double[data.ntypes+1];
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data.pair_gauss_rmh = new double[data.ntypes+1];
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for (i = 1; i <= data.ntypes; i++)
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for (j = i; j <= data.ntypes; j++) {
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itmp = read_int(fp);
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if (i == j && itmp == 0) {
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printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
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exit(1);
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}
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if (itmp) {
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if (i == j) {
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data.pair_gauss_hgauss[i] = read_double(fp);
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data.pair_gauss_rmh[i] = read_double(fp);
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double cut_lj = read_double(fp);
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} else {
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double dipole_hgauss = read_double(fp);
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double dipole_rmh = read_double(fp);
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double cut_lj = read_double(fp);
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}
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}
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}
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} else if (strcmp(style,"gauss/cut") == 0) {
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double cut_lj_global = 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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if (!flag) return;
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data.pair_gauss_hgauss = new double[data.ntypes+1];
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data.pair_gauss_rmh = new double[data.ntypes+1];
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data.pair_gauss_sigmah = new double[data.ntypes+1];
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for (i = 1; i <= data.ntypes; i++)
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for (j = i; j <= data.ntypes; j++) {
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itmp = read_int(fp);
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if (i == j && itmp == 0) {
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printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
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exit(1);
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}
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if (itmp) {
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if (i == j) {
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data.pair_gauss_hgauss[i] = read_double(fp);
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data.pair_gauss_rmh[i] = read_double(fp);
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data.pair_gauss_sigmah[i] = read_double(fp);
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double cut_lj = read_double(fp);
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} else {
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double dipole_hgauss = read_double(fp);
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double dipole_rmh = read_double(fp);
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double dipole_sigmah = read_double(fp);
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double cut_lj = read_double(fp);
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}
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}
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}
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} else if ((strcmp(style,"gran/hooke") == 0) ||
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(strcmp(style,"gran/hooke/history") == 0) ||
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(strcmp(style,"gran/hertz/history") == 0)) {
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@ -2157,6 +2248,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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int n = read_int(fp);
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} else if (strcmp(style,"tersoff") == 0) {
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} else if (strcmp(style,"tersoff/table") == 0) {
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} else if (strcmp(style,"tersoff/zbl") == 0) {
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} else if ((strcmp(style,"yukawa") == 0) ||
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@ -2190,11 +2282,57 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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} else if ((strcmp(style,"cg/cmm") == 0) ||
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(strcmp(style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(style,"cg/cmm/coul/long") == 0)) {
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(strcmp(style,"cg/cmm/coul/long") == 0) ||
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(strcmp(style,"lj/sdk") == 0) ||
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(strcmp(style,"lj/sdk/coul/long") == 0)) {
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m = 0;
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data.cut_lj_global = read_double(fp);
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if ((strcmp(style,"cg/cmm/coul/long") == 0) ||
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(strcmp(style,"lj/sdk/coul/long") == 0)) {
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data.cut_coul_global = read_double(fp);
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}
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data.offset_flag = read_int(fp);
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data.mix_flag = read_int(fp);
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if (!flag) return;
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const int numtyp=data.ntypes+1;
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data.pair_cg_cmm_type = new int*[numtyp];
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data.pair_setflag = new int*[numtyp];
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data.pair_cg_epsilon = new double*[numtyp];
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data.pair_cg_sigma = new double*[numtyp];
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data.pair_cut_lj = new double*[numtyp];
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data.pair_cut_coul = NULL;
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m=0;
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for (i = 1; i <= data.ntypes; i++) {
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data.pair_cg_cmm_type[i] = new int[numtyp];
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data.pair_setflag[i] = new int[numtyp];
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data.pair_cg_epsilon[i] = new double[numtyp];
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data.pair_cg_sigma[i] = new double[numtyp];
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data.pair_cut_lj[i] = new double[numtyp];
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for (j = i; j <= data.ntypes; j++) {
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itmp = read_int(fp);
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data.pair_setflag[i][j] = itmp;
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if (i == j && itmp == 0) {
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printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
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exit(1);
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}
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if (itmp) {
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data.pair_cg_cmm_type[i][j] = read_int(fp);
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data.pair_cg_epsilon[i][j] = read_double(fp);
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data.pair_cg_sigma[i][j] = read_double(fp);
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data.pair_cut_lj[i][j] = read_double(fp);
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}
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}
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}
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} else if ((strcmp(style,"cg/cmm/old") == 0) ||
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(strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
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(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
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m = 0;
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data.cut_lj_global = read_double(fp);
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data.cut_coul_global = read_double(fp);
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data.kappa = read_double(fp);
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data.offset_flag = read_int(fp);
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@ -2208,8 +2346,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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data.pair_cg_epsilon = new double*[numtyp];
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data.pair_cg_sigma = new double*[numtyp];
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data.pair_cut_lj = new double*[numtyp];
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if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(style,"cg/cmm/coul/long") == 0)) {
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if ((strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
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(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
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data.pair_cut_coul = new double*[numtyp];
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m=1;
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} else {
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@ -2223,8 +2361,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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data.pair_cg_epsilon[i] = new double[numtyp];
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data.pair_cg_sigma[i] = new double[numtyp];
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data.pair_cut_lj[i] = new double[numtyp];
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if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(style,"cg/cmm/coul/long") == 0)) {
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if ((strcmp(style,"cg/cmm/coul/cut/old") == 0) ||
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(strcmp(style,"cg/cmm/coul/long/old") == 0)) {
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data.pair_cut_coul[i] = new double[numtyp];
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}
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@ -2247,7 +2385,6 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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}
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}
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} else if ((strcmp(style,"hybrid") == 0) ||
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(strcmp(style,"hybrid/overlay") == 0)) {
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@ -2394,7 +2531,8 @@ void angle(FILE *fp, Data &data)
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{
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if (strcmp(data.angle_style,"none") == 0) {
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} else if (strcmp(data.angle_style,"cg/cmm") == 0) {
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} else if ((strcmp(data.angle_style,"cg/cmm") == 0) ||
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(strcmp(data.angle_style,"sdk") == 0)) {
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data.angle_harmonic_k = new double[data.nangletypes+1];
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data.angle_harmonic_theta0 = new double[data.nangletypes+1];
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@ -2818,18 +2956,18 @@ void Data::stats()
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if (nellipsoids) printf(" Nellipsoids = " BIGINT_FORMAT "\n",nellipsoids);
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printf(" Nbonds = " BIGINT_FORMAT "\n",nbonds);
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printf(" Nangles = " BIGINT_FORMAT "\n",nangles);
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printf(" Ndihedrals = " BIGINT_FORMAT "\n",ndihedrals);
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printf(" Nimpropers = " BIGINT_FORMAT "\n",nimpropers);
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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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printf(" Unit style = %s\n",unit_style);
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printf(" Atom style = %s\n",atom_style);
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printf(" Pair style = %s\n",pair_style);
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printf(" Bond style = %s\n",bond_style);
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printf(" Angle style = %s\n",angle_style);
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printf(" Dihedral style = %s\n",dihedral_style);
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printf(" Improper style = %s\n",improper_style);
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if (pair_style) printf(" Pair style = %s\n",pair_style);
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if (bond_style) printf(" Bond style = %s\n",bond_style);
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if (angle_style) printf(" Angle style = %s\n",angle_style);
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if (dihedral_style) printf(" Dihedral style = %s\n",dihedral_style);
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if (improper_style) printf(" Improper style = %s\n",improper_style);
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printf(" Xlo xhi = %g %g\n",xlo,xhi);
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printf(" Ylo yhi = %g %g\n",ylo,yhi);
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@ -2882,7 +3020,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (angle_style) fprintf(fp2,"angle_style %s\n",angle_style);
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if (dihedral_style) fprintf(fp2,"dihedral_style %s\n",dihedral_style);
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if (improper_style) fprintf(fp2,"improper_style %s\n",improper_style);
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fprintf(fp2,"special_bonds %g %g %g %g %g %g\n",
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fprintf(fp2,"special_bonds lj %g %g %g coul %g %g %g\n",
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special_lj[1],special_lj[2],special_lj[3],
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special_lj[1],special_coul[2],special_coul[3]);
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fprintf(fp2,"\n");
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@ -2910,23 +3048,28 @@ void Data::write(FILE *fp, FILE *fp2)
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(strcmp(pair_style,"brownian") != 0) &&
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(strcmp(pair_style,"coul/cut") != 0) &&
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(strcmp(pair_style,"coul/debye") != 0) &&
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(strcmp(pair_style,"coul/diel") != 0) &&
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(strcmp(pair_style,"coul/long") != 0) &&
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(strcmp(pair_style,"eam") != 0) &&
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(strcmp(pair_style,"eam/alloy") != 0) &&
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(strcmp(pair_style,"eam/fs") != 0) &&
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(strcmp(pair_style,"eim") != 0) &&
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(strcmp(pair_style,"eff/cut") != 0) &&
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(strcmp(pair_style,"gauss") != 0) &&
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(strcmp(pair_style,"gauss/cut") != 0) &&
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(strcmp(pair_style,"gran/history") != 0) &&
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(strcmp(pair_style,"gran/no_history") != 0) &&
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(strcmp(pair_style,"gran/hertzian") != 0) &&
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(strcmp(pair_style,"lubricate2") != 0) &&
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(strcmp(pair_style,"lubricateU") != 0) &&
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(strcmp(pair_style,"meam") != 0) &&
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(strcmp(pair_style,"rebo") != 0) &&
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(strcmp(pair_style,"reax") != 0) &&
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(strcmp(pair_style,"reax/c") != 0) &&
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(strcmp(pair_style,"sw") != 0) &&
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(strcmp(pair_style,"table") != 0) &&
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(strcmp(pair_style,"tersoff") != 0) &&
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(strcmp(pair_style,"tersoff/table") != 0) &&
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(strcmp(pair_style,"tersoff/zbl") != 0) &&
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(strcmp(pair_style,"hybrid") != 0) &&
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(strcmp(pair_style,"hybrid/overlay") != 0))
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@ -3035,7 +3178,9 @@ void Data::write(FILE *fp, FILE *fp2)
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} else if ((strcmp(pair_style,"cg/cmm") == 0) ||
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(strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(pair_style,"cg/cmm/coul/long") == 0)) {
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(strcmp(pair_style,"cg/cmm/coul/long") == 0) ||
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(strcmp(pair_style,"lj/sdk") == 0) ||
|
||||
(strcmp(pair_style,"lj/sdk/coul/long") == 0)) {
|
||||
printf("ERROR: Cannot write pair_style %s to data file\n",
|
||||
pair_style);
|
||||
exit(1);
|
||||
|
|
@ -3046,9 +3191,13 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
// only supported styles = cg/cmm
|
||||
|
||||
if (pair_style && fp2) {
|
||||
if ((strcmp(pair_style,"cg/cmm") == 0) ||
|
||||
if ((strcmp(pair_style,"lj/sdk") == 0) ||
|
||||
(strcmp(pair_style,"lj/sdk/coul/long") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm/coul/long") == 0)) {
|
||||
(strcmp(pair_style,"cg/cmm/old") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm/coul/cut/old") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm/coul/long/old") == 0)) {
|
||||
for (int i = 1; i <= ntypes; i++) {
|
||||
for (int j = i; j <= ntypes; j++) {
|
||||
fprintf(fp2,"pair_coeff %d %d %s %g %g\n",i,j,
|
||||
|
|
|
|||
Loading…
Reference in New Issue