mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1484 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8df0490986
commit
bd89b8239f
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@ -13,7 +13,11 @@
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// Convert a LAMMPS binary restart file into an ASCII text data file
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//
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// Syntax: restart2data restart-file data-file
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// Syntax: restart2data restart-file data-file (parameter-file)
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// parameter-file is optional
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// if specified it will contain LAMMPS input script commands
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// for mass and force field info
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// only a few force field styles support this option
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//
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// this serial code must be compiled on a platform that can read the binary
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// restart file since binary formats are not compatible across all platforms
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@ -45,6 +49,9 @@ enum{VERSION,UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
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enum{MASS,SHAPE,DIPOLE};
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enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
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static const char * const cg_type_list[] =
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{"none", "lj9_6", "lj12_4", "lj12_6"};
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// ---------------------------------------------------------------------
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// Data class to hold problem
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// ---------------------------------------------------------------------
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@ -73,9 +80,13 @@ class Data {
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int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
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int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
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int triclinic;
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double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
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double special_lj[4],special_coul[4];
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double cut_lj_global,cut_coul_global,kappa;
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int offset_flag,mix_flag;
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// force fields
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char *pair_style,*bond_style,*angle_style,*dihedral_style,*improper_style;
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@ -91,6 +102,9 @@ 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_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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double *pair_ljexpand_epsilon,*pair_ljexpand_sigma,*pair_ljexpand_shift;
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double *pair_ljsmooth_epsilon,*pair_ljsmooth_sigma;
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double *pair_morse_d0,*pair_morse_alpha,*pair_morse_r0;
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@ -116,6 +130,8 @@ class Data {
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double *angle_cosine_k;
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double *angle_cosine_squared_k,*angle_cosine_squared_theta0;
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double *angle_harmonic_k,*angle_harmonic_theta0;
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double *angle_cg_cmm_epsilon,*angle_cg_cmm_sigma;
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int *angle_cg_cmm_type;
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double *dihedral_charmm_k,*dihedral_charmm_weight;
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int *dihedral_charmm_multiplicity,*dihedral_charmm_sign;
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@ -172,7 +188,7 @@ class Data {
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Data();
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void stats();
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void write(FILE *);
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void write(FILE *fp, FILE *fp2=NULL);
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void write_atom_angle(FILE *, int, int, int, int);
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void write_atom_atomic(FILE *, int, int, int, int);
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@ -266,13 +282,13 @@ char *read_char(FILE *fp);
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// main program
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// ---------------------------------------------------------------------
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main (int argc, char **argv)
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int main (int argc, char **argv)
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{
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// syntax error check
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if (argc != 3) {
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printf("Syntax: restart2data restart-file data-file\n");
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exit(1);
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if ((argc != 3) && (argc !=4)) {
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printf("Syntax: restart2data restart-file data-file [parameter-file]\n");
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return 1;
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}
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// if restart file contains '%', file = filename with % replaced by "base"
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@ -297,7 +313,7 @@ main (int argc, char **argv)
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FILE *fp = fopen(file,"rb");
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if (fp == NULL) {
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printf("ERROR: Cannot open restart file %s\n",file);
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exit(1);
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return 1;
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}
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// read beginning of restart file
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@ -324,8 +340,8 @@ main (int argc, char **argv)
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sprintf(file,"%s%d%s",argv[1],iproc,ptr+1);
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fp = fopen(file,"rb");
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if (fp == NULL) {
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printf("ERROR: Cannot open restart file %s\n",file);
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exit(1);
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printf("ERROR: Cannot open restart file %s\n",file);
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return 1;
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}
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}
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n = read_int(fp);
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@ -348,17 +364,40 @@ main (int argc, char **argv)
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data.stats();
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// write out data file
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// write out data file and no parameter file
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printf("Writing data file ...\n");
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fp = fopen(argv[2],"w");
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if (fp == NULL) {
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printf("ERROR: Cannot open data file %s\n",argv[2]);
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exit(1);
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if (argc == 3) {
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printf("Writing data file ...\n");
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fp = fopen(argv[2],"w");
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if (fp == NULL) {
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printf("ERROR: Cannot open data file %s\n",argv[2]);
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return 1;
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}
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data.write(fp);
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fclose(fp);
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// write out data file and parameter file
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} else {
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printf("Writing data file ...\n");
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fp = fopen(argv[2],"w");
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if (fp == NULL) {
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printf("ERROR: Cannot open data file %s\n",argv[2]);
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return 1;
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}
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printf("Writing parameter file ...\n");
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FILE *fp2 = fopen(argv[3],"w");
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if (fp2 == NULL) {
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printf("ERROR: Cannot open parameter file %s\n",argv[3]);
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return 1;
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}
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data.write(fp,fp2);
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fclose(fp);
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fclose(fp2);
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}
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data.write(fp);
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fclose(fp);
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return 0;
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}
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// ---------------------------------------------------------------------
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@ -1768,6 +1807,61 @@ 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,"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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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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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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if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(style,"cg/cmm/coul/long") == 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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data.pair_cut_coul = NULL;
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m=0;
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}
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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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if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
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(strcmp(style,"cg/cmm/coul/long") == 0) ) {
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data.pair_cut_coul[i] = new double[numtyp];
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}
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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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if (m) data.pair_cut_coul[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,"hybrid") == 0) {
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// for each substyle of hybrid,
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@ -1922,7 +2016,8 @@ void angle(FILE *fp, Data &data)
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data.angle_cosine_k = new double[data.nangletypes+1];
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fread(&data.angle_cosine_k[1],sizeof(double),data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cosine/squared") == 0) {
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} else if ((strcmp(data.angle_style,"cosine/squared") == 0) ||
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(strcmp(data.angle_style,"cosine/delta") == 0)) {
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data.angle_cosine_squared_k = new double[data.nangletypes+1];
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data.angle_cosine_squared_theta0 = new double[data.nangletypes+1];
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@ -1937,6 +2032,22 @@ void angle(FILE *fp, Data &data)
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fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"cg/cmm") == 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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data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
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data.angle_cg_cmm_sigma = new double[data.nangletypes+1];
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double *angle_cg_cmm_rcut = new double[data.nangletypes+1];
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data.angle_cg_cmm_type = new int[data.nangletypes+1];
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fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_sigma[1],sizeof(double),data.nangletypes,fp);
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fread(angle_cg_cmm_rcut,sizeof(double),data.nangletypes,fp);
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fread(&data.angle_cg_cmm_type[1],sizeof(int),data.nangletypes,fp);
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} else if (strcmp(data.angle_style,"hybrid") == 0) {
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int nstyles = read_int(fp);
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@ -2243,7 +2354,7 @@ void Data::stats()
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// write the data file
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// ---------------------------------------------------------------------
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void Data::write(FILE *fp)
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void Data::write(FILE *fp, FILE *fp2)
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{
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fprintf(fp,"LAMMPS data file from restart file: timestep = %d, procs = %d\n",
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ntimestep,nprocs);
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@ -2271,9 +2382,33 @@ void Data::write(FILE *fp)
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fprintf(fp,"%g %g zlo zhi\n",zlo,zhi);
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if (triclinic) fprintf(fp,"%g %g %g xy xz yz\n",xy,xz,yz);
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// write ff styles to parameter file
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if (fp2) {
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fprintf(fp2,"# LAMMPS parameter file from restart file: timestep = %d, procs = %d\n\n",
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ntimestep,nprocs);
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if (pair_style) fprintf(fp2,"pair_style %s\n",pair_style);
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if (bond_style) fprintf(fp2,"bond_style %s\n",bond_style);
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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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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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}
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// mass to either data file or parameter file
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if (mass) {
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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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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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}
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if (shape) {
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@ -2286,8 +2421,10 @@ void Data::write(FILE *fp)
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fprintf(fp,"\nDipoles\n\n");
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for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,dipole[i]);
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}
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if (pair_style) {
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// pair coeffs to data file
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if (pair_style && fp2 == NULL) {
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if ((strcmp(pair_style,"none") != 0) &&
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(strcmp(pair_style,"eam") != 0) &&
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(strcmp(pair_style,"eam/opt") != 0) &&
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@ -2389,10 +2526,41 @@ void Data::write(FILE *fp)
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for (int i = 1; i <= ntypes; i++)
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fprintf(fp,"%d %g\n",i,
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pair_yukawa_A[i]);
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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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printf("ERROR: Cannot write pair_style %s to data file\n",
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pair_style);
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exit(1);
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}
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}
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if (bond_style) {
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// pair coeffs to parameter file
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// only supported styles = cg/cmm
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if (pair_style && fp2) {
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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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for (int i = 1; i <= ntypes; i++) {
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for (int j = i; j <= ntypes; j++) {
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fprintf(fp2,"pair_coeff %d %d %s %g %g\n",i,j,
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cg_type_list[pair_cg_cmm_type[i][j]],
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pair_cg_epsilon[i][j],pair_cg_sigma[i][j]);
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}
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}
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} else {
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printf("ERROR: Cannot write pair_style %s to parameter file\n",
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pair_style);
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exit(1);
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}
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}
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// bond coeffs to data file
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if (bond_style && fp2 == NULL) {
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if ((strcmp(bond_style,"none") != 0) &&
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(strcmp(bond_style,"hybrid") != 0))
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fprintf(fp,"\nBond Coeffs\n\n");
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@ -2434,7 +2602,25 @@ void Data::write(FILE *fp)
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}
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}
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if (angle_style) {
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// bond coeffs to parameter file
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// only supported styles = harmonic
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if (bond_style && fp2) {
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if (strcmp(bond_style,"harmonic") == 0) {
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for (int i = 1; i <= nbondtypes; i++)
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fprintf(fp2,"bond_coeff %d %g %g\n",i,
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bond_harmonic_k[i],bond_harmonic_r0[i]);
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} else {
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printf("ERROR: Cannot write bond_style %s to parameter file\n",
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bond_style);
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exit(1);
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}
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}
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// angle coeffs to data file
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if (angle_style && fp2 == NULL) {
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double PI = 3.1415926; // convert back to degrees
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if ((strcmp(angle_style,"none") != 0) &&
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@ -2452,13 +2638,13 @@ void Data::write(FILE *fp)
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fprintf(fp,"%d %g %g %g %g\n",i,
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angle_class2_theta0[i]/PI*180.0,angle_class2_k2[i],
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angle_class2_k3[i],angle_class2_k4[i]);
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fprintf(fp,"\nBondBond Coeffs\n\n");
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for (int i = 1; i <= nangletypes; i++)
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fprintf(fp,"%d %g %g %g\n",i,
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angle_class2_bb_k[i],
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angle_class2_bb_r1[i],angle_class2_bb_r2[i]);
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fprintf(fp,"\nBondAngle Coeffs\n\n");
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for (int i = 1; i <= nangletypes; i++)
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fprintf(fp,"%d %g %g %g %g\n",i,
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@ -2467,13 +2653,56 @@ void Data::write(FILE *fp)
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} else if (strcmp(angle_style,"cosine") == 0) {
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for (int i = 1; i <= nangletypes; i++)
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fprintf(fp,"%d %g\n",i,
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angle_cosine_k[i]);
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} if (strcmp(angle_style,"harmonic") == 0) {
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fprintf(fp,"%d %g\n",i,angle_cosine_k[i]);
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} else if (strcmp(angle_style,"cosine/squared") == 0) {
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for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,
|
||||
angle_cosine_squared_k[i],
|
||||
angle_cosine_squared_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"harmonic") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,
|
||||
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"cg/cmm") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g %s %g %g\n",i,
|
||||
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
|
||||
cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
|
||||
angle_cg_cmm_sigma[i]);
|
||||
}
|
||||
}
|
||||
|
||||
// angle coeffs to parameter file
|
||||
// only supported styles = cosine/squared, harmonic, cg/cmm
|
||||
|
||||
if (angle_style && fp2) {
|
||||
double PI = 3.1415926; // convert back to degrees
|
||||
|
||||
if (strcmp(angle_style,"cosine/squared") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp2,"angle_coeffs %d %g %g\n",i,
|
||||
angle_cosine_squared_k[i],
|
||||
angle_cosine_squared_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"harmonic") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp2,"angle_coeffs %d %g %g\n",i,
|
||||
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"cg/cmm") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp2,"angle_coeffs %d %g %g %s %g %g\n",i,
|
||||
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
|
||||
cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
|
||||
angle_cg_cmm_sigma[i]);
|
||||
|
||||
} else {
|
||||
printf("ERROR: Cannot write angle_style %s to parameter file\n",
|
||||
angle_style);
|
||||
exit(1);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue