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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6338 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-06-08 20:23:37 +00:00
parent 02ea2aaf33
commit b303b5b852
1 changed files with 125 additions and 104 deletions
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229
tools/restart2data.cpp
View File

@ -13,11 +13,14 @@
// Convert a LAMMPS binary restart file into an ASCII text data file
//
// Syntax: restart2data restart-file data-file (input-file)
// Syntax: restart2data switch arg ... restart-file data-file (input-file)
// optional switch = -s
// arg = suffix to remove from style names
// restart-file and data-file are mandatory
// input-file is optional
// if specified it will contain LAMMPS input script commands
// for mass and force field info
// only a few force field styles support this option
// if specified it will contain LAMMPS input script commands
// for mass and force field info
// only a few force field styles support this option
//
// this serial code must be compiled on a platform that can read the binary
// restart file since binary formats are not compatible across all platforms
@ -77,6 +80,7 @@ class Data {
char *version;
int size_smallint,size_tagint,size_bigint;
char *suffix;
bigint ntimestep;
int nprocs;
char *unit_style;
@ -85,7 +89,7 @@ class Data {
int newton_pair,newton_bond;
int xperiodic,yperiodic,zperiodic;
int boundary[3][2];
char *atom_style;
int style_angle,style_atomic,style_bond,style_charge,style_dipole;
int style_ellipsoid,style_full;
@ -300,6 +304,8 @@ int atom_molecular(double *, Data &, int);
int atom_peri(double *, Data &, int);
int atom_sphere(double *, Data &, int);
void strip_suffix(char *, char *);
int read_int(FILE *fp);
double read_double(FILE *fp);
char *read_char(FILE *fp);
@ -309,44 +315,74 @@ bigint read_bigint(FILE *fp);
// main program
// ---------------------------------------------------------------------
int main (int argc, char **argv)
int main (int narg, char **arg)
{
// syntax error check
// process command-line args
if ((argc != 3) && (argc !=4)) {
printf("Syntax: restart2data restart-file data-file (input-file)\n");
char *suffix = NULL;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"-s") == 0) {
if (iarg+2 > narg) {
printf("Syntax: restart2data switch arg ... "
"restart-file data-file (input-file)\n");
return 1;
}
suffix = arg[iarg+1];
iarg += 2;
} else break;
}
if ((narg-iarg != 2) && (narg-iarg != 3)) {
printf("Syntax: restart2data switch arg ... "
"restart-file data-file (input-file)\n");
return 1;
}
char *restartfile = arg[iarg];
char *datafile = arg[iarg+1];
char *inputfile = NULL;
if (narg-iarg == 3) inputfile = arg[iarg+2];
// if restart file contains '%', file = filename with % replaced by "base"
// else file = single file
int multiproc;
char *file,*ptr;
if (ptr = strchr(argv[1],'%')) {
multiproc = 1;
file = new char[strlen(argv[1]) + 16];
*ptr = '\0';
sprintf(file,"%s%s%s",argv[1],"base",ptr+1);
} else {
multiproc = 0;
file = argv[1];
}
// open single restart file or base file for multiproc case
printf("Reading restart file ...\n");
FILE *fp = fopen(file,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",file);
return 1;
char *ptr;
FILE *fp;
int multiproc = 0;
if (ptr = strchr(restartfile,'%')) {
multiproc = 1;
char *basefile = new char[strlen(restartfile) + 16];
*ptr = '\0';
sprintf(basefile,"%s%s%s",restartfile,"base",ptr+1);
fp = fopen(basefile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",basefile);
return 1;
}
} else {
fp = fopen(restartfile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",restartfile);
return 1;
}
}
// read beginning of restart file
Data data;
if (suffix) {
int n = strlen(suffix) + 1;
data.suffix = new char[n];
strcpy(data.suffix,suffix);
} else data.suffix = NULL;
header(fp,data);
if (data.size_smallint != sizeof(int) ||
data.size_tagint != sizeof(tagint) ||
@ -372,10 +408,11 @@ int main (int argc, char **argv)
for (int iproc = 0; iproc < data.nprocs; iproc++) {
if (multiproc) {
fclose(fp);
sprintf(file,"%s%d%s",argv[1],iproc,ptr+1);
fp = fopen(file,"rb");
char *procfile;
sprintf(procfile,"%s%d%s",restartfile,iproc,ptr+1);
fp = fopen(procfile,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",file);
printf("ERROR: Cannot open restart file %s\n",procfile);
return 1;
}
}
@ -401,11 +438,11 @@ int main (int argc, char **argv)
// write out data file and no input file
if (argc == 3) {
if (!inputfile) {
printf("Writing data file ...\n");
fp = fopen(argv[2],"w");
fp = fopen(datafile,"w");
if (fp == NULL) {
printf("ERROR: Cannot open data file %s\n",argv[2]);
printf("ERROR: Cannot open data file %s\n",datafile);
return 1;
}
data.write(fp);
@ -415,15 +452,15 @@ int main (int argc, char **argv)
} else {
printf("Writing data file ...\n");
fp = fopen(argv[2],"w");
fp = fopen(datafile,"w");
if (fp == NULL) {
printf("ERROR: Cannot open data file %s\n",argv[2]);
printf("ERROR: Cannot open data file %s\n",datafile);
return 1;
}
printf("Writing input file ...\n");
FILE *fp2 = fopen(argv[3],"w");
FILE *fp2 = fopen(inputfile,"w");
if (fp2 == NULL) {
printf("ERROR: Cannot open input file %s\n",argv[3]);
printf("ERROR: Cannot open input file %s\n",inputfile);
return 1;
}
@ -492,6 +529,7 @@ void header(FILE *fp, Data &data)
data.style_molecular = data.style_peri = data.style_sphere = 0;
data.atom_style = read_char(fp);
strip_suffix(data.atom_style,data.suffix);
set_style(data.atom_style,data,1);
if (strcmp(data.atom_style,"hybrid") == 0) {
@ -638,18 +676,23 @@ void force_fields(FILE *fp, Data &data)
if (flag == PAIR) {
data.pair_style = read_char(fp);
strip_suffix(data.pair_style,data.suffix);
pair(fp,data,data.pair_style,1);
} else if (flag == BOND) {
data.bond_style = read_char(fp);
strip_suffix(data.bond_style,data.suffix);
bond(fp,data);
} else if (flag == ANGLE) {
data.angle_style = read_char(fp);
strip_suffix(data.angle_style,data.suffix);
angle(fp,data);
} else if (flag == DIHEDRAL) {
data.dihedral_style = read_char(fp);
strip_suffix(data.dihedral_style,data.suffix);
dihedral(fp,data);
} else if (flag == IMPROPER) {
data.improper_style = read_char(fp);
strip_suffix(data.improper_style,data.suffix);
improper(fp,data);
} else {
printf("ERROR: Invalid flag in force fields section of restart file %d\n",
@ -1338,9 +1381,9 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
} else if ((strcmp(style,"buck") == 0) ||
(strcmp(style,"buck/coul/cut") == 0) ||
(strcmp(style,"buck/coul/long") == 0) ||
(strcmp(style,"buck/coul") == 0)) {
(strcmp(style,"buck/coul/cut") == 0) ||
(strcmp(style,"buck/coul/long") == 0) ||
(strcmp(style,"buck/coul") == 0)) {
if (strcmp(style,"buck") == 0) {
m = 0;
@ -1573,11 +1616,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
} else if (strcmp(style,"eam") == 0) {
} else if (strcmp(style,"eam/opt") == 0) {
} else if (strcmp(style,"eam/alloy") == 0) {
} else if (strcmp(style,"eam/alloy/opt") == 0) {
} else if (strcmp(style,"eam/fs") == 0) {
} else if (strcmp(style,"eam/fs/opt") == 0) {
} else if (strcmp(style,"eim") == 0) {
} else if (strcmp(style,"eff/cut") == 0) {
@ -1666,11 +1706,9 @@ void pair(FILE *fp, Data &data, char *style, int flag)
int dampflag = read_int(fp);
} else if ((strcmp(style,"lj/charmm/coul/charmm") == 0) ||
(strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) ||
(strcmp(style,"lj/charmm/coul/long") == 0) ||
(strcmp(style,"lj/charmm/coul/long/gpu") == 0) ||
(strcmp(style,"lj/charmm/coul/long/opt") == 0)) {
(strcmp(style,"lj/charmm/coul/charmm/implicit") == 0) ||
(strcmp(style,"lj/charmm/coul/long") == 0)) {
if (strcmp(style,"lj/charmm/coul/charmm") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
@ -1685,9 +1723,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
double cut_coul = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if ((strcmp(style,"lj/charmm/coul/long") == 0) ||
(strcmp(style,"lj/charmm/coul/long/gpu") == 0) ||
(strcmp(style,"lj/charmm/coul/long/opt") == 0)) {
} else if (strcmp(style,"lj/charmm/coul/long") == 0) {
double cut_lj_inner = read_double(fp);
double cut_lj = read_double(fp);
double cut_coul = read_double(fp);
@ -1726,7 +1762,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
} else if ((strcmp(style,"lj/class2") == 0) ||
(strcmp(style,"lj/class2/coul/cut") == 0) ||
(strcmp(style,"lj/class2/coul/long") == 0)) {
(strcmp(style,"lj/class2/coul/long") == 0)) {
if (strcmp(style,"lj/class2") == 0) {
m = 0;
@ -1775,25 +1811,18 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
} else if ((strcmp(style,"lj/cut") == 0) ||
(strcmp(style,"lj/cut/gpu") == 0) ||
(strcmp(style,"lj/cut/opt") == 0) ||
(strcmp(style,"lj/cut/coul/cut") == 0) ||
(strcmp(style,"lj/cut/coul/cut/gpu") == 0) ||
(strcmp(style,"lj/cut/coul/debye") == 0) ||
(strcmp(style,"lj/cut/coul/long") == 0) ||
(strcmp(style,"lj/cut/coul/long/gpu") == 0) ||
(strcmp(style,"lj/cut/coul/long/tip4p") == 0) ||
(strcmp(style,"lj/coul") == 0)) {
(strcmp(style,"lj/cut/coul/cut") == 0) ||
(strcmp(style,"lj/cut/coul/debye") == 0) ||
(strcmp(style,"lj/cut/coul/long") == 0) ||
(strcmp(style,"lj/cut/coul/long/tip4p") == 0) ||
(strcmp(style,"lj/coul") == 0)) {
if ((strcmp(style,"lj/cut") == 0) ||
(strcmp(style,"lj/cut/gpu") == 0) ||
(strcmp(style,"lj/cut/opt") == 0)) {
if (strcmp(style,"lj/cut") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if ((strcmp(style,"lj/cut/coul/cut") == 0) ||
(strcmp(style,"lj/cut/coul/cut/gpu") == 0)) {
} else if (strcmp(style,"lj/cut/coul/cut") == 0) {
m = 1;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
@ -1806,8 +1835,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
double kappa = read_double(fp);
int offset_flag = read_int(fp);
int mix_flag = read_int(fp);
} else if ((strcmp(style,"lj/cut/coul/long") == 0) ||
(strcmp(style,"lj/cut/coul/long/gpu") == 0)) {
} else if (strcmp(style,"lj/cut/coul/long") == 0) {
m = 0;
double cut_lj_global = read_double(fp);
double cut_lj_coul = read_double(fp);
@ -1860,8 +1888,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
}
} else if ((strcmp(style,"lj/expand") == 0) ||
(strcmp(style,"lj/expand/gpu") == 0)) {
} else if (strcmp(style,"lj/expand") == 0) {
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
@ -1897,7 +1924,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
} else if ((strcmp(style,"lj/gromacs") == 0) ||
(strcmp(style,"lj/gromacs/coul/gromacs") == 0)) {
if (strcmp(style,"lj/gromacs") == 0) {
m = 1;
double cut_inner_global = read_double(fp);
@ -1981,9 +2008,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
} else if (strcmp(style,"meam") == 0) {
} else if ((strcmp(style,"morse") == 0) ||
(strcmp(style,"morse/gpu") == 0) ||
(strcmp(style,"morse/opt") == 0)) {
} else if (strcmp(style,"morse") == 0) {
double cut_global = read_double(fp);
int offset_flag = read_int(fp);
@ -2087,10 +2112,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
} else if ((strcmp(style,"cg/cmm") == 0) ||
(strcmp(style,"cg/cmm/gpu") == 0) ||
(strcmp(style,"cg/cmm/coul/cut") == 0) ||
(strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"cg/cmm/coul/long/gpu") == 0)) {
(strcmp(style,"cg/cmm/coul/long") == 0)) {
m = 0;
data.cut_lj_global = read_double(fp);
data.cut_coul_global = read_double(fp);
@ -2106,9 +2129,8 @@ void pair(FILE *fp, Data &data, char *style, int flag)
data.pair_cg_epsilon = new double*[numtyp];
data.pair_cg_sigma = new double*[numtyp];
data.pair_cut_lj = new double*[numtyp];
if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
(strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"cg/cmm/coul/long/gpu") == 0)) {
if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
(strcmp(style,"cg/cmm/coul/long") == 0)) {
data.pair_cut_coul = new double*[numtyp];
m=1;
} else {
@ -2123,8 +2145,7 @@ void pair(FILE *fp, Data &data, char *style, int flag)
data.pair_cg_sigma[i] = new double[numtyp];
data.pair_cut_lj[i] = new double[numtyp];
if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
(strcmp(style,"cg/cmm/coul/long") == 0) ||
(strcmp(style,"cg/cmm/coul/long/gpu") == 0)) {
(strcmp(style,"cg/cmm/coul/long") == 0)) {
data.pair_cut_coul[i] = new double[numtyp];
}
@ -2745,11 +2766,8 @@ void Data::write(FILE *fp, FILE *fp2)
(strcmp(pair_style,"coul/debye") != 0) &&
(strcmp(pair_style,"coul/long") != 0) &&
(strcmp(pair_style,"eam") != 0) &&
(strcmp(pair_style,"eam/opt") != 0) &&
(strcmp(pair_style,"eam/alloy") != 0) &&
(strcmp(pair_style,"eam/alloy/opt") != 0) &&
(strcmp(pair_style,"eam/fs") != 0) &&
(strcmp(pair_style,"eam/fs/opt") != 0) &&
(strcmp(pair_style,"eim") != 0) &&
(strcmp(pair_style,"eff/cut") != 0) &&
(strcmp(pair_style,"gran/history") != 0) &&
@ -2773,9 +2791,9 @@ void Data::write(FILE *fp, FILE *fp2)
pair_born_C[i],pair_born_D[i]);
} else if ((strcmp(pair_style,"buck") == 0) ||
(strcmp(pair_style,"buck/coul/cut") == 0) ||
(strcmp(pair_style,"buck/coul/long") == 0) ||
(strcmp(pair_style,"buck/long") == 0)) {
(strcmp(pair_style,"buck/coul/cut") == 0) ||
(strcmp(pair_style,"buck/coul/long") == 0) ||
(strcmp(pair_style,"buck/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_buck_A[i],pair_buck_rho[i],pair_buck_C[i]);
@ -2801,8 +2819,7 @@ void Data::write(FILE *fp, FILE *fp2)
fprintf(fp,"%d %g\n",i,
pair_dpd_gamma[i]);
} else if ((strcmp(pair_style,"gayberne") == 0) ||
(strcmp(pair_style,"gayberne/gpu") == 0)) {
} else if (strcmp(pair_style,"gayberne") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
pair_gb_epsilon[i],pair_gb_sigma[i],
@ -2811,7 +2828,6 @@ void Data::write(FILE *fp, FILE *fp2)
} else if ((strcmp(pair_style,"lj/charmm/coul/charmm") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/charmm/implicit") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/long") == 0) ||
(strcmp(pair_style,"lj/charmm/coul/long") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
@ -2824,23 +2840,18 @@ void Data::write(FILE *fp, FILE *fp2)
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_class2_epsilon[i],pair_class2_sigma[i]);
} else if ((strcmp(pair_style,"lj/cut") == 0) ||
(strcmp(pair_style,"lj/cut/gpu") == 0) ||
(strcmp(pair_style,"lj/cut/opt") == 0) ||
(strcmp(pair_style,"lj/cut/coul/cut") == 0) ||
(strcmp(pair_style,"lj/cut/coul/cut/gpu") == 0) ||
(strcmp(pair_style,"lj/cut/coul/debye") == 0) ||
(strcmp(pair_style,"lj/cut/coul/long") == 0) ||
(strcmp(pair_style,"lj/cut/coul/long/gpu") == 0) ||
(strcmp(pair_style,"lj/cut/coul/long/tip4p") == 0) ||
(strcmp(pair_style,"lj/coul") == 0)) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g\n",i,
pair_lj_epsilon[i],pair_lj_sigma[i]);
} else if ((strcmp(pair_style,"lj/expand") == 0) ||
(strcmp(pair_style,"lj/expand/gpu")==0)) {
} else if (strcmp(pair_style,"lj/expand") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_ljexpand_epsilon[i],pair_ljexpand_sigma[i],
@ -2857,9 +2868,7 @@ void Data::write(FILE *fp, FILE *fp2)
fprintf(fp,"%d %g %g\n",i,
pair_ljsmooth_epsilon[i],pair_ljsmooth_sigma[i]);
} else if ((strcmp(pair_style,"morse") == 0) ||
(strcmp(pair_style,"morse/gpu") == 0) ||
(strcmp(pair_style,"morse/opt") == 0)) {
} else if (strcmp(pair_style,"morse") == 0) {
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
pair_morse_d0[i],pair_morse_alpha[i],pair_morse_r0[i]);
@ -2888,10 +2897,8 @@ void Data::write(FILE *fp, FILE *fp2)
if (pair_style && fp2) {
if ((strcmp(pair_style,"cg/cmm") == 0) ||
(strcmp(pair_style,"cg/cmm/gpu") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/long") == 0) ||
(strcmp(pair_style,"cg/cmm/coul/long/gpu") == 0)) {
(strcmp(pair_style,"cg/cmm/coul/long") == 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,
@ -3502,6 +3509,20 @@ void Data::write_vel_sphere_extra(FILE *fp, int i)
void Data::write_vel_molecular_extra(FILE *fp, int i) {}
void Data::write_vel_peri_extra(FILE *fp, int i) {}
// ---------------------------------------------------------------------
// strip suffix from style name if suffix is defined
// ---------------------------------------------------------------------
void strip_suffix(char *style, char *suffix)
{
if (!suffix) return;
int n = strlen(suffix) + 2;
char *esuffix = new char[n];
sprintf(esuffix,"/%s",suffix);
char *ptr = strstr(style,esuffix);
if (ptr && ptr-style+1+strlen(suffix) == strlen(style)) *ptr = '\0';
}
// ---------------------------------------------------------------------
// binary reads from restart file
// ---------------------------------------------------------------------