mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7017 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8e637f06fa
commit
4c107e07a4
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@ -13,9 +13,7 @@
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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 switch arg ... restart-file data-file (input-file)
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// optional switch = -s
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// arg = suffix to remove from style names
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// Syntax: restart2data restart-file data-file (input-file)
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// restart-file and data-file are mandatory
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// input-file is optional
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// if specified it will contain LAMMPS input script commands
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@ -80,7 +78,6 @@ class Data {
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char *version;
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int size_smallint,size_tagint,size_bigint;
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char *suffix;
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bigint ntimestep;
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int nprocs;
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char *unit_style;
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@ -316,7 +313,7 @@ int atom_molecular(double *, Data &, int);
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int atom_peri(double *, Data &, int);
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int atom_sphere(double *, Data &, int);
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void strip_suffix(char *, char *);
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void strip_suffix(char *);
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int read_int(FILE *fp);
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double read_double(FILE *fp);
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@ -331,29 +328,16 @@ int main (int narg, char **arg)
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{
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// process command-line args
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char *suffix = NULL;
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"-h") == 0) {
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printf("Syntax: restart2data switch arg ... "
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"restart-file data-file (input-file)\n");
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printf(" optional switch = -s");
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printf(" arg = suffix to remove from style names");
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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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} else if (strcmp(arg[iarg],"-s") == 0) {
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if (iarg+2 > narg) {
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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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suffix = arg[iarg+1];
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iarg += 2;
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} else break;
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if (strcmp(arg[iarg],"-h") == 0) {
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printf("Syntax: restart2data switch arg ... "
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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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return 0;
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}
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if ((narg-iarg != 2) && (narg-iarg != 3)) {
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@ -377,7 +361,7 @@ int main (int narg, char **arg)
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FILE *fp;
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int multiproc = 0;
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if (ptr = strchr(restartfile,'%')) {
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if ( (ptr = strchr(restartfile,'%')) ) {
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multiproc = 1;
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char *basefile = new char[strlen(restartfile) + 16];
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*ptr = '\0';
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@ -399,12 +383,6 @@ int main (int narg, char **arg)
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Data data;
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if (suffix) {
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int n = strlen(suffix) + 1;
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data.suffix = new char[n];
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strcpy(data.suffix,suffix);
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} else data.suffix = NULL;
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header(fp,data);
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if (data.size_smallint != sizeof(int) ||
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data.size_tagint != sizeof(tagint) ||
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@ -500,7 +478,7 @@ 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 = "25 Jun 2011";
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char *version = "19 Aug 2011";
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data.triclinic = 0;
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@ -551,7 +529,7 @@ void header(FILE *fp, Data &data)
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data.style_molecular = data.style_peri = data.style_sphere = 0;
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data.atom_style = read_char(fp);
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strip_suffix(data.atom_style,data.suffix);
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strip_suffix(data.atom_style);
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set_style(data.atom_style,data,1);
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if (strcmp(data.atom_style,"hybrid") == 0) {
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@ -641,7 +619,6 @@ void groups(FILE *fp)
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{
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int ngroup = read_int(fp);
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int n;
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char *name;
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// use count to not change restart format with deleted groups
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@ -698,23 +675,23 @@ void force_fields(FILE *fp, Data &data)
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if (flag == PAIR) {
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data.pair_style = read_char(fp);
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strip_suffix(data.pair_style,data.suffix);
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strip_suffix(data.pair_style);
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pair(fp,data,data.pair_style,1);
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} else if (flag == BOND) {
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data.bond_style = read_char(fp);
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strip_suffix(data.bond_style,data.suffix);
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strip_suffix(data.bond_style);
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bond(fp,data);
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} else if (flag == ANGLE) {
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data.angle_style = read_char(fp);
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strip_suffix(data.angle_style,data.suffix);
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strip_suffix(data.angle_style);
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angle(fp,data);
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} else if (flag == DIHEDRAL) {
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data.dihedral_style = read_char(fp);
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strip_suffix(data.dihedral_style,data.suffix);
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strip_suffix(data.dihedral_style);
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dihedral(fp,data);
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} else if (flag == IMPROPER) {
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data.improper_style = read_char(fp);
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strip_suffix(data.improper_style,data.suffix);
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strip_suffix(data.improper_style);
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improper(fp,data);
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} else {
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printf("ERROR: Invalid flag in force fields section of restart file %d\n",
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@ -3330,7 +3307,7 @@ void Data::write(FILE *fp, FILE *fp2)
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fprintf(fp,"\nAtoms\n\n");
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int ix,iy,iz;
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for (uint64_t i = 0; i < natoms; i++) {
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for (bigint i = 0; i < natoms; i++) {
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ix = (image[i] & 1023) - 512;
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iy = (image[i] >> 10 & 1023) - 512;
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@ -3371,7 +3348,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (natoms) {
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fprintf(fp,"\nVelocities\n\n");
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for (uint64_t i = 0; i < natoms; i++)
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for (bigint i = 0; i < natoms; i++)
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if (style_hybrid == 0) {
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if (style_angle) write_vel_angle(fp,i);
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@ -3406,7 +3383,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (nellipsoids) {
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fprintf(fp,"\nEllipsoids\n\n");
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for (uint64_t i = 0; i < natoms; i++) {
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for (bigint i = 0; i < natoms; i++) {
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if (ellipsoid[i])
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fprintf(fp,"%d %-1.16e %-1.16e %-1.16e "
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"%-1.16e %-1.16e %-1.16e %-1.16e \n",
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@ -3417,21 +3394,21 @@ void Data::write(FILE *fp, FILE *fp2)
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if (nbonds) {
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fprintf(fp,"\nBonds\n\n");
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for (uint64_t i = 0; i < nbonds; i++)
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for (bigint i = 0; i < nbonds; 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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fprintf(fp,"\nAngles\n\n");
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for (uint64_t i = 0; i < nangles; i++)
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for (bigint i = 0; i < nangles; 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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fprintf(fp,"\nDihedrals\n\n");
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for (uint64_t i = 0; i < ndihedrals; i++)
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for (bigint i = 0; i < ndihedrals; 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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@ -3439,7 +3416,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (nimpropers) {
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fprintf(fp,"\nImpropers\n\n");
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for (uint64_t i = 0; i < nimpropers; i++)
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for (bigint i = 0; i < nimpropers; 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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@ -3509,7 +3486,7 @@ void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz)
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void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)
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{
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fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
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fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
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tag[i],type[i],vfrac[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
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}
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@ -3562,7 +3539,7 @@ void Data::write_atom_molecular_extra(FILE *fp, int i)
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void Data::write_atom_peri_extra(FILE *fp, int i)
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{
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fprintf(fp," %-1.16e %-1.16e %-1.16e",vfrac[i],rmass[i]);
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fprintf(fp," %-1.16e %-1.16e",vfrac[i],rmass[i]);
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}
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// ---------------------------------------------------------------------
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@ -3649,17 +3626,26 @@ void Data::write_vel_molecular_extra(FILE *fp, int i) {}
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void Data::write_vel_peri_extra(FILE *fp, int i) {}
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// ---------------------------------------------------------------------
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// strip suffix from style name if suffix is defined
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// strip known accelerator suffixes from style name
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// ---------------------------------------------------------------------
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void strip_suffix(char *style, char *suffix)
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void strip_suffix(char *style)
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{
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if (!suffix) return;
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int n = strlen(suffix) + 2;
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char *esuffix = new char[n];
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sprintf(esuffix,"/%s",suffix);
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char *ptr = strstr(style,esuffix);
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if (ptr && ptr-style+1+strlen(suffix) == strlen(style)) *ptr = '\0';
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char *slash = strrchr(style,'/');
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if (slash == NULL) return;
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int i=0;
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const char *suffix_list[] = { "/opt", "/gpu", "/cuda", "/omp", NULL };
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const char *suffix = suffix_list[0];
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while (suffix != NULL) {
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if (strcmp(slash,suffix) == 0) {
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*slash = '\0';
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return;
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}
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++i;
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suffix = suffix_list[i];
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}
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}
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// ---------------------------------------------------------------------
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