git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -71,7 +71,7 @@ void ReadRestart::command(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal read_restart command");
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if (domain->box_exist)
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if (domain->box_exist)
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error->all(FLERR,"Cannot read_restart after simulation box is defined");
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MPI_Comm_rank(world,&me);
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@ -181,30 +181,30 @@ void ReadRestart::command(int narg, char **arg)
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for (int iproc = 0; iproc < nprocs_file; iproc++) {
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n = read_int();
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if (n > maxbuf) {
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maxbuf = n;
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memory->destroy(buf);
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memory->create(buf,maxbuf,"read_restart:buf");
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maxbuf = n;
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memory->destroy(buf);
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memory->create(buf,maxbuf,"read_restart:buf");
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}
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if (n > 0) {
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if (me == 0) nread_double(buf,n,fp);
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MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
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if (me == 0) nread_double(buf,n,fp);
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MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
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}
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m = 0;
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while (m < n) {
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x = &buf[m+1];
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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m += avec->unpack_restart(&buf[m]);
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}
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else m += static_cast<int> (buf[m]);
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x = &buf[m+1];
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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m += avec->unpack_restart(&buf[m]);
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}
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else m += static_cast<int> (buf[m]);
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}
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}
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@ -227,16 +227,16 @@ void ReadRestart::command(int narg, char **arg)
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*ptr = '%';
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fp = fopen(perproc,"rb");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open restart file %s",perproc);
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error->one(FLERR,str);
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char str[128];
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sprintf(str,"Cannot open restart file %s",perproc);
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error->one(FLERR,str);
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}
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nread_int(&n,1,fp);
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if (n > maxbuf) {
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maxbuf = n;
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memory->destroy(buf);
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memory->create(buf,maxbuf,"read_restart:buf");
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maxbuf = n;
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memory->destroy(buf);
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memory->create(buf,maxbuf,"read_restart:buf");
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}
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if (n > 0) nread_double(buf,n,fp);
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@ -288,8 +288,8 @@ void ReadRestart::command(int narg, char **arg)
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double **atom_extra = atom->extra;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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for (int j = 0; j < count[i]; j++)
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atom_extra[i][j] = extra[i][j];
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for (int j = 0; j < count[i]; j++)
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atom_extra[i][j] = extra[i][j];
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modify->delete_fix("_read_restart");
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}
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}
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@ -310,7 +310,7 @@ void ReadRestart::command(int narg, char **arg)
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
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}
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if (natoms != atom->natoms)
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if (natoms != atom->natoms)
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error->all(FLERR,"Did not assign all atoms correctly");
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if (me == 0) {
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@ -320,21 +320,21 @@ void ReadRestart::command(int narg, char **arg)
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}
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if (atom->nangles) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
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atom->nangles);
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atom->nangles);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
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atom->nangles);
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atom->nangles);
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}
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if (atom->ndihedrals) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
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atom->ndihedrals);
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atom->ndihedrals);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
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atom->ndihedrals);
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atom->ndihedrals);
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}
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if (atom->nimpropers) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
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atom->nimpropers);
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atom->nimpropers);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
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atom->nimpropers);
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atom->nimpropers);
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}
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}
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@ -414,7 +414,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
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struct dirent *ep;
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DIR *dp = opendir(dirname);
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if (dp == NULL)
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if (dp == NULL)
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error->one(FLERR,"Cannot open dir to search for restart file");
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while (ep = readdir(dp)) {
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if (strstr(ep->d_name,begin) != ep->d_name) continue;
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@ -448,7 +448,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
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}
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/* ----------------------------------------------------------------------
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read header of restart file
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read header of restart file
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------------------------------------------------------------------------- */
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void ReadRestart::header()
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@ -467,27 +467,27 @@ void ReadRestart::header()
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if (flag == VERSION) {
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char *version = read_char();
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if (strcmp(version,universe->version) != 0 && me == 0) {
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error->warning(FLERR,
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"Restart file version does not match LAMMPS version");
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if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
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version,universe->version);
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error->warning(FLERR,
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"Restart file version does not match LAMMPS version");
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if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
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version,universe->version);
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}
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delete [] version;
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// check lmptype.h sizes, error if different
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} else if (flag == SMALLINT) {
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int size = read_int();
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if (size != sizeof(smallint))
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error->all(FLERR,"Smallint setting in lmptype.h is not compatible");
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error->all(FLERR,"Smallint setting in lmptype.h is not compatible");
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} else if (flag == TAGINT) {
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int size = read_int();
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if (size != sizeof(tagint))
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error->all(FLERR,"Tagint setting in lmptype.h is not compatible");
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error->all(FLERR,"Tagint setting in lmptype.h is not compatible");
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} else if (flag == BIGINT) {
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int size = read_int();
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if (size != sizeof(bigint))
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error->all(FLERR,"Bigint setting in lmptype.h is not compatible");
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error->all(FLERR,"Bigint setting in lmptype.h is not compatible");
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// reset unit_style only if different
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// so that timestep,neighbor-skin are not changed
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@ -506,15 +506,15 @@ void ReadRestart::header()
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int dimension = read_int();
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domain->dimension = dimension;
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if (domain->dimension == 2 && domain->zperiodic == 0)
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error->all(FLERR,
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"Cannot run 2d simulation with nonperiodic Z dimension");
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error->all(FLERR,
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"Cannot run 2d simulation with nonperiodic Z dimension");
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// read nprocs from restart file, warn if different
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} else if (flag == NPROCS) {
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nprocs_file = read_int();
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if (nprocs_file != comm->nprocs && me == 0)
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error->warning(FLERR,"Restart file used different # of processors");
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error->warning(FLERR,"Restart file used different # of processors");
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// don't set procgrid, warn if different
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@ -524,10 +524,10 @@ void ReadRestart::header()
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py = read_int();
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} else if (flag == PROCGRID_2) {
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pz = read_int();
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if (comm->user_procgrid[0] != 0 &&
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(px != comm->user_procgrid[0] || py != comm->user_procgrid[1] ||
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pz != comm->user_procgrid[2]) && me == 0)
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error->warning(FLERR,"Restart file used different 3d processor grid");
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if (comm->user_procgrid[0] != 0 &&
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(px != comm->user_procgrid[0] || py != comm->user_procgrid[1] ||
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pz != comm->user_procgrid[2]) && me == 0)
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error->warning(FLERR,"Restart file used different 3d processor grid");
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// don't set newton_pair, leave input script value unchanged
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// set newton_bond from restart file
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@ -536,18 +536,18 @@ void ReadRestart::header()
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} else if (flag == NEWTON_PAIR) {
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int newton_pair_file = read_int();
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if (force->newton_pair != 1) {
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if (newton_pair_file != force->newton_pair && me == 0)
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error->warning(FLERR,
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"Restart file used different newton pair setting, "
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"using input script value");
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if (newton_pair_file != force->newton_pair && me == 0)
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error->warning(FLERR,
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"Restart file used different newton pair setting, "
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"using input script value");
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}
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} else if (flag == NEWTON_BOND) {
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int newton_bond_file = read_int();
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if (force->newton_bond != 1) {
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if (newton_bond_file != force->newton_bond && me == 0)
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error->warning(FLERR,
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"Restart file used different newton bond setting, "
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"using restart file value");
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if (newton_bond_file != force->newton_bond && me == 0)
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error->warning(FLERR,
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"Restart file used different newton bond setting, "
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"using restart file value");
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}
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force->newton_bond = newton_bond_file;
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if (force->newton_pair || force->newton_bond) force->newton = 1;
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@ -575,20 +575,20 @@ void ReadRestart::header()
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} else if (flag == BOUNDARY_21) {
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boundary[2][1] = read_int();
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if (domain->boundary[0][0] || domain->boundary[0][1] ||
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domain->boundary[1][0] || domain->boundary[1][1] ||
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domain->boundary[2][0] || domain->boundary[2][1]) {
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if (boundary[0][0] != domain->boundary[0][0] ||
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boundary[0][1] != domain->boundary[0][1] ||
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boundary[1][0] != domain->boundary[1][0] ||
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boundary[1][1] != domain->boundary[1][1] ||
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boundary[2][0] != domain->boundary[2][0] ||
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boundary[2][1] != domain->boundary[2][1]) {
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if (me == 0)
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error->warning(FLERR,
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"Restart file used different boundary settings, "
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"using restart file values");
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}
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if (domain->boundary[0][0] || domain->boundary[0][1] ||
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domain->boundary[1][0] || domain->boundary[1][1] ||
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domain->boundary[2][0] || domain->boundary[2][1]) {
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if (boundary[0][0] != domain->boundary[0][0] ||
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boundary[0][1] != domain->boundary[0][1] ||
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boundary[1][0] != domain->boundary[1][0] ||
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boundary[1][1] != domain->boundary[1][1] ||
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boundary[2][0] != domain->boundary[2][0] ||
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boundary[2][1] != domain->boundary[2][1]) {
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if (me == 0)
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error->warning(FLERR,
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"Restart file used different boundary settings, "
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"using restart file values");
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}
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}
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domain->boundary[0][0] = boundary[0][0];
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@ -601,14 +601,14 @@ void ReadRestart::header()
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domain->periodicity[0] = domain->xperiodic = xperiodic;
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domain->periodicity[1] = domain->yperiodic = yperiodic;
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domain->periodicity[2] = domain->zperiodic = zperiodic;
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domain->nonperiodic = 0;
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if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
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domain->nonperiodic = 1;
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if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
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boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
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boundary[2][0] >= 2 || boundary[2][1] >= 2)
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domain->nonperiodic = 2;
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domain->nonperiodic = 1;
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if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
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boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
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boundary[2][0] >= 2 || boundary[2][1] >= 2)
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domain->nonperiodic = 2;
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}
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// create new AtomVec class
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@ -621,9 +621,9 @@ void ReadRestart::header()
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char **words = NULL;
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if (strcmp(style,"hybrid") == 0) {
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nwords = read_int();
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words = new char*[nwords];
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for (int i = 0; i < nwords; i++) words[i] = read_char();
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nwords = read_int();
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words = new char*[nwords];
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for (int i = 0; i < nwords; i++) words[i] = read_char();
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}
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atom->create_avec(style,nwords,words);
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@ -717,7 +717,7 @@ void ReadRestart::type_arrays()
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delete [] mass;
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} else error->all(FLERR,
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"Invalid flag in type arrays section of restart file");
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"Invalid flag in type arrays section of restart file");
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flag = read_int();
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}
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@ -743,8 +743,8 @@ void ReadRestart::force_fields()
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delete [] style;
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if (force->pair->restartinfo) force->pair->read_restart(fp);
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else {
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delete force->pair;
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force->pair = NULL;
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delete force->pair;
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force->pair = NULL;
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}
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} else if (flag == BOND) {
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@ -752,7 +752,7 @@ void ReadRestart::force_fields()
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style = new char[n];
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if (me == 0) nread_char(style,n,fp);
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MPI_Bcast(style,n,MPI_CHAR,0,world);
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force->create_bond(style);
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delete [] style;
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force->bond->read_restart(fp);
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@ -788,7 +788,7 @@ void ReadRestart::force_fields()
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force->improper->read_restart(fp);
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} else error->all(FLERR,
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"Invalid flag in force field section of restart file");
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"Invalid flag in force field section of restart file");
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flag = read_int();
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}
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Reference in New Issue
Block a user