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lammps/src/read_restart.cpp
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read_restart.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include <dirent.h>
#include "read_restart.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "comm.h"
#include "irregular.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_read_restart.h"
#include "group.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "special.h"
#include "universe.h"
#include "mpiio.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// same as write_restart.cpp
#define MAGIC_STRING "LammpS RestartT"
#define ENDIAN 0x0001
#define ENDIANSWAP 0x1000
#define VERSION_NUMERIC 0
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID,
NEWTON_PAIR,NEWTON_BOND,
XPERIODIC,YPERIODIC,ZPERIODIC,BOUNDARY,
ATOM_STYLE,NATOMS,NTYPES,
NBONDS,NBONDTYPES,BOND_PER_ATOM,
NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
TRICLINIC,BOXLO,BOXHI,XY,XZ,YZ,
SPECIAL_LJ,SPECIAL_COUL,
MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER,
MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
IMAGEINT,BOUNDMIN,TIMESTEP,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL};
#define LB_FACTOR 1.1
/* ---------------------------------------------------------------------- */
ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void ReadRestart::command(int narg, char **arg)
{
if (narg != 1 && narg != 2) error->all(FLERR,"Illegal read_restart command");
if (domain->box_exist)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// check for remap option
int remapflag = 0;
if (narg == 2) {
if (strcmp(arg[1],"remap") == 0) remapflag = 1;
else error->all(FLERR,"Illegal read_restart command");
}
// if filename contains "*", search dir for latest restart file
char *file = new char[strlen(arg[0]) + 16];
if (strchr(arg[0],'*')) {
int n;
if (me == 0) {
file_search(arg[0],file);
n = strlen(file) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(file,n,MPI_CHAR,0,world);
} else strcpy(file,arg[0]);
// check for multiproc files and an MPI-IO filename
if (strchr(arg[0],'%')) multiproc = 1;
else multiproc = 0;
if (strstr(arg[0],".mpiio")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiioflag)
error->all(FLERR,
"Read restart MPI-IO input not allowed with % in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
if (!mpiio->mpiio_exists)
error->all(FLERR,"Reading from MPI-IO filename when "
"MPIIO package is not installed");
}
// open single restart file or base file for multiproc case
if (me == 0) {
if (screen) fprintf(screen,"Reading restart file ...\n");
char *hfile;
if (multiproc) {
hfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(hfile,"%s%s%s",file,"base",ptr+1);
*ptr = '%';
} else hfile = file;
fp = fopen(hfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
if (multiproc) delete [] hfile;
}
// read magic string, endian flag, numeric version
magic_string();
endian();
int incompatible = version_numeric();
// read header info which creates simulation box
header(incompatible);
domain->box_exist = 1;
// problem setup using info from header
int n;
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
atom->deallocate_topology();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box(0);
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
// read groups, ntype-length arrays, force field, fix info from file
// nextra = max # of extra quantities stored with each atom
group->read_restart(fp);
type_arrays();
force_fields();
int nextra = modify->read_restart(fp);
atom->nextra_store = nextra;
memory->create(atom->extra,n,nextra,"atom:extra");
// read file layout info
file_layout();
// close header file if in multiproc mode
if (multiproc && me == 0) {
fclose(fp);
fp = NULL;
}
// read per-proc info
AtomVec *avec = atom->avec;
int maxbuf = 0;
double *buf = NULL;
int m,flag;
// MPI-IO input from single file
if (mpiioflag) {
mpiio->openForRead(file);
memory->create(buf,assignedChunkSize,"read_restart:buf");
mpiio->read((headerOffset+assignedChunkOffset),assignedChunkSize,buf);
mpiio->close();
m = 0;
while (m < assignedChunkSize) m += avec->unpack_restart(&buf[m]);
}
// input of single native file
// nprocs_file = # of chunks in file
// proc 0 reads a chunk and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// if remapflag set, remap the atom to box before checking sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
else if (multiproc == 0) {
int triclinic = domain->triclinic;
imageint *iptr;
double *x,lamda[3];
double *coord,*sublo,*subhi;
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
if (read_int() != PERPROC)
error->all(FLERR,"Invalid flag in peratom section of restart file");
n = read_int();
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
read_double_vec(n,buf);
m = 0;
while (m < n) {
x = &buf[m+1];
if (remapflag) {
iptr = (imageint *) &buf[m+7];
domain->remap(x,*iptr);
}
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
} else m += static_cast<int> (buf[m]);
}
}
if (me == 0) {
fclose(fp);
fp = NULL;
}
}
// input of multiple native files with procs <= files
// # of files = multiproc_file
// each proc reads a subset of files, striding by nprocs
// each proc keeps all atoms in all perproc chunks in its files
else if (nprocs <= multiproc_file) {
char *procfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
for (int iproc = me; iproc < multiproc_file; iproc += nprocs) {
*ptr = '\0';
sprintf(procfile,"%s%d%s",file,iproc,ptr+1);
*ptr = '%';
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
int procsperfile;
fread(&procsperfile,sizeof(int),1,fp);
for (int i = 0; i < procsperfile; i++) {
fread(&flag,sizeof(int),1,fp);
if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
fread(buf,sizeof(double),n,fp);
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
}
fclose(fp);
fp = NULL;
}
delete [] procfile;
}
// input of multiple native files with procs > files
// # of files = multiproc_file
// cluster procs based on # of files
// 1st proc in each cluster reads per-proc chunks from file
// sends chunks round-robin to other procs in its cluster
// each proc keeps all atoms in its perproc chunks in file
else {
// nclusterprocs = # of procs in my cluster that read from one file
// filewriter = 1 if this proc reads file, else 0
// fileproc = ID of proc in my cluster who reads from file
// clustercomm = MPI communicator within my cluster of procs
int nfile = multiproc_file;
int icluster = static_cast<int> ((bigint) me * nfile/nprocs);
int fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
int nclusterprocs = fileprocnext - fileproc;
int filereader = 0;
if (me == fileproc) filereader = 1;
MPI_Comm clustercomm;
MPI_Comm_split(world,icluster,0,&clustercomm);
if (filereader) {
char *procfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(procfile,"%s%d%s",file,icluster,ptr+1);
*ptr = '%';
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
delete [] procfile;
}
int flag,procsperfile;
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&procsperfile,sizeof(int),1,fp);
}
MPI_Bcast(&procsperfile,1,MPI_INT,0,clustercomm);
int tmp,iproc;
MPI_Request request;
for (int i = 0; i < procsperfile; i++) {
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
fread(buf,sizeof(double),n,fp);
if (i % nclusterprocs) {
iproc = me + (i % nclusterprocs);
MPI_Send(&n,1,MPI_INT,iproc,0,world);
MPI_Recv(&tmp,0,MPI_INT,iproc,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(buf,n,MPI_DOUBLE,iproc,0,world);
}
} else if (i % nclusterprocs == me - fileproc) {
MPI_Recv(&n,1,MPI_INT,fileproc,0,world,MPI_STATUS_IGNORE);
if (n > maxbuf) {
maxbuf = n;
memory->destroy(buf);
memory->create(buf,maxbuf,"read_restart:buf");
}
MPI_Irecv(buf,n,MPI_DOUBLE,fileproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,fileproc,0,world);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
if (i % nclusterprocs == me - fileproc) {
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
}
}
if (filereader && fp != NULL) {
fclose(fp);
fp = NULL;
}
MPI_Comm_free(&clustercomm);
}
// clean-up memory
delete [] file;
memory->destroy(buf);
// for multiproc or MPI-IO files:
// perform irregular comm to migrate atoms to correct procs
if (multiproc || mpiioflag) {
// if remapflag set, remap all atoms I read back to box before migrating
if (remapflag) {
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
domain->remap(x[i],image[i]);
}
// create a temporary fix to hold and migrate extra atom info
// necessary b/c irregular will migrate atoms
if (nextra) {
char cextra[8],fixextra[8];
sprintf(cextra,"%d",nextra);
sprintf(fixextra,"%d",modify->nfix_restart_peratom);
char **newarg = new char*[5];
newarg[0] = (char *) "_read_restart";
newarg[1] = (char *) "all";
newarg[2] = (char *) "READ_RESTART";
newarg[3] = cextra;
newarg[4] = fixextra;
modify->add_fix(5,newarg);
delete [] newarg;
}
// move atoms to new processors via irregular()
// turn sorting on in migrate_atoms() to avoid non-reproducible restarts
// in case read by different proc than wrote restart file
// first do map_init() since irregular->migrate_atoms() will do map_clear()
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// put extra atom info held by fix back into atom->extra
// destroy temporary fix
if (nextra) {
memory->destroy(atom->extra);
memory->create(atom->extra,atom->nmax,nextra,"atom:extra");
int ifix = modify->find_fix("_read_restart");
FixReadRestart *fix = (FixReadRestart *) modify->fix[ifix];
int *count = fix->count;
double **extra = fix->extra;
double **atom_extra = atom->extra;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < count[i]; j++)
atom_extra[i][j] = extra[i][j];
modify->delete_fix("_read_restart");
}
}
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all restart atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
}
}
// check that atom IDs are valid
atom->tag_check();
// create global mapping of atoms
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
// create special bond lists for molecular systems
if (atom->molecular == 1) {
Special special(lmp);
special.build();
}
}
/* ----------------------------------------------------------------------
infile contains a "*"
search for all files which match the infile pattern
replace "*" with latest timestep value to create outfile name
search dir referenced by initial pathname of file
if infile also contains "%", use "base" when searching directory
only called by proc 0
------------------------------------------------------------------------- */
void ReadRestart::file_search(char *infile, char *outfile)
{
char *ptr;
// separate infile into dir + filename
char *dirname = new char[strlen(infile) + 1];
char *filename = new char[strlen(infile) + 1];
if (strchr(infile,'/')) {
ptr = strrchr(infile,'/');
*ptr = '\0';
strcpy(dirname,infile);
strcpy(filename,ptr+1);
*ptr = '/';
} else {
strcpy(dirname,"./");
strcpy(filename,infile);
}
// if filename contains "%" replace "%" with "base"
char *pattern = new char[strlen(filename) + 16];
if ((ptr = strchr(filename,'%'))) {
*ptr = '\0';
sprintf(pattern,"%s%s%s",filename,"base",ptr+1);
*ptr = '%';
} else strcpy(pattern,filename);
// scan all files in directory, searching for files that match pattern
// maxnum = largest int that matches "*"
int n = strlen(pattern) + 16;
char *begin = new char[n];
char *middle = new char[n];
char *end = new char[n];
ptr = strchr(pattern,'*');
*ptr = '\0';
strcpy(begin,pattern);
strcpy(end,ptr+1);
int nbegin = strlen(begin);
bigint maxnum = -1;
struct dirent *ep;
DIR *dp = opendir(dirname);
if (dp == NULL)
error->one(FLERR,"Cannot open dir to search for restart file");
while ((ep = readdir(dp))) {
if (strstr(ep->d_name,begin) != ep->d_name) continue;
if ((ptr = strstr(&ep->d_name[nbegin],end)) == NULL) continue;
if (strlen(end) == 0) ptr = ep->d_name + strlen(ep->d_name);
*ptr = '\0';
if (strlen(&ep->d_name[nbegin]) < n) {
strcpy(middle,&ep->d_name[nbegin]);
if (ATOBIGINT(middle) > maxnum) maxnum = ATOBIGINT(middle);
}
}
closedir(dp);
if (maxnum < 0) error->one(FLERR,"Found no restart file matching pattern");
// create outfile with maxint substituted for "*"
// use original infile, not pattern, since need to retain "%" in filename
ptr = strchr(infile,'*');
*ptr = '\0';
sprintf(outfile,"%s" BIGINT_FORMAT "%s",infile,maxnum,ptr+1);
*ptr = '*';
// clean up
delete [] dirname;
delete [] filename;
delete [] pattern;
delete [] begin;
delete [] middle;
delete [] end;
}
/* ----------------------------------------------------------------------
read header of restart file
------------------------------------------------------------------------- */
void ReadRestart::header(int incompatible)
{
int xperiodic(-1),yperiodic(-1),zperiodic(-1);
// read flags and fields until flag = -1
int flag = read_int();
while (flag >= 0) {
// check restart file version, warn if different
if (flag == VERSION) {
char *version = read_string();
if (me == 0) {
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
version,universe->version);
}
if (incompatible)
error->all(FLERR,"Restart file incompatible with current version");
delete [] version;
// check lmptype.h sizes, error if different
} else if (flag == SMALLINT) {
int size = read_int();
if (size != sizeof(smallint))
error->all(FLERR,"Smallint setting in lmptype.h is not compatible");
} else if (flag == IMAGEINT) {
int size = read_int();
if (size != sizeof(imageint))
error->all(FLERR,"Imageint setting in lmptype.h is not compatible");
} else if (flag == TAGINT) {
int size = read_int();
if (size != sizeof(tagint))
error->all(FLERR,"Tagint setting in lmptype.h is not compatible");
} else if (flag == BIGINT) {
int size = read_int();
if (size != sizeof(bigint))
error->all(FLERR,"Bigint setting in lmptype.h is not compatible");
// reset unit_style only if different
// so that timestep,neighbor-skin are not changed
} else if (flag == UNITS) {
char *style = read_string();
if (strcmp(style,update->unit_style) != 0) update->set_units(style);
delete [] style;
} else if (flag == NTIMESTEP) {
update->ntimestep = read_bigint();
// set dimension from restart file
} else if (flag == DIMENSION) {
int dimension = read_int();
domain->dimension = dimension;
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,
"Cannot run 2d simulation with nonperiodic Z dimension");
// read nprocs from restart file, warn if different
} else if (flag == NPROCS) {
nprocs_file = read_int();
if (nprocs_file != comm->nprocs && me == 0)
error->warning(FLERR,"Restart file used different # of processors");
// don't set procgrid, warn if different
} else if (flag == PROCGRID) {
int procgrid[3];
read_int();
read_int_vec(3,procgrid);
int flag = 0;
if (comm->user_procgrid[0] != 0 &&
procgrid[0] != comm->user_procgrid[0]) flag = 1;
if (comm->user_procgrid[1] != 0 &&
procgrid[1] != comm->user_procgrid[1]) flag = 1;
if (comm->user_procgrid[2] != 0 &&
procgrid[2] != comm->user_procgrid[2]) flag = 1;
if (flag && me == 0)
error->warning(FLERR,"Restart file used different 3d processor grid");
// don't set newton_pair, leave input script value unchanged
// set newton_bond from restart file
// warn if different and input script settings are not default
} else if (flag == NEWTON_PAIR) {
int newton_pair_file = read_int();
if (force->newton_pair != 1) {
if (newton_pair_file != force->newton_pair && me == 0)
error->warning(FLERR,
"Restart file used different newton pair setting, "
"using input script value");
}
} else if (flag == NEWTON_BOND) {
int newton_bond_file = read_int();
if (force->newton_bond != 1) {
if (newton_bond_file != force->newton_bond && me == 0)
error->warning(FLERR,
"Restart file used different newton bond setting, "
"using restart file value");
}
force->newton_bond = newton_bond_file;
if (force->newton_pair || force->newton_bond) force->newton = 1;
else force->newton = 0;
// set boundary settings from restart file
// warn if different and input script settings are not default
} else if (flag == XPERIODIC) {
xperiodic = read_int();
} else if (flag == YPERIODIC) {
yperiodic = read_int();
} else if (flag == ZPERIODIC) {
zperiodic = read_int();
} else if (flag == BOUNDARY) {
int boundary[3][2];
read_int();
read_int_vec(6,&boundary[0][0]);
if (domain->boundary[0][0] || domain->boundary[0][1] ||
domain->boundary[1][0] || domain->boundary[1][1] ||
domain->boundary[2][0] || domain->boundary[2][1]) {
if (boundary[0][0] != domain->boundary[0][0] ||
boundary[0][1] != domain->boundary[0][1] ||
boundary[1][0] != domain->boundary[1][0] ||
boundary[1][1] != domain->boundary[1][1] ||
boundary[2][0] != domain->boundary[2][0] ||
boundary[2][1] != domain->boundary[2][1]) {
if (me == 0)
error->warning(FLERR,
"Restart file used different boundary settings, "
"using restart file values");
}
}
domain->boundary[0][0] = boundary[0][0];
domain->boundary[0][1] = boundary[0][1];
domain->boundary[1][0] = boundary[1][0];
domain->boundary[1][1] = boundary[1][1];
domain->boundary[2][0] = boundary[2][0];
domain->boundary[2][1] = boundary[2][1];
if (xperiodic < 0 || yperiodic < 0 || zperiodic < 0)
error->all(FLERR,"Illegal or unset periodicity in restart");
domain->periodicity[0] = domain->xperiodic = xperiodic;
domain->periodicity[1] = domain->yperiodic = yperiodic;
domain->periodicity[2] = domain->zperiodic = zperiodic;
domain->nonperiodic = 0;
if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
domain->nonperiodic = 1;
if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
boundary[2][0] >= 2 || boundary[2][1] >= 2)
domain->nonperiodic = 2;
}
} else if (flag == BOUNDMIN) {
double minbound[6];
read_int();
read_double_vec(6,minbound);
domain->minxlo = minbound[0]; domain->minxhi = minbound[1];
domain->minylo = minbound[2]; domain->minyhi = minbound[3];
domain->minzlo = minbound[4]; domain->minzhi = minbound[5];
// create new AtomVec class using any stored args
} else if (flag == ATOM_STYLE) {
char *style = read_string();
int nargcopy = read_int();
char **argcopy = new char*[nargcopy];
for (int i = 0; i < nargcopy; i++)
argcopy[i] = read_string();
atom->create_avec(style,nargcopy,argcopy,1);
for (int i = 0; i < nargcopy; i++) delete [] argcopy[i];
delete [] argcopy;
delete [] style;
} else if (flag == NATOMS) {
atom->natoms = read_bigint();
} else if (flag == NTYPES) {
atom->ntypes = read_int();
} else if (flag == NBONDS) {
atom->nbonds = read_bigint();
} else if (flag == NBONDTYPES) {
atom->nbondtypes = read_int();
} else if (flag == BOND_PER_ATOM) {
atom->bond_per_atom = read_int();
} else if (flag == NANGLES) {
atom->nangles = read_bigint();
} else if (flag == NANGLETYPES) {
atom->nangletypes = read_int();
} else if (flag == ANGLE_PER_ATOM) {
atom->angle_per_atom = read_int();
} else if (flag == NDIHEDRALS) {
atom->ndihedrals = read_bigint();
} else if (flag == NDIHEDRALTYPES) {
atom->ndihedraltypes = read_int();
} else if (flag == DIHEDRAL_PER_ATOM) {
atom->dihedral_per_atom = read_int();
} else if (flag == NIMPROPERS) {
atom->nimpropers = read_bigint();
} else if (flag == NIMPROPERTYPES) {
atom->nimpropertypes = read_int();
} else if (flag == IMPROPER_PER_ATOM) {
atom->improper_per_atom = read_int();
} else if (flag == TRICLINIC) {
domain->triclinic = read_int();
} else if (flag == BOXLO) {
read_int();
read_double_vec(3,domain->boxlo);
} else if (flag == BOXHI) {
read_int();
read_double_vec(3,domain->boxhi);
} else if (flag == XY) {
domain->xy = read_double();
} else if (flag == XZ) {
domain->xz = read_double();
} else if (flag == YZ) {
domain->yz = read_double();
} else if (flag == SPECIAL_LJ) {
read_int();
read_double_vec(3,&force->special_lj[1]);
} else if (flag == SPECIAL_COUL) {
read_int();
read_double_vec(3,&force->special_coul[1]);
} else if (flag == TIMESTEP) {
update->dt = read_double();
} else if (flag == ATOM_ID) {
atom->tag_enable = read_int();
} else if (flag == ATOM_MAP_STYLE) {
atom->map_style = read_int();
} else if (flag == ATOM_MAP_USER) {
atom->map_user = read_int();
} else if (flag == ATOM_SORTFREQ) {
atom->sortfreq = read_int();
} else if (flag == ATOM_SORTBIN) {
atom->userbinsize = read_double();
} else if (flag == COMM_MODE) {
comm->mode = read_int();
} else if (flag == COMM_CUTOFF) {
comm->cutghostuser = read_double();
} else if (flag == COMM_VEL) {
comm->ghost_velocity = read_int();
} else error->all(FLERR,"Invalid flag in header section of restart file");
flag = read_int();
}
}
/* ---------------------------------------------------------------------- */
void ReadRestart::type_arrays()
{
int flag = read_int();
while (flag >= 0) {
if (flag == MASS) {
read_int();
double *mass = new double[atom->ntypes+1];
read_double_vec(atom->ntypes,&mass[1]);
atom->set_mass(mass);
delete [] mass;
} else error->all(FLERR,
"Invalid flag in type arrays section of restart file");
flag = read_int();
}
}
/* ---------------------------------------------------------------------- */
void ReadRestart::force_fields()
{
char *style;
int flag = read_int();
while (flag >= 0) {
if (flag == PAIR) {
style = read_string();
force->create_pair(style,1);
delete [] style;
force->pair->read_restart(fp);
} else if (flag == BOND) {
style = read_string();
force->create_bond(style,1);
delete [] style;
force->bond->read_restart(fp);
} else if (flag == ANGLE) {
style = read_string();
force->create_angle(style,1);
delete [] style;
force->angle->read_restart(fp);
} else if (flag == DIHEDRAL) {
style = read_string();
force->create_dihedral(style,1);
delete [] style;
force->dihedral->read_restart(fp);
} else if (flag == IMPROPER) {
style = read_string();
force->create_improper(style,1);
delete [] style;
force->improper->read_restart(fp);
} else error->all(FLERR,
"Invalid flag in force field section of restart file");
flag = read_int();
}
}
/* ---------------------------------------------------------------------- */
void ReadRestart::file_layout()
{
int flag = read_int();
while (flag >= 0) {
if (flag == MULTIPROC) {
multiproc_file = read_int();
if (multiproc == 0 && multiproc_file)
error->all(FLERR,"Restart file is not a multi-proc file");
if (multiproc && multiproc_file == 0)
error->all(FLERR,"Restart file is a multi-proc file");
} else if (flag == MPIIO) {
int mpiioflag_file = read_int();
if (mpiioflag == 0 && mpiioflag_file)
error->all(FLERR,"Restart file is a MPI-IO file");
if (mpiioflag && mpiioflag_file == 0)
error->all(FLERR,"Restart file is not a MPI-IO file");
if (mpiioflag) {
bigint *nproc_chunk_offsets;
memory->create(nproc_chunk_offsets,nprocs,
"write_restart:nproc_chunk_offsets");
bigint *nproc_chunk_sizes;
memory->create(nproc_chunk_sizes,nprocs,
"write_restart:nproc_chunk_sizes");
// on rank 0 read in the chunk sizes that were written out
// then consolidate them and compute offsets relative to the
// end of the header info to fit the current partition size
// if the number of ranks that did the writing is different
if (me == 0) {
int *all_written_send_sizes;
memory->create(all_written_send_sizes,nprocs_file,
"write_restart:all_written_send_sizes");
int *nproc_chunk_number;
memory->create(nproc_chunk_number,nprocs,
"write_restart:nproc_chunk_number");
fread(all_written_send_sizes,sizeof(int),nprocs_file,fp);
int init_chunk_number = nprocs_file/nprocs;
int num_extra_chunks = nprocs_file - (nprocs*init_chunk_number);
for (int i = 0; i < nprocs; i++) {
if (i < num_extra_chunks)
nproc_chunk_number[i] = init_chunk_number+1;
else
nproc_chunk_number[i] = init_chunk_number;
}
int all_written_send_sizes_index = 0;
bigint current_offset = 0;
for (int i=0;i<nprocs;i++) {
nproc_chunk_offsets[i] = current_offset;
nproc_chunk_sizes[i] = 0;
for (int j=0;j<nproc_chunk_number[i];j++) {
nproc_chunk_sizes[i] +=
all_written_send_sizes[all_written_send_sizes_index];
current_offset +=
(all_written_send_sizes[all_written_send_sizes_index] *
sizeof(double));
all_written_send_sizes_index++;
}
}
memory->destroy(all_written_send_sizes);
memory->destroy(nproc_chunk_number);
}
// scatter chunk sizes and offsets to all procs
MPI_Scatter(nproc_chunk_sizes, 1, MPI_LMP_BIGINT,
&assignedChunkSize , 1, MPI_LMP_BIGINT, 0,world);
MPI_Scatter(nproc_chunk_offsets, 1, MPI_LMP_BIGINT,
&assignedChunkOffset , 1, MPI_LMP_BIGINT, 0,world);
memory->destroy(nproc_chunk_sizes);
memory->destroy(nproc_chunk_offsets);
}
}
flag = read_int();
}
// if MPI-IO file, broadcast the end of the header offste
// this allows all ranks to compute offset to their data
if (mpiioflag) {
if (me == 0) headerOffset = ftell(fp);
MPI_Bcast(&headerOffset,1,MPI_LMP_BIGINT,0,world);
}
}
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
// low-level fread methods
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void ReadRestart::magic_string()
{
int n = strlen(MAGIC_STRING) + 1;
char *str = new char[n];
int count;
if (me == 0) count = fread(str,sizeof(char),n,fp);
MPI_Bcast(&count,1,MPI_INT,0,world);
if (count < n)
error->all(FLERR,"Invalid LAMMPS restart file");
MPI_Bcast(str,n,MPI_CHAR,0,world);
if (strcmp(str,MAGIC_STRING) != 0)
error->all(FLERR,"Invalid LAMMPS restart file");
delete [] str;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void ReadRestart::endian()
{
int endian = read_int();
if (endian == ENDIAN) return;
if (endian == ENDIANSWAP)
error->all(FLERR,"Restart file byte ordering is swapped");
else error->all(FLERR,"Restart file byte ordering is not recognized");
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int ReadRestart::version_numeric()
{
int vn = read_int();
if (vn != VERSION_NUMERIC) return 1;
return 0;
}
/* ----------------------------------------------------------------------
read an int from restart file and bcast it
------------------------------------------------------------------------- */
int ReadRestart::read_int()
{
int value;
if ((me == 0) && (fread(&value,sizeof(int),1,fp) < 1))
value = -1;
MPI_Bcast(&value,1,MPI_INT,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a bigint from restart file and bcast it
------------------------------------------------------------------------- */
bigint ReadRestart::read_bigint()
{
bigint value;
if ((me == 0) && (fread(&value,sizeof(bigint),1,fp) < 1))
value = -1;
MPI_Bcast(&value,1,MPI_LMP_BIGINT,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a double from restart file and bcast it
------------------------------------------------------------------------- */
double ReadRestart::read_double()
{
double value;
if ((me == 0) && (fread(&value,sizeof(double),1,fp) < 1))
value = 0.0;
MPI_Bcast(&value,1,MPI_DOUBLE,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a char string (including NULL) and bcast it
str is allocated here, ptr is returned, caller must deallocate
------------------------------------------------------------------------- */
char *ReadRestart::read_string()
{
int n = read_int();
if (n < 0) error->all(FLERR,"Illegal size string or corrupt restart");
char *value = new char[n];
if (me == 0) fread(value,sizeof(char),n,fp);
MPI_Bcast(value,n,MPI_CHAR,0,world);
return value;
}
/* ----------------------------------------------------------------------
read vector of N ints from restart file and bcast them
------------------------------------------------------------------------- */
void ReadRestart::read_int_vec(int n, int *vec)
{
if (n < 0) error->all(FLERR,"Illegal size integer vector read requested");
if (me == 0) fread(vec,sizeof(int),n,fp);
MPI_Bcast(vec,n,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
read vector of N doubles from restart file and bcast them
------------------------------------------------------------------------- */
void ReadRestart::read_double_vec(int n, double *vec)
{
if (n < 0) error->all(FLERR,"Illegal size double vector read requested");
if (me == 0) fread(vec,sizeof(double),n,fp);
MPI_Bcast(vec,n,MPI_DOUBLE,0,world);
}
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