read_restart.cpp
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Created: Fri, May 24, 07:53

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 "lmptype.h"
	#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};

	#define LB_FACTOR 1.1

	/* ---------------------------------------------------------------------- */

	ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {}

	/* ---------------------------------------------------------------------- */

	void ReadRestart::command(int narg, char **arg)
	{
	if (narg != 1) 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);

	// 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],".mpi")) mpiioflag = 1;
	else mpiioflag = 0;

	if (multiproc && mpiioflag)
	error->all(FLERR,
	"Read restart MPI-IO output 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->avec->grow(n);
	n = atom->nmax;

	domain->print_box(" ");
	domain->set_initial_box();
	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);

	// 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) {
	// add calls to RestartMPIIO class
	// reopen header file
	// perform reads
	// allow for different # of procs reading than wrote the file

	// mpiio->open(file);
	// mpiio->read();
	// mpiio->close();

	// then process atom info as

	//m = 0;
	//while (m < n) 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
	// check for atom in sub-domain differs for orthogonal vs triclinic box

	else if (multiproc == 0) {

	int triclinic = domain->triclinic;
	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 (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);
	}

	// 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);
	}

	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_Status status;
	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,&status);
	MPI_Rsend(buf,n,MPI_DOUBLE,iproc,0,world);
	}

	} else if (i % nclusterprocs == me - fileproc) {
	MPI_Recv(&n,1,MPI_INT,fileproc,0,world,&status);
	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,&status);
	}

	if (i % nclusterprocs == me - fileproc) {
	m = 0;
	while (m < n) m += avec->unpack_restart(&buf[m]);
	}
	}

	if (filereader) fclose(fp);
	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) {

	// 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()
	// 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();
	if (domain->triclinic) domain->x2lamda(atom->nlocal);
	Irregular *irregular = new Irregular(lmp);
	irregular->migrate_atoms();
	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 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();

	// if molecular system or user-requested, create global mapping of atoms

	if (atom->molecular \|\| atom->map_user) {
	atom->map_init();
	atom->map_set();
	}

	// create special bond lists for molecular systems

	if (atom->molecular) {
	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 px,py,pz;
	int xperiodic,yperiodic,zperiodic;
	int boundary[3][2];

	// 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);
	if (comm->user_procgrid[0] != 0 &&
	(procgrid[0] != comm->user_procgrid[0] \|\|
	procgrid[1] != comm->user_procgrid[1] \|\|
	procgrid[2] != comm->user_procgrid[2]) && 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];

	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;
	}

	// create new AtomVec class
	// if style = hybrid, read additional sub-class arguments

	} else if (flag == ATOM_STYLE) {
	char *style = read_string();

	int nwords = 0;
	char **words = NULL;

	if (strcmp(style,"hybrid") == 0) {
	nwords = read_int();
	words = new char*[nwords];
	for (int i = 0; i < nwords; i++) words[i] = read_string();
	}

	atom->create_avec(style,nwords,words);
	atom->avec->read_restart_settings(fp);

	for (int i = 0; i < nwords; i++) delete [] words[i];
	delete [] words;
	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 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()
	{
	int n;
	char *style;

	int flag = read_int();
	while (flag >= 0) {

	if (flag == PAIR) {
	style = read_string();
	force->create_pair(style);
	delete [] style;
	force->pair->read_restart(fp);

	} else if (flag == BOND) {
	style = read_string();
	force->create_bond(style);
	delete [] style;
	force->bond->read_restart(fp);

	} else if (flag == ANGLE) {
	style = read_string();
	force->create_angle(style);
	delete [] style;
	force->angle->read_restart(fp);

	} else if (flag == DIHEDRAL) {
	style = read_string();
	force->create_dihedral(style);
	delete [] style;
	force->dihedral->read_restart(fp);

	} else if (flag == IMPROPER) {
	style = read_string();
	force->create_improper(style);
	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");
	}

	// NOTE: could add reading of MPI-IO specific fields to header here
	// e.g. read vector of PERPROCSIZE values

	flag = read_int();
	}
	}

	// ----------------------------------------------------------------------
	// ----------------------------------------------------------------------
	// 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;
	if (me == 0) fread(&endian,sizeof(int),1,fp);
	MPI_Bcast(&endian,1,MPI_INT,0,world);
	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;
	if (me == 0) fread(&vn,sizeof(int),1,fp);
	MPI_Bcast(&vn,1,MPI_INT,0,world);
	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);
	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);
	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);
	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;
	if (me == 0) fread(&n,sizeof(int),1,fp);
	MPI_Bcast(&n,1,MPI_INT,0,world);
	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
	do not bcast them, caller does that if required
	------------------------------------------------------------------------- */

	void ReadRestart::read_int_vec(int n, int *vec)
	{
	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
	do not bcast them, caller does that if required
	------------------------------------------------------------------------- */

	void ReadRestart::read_double_vec(int n, double *vec)
	{
	if (me == 0) fread(vec,sizeof(double),n,fp);
	MPI_Bcast(vec,n,MPI_DOUBLE,0,world);
	}

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