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lammps/src/write_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 "write_restart.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "group.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "update.h"
#include "neighbor.h"
#include "domain.h"
#include "modify.h"
#include "universe.h"
#include "comm.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// same as read_restart.cpp and tools/restart2data.cpp
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
ATOM_STYLE,NATOMS,NTYPES,
NBONDS,NBONDTYPES,BOND_PER_ATOM,
NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
XY,XZ,YZ};
enum{MASS};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
/* ---------------------------------------------------------------------- */
WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
}
/* ----------------------------------------------------------------------
called as write_restart command in input script
------------------------------------------------------------------------- */
void WriteRestart::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Write_restart command before simulation box is defined");
if (narg != 1) error->all(FLERR,"Illegal write_restart command");
// if filename contains a "*", replace with current timestep
char *ptr;
int n = strlen(arg[0]) + 16;
char *file = new char[n];
if (ptr = strchr(arg[0],'*')) {
*ptr = '\0';
sprintf(file,"%s" BIGINT_FORMAT "%s",arg[0],update->ntimestep,ptr+1);
} else strcpy(file,arg[0]);
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if (comm->me == 0 && screen)
fprintf(screen,"System init for write_restart ...\n");
lmp->init();
// move atoms to new processors before writing file
// do setup_pre_exchange to force update of per-atom info if needed
// enforce PBC in case atoms are outside box
// call borders() to rebuild atom map since exchange() destroys map
modify->setup_pre_exchange();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
write(file);
delete [] file;
}
/* ----------------------------------------------------------------------
called from command() and directly from output within run/minimize loop
file = final file name to write, except may contain a "%"
------------------------------------------------------------------------- */
void WriteRestart::write(char *file)
{
// special case where reneighboring is not done in integrator
// on timestep restart file is written (due to build_once being set)
// if box is changing, must be reset, else restart file will have
// wrong box size and atoms will be lost when restart file is read
// other calls to pbc and domain and comm are not made,
// b/c they only make sense if reneighboring is actually performed
if (neighbor->build_once) domain->reset_box();
// natoms = sum of nlocal = value to write into restart file
// if unequal and thermo lostflag is "error", don't write restart file
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write restart file");
// check if filename contains "%"
int multiproc;
if (strchr(file,'%')) multiproc = 1;
else multiproc = 0;
// open single restart file or base file for multiproc case
if (me == 0) {
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,"wb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
if (multiproc) delete [] hfile;
}
// proc 0 writes header, groups, ntype-length arrays, force field
// all procs write fix info
if (me == 0) {
header();
group->write_restart(fp);
type_arrays();
force_fields();
}
modify->write_restart(fp);
// communication buffer for all my atom's info
// max_size = largest buffer needed by any proc
int max_size;
int send_size = atom->avec->size_restart();
MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf;
if (me == 0) memory->create(buf,max_size,"write_restart:buf");
else memory->create(buf,send_size,"write_restart:buf");
// pack my atom data into buf
AtomVec *avec = atom->avec;
int n = 0;
for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);
// if any fix requires it, remap each atom's coords via PBC
// is because fix changes atom coords (excepting an integrate fix)
// just remap in buffer, not actual atoms
if (modify->restart_pbc_any) {
int triclinic = domain->triclinic;
double *lo,*hi,*period;
if (triclinic == 0) {
lo = domain->boxlo;
hi = domain->boxhi;
period = domain->prd;
} else {
lo = domain->boxlo_lamda;
hi = domain->boxhi_lamda;
period = domain->prd_lamda;
}
int xperiodic = domain->xperiodic;
int yperiodic = domain->yperiodic;
int zperiodic = domain->zperiodic;
double *x;
int m = 0;
for (int i = 0; i < atom->nlocal; i++) {
x = &buf[m+1];
if (triclinic) domain->x2lamda(x,x);
if (xperiodic) {
if (x[0] < lo[0]) x[0] += period[0];
if (x[0] >= hi[0]) x[0] -= period[0];
x[0] = MAX(x[0],lo[0]);
}
if (yperiodic) {
if (x[1] < lo[1]) x[1] += period[1];
if (x[1] >= hi[1]) x[1] -= period[1];
x[1] = MAX(x[1],lo[1]);
}
if (zperiodic) {
if (x[2] < lo[2]) x[2] += period[2];
if (x[2] >= hi[2]) x[2] -= period[2];
x[2] = MAX(x[2],lo[2]);
}
if (triclinic) domain->lamda2x(x,x);
m += static_cast<int> (buf[m]);
}
}
// if single file:
// write one chunk of atoms per proc to file
// proc 0 pings each proc, receives its chunk, writes to file
// all other procs wait for ping, send their chunk to proc 0
// else if one file per proc:
// each proc opens its own file and writes its chunk directly
if (multiproc == 0) {
int tmp,recv_size;
MPI_Status status;
MPI_Request request;
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,max_size,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
} else recv_size = send_size;
fwrite(&recv_size,sizeof(int),1,fp);
fwrite(buf,sizeof(double),recv_size,fp);
}
fclose(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,send_size,MPI_DOUBLE,0,0,world);
}
} else {
if (me == 0) fclose(fp);
char *perproc = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(perproc,"%s%d%s",file,me,ptr+1);
*ptr = '%';
fp = fopen(perproc,"wb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",perproc);
error->one(FLERR,str);
}
delete [] perproc;
fwrite(&send_size,sizeof(int),1,fp);
fwrite(buf,sizeof(double),send_size,fp);
fclose(fp);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
proc 0 writes out problem description
------------------------------------------------------------------------- */
void WriteRestart::header()
{
write_char(VERSION,universe->version);
write_int(SMALLINT,sizeof(smallint));
write_int(TAGINT,sizeof(tagint));
write_int(BIGINT,sizeof(bigint));
write_char(UNITS,update->unit_style);
write_bigint(NTIMESTEP,update->ntimestep);
write_int(DIMENSION,domain->dimension);
write_int(NPROCS,nprocs);
write_int(PROCGRID_0,comm->procgrid[0]);
write_int(PROCGRID_1,comm->procgrid[1]);
write_int(PROCGRID_2,comm->procgrid[2]);
write_int(NEWTON_PAIR,force->newton_pair);
write_int(NEWTON_BOND,force->newton_bond);
write_int(XPERIODIC,domain->xperiodic);
write_int(YPERIODIC,domain->yperiodic);
write_int(ZPERIODIC,domain->zperiodic);
write_int(BOUNDARY_00,domain->boundary[0][0]);
write_int(BOUNDARY_01,domain->boundary[0][1]);
write_int(BOUNDARY_10,domain->boundary[1][0]);
write_int(BOUNDARY_11,domain->boundary[1][1]);
write_int(BOUNDARY_20,domain->boundary[2][0]);
write_int(BOUNDARY_21,domain->boundary[2][1]);
// atom_style must be written before atom class values
// so read_restart can create class before reading class values
// if style = hybrid, also write sub-class styles
// avec->write_restart() writes atom_style specific info
write_char(ATOM_STYLE,atom->atom_style);
if (strcmp(atom->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
int nstyles = avec_hybrid->nstyles;
char **keywords = avec_hybrid->keywords;
fwrite(&nstyles,sizeof(int),1,fp);
for (int i = 0; i < nstyles; i++) {
int n = strlen(keywords[i]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(keywords[i],sizeof(char),n,fp);
}
}
if (me == 0) atom->avec->write_restart_settings(fp);
write_bigint(NATOMS,natoms);
write_int(NTYPES,atom->ntypes);
write_bigint(NBONDS,atom->nbonds);
write_int(NBONDTYPES,atom->nbondtypes);
write_int(BOND_PER_ATOM,atom->bond_per_atom);
write_bigint(NANGLES,atom->nangles);
write_int(NANGLETYPES,atom->nangletypes);
write_int(ANGLE_PER_ATOM,atom->angle_per_atom);
write_bigint(NDIHEDRALS,atom->ndihedrals);
write_int(NDIHEDRALTYPES,atom->ndihedraltypes);
write_int(DIHEDRAL_PER_ATOM,atom->dihedral_per_atom);
write_bigint(NIMPROPERS,atom->nimpropers);
write_int(NIMPROPERTYPES,atom->nimpropertypes);
write_int(IMPROPER_PER_ATOM,atom->improper_per_atom);
write_double(BOXLO_0,domain->boxlo[0]);
write_double(BOXHI_0,domain->boxhi[0]);
write_double(BOXLO_1,domain->boxlo[1]);
write_double(BOXHI_1,domain->boxhi[1]);
write_double(BOXLO_2,domain->boxlo[2]);
write_double(BOXHI_2,domain->boxhi[2]);
write_double(SPECIAL_LJ_1,force->special_lj[1]);
write_double(SPECIAL_LJ_2,force->special_lj[2]);
write_double(SPECIAL_LJ_3,force->special_lj[3]);
write_double(SPECIAL_COUL_1,force->special_coul[1]);
write_double(SPECIAL_COUL_2,force->special_coul[2]);
write_double(SPECIAL_COUL_3,force->special_coul[3]);
if (domain->triclinic) {
write_double(XY,domain->xy);
write_double(XZ,domain->xz);
write_double(YZ,domain->yz);
}
// -1 flag signals end of header
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out any type-based arrays that are defined
------------------------------------------------------------------------- */
void WriteRestart::type_arrays()
{
if (atom->mass) {
int flag = MASS;
fwrite(&flag,sizeof(int),1,fp);
fwrite(&atom->mass[1],sizeof(double),atom->ntypes,fp);
}
// -1 flag signals end of type arrays
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out and force field styles and data that are defined
------------------------------------------------------------------------- */
void WriteRestart::force_fields()
{
if (force->pair) {
int flag = PAIR;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->pair_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->pair_style,sizeof(char),n,fp);
force->pair->write_restart(fp);
}
if (atom->avec->bonds_allow && force->bond) {
int flag = BOND;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->bond_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->bond_style,sizeof(char),n,fp);
force->bond->write_restart(fp);
}
if (atom->avec->angles_allow && force->angle) {
int flag = ANGLE;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->angle_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->angle_style,sizeof(char),n,fp);
force->angle->write_restart(fp);
}
if (atom->avec->dihedrals_allow && force->dihedral) {
int flag = DIHEDRAL;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->dihedral_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->dihedral_style,sizeof(char),n,fp);
force->dihedral->write_restart(fp);
}
if (atom->avec->impropers_allow && force->improper) {
int flag = IMPROPER;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->improper_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->improper_style,sizeof(char),n,fp);
force->improper->write_restart(fp);
}
// -1 flag signals end of force field info
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and an int into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_int(int flag, int value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and a double into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_double(int flag, double value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and a char str into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_char(int flag, char *value)
{
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(value) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(value,sizeof(char),n,fp);
}
/* ----------------------------------------------------------------------
write a flag and a bigint into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_bigint(int flag, bigint value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(bigint),1,fp);
}
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