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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11095 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-12-06 22:32:32 +00:00
parent 6831bc9d32
commit 6bfbfa78f4
6 changed files with 691 additions and 389 deletions
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411
src/write_restart.cpp
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@ -39,23 +39,26 @@
using namespace LAMMPS_NS;
// same as read_restart.cpp and tools/restart2data.cpp
// same as read_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_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};
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};
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
@ -65,6 +68,7 @@ WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
multiproc = 0;
}
/* ----------------------------------------------------------------------
@ -75,7 +79,7 @@ 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 (narg < 1) error->all(FLERR,"Illegal write_restart command");
// if filename contains a "*", replace with current timestep
@ -88,6 +92,21 @@ void WriteRestart::command(int narg, char **arg)
sprintf(file,"%s" BIGINT_FORMAT "%s",arg[0],update->ntimestep,ptr+1);
} else strcpy(file,arg[0]);
// check for multiproc output and an MPI-IO filename
if (strchr(arg[0],'%')) multiproc = nprocs;
else multiproc = 0;
if (strstr(arg[0],".mpi")) mpiio = 1;
else mpiio = 0;
if (multiproc && mpiio)
error->all(FLERR,
"Write restart MPI-IO output not allowed with '%' in filename");
// setup output style and process optional args
// also called by Output class for periodic restart files
multiproc_options(multiproc,mpiio,narg-1,&arg[1]);
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
@ -114,6 +133,78 @@ void WriteRestart::command(int narg, char **arg)
delete [] file;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void WriteRestart::multiproc_options(int multiproc_caller, int mpiio_caller,
int narg, char **arg)
{
multiproc = multiproc_caller;
mpiio = mpiio_caller;
// defaults for multiproc file writing
nclusterprocs = nprocs;
filewriter = 0;
if (me == 0) filewriter = 1;
fileproc = 0;
if (multiproc) {
nclusterprocs = 1;
filewriter = 1;
fileproc = me;
icluster = me;
}
// optional args
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart fileper "
"without % in restart file name");
int nper = force->inumeric(FLERR,arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal write_restart command");
multiproc = nprocs/nper;
if (nprocs % nper) multiproc++;
fileproc = me/nper * nper;
int fileprocnext = MIN(fileproc+nper,nprocs);
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
icluster = fileproc/nper;
iarg += 2;
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_restart command");
if (!multiproc)
error->all(FLERR,"Cannot use write_restart nfile "
"without % in restart file name");
int nfile = force->inumeric(FLERR,arg[iarg+1]);
if (nfile <= 0) error->all(FLERR,"Illegal write_restart command");
nfile = MIN(nfile,nprocs);
multiproc = nfile;
icluster = static_cast<int> ((bigint) me * nfile/nprocs);
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++;
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
iarg += 2;
} else error->all(FLERR,"Illegal write_restart command");
}
}
/* ----------------------------------------------------------------------
called from command() and directly from output within run/minimize loop
file = final file name to write, except may contain a "%"
@ -138,12 +229,6 @@ void WriteRestart::write(char *file)
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) {
@ -164,8 +249,15 @@ void WriteRestart::write(char *file)
if (multiproc) delete [] hfile;
}
// proc 0 writes header, groups, ntype-length arrays, force field
// all procs write fix info
// proc 0 writes magic string, endian flag, numeric version
if (me == 0) {
magic_string();
endian();
version_numeric();
}
// proc 0 writes header, groups, pertype info, force field info
if (me == 0) {
header();
@ -174,9 +266,11 @@ void WriteRestart::write(char *file)
force_fields();
}
// all procs write fix info
modify->write_restart(fp);
// communication buffer for all my atom's info
// communication buffer for my atom info
// max_size = largest buffer needed by any proc
int max_size;
@ -184,8 +278,35 @@ void WriteRestart::write(char *file)
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");
memory->create(buf,max_size,"write_restart:buf");
// all procs write file layout info which may include per-proc sizes
file_layout(send_size);
// header info is complete
// if multiproc output:
// close header file, open multiname file on each writing proc
if (multiproc) {
if (me == 0) fclose(fp);
char *multiname = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(multiname,"%s%d%s",file,icluster,ptr+1);
if (filewriter) {
fp = fopen(multiname,"wb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",multiname);
error->one(FLERR,str);
}
}
delete [] multiname;
}
// pack my atom data into buf
@ -242,55 +363,31 @@ void WriteRestart::write(char *file)
}
}
// 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
// filewriter = 1 = this proc writes to file
// ping each proc in my cluster, receive its data, write data to file
// else wait for ping from fileproc, send my data to fileproc
if (multiproc == 0) {
int tmp,recv_size;
MPI_Status status;
MPI_Request request;
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;
if (filewriter) {
write_int(PROCSPERFILE,nclusterprocs);
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,max_size,MPI_DOUBLE,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+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);
write_double_vec(PERPROC,recv_size,buf);
}
fclose(fp);
} 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);
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,send_size,MPI_DOUBLE,fileproc,0,world);
}
memory->destroy(buf);
@ -308,35 +405,28 @@ void WriteRestart::write(char *file)
void WriteRestart::header()
{
write_char(VERSION,universe->version);
write_string(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_string(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_vec(PROCGRID,3,comm->procgrid);
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]);
write_int_vec(BOUNDARY,6,&domain->boundary[0][0]);
// 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);
write_string(ATOM_STYLE,atom->atom_style);
if (strcmp(atom->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
@ -349,8 +439,7 @@ void WriteRestart::header()
fwrite(keywords[i],sizeof(char),n,fp);
}
}
if (me == 0) atom->avec->write_restart_settings(fp);
atom->avec->write_restart_settings(fp);
write_bigint(NATOMS,natoms);
write_int(NTYPES,atom->ntypes);
@ -367,25 +456,15 @@ void WriteRestart::header()
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_int(TRICLINIC,domain->triclinic);
write_double_vec(BOXLO,3,domain->boxlo);
write_double_vec(BOXHI,3,domain->boxhi);
write_double(XY,domain->xy);
write_double(XZ,domain->xz);
write_double(YZ,domain->yz);
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);
}
write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]);
write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]);
// -1 flag signals end of header
@ -399,11 +478,7 @@ void WriteRestart::header()
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);
}
if (atom->mass) write_double_vec(MASS,atom->ntypes,&atom->mass[1]);
// -1 flag signals end of type arrays
@ -417,44 +492,24 @@ void WriteRestart::type_arrays()
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);
if (force->pair && force->pair->restartinfo) {
write_string(PAIR,force->pair_style);
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);
write_string(BOND,force->bond_style);
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);
write_string(ANGLE,force->angle_style);
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);
write_string(DIHEDRAL,force->dihedral_style);
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);
write_string(IMPROPER,force->improper_style);
force->improper->write_restart(fp);
}
@ -464,6 +519,62 @@ void WriteRestart::force_fields()
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out file layout info
all procs call this method, only proc 0 writes to file
------------------------------------------------------------------------- */
void WriteRestart::file_layout(int send_size)
{
if (me == 0) {
write_int(MULTIPROC,multiproc);
write_int(MPIIO,mpiio);
}
// -1 flag signals end of file layout info
if (me == 0) {
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
}
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
// low-level fwrite methods
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void WriteRestart::magic_string()
{
int n = strlen(MAGIC_STRING) + 1;
char *str = new char[n];
strcpy(str,MAGIC_STRING);
fwrite(str,sizeof(char),n,fp);
delete [] str;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void WriteRestart::endian()
{
int endian = ENDIAN;
fwrite(&endian,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void WriteRestart::version_numeric()
{
int vn = VERSION_NUMERIC;
fwrite(&vn,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and an int into restart file
------------------------------------------------------------------------- */
@ -474,6 +585,16 @@ void WriteRestart::write_int(int flag, int value)
fwrite(&value,sizeof(int),1,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);
}
/* ----------------------------------------------------------------------
write a flag and a double into restart file
------------------------------------------------------------------------- */
@ -485,23 +606,35 @@ void WriteRestart::write_double(int flag, double value)
}
/* ----------------------------------------------------------------------
write a flag and a char str into restart file
write a flag and a char string (including NULL) into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_char(int flag, char *value)
void WriteRestart::write_string(int flag, char *value)
{
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(value) + 1;
fwrite(&flag,sizeof(int),1,fp);
fwrite(&n,sizeof(int),1,fp);
fwrite(value,sizeof(char),n,fp);
}
/* ----------------------------------------------------------------------
write a flag and a bigint into restart file
write a flag and vector of N ints into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_bigint(int flag, bigint value)
void WriteRestart::write_int_vec(int flag, int n, int *vec)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(bigint),1,fp);
fwrite(&n,sizeof(int),1,fp);
fwrite(vec,sizeof(int),n,fp);
}
/* ----------------------------------------------------------------------
write a flag and vector of N doubles into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_double_vec(int flag, int n, double *vec)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&n,sizeof(int),1,fp);
fwrite(vec,sizeof(double),n,fp);
}