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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-10-30 20:04:06 +00:00
parent 0aa77408f8
commit 354e20f431
1219 changed files with 10111 additions and 10111 deletions
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58
src/read_restart.cpp
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@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "dirent.h"
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include <dirent.h>
#include "read_restart.h"
#include "atom.h"
#include "atom_vec.h"
@ -110,13 +110,13 @@ void ReadRestart::command(int narg, char **arg)
if (strstr(arg[0],".mpiio")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiioflag)
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)
if (!mpiio->mpiio_exists)
error->all(FLERR,"Reading from MPI-IO filename when "
"MPIIO package is not installed");
}
@ -234,7 +234,7 @@ void ReadRestart::command(int narg, char **arg)
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
if (read_int() != PERPROC)
if (read_int() != PERPROC)
error->all(FLERR,"Invalid flag in peratom section of restart file");
n = read_int();
@ -294,16 +294,16 @@ void ReadRestart::command(int narg, char **arg)
}
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
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)
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;
@ -342,7 +342,7 @@ void ReadRestart::command(int narg, char **arg)
int fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
int fileprocnext =
int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
@ -371,7 +371,7 @@ void ReadRestart::command(int narg, char **arg)
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PROCSPERFILE)
if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&procsperfile,sizeof(int),1,fp);
}
@ -383,7 +383,7 @@ void ReadRestart::command(int narg, char **arg)
for (int i = 0; i < procsperfile; i++) {
if (filereader) {
fread(&flag,sizeof(int),1,fp);
if (flag != PERPROC)
if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
@ -666,7 +666,7 @@ void ReadRestart::header(int incompatible)
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
version,universe->version);
}
if (incompatible)
if (incompatible)
error->all(FLERR,"Restart file incompatible with current version");
delete [] version;
@ -729,7 +729,7 @@ void ReadRestart::header(int incompatible)
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)
if (flag && me == 0)
error->warning(FLERR,"Restart file used different 3d processor grid");
// don't set newton_pair, leave input script value unchanged
@ -894,7 +894,7 @@ void ReadRestart::header(int incompatible)
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) {
@ -996,7 +996,7 @@ void ReadRestart::file_layout()
if (mpiioflag && mpiioflag_file == 0)
error->all(FLERR,"Restart file is not a MPI-IO file");
if (mpiioflag) {
if (mpiioflag) {
bigint *nproc_chunk_offsets;
memory->create(nproc_chunk_offsets,nprocs,
"write_restart:nproc_chunk_offsets");
@ -1016,45 +1016,45 @@ void ReadRestart::file_layout()
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] +=
nproc_chunk_sizes[i] +=
all_written_send_sizes[all_written_send_sizes_index];
current_offset +=
(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);
}
@ -1089,10 +1089,10 @@ void ReadRestart::magic_string()
int count;
if (me == 0) count = fread(str,sizeof(char),n,fp);
MPI_Bcast(&count,1,MPI_INT,0,world);
if (count < n)
if (count < n)
error->all(FLERR,"Invalid LAMMPS restart file");
MPI_Bcast(str,n,MPI_CHAR,0,world);
if (strcmp(str,MAGIC_STRING) != 0)
if (strcmp(str,MAGIC_STRING) != 0)
error->all(FLERR,"Invalid LAMMPS restart file");
delete [] str;
}