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Merge pull request #673 from pastewka/17_dump_nc2

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Multi file support for NetCDF dump style
This commit is contained in:
Steve Plimpton
2017-10-06 09:14:12 -06:00
committed by GitHub
parent 4cfa88b70f 352a20fc1c
commit f7cbdcf995
5 changed files with 116 additions and 98 deletions
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6
doc/src/dump_modify.txt
View File

@ -15,9 +15,11 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
these keywords apply to various dump styles :l
keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no} or {at} N
keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
only available after "append yes"
{buffer} arg = {yes} or {no}
{element} args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name, e.g. C or Fe or Ga

4
doc/src/dump_netcdf.txt
View File

@ -25,7 +25,8 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
dump 1 all netcdf 100 traj.nc type x y z vx vy vz
dump_modify 1 append yes at -1 thermo yes
dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
dump 1 all netcdf 1000 traj.*.nc id type x y z :pre
[Description:]
@ -73,4 +74,3 @@ section for more info.
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html

131
src/USER-NETCDF/dump_netcdf.cpp
View File

@ -88,8 +88,8 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
if (multiproc)
error->all(FLERR,"Multi-processor writes are not supported.");
if (multifile)
error->all(FLERR,"Multiple files are not supported.");
if (append_flag && multifile)
error->all(FLERR,"Cannot append when writing to multiple files.");
perat = new nc_perat_t[nfield];
@ -224,6 +224,24 @@ DumpNetCDF::~DumpNetCDF()
void DumpNetCDF::openfile()
{
char *filecurrent = filename;
if (multifile && !singlefile_opened) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
if (thermo && !singlefile_opened) {
if (thermovar) delete [] thermovar;
thermovar = new int[output->thermo->nfield];
@ -268,14 +286,14 @@ void DumpNetCDF::openfile()
ntotalgr = group->count(igroup);
if (filewriter) {
if (append_flag && access(filename, F_OK) != -1) {
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
// Fixme! Perform checks if dimensions and variables conform with
// data structure standard.
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( nc_open(filename, NC_WRITE, &ncid), filename );
NCERRX( nc_open(filecurrent, NC_WRITE, &ncid), filecurrent );
// dimensions
NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
@ -348,8 +366,8 @@ void DumpNetCDF::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( nc_create(filename, NC_64BIT_DATA, &ncid),
filename );
NCERRX( nc_create(filecurrent, NC_64BIT_DATA, &ncid),
filecurrent );
// dimensions
NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
@ -598,15 +616,39 @@ void DumpNetCDF::closefile()
if (filewriter && singlefile_opened) {
NCERR( nc_close(ncid) );
singlefile_opened = 0;
// append next time DumpNetCDF::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
if (multifile)
framei = 1;
else {
// append next time DumpNetCDF::openfile is called
append_flag = 1;
framei++;
}
}
}
/* ---------------------------------------------------------------------- */
template <typename T>
int nc_put_var1_bigint(int ncid, int varid, const size_t index[], const T* tp)
{
return nc_put_var1_int(ncid, varid, index, tp);
}
template <>
int nc_put_var1_bigint<long>(int ncid, int varid, const size_t index[],
const long* tp)
{
return nc_put_var1_long(ncid, varid, index, tp);
}
template <>
int nc_put_var1_bigint<long long>(int ncid, int varid, const size_t index[],
const long long* tp)
{
return nc_put_var1_longlong(ncid, varid, index, tp);
}
void DumpNetCDF::write()
{
// open file
@ -638,13 +680,8 @@ void DumpNetCDF::write()
th->keyword[i] );
}
else if (th->vtype[i] == BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( nc_put_var1_long(ncid, thermovar[i], start, &th->bivalue),
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i] );
#else
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i] );
#endif
}
}
}
@ -887,6 +924,8 @@ int DumpNetCDF::modify_param(int narg, char **arg)
return 2;
}
else if (strcmp(arg[iarg],"at") == 0) {
if (!append_flag)
error->all(FLERR,"expected 'append yes' before 'at' keyword");
iarg++;
framei = force->inumeric(FLERR,arg[iarg]);
if (framei < 0) framei--;
@ -911,68 +950,6 @@ int DumpNetCDF::modify_param(int narg, char **arg)
/* ---------------------------------------------------------------------- */
void DumpNetCDF::write_prmtop()
{
char fn[1024];
char tmp[81];
FILE *f;
strcpy(fn, filename);
strcat(fn, ".prmtop");
f = fopen(fn, "w");
fprintf(f, "%%VERSION LAMMPS\n");
fprintf(f, "%%FLAG TITLE\n");
fprintf(f, "%%FORMAT(20a4)\n");
memset(tmp, ' ', 76);
tmp[76] = '\0';
fprintf(f, "NASN%s\n", tmp);
fprintf(f, "%%FLAG POINTERS\n");
fprintf(f, "%%FORMAT(10I8)\n");
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
fprintf(f, "%8li", ntotalgr);
#else
fprintf(f, "%8i", ntotalgr);
#endif
for (int i = 0; i < 11; i++)
fprintf(f, "%8i", 0);
fprintf(f, "\n");
for (int i = 0; i < 12; i++)
fprintf(f, "%8i", 0);
fprintf(f, "\n");
for (int i = 0; i < 6; i++)
fprintf(f, "%8i", 0);
fprintf(f, "\n");
fprintf(f, "%%FLAG ATOM_NAME\n");
fprintf(f, "%%FORMAT(20a4)\n");
for (int i = 0; i < ntotalgr; i++) {
fprintf(f, "%4s", "He");
if ((i+1) % 20 == 0)
fprintf(f, "\n");
}
fprintf(f, "%%FLAG CHARGE\n");
fprintf(f, "%%FORMAT(5E16.5)\n");
for (int i = 0; i < ntotalgr; i++) {
fprintf(f, "%16.5e", 0.0);
if ((i+1) % 5 == 0)
fprintf(f, "\n");
}
fprintf(f, "%%FLAG MASS\n");
fprintf(f, "%%FORMAT(5E16.5)\n");
for (int i = 0; i < ntotalgr; i++) {
fprintf(f, "%16.5e", 1.0);
if ((i+1) % 5 == 0)
fprintf(f, "\n");
}
fclose(f);
}
/* ---------------------------------------------------------------------- */
void DumpNetCDF::ncerr(int err, const char *descr, int line)
{
if (err != NC_NOERR) {

1
src/USER-NETCDF/dump_netcdf.h
View File

@ -92,7 +92,6 @@ class DumpNetCDF : public DumpCustom {
void closefile();
virtual void write_header(bigint);
virtual void write_data(int, double *);
void write_prmtop();
virtual int modify_param(int, char **);

72
src/USER-NETCDF/dump_netcdf_mpiio.cpp
View File

@ -88,8 +88,8 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
if (multiproc)
error->all(FLERR,"Multi-processor writes are not supported.");
if (multifile)
error->all(FLERR,"Multiple files are not supported.");
if (append_flag && multifile)
error->all(FLERR,"Cannot append when writing to multiple files.");
perat = new nc_perat_t[nfield];
@ -217,6 +217,24 @@ DumpNetCDFMPIIO::~DumpNetCDFMPIIO()
void DumpNetCDFMPIIO::openfile()
{
char *filecurrent = filename;
if (multifile && !singlefile_opened) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
if (thermo && !singlefile_opened) {
if (thermovar) delete [] thermovar;
thermovar = new int[output->thermo->nfield];
@ -260,7 +278,7 @@ void DumpNetCDFMPIIO::openfile()
// get total number of atoms
ntotalgr = group->count(igroup);
if (append_flag && access(filename, F_OK) != -1) {
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
// Fixme! Perform checks if dimensions and variables conform with
// data structure standard.
@ -270,8 +288,8 @@ void DumpNetCDFMPIIO::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( ncmpi_open(MPI_COMM_WORLD, filename, NC_WRITE, MPI_INFO_NULL,
&ncid), filename );
NCERRX( ncmpi_open(MPI_COMM_WORLD, filecurrent, NC_WRITE, MPI_INFO_NULL,
&ncid), filecurrent );
// dimensions
NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
@ -344,8 +362,8 @@ void DumpNetCDFMPIIO::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( ncmpi_create(MPI_COMM_WORLD, filename, NC_64BIT_DATA,
MPI_INFO_NULL, &ncid), filename );
NCERRX( ncmpi_create(MPI_COMM_WORLD, filecurrent, NC_64BIT_DATA,
MPI_INFO_NULL, &ncid), filecurrent );
// dimensions
NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
@ -574,15 +592,40 @@ void DumpNetCDFMPIIO::closefile()
if (singlefile_opened) {
NCERR( ncmpi_close(ncid) );
singlefile_opened = 0;
// append next time DumpNetCDFMPIIO::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
if (multifile)
framei = 1;
else {
// append next time DumpNetCDFMPIIO::openfile is called
append_flag = 1;
framei++;
}
}
}
/* ---------------------------------------------------------------------- */
template <typename T>
int ncmpi_put_var1_bigint(int ncid, int varid, const MPI_Offset index[],
const T* tp)
{
return ncmpi_put_var1_int(ncid, varid, index, tp);
}
template <>
int ncmpi_put_var1_bigint<long>(int ncid, int varid, const MPI_Offset index[],
const long* tp)
{
return ncmpi_put_var1_long(ncid, varid, index, tp);
}
template <>
int ncmpi_put_var1_bigint<long long>(int ncid, int varid, const MPI_Offset index[],
const long long* tp)
{
return ncmpi_put_var1_longlong(ncid, varid, index, tp);
}
void DumpNetCDFMPIIO::write()
{
// open file
@ -616,13 +659,8 @@ void DumpNetCDFMPIIO::write()
th->keyword[i] );
}
else if (th->vtype[i] == BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( ncmpi_put_var1_long(ncid, thermovar[i], start, &th->bivalue),
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i] );
#else
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i] );
#endif
}
}
}
@ -882,6 +920,8 @@ int DumpNetCDFMPIIO::modify_param(int narg, char **arg)
return 2;
}
else if (strcmp(arg[iarg],"at") == 0) {
if (!append_flag)
error->all(FLERR,"expected 'append yes' before 'at' keyword");
iarg++;
framei = force->inumeric(FLERR,arg[iarg]);
if (framei < 0) framei--;