Merge pull request #673 from pastewka/17_dump_nc2 (f7cbdcf9) · Commits · 郑智淋 / lammps

doc/src/dump_modify.txt

+4 −2

Original line number	Diff line number	Diff line
		@@ -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

doc/src/dump_netcdf.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -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

src/USER-NETCDF/dump_netcdf.cpp

+54 −77

Original line number	Diff line number	Diff line
		@@ -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;
		// write to next frame upon next open
		if (multifile)
		framei = 1;
		else {
		// append next time DumpNetCDF::openfile is called
		append_flag = 1;
		// write to next frame upon next open
		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),
		th->keyword[i] );
		#else
		NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->bivalue),
		NCERRX( nc_put_var1_bigint(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) {

src/USER-NETCDF/dump_netcdf.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -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 **);

src/USER-NETCDF/dump_netcdf_mpiio.cpp

+56 −16

Original line number	Diff line number	Diff line
		@@ -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;
		// write to next frame upon next open
		if (multifile)
		framei = 1;
		else {
		// append next time DumpNetCDFMPIIO::openfile is called
		append_flag = 1;
		// write to next frame upon next open
		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--;

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