Merge pull request #733 from pastewka/17_dump_nc3 (83ec9815) · Commits · 郑智淋 / lammps

src/USER-NETCDF/dump_netcdf.cpp

+96 −44

Original line number	Diff line number	Diff line
		@@ -43,7 +43,8 @@
		using namespace LAMMPS_NS;
		using namespace MathConst;

		enum{INT,FLOAT,BIGINT}; // same as in thermo.cpp
		enum{THERMO_INT,THERMO_FLOAT,THERMO_BIGINT}; // same as in thermo.cpp
		enum{DUMP_INT,DUMP_DOUBLE,DUMP_STRING,DUMP_BIGINT}; // same as in DumpCFG

		const char NC_FRAME_STR[] = "frame";
		const char NC_SPATIAL_STR[] = "spatial";
		@@ -121,10 +122,6 @@ DumpNetCDF::DumpNetCDF(LAMMPS lmp, int narg, char *arg) :
		ndims = 3;
		strcpy(mangled, "velocities");
		}
		// extensions to the AMBER specification
		else if (!strcmp(mangled, "type")) {
		strcpy(mangled, "atom_types");
		}
		else if (!strcmp(mangled, "xs") \|\| !strcmp(mangled, "ys") \|\|
		!strcmp(mangled, "zs")) {
		idim = mangled[0] - 'x';
		@@ -325,18 +322,6 @@ void DumpNetCDF::openfile()

		// variables specified in the input file
		for (int i = 0; i < n_perat; i++) {
		nc_type xtype;

		// Type mangling
		if (vtype[perat[i].field[0]] == INT) {
		xtype = NC_INT;
		} else {
		if (double_precision)
		xtype = NC_DOUBLE;
		else
		xtype = NC_FLOAT;
		}

		NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var),
		perat[i].name );
		}
		@@ -421,10 +406,11 @@ void DumpNetCDF::openfile()
		nc_type xtype;

		// Type mangling
		if (vtype[perat[i].field[0]] == INT) {
		if (vtype[perat[i].field[0]] == DUMP_INT) {
		xtype = NC_INT;
		}
		else {
		} else if (vtype[perat[i].field[0]] == DUMP_BIGINT) {
		xtype = NC_INT64;
		} else {
		if (double_precision)
		xtype = NC_DOUBLE;
		else
		@@ -488,17 +474,22 @@ void DumpNetCDF::openfile()
		if (thermo) {
		Thermo *th = output->thermo;
		for (int i = 0; i < th->nfield; i++) {
		if (th->vtype[i] == FLOAT) {
		if (th->vtype[i] == THERMO_FLOAT) {
		NCERRX( nc_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims,
		&thermovar[i]), th->keyword[i] );
		}
		else if (th->vtype[i] == INT) {
		else if (th->vtype[i] == THERMO_INT) {
		NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT, 1, dims,
		&thermovar[i]), th->keyword[i] );
		}
		else if (th->vtype[i] == BIGINT) {
		else if (th->vtype[i] == THERMO_BIGINT) {
		#if defined(LAMMPS_SMALLBIG) \|\| defined(LAMMPS_BIGBIG)
		NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT64, 1, dims,
		&thermovar[i]), th->keyword[i] );
		#else
		NCERRX( nc_def_var(ncid, th->keyword[i], NC_LONG, 1, dims,
		&thermovar[i]), th->keyword[i] );
		#endif
		}
		}
		}
		@@ -606,6 +597,7 @@ void DumpNetCDF::openfile()
		count[1] = 5;
		NCERR( nc_put_vara_text(ncid, cell_angular_var, index, count, "gamma") );

		append_flag = 1;
		framei = 1;
		}
		}
		@@ -651,6 +643,52 @@ int nc_put_var1_bigint<long long>(int ncid, int varid, const size_t index[],
		return nc_put_var1_longlong(ncid, varid, index, tp);
		}

		template <typename T>
		int nc_put_vara_bigint(int ncid, int varid, const size_t start[],
		const size_t count[], const T* tp)
		{
		return nc_put_vara_int(ncid, varid, start, count, tp);
		}

		template <>
		int nc_put_vara_bigint<long>(int ncid, int varid, const size_t start[],
		const size_t count[], const long* tp)
		{
		return nc_put_vara_long(ncid, varid, start, count, tp);
		}

		template <>
		int nc_put_vara_bigint<long long>(int ncid, int varid, const size_t start[],
		const size_t count[], const long long* tp)
		{
		return nc_put_vara_longlong(ncid, varid, start, count, tp);
		}

		template <typename T>
		int nc_put_vars_bigint(int ncid, int varid, const size_t start[],
		const size_t count[], const ptrdiff_t stride[],
		const T* tp)
		{
		return nc_put_vars_int(ncid, varid, start, count, stride, tp);
		}

		template <>
		int nc_put_vars_bigint<long>(int ncid, int varid, const size_t start[],
		const size_t count[], const ptrdiff_t stride[],
		const long* tp)
		{
		return nc_put_vars_long(ncid, varid, start, count, stride, tp);
		}

		template <>
		int nc_put_vars_bigint<long long>(int ncid, int varid, const size_t start[],
		const size_t count[],
		const ptrdiff_t stride[],
		const long long* tp)
		{
		return nc_put_vars_longlong(ncid, varid, start, count, stride, tp);
		}

		void DumpNetCDF::write()
		{
		// open file
		@@ -672,16 +710,16 @@ void DumpNetCDF::write()
		for (int i = 0; i < th->nfield; i++) {
		th->call_vfunc(i);
		if (filewriter) {
		if (th->vtype[i] == FLOAT) {
		if (th->vtype[i] == THERMO_FLOAT) {
		NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
		&th->dvalue),
		th->keyword[i] );
		}
		else if (th->vtype[i] == INT) {
		else if (th->vtype[i] == THERMO_INT) {
		NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
		th->keyword[i] );
		}
		else if (th->vtype[i] == BIGINT) {
		else if (th->vtype[i] == THERMO_BIGINT) {
		NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
		th->keyword[i] );
		}
		@@ -782,16 +820,16 @@ void DumpNetCDF::write_data(int n, double *mybuf)

		if (!int_buffer) {
		n_buffer = n;
		int_buffer = (int *)
		memory->smalloc(n*sizeof(int),"dump::int_buffer");
		int_buffer = (bigint *)
		memory->smalloc(n*sizeof(bigint),"dump::int_buffer");
		double_buffer = (double *)
		memory->smalloc(n*sizeof(double),"dump::double_buffer");
		}

		if (n > n_buffer) {
		n_buffer = n;
		int_buffer = (int *)
		memory->srealloc(int_buffer, n*sizeof(int),"dump::int_buffer");
		int_buffer = (bigint *)
		memory->srealloc(int_buffer, n*sizeof(bigint),"dump::int_buffer");
		double_buffer = (double *)
		memory->srealloc(double_buffer, n*sizeof(double),"dump::double_buffer");
		}
		@@ -811,7 +849,7 @@ void DumpNetCDF::write_data(int n, double *mybuf)
		for (int i = 0; i < n_perat; i++) {
		int iaux = perat[i].field[0];

		if (vtype[iaux] == INT) {
		if (vtype[iaux] == DUMP_INT \|\| vtype[iaux] == DUMP_BIGINT) {
		// integers
		if (perat[i].dims > 1) {

		@@ -819,40 +857,54 @@ void DumpNetCDF::write_data(int n, double *mybuf)
		iaux = perat[i].field[idim];

		if (iaux >= 0) {
		if (vtype[iaux] == DUMP_INT) {
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = mybuf[iaux];
		int_buffer[j] = static_cast<int>(mybuf[iaux]);
		}
		}
		else { // DUMP_BIGINT
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = static_cast<bigint>(mybuf[iaux]);
		}
		}

		start[2] = idim;

		if (perat[i].constant) {
		if (perat[i].ndumped < ntotalgr) {
		NCERR( nc_put_vars_int(ncid, perat[i].var,
		NCERR( nc_put_vars_bigint(ncid, perat[i].var,
		start+1, count+1, stride+1,
		int_buffer) );
		perat[i].ndumped += n;
		}
		}
		else
		NCERR( nc_put_vars_int(ncid, perat[i].var, start, count, stride,
		NCERR( nc_put_vars_bigint(ncid, perat[i].var, start, count, stride,
		int_buffer) );
		}
		}
		}
		else {
		if (vtype[iaux] == DUMP_INT) {
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = static_cast<int>(mybuf[iaux]);
		}
		}
		else { // DUMP_BIGINT
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = mybuf[iaux];
		int_buffer[j] = static_cast<bigint>(mybuf[iaux]);
		}
		}

		if (perat[i].constant) {
		if (perat[i].ndumped < ntotalgr) {
		NCERR( nc_put_vara_int(ncid, perat[i].var, start+1, count+1,
		NCERR( nc_put_vara_bigint(ncid, perat[i].var, start+1, count+1,
		int_buffer) );
		perat[i].ndumped += n;
		}
		}
		else
		NCERR( nc_put_vara_int(ncid, perat[i].var, start, count,
		NCERR( nc_put_vara_bigint(ncid, perat[i].var, start, count,
		int_buffer) );
		}
		}

src/USER-NETCDF/dump_netcdf.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -66,7 +66,7 @@ class DumpNetCDF : public DumpCustom {
		bool thermo; // write thermo output to netcdf file

		bigint n_buffer; // size of buffer
		int *int_buffer; // buffer for passing data to netcdf
		bigint *int_buffer; // buffer for passing data to netcdf
		double *double_buffer; // buffer for passing data to netcdf

		int ncid;

src/USER-NETCDF/dump_netcdf_mpiio.cpp

+93 −38

Original line number	Diff line number	Diff line
		@@ -43,7 +43,8 @@
		using namespace LAMMPS_NS;
		using namespace MathConst;

		enum{INT,FLOAT,BIGINT}; // same as in thermo.cpp
		enum{THERMO_INT,THERMO_FLOAT,THERMO_BIGINT}; // same as in thermo.cpp
		enum{DUMP_INT,DUMP_DOUBLE,DUMP_STRING,DUMP_BIGINT}; // same as in DumpCFG

		const char NC_FRAME_STR[] = "frame";
		const char NC_SPATIAL_STR[] = "spatial";
		@@ -321,19 +322,6 @@ void DumpNetCDFMPIIO::openfile()

		// variables specified in the input file
		for (int i = 0; i < n_perat; i++) {
		nc_type xtype;

		// Type mangling
		if (vtype[perat[i].field[0]] == INT) {
		xtype = NC_INT;
		}
		else {
		if (double_precision)
		xtype = NC_DOUBLE;
		else
		xtype = NC_FLOAT;
		}

		NCERRX( ncmpi_inq_varid(ncid, perat[i].name, &perat[i].var),
		perat[i].name );
		}
		@@ -417,10 +405,11 @@ void DumpNetCDFMPIIO::openfile()
		nc_type xtype;

		// Type mangling
		if (vtype[perat[i].field[0]] == INT) {
		if (vtype[perat[i].field[0]] == DUMP_INT) {
		xtype = NC_INT;
		}
		else {
		} else if (vtype[perat[i].field[0]] == DUMP_BIGINT) {
		xtype = NC_INT64;
		} else {
		if (double_precision)
		xtype = NC_DOUBLE;
		else
		@@ -456,17 +445,22 @@ void DumpNetCDFMPIIO::openfile()
		if (thermo) {
		Thermo *th = output->thermo;
		for (int i = 0; i < th->nfield; i++) {
		if (th->vtype[i] == FLOAT) {
		if (th->vtype[i] == THERMO_FLOAT) {
		NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims,
		&thermovar[i]), th->keyword[i] );
		}
		else if (th->vtype[i] == INT) {
		else if (th->vtype[i] == THERMO_INT) {
		NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT, 1, dims,
		&thermovar[i]), th->keyword[i] );
		}
		else if (th->vtype[i] == BIGINT) {
		else if (th->vtype[i] == THERMO_BIGINT) {
		#if defined(LAMMPS_SMALLBIG) \|\| defined(LAMMPS_BIGBIG)
		NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_INT64, 1, dims,
		&thermovar[i]), th->keyword[i] );
		#else
		NCERRX( ncmpi_def_var(ncid, th->keyword[i], NC_LONG, 1, dims,
		&thermovar[i]), th->keyword[i] );
		#endif
		}
		}
		}
		@@ -583,6 +577,7 @@ void DumpNetCDFMPIIO::openfile()

		NCERR( ncmpi_end_indep_data(ncid) );

		append_flag = 1;
		framei = 1;
		}
		}
		@@ -622,12 +617,64 @@ int ncmpi_put_var1_bigint<long>(int ncid, int varid, const MPI_Offset index[],
		}

		template <>
		int ncmpi_put_var1_bigint<long long>(int ncid, int varid, const MPI_Offset index[],
		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);
		}

		template <typename T>
		int ncmpi_put_vara_bigint_all(int ncid, int varid, const MPI_Offset start[],
		const MPI_Offset count[], const T* tp)
		{
		return ncmpi_put_vara_int_all(ncid, varid, start, count, tp);
		}

		template <>
		int ncmpi_put_vara_bigint_all<long>(int ncid, int varid,
		const MPI_Offset start[],
		const MPI_Offset count[], const long* tp)
		{
		return ncmpi_put_vara_long_all(ncid, varid, start, count, tp);
		}

		template <>
		int ncmpi_put_vara_bigint_all<long long>(int ncid, int varid,
		const MPI_Offset start[],
		const MPI_Offset count[],
		const long long* tp)
		{
		return ncmpi_put_vara_longlong_all(ncid, varid, start, count, tp);
		}

		template <typename T>
		int ncmpi_put_vars_bigint_all(int ncid, int varid, const MPI_Offset start[],
		const MPI_Offset count[],
		const MPI_Offset stride[], const T* tp)
		{
		return ncmpi_put_vars_int_all(ncid, varid, start, count, stride, tp);
		}

		template <>
		int ncmpi_put_vars_bigint_all<long>(int ncid, int varid,
		const MPI_Offset start[],
		const MPI_Offset count[],
		const MPI_Offset stride[], const long* tp)
		{
		return ncmpi_put_vars_long_all(ncid, varid, start, count, stride, tp);
		}

		template <>
		int ncmpi_put_vars_bigint_all<long long>(int ncid, int varid,
		const MPI_Offset start[],
		const MPI_Offset count[],
		const MPI_Offset stride[],
		const long long* tp)
		{
		return ncmpi_put_vars_longlong_all(ncid, varid, start, count, stride, tp);
		}

		void DumpNetCDFMPIIO::write()
		{
		// open file
		@@ -651,16 +698,16 @@ void DumpNetCDFMPIIO::write()
		for (int i = 0; i < th->nfield; i++) {
		th->call_vfunc(i);
		if (filewriter) {
		if (th->vtype[i] == FLOAT) {
		if (th->vtype[i] == THERMO_FLOAT) {
		NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start,
		&th->dvalue),
		th->keyword[i] );
		}
		else if (th->vtype[i] == INT) {
		else if (th->vtype[i] == THERMO_INT) {
		NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
		th->keyword[i] );
		}
		else if (th->vtype[i] == BIGINT) {
		else if (th->vtype[i] == THERMO_BIGINT) {
		NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
		th->keyword[i] );
		}
		@@ -789,16 +836,16 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf)

		if (!int_buffer) {
		n_buffer = std::max(1, n);
		int_buffer = (int *)
		memory->smalloc(n_buffer*sizeof(int),"dump::int_buffer");
		int_buffer = (bigint *)
		memory->smalloc(n_buffer*sizeof(bigint),"dump::int_buffer");
		double_buffer = (double *)
		memory->smalloc(n_buffer*sizeof(double),"dump::double_buffer");
		}

		if (n > n_buffer) {
		n_buffer = std::max(1, n);
		int_buffer = (int *)
		memory->srealloc(int_buffer, n_buffer*sizeof(int),"dump::int_buffer");
		int_buffer = (bigint *)
		memory->srealloc(int_buffer, n_buffer*sizeof(bigint),"dump::int_buffer");
		double_buffer = (double *)
		memory->srealloc(double_buffer, n_buffer*sizeof(double),
		"dump::double_buffer");
		@@ -831,7 +878,7 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
		error->one(FLERR,errmsg);
		}

		if (vtype[iaux] == INT) {
		if (vtype[iaux] == DUMP_INT \|\| vtype[iaux] == DUMP_BIGINT) {
		// integers
		if (perat[i].dims > 1) {

		@@ -846,13 +893,21 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
		error->one(FLERR,errmsg);
		}

		if (vtype[iaux] == DUMP_INT) {
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = mybuf[iaux];
		int_buffer[j] = static_cast<int>(mybuf[iaux]);
		}
		}
		else { // DUMP_BIGINT
		for (int j = 0; j < n; j++, iaux+=size_one) {
		int_buffer[j] = static_cast<bigint>(mybuf[iaux]);
		}
		}

		start[2] = idim;
		NCERRX( ncmpi_put_vars_int_all(ncid, perat[i].var, start, count,
		stride, int_buffer), perat[i].name );
		NCERRX( ncmpi_put_vars_bigint_all(ncid, perat[i].var, start, count,
		stride, int_buffer),
		perat[i].name );
		}
		}
		}
		@@ -861,7 +916,7 @@ void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
		int_buffer[j] = mybuf[iaux];
		}

		NCERRX( ncmpi_put_vara_int_all(ncid, perat[i].var, start, count,
		NCERRX( ncmpi_put_vara_bigint_all(ncid, perat[i].var, start, count,
		int_buffer), perat[i].name );
		}
		}

src/USER-NETCDF/dump_netcdf_mpiio.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -65,7 +65,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
		bool thermo; // write thermo output to netcdf file

		bigint n_buffer; // size of buffer
		int *int_buffer; // buffer for passing data to netcdf
		bigint *int_buffer; // buffer for passing data to netcdf
		double *double_buffer; // buffer for passing data to netcdf

		int ncid;

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