Merge pull request #1303 from pastewka/19_dump_nc1 (fb30d2d0) · Commits · 郑智淋 / lammps

src/USER-NETCDF/dump_netcdf.cpp

+57 −48

Original line number	Diff line number	Diff line
		@@ -281,6 +281,9 @@ void DumpNetCDF::openfile()

		// get total number of atoms
		ntotalgr = group->count(igroup);
		for (int i = 0; i < DUMP_NC_MAX_DIMS; i++) {
		vector_dim[i] = -1;
		}

		if (filewriter) {
		if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
		@@ -294,9 +297,6 @@ void DumpNetCDF::openfile()

		// dimensions
		NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
		NCERRX( nc_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim),
		NC_SPATIAL_STR );
		NCERRX( nc_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR );
		NCERRX( nc_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR );
		NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim),
		NC_CELL_SPATIAL_STR );
		@@ -304,6 +304,26 @@ void DumpNetCDF::openfile()
		NC_CELL_ANGULAR_STR );
		NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );

		for (int i = 0; i < n_perat; i++) {
		int dims = perat[i].dims;
		if (vector_dim[dims] < 0) {
		char dimstr[1024];
		if (dims == 3) {
		strcpy(dimstr, NC_SPATIAL_STR);
		}
		else if (dims == 6) {
		strcpy(dimstr, NC_VOIGT_STR);
		}
		else {
		sprintf(dimstr, "vec%i", dims);
		}
		if (dims != 1) {
		NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]),
		dimstr );
		}
		}
		}

		// default variables
		NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var),
		NC_SPATIAL_STR );
		@@ -320,7 +340,6 @@ void DumpNetCDF::openfile()
		NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var),
		NC_CELL_ANGLES_STR);

		// variables specified in the input file
		for (int i = 0; i < n_perat; i++) {
		NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var),
		perat[i].name );
		@@ -359,10 +378,6 @@ void DumpNetCDF::openfile()
		// dimensions
		NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
		NC_FRAME_STR );
		NCERRX( nc_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim),
		NC_SPATIAL_STR );
		NCERRX( nc_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim),
		NC_VOIGT_STR );
		NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim),
		NC_ATOM_STR );
		NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim),
		@@ -372,13 +387,33 @@ void DumpNetCDF::openfile()
		NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim),
		NC_LABEL_STR );

		for (int i = 0; i < n_perat; i++) {
		int dims = perat[i].dims;
		if (vector_dim[dims] < 0) {
		char dimstr[1024];
		if (dims == 3) {
		strcpy(dimstr, NC_SPATIAL_STR);
		}
		else if (dims == 6) {
		strcpy(dimstr, NC_VOIGT_STR);
		}
		else {
		sprintf(dimstr, "vec%i", dims);
		}
		if (dims != 1) {
		NCERRX( nc_def_dim(ncid, dimstr, dims, &vector_dim[dims]),
		dimstr );
		}
		}
		}

		// default variables
		dims[0] = spatial_dim;
		dims[0] = vector_dim[3];
		NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var),
		NC_SPATIAL_STR );
		NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims,
		&cell_spatial_var), NC_CELL_SPATIAL_STR );
		dims[0] = spatial_dim;
		dims[0] = vector_dim[3];
		dims[1] = label_dim;
		NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims,
		&cell_angular_var), NC_CELL_ANGULAR_STR );
		@@ -400,7 +435,7 @@ void DumpNetCDF::openfile()
		// variables specified in the input file
		dims[0] = frame_dim;
		dims[1] = atom_dim;
		dims[2] = spatial_dim;
		dims[2] = vector_dim[3];

		for (int i = 0; i < n_perat; i++) {
		nc_type xtype;
		@@ -419,53 +454,27 @@ void DumpNetCDF::openfile()

		if (perat[i].constant) {
		// this quantity will only be written once
		if (perat[i].dims == 6) {
		// this is a tensor in Voigt notation
		dims[2] = Voigt_dim;
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 3) {
		// this is a vector, we need to store x-, y- and z-coordinates
		dims[2] = spatial_dim;
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 1) {
		if (perat[i].dims == 1) {
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1,
		&perat[i].var), perat[i].name );
		}
		else {
		char errstr[1024];
		sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
		"this to the NetCDF trajectory file.", perat[i].dims,
		perat[i].name);
		error->all(FLERR,errstr);
		}
		}
		else {
		if (perat[i].dims == 6) {
		// this is a tensor in Voigt notation
		dims[2] = Voigt_dim;
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
		// this is a vector
		dims[1] = vector_dim[perat[i].dims];
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 3) {
		// this is a vector, we need to store x-, y- and z-coordinates
		dims[2] = spatial_dim;
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 1) {
		else {
		if (perat[i].dims == 1) {
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims,
		&perat[i].var), perat[i].name );
		}
		else {
		char errstr[1024];
		sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
		"this to the NetCDF trajectory file.", perat[i].dims,
		perat[i].name);
		error->all(FLERR,errstr);
		// this is a vector
		dims[2] = vector_dim[perat[i].dims];
		NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
		&perat[i].var), perat[i].name );
		}
		}
		}

src/USER-NETCDF/dump_netcdf.h

+1 −2

Original line number	Diff line number	Diff line
		@@ -72,8 +72,7 @@ class DumpNetCDF : public DumpCustom {
		int ncid;

		int frame_dim;
		int spatial_dim;
		int Voigt_dim;
		int vector_dim[DUMP_NC_MAX_DIMS];
		int atom_dim;
		int cell_spatial_dim;
		int cell_angular_dim;

src/USER-NETCDF/dump_netcdf_mpiio.cpp

+51 −28

Original line number	Diff line number	Diff line
		@@ -278,6 +278,9 @@ void DumpNetCDFMPIIO::openfile()

		// get total number of atoms
		ntotalgr = group->count(igroup);
		for (int i = 0; i < DUMP_NC_MPIIO_MAX_DIMS; i++) {
		vector_dim[i] = -1;
		}

		if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
		// Fixme! Perform checks if dimensions and variables conform with
		@@ -294,9 +297,6 @@ void DumpNetCDFMPIIO::openfile()

		// dimensions
		NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
		NCERRX( ncmpi_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim),
		NC_SPATIAL_STR );
		NCERRX( ncmpi_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR );
		NCERRX( ncmpi_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR );
		NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim),
		NC_CELL_SPATIAL_STR );
		@@ -304,6 +304,26 @@ void DumpNetCDFMPIIO::openfile()
		NC_CELL_ANGULAR_STR );
		NCERRX( ncmpi_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );

		for (int i = 0; i < n_perat; i++) {
		int dims = perat[i].dims;
		if (vector_dim[dims] < 0) {
		char dimstr[1024];
		if (dims == 3) {
		strcpy(dimstr, NC_SPATIAL_STR);
		}
		else if (dims == 6) {
		strcpy(dimstr, NC_VOIGT_STR);
		}
		else {
		sprintf(dimstr, "vec%i", dims);
		}
		if (dims != 1) {
		NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]),
		dimstr );
		}
		}
		}

		// default variables
		NCERRX( ncmpi_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var),
		NC_SPATIAL_STR );
		@@ -358,10 +378,6 @@ void DumpNetCDFMPIIO::openfile()
		// dimensions
		NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
		NC_FRAME_STR );
		NCERRX( ncmpi_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim),
		NC_SPATIAL_STR );
		NCERRX( ncmpi_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim),
		NC_VOIGT_STR );
		NCERRX( ncmpi_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim),
		NC_ATOM_STR );
		NCERRX( ncmpi_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim),
		@@ -371,13 +387,33 @@ void DumpNetCDFMPIIO::openfile()
		NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim),
		NC_LABEL_STR );

		for (int i = 0; i < n_perat; i++) {
		int dims = perat[i].dims;
		if (vector_dim[dims] < 0) {
		char dimstr[1024];
		if (dims == 3) {
		strcpy(dimstr, NC_SPATIAL_STR);
		}
		else if (dims == 6) {
		strcpy(dimstr, NC_VOIGT_STR);
		}
		else {
		sprintf(dimstr, "vec%i", dims);
		}
		if (dims != 1) {
		NCERRX( ncmpi_def_dim(ncid, dimstr, dims, &vector_dim[dims]),
		dimstr );
		}
		}
		}

		// default variables
		dims[0] = spatial_dim;
		dims[0] = vector_dim[3];
		NCERRX( ncmpi_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var),
		NC_SPATIAL_STR );
		NCERRX( ncmpi_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims,
		&cell_spatial_var), NC_CELL_SPATIAL_STR );
		dims[0] = spatial_dim;
		dims[0] = vector_dim[3];
		dims[1] = label_dim;
		NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims,
		&cell_angular_var), NC_CELL_ANGULAR_STR );
		@@ -399,7 +435,7 @@ void DumpNetCDFMPIIO::openfile()
		// variables specified in the input file
		dims[0] = frame_dim;
		dims[1] = atom_dim;
		dims[2] = spatial_dim;
		dims[2] = vector_dim[3];

		for (int i = 0; i < n_perat; i++) {
		nc_type xtype;
		@@ -416,28 +452,15 @@ void DumpNetCDFMPIIO::openfile()
		xtype = NC_FLOAT;
		}

		if (perat[i].dims == 6) {
		// this is a tensor in Voigt notation
		dims[2] = Voigt_dim;
		NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 3) {
		// this is a vector, we need to store x-, y- and z-coordinates
		dims[2] = spatial_dim;
		NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
		&perat[i].var), perat[i].name );
		}
		else if (perat[i].dims == 1) {
		if (perat[i].dims == 1) {
		NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 2, dims,
		&perat[i].var), perat[i].name );
		}
		else {
		char errstr[1024];
		sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
		"this to the NetCDF trajectory file.", perat[i].dims,
		perat[i].name);
		error->all(FLERR,errstr);
		// this is a vector
		dims[2] = vector_dim[perat[i].dims];
		NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
		&perat[i].var), perat[i].name );
		}
		}

src/USER-NETCDF/dump_netcdf_mpiio.h

+1 −2

Original line number	Diff line number	Diff line
		@@ -71,8 +71,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
		int ncid;

		int frame_dim;
		int spatial_dim;
		int Voigt_dim;
		int vector_dim[DUMP_NC_MPIIO_MAX_DIMS];
		int atom_dim;
		int cell_spatial_dim;
		int cell_angular_dim;

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