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ENH: Support for outputting computes and fixes with arbitrary number of columns.

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This commit is contained in:
Lars Pastewka
2019-01-21 23:04:22 +01:00
parent bd3b712902
commit 0fde0f99bc
4 changed files with 110 additions and 80 deletions
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105
src/USER-NETCDF/dump_netcdf.cpp
View File

@ -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 );
&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[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 == 6) {
// this is a tensor in Voigt notation
dims[2] = Voigt_dim;
NCERRX( nc_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( nc_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( 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 );
}
}
}

3
src/USER-NETCDF/dump_netcdf.h
View File

@ -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;

79
src/USER-NETCDF/dump_netcdf_mpiio.cpp
View File

@ -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 );
}
}

3
src/USER-NETCDF/dump_netcdf_mpiio.h
View File

@ -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;