diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp
index e4c0115793482efc11e54bd784f664bea89293d9..c095c4f44b0c4f481ae7b5a7011cdb693b32ed4b 100644
--- a/src/USER-NETCDF/dump_netcdf.cpp
+++ b/src/USER-NETCDF/dump_netcdf.cpp
@@ -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)Â {
+ 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 );
}
}
}
diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/USER-NETCDF/dump_netcdf.h
index f97fd58409fa952ebe44e0bcb97ccd776227d619..f74e95be386fef261c2ad1ad1cce4a615c634446 100644
--- a/src/USER-NETCDF/dump_netcdf.h
+++ b/src/USER-NETCDF/dump_netcdf.h
@@ -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;
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
index 733fae10f33d1c536d7ea79e451bb4d856785434..026a6eaa3aadc7c41db1f3b4e70c917e4fa70f8e 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
@@ -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 );
}
}
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h
index 330fa46c045b8eee761dce3958422f9db41bed1a..98ccb87927605182b4d1ffbbb1f99abe23c0e54e 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.h
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.h
@@ -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;