herr_t H5IMmake_palette( hid_t loc_id,
const char *pal_name,
const hsize_t *pal_dims,
const unsigned char *pal_data )
{
int has_pal;
/* check the arguments */
if (pal_name == NULL)
return -1;
/* Check if the dataset already exists */
has_pal = H5LTfind_dataset( loc_id, pal_name );
/* It exists. Return */
if ( has_pal == 1 )
return 0;
/* Make the palette dataset. */
if ( H5LTmake_dataset( loc_id, pal_name, 2, pal_dims, H5T_NATIVE_UCHAR, pal_data ) < 0 )
return -1;
/* Attach the attribute "CLASS" to the >>palette<< dataset*/
if ( H5LTset_attribute_string( loc_id, pal_name, "CLASS", PALETTE_CLASS ) < 0)
return -1;
/* Attach the attribute "PAL_VERSION" to the >>palette<< dataset*/
if ( H5LTset_attribute_string( loc_id, pal_name, "PAL_VERSION", "1.2" ) < 0)
return -1;
return 0;
}
/*+++++++++++++++++++++++++
.IDENTifer PYTABLE_open_group
.PURPOSE Open/Create a group in an exsisting HDF5-file
.INPUT/OUTPUT
call as grpID = PYTABLE_open_group( locID, name, sz_hint );
input:
hid_t locID : HDF5 object id
char name[] : name of the group
.RETURNS A negative value is returned on failure.
.COMMENTS none
-------------------------*/
hid_t PYTABLE_open_group( hid_t locID, const char *name )
{
hid_t grpID;
/*
* check if the group exists, if not create it
*/
H5E_BEGIN_TRY {
if ( (grpID = H5Gopen( locID, name, H5P_DEFAULT )) < 0 ) {
grpID = H5Gcreate( locID, name,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
(void) H5LTset_attribute_string( locID, name, "CLASS",
PY_GROUP_CLASS );
(void) H5LTset_attribute_string( locID, name,
"PYTABLES_FORMAT_VERSION",
PY_FORMAT_VERSION );
(void) H5LTset_attribute_string( locID, name, "TITLE",
name );
(void) H5LTset_attribute_string( locID, name, "VERSION",
PY_GROUP_VERSION );
}
} H5E_END_TRY;
/*
* return id of the group
*/
return grpID;
}
/*+++++++++++++++++++++++++
.IDENTifer PYTABLE_open_file
.PURPOSE Open/Create a PyTable file
.INPUT/OUTPUT
call as grpID = PYTABLE_open_file( filename, title );
input:
char filename[] : file name
char title[] : title of the PyTable database
.RETURNS A negative value is returned on failure.
.COMMENTS none
-------------------------*/
hid_t PYTABLE_open_file( const char *filename, const char *title )
{
hid_t fileID;
/*
* check if the file exists, if not create it
*/
H5E_BEGIN_TRY {
fileID = H5Fopen( filename, H5F_ACC_RDWR, H5P_DEFAULT );
if ( fileID < 0 ) {
fileID = H5Fcreate( filename, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT );
if ( fileID < 0 ) return -1;
/*
* attach PyTables required attributes
*/
(void) H5LTset_attribute_string( fileID, "/", "CLASS",
PY_GROUP_CLASS );
(void) H5LTset_attribute_string( fileID, "/",
"PYTABLES_FORMAT_VERSION",
PY_FORMAT_VERSION );
(void) H5LTset_attribute_string( fileID, "/", "TITLE",
title );
(void) H5LTset_attribute_string( fileID, "/", "VERSION",
PY_GROUP_VERSION );
}
} H5E_END_TRY;
/*
* return id of the file
*/
return fileID;
}
herr_t H5IMmake_image_8bit( hid_t loc_id,
const char *dset_name,
hsize_t width,
hsize_t height,
const unsigned char *buf )
{
hsize_t dims[IMAGE8_RANK];
/* check the arguments */
if (dset_name == NULL)
return -1;
/* Initialize the image dimensions */
dims[0] = height;
dims[1] = width;
/* Make the dataset */
if ( H5LTmake_dataset( loc_id, dset_name, IMAGE8_RANK, dims, H5T_NATIVE_UCHAR, buf ) < 0)
return -1;
/* Attach the CLASS attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "CLASS", IMAGE_CLASS ) < 0)
return -1;
/* Attach the VERSION attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "IMAGE_VERSION", IMAGE_VERSION ) < 0)
return -1;
/* Attach the IMAGE_SUBCLASS attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "IMAGE_SUBCLASS", "IMAGE_INDEXED" ) < 0)
return -1;
return 0;
}
herr_t H5IMmake_image_24bit( hid_t loc_id,
const char *dset_name,
hsize_t width,
hsize_t height,
const char *interlace,
const unsigned char *buf )
{
hsize_t dims[IMAGE24_RANK];
/* check the arguments */
if (interlace == NULL)
return -1;
if (dset_name == NULL)
return -1;
/* Initialize the image dimensions */
if ( HDstrncmp( interlace, "INTERLACE_PIXEL",15 ) == 0 )
{
/* Number of color planes is defined as the third dimension */
dims[0] = height;
dims[1] = width;
dims[2] = IMAGE24_RANK;
}
else
if ( HDstrncmp( interlace, "INTERLACE_PLANE",15 ) == 0 )
{
/* Number of color planes is defined as the first dimension */
dims[0] = IMAGE24_RANK;
dims[1] = height;
dims[2] = width;
}
else return -1;
/* Make the dataset */
if ( H5LTmake_dataset( loc_id, dset_name, IMAGE24_RANK, dims, H5T_NATIVE_UCHAR, buf ) < 0)
return -1;
/* Attach the CLASS attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "CLASS", IMAGE_CLASS ) < 0)
return -1;
/* Attach the VERSION attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "IMAGE_VERSION", IMAGE_VERSION ) < 0)
return -1;
/* Attach the IMAGE_SUBCLASS attribute */
if ( H5LTset_attribute_string( loc_id, dset_name, "IMAGE_SUBCLASS", "IMAGE_TRUECOLOR" ) < 0)
return -1;
/* Attach the INTERLACE_MODE attribute. This attributes is only for true color images */
if ( H5LTset_attribute_string( loc_id, dset_name, "INTERLACE_MODE", interlace ) < 0)
return -1;
return 0;
}
/*writes properties of the current run related to implementation and command line choices*/
herr_t /*hdf5 error*/
append_meta_properties(hdf5block_t *h5block,/*hdf5 file ids*/
double *seed,/*random number seed*/
size_t *BurnInSampleSize, /*tuning iterations*/
char *h5file, /*name of hdf5 file containing the experimental data and prior set-up*/
char *lib_base)/*basename of the library file @code .so@ file*/{
herr_t status;
int omp_n,omp_np,i;
status&=H5LTset_attribute_double(h5block->file_id, "LogParameters", "seed", seed, 1);
status&=H5LTset_attribute_ulong(h5block->file_id, "LogParameters", "BurnIn", BurnInSampleSize, 1);
status&=H5LTset_attribute_string(h5block->file_id, "LogParameters", "DataFrom", h5file);
status&=H5LTmake_dataset_string(h5block->file_id,"Model",lib_base);
// here we make a short test to see what the automatic choice of the
// number of threads turns out to be.
#pragma omp parallel private(omp_n,omp_np) reduction(+:i)
{
i=1;
omp_n=omp_get_num_threads();
omp_np=omp_get_num_procs();
}
if (i!=omp_n){
fprintf(stderr,"[append_meta_properties] warning: finding out number of threads possibly failed reduction of (n×1: %i) != get_num_threads():%i.\n",i,omp_n);
} else {
h5block->size[0]=1;
h5block->size[1]=1;
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_THREADS",1,h5block->size,&omp_n);
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_PROCS",1,h5block->size,&omp_np);
}
return status;
}
void Grid::initData(FileIO *fileIO)
{
hid_t gridGroup = fileIO->newGroup("/Grid");
// set lengths
check(H5LTset_attribute_double(gridGroup, ".", "Lx", &Lx, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Ly", &Ly, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lz", &Lz, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lv", &Lv, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Lm", &Lm, 1), DMESG("HDF-5 Error"));
// set grid point number
check(H5LTset_attribute_int(gridGroup, ".", "Nx", &Nx , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nky",&Nky, 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nz", &Nz , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nv", &Nv , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Nm", &Nm , 1), DMESG("HDF-5 Error"));
check(H5LTset_attribute_int(gridGroup, ".", "Ns", &Ns , 1), DMESG("HDF-5 Error"));
// set grids
check(H5LTset_attribute_double(gridGroup, ".", "X", &X[NxGlD], Nx), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "Z", &Z[NzGlD], Nz), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "V", &V[NvGlD], Nv), DMESG("HDF-5 Error"));
check(H5LTset_attribute_double(gridGroup, ".", "M", &M[NmGlD], Nm), DMESG("HDF-5 Error"));
check(H5LTset_attribute_string(gridGroup, ".", "MuIntegrationType", muIntegrationType.c_str()), DMESG("HDF-5 Error"));
H5Gclose(gridGroup);
}
// Write string attribute <attr_name> given by address <path>
char AH5_write_str_attr(hid_t loc_id, const char *path, char *attr_name, const char *wdata)
{
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path))
if (H5LTset_attribute_string(loc_id, path, attr_name, wdata) >= 0)
success = AH5_TRUE;
return success;
}
/**
* Write integer attribute.
*
* @param [in] DatasetName
* @param [in] AttributeName
* @param [in] Value
* @throw ios::failure
*/
inline void THDF5_File::WriteStringAttribute(const char * DatasetName, const char * AttributeName, const string & Value){
herr_t status = H5LTset_attribute_string(HDF5_FileId, DatasetName, AttributeName, Value.c_str());
if (status < 0) {
char ErrorMessage[256];
sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteToAttribute,AttributeName, DatasetName);
throw ios::failure(ErrorMessage);
}
}// end of WriteIntAttribute
int pioAddAttributeString(PIOObject pioObject,
const char* attr_name, const char* attr_value)
{
if (pioAttributeIsProtected(attr_name))
{
fprintf(stdout,
"WARNING: Attribute name %s is a reserved for pinocchIO internal use.\n",
attr_name);
return -1;
}
return H5LTset_attribute_string(pioObject.identifier, ".",
attr_name, attr_value);
}
void Particle_interaction_model::write_to_file( hid_t hdf5_file_id )
{
hid_t group_id;
herr_t status;
std::string hdf5_groupname = "/Particle_interaction_model";
group_id = H5Gcreate( hdf5_file_id, hdf5_groupname.c_str(),
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); hdf5_status_check( group_id );
status = H5LTset_attribute_string( hdf5_file_id, hdf5_groupname.c_str(),
"particle_interaction_model",
particle_interaction_model.c_str() ); hdf5_status_check( status );
status = H5Gclose(group_id); hdf5_status_check( status );
return;
}
int_f
nh5ltset_attribute_string_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name;
char *c_attrname;
int c_namelen;
int c_attrnamelen;
/*
* Convert FORTRAN name to C name
*/
c_namelen = *namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL) return ret_value;
c_attrnamelen = *attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL) return ret_value;
/*
* Call H5LTset_attribute_string function.
*/
c_loc_id = (hid_t)*loc_id;
ret = H5LTset_attribute_string(c_loc_id,c_name,c_attrname,buf);
if (ret < 0) return ret_value;
ret_value = 0;
return ret_value;
}
/* ------- begin -------------------------- init_hdf5_indata.c --- */
void init_hdf5_indata_new(void)
/* Creates the netCDF file for the input data */
{
const char routineName[] = "init_hdf5_indata_new";
int i, PRD_angle_dep;
double *eweight, *eabund, *x, *y;
/* This value is harcoded for efficiency.
Maximum number of iterations ever needed */
int NMaxIter = 1500;
hid_t plist, ncid, file_dspace, ncid_input, ncid_atmos, ncid_mpi;
hsize_t dims[4];
bool_t XRD;
char startJ[MAX_LINE_SIZE], StokesMode[MAX_LINE_SIZE], angleSet[MAX_LINE_SIZE];
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(INPUTDATA_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Create groups */
if (( ncid_input = H5Gcreate(ncid, "/input", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_atmos = H5Gcreate(ncid, "/atmos", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_mpi = H5Gcreate(ncid, "/mpi", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* --- Definitions for the INPUT group --- */
/* attributes */
if ( atmos.NPRDactive > 0)
PRD_angle_dep = input.PRD_angle_dep;
else
PRD_angle_dep=0;
XRD = (input.XRD && atmos.NPRDactive > 0);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Magneto_optical",
(unsigned char *) &input.magneto_optical, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "PRD_angle_dep",
(unsigned char *) &PRD_angle_dep, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "XRD",
(unsigned char *) &XRD, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Background_polarization",
(unsigned char *) &input.backgr_pol, 1)) < 0) HERR(routineName);
switch (input.startJ) {
case UNKNOWN:
strcpy(startJ, "Unknown");
break;
case LTE_POPULATIONS:
strcpy(startJ, "LTE_POPULATIONS");
break;
case ZERO_RADIATION:
strcpy(startJ, "ZERO_RADIATION");
break;
case OLD_POPULATIONS:
strcpy(startJ, "OLD_POPULATIONS");
break;
case ESCAPE_PROBABILITY:
strcpy(startJ, "ESCAPE_PROBABILITY");
break;
case NEW_J:
strcpy(startJ, "NEW_J");
break;
case OLD_J:
strcpy(startJ, "OLD_J");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Start_J", startJ)) < 0)
HERR(routineName);
switch (input.StokesMode) {
case NO_STOKES:
strcpy(StokesMode, "NO_STOKES");
break;
case FIELD_FREE:
strcpy(StokesMode, "FIELD_FREE");
break;
case POLARIZATION_FREE:
strcpy(StokesMode, "POLARIZATION_FREE");
break;
case FULL_STOKES:
strcpy(StokesMode, "FULL_STOKES");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Stokes_mode",
StokesMode) ) < 0) HERR(routineName);
switch (atmos.angleSet.set) {
case SET_VERTICAL:
strcpy(angleSet, "SET_VERTICAL");
break;
case SET_GL:
strcpy(angleSet, "SET_GL");
break;
case SET_A2:
strcpy(angleSet, "SET_A2");
break;
case SET_A4:
strcpy(angleSet, "SET_A4");
break;
case SET_A6:
strcpy(angleSet, "SET_A6");
break;
case SET_A8:
strcpy(angleSet, "SET_A8");
break;
case SET_B4:
strcpy(angleSet, "SET_B4");
break;
case SET_B6:
strcpy(angleSet, "SET_B6");
break;
case SET_B8:
strcpy(angleSet, "SET_B8");
break;
case NO_SET:
strcpy(angleSet, "NO_SET");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Angle_set",
angleSet) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Atmos_file",
input.atmos_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Abundances_file",
input.abund_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Kurucz_PF_data",
input.pfData) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Iteration_limit",
&input.iterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "PRD_Iteration_limit",
&input.PRDiterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "N_max_iter",
&input.NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_delay",
&input.Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_order",
&input.Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_period",
&input.Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_N_max_iter",
&input.PRD_NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_delay",
&input.PRD_Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_order",
&input.PRD_Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_period",
&input.PRD_Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Metallicity",
&input.metallicity, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Lambda_reference",
&atmos.lambda_ref, 1) ) < 0) HERR(routineName);
/* --- Definitions for the ATMOS group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_atmos, ".", "nhydr",
&atmos.H->Nlevel, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nelements",
&atmos.Nelem, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nrays",
&geometry.Nrays, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = infile.nz;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_atmos_T = H5Dcreate(ncid_atmos, "temperature", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dcreate(ncid_atmos, "velocity_z", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dcreate(ncid_atmos, "height", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* --- Write some data that does not depend on xi, yi, ATMOS group --- */
/* arrays of number of elements */
eweight = (double *) malloc(atmos.Nelem * sizeof(double));
eabund = (double *) malloc(atmos.Nelem * sizeof(double));
for (i=0; i < atmos.Nelem; i++) {
eweight[i] = atmos.elements[i].weight;
eabund[i] = atmos.elements[i].abund;
}
dims[0] = atmos.Nelem;
if (( H5LTmake_dataset(ncid_atmos, "element_weight", 1, dims,
H5T_NATIVE_DOUBLE, eweight) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "element_abundance", 1, dims,
H5T_NATIVE_DOUBLE, eabund) ) < 0) HERR(routineName);
/* Not writing element_id for now
dims[1] = strlen;
if (( H5LTmake_dataset(ncid_atmos, "element_id", 2, dims,
H5T_C_S1, eID) ) < 0) HERR(routineName);
*/
free(eweight);
free(eabund);
dims[0] = geometry.Nrays;
if (( H5LTmake_dataset(ncid_atmos, "muz", 1, dims,
H5T_NATIVE_DOUBLE, geometry.muz) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "wmu", 1, dims,
H5T_NATIVE_DOUBLE, geometry.wmu) ) < 0) HERR(routineName);
x = (double *) malloc(mpi.nx * sizeof(double));
y = (double *) malloc(mpi.ny * sizeof(double));
for (i=0; i < mpi.nx; i++) x[i] = infile.x[mpi.xnum[i]];
for (i=0; i < mpi.ny; i++) y[i] = infile.y[mpi.ynum[i]];
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atmos, "x", 1, dims,
H5T_NATIVE_DOUBLE, x) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atmos, "y", 1, dims,
H5T_NATIVE_DOUBLE, y) ) < 0) HERR(routineName);
free(x);
free(y);
/* attributes */
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "moving",
(unsigned char *) &atmos.moving, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "stokes",
(unsigned char *) &atmos.Stokes, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "temperature", "units",
"K") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "velocity_z", "units",
"m s^-1") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "height", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "element_weight", "units",
"atomic_mass_units") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "x", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "y", "units",
"m") ) < 0) HERR(routineName);
/* --- Definitions for the MPI group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_mpi, ".", "nprocesses",
&mpi.size, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "niterations",
&NMaxIter, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mpi, XNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.xnum) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mpi, YNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.ynum) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
if (( file_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dcreate(ncid_mpi, TASK_MAP, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dcreate(ncid_mpi, TASK_NUMBER, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dcreate(ncid_mpi, ITER_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dcreate(ncid_mpi, CONV_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dcreate(ncid_mpi, DM_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dcreate(ncid_mpi, ZC_NAME, H5T_NATIVE_INT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = NMaxIter;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dcreate(ncid_mpi, DMH_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* attributes */
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_start",
&input.p15d_x0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_end",
&input.p15d_x1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_step",
&input.p15d_xst, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_start",
&input.p15d_y0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_end",
&input.p15d_y1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_step",
&input.p15d_yst, 1) ) < 0) HERR(routineName);
/* Tiago: most of the arrays involving Ntasks or rank as index are not
currently being written. They should eventually be migrated into
arrays of [ix, iy] and be written for each task. This is to
avoid causing problems with pool mode, where these quantities are
not known from the start.
*/
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
/* --- Copy stuff to the IO data struct --- */
io.in_ncid = ncid;
io.in_input_ncid = ncid_input;
io.in_atmos_ncid = ncid_atmos;
io.in_mpi_ncid = ncid_mpi;
return;
}
int SpIO_FwriteModel(SpFile *sfp, SpModel model)
{
int status = 0;
herr_t hstatus;
/* Write the version of format */
if(!status) {
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "format", "SPARX format v3");
if(hstatus < 0)
status = 1;
}
/* Write the type of coordinat system */
if(!status) {
DatINode *geom = Dat_IList_IdxLookup(GEOM_TYPES, model.parms.geom);
Deb_ASSERT(geom != NULL);
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "geom", geom->name);
if(hstatus < 0)
status = 1;
}
/* Write T_cmb */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "T_cmb", &model.parms.T_cmb, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write T_in */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "T_in", &model.parms.T_in, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write molecule name */
if(!status) {
Molec *mol = model.parms.mol;
hstatus = H5LTset_attribute_string(sfp->h5f_id, "/", "molec", mol ? mol->name : "");
if(hstatus < 0)
status = 1;
}
/* Write pops-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "pops", &model.parms.pops, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write dust-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "dust", &model.parms.dust, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write polariz-switch */
if(!status) {
hstatus = H5LTset_attribute_int(sfp->h5f_id, "/", "polariz", &model.parms.polariz, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write polariz-switch */
if(!status) {
hstatus = H5LTset_attribute_double(sfp->h5f_id, "/", "z", &model.parms.z, (size_t)1);
if(hstatus < 0)
status = 1;
}
/* Write grid */
if(!status)
status = SpIO_H5WriteGrid(sfp->h5f_id, model.grid, &model.parms);
if(status)
status = Err_SETSTRING("Error writing model to file `%s'", sfp->name);
return status;
}
herr_t H5IMmake_image_8bitf(hid_t loc_id,
const char *dset_name,
hsize_t width,
hsize_t height,
int_f *buf)
{
hid_t did; /* dataset ID */
hid_t sid; /* space ID */
hsize_t dims[IMAGE8_RANK]; /* dimensions */
/* initialize the image dimensions */
dims[0] = height;
dims[1] = width;
/*-------------------------------------------------------------------------
* create and write the dataset
*-------------------------------------------------------------------------
*/
/* create the data space for the dataset. */
if((sid = H5Screate_simple(IMAGE8_RANK, dims, NULL)) < 0)
return -1;
/* create the dataset as H5T_NATIVE_UCHAR */
if((did = H5Dcreate2(loc_id, dset_name, H5T_NATIVE_UINT8, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
return -1;
/* write with memory type H5T_NATIVE_INT */
/* Use long type if Fortran integer is 8 bytes and C long long is also 8 bytes*/
/* Fail if otherwise */
if(buf) {
if(sizeof(int_f) == sizeof(int)) {
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long)) {
if(H5Dwrite(did, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long long)) {
if(H5Dwrite(did, H5T_NATIVE_LLONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else
return -1;
}
/* close */
if(H5Dclose(did) < 0)
return -1;
if(H5Sclose(sid) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the specification attributes
*-------------------------------------------------------------------------
*/
/* attach the CLASS attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "CLASS", IMAGE_CLASS) < 0)
return -1;
/* attach the VERSION attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "IMAGE_VERSION", IMAGE_VERSION) < 0)
return -1;
/* attach the IMAGE_SUBCLASS attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "IMAGE_SUBCLASS", "IMAGE_INDEXED") < 0)
return -1;
return 0;
}
herr_t H5IMmake_palettef(hid_t loc_id,
const char *pal_name,
const hsize_t *pal_dims,
int_f *pal_data)
{
hid_t did; /* dataset ID */
hid_t sid; /* space ID */
int has_pal;
/* Check if the dataset already exists */
has_pal = H5LTfind_dataset(loc_id, pal_name);
/* It exists. Return */
if(has_pal == 1)
return 0;
/*-------------------------------------------------------------------------
* create and write the dataset
*-------------------------------------------------------------------------
*/
/* create the data space for the dataset. */
if((sid = H5Screate_simple(2, pal_dims, NULL)) < 0)
return -1;
/* create the dataset as H5T_NATIVE_UCHAR */
if((did = H5Dcreate2(loc_id, pal_name, H5T_NATIVE_UCHAR, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
return -1;
/* write with memory type H5T_NATIVE_INT */
if(pal_data) {
if(sizeof(int_f) == sizeof(int)) {
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, pal_data) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long)) {
if(H5Dwrite(did, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, pal_data) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long long)) {
if(H5Dwrite(did, H5T_NATIVE_LLONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, pal_data) < 0)
return -1;
} else
return -1;
}
/* close */
if(H5Dclose(did) < 0)
return -1;
if(H5Sclose(sid) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the specification attributes
*-------------------------------------------------------------------------
*/
/* Attach the attribute "CLASS" to the >>palette<< dataset*/
if(H5LTset_attribute_string(loc_id, pal_name, "CLASS", PALETTE_CLASS) < 0)
return -1;
/* Attach the attribute "PAL_VERSION" to the >>palette<< dataset*/
if(H5LTset_attribute_string(loc_id, pal_name, "PAL_VERSION", "1.2") < 0)
return -1;
return 0;
}
herr_t H5IMmake_image_24bitf(hid_t loc_id,
const char *dset_name,
hsize_t width,
hsize_t height,
const char *interlace,
int_f *buf)
{
hid_t did; /* dataset ID */
hid_t sid; /* space ID */
hsize_t dims[IMAGE24_RANK]; /* dimensions */
/*-------------------------------------------------------------------------
* attach the image dimensions according to the interlace mode
*-------------------------------------------------------------------------
*/
if(strcmp(interlace, "INTERLACE_PIXEL") == 0) {
/* Number of color planes is defined as the third dimension */
dims[0] = height;
dims[1] = width;
dims[2] = IMAGE24_RANK;
}
else
if(strcmp(interlace, "INTERLACE_PLANE") == 0) {
/* Number of color planes is defined as the first dimension */
dims[0] = IMAGE24_RANK;
dims[1] = height;
dims[2] = width;
}
else
return -1;
/*-------------------------------------------------------------------------
* create and write the dataset
*-------------------------------------------------------------------------
*/
/* create the data space for the dataset. */
if((sid = H5Screate_simple(IMAGE24_RANK, dims, NULL)) < 0)
return -1;
/* create the dataset as H5T_NATIVE_UCHAR */
if((did = H5Dcreate2(loc_id, dset_name, H5T_NATIVE_UCHAR, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
return -1;
/* write with memory type H5T_NATIVE_INT */
if(buf) {
if(sizeof(int_f) == sizeof(int)) {
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long)) {
if(H5Dwrite(did, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else if(sizeof(int_f) == sizeof(long long)) {
if(H5Dwrite(did, H5T_NATIVE_LLONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
return -1;
} else
return -1;
}
/* close */
if(H5Dclose(did) < 0)
return -1;
if(H5Sclose(sid) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the specification attributes
*-------------------------------------------------------------------------
*/
/* Attach the CLASS attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "CLASS", IMAGE_CLASS) < 0)
return -1;
/* Attach the VERSION attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "IMAGE_VERSION", IMAGE_VERSION) < 0)
return -1;
/* Attach the IMAGE_SUBCLASS attribute */
if(H5LTset_attribute_string(loc_id, dset_name, "IMAGE_SUBCLASS", "IMAGE_TRUECOLOR") < 0)
return -1;
/* Attach the INTERLACE_MODE attribute. This attributes is only for true color images */
if(H5LTset_attribute_string(loc_id, dset_name, "INTERLACE_MODE", interlace) < 0)
return -1;
return 0;
}
void write_string_attribute (std::string const & obj_name, std::string const & attr_name, std::string const & value){
herr_t err = H5LTset_attribute_string(_g.getId(),obj_name.c_str(),attr_name.c_str(), value.c_str() ) ;
if (err<0) TRIQS_RUNTIME_ERROR << "Error in setting attribute of "<< obj_name<<" named "<< attr_name << " to " << value;
}
/*+++++++++++++++++++++++++
.IDENTifer PYTABLE_make_array
.PURPOSE create extensible HDF5 dataset
.INPUT/OUTPUT
call as stat = PYTABLE_make_array( locID, dset_name, title, rank, dims,
extdim, typeID, dims_chunk, fill_data,
compress, shuffle, fletcher32, buff );
input:
hid_t locID : HDF5 identifier of file or group
char *dset_name : name of dataset
char *title :
int rank : number of dimensions
hsize_t *dims : size of each dimension
int extdim : index of expendable dimension
hid_t typeID : data type (HDF5 identifier)
hsize_t *dims_chunk : chunk sizes
void *fill_data : Fill value for data
unsigned int compress : compression level (zero for no compression)
bool shuffle : shuffel data for better compression
bool fletcher32 :
void *buffer : buffer with data to write (or NULL)
.RETURNS A negative value is returned on failure.
.COMMENTS none
-------------------------*/
herr_t PYTABLE_make_array( hid_t locID, const char *dset_name,
const char *title, const int rank,
const hsize_t *dims, int extdim, hid_t typeID,
const hsize_t *dims_chunk, void *fill_data,
unsigned int compress, bool shuffle,
bool fletcher32, const void *buffer )
{
register int ni;
hid_t dataID = -1, spaceID = -1;
herr_t stat;
/* check if the array has to be chunked or not */
if ( dims_chunk != NULL ) {
hid_t plistID;
hsize_t *maxdims = (hsize_t *) malloc( rank * sizeof(hsize_t) );
if ( maxdims == NULL )
NADC_GOTO_ERROR( NADC_ERR_ALLOC, "maxdims" );
for ( ni = 0; ni < rank; ni++ ) {
if ( ni == extdim )
maxdims[ni] = H5S_UNLIMITED;
else
maxdims[ni] =
dims[ni] < dims_chunk[ni] ? dims_chunk[ni] : dims[ni];
}
spaceID = H5Screate_simple( rank, dims, maxdims );
free( maxdims );
if ( spaceID < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_SPACE, "" );
/* Modify dataset creation properties, i.e. enable chunking */
plistID = H5Pcreate( H5P_DATASET_CREATE );
if ( H5Pset_chunk( plistID, rank, dims_chunk ) < 0 ) goto done;
/* set the fill value using a struct as the data type */
if ( fill_data != NULL
&& H5Pset_fill_value( plistID, typeID, fill_data ) < 0 )
goto done;
/* dataset creation property list is modified to use */
/* fletcher must be first */
if ( fletcher32 ) {
if ( H5Pset_fletcher32( plistID ) < 0 ) goto done;
}
/* then shuffle */
if ( shuffle ) {
if ( H5Pset_shuffle( plistID ) < 0 ) goto done;
}
/* finally compression */
if ( compress > 0 ) {
if ( H5Pset_deflate( plistID, compress ) < 0 ) goto done;
}
/* create the (chunked) dataset */
dataID = H5Dcreate( locID, dset_name, typeID, spaceID,
H5P_DEFAULT, plistID, H5P_DEFAULT );
if ( dataID < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, dset_name );
/* end access to the property list */
if ( H5Pclose( plistID ) < 0 ) goto done;
} else {
spaceID = H5Screate_simple( rank, dims, NULL );
if ( spaceID < 0 ) return -1;
/* create the dataset (not chunked) */
dataID = H5Dcreate( locID, dset_name, typeID, spaceID,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
if ( dataID < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, dset_name );
}
/*
* write the data
*/
stat = H5Dwrite( dataID, typeID, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer );
if ( stat < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_WR, "" );
(void) H5Dclose( dataID );
(void) H5Sclose( spaceID );
/*
* Set the conforming array attributes
*
* attach the CLASS attribute
*/
(void) H5LTset_attribute_string( locID, dset_name, "CLASS",
PY_ARRAY_CLASS );
/* attach the EXTDIM attribute in case of enlargeable arrays */
(void) H5LTset_attribute_int( locID, dset_name, "EXTDIM", &extdim, 1 );
/* attach the FLAVOR attribute */
(void) H5LTset_attribute_string( locID, dset_name, "FLAVOR",
PY_ARRAY_FLAVOR );
/* attach the VERSION attribute */
(void) H5LTset_attribute_string( locID, dset_name, "VERSION",
PY_ARRAY_VERSION );
/* attach the TITLE attribute */
(void) H5LTset_attribute_string( locID, dset_name, "TITLE", title );
return 0;
done:
if ( dataID > 0 ) (void) H5Dclose( dataID );
if ( spaceID > 0 ) (void) H5Sclose( spaceID );
return -1;
}
int FileIO::create(Setup *setup) {
hid_t file_plist = H5Pcreate(H5P_FILE_ACCESS);
#ifdef GKC_PARALLEL_MPI
// pass some information onto the underlying MPI_File_open call
MPI_Info file_info;
check(MPI_Info_create(&file_info), DMESG("File info"));
/*
H5Pset_sieve_buf_size(file_plist, 262144);
H5Pset_alignment(file_plist, 524288, 262144);
MPI_Info_set(file_info, (char *) "access_style" , (char *) "write_once");
MPI_Info_set(file_info, (char *) "collective_buffering", (char *) "true");
MPI_Info_set(file_info, (char *) "cb_block_size" , (char *) "1048576");
MPI_Info_set(file_info, (char *) "cb_buffer_size" , (char *) "4194304");
* */
check( H5Pset_fapl_mpio(file_plist, parallel->Comm[DIR_ALL], file_info), DMESG("Set MPI Property"));
#endif
file = check(H5Fcreate(outputFileName.c_str(), (overwriteFile ? H5F_ACC_TRUNC : H5F_ACC_EXCL),
H5P_DEFAULT, file_plist ), DMESG("H5FCreate : HDF5 File (File already exists ? use -f to overwrite) : " + outputFileName));
check( H5Pclose(file_plist), DMESG("H5Pclose"));
#ifdef GKC_PARALLEL_MPI
MPI_Info_free(&file_info);
#endif
//////////////////////////////////////////////////////////////// Info Group ////////////////////////////////////////////////////////
hid_t infoGroup = check(H5Gcreate(file, "/Info",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
check(H5LTset_attribute_string(infoGroup, ".", "Output", outputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Input", inputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Version", PACKAGE_VERSION), DMESG("H5LTset_attribute"));
// Some Simulation specific stuff
//check(H5LTset_attribute_string(infoGroup, ".", "Solver", ((setup->Solver & VL_LIN) ? "Linear" : "Non-Linear")), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "Type", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "FFTSolverS", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_string(infoGroup, ".", "Initial Condition", setup->PerturbationMethod.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Info", info.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Config", setup->configFileString.c_str()), DMESG("H5LTset_attribute"));
H5Gclose(infoGroup);
/// Wrote setup constants, ugly here ////
hid_t constantsGroup = check(H5Gcreate(file, "/Constants",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
//
if (!setup->parser_constants.empty()) {
std::vector<std::string> const_vec = Setup::split(setup->parser_constants, ",");
for(int s = 0; s < const_vec.size(); s++) {
std::vector<std::string> key_value = Setup::split(const_vec[s],"=");
double value = Setup::string_to_double(key_value[1]);
int dim[] = { 1 };
// check(H5LTmake_dataset_double(constantsGroup, Setup::trimLower(key_value[0], false).c_str(), 1, dim, &value ), DMESG("Write Constants Attributes"));
check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &value, 1), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &(Setup::string_to_double(key_value[1])), 1), DMESG("H5LTset_attribute"));
};
}
H5Gclose(constantsGroup);
// ********************* setup Table for CFL *****************88
cfl_table = new CFLTable();
cfl_offset[0] = HOFFSET( CFLTable, timeStep );
cfl_offset[1] = HOFFSET( CFLTable, time );
cfl_offset[2] = HOFFSET( CFLTable, Fx );
cfl_offset[3] = HOFFSET( CFLTable, Fy );
cfl_offset[4] = HOFFSET( CFLTable, Fz );
cfl_offset[5] = HOFFSET( CFLTable, Fv );
cfl_offset[6] = HOFFSET( CFLTable, total );
for(int i = 1; i < 7; i++) cfl_sizes[i] = sizeof(double); cfl_sizes[0] = sizeof(int);
hid_t cfl_type[7]; for(int i = 1; i < 7; i++) cfl_type [i] = H5T_NATIVE_DOUBLE; cfl_type[0] = H5T_NATIVE_INT;
const char *cfl_names[7];
cfl_names[0] = "timeStep";
cfl_names[1] = "time";
cfl_names[2] = "Fx"; cfl_names[3] = "Fy"; cfl_names[4] = "Fz"; cfl_names[5] = "Fv"; cfl_names[6] = "Total";
check(H5TBmake_table("cflTable", file, "cfl", (hsize_t) 7, (hsize_t) 0, sizeof(CFLTable), (const char**) cfl_names,
cfl_offset, cfl_type, 32, NULL, 0, cfl_table ), DMESG("H5Tmake_table : cfl"));
return HELIOS_SUCCESS;
}
int_f
h5ltset_attribute_c(hid_t_f *loc_id,
size_t_f *namelen,
_fcd dsetname,
size_t_f *attrnamelen,
_fcd attrname,
size_t_f *size,
void *buf, char *dtype, size_t_f *sizeof_val)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
char *c_buf = NULL;
size_t c_size;
/*
* convert FORTRAN name to C name
*/
c_name = (char *)HD5f2cstring(dsetname, (size_t)*namelen);
if (c_name == NULL)
goto done;
c_attrname = (char *)HD5f2cstring(attrname, (size_t)*attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* call H5LTset_attribute_int function.
*/
c_loc_id = (hid_t)*loc_id;
c_size = (size_t)*size;
if( HDstrncmp(dtype,"I",1) == 0 ) {
if ((size_t)*sizeof_val == sizeof(int))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_INT, (const int *)buf);
else if ((size_t)*sizeof_val == sizeof(long))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_LONG, (const long *)buf);
else if ((size_t)*sizeof_val == sizeof(long long))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_LLONG, (const long long *)buf);
else
goto done;
} else if ( HDstrncmp(dtype,"R",1) == 0 ) {
if((size_t)*sizeof_val == sizeof(float))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_FLOAT, (const float *)buf);
else if((size_t)*sizeof_val == sizeof(double))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_DOUBLE, (const double *)buf);
#if H5_SIZEOF_LONG_DOUBLE !=0
else if((size_t)*sizeof_val == sizeof(long double))
ret = H5LT_set_attribute_numerical(c_loc_id,c_name,c_attrname, c_size, H5T_NATIVE_LDOUBLE, (const long double *)buf);
#endif
else
goto done;
} else if ( HDstrncmp(dtype,"C",1) == 0 ) {
c_buf = (char *)HD5f2cstring((_fcd)buf, c_size);
if (c_buf == NULL)
goto done;
ret = H5LTset_attribute_string(c_loc_id,c_name,c_attrname,c_buf);
}
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
HDfree(c_name);
if(c_attrname!=NULL)
HDfree(c_attrname);
if(c_buf!=NULL)
HDfree(c_buf);
return ret_value;
}
/* ------- begin -------------------------- init_aux_new.c -- --- */
void init_aux_new(void) {
/* Creates the HDF5 file for the auxiliary data */
const char routineName[] = "init_aux_new";
unsigned int *tmp;
double *tmp_double;
int i;
hid_t plist, ncid, file_dspace, ncid_atom, ncid_mol;
hid_t id_x, id_y, id_z, id_n, id_tmp;
hsize_t dims[4];
char group_name[ARR_STRLEN];
Atom *atom;
Molecule *molecule;
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS) ) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(AUX_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* Fill value */
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* Get group name */
sprintf(group_name, (atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s",
atom->ID);
if (( ncid_atom = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_atom_ncid[i] = ncid_atom;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_atom, ".", "nlevel",
&atom->Nlevel, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "nline",
&atom->Nline, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "ncontinuum",
&atom->Ncont, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atom, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_atom, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atom, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_atom, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_atom, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_atom, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = atom->Nlevel;
tmp = (unsigned int *) calloc(atom->Nlevel , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = atom->Nline;
tmp = (unsigned int *) calloc(atom->Nline , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
tmp = (unsigned int *) calloc(atom->Ncont , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, CONT_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
}
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_atom, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( H5LTset_attribute_string(ncid_atom, CONT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
}
/* --- variables --- */
dims[0] = atom->Nlevel;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (atom->n != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POP_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_pop[i] = id_tmp;
}
if (atom->nstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POPLTE_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Radiative rates */
dims[0] = atom->Nline;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0) HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LINE_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijL[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiL[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, CONT_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijC[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiC[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* Get group name */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( ncid_mol = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_mol_ncid[i] = ncid_mol;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_mol, ".", "nlevel_vibr",
&molecule->Nv, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nline_molecule",
&molecule->Nrt, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nJ",
&molecule->NJ, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mol, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_mol, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mol, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_mol, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_mol, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_mol, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = molecule->Nv;
tmp = (unsigned int *) calloc(molecule->Nv, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->Nrt;
tmp = (unsigned int *) calloc(molecule->Nrt, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->NJ;
tmp = (unsigned int *) calloc(molecule->NJ, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, NJ_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_mol, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, NJ_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
/* --- variables --- */
dims[0] = molecule->Nv;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_mol, VLEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (molecule->nv != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_pop[i] = id_tmp;
}
if (molecule->nvstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
// TODO: molecule->Ediss, molecule->Tmin, molecule->Tmax
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active MOLECULES loop */
io.aux_ncid = ncid; /* Copy stuff to the IO data struct */
if (( H5Pclose(plist) ) < 0) HERR(routineName); /* Free hdf5 resources */
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
return;
}
int_f
nh5ltset_attribute_string_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
int_f *buflen,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
int c_namelen;
int c_attrnamelen;
char *c_buf = NULL;
int c_buflen;
/*
* convert FORTRAN name to C name
*/
c_namelen = *namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL)
goto done;
c_attrnamelen = *attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL)
goto done;
c_buflen = *buflen;
c_buf = (char *)HD5f2cstring(buf, c_buflen);
if (c_buf == NULL)
goto done;
/*
* call H5LTset_attribute_string function.
*/
c_loc_id = (hid_t)*loc_id;
ret = H5LTset_attribute_string(c_loc_id,c_name,c_attrname,c_buf);
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
free(c_name);
if(c_attrname!=NULL)
free(c_attrname);
if(c_buf!=NULL)
free(c_buf);
return ret_value;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
