int_f
nh5sset_extent_simple_c ( hid_t_f *space_id , int_f *rank, hsize_t_f *current_size, hsize_t_f *maximum_size)
{
int ret_value = -1;
hid_t c_space_id;
int c_rank;
hsize_t *c_current_size;
hsize_t *c_maximum_size;
herr_t status;
int i;
c_current_size = malloc(sizeof(hsize_t)*(*rank));
if (!c_current_size) return ret_value;
c_maximum_size = malloc(sizeof(hsize_t)*(*rank));
if (!c_maximum_size) return ret_value;
/*
* Reverse dimensions due to C-FORTRAN storage order.
*/
for (i=0; i < *rank; i++) {
c_current_size[i] = (hsize_t)current_size[*rank - i - 1];
c_maximum_size[i] = (hsize_t)maximum_size[*rank - i - 1];
}
c_space_id = *space_id;
c_rank = *rank;
status = H5Sset_extent_simple(c_space_id, c_rank, c_current_size, c_maximum_size);
if ( status >= 0 ) ret_value = 0;
HDfree(c_current_size);
HDfree(c_maximum_size);
return ret_value;
}
void DCDataSet::append(size_t count, size_t offset, size_t stride, const void* data)
throw (DCException)
{
log_msg(2, "DCDataSet::append");
if (!opened)
throw DCException(getExceptionString("append: Dataset has not been opened/created."));
log_msg(3, "logical_size = %s", getLogicalSize().toString().c_str());
Dimensions target_offset(getLogicalSize());
// extend size (dataspace) of existing dataset with count elements
getLogicalSize()[0] += count;
hsize_t * max_dims = new hsize_t[ndims];
for (size_t i = 0; i < ndims; ++i)
max_dims[i] = H5F_UNLIMITED;
if (H5Sset_extent_simple(dataspace, 1, getLogicalSize().getPointer(), max_dims) < 0)
throw DCException(getExceptionString("append: Failed to set new extent"));
delete[] max_dims;
max_dims = NULL;
log_msg(3, "logical_size = %s", getLogicalSize().toString().c_str());
if (H5Dset_extent(dataset, getLogicalSize().getPointer()) < 0)
throw DCException(getExceptionString("append: Failed to extend dataset"));
// select the region in the target DataSpace to write to
Dimensions dim_data(count, 1, 1);
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, target_offset.getPointer(),
NULL, dim_data.getPointer(), NULL) < 0 ||
H5Sselect_valid(dataspace) < 0)
throw DCException(getExceptionString("append: Invalid target hyperslap selection"));
// append data to the dataset.
// select the region in the source DataSpace to read from
Dimensions dim_src(offset + count * stride, 1, 1);
hid_t dsp_src = H5Screate_simple(1, dim_src.getPointer(), NULL);
if (dsp_src < 0)
throw DCException(getExceptionString("append: Failed to create src dataspace while appending"));
if (H5Sselect_hyperslab(dsp_src, H5S_SELECT_SET, Dimensions(offset, 0, 0).getPointer(),
Dimensions(stride, 1, 1).getPointer(), dim_data.getPointer(), NULL) < 0 ||
H5Sselect_valid(dsp_src) < 0)
throw DCException(getExceptionString("append: Invalid source hyperslap selection"));
if (!data || (count == 0))
{
H5Sselect_none(dataspace);
data = NULL;
}
if (H5Dwrite(dataset, this->datatype, dsp_src, dataspace, dsetWriteProperties, data) < 0)
throw DCException(getExceptionString("append: Failed to append dataset"));
H5Sclose(dsp_src);
}
hid_t _write_grid(hid_t loc_id, std::string attr_name, double *attr_array, const hsize_t size)
{
herr_t status;
hid_t attr_id;
DataspaceCreate x_grid_space(H5S_SCALAR);
status = H5Sset_extent_simple(x_grid_space.dataspace_id, 1, &size, NULL);
attr_id = H5Acreate(loc_id, attr_name.c_str(), H5T_NATIVE_DOUBLE, x_grid_space.dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
status = H5Awrite(attr_id, H5T_NATIVE_DOUBLE, attr_array);
H5Aclose(attr_id);
return status;
}
void writeInt32Attribute(hid_t element, const char *attr_name, hsize_t dims, int *attr_value)
{
herr_t hdfstatus = -1;
hid_t hdfdatatype = -1;
hid_t hdfattr = -1;
hid_t hdfattrdataspace = -1;
hdfattrdataspace = H5Screate(H5S_SCALAR);
hdfdatatype = H5Tcopy(H5T_NATIVE_INT32);
if (dims == 1) {
} else {
hdfattrdataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdfattrdataspace, 1, &dims, NULL);
}
hdfattr = H5Acreate2(element, attr_name, hdfdatatype, hdfattrdataspace, H5P_DEFAULT, H5P_DEFAULT);
hdfstatus = H5Awrite(hdfattr, hdfdatatype, attr_value);
H5Aclose (hdfattr);
H5Sclose(hdfattrdataspace);
return;
}
void write_header_attributes_in_hdf5(hid_t handle)
{
hsize_t adim[1] = { 6 };
hid_t hdf5_dataspace, hdf5_attribute;
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, adim, NULL);
hdf5_attribute = H5Acreate(handle, "NumPart_ThisFile", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, header.npart);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, adim, NULL);
hdf5_attribute = H5Acreate(handle, "NumPart_Total", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotal);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, adim, NULL);
hdf5_attribute = H5Acreate(handle, "NumPart_Total_HW", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, header.npartTotalHighWord);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, adim, NULL);
hdf5_attribute = H5Acreate(handle, "MassTable", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, header.mass);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Time", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.time);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Redshift", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.redshift);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "BoxSize", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.BoxSize);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "NumFilesPerSnapshot", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.num_files);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Omega0", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.Omega0);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "OmegaLambda", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.OmegaLambda);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "HubbleParam", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &header.HubbleParam);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Flag_Sfr", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.flag_sfr);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Flag_Cooling", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.flag_cooling);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Flag_StellarAge", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.flag_stellarage);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Flag_Metals", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.flag_metals);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(handle, "Flag_Feedback", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &header.flag_feedback);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
header.flag_entropy_instead_u = 0;
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, adim, NULL);
hdf5_attribute = H5Acreate(handle, "Flag_Entropy_ICs", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, &header.flag_entropy_instead_u);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
}
/*-------------------------------------------------------------------------
* Function: addrem_records
*
* Purpose: Adds/removes a specified number of records to random datasets
* to the SWMR test file.
*
* Parameters: hid_t fid
* The file ID of the SWMR HDF5 file
*
* unsigned verbose
* Whether or not to emit verbose console messages
*
* unsigned long nops
* # of records to read/write in the datasets
*
* unsigned long flush_count
* # of records to write before flushing the file to disk
*
* Return: Success: 0
* Failure: -1
*
*-------------------------------------------------------------------------
*/
static int
addrem_records(hid_t fid, unsigned verbose, unsigned long nops, unsigned long flush_count)
{
hid_t tid; /* Datatype ID for records */
hid_t mem_sid; /* Memory dataspace ID */
hsize_t start[2] = {0, 0}, count[2] = {1, 1}; /* Hyperslab selection values */
hsize_t dim[2] = {1, 0}; /* Dataspace dimensions */
symbol_t buf[MAX_SIZE_CHANGE]; /* Write buffer */
H5AC_cache_config_t mdc_config_orig; /* Original metadata cache configuration */
H5AC_cache_config_t mdc_config_cork; /* Corked metadata cache configuration */
unsigned long op_to_flush; /* # of operations before flush */
unsigned long u, v; /* Local index variables */
assert(fid > 0);
/* Reset the buffer */
memset(&buf, 0, sizeof(buf));
/* Create a dataspace for the record to add */
if((mem_sid = H5Screate_simple(2, count, NULL)) < 0)
return -1;
/* Create datatype for appending records */
if((tid = create_symbol_datatype()) < 0)
return -1;
/* Get the current metadata cache configuration, and set up the corked
* configuration */
mdc_config_orig.version = H5AC__CURR_CACHE_CONFIG_VERSION;
if(H5Fget_mdc_config(fid, &mdc_config_orig) < 0)
return -1;
memcpy(&mdc_config_cork, &mdc_config_orig, sizeof(mdc_config_cork));
mdc_config_cork.evictions_enabled = FALSE;
mdc_config_cork.incr_mode = H5C_incr__off;
mdc_config_cork.flash_incr_mode = H5C_flash_incr__off;
mdc_config_cork.decr_mode = H5C_decr__off;
/* Add and remove records to random datasets, according to frequency
* distribution */
op_to_flush = flush_count;
for(u=0; u<nops; u++) {
symbol_info_t *symbol; /* Symbol to write record to */
hid_t file_sid; /* Dataset's space ID */
/* Get a random dataset, according to the symbol distribution */
symbol = choose_dataset();
/* Decide whether to shrink or expand, and by how much */
count[1] = (hsize_t)random() % (MAX_SIZE_CHANGE * 2) + 1;
if(count[1] > MAX_SIZE_CHANGE) {
/* Add records */
count[1] -= MAX_SIZE_CHANGE;
/* Set the buffer's IDs (equal to its position) */
for(v=0; v<count[1]; v++)
buf[v].rec_id = (uint64_t)symbol->nrecords + (uint64_t)v;
/* Set the memory space to the correct size */
if(H5Sset_extent_simple(mem_sid, 2, count, NULL) < 0)
return -1;
/* Get the coordinates to write */
start[1] = symbol->nrecords;
/* Cork the metadata cache, to prevent the object header from being
* flushed before the data has been written */
/*if(H5Fset_mdc_config(fid, &mdc_config_cork) < 0)
return(-1);*/
/* Extend the dataset's dataspace to hold the new record */
symbol->nrecords+= count[1];
dim[1] = symbol->nrecords;
if(H5Dset_extent(symbol->dsid, dim) < 0)
return -1;
/* Get the dataset's dataspace */
if((file_sid = H5Dget_space(symbol->dsid)) < 0)
return -1;
/* Choose the last record in the dataset */
if(H5Sselect_hyperslab(file_sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
return -1;
/* Write record to the dataset */
if(H5Dwrite(symbol->dsid, tid, mem_sid, file_sid, H5P_DEFAULT, &buf) < 0)
return -1;
/* Uncork the metadata cache */
/*if(H5Fset_mdc_config(fid, &mdc_config_orig) < 0)
return -1;*/
/* Close the dataset's dataspace */
if(H5Sclose(file_sid) < 0)
return -1;
} /* end if */
else {
/* Shrink the dataset's dataspace */
if(count[1] > symbol->nrecords)
symbol->nrecords = 0;
else
symbol->nrecords -= count[1];
dim[1] = symbol->nrecords;
if(H5Dset_extent(symbol->dsid, dim) < 0)
return -1;
} /* end else */
/* Check for flushing file */
if(flush_count > 0) {
/* Decrement count of records to write before flushing */
op_to_flush--;
/* Check for counter being reached */
if(0 == op_to_flush) {
/* Flush contents of file */
if(H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0)
return -1;
/* Reset flush counter */
op_to_flush = flush_count;
} /* end if */
} /* end if */
} /* end for */
/* Emit informational message */
if(verbose)
fprintf(stderr, "Closing datasets\n");
/* Close the datasets */
for(u = 0; u < NLEVELS; u++)
for(v = 0; v < symbol_count[u]; v++)
if(H5Dclose(symbol_info[u][v].dsid) < 0)
return -1;
return 0;
}
/*
* Function: dset_write
* Purpose: Write buffer into the dataset.
* Return: SUCCESS or FAIL
* Programmer: Christian Chilan, April, 2008
* Modifications:
*/
static herr_t
dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer)
{
int cur_dim = order[local_dim]-1;
int ret_code = SUCCESS;
int k;
hsize_t dims[MAX_DIMS], maxdims[MAX_DIMS];
hsize_t i;
int j;
herr_t hrc;
/* iterates according to the dimensions in order array */
for (i=0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]){
h5offset[cur_dim] = (hssize_t)i;
offset[cur_dim] = (HDoff_t)i;
if (local_dim > 0){
dset_write(local_dim-1, fd, parms, buffer);
}else{
switch (parms->io_type) {
case POSIXIO:
/* initialize POSIX offset in the buffer */
for(j = 0; j < parms->rank; j++)
buf_offset[j] = 0;
buf_p = (unsigned char *)buffer;
/* write POSIX buffer */
posix_buffer_write(0, fd, parms, buffer);
break;
case HDF5:
/* if dimensions are extendable, extend them as needed during access */
if (parms->h5_use_chunks && parms->h5_extendable) {
hrc=H5Sget_simple_extent_dims(h5dset_space_id,dims,maxdims);
VRFY((hrc >= 0), "H5Sget_simple_extent_dims");
for (k=0; k < parms->rank; k++){
HDassert(h5offset[k] >= 0);
if (dims[k] <= (hsize_t)h5offset[k]) {
dims[k] = dims[k]+h5count[k];
hrc=H5Sset_extent_simple(h5dset_space_id,parms->rank,dims,maxdims);
VRFY((hrc >= 0), "H5Sset_extent_simple");
hrc=H5Dset_extent(h5ds_id,dims);
VRFY((hrc >= 0), "H5Dextend");
}
}
}
/* applies offset */
hrc = H5Soffset_simple(h5dset_space_id, h5offset);
VRFY((hrc >= 0), "H5Soffset_simple");
/* Write the buffer out */
hrc=H5Sget_simple_extent_dims(h5dset_space_id,dims,maxdims);
hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id,
h5dset_space_id, h5dxpl, buffer);
VRFY((hrc >= 0), "H5Dwrite");
break;
default:
/* unknown request */
HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
HDassert(0 && "Unknown IO type");
break;
} /* switch (parms->io_type) */
}
}
done:
return ret_code;
}
bool Hdf5Dataset::saveMap(const VecVecDouble &pose_reach, const VecVecDouble &spheres, const VecDouble &ri, const double resolution)
{
if(!checkPath(this->path_))
{
createPath(this->path_);
}
const char *filepath = this->path_.c_str();
const char *name = this->filename_.c_str();
char fullpath[100];
strcpy(fullpath, filepath);
strcat(fullpath, name);
ROS_INFO("Saving map %s", this->filename_.c_str());
this->file_ = H5Fcreate(fullpath, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
this->group_poses_ = H5Gcreate(this->file_, "/Poses", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
this->group_spheres_ = H5Gcreate(this->file_, "/Spheres", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ROS_INFO("Saving poses in reachability map");
const hsize_t ndims = 2;
const hsize_t ncols = 10;
int posSize =pose_reach.size();
int chunk_size;
int PY = 10;
if (posSize % 2)
{
chunk_size = (posSize / 2) + 1;
}
else
{
chunk_size = (posSize / 2);
}
// Create Dataspace
hsize_t dims[ndims] = {0, ncols}; // Starting with an empty buffer
hsize_t max_dims[ndims] = {H5S_UNLIMITED, ncols}; // Creating dataspace
hid_t file_space = H5Screate_simple(ndims, dims, max_dims);
// Create Dataset Property list
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk_dims[ndims] = {chunk_size, ncols};
H5Pset_chunk(plist, ndims, chunk_dims);
// Create the datset
this->poses_dataset_ = H5Dcreate(this->group_poses_, "poses_dataset", H5T_NATIVE_FLOAT, file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
// Closing resources
H5Pclose(plist);
H5Sclose(file_space);
// Creating the first buffer
hsize_t nlines = chunk_size;
float *buffer = new float[nlines * ncols];
float **dset1_data = new float *[nlines];
for (hsize_t i = 0; i < nlines; ++i)
{
dset1_data[i] = &buffer[i * ncols];
}
// Data for the first chunk
for (int i = 0; i < chunk_size; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i][j] = pose_reach[i][j];
}
}
// Memory dataspace indicating size of the buffer
dims[0] = chunk_size;
dims[1] = ncols;
hid_t mem_space = H5Screate_simple(ndims, dims, NULL);
// Extending dataset
dims[0] = chunk_size;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab on the dataset
file_space = H5Dget_space(this->poses_dataset_);
hsize_t start[2] = {0, 0};
hsize_t count[2] = {chunk_size, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to the dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing file dataspace
H5Sclose(file_space);
// Data for the Second chunk
for (int i = chunk_size; i < posSize; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i - chunk_size][j] = pose_reach[i][j];
}
}
// Resizing new memory dataspace indicating new size of the buffer
dims[0] = posSize - chunk_size;
dims[1] = ncols;
H5Sset_extent_simple(mem_space, ndims, dims, NULL);
// Extend dataset
dims[0] = posSize;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab
file_space = H5Dget_space(this->poses_dataset_);
start[0] = chunk_size;
start[1] = 0;
count[0] = posSize - chunk_size;
count[1] = ncols;
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing all the resources
delete[] dset1_data;
delete[] buffer;
// Creating Sphere dataset
ROS_INFO("Saving spheres in Reachability map");
hid_t sphere_dataspace;
const int SX = spheres.size();
const int SY = 4;
hsize_t dims2[2]; // dataset dimensions
dims2[0] = SX;
dims2[1] = SY;
double dset2_data[SX][SY];
for(int i=0;i<spheres.size();++i)
{
for(int j=0;j<spheres[i].size();++j)
{
dset2_data[i][j] = spheres[i][j];
}
for (int j = 3; j < SY; j++)
{
dset2_data[i][j] = ri[i];
}
}
sphere_dataspace = H5Screate_simple(2, dims2, NULL);
this->sphere_dataset_ = H5Dcreate2(this->group_spheres_, "sphere_dataset", H5T_NATIVE_DOUBLE,
sphere_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(this->sphere_dataset_, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_data);
// Creating attribute
hsize_t attr_dims;
float attr_data[1];
attr_data[0] = resolution;
attr_dims = 1;
sphere_dataspace = H5Screate_simple(1, &attr_dims, NULL);
this->attr_ = H5Acreate2(this->sphere_dataset_, "Resolution", H5T_NATIVE_FLOAT, sphere_dataspace,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(this->attr_, H5T_NATIVE_FLOAT, attr_data);
//H5Aclose(this->attr_);
// Closing all
H5Sclose(sphere_dataspace);
H5Sclose(file_space);
H5Sclose(mem_space);
close();
}
int
main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t fid; /* Dataspace identifier */
hid_t attr1, attr2, attr3; /* Attribute identifiers */
hid_t attr;
hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */
hid_t atype, atype_mem; /* Attribute type */
H5T_class_t type_class;
hsize_t fdim[] = {SIZE};
hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */
float matrix[ADIM1][ADIM2]; /* Attribute data */
herr_t ret; /* Return value */
H5O_info_t oinfo; /* Object info */
unsigned i, j; /* Counters */
char string_out[80]; /* Buffer to read string attribute back */
int point_out; /* Buffer to read scalar attribute back */
/*
* Data initialization.
*/
int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */
int point = 1; /* Value of the scalar attribute */
char string[] = "ABCD"; /* Value of the string attribute */
for (i=0; i < ADIM1; i++) { /* Values of the array attribute */
for (j=0; j < ADIM2; j++)
matrix[i][j] = -1.;
}
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the dataspace for the dataset in the file.
*/
fid = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);
/*
* Create the dataset in the file.
*/
dataset = H5Dcreate2(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);
/*
* Create dataspace for the first attribute.
*/
aid1 = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL);
/*
* Create array attribute.
*/
attr1 = H5Acreate2(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write array attribute.
*/
ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);
/*
* Create scalar attribute.
*/
aid2 = H5Screate(H5S_SCALAR);
attr2 = H5Acreate2(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
H5P_DEFAULT, H5P_DEFAULT);
/*
* Write scalar attribute.
*/
ret = H5Awrite(attr2, H5T_NATIVE_INT, &point);
/*
* Create string attribute.
*/
aid3 = H5Screate(H5S_SCALAR);
atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 5);
H5Tset_strpad(atype,H5T_STR_NULLTERM);
attr3 = H5Acreate2(dataset, ANAMES, atype, aid3, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write string attribute.
*/
ret = H5Awrite(attr3, atype, string);
/*
* Close attribute and file dataspaces, and datatype.
*/
ret = H5Sclose(aid1);
ret = H5Sclose(aid2);
ret = H5Sclose(aid3);
ret = H5Sclose(fid);
ret = H5Tclose(atype);
/*
* Close the attributes.
*/
ret = H5Aclose(attr1);
ret = H5Aclose(attr2);
ret = H5Aclose(attr3);
/*
* Close the dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Reopen the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = H5Dopen2(file, "Dataset", H5P_DEFAULT);
/*
* Attach to the scalar attribute using attribute name, then read and
* display its value.
*/
attr = H5Aopen(dataset, "Integer attribute", H5P_DEFAULT);
ret = H5Aread(attr, H5T_NATIVE_INT, &point_out);
printf("The value of the attribute \"Integer attribute\" is %d \n", point_out);
ret = H5Aclose(attr);
/*
* Find string attribute by iterating through all attributes
*/
ret = H5Oget_info(dataset, &oinfo);
for(i = 0; i < (unsigned)oinfo.num_attrs; i++) {
attr = H5Aopen_by_idx(dataset, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)i, H5P_DEFAULT, H5P_DEFAULT);
atype = H5Aget_type(attr);
type_class = H5Tget_class(atype);
if (type_class == H5T_STRING) {
atype_mem = H5Tget_native_type(atype, H5T_DIR_ASCEND);
ret = H5Aread(attr, atype_mem, string_out);
printf("Found string attribute; its index is %d , value = %s \n", i, string_out);
ret = H5Tclose(atype_mem);
}
ret = H5Aclose(attr);
ret = H5Tclose(atype);
}
/*
* Get attribute info using iteration function.
*/
ret = H5Aiterate2(dataset, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_info, NULL);
/*
* Close the dataset and the file.
*/
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
int gal2gad2(NbodyModel *theModel, const char * prefix, const char * path,
double length, double mass, double velocity) {
#ifdef HAS_HDF5
int n=theModel->n;
hid_t file_id,group_id,header_id;
hid_t hdf5_dataspace,hdf5_attribute;
hsize_t pdims[2];
hsize_t mdims[1];
hsize_t tdims[1];
hsize_t fdims[1];
float *positions;
float *velocities;
int *IDs;
int nFiles=1;
int Npart[6]={0,0,0,0,n,0};
int Npart_hw[6]={0,0,0,0,0,0};
float *masses;
herr_t status;
int i_zero=0;
double d_zero=0.0;
double d_one=1.0;
int i;
char hdf5file[100];
char paramfile[100];
FILE * pfile;
sprintf(hdf5file,"%s%s.hdf5",path,prefix);
sprintf(paramfile,"%s%s.param",path,prefix);
positions = (float *)malloc(sizeof(float)*3*n);
velocities = (float *)malloc(sizeof(float)*3*n);
masses = (float *)malloc(sizeof(float)*n);
IDs = (int *)malloc(sizeof(int)*n);
printf("HDF5FILE BEING GENERATED\n");
for(i=0;i<n;i++) {
positions[i*3+0] = (float)theModel->x[i];
positions[i*3+1] = (float)theModel->y[i];
positions[i*3+2] = (float)theModel->z[i];
velocities[i*3+0] = (float)theModel->vx[i];
velocities[i*3+1] = (float)theModel->vy[i];
velocities[i*3+2] = (float)theModel->vz[i];
masses[i] = (float)theModel->mass[i];
IDs[i]=i;
}
file_id = H5Fcreate (hdf5file,
H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
group_id = H5Gcreate1(file_id, "PartType4", 0);
header_id = H5Gcreate1(file_id, "Header", 0);
pdims[0] = n;
pdims[1] = 3;
mdims[0] = n;
tdims[0] = 6;
fdims[0] = 1;
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate1(header_id, "NumPart_ThisFile",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, Npart);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate1(header_id, "NumPart_Total",
H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate1(header_id, "NumPart_Total_HW",
H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart_hw);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Time",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &time);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Redshift",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &d_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "BoxSize",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &d_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "NumFilesPerSnapshot",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &nFiles);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Omega0",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &d_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "OmegaLambda",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &d_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "HubbleParam",
H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &d_one);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Flag_Sfr",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &i_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Flag_Cooling",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &i_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Flag_StellarAge",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &i_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Flag_Metals",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &i_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate1(header_id, "Flag_Feedback",
H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &i_zero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate1(header_id, "Flag_Entropy_ICs",
H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart_hw);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
status = H5LTmake_dataset(file_id,"PartType4/Coordinates",2,
pdims,H5T_NATIVE_FLOAT,positions);
status = H5LTmake_dataset(file_id,"PartType4/ParticleIDs",1,
mdims,H5T_NATIVE_UINT,IDs);
status = H5LTmake_dataset(file_id,"PartType4/Velocities",2,
pdims,H5T_NATIVE_FLOAT,velocities);
status = H5LTmake_dataset(file_id,"PartType4/Masses",1,
mdims,H5T_NATIVE_FLOAT,masses);
status = H5Fclose (file_id);
free(positions);
free(velocities);
free(masses);
free(IDs);
pfile = fopen(paramfile,"w");
fprintf(pfile,"InitCondFile\t%s\n",prefix);
fprintf(pfile,"OutputDir\tout\n");
fprintf(pfile,"EnergyFile\tenergy.txt\n");
fprintf(pfile,"InfoFile\tinfo.txt\n");
fprintf(pfile,"TimingsFile\ttimings.txt\n");
fprintf(pfile,"CpuFile\tcpu.txt\n");
fprintf(pfile,"RestartFile\trestart\n");
fprintf(pfile,"SnapshotFileBase\tsnapshot\n");
fprintf(pfile,"OutputListFilename\toutput_list.txt\n");
fprintf(pfile,"ICFormat\t3\n");
fprintf(pfile,"SnapFormat\t3\n");
fprintf(pfile,"TypeOfTimestepCriterion\t0\n");
fprintf(pfile,"OutputListOn\t0\n");
fprintf(pfile,"PeriodicBoundariesOn\t0\n");
fprintf(pfile,"TimeBegin\t0.0\n");
fprintf(pfile,"TimeMax\t%le\n",theModel->tFinal);
fprintf(pfile,"Omega0\t0\n");
fprintf(pfile,"OmegaLambda\t0\n");
fprintf(pfile,"OmegaBaryon\t0\n");
fprintf(pfile,"HubbleParam\t1.0\n");
fprintf(pfile,"BoxSize\t0\n");
fprintf(pfile,"TimeBetSnapshot\t%le\n",theModel->tFinal/100); //change this
fprintf(pfile,"TimeOfFirstSnapshot\t0\n");
fprintf(pfile,"CpuTimeBetRestartFile\t300.0\n");
fprintf(pfile,"TimeBetStatistics\t0.1\n");
fprintf(pfile,"NumFilesPerSnapshot\t1\n");
fprintf(pfile,"NumFilesWrittenInParallel\t1\n");
fprintf(pfile,"ErrTolIntAccuracy\t0.0025\n");
fprintf(pfile,"CourantFac\t0.15\n");
fprintf(pfile,"MaxSizeTimestep\t0.01\n");
fprintf(pfile,"MinSizeTimestep\t0.0\n");
fprintf(pfile,"ErrTolTheta\t0.05\n");
fprintf(pfile,"TypeOfOpeningCriterion\t1\n");
fprintf(pfile,"ErrTolForceAcc\t0.0005\n");
fprintf(pfile,"TreeDomainUpdateFrequency\t0.01\n");
fprintf(pfile,"DesNumNgb\t50\n");
fprintf(pfile,"MaxNumNgbDeviation\t2\n");
fprintf(pfile,"ArtBulkViscConst\t0.8\n");
fprintf(pfile,"InitGasTemp\t0\n");
fprintf(pfile,"MinGasTemp\t0\n");
fprintf(pfile,"PartAllocFactor\t1.5\n");
fprintf(pfile,"TreeAllocFactor\t0.8\n");
fprintf(pfile,"BufferSize\t25\n");
fprintf(pfile,"UnitLength_in_cm\t%le \n",length);
fprintf(pfile,"UnitMass_in_g\t%le \n",mass);
fprintf(pfile,"UnitVelocity_in_cm_per_s\t%le \n",velocity);
fprintf(pfile,"GravityConstantInternal\t0\n");
fprintf(pfile,"MinGasHsmlFractional\t0.25\n");
fprintf(pfile,"SofteningGas\t0\n");
fprintf(pfile,"SofteningHalo\t1.0\n");
fprintf(pfile,"SofteningDisk\t0.4\n");
fprintf(pfile,"SofteningBulge\t0\n");
fprintf(pfile,"SofteningStars\t1.0e-2\n");
fprintf(pfile,"SofteningBndry\t0\n");
fprintf(pfile,"SofteningGasMaxPhys\t0\n");
fprintf(pfile,"SofteningHaloMaxPhys\t1.0\n");
fprintf(pfile,"SofteningDiskMaxPhys\t0.4\n");
fprintf(pfile,"SofteningBulgeMaxPhys\t0\n");
fprintf(pfile,"SofteningStarsMaxPhys\t1.0e-2\n");
fprintf(pfile,"SofteningBndryMaxPhys\t0\n");
fprintf(pfile,"MaxRMSDisplacementFac\t0.2\n");
fprintf(pfile,"TimeLimitCPU\t36000\n");
fprintf(pfile,"ResubmitOn\t0\n");
fprintf(pfile,"ResubmitCommand\tmy-scriptfile\n");
fprintf(pfile,"ComovingIntegrationOn\t0\n");
fclose(pfile);
return 0;
#else
printf("ATTEMTPING TO RUN GAL2GAD2 ROUTINE WITHOUT HDF5 SUPPORT!\n");
printf("EXITING!\n");
exit(0);
return 1;
#endif
}
int main( int argc, char ** argv ) {
hid_t file_id,group_id,header_id;
hid_t hdf5_dataspace,hdf5_attribute;
hsize_t pdims[2];
hsize_t mdims[1];
hsize_t tdims[1];
hsize_t fdims[1];
float positions[NPARTS*NDIMS];
float velocities[NPARTS*NDIMS];
int IDs[NPARTS];
int nFiles=1;
int Npart[NTYPES]={0,0,0,0,NPARTS,0};
int Npart_hw[NTYPES]={0,0,0,0,0,0};
#ifdef HAS_CORE
double core_fraction=0.1;
double disk_mass=(1.0-core_fraction)*(500*400/1.0e10);
double core_mass=disk_mass*core_fraction/(1.0-core_fraction);
double mass_per=disk_mass/(NPARTS-1);
#else
double disk_mass=(500*400/1.0e10);
double mass_per=disk_mass/(NPARTS);
#endif
//double Massarr[NTYPES]={0.0,0.0,0.0,0.0,mass_per,0.0};
float masses[NPARTS];
herr_t status;
double redshift=0.0;
double time=0.0;
double boxsize=0.0;
double dzero=0.0;
double done=1.0;
int izero=0;
int ione=1;
double distance;
double radius=0.77;
double base_vel=0.0;
double r,rscaled,a,v,cosine,sine,con,posx,posy;
double rotate_factor=1.0;
double G=6.67e-8; // cm^3 g^-1 s^-2
char filename[80];
int i,j,k;
seed_by_time(0);
if (argc>1) {
sscanf(argv[1],"%s",filename);
} else {
strcpy(filename,"gal_test.hdf5");
}
#ifdef HAS_CORE
masses[0]=core_mass;
for(i=1;i<NPARTS;i++) {
masses[i]=mass_per;
}
#else
for(i=0;i<NPARTS;i++) {
masses[i]=mass_per;
}
#endif
positions[0]=0.0;
positions[1]=0.0;
positions[2]=0.0;
for(i=1;i<NPARTS;i++) {
distance=2.0*radius;
while(distance>radius) {
distance=0.0;
for(j=0;j<NDIMS;j++) {
positions[3*i+j] = radius*(1.0-2.0*(double)rand()/(double)RAND_MAX);
distance+=pow(positions[3*i+j],2.0);
}
distance=sqrt(distance);
}
}
/* random velocity
for(i=0;i<NPARTS;i++) {
for(j=0;j<NDIMS;j++) {
velocities[3*i+j] = base_vel*(1.0-2.0*(double)rand()/(double)RAND_MAX);
}
}
*/
velocities[0]=0.0;
velocities[1]=0.0;
velocities[2]=0.0;
for(i=1;i<NPARTS;i++) {
posx = positions[NDIMS*i];
posy = positions[NDIMS*i+1];
r=sqrt(pow(posx,2.0)+pow(posy,2.0));
#ifdef HAS_CORE
con = G*(disk_mass+core_mass)*1.99e43*pow((r/radius),3.0);
#else
con = G*(disk_mass)*1.99e43*pow((r/radius),3.0);
#endif
rscaled=r*3.089e21; // convert to cm
if(r>0.0) {
v=sqrt(con/rscaled)*1.0e-5;
cosine=posx/r;
sine=posy/r;
velocities[NDIMS*i+0]=v*rotate_factor*(-sine);
velocities[NDIMS*i+1]=v*rotate_factor*cosine;
velocities[NDIMS*i+2]=0.0;
}
}
for(i=0;i<NPARTS;i++) {
IDs[i]=i;
}
// EXAMPLE("make a dataset");
file_id = H5Fcreate (filename,
H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
group_id = H5Gcreate(file_id, "PartType4", 0);
header_id = H5Gcreate(file_id, "Header", 0);
pdims[0] = NPARTS;
pdims[1] = NDIMS;
mdims[0] = NPARTS;
tdims[0] = NTYPES;
fdims[0] = 1;
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate(header_id, "NumPart_ThisFile", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, Npart);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate(header_id, "NumPart_Total", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate(header_id, "NumPart_Total_HW", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart_hw);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
/*
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate(header_id, "MassTable", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, Massarr);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
*/
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Time", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &time);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Redshift", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &redshift);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "BoxSize", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &boxsize);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "NumFilesPerSnapshot", H5T_NATIVE_INT,
hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &nFiles);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Omega0", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &dzero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "OmegaLambda", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &dzero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "HubbleParam", H5T_NATIVE_DOUBLE, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_DOUBLE, &done);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Flag_Sfr", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &izero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Flag_Cooling", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &izero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Flag_StellarAge", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &izero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Flag_Metals", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &izero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute = H5Acreate(header_id, "Flag_Feedback", H5T_NATIVE_INT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_INT, &izero);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
hdf5_dataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdf5_dataspace, 1, tdims, NULL);
hdf5_attribute = H5Acreate(header_id, "Flag_Entropy_ICs", H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
H5Awrite(hdf5_attribute, H5T_NATIVE_UINT, Npart_hw);
H5Aclose(hdf5_attribute);
H5Sclose(hdf5_dataspace);
status = H5LTmake_dataset(file_id,"PartType4/Coordinates",2,
pdims,H5T_NATIVE_FLOAT,positions);
status = H5LTmake_dataset(file_id,"PartType4/ParticleIDs",1,
mdims,H5T_NATIVE_UINT,IDs);
status = H5LTmake_dataset(file_id,"PartType4/Velocities",2,
pdims,H5T_NATIVE_FLOAT,velocities);
status = H5LTmake_dataset(file_id,"PartType4/Masses",1,
mdims,H5T_NATIVE_FLOAT,masses);
status = H5Fclose (file_id);
// PASSED();
return 0;
}
