extern "C" bool write_h5(char* fname, dtype* data_array){
#ifdef _HDF5_H
hid_t out_type_id = H5T_NATIVE_FLOAT;
hid_t file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t dataspace_id, dataset_id;
int ndims = 2; hsize_t dimsH[2];
dimsH[0] = 1679;
dimsH[1] = 1475;
hid_t gid2 = H5Gcreate1(file_id,"data",0);
dataspace_id = H5Screate_simple(ndims, dimsH, NULL);
bool compress = false;
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
hsize_t chunk[2] = {64, 64};
if (compress)
{ H5Pset_deflate (dcpl, 9);
H5Pset_chunk (dcpl, 2, chunk);
}
dataset_id = H5Dcreate(file_id, "/data/data", out_type_id, dataspace_id,
H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_array);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
H5Gclose(gid2);
H5Fclose(file_id);
return true;
#endif
return false;
}
// save the population
void logger_save_population(logger_t *logger, GString *profiles, GString *hosts) {
// create population group
hid_t group_id;
group_id = H5Gcreate1(logger->file_id, "/population", H5P_DEFAULT);
H5LTmake_dataset_string(group_id, "/population/profiles", profiles->str);
H5LTmake_dataset_string(group_id, "/population/hosts", hosts->str);
H5Gclose(group_id);
}
/*-------------------------------------------------------------------------
*
* Function: group_version_macros
*
* Purpose: Test H5G version compatibility macros.
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Neil Fortner
* Saturday, October 11, 2008
*
*-------------------------------------------------------------------------
*/
static int
group_version_macros(hid_t fapl)
{
hid_t fid, gid;
char filename[NAME_BUF_SIZE];
/* Output message about test being performed */
TESTING("H5G version compatibility macros");
/* Create file */
h5_fixname(FILENAME[1], fapl, filename, sizeof filename);
if ((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) TEST_ERROR;
/* Create a group (test H5Gcreate1) */
if ((gid = H5Gcreate1(fid, "group", 0)) < 0) TEST_ERROR;
/* Close group */
if (H5Gclose(gid) < 0) TEST_ERROR;
/* Open group (test H5Gopen1) */
if ((gid = H5Gopen1(fid, "group")) < 0) TEST_ERROR;
/* Close group */
if (H5Gclose(gid) < 0) TEST_ERROR;
/* Close file */
if (H5Fclose(fid) < 0) TEST_ERROR;
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(gid);
H5Gclose(fid);
} H5E_END_TRY
return -1;
} /* end group_version_macros() */
void logger_write_params(logger_t *logger) {
// create settings group
hid_t group_id = H5Gcreate1(logger->file_id, "/settings", H5P_DEFAULT);
H5Gclose(group_id);
// create dataspace
hsize_t dim = 1;
H5LTmake_dataset(logger->file_id, "/settings/psize", 1, &dim,
H5T_NATIVE_INT, &logger->params->psize);
H5LTmake_dataset(logger->file_id, "/settings/steps", 1, &dim,
H5T_NATIVE_INT, &logger->params->steps);
H5LTmake_dataset(logger->file_id, "/settings/fparts", 1, &dim,
H5T_NATIVE_INT, &logger->params->fparts);
H5LTmake_dataset(logger->file_id, "/settings/seed", 1, &dim,
H5T_NATIVE_INT, &logger->params->seed);
H5LTmake_dataset(logger->file_id, "/settings/seg_type", 1, &dim,
H5T_NATIVE_INT, &logger->params->seg_type);
H5LTmake_dataset(logger->file_id, "/settings/mu", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->mu);
H5LTmake_dataset(logger->file_id, "/settings/pconj", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->pconj);
H5LTmake_dataset(logger->file_id, "/settings/beta", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->beta);
H5LTmake_dataset(logger->file_id, "/settings/kappa", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->kappa);
H5LTmake_dataset(logger->file_id, "/settings/alpha", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->alpha);
H5LTmake_dataset(logger->file_id, "/settings/max_beta", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->max_beta);
H5LTmake_dataset(logger->file_id, "/settings/max_kappa", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->max_kappa);
H5LTmake_dataset(logger->file_id, "/settings/max_alpha", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->max_alpha);
H5LTmake_dataset(logger->file_id, "/settings/max_cn", 1, &dim,
H5T_NATIVE_INT, &logger->params->max_cn);
H5LTmake_dataset(logger->file_id, "/settings/phi", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->phi);
H5LTmake_dataset(logger->file_id, "/settings/gamma", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->gamma);
H5LTmake_dataset(logger->file_id, "/settings/gamma.alpha", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->gamma_alpha);
H5LTmake_dataset(logger->file_id, "/settings/lambda", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->lambda);
H5LTmake_dataset(logger->file_id, "/settings/omega.0", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->omega_0);
H5LTmake_dataset(logger->file_id, "/settings/dilution", 1, &dim,
H5T_NATIVE_INT, &logger->params->dilution);
H5LTmake_dataset(logger->file_id, "/settings/mut.rng", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->mut_rng);
H5LTmake_dataset(logger->file_id, "/settings/duration", 1, &dim,
H5T_NATIVE_DOUBLE, &logger->params->duration);
}
// create groups -- then create tseriess
logger_t *logger_new(params_t *params) {
logger_t *logger = malloc(sizeof(logger_t));
// store params
logger->params = params;
// open file
logger->file_id = H5Fcreate(params->log_path->str, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
// initialize inter- stats
logger->inter_stats = nvar_init(P_INTER_IDX_ALL);
// reset counters
memset(&logger->counters, 0, sizeof(counters_t));
// create group of dynamics
hid_t group_id = H5Gcreate1(logger->file_id, "/dynamics", H5P_DEFAULT);
H5Gclose(group_id);
// ================== CREATE TABLES ===================
// create COUNTERS table
const char *counter_labels[] = {"n", "cn", "inf", "ptypes", "loss", "div.inf",
"div.all", "death", "rep", "ht", "mut"};
hdf_table_initialize(&logger->tbl_counters, logger->file_id, "/dynamics/counters",
TBL_COUNTERS_LEN, Q_HDF_TYPE_INT, counter_labels);
// create COMPETITION data??
if (logger->params->compete) {
// create competition group
group_id = H5Gcreate1(logger->file_id, "/competition", H5P_DEFAULT);
H5Gclose(group_id);
hdf_table_initialize(&logger->tbl_competition, logger->file_id,
"/competition/frequencies",
params->contenders, Q_HDF_TYPE_INT, NULL);
// create contenders group
group_id = H5Gcreate1(logger->file_id, "/competition/contenders", H5P_DEFAULT);
H5Gclose(group_id);
// write all the contenders in the group
const char *labels[] = {"beta", "kappa", "alpha"};
double data[3];
GHashTableIter iter;
profile_t *profile;
pdata_t *pdata;
GString *name;
hdf_table_t table;
g_hash_table_iter_init(&iter, params->pool->profiles);
while (g_hash_table_iter_next(&iter, (void **)&profile, (void **)&pdata)) {
assert(pdata->pid < params->contenders);
// convert profile id to a string
name = g_string_new_itol(pdata->pid);
g_string_prepend(name, "/competition/contenders/");
// get data into buffer
data[0] = profile->beta;
data[1] = profile->kappa;
data[2] = profile->alpha;
// create table in group contenders
hdf_table_initialize(&table, logger->file_id, name->str,
3, Q_HDF_TYPE_DOUBLE, labels);
hdf_table_append_record(&table, data);
hdf_table_finalize(&table);
// free string
g_string_free(name, TRUE);
}
}
nvar_t *nvar;
// create INTER tables
group_id = H5Gcreate1(logger->file_id, "/dynamics/inter", H5P_DEFAULT);
H5Gclose(group_id);
const char *inter_m_labels[] = {"domg", "cn", "dev", "absdev", "beta", "kappa",
"alpha", "bk", "rate", "nr", "ht", "death", "fitness",
"tbeta", "tkappa", "talpha", "tbk"};
hdf_table_initialize(&logger->tbl_inter_m, logger->file_id, "/dynamics/inter/M",
P_INTER_IDX_ALL, Q_HDF_TYPE_DOUBLE, inter_m_labels);
hdf_table_initialize(&logger->tbl_inter_v, logger->file_id, "/dynamics/inter/V",
P_INTER_IDX_ALL, Q_HDF_TYPE_DOUBLE, inter_m_labels);
// create an nvar object (just to get the covariance labels)
nvar = nvar_init(P_INTER_IDX_ALL);
nvar_assign_labels(nvar, inter_m_labels);
hdf_table_initialize(&logger->tbl_inter_c, logger->file_id, "/dynamics/inter/C",
P_INTER_IDX_ALL*(P_INTER_IDX_ALL-1)/2, Q_HDF_TYPE_DOUBLE,
(const char **)nvar->plabels);
nvar_free(nvar);
// create INTRA tables
group_id = H5Gcreate1(logger->file_id, "/dynamics/intra", H5P_DEFAULT);
H5Gclose(group_id);
const char *intra_m_labels[] = {"cn", "beta", "kappa", "alpha", "bk", "rate",
"nr", "ht", "death", "fitness",
"tbeta", "tkappa", "talpha", "tbk"};
hdf_table_initialize(&logger->tbl_intra_m, logger->file_id, "/dynamics/intra/M",
P_INTRA_IDX_ALL, Q_HDF_TYPE_DOUBLE, intra_m_labels);
hdf_table_initialize(&logger->tbl_intra_v, logger->file_id, "/dynamics/intra/V",
P_INTRA_IDX_ALL, Q_HDF_TYPE_DOUBLE, intra_m_labels);
// create an nvar object (just to get the covariance labels)
nvar = nvar_init(P_INTRA_IDX_ALL);
nvar_assign_labels(nvar, intra_m_labels);
hdf_table_initialize(&logger->tbl_intra_c, logger->file_id, "/dynamics/intra/C",
P_INTRA_IDX_ALL*(P_INTRA_IDX_ALL-1)/2, Q_HDF_TYPE_DOUBLE,
(const char **)nvar->plabels);
// create GLOBAL tables (all writing occurring within the pool)
group_id = H5Gcreate1(logger->file_id, "/dynamics/global", H5P_DEFAULT);
H5Gclose(group_id);
hdf_table_initialize(&logger->tbl_global_m, logger->file_id, "/dynamics/global/M",
P_INTRA_IDX_ALL, Q_HDF_TYPE_DOUBLE, intra_m_labels);
hdf_table_initialize(&logger->tbl_global_v, logger->file_id, "/dynamics/global/V",
P_INTRA_IDX_ALL, Q_HDF_TYPE_DOUBLE, intra_m_labels);
hdf_table_initialize(&logger->tbl_global_c, logger->file_id, "/dynamics/global/C",
P_INTRA_IDX_ALL*(P_INTRA_IDX_ALL-1)/2, Q_HDF_TYPE_DOUBLE,
(const char **)nvar->plabels);
// free the nvar object
nvar_free(nvar);
// create the RELATEDNESS2 tables
group_id = H5Gcreate1(logger->file_id, "/dynamics/relatedness", H5P_DEFAULT);
H5Gclose(group_id);
group_id = H5Gcreate1(logger->file_id, "/dynamics/relatedness/wg", H5P_DEFAULT);
H5Gclose(group_id);
group_id = H5Gcreate1(logger->file_id, "/dynamics/relatedness/oo", H5P_DEFAULT);
H5Gclose(group_id);
const char *relatedness_labels[] = {"beta", "kappa", "alpha"};
hdf_table_initialize(&logger->tbl_relatedness_wg_cov, logger->file_id,
"/dynamics/relatedness/wg/cov", P_PARAMS_IDX_ALL,
Q_HDF_TYPE_DOUBLE, relatedness_labels);
hdf_table_initialize(&logger->tbl_relatedness_wg_var, logger->file_id,
"/dynamics/relatedness/wg/var", P_PARAMS_IDX_ALL,
Q_HDF_TYPE_DOUBLE, relatedness_labels);
hdf_table_initialize(&logger->tbl_relatedness_oo_cov, logger->file_id,
"/dynamics/relatedness/oo/cov", P_PARAMS_IDX_ALL,
Q_HDF_TYPE_DOUBLE, relatedness_labels);
hdf_table_initialize(&logger->tbl_relatedness_oo_var, logger->file_id,
"/dynamics/relatedness/oo/var", P_PARAMS_IDX_ALL,
Q_HDF_TYPE_DOUBLE, relatedness_labels);
// reset the intra-buffers
BFILL(logger->MM, P_INTRA_IDX_ALL, 0);
BFILL(logger->VV, P_INTRA_IDX_ALL, 0);
BFILL(logger->CC, P_INTRA_IDX_ALL * (P_INTRA_IDX_ALL-1) / 2, 0);
// === CREATE HISTOGRAMS ===
// create group
group_id = H5Gcreate1(logger->file_id, "/histograms", H5P_DEFAULT);
H5Gclose(group_id);
// initialize CN histogram
double xlim[] = {-0.5, params->max_cn - 0.5};
hdf_histogram_initialize(&logger->hist_cn, logger->file_id, "/histograms/cn",
params->fparts, params->max_cn, 0,
xlim, NULL, FALSE);
// initialize AGE histogram
xlim[0] = 0;
xlim[1] = 50;
hdf_histogram_initialize(&logger->hist_age, logger->file_id, "/histograms/age",
params->fparts, 50, 0,
xlim, NULL, FALSE);
// initialize BK histogram
xlim[1] = logger->params->max_beta;
double ylim[] = {0, logger->params->max_kappa};
hdf_histogram_initialize(&logger->hist_beta_kappa, logger->file_id, "/histograms/bk",
params->fparts, logger->params->nbins, logger->params->nbins,
xlim, ylim, TRUE);
// initialize BA histogram
xlim[0] = 0; xlim[1] = logger->params->max_beta;
ylim[0] = 0; ylim[1] = logger->params->max_alpha;
hdf_histogram_initialize(&logger->hist_beta_alpha, logger->file_id, "/histograms/ba",
params->fparts, logger->params->nbins, logger->params->nbins,
xlim, ylim, TRUE);
// initialize KA histogram
xlim[0] = 0; xlim[1] = logger->params->max_kappa;
ylim[0] = 0; ylim[1] = logger->params->max_alpha;
hdf_histogram_initialize(&logger->hist_kappa_alpha, logger->file_id, "/histograms/ka",
params->fparts, logger->params->nbins, logger->params->nbins,
xlim, ylim, TRUE);
return logger;
}
bool WriteHDF5file(char* fname, dtype* outArray, int* dims, float* pixel,
float* expo, float* waveLen, float* dist, float* beamxy,
float* flux, bool compress, unsigned short* badmask)
{
#ifdef _HDF5_H
hid_t out_type_id = H5T_NATIVE_FLOAT;
hid_t file_id = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
hid_t gid = H5Gcreate1(file_id,"LCLS",0);
hid_t dataspace_id, dataset_id;
int ndims = 1;
hsize_t dimsH[2];
dimsH[0] = 1;
dimsH[1] = 0;
dataspace_id = H5Screate_simple(1, dimsH, NULL);
dataset_id = H5Dcreate1(gid, "detectorPosition", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, dist)< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "photon_wavelength_A", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, waveLen)< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "exposure_s", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, expo)< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "pixelX_m", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, &pixel[0])< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "pixelY_m", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, &pixel[1])< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "flux_ph_s", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, flux)< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "beamX_px", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, &beamxy[0])< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
dataset_id = H5Dcreate1(gid, "beamY_px", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL,H5P_DEFAULT, &beamxy[1])< 0)
printf("Error writing 1D data to file\n");
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
ndims = 2;
dimsH[0] = dims[1];
dimsH[1] = dims[0];
hid_t gid2 = H5Gcreate1(file_id,"data",0);
dataspace_id = H5Screate_simple(ndims, dimsH, NULL);
//COMPRESSION
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
// hsize_t chunk[2] = {dimsH[0], dimsH[1]};
//#ifdef ZLIB_H
//CASS hsize_t chunk[2] = {40,2};
hsize_t chunk[2] = {64, 64};
if (compress)
{ H5Pset_deflate (dcpl, 9);
H5Pset_chunk (dcpl, 2, chunk);
}
//#endif
// H5Pset_szip (dcpl, H5_SZIP_NN_OPTION_MASK, 8);
// H5Pset_chunk (dcpl, 2, chunk);
dataset_id = H5Dcreate(file_id, "/data/data", out_type_id, dataspace_id,
H5P_DEFAULT, dcpl, H5P_DEFAULT);
// dataset_id = H5Dcreate1(file_id, "/data/data", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id, out_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, outArray)< 0)
printf("Error writing 2D data to file\n");
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
H5Gclose(gid2);
//Here badmask
H5Gclose(gid);
H5Fclose(file_id);
return true;
#endif
return false;
}
/*
* Write 2D data to HDF5 file
*/
void cData2d::writeHDF5(char* filename){
// Figure out the HDF5 data type
hid_t out_type_id = 0;
if(sizeof(tData2d) == sizeof(float))
out_type_id = H5T_NATIVE_FLOAT;
else if(sizeof(tData2d) == sizeof(double))
out_type_id = H5T_NATIVE_DOUBLE;
else {
printf("2dData::writeHDF5: unsuppoted data type\n");
exit(1);
}
// Create the file and data group
hid_t file_id;
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
H5Gcreate1(file_id,"data",0);
// Data space dimensions
int ndims = 2;
hsize_t dims[ndims];
dims[0] = ny;
dims[1] = nx;
// Write the data
hid_t dataspace_id;
hid_t dataset_id;
dataspace_id = H5Screate_simple(ndims, dims, NULL);
dataset_id = H5Dcreate1(file_id, "/data/data", out_type_id, dataspace_id, H5P_DEFAULT);
if(H5Dwrite(dataset_id,out_type_id , H5S_ALL, H5S_ALL,H5P_DEFAULT, data)< 0){
printf("2dData::writeHDF5: Error writing data to file\n");
exit(1);
}
// Close and exit
H5Dclose(dataset_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
}
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
}