int
main (void)
{
FILE *f;
mdl_t source_mdl;
inp_t fake;
fake.output.time_steps = 128;
fake.solver.ti = 0.000001 * CONST_MKSA_YEAR;
fake.solver.tf = 10000000 * CONST_MKSA_YEAR;
int verbose = 0;
/* Create the input.ini file */
f = fopen ("source.mdl", "w");
fprintf (f, "# This source model file was created by source_test\n");
fprintf (f, "# cell number, Av [mag], n(H) [cm^-3], Tgas [K], Tdust [K]\n");
fprintf (f, "0 0.1 1e+02 15.0 12.0\n");
fprintf (f, "1 1.0 1e+03 11.0 10.0\n");
fprintf (f, "2 10.0 1e+04 8.0 7.0\n");
fclose (f);
/* Read it */
if( read_source ("source.mdl", &source_mdl, &fake, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Check that the values are correct */
if ((source_mdl.n_cells == 3) &&
(source_mdl.cell[0].av[0] == 0.1) &&
(source_mdl.cell[0].nh[0] == 1e2) &&
(source_mdl.cell[0].tgas[0] == 15) &&
(source_mdl.cell[0].tdust[0] == 12) &&
(source_mdl.cell[1].av[0] == 1.0) &&
(source_mdl.cell[1].nh[0] == 1e3) &&
(source_mdl.cell[1].tgas[0] == 11) &&
(source_mdl.cell[1].tdust[0] == 10) &&
(source_mdl.cell[2].av[0] == 10.0) &&
(source_mdl.cell[2].nh[0] == 1e4) &&
(source_mdl.cell[2].tgas[0] == 8) &&
(source_mdl.cell[2].tdust[0] == 7) &&
(source_mdl.ts.time_steps[10] - 332.988055 < 0.0001) &&
(source_mdl.ts.time_steps[23] - 7130.784562 < 0.0001) &&
(source_mdl.ts.time_steps[47] - 2040939.960351 < 0.0001) )
{
free_mdl(&source_mdl);
return EXIT_SUCCESS;
}
else
{
free_mdl(&source_mdl);
return EXIT_FAILURE;
}
}
int
main (void)
{
FILE *f;
mdl_t source_mdl;
inp_t fake;
int verbose = 0;
/* Create the input.ini file */
f = fopen ("source_dyn.mdl", "w");
fprintf (f, "# Source model file example for a time-dependant source structure\n"
"[times]\n"
" 0 1.00e-06\n"
" 1 1.24e-06\n"
" 2 1.55e-06\n"
" 3 1.92e-06\n"
" 4 2.39e-06\n"
" 5 2.97e-06\n"
" 6 3.69e-06\n"
" 7 4.59e-06\n"
" 8 5.70e-06\n"
" 9 7.09e-06\n"
" 10 8.81e-06\n"
"[cells]\n"
"# cell (= shell) number, time index, Av [mag], nH [cm^-3], Tgas [K], Tdust [K]\n"
" 0 0 0.00 1.00e+04 10.00 10.00\n"
" 0 1 0.16 1.11e+04 11.50 11.50\n"
" 0 2 0.31 1.24e+04 12.99 12.99\n"
" 0 3 0.47 1.39e+04 14.49 14.49\n"
" 0 4 0.63 1.55e+04 15.98 15.98\n"
" 0 5 0.79 1.72e+04 17.48 17.48\n"
" 0 6 0.94 1.92e+04 18.98 18.98\n"
" 0 7 1.10 2.14e+04 20.47 20.47\n"
" 0 8 1.26 2.39e+04 21.97 21.97\n"
" 0 9 1.42 2.66e+04 23.46 23.46\n"
" 0 10 1.57 2.97e+04 24.96 24.96\n"
" 1 0 0.00 1.00e+04 10.00 10.00\n"
" 1 1 0.16 1.11e+04 11.50 11.50\n"
" 1 2 0.31 1.24e+04 12.99 12.99\n"
" 1 3 0.47 1.39e+04 14.49 14.49\n"
" 1 4 0.63 1.55e+04 15.98 15.98\n"
" 1 5 0.79 1.72e+04 17.48 17.48\n"
" 1 6 0.94 1.92e+04 18.98 18.98\n"
" 1 7 1.10 2.14e+04 20.47 20.47\n"
" 1 8 1.26 2.39e+04 21.97 21.97\n"
" 1 9 1.42 2.66e+04 23.46 23.46\n"
" 1 10 1.57 2.97e+04 24.96 24.96\n"
" 2 0 0.00 1.00e+04 10.00 10.00\n"
" 2 1 0.16 1.11e+04 11.50 11.50\n"
" 2 2 0.31 1.24e+04 12.99 12.99\n"
" 2 3 0.47 1.39e+04 14.49 14.49\n"
" 2 4 0.63 1.55e+04 15.98 15.98\n"
" 2 5 0.79 1.72e+04 17.48 17.48\n"
" 2 6 0.94 1.92e+04 18.98 18.98\n"
" 2 7 1.10 2.14e+04 20.47 20.47\n"
" 2 8 1.26 2.39e+04 21.97 21.97\n"
" 2 9 1.42 2.66e+04 23.46 23.46\n"
" 2 10 1.57 2.97e+04 24.96 24.96\n");
fclose (f);
/* Read it */
if( read_source ("./source_dyn.mdl", &source_mdl, &fake, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Check that the values are correct */
if ((source_mdl.n_cells == 3) &&
(source_mdl.ts.n_time_steps == 11) &&
(source_mdl.cell[0].av[0] == 0.0) &&
(source_mdl.cell[0].nh[0] == 1e4) &&
(source_mdl.cell[0].tgas[0] == 10) &&
(source_mdl.cell[0].tdust[0] == 10) &&
(source_mdl.cell[1].av[5] == 0.79) &&
(source_mdl.cell[1].nh[5] == 1.72e4) &&
(source_mdl.cell[1].tgas[5] == 17.48) &&
(source_mdl.cell[1].tdust[5] == 17.48) &&
(source_mdl.cell[2].av[10] == 1.57) &&
(source_mdl.cell[2].nh[10] == 2.97e4) &&
(source_mdl.cell[2].tgas[10] == 24.96) &&
(source_mdl.cell[2].tdust[10] == 24.96) &&
(source_mdl.ts.time_steps[5] / CONST_MKSA_YEAR - 2.97e-6 < 0.01e-6 ))
{
free_mdl(&source_mdl);
return EXIT_SUCCESS;
}
else
{
free_mdl(&source_mdl);
return EXIT_FAILURE;
}
}
int
main (int argc, char *argv[])
{
inp_t input_params;
mdl_t source_mdl;
net_t network;
int cell_index;
int verbose = 1;
char *input_file;
/* Parse options and command line arguments. Diplay help
message if no (or more than one) argument is given. */
{
int opt;
static struct option longopts[] = {
{"help", no_argument, NULL, 'h'},
{"version", no_argument, NULL, 'V'},
{"verbose", no_argument, NULL, 'v'},
{"quiet", no_argument, NULL, 'q'},
{0, 0, 0, 0}
};
while ((opt = getopt_long (argc, argv, "hVvq", longopts, NULL)) != -1)
{
switch (opt)
{
case 'h':
usage ();
return EXIT_SUCCESS;
break;
case 'V':
version ();
return EXIT_SUCCESS;
break;
case 'v':
verbose = 2;
break;
case 'q':
verbose = 0;
break;
default:
usage ();
return EXIT_FAILURE;
}
};
argc -= optind;
argv += optind;
if (argc != 1)
{
usage ();
return EXIT_FAILURE;
}
input_file = argv[0];
}
/* Read the input file */
if( read_input_file_names (input_file, &input_params.files, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the chemical network file */
if( read_network (input_params.files.chem_file, &network, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the input file */
if( read_input (input_file, &input_params, &network, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the source model file */
if( read_source (input_params.files.source_file, &source_mdl, &input_params,
verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
// Hdf5 files, datatype and dataspace
hid_t fid, datatype, dataspace, dataset, tsDataset, tsDataspace, speciesDataset, speciesDataspace, speciesType;
datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
hsize_t dimsf[ ROUTE_DATASET_RANK ]={ source_mdl.n_cells, source_mdl.ts.n_time_steps, input_params.output.n_output_species, N_OUTPUT_ROUTES };
fid = H5Fcreate( "astrochem_output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dataspace = H5Screate_simple( ABUNDANCE_DATASET_RANK, dimsf, NULL);
// Add Atributes
hid_t simpleDataspace = H5Screate(H5S_SCALAR);
hid_t attrType = H5Tcopy(H5T_C_S1);
H5Tset_size ( attrType, MAX_CHAR_FILENAME );
H5Tset_strpad(attrType,H5T_STR_NULLTERM);
hid_t attrNetwork = H5Acreate( fid, "chem_file", attrType, simpleDataspace, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite( attrNetwork, attrType, realpath( input_params.files.chem_file, NULL ) );
H5Aclose( attrNetwork );
hid_t attrModel = H5Acreate( fid, "source_file", attrType, simpleDataspace, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite( attrModel, attrType, realpath( input_params.files.source_file, NULL ) );
H5Aclose( attrModel );
H5Tclose( attrType );
H5Sclose( simpleDataspace );
// Define chunk property
hsize_t chunk_dims[ ROUTE_DATASET_RANK ] = { 1, 1, input_params.output.n_output_species, N_OUTPUT_ROUTES };
hid_t prop_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(prop_id, ABUNDANCE_DATASET_RANK , chunk_dims);
// Create dataset
dataset = H5Dcreate(fid, "Abundances", datatype, dataspace, H5P_DEFAULT, prop_id, H5P_DEFAULT);
int i;
hid_t dataspaceRoute, route_t_datatype, r_t_datatype, route_prop_id, routeGroup;
hid_t routeDatasets[ input_params.output.n_output_species ];
if (input_params.output.trace_routes)
{
// Create route dataspace
dataspaceRoute = H5Screate_simple( ROUTE_DATASET_RANK, dimsf, NULL);
// Create route datatype
r_t_datatype = H5Tcreate (H5T_COMPOUND, sizeof(r_t));
H5Tinsert( r_t_datatype, "reaction_number", HOFFSET(r_t, reaction_no ), H5T_NATIVE_INT);
H5Tinsert( r_t_datatype, "reaction_rate", HOFFSET(r_t, rate), H5T_NATIVE_DOUBLE);
route_t_datatype = H5Tcreate (H5T_COMPOUND, sizeof(rout_t));
H5Tinsert( route_t_datatype, "formation_rate", HOFFSET(rout_t, formation ), r_t_datatype );
H5Tinsert( route_t_datatype, "destruction_rate", HOFFSET(rout_t, destruction ), r_t_datatype );
// Define route chunk property
route_prop_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk( route_prop_id, ROUTE_DATASET_RANK, chunk_dims);
// Create each named route dataset
routeGroup = H5Gcreate( fid, "Routes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
char routeName[6] = "route_";
char tempName[ MAX_CHAR_SPECIES + sizeof( routeName ) ];
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
strcpy( tempName, routeName );
strcat( tempName, network.species[input_params.output.output_species_idx[i]].name );
routeDatasets[i] = H5Dcreate( routeGroup, tempName, route_t_datatype, dataspaceRoute, H5P_DEFAULT, route_prop_id, H5P_DEFAULT);
}
}
// Timesteps and species
hsize_t n_ts = source_mdl.ts.n_time_steps;
hsize_t n_species = input_params.output.n_output_species ;
tsDataspace = H5Screate_simple( 1, &n_ts, NULL);
speciesDataspace = H5Screate_simple( 1, &n_species, NULL);
speciesType = H5Tcopy (H5T_C_S1);
H5Tset_size (speciesType, MAX_CHAR_SPECIES );
H5Tset_strpad(speciesType,H5T_STR_NULLTERM);
// Create ts and species datasets
tsDataset = H5Dcreate(fid, "TimeSteps", datatype, tsDataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
speciesDataset = H5Dcreate(fid, "Species", speciesType, speciesDataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
double* convTs = (double*) malloc( sizeof(double)* source_mdl.ts.n_time_steps );
for( i=0; i< source_mdl.ts.n_time_steps; i++ )
{
convTs[i] = source_mdl.ts.time_steps[i] / CONST_MKSA_YEAR;
}
H5Dwrite( tsDataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, convTs );
char speciesName [ input_params.output.n_output_species ][ MAX_CHAR_SPECIES ];
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
strcpy( speciesName[i], network.species[input_params.output.output_species_idx[i]].name );
}
H5Dwrite( speciesDataset, speciesType, H5S_ALL, H5S_ALL, H5P_DEFAULT, speciesName );
free( convTs );
H5Dclose( tsDataset );
H5Dclose( speciesDataset );
H5Tclose( speciesType );
H5Sclose( tsDataspace );
H5Sclose( speciesDataspace );
#ifdef HAVE_OPENMP
/*Initialize lock*/
omp_init_lock(&lock);
/* Solve the ODE system for each cell. */
{
#pragma omp parallel for schedule (dynamic, 1)
#endif
for (cell_index = 0; cell_index < source_mdl.n_cells; cell_index++)
{
if (verbose >= 1)
fprintf (stdout, "Computing abundances in cell %d...\n",
cell_index);
if( full_solve ( fid, dataset, routeDatasets, dataspace, dataspaceRoute, datatype, route_t_datatype, cell_index, &input_params, source_mdl.mode,
&source_mdl.cell[cell_index], &network, &source_mdl.ts, verbose) != EXIT_SUCCESS )
{
exit (EXIT_FAILURE);
}
if (verbose >= 1)
fprintf (stdout, "Done with cell %d.\n", cell_index);
}
#ifdef HAVE_OPENMP
}
/*Finished lock mechanism, destroy it*/
omp_destroy_lock(&lock);
#endif
/*
* Close/release hdf5 resources.
*/
if (input_params.output.trace_routes)
{
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
H5Dclose(routeDatasets[i] );
}
H5Sclose(dataspaceRoute);
H5Gclose(routeGroup);
H5Pclose(route_prop_id);
H5Tclose(r_t_datatype);
H5Tclose(route_t_datatype);
}
H5Dclose(dataset);
H5Pclose(prop_id);
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(fid);
free_input (&input_params);
free_mdl (&source_mdl);
free_network (&network);
return (EXIT_SUCCESS);
}
