int main(int argc, char* argv[]) { if (argc == 1) Usage(); // Initialize PETSc/MPI for command line options and engines that // require it. char help[] = "Alquimia advective, nondispersive reactive transport driver"; PetscInitialize(&argc, &argv, (char*)0, help); PetscInitializeFortran(); char input_file[FILENAME_MAX]; strncpy(input_file, argv[1], FILENAME_MAX-1); // Parse the input file. TransportDriverInput* input = TransportDriverInput_New(input_file); if (input == NULL) alquimia_error("transport: error encountered reading input file '%s'.", input_file); // Set up output. DriverOutput* output = NULL; if (AlquimiaCaseInsensitiveStringCompare(input->output_type, "python")) output = PythonDriverOutput_New(); else if (AlquimiaCaseInsensitiveStringCompare(input->output_type, "gnuplot")) output = GnuplotDriverOutput_New(); // Create a TransportDriver from the parsed input. TransportDriver* transport = TransportDriver_New(input); // Run the simulation. int status = TransportDriver_Run(transport); // Get the solution out of the driver and write it out. if (output != NULL) { double final_time; AlquimiaVectorString var_names = {.size = 0}; AlquimiaVectorDouble var_data = {.size = 0}; TransportDriver_GetSoluteAndAuxData(transport, &final_time, &var_names, &var_data); DriverOutput_WriteMulticompVector(output, input->output_file, var_names, var_data); FreeAlquimiaVectorString(&var_names); FreeAlquimiaVectorDouble(&var_data); } // Clean up. TransportDriverInput_Free(input); TransportDriver_Free(transport); PetscInt petsc_error = PetscFinalize(); if (status == EXIT_SUCCESS && petsc_error == 0) printf("Success!\n"); else printf("Failed!\n"); return status; }
void FreeAlquimiaProblemMetaData(AlquimiaProblemMetaData* meta_data) { if (meta_data != NULL) { FreeAlquimiaVectorString(&(meta_data->primary_names)); FreeAlquimiaVectorInt(&(meta_data->positivity)); FreeAlquimiaVectorString(&(meta_data->mineral_names)); FreeAlquimiaVectorString(&(meta_data->surface_site_names)); FreeAlquimiaVectorString(&(meta_data->ion_exchange_names)); FreeAlquimiaVectorString(&(meta_data->isotherm_species_names)); FreeAlquimiaVectorString(&(meta_data->aqueous_kinetic_names)); } } /* end FreeAlquimiaProblemMetaData() */
void TransportDriver_GetSoluteAndAuxData(TransportDriver* driver, double* time, AlquimiaVectorString* var_names, AlquimiaVectorDouble* var_data) { // Destroy the contents of the vectors we're given. if (var_names->size > 0) FreeAlquimiaVectorString(var_names); if (var_data->size > 0) FreeAlquimiaVectorDouble(var_data); // Construct a list of all variables, which are those in the state and // the auxiliary output data, and fill their data. int num_cells = driver->num_cells; int num_primary = driver->chem_sizes.num_primary; int num_sorbed = driver->chem_sizes.num_sorbed; int num_minerals = driver->chem_sizes.num_minerals; int num_surface_sites = driver->chem_sizes.num_surface_sites; int num_ion_exchange_sites = driver->chem_sizes.num_ion_exchange_sites; int num_aqueous_complexes = driver->chem_sizes.num_aqueous_complexes; int num_aqueous_kinetics = driver->chem_sizes.num_aqueous_kinetics; int num_vars = 1 + // grid cell locations num_primary + // total mobile num_sorbed + // total immobile 2 * num_minerals + // mineral volume fractions, specific surface area num_surface_sites + // surface site density num_ion_exchange_sites + // cation exchange capacity 1 + // pH num_aqueous_kinetics + // aqueous kinetic rate 2 * num_minerals + // mineral saturation index, reaction rate 2 * num_primary + // primary free ion concentration, activity coeff 2 * num_aqueous_complexes; // secondary free ion concentration, activity coeff int counter = 0; AllocateAlquimiaVectorString(num_vars, var_names); AllocateAlquimiaVectorDouble(num_vars * driver->num_cells, var_data); { var_names->data[counter] = AlquimiaStringDup("x"); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->x_min + (j+0.5) * (driver->x_max - driver->x_min) / driver->num_cells; ++counter; } for (int i = 0; i < num_primary; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "total_mobile[%s]", driver->chem_metadata.primary_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].total_mobile.data[i]; } for (int i = 0; i < num_sorbed; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "total_immobile[%d]", i); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].total_immobile.data[i]; } for (int i = 0; i < num_minerals; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "mineral_volume_fractions[%s]", driver->chem_metadata.mineral_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].mineral_volume_fraction.data[i]; } for (int i = 0; i < num_minerals; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "mineral_specific_surface_area[%s]", driver->chem_metadata.mineral_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].mineral_specific_surface_area.data[i]; } for (int i = 0; i < num_surface_sites; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "surface_site_density[%s]", driver->chem_metadata.surface_site_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].surface_site_density.data[i]; } for (int i = 0; i < num_ion_exchange_sites; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "cation_exchange_capacity[%s]", driver->chem_metadata.ion_exchange_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_state[j].cation_exchange_capacity.data[i]; } { var_names->data[counter] = AlquimiaStringDup("pH"); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].pH; ++counter; } for (int i = 0; i < num_aqueous_kinetics; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "aqueous_kinetic_rate[%s]", driver->chem_metadata.aqueous_kinetic_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].aqueous_kinetic_rate.data[i]; } for (int i = 0; i < num_minerals; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "mineral_saturation_index[%s]", driver->chem_metadata.mineral_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].mineral_saturation_index.data[i]; } for (int i = 0; i < num_minerals; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "mineral_reaction_rate[%s]", driver->chem_metadata.mineral_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].mineral_reaction_rate.data[i]; } for (int i = 0; i < num_primary; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "primary_free_ion_concentration[%s]", driver->chem_metadata.primary_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].primary_free_ion_concentration.data[i]; } for (int i = 0; i < num_primary; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "primary_activity_coeff[%s]", driver->chem_metadata.primary_names.data[i]); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].primary_activity_coeff.data[i]; } for (int i = 0; i < num_aqueous_complexes; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "secondary_free_ion_concentration[%d]", i); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].secondary_free_ion_concentration.data[i]; } for (int i = 0; i < num_aqueous_complexes; ++i, ++counter) { char var_name[1024]; snprintf(var_name, 1023, "secondary_activity_coeff[%d]", i); var_names->data[counter] = AlquimiaStringDup(var_name); for (int j = 0; j < num_cells; ++j) var_data->data[num_vars*j + counter] = driver->chem_aux_output[j].secondary_activity_coeff.data[i]; } }