void FreeAlquimiaProperties(AlquimiaProperties* props) {
if (props != NULL) {
FreeAlquimiaVectorDouble(&(props->isotherm_kd));
FreeAlquimiaVectorDouble(&(props->freundlich_n));
FreeAlquimiaVectorDouble(&(props->langmuir_b));
FreeAlquimiaVectorDouble(&(props->mineral_rate_cnst));
FreeAlquimiaVectorDouble(&(props->aqueous_kinetic_rate_cnst));
}
} /* end FreeAlquimiaProperties() */
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 FreeAlquimiaAuxiliaryOutputData(AlquimiaAuxiliaryOutputData* aux_output) {
if (aux_output != NULL) {
FreeAlquimiaVectorDouble(&(aux_output->aqueous_kinetic_rate));
FreeAlquimiaVectorDouble(&(aux_output->mineral_saturation_index));
FreeAlquimiaVectorDouble(&(aux_output->mineral_reaction_rate));
FreeAlquimiaVectorDouble(&(aux_output->primary_free_ion_concentration));
FreeAlquimiaVectorDouble(&(aux_output->primary_activity_coeff));
FreeAlquimiaVectorDouble(&(aux_output->secondary_free_ion_concentration));
FreeAlquimiaVectorDouble(&(aux_output->secondary_activity_coeff));
}
} /* end FreeAlquimiaAuxiliaryOutputData() */
void FreeAlquimiaState(AlquimiaState* state) {
if (state != NULL) {
FreeAlquimiaVectorDouble(&(state->total_mobile));
FreeAlquimiaVectorDouble(&(state->total_immobile));
FreeAlquimiaVectorDouble(&(state->mineral_volume_fraction));
FreeAlquimiaVectorDouble(&(state->mineral_specific_surface_area));
FreeAlquimiaVectorDouble(&(state->cation_exchange_capacity));
FreeAlquimiaVectorDouble(&(state->surface_site_density));
}
} /* end FreeAlquimiaState() */
void DriverOutput_WriteMulticompVector(DriverOutput* output,
const char* filename,
AlquimiaVectorString comp_names,
AlquimiaVectorDouble multicomp_vector)
{
int num_comps = comp_names.size;
if ((multicomp_vector.size % num_comps) != 0)
{
alquimia_error("DriverOutput_WriteMulticompVector: multicomp_vector data has invalid size for %d components (%d).",
num_comps, multicomp_vector.size);
}
int vec_size = multicomp_vector.size / num_comps;
AlquimiaVectorDouble var_vectors[num_comps];
for (int i = 0; i < num_comps; ++i)
{
AllocateAlquimiaVectorDouble(vec_size, &var_vectors[i]);
for (int j = 0; j < vec_size; ++j)
var_vectors[i].data[j] = multicomp_vector.data[num_comps*j+i];
}
DriverOutput_WriteVectors(output, filename, comp_names, var_vectors);
for (int i = 0; i < num_comps; ++i)
FreeAlquimiaVectorDouble(&var_vectors[i]);
}
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];
}
}
void FreeAlquimiaAuxiliaryData(AlquimiaAuxiliaryData* aux_data) {
if (aux_data != NULL) {
FreeAlquimiaVectorInt(&(aux_data->aux_ints));
FreeAlquimiaVectorDouble(&(aux_data->aux_doubles));
}
} /* end FreeAlquimiaAuxiliaryData() */
