Welcome to PyTOUGHREACT’s documentation!
Getting started
Installation
Technical
Repository API Code
- Chemical Class
- Biodegradation Processes
- Biomass Composition
BiomassGasBaseComponentBaseComponent.__init__()BaseComponent.add_to_process()BaseComponent.default_benzene()BaseComponent.default_n_decane()BaseComponent.default_n_pentane()BaseComponent.default_n_propyl_benzene()BaseComponent.default_p_xylene()BaseComponent.default_toluene()BaseComponent.get_fifth_set()BaseComponent.get_first_set()BaseComponent.get_fourth_set()BaseComponent.get_second_set()BaseComponent.get_seventh_set()BaseComponent.get_sixth_set()BaseComponent.get_third_set()
ComponentSolids
- Chemical Composition
- Chemical Kinetic Properties
- Chemical Mineral Composition
- Chemical Mineral Description
- Chemical Mineral Zone
- Chemical Permeability Porosity Zone
- Plotting Class
- Results Class
- Results for Tough 3
ResultTough3ResultTough3.__init__()ResultTough3.check_strictly_increasing()ResultTough3.convert_times()ResultTough3.del_index()ResultTough3.duplicate_index()ResultTough3.get_coord_data()ResultTough3.get_element_data()ResultTough3.get_elements()ResultTough3.get_generation_data()ResultTough3.get_layer_data()ResultTough3.get_number_of_layers()ResultTough3.get_parameters()ResultTough3.get_result_dictionary()ResultTough3.get_time_index()ResultTough3.get_times()ResultTough3.get_timeseries_data()ResultTough3.get_unique_coord_data()ResultTough3.get_unique_x_data()ResultTough3.get_unique_y_data()ResultTough3.get_unique_z_data()ResultTough3.get_x_data()ResultTough3.get_x_depth_data()ResultTough3.get_x_start_points()ResultTough3.get_y_data()ResultTough3.get_z_data()ResultTough3.get_z_layer_data()ResultTough3.read_file()ResultTough3.remove_non_increasing()
- Results for Tough React
ResultReactResultReact.__init__()ResultReact.convert_times()ResultReact.get_coord_data()ResultReact.get_element_data()ResultReact.get_elements()ResultReact.get_layer_data()ResultReact.get_number_of_layers()ResultReact.get_parameters()ResultReact.get_times()ResultReact.get_timeseries_data()ResultReact.get_unique_coord_data()ResultReact.get_unique_x_data()ResultReact.get_unique_y_data()ResultReact.get_unique_z_data()ResultReact.get_x_data()ResultReact.get_x_depth_data()ResultReact.get_x_start_points()ResultReact.get_y_data()ResultReact.get_z_data()ResultReact.get_z_layer_data()
- Results for Multiple Files Tough 3
- Results for Multiple Files Tough React
MultiResultReactMultiResultReact.__init__()MultiResultReact.get_multi_element_data()MultiResultReact.get_multi_file_distance()MultiResultReact.get_multi_prop_distance()MultiResultReact.retrieve_data_multi_file_fixed_time()MultiResultReact.retrieve_data_multi_file_fixed_time_layer()MultiResultReact.retrieve_data_multi_timeseries()
- Results for Single Files
- Results for Multiple Files
- Results for Experimental Data
- Results for t2result
- Results for Tough 3
- Utilities Class
- TOUGHREACT Utilities
- TOUGH3 Utilities
T2UtilitiesT2Utilities.__init__()T2Utilities.chop_list()T2Utilities.convert_parameter_name()T2Utilities.convert_times()T2Utilities.cust_range()T2Utilities.fmt()T2Utilities.get_grid_number()T2Utilities.get_number_of_grids()T2Utilities.param_label_full()T2Utilities.remove_repetiting()T2Utilities.trim_data_points()
- Wrapper Class
- Writers Class
- Biodegradation Writing
T2BioParserT2BioT2Bio.__init__()T2Bio.get_present_sections()T2Bio.present_sectionsT2Bio.read()T2Bio.read_biodg()T2Bio.read_chem()T2Bio.read_gas()T2Bio.read_more_options()T2Bio.read_multi()T2Bio.read_parameters()T2Bio.read_rocktypes()T2Bio.read_solids()T2Bio.reset_bio_dicta()T2Bio.run()T2Bio.section_insertion_index()T2Bio.update_read_write_functions()T2Bio.write()T2Bio.write_biodg()T2Bio.write_chem()T2Bio.write_gas()T2Bio.write_parameters()T2Bio.write_solids()T2Bio.write_start()
- Chemical Writing
T2ChemicalDataT2ChemicalData.__init__()T2ChemicalData.find_gas()T2ChemicalData.find_minerals()T2ChemicalData.find_primary_aqueous()T2ChemicalData.get_default_chemical_zone_to_nodes()T2ChemicalData.get_default_chemical_zones()T2ChemicalData.get_minerals_to_write()T2ChemicalData.get_nodes_to_read()T2ChemicalData.get_param_values()T2ChemicalData.get_param_values_decay_species()T2ChemicalData.get_param_values_exchangeable_cations()T2ChemicalData.get_param_values_gas()T2ChemicalData.get_param_values_ib_waters()T2ChemicalData.get_param_values_ij_gases()T2ChemicalData.get_param_values_mineral()T2ChemicalData.get_param_values_mineral_zones()T2ChemicalData.get_param_values_perm_poro()T2ChemicalData.get_param_values_surface_complex()T2ChemicalData.get_primary_species_to_read()T2ChemicalData.get_printout_options()T2ChemicalData.get_reactive_constraints()T2ChemicalData.get_reactive_options()T2ChemicalData.get_readio()T2ChemicalData.get_tolerance_values()T2ChemicalData.get_weight_diffusion()T2ChemicalData.search_for_node_index()
T2ChemicalT2Chemical.__init__()T2Chemical.boundary_water_indexT2Chemical.convert_to_t2chemical()T2Chemical.count_mineral_zones()T2Chemical.count_zones()T2Chemical.get_boundary_water_index()T2Chemical.get_initial_gas_index()T2Chemical.get_initial_water_index()T2Chemical.get_injection_gas_index()T2Chemical.get_mineral_index()T2Chemical.get_mineral_zones()T2Chemical.get_perm_poro_index()T2Chemical.get_perm_poro_zones()T2Chemical.get_present_sections()T2Chemical.getib_waters()T2Chemical.getij_gas()T2Chemical.initial_gas_indexT2Chemical.initial_water_indexT2Chemical.injection_gas_indexT2Chemical.map_mineral_to_zone()T2Chemical.mineral_indexT2Chemical.mineral_zonesT2Chemical.perm_poroT2Chemical.perm_poro_indexT2Chemical.present_sectionsT2Chemical.read()T2Chemical.read_aqueous_complexes()T2Chemical.read_aqueous_kinetics()T2Chemical.read_cation_exchange()T2Chemical.read_decay_species()T2Chemical.read_exchangeable_cations()T2Chemical.read_gases()T2Chemical.read_ib_waters()T2Chemical.read_ij_gas()T2Chemical.read_linear_equilibrium()T2Chemical.read_mineral_zones()T2Chemical.read_minerals()T2Chemical.read_perm_poro()T2Chemical.read_primary_aqueous()T2Chemical.read_surface_adsorption()T2Chemical.read_surface_complexes()T2Chemical.section_insertion_index()T2Chemical.update_read_write_functions()T2Chemical.write()T2Chemical.write_aqueous_complexes()T2Chemical.write_aqueous_kinetics()T2Chemical.write_cation_exchange()T2Chemical.write_decay_species()T2Chemical.write_dissolution_precipitation()T2Chemical.write_equilibrium()T2Chemical.write_exchangeable_cations()T2Chemical.write_gases()T2Chemical.write_ib_waters()T2Chemical.write_ij_gas()T2Chemical.write_linear_equilibrium()T2Chemical.write_mineral_zones()T2Chemical.write_minerals()T2Chemical.write_perm_poro()T2Chemical.write_primary_aqueous()T2Chemical.write_surface_adsorption()T2Chemical.write_surface_complexes()T2Chemical.write_title()
- React Writing
T2ReactParserT2ExtraPrecisionDataParserT2ReactT2React.__init__()T2React.check_for_executable()T2React.check_for_thermodynamic_database()T2React.get_present_sections()T2React.present_sectionsT2React.read()T2React.read_blocks()T2React.read_connections()T2React.read_parameters()T2React.read_rocktypes()T2React.run()T2React.section_insertion_index()T2React.update_read_write_functions()T2React.write()T2React.write_react()
- Solute Writing
T2SoluteParserT2SoluteParser.__init__()T2SoluteParser.find_minerals()T2SoluteParser.find_primary_aqueous()T2SoluteParser.get_default_chemical_zone_to_nodes()T2SoluteParser.get_default_chemical_zones()T2SoluteParser.get_minerals_to_write()T2SoluteParser.get_nodes_to_read()T2SoluteParser.get_primary_species_to_read()T2SoluteParser.get_printout_options()T2SoluteParser.get_reactive_constraints()T2SoluteParser.get_reactive_options()T2SoluteParser.get_readio()T2SoluteParser.get_tolerance_values()T2SoluteParser.get_weight_diffusion()T2SoluteParser.search_for_node_index()
T2SoluteT2Solute.__init__()T2Solute.convert_to_t2solute()T2Solute.generate_zone_to_blocks()T2Solute.get_boundary_water()T2Solute.get_boundary_water_index()T2Solute.get_grid_blocks()T2Solute.get_initial_water()T2Solute.get_initial_water_index()T2Solute.get_mineral()T2Solute.get_present_sections()T2Solute.get_zone_value()T2Solute.getgrid_info()T2Solute.map_zone_to_blocks()T2Solute.present_sectionsT2Solute.read()T2Solute.read_adsorption_species()T2Solute.read_aqueous_species()T2Solute.read_chemical_zones()T2Solute.read_chemical_zones_to_nodes()T2Solute.read_constraints()T2Solute.read_exchange_species()T2Solute.read_minerals()T2Solute.read_nodes()T2Solute.read_options()T2Solute.read_primary_species()T2Solute.read_printout()T2Solute.read_readio()T2Solute.read_tolerance()T2Solute.read_weight_diffu()T2Solute.section_insertion_index()T2Solute.update_read_write_functions()T2Solute.write()T2Solute.write_adsorption_species()T2Solute.write_aqueous_species()T2Solute.write_chemical_zones()T2Solute.write_chemical_zones_to_nodes()T2Solute.write_constraints()T2Solute.write_exchange_species()T2Solute.write_minerals()T2Solute.write_nodes()T2Solute.write_options()T2Solute.write_primary_species()T2Solute.write_printout()T2Solute.write_readio()T2Solute.write_title()T2Solute.write_tolerance()T2Solute.write_weight_diffu()
- Biodegradation Writing
- Source Code
- pytoughreact package
- Subpackages
- pytoughreact.assembler package
- pytoughreact.chemical package
- Submodules
- pytoughreact.chemical.bio_process_description module
- pytoughreact.chemical.biomass_composition module
BaseComponentBaseComponent.__init__()BaseComponent.add_to_process()BaseComponent.default_benzene()BaseComponent.default_n_decane()BaseComponent.default_n_pentane()BaseComponent.default_n_propyl_benzene()BaseComponent.default_p_xylene()BaseComponent.default_toluene()BaseComponent.get_fifth_set()BaseComponent.get_first_set()BaseComponent.get_fourth_set()BaseComponent.get_second_set()BaseComponent.get_seventh_set()BaseComponent.get_sixth_set()BaseComponent.get_third_set()
BiomassComponentGasSolidsWaterBio
- pytoughreact.chemical.chemical_composition module
- pytoughreact.chemical.kinetic_properties module
- pytoughreact.chemical.mineral_composition module
- pytoughreact.chemical.mineral_description module
MineralMineral.__init__()Mineral.get_composition()Mineral.get_dissolution_parameters()Mineral.get_equilibrium_data()Mineral.get_first_row()Mineral.get_number_of_ph_dependence()Mineral.get_ph_dependency_1()Mineral.get_ph_dependency_2()Mineral.get_precipitation_parameters()Mineral.get_precipitation_parameters_2()
- pytoughreact.chemical.mineral_zone module
- pytoughreact.chemical.perm_poro_zone module
- Module contents
- pytoughreact.constants package
- Submodules
- pytoughreact.constants.cap_pressure_constants module
- pytoughreact.constants.default_minerals module
- pytoughreact.constants.defaults_constants module
- pytoughreact.constants.format_specifications module
- pytoughreact.constants.generalconstants module
- pytoughreact.constants.grid_constants module
- pytoughreact.constants.plotconstants module
- pytoughreact.constants.reactionconstants module
- pytoughreact.constants.rel_perm_constants module
- pytoughreact.constants.sections module
- Module contents
- pytoughreact.exceptions package
- pytoughreact.model package
- pytoughreact.numerical package
- pytoughreact.plotting package
- Submodules
- pytoughreact.plotting.plot_multiple_files_routine module
- pytoughreact.plotting.plot_multiple_tough_routine module
PlotMultiToughPlotMultiTough.__init__()PlotMultiTough.get_restart_data_element()PlotMultiTough.get_restart_data_time()PlotMultiTough.get_restart_locations()PlotMultiTough.multi_param_multi_file_plot()PlotMultiTough.multi_time_plot()PlotMultiTough.multi_time_plot_restart()PlotMultiTough.plot_multi_param_single_plot()PlotMultiTough.read_file()PlotMultiTough.read_file_multi()
- pytoughreact.plotting.plot_tough_routine module
- Module contents
- pytoughreact.pytough_wrapper package
- pytoughreact.results package
- Submodules
- pytoughreact.results.multi_result_tough_3 module
- pytoughreact.results.multi_result_tough_react module
MultiResultReactMultiResultReact.__init__()MultiResultReact.get_multi_element_data()MultiResultReact.get_multi_file_distance()MultiResultReact.get_multi_prop_distance()MultiResultReact.retrieve_data_multi_file_fixed_time()MultiResultReact.retrieve_data_multi_file_fixed_time_layer()MultiResultReact.retrieve_data_multi_timeseries()
- pytoughreact.results.result_multiple module
- pytoughreact.results.result_single module
- pytoughreact.results.result_tough_3 module
ResultTough3ResultTough3.__init__()ResultTough3.check_strictly_increasing()ResultTough3.convert_times()ResultTough3.del_index()ResultTough3.duplicate_index()ResultTough3.get_coord_data()ResultTough3.get_element_data()ResultTough3.get_elements()ResultTough3.get_generation_data()ResultTough3.get_layer_data()ResultTough3.get_number_of_layers()ResultTough3.get_parameters()ResultTough3.get_result_dictionary()ResultTough3.get_time_index()ResultTough3.get_times()ResultTough3.get_timeseries_data()ResultTough3.get_unique_coord_data()ResultTough3.get_unique_x_data()ResultTough3.get_unique_y_data()ResultTough3.get_unique_z_data()ResultTough3.get_x_data()ResultTough3.get_x_depth_data()ResultTough3.get_x_start_points()ResultTough3.get_y_data()ResultTough3.get_z_data()ResultTough3.get_z_layer_data()ResultTough3.read_file()ResultTough3.remove_non_increasing()
- pytoughreact.results.result_tough_react module
ResultReactResultReact.__init__()ResultReact.convert_times()ResultReact.get_coord_data()ResultReact.get_element_data()ResultReact.get_elements()ResultReact.get_layer_data()ResultReact.get_number_of_layers()ResultReact.get_parameters()ResultReact.get_times()ResultReact.get_timeseries_data()ResultReact.get_unique_coord_data()ResultReact.get_unique_x_data()ResultReact.get_unique_y_data()ResultReact.get_unique_z_data()ResultReact.get_x_data()ResultReact.get_x_depth_data()ResultReact.get_x_start_points()ResultReact.get_y_data()ResultReact.get_z_data()ResultReact.get_z_layer_data()
- pytoughreact.results.simple_experiment_data module
- Module contents
- pytoughreact.utilities package
- pytoughreact.writers package
- Submodules
- pytoughreact.writers.bio_writing module
T2BioT2Bio.__init__()T2Bio.get_present_sections()T2Bio.present_sectionsT2Bio.read()T2Bio.read_biodg()T2Bio.read_chem()T2Bio.read_gas()T2Bio.read_more_options()T2Bio.read_multi()T2Bio.read_parameters()T2Bio.read_rocktypes()T2Bio.read_solids()T2Bio.reset_bio_dicta()T2Bio.run()T2Bio.section_insertion_index()T2Bio.set_echo_extra_precision()T2Bio.update_read_write_functions()T2Bio.write()T2Bio.write_biodg()T2Bio.write_chem()T2Bio.write_gas()T2Bio.write_parameters()T2Bio.write_solids()T2Bio.write_start()
T2BioParser
- pytoughreact.writers.chemical_writing module
T2ChemicalT2Chemical.__init__()T2Chemical.boundary_water_indexT2Chemical.convert_to_t2chemical()T2Chemical.count_mineral_zones()T2Chemical.count_zones()T2Chemical.get_boundary_water_index()T2Chemical.get_boundary_waters()T2Chemical.get_initial_gas_index()T2Chemical.get_initial_water_index()T2Chemical.get_initial_water_row()T2Chemical.get_initial_waters_pressure()T2Chemical.get_initial_waters_temperature()T2Chemical.get_injection_gas_index()T2Chemical.get_mineral_index()T2Chemical.get_mineral_zones()T2Chemical.get_perm_poro_index()T2Chemical.get_perm_poro_zones()T2Chemical.get_present_sections()T2Chemical.getib_waters()T2Chemical.getij_gas()T2Chemical.initial_gas_indexT2Chemical.initial_water_indexT2Chemical.injection_gas_indexT2Chemical.map_mineral_to_zone()T2Chemical.mineral_indexT2Chemical.mineral_zonesT2Chemical.perm_poroT2Chemical.perm_poro_indexT2Chemical.present_sectionsT2Chemical.read()T2Chemical.read_aqueous_complexes()T2Chemical.read_aqueous_kinetics()T2Chemical.read_cation_exchange()T2Chemical.read_decay_species()T2Chemical.read_exchangeable_cations()T2Chemical.read_gases()T2Chemical.read_ib_waters()T2Chemical.read_ij_gas()T2Chemical.read_linear_equilibrium()T2Chemical.read_mineral_zones()T2Chemical.read_minerals()T2Chemical.read_perm_poro()T2Chemical.read_primary_aqueous()T2Chemical.read_surface_adsorption()T2Chemical.read_surface_complexes()T2Chemical.section_insertion_index()T2Chemical.update_read_write_functions()T2Chemical.write()T2Chemical.write_aqueous_complexes()T2Chemical.write_aqueous_kinetics()T2Chemical.write_cation_exchange()T2Chemical.write_decay_species()T2Chemical.write_dissolution_precipitation()T2Chemical.write_equilibrium()T2Chemical.write_exchangeable_cations()T2Chemical.write_gases()T2Chemical.write_ib_waters()T2Chemical.write_ij_gas()T2Chemical.write_linear_equilibrium()T2Chemical.write_mineral_zones()T2Chemical.write_minerals()T2Chemical.write_perm_poro()T2Chemical.write_primary_aqueous()T2Chemical.write_surface_adsorption()T2Chemical.write_surface_complexes()T2Chemical.write_title()
T2ChemicalDataT2ChemicalData.__init__()T2ChemicalData.find_gas()T2ChemicalData.find_minerals()T2ChemicalData.find_primary_aqueous()T2ChemicalData.get_default_chemical_zone_to_nodes()T2ChemicalData.get_default_chemical_zones()T2ChemicalData.get_minerals_to_write()T2ChemicalData.get_nodes_to_read()T2ChemicalData.get_param_values()T2ChemicalData.get_param_values_decay_species()T2ChemicalData.get_param_values_exchangeable_cations()T2ChemicalData.get_param_values_gas()T2ChemicalData.get_param_values_ib_waters()T2ChemicalData.get_param_values_ij_gases()T2ChemicalData.get_param_values_mineral()T2ChemicalData.get_param_values_mineral_zones()T2ChemicalData.get_param_values_perm_poro()T2ChemicalData.get_param_values_surface_complex()T2ChemicalData.get_primary_species_to_read()T2ChemicalData.get_printout_options()T2ChemicalData.get_reactive_constraints()T2ChemicalData.get_reactive_options()T2ChemicalData.get_readio()T2ChemicalData.get_tolerance_values()T2ChemicalData.get_weight_diffusion()T2ChemicalData.search_for_node_index()
- pytoughreact.writers.react_writing module
T2ExtraPrecisionDataParserT2ReactT2React.__init__()T2React.check_for_executable()T2React.check_for_thermodynamic_database()T2React.get_present_sections()T2React.present_sectionsT2React.read()T2React.read_blocks()T2React.read_connections()T2React.read_parameters()T2React.read_react()T2React.read_rocktypes()T2React.run()T2React.section_insertion_index()T2React.update_read_write_functions()T2React.write()T2React.write_react()
T2ReactParser
- pytoughreact.writers.solute_writing module
T2SoluteT2Solute.__init__()T2Solute.convert_to_t2solute()T2Solute.generate_zone_to_blocks()T2Solute.get_boundary_water()T2Solute.get_boundary_water_index()T2Solute.get_grid_blocks()T2Solute.get_initial_water()T2Solute.get_initial_water_index()T2Solute.get_mineral()T2Solute.get_present_sections()T2Solute.get_zone_value()T2Solute.getgrid_info()T2Solute.map_zone_to_blocks()T2Solute.present_sectionsT2Solute.read()T2Solute.read_adsorption_species()T2Solute.read_aqueous_species()T2Solute.read_chemical_zones()T2Solute.read_chemical_zones_to_nodes()T2Solute.read_constraints()T2Solute.read_exchange_species()T2Solute.read_minerals()T2Solute.read_nodes()T2Solute.read_options()T2Solute.read_primary_species()T2Solute.read_printout()T2Solute.read_readio()T2Solute.read_tolerance()T2Solute.read_weight_diffu()T2Solute.section_insertion_index()T2Solute.update_read_write_functions()T2Solute.write()T2Solute.write_adsorption_species()T2Solute.write_aqueous_species()T2Solute.write_chemical_zones()T2Solute.write_chemical_zones_to_nodes()T2Solute.write_constraints()T2Solute.write_exchange_species()T2Solute.write_minerals()T2Solute.write_nodes()T2Solute.write_options()T2Solute.write_primary_species()T2Solute.write_printout()T2Solute.write_readio()T2Solute.write_title()T2Solute.write_tolerance()T2Solute.write_weight_diffu()
T2SoluteParserT2SoluteParser.__init__()T2SoluteParser.find_minerals()T2SoluteParser.find_primary_aqueous()T2SoluteParser.get_default_chemical_zone_to_nodes()T2SoluteParser.get_default_chemical_zones()T2SoluteParser.get_minerals_to_write()T2SoluteParser.get_nodes_to_read()T2SoluteParser.get_primary_species_to_read()T2SoluteParser.get_printout_options()T2SoluteParser.get_reactive_constraints()T2SoluteParser.get_reactive_options()T2SoluteParser.get_readio()T2SoluteParser.get_tolerance_values()T2SoluteParser.get_weight_diffusion()T2SoluteParser.search_for_node_index()
- Module contents
- Submodules
- pytoughreact.result_bio module
- pytoughreact.run module
- pytoughreact.run_bio module
- pytoughreact.run_react module
- pytoughreact.run_result module
- pytoughreact.version module
- Module contents
- Subpackages
- pytoughreact package
Community Guidelines
Requirements
Developer Notes