pytoughreact package

Subpackages

• pytoughreact.assembler package
  • Module contents
• pytoughreact.chemical package
  • Submodules
  • pytoughreact.chemical.bio_process_description module
    • BIODG
      • BIODG.__init__()
      • BIODG.get_base_parameter_and_index()
      • BIODG.get_first_set()
      • BIODG.get_number_of_biomasses()
    • Process
      • Process.__init__()
      • Process.get_kc()
      • Process.get_kh()
      • Process.get_knc()
      • Process.get_ks()
      • Process.get_number_of_competiting()
      • Process.get_uptake()
  • pytoughreact.chemical.biomass_composition module
    • BaseComponent
      • BaseComponent.__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()
    • Biomass
      • Biomass.__init__()
    • Component
      • Component.__init__()
      • Component.get_toluene()
    • Gas
      • Gas.__init__()
      • Gas.add_to_process()
    • Solids
      • Solids.__init__()
      • Solids.get_first_set()
    • WaterBio
      • WaterBio.__init__()
      • WaterBio.add_to_process()
  • pytoughreact.chemical.chemical_composition module
    • PrimarySpecies
      • PrimarySpecies.__init__()
      • PrimarySpecies.get_name_trans()
    • ReactGas
      • ReactGas.__init__()
    • Water
      • Water.__init__()
    • WaterComp
      • WaterComp.__init__()
  • pytoughreact.chemical.kinetic_properties module
    • Dissolution
      • Dissolution.__init__()
    • Equilibrium
      • Equilibrium.__init__()
    • Kinetic
      • Kinetic.__init__()
    • PHDependenceType1
      • PHDependenceType1.__init__()
    • PHDependenceType2
      • PHDependenceType2.__init__()
    • Precipitation
      • Precipitation.__init__()
  • pytoughreact.chemical.mineral_composition module
    • MineralComp
      • MineralComp.__init__()
  • pytoughreact.chemical.mineral_description module
    • Mineral
      • Mineral.__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
    • MineralZone
      • MineralZone.__init__()
  • pytoughreact.chemical.perm_poro_zone module
    • PermPoro
      • PermPoro.__init__()
    • PermPoroZone
      • PermPoroZone.__init__()
  • Module contents
• pytoughreact.constants package
  • Submodules
  • pytoughreact.constants.cap_pressure_constants module
  • pytoughreact.constants.default_minerals module
    • get_kinetics_minerals()
    • get_specific_mineral()
  • 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
  • Submodules
  • pytoughreact.exceptions.custom_error module
    • CapillaryPressureTypeError
      • CapillaryPressureTypeError.__init__()
    • Error
    • MissingParameterError
      • MissingParameterError.__init__()
    • NotFoundError
      • NotFoundError.__init__()
    • ParameterLessThanThreeError
      • ParameterLessThanThreeError.__init__()
    • ReactiveConstraintsError
    • ReactiveOptionsError
    • RelativePermeabilityTypeError
      • RelativePermeabilityTypeError.__init__()
    • RequiredInputError
      • RequiredInputError.__init__()
    • RestrictionError
      • RestrictionError.__init__()
  • Module contents
• pytoughreact.model package
  • Submodules
  • pytoughreact.model.capillary_pressure module
  • pytoughreact.model.grid module
  • pytoughreact.model.physical_model module
  • pytoughreact.model.relative_permeability module
  • Module contents
• pytoughreact.numerical package
  • Submodules
  • pytoughreact.numerical.physical_model_numericals module
  • Module contents
• pytoughreact.plotting package
  • Submodules
  • pytoughreact.plotting.plot_multiple_files_routine module
    • PlotMultiFiles
      • PlotMultiFiles.__init__()
      • PlotMultiFiles.multi_file_single_plot()
      • PlotMultiFiles.plot_multi_element_multi_file()
      • PlotMultiFiles.plot_multi_file_distance()
      • PlotMultiFiles.plot_multi_per_panel()
  • pytoughreact.plotting.plot_multiple_tough_routine module
    • PlotMultiTough
      • PlotMultiTough.__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
    • PlotTough
      • PlotTough.__init__()
      • PlotTough.plot_2d_one()
      • PlotTough.plot_2d_with_grid()
      • PlotTough.plot_param_with_layer()
      • PlotTough.plot_param_with_param()
      • PlotTough.plot_param_with_time()
      • PlotTough.plot_param_with_time_restart()
  • Module contents
• pytoughreact.pytough_wrapper package
  • Subpackages
    • pytoughreact.pytough_wrapper.wrapper package
      • Submodules
      • pytoughreact.pytough_wrapper.wrapper.reactblock module
      • pytoughreact.pytough_wrapper.wrapper.reactgrid module
      • pytoughreact.pytough_wrapper.wrapper.reactzone module
      • Module contents
  • Module contents
• pytoughreact.results package
  • Submodules
  • pytoughreact.results.multi_result_tough_3 module
    • MultiResultTough3
      • MultiResultTough3.__init__()
      • MultiResultTough3.get_multi_element_data()
      • MultiResultTough3.get_multi_element_data_per_panel()
      • MultiResultTough3.retrieve_data_multi_file_fixed_time()
      • MultiResultTough3.retrieve_data_multi_file_fixed_time_layer()
      • MultiResultTough3.retrieve_data_multi_timeseries()
  • pytoughreact.results.multi_result_tough_react module
    • MultiResultReact
      • MultiResultReact.__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
    • FileReadMultiple
      • FileReadMultiple.__init__()
      • FileReadMultiple.plot_param_with_layer()
      • FileReadMultiple.plot_time()
      • FileReadMultiple.plot_time_per_panel()
  • pytoughreact.results.result_single module
    • FileReadSingle
      • FileReadSingle.__init__()
      • FileReadSingle.get_simulator_type()
      • FileReadSingle.plot_2d()
      • FileReadSingle.plot_param_with_layer()
      • FileReadSingle.plot_param_with_param()
      • FileReadSingle.plot_time()
      • FileReadSingle.validate_file()
  • pytoughreact.results.result_tough_3 module
    • ResultTough3
      • ResultTough3.__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
    • ResultReact
      • ResultReact.__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
    • Experiment
      • Experiment.__init__()
      • Experiment.get_column_names()
      • Experiment.get_times()
      • Experiment.get_timeseries_data()
      • Experiment.read_file()
  • Module contents
• pytoughreact.utilities package
  • Submodules
  • pytoughreact.utilities.synergy_general_utilities module
  • pytoughreact.utilities.synergy_tough_react_utilities module
  • Module contents
• pytoughreact.writers package
  • Submodules
  • pytoughreact.writers.bio_writing module
    • T2Bio
      • T2Bio.__init__()
      • T2Bio.get_present_sections()
      • T2Bio.present_sections
      • T2Bio.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
      • T2BioParser.__init__()
      • T2BioParser.read_multi_value_line()
      • T2BioParser.read_params_value_line()
  • pytoughreact.writers.chemical_writing module
    • T2Chemical
      • T2Chemical.__init__()
      • T2Chemical.boundary_water_index
      • T2Chemical.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_index
      • T2Chemical.initial_water_index
      • T2Chemical.injection_gas_index
      • T2Chemical.map_mineral_to_zone()
      • T2Chemical.mineral_index
      • T2Chemical.mineral_zones
      • T2Chemical.perm_poro
      • T2Chemical.perm_poro_index
      • T2Chemical.present_sections
      • T2Chemical.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()
    • T2ChemicalData
      • T2ChemicalData.__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
    • T2ExtraPrecisionDataParser
      • T2ExtraPrecisionDataParser.__init__()
    • T2React
      • T2React.__init__()
      • T2React.check_for_executable()
      • T2React.check_for_thermodynamic_database()
      • T2React.get_present_sections()
      • T2React.present_sections
      • T2React.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
      • T2ReactParser.__init__()
  • pytoughreact.writers.solute_writing module
    • T2Solute
      • T2Solute.__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_sections
      • T2Solute.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()
    • T2SoluteParser
      • T2SoluteParser.__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