Index

_

__init__() (pytoughreact.chemical.bio_process_description.BIODG method), [1] (pytoughreact.chemical.bio_process_description.Process method), [1] (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] (pytoughreact.chemical.biomass_composition.Biomass method), [1] (pytoughreact.chemical.biomass_composition.Component method), [1] (pytoughreact.chemical.biomass_composition.Gas method), [1] (pytoughreact.chemical.biomass_composition.Solids method), [1] (pytoughreact.chemical.biomass_composition.WaterBio method) (pytoughreact.chemical.chemical_composition.PrimarySpecies method), [1] (pytoughreact.chemical.chemical_composition.ReactGas method), [1] (pytoughreact.chemical.chemical_composition.Water method), [1] (pytoughreact.chemical.chemical_composition.WaterComp method), [1] (pytoughreact.chemical.kinetic_properties.Dissolution method), [1] (pytoughreact.chemical.kinetic_properties.Equilibrium method), [1] (pytoughreact.chemical.kinetic_properties.Kinetic method), [1] (pytoughreact.chemical.kinetic_properties.PHDependenceType1 method) (pytoughreact.chemical.kinetic_properties.PHDependenceType2 method) (pytoughreact.chemical.kinetic_properties.Precipitation method), [1] (pytoughreact.chemical.mineral_composition.MineralComp method), [1] (pytoughreact.chemical.mineral_description.Mineral method), [1] (pytoughreact.chemical.mineral_zone.MineralZone method), [1] (pytoughreact.chemical.perm_poro_zone.PermPoro method), [1] (pytoughreact.chemical.perm_poro_zone.PermPoroZone method), [1] (pytoughreact.exceptions.custom_error.CapillaryPressureTypeError method) (pytoughreact.exceptions.custom_error.MissingParameterError method) (pytoughreact.exceptions.custom_error.NotFoundError method) (pytoughreact.exceptions.custom_error.ParameterLessThanThreeError method) (pytoughreact.exceptions.custom_error.RelativePermeabilityTypeError method) (pytoughreact.exceptions.custom_error.RequiredInputError method) (pytoughreact.exceptions.custom_error.RestrictionError method) (pytoughreact.plotting.plot_multiple_files_routine.PlotMultiFiles method), [1] (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method), [1] (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] (pytoughreact.results.result_multiple.FileReadMultiple method), [1] (pytoughreact.results.result_single.FileReadSingle method), [1] (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] (pytoughreact.results.simple_experiment_data.Experiment method), [1] (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) (pytoughreact.utilities.t2_utilities.T2Utilities method) (pytoughreact.wrapper.react_data.ReactData method) (pytoughreact.wrapper.reactblock.T2Block method) (pytoughreact.wrapper.reactgrid.T2ReactGrid method) (pytoughreact.wrapper.reactzone.T2Zone method) (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.bio_writing.T2BioParser method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.react_writing.T2ExtraPrecisionDataParser method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.react_writing.T2ReactParser method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1]

__weakref__ (pytoughreact.chemical.bio_process_description.BIODG attribute) (pytoughreact.chemical.bio_process_description.Process attribute)

A

add_block() (pytoughreact.wrapper.reactgrid.T2ReactGrid method) add_to_process() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] (pytoughreact.chemical.biomass_composition.Gas method), [1] (pytoughreact.chemical.biomass_composition.WaterBio method)

add_zone() (pytoughreact.wrapper.reactgrid.T2ReactGrid method)

B

BaseComponent (class in pytoughreact.chemical.biomass_composition), [1] BIODG (class in pytoughreact.chemical.bio_process_description), [1]

Biomass (class in pytoughreact.chemical.biomass_composition), [1] boundary_water_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1]

C

CapillaryPressureTypeError check_for_executable() (pytoughreact.writers.react_writing.T2React method), [1] check_for_thermodynamic_database() (pytoughreact.writers.react_writing.T2React method), [1] check_strictly_increasing() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] chop_list() (pytoughreact.utilities.t2_utilities.T2Utilities method) Component (class in pytoughreact.chemical.biomass_composition), [1] convert_parameter_name() (pytoughreact.utilities.t2_utilities.T2Utilities method) convert_times() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] (pytoughreact.utilities.t2_utilities.T2Utilities method)

convert_to_t2chemical() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] convert_to_t2solute() (pytoughreact.writers.solute_writing.T2Solute method), [1] copy_all_files() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) copy_file() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) count_mineral_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] count_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] cust_range() (pytoughreact.utilities.t2_utilities.T2Utilities method)

D

default_benzene() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] default_n_decane() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] default_n_pentane() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] default_n_propyl_benzene() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1]

default_p_xylene() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] default_toluene() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] del_index() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] Dissolution (class in pytoughreact.chemical.kinetic_properties), [1] duplicate_index() (pytoughreact.results.result_tough_3.ResultTough3 method), [1]

E

empty() (pytoughreact.wrapper.reactgrid.T2ReactGrid method) Equilibrium (class in pytoughreact.chemical.kinetic_properties), [1]

Error Experiment (class in pytoughreact.results.simple_experiment_data), [1]

F

FileReadMultiple (class in pytoughreact.results.result_multiple), [1] FileReadSingle (class in pytoughreact.results.result_single), [1] find_gas() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] find_minerals() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1]

find_primary_aqueous() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] find_word() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) fmt() (pytoughreact.utilities.t2_utilities.T2Utilities method) fromgeo() (pytoughreact.wrapper.reactgrid.T2ReactGrid method)

G

Gas (class in pytoughreact.chemical.biomass_composition), [1] generate_zone_to_blocks() (pytoughreact.writers.solute_writing.T2Solute method), [1] get_base_parameter_and_index() (pytoughreact.chemical.bio_process_description.BIODG method), [1] get_boundary_water() (pytoughreact.writers.solute_writing.T2Solute method), [1] get_boundary_water_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] get_boundary_waters() (pytoughreact.writers.chemical_writing.T2Chemical method) get_column_names() (pytoughreact.results.simple_experiment_data.Experiment method), [1] get_composition() (pytoughreact.chemical.mineral_description.Mineral method) get_coord_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_default_chemical_zone_to_nodes() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_default_chemical_zones() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_dissolution_parameters() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_element_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_elements() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_equilibrium_data() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_fifth_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_first_row() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_first_set() (pytoughreact.chemical.bio_process_description.BIODG method), [1] (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] (pytoughreact.chemical.biomass_composition.Solids method), [1] get_fourth_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_generation_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] get_grid_blocks() (pytoughreact.writers.solute_writing.T2Solute method), [1] get_grid_number() (pytoughreact.utilities.t2_utilities.T2Utilities method) get_initial_gas_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_initial_water() (pytoughreact.writers.solute_writing.T2Solute method), [1] get_initial_water_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] get_initial_water_row() (pytoughreact.writers.chemical_writing.T2Chemical method) get_initial_waters_pressure() (pytoughreact.writers.chemical_writing.T2Chemical method) get_initial_waters_temperature() (pytoughreact.writers.chemical_writing.T2Chemical method) get_injection_gas_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_kc() (pytoughreact.chemical.bio_process_description.Process method), [1] get_kh() (pytoughreact.chemical.bio_process_description.Process method), [1] get_kinetics_minerals() (in module pytoughreact.constants.default_minerals) get_knc() (pytoughreact.chemical.bio_process_description.Process method), [1] get_ks() (pytoughreact.chemical.bio_process_description.Process method), [1] get_layer_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_mineral() (pytoughreact.writers.solute_writing.T2Solute method), [1] get_mineral_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_mineral_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_minerals_to_write() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_multi_element_data() (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] get_multi_element_data_per_panel() (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] get_multi_file_distance() (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] get_multi_prop_distance() (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] get_name_trans() (pytoughreact.chemical.chemical_composition.PrimarySpecies method), [1] get_nodes_to_read() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_num_zones() (pytoughreact.wrapper.reactgrid.T2ReactGrid method) get_number_of_biomasses() (pytoughreact.chemical.bio_process_description.BIODG method), [1] get_number_of_competiting() (pytoughreact.chemical.bio_process_description.Process method), [1] get_number_of_grids() (pytoughreact.utilities.t2_utilities.T2Utilities method) get_number_of_layers() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_number_of_ph_dependence() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_param_values() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_decay_species() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_exchangeable_cations() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_gas() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_ib_waters() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_ij_gases() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_mineral() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1]

get_param_values_mineral_zones() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_perm_poro() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_param_values_surface_complex() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] get_parameters() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_perm_poro_index() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_perm_poro_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] get_ph_dependency_1() (pytoughreact.chemical.mineral_description.Mineral method) get_ph_dependency_2() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_precipitation_parameters() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_precipitation_parameters_2() (pytoughreact.chemical.mineral_description.Mineral method), [1] get_present_sections() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] get_primary_species_to_read() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_printout_options() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_reactive_constraints() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_reactive_options() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_readio() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_restart_data_element() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method) get_restart_data_time() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method) get_restart_locations() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method) get_result_dictionary() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] get_second_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_seventh_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_simulator_type() (pytoughreact.results.result_single.FileReadSingle method), [1] get_sixth_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_specific_mineral() (in module pytoughreact.constants.default_minerals) get_third_set() (pytoughreact.chemical.biomass_composition.BaseComponent method), [1] get_time_index() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] get_times() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] (pytoughreact.results.simple_experiment_data.Experiment method), [1] get_timeseries_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] (pytoughreact.results.simple_experiment_data.Experiment method), [1] get_tolerance_values() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_toluene() (pytoughreact.chemical.biomass_composition.Component method) get_unique_coord_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_unique_x_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_unique_y_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_unique_z_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_uptake() (pytoughreact.chemical.bio_process_description.Process method), [1] get_weight_diffusion() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] get_x_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_x_depth_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_x_start_points() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_y_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_z_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_z_layer_data() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.result_tough_react.ResultReact method), [1] get_zone_value() (pytoughreact.writers.solute_writing.T2Solute method), [1] getgrid_info() (pytoughreact.writers.solute_writing.T2Solute method), [1] getib_waters() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] getij_gas() (pytoughreact.writers.chemical_writing.T2Chemical method), [1]

I

initial_gas_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1]

initial_water_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1] injection_gas_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1]

K

Kinetic (class in pytoughreact.chemical.kinetic_properties), [1]

M

map_mineral_to_zone() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] map_zone_to_blocks() (pytoughreact.writers.solute_writing.T2Solute method), [1] Mineral (class in pytoughreact.chemical.mineral_description), [1] mineral_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1] mineral_zones (pytoughreact.writers.chemical_writing.T2Chemical property), [1] MineralComp (class in pytoughreact.chemical.mineral_composition), [1] MineralZone (class in pytoughreact.chemical.mineral_zone), [1] MissingParameterError module pytoughreact pytoughreact.chemical pytoughreact.chemical.bio_process_description pytoughreact.chemical.biomass_composition pytoughreact.chemical.chemical_composition pytoughreact.chemical.kinetic_properties pytoughreact.chemical.mineral_composition pytoughreact.chemical.mineral_description pytoughreact.chemical.mineral_zone pytoughreact.chemical.perm_poro_zone pytoughreact.constants pytoughreact.constants.cap_pressure_constants, [1] pytoughreact.constants.default_minerals, [1] pytoughreact.constants.defaults_constants pytoughreact.constants.format_specifications, [1] pytoughreact.constants.generalconstants, [1] pytoughreact.constants.grid_constants, [1] pytoughreact.constants.plotconstants, [1] pytoughreact.constants.reactionconstants, [1] pytoughreact.constants.rel_perm_constants, [1] pytoughreact.constants.sections, [1] pytoughreact.exceptions pytoughreact.exceptions.custom_error pytoughreact.plotting pytoughreact.plotting.plot_multiple_files_routine pytoughreact.plotting.plot_multiple_tough_routine pytoughreact.plotting.plot_tough_routine pytoughreact.results pytoughreact.results.multi_result_tough_3 pytoughreact.results.multi_result_tough_react pytoughreact.results.result_multiple pytoughreact.results.result_single pytoughreact.results.result_tough_3 pytoughreact.results.result_tough_react pytoughreact.results.simple_experiment_data pytoughreact.utilities pytoughreact.version pytoughreact.writers pytoughreact.writers.bio_writing pytoughreact.writers.chemical_writing pytoughreact.writers.react_writing pytoughreact.writers.solute_writing

multi_file_single_plot() (pytoughreact.plotting.plot_multiple_files_routine.PlotMultiFiles method), [1] multi_param_multi_file_plot() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method), [1] multi_time_plot() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method), [1] multi_time_plot_restart() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method), [1] MultiResultReact (class in pytoughreact.results.multi_result_tough_react), [1] MultiResultTough3 (class in pytoughreact.results.multi_result_tough_3), [1]

N

NotFoundError

num_zones (pytoughreact.wrapper.reactgrid.T2ReactGrid property)

P

param_label_full() (pytoughreact.utilities.t2_utilities.T2Utilities method) ParameterLessThanThreeError perm_poro (pytoughreact.writers.chemical_writing.T2Chemical property), [1] perm_poro_index (pytoughreact.writers.chemical_writing.T2Chemical property), [1] PermPoro (class in pytoughreact.chemical.perm_poro_zone), [1] PermPoroZone (class in pytoughreact.chemical.perm_poro_zone), [1] PHDependenceType1 (class in pytoughreact.chemical.kinetic_properties) PHDependenceType2 (class in pytoughreact.chemical.kinetic_properties) plot_2d() (pytoughreact.results.result_single.FileReadSingle method), [1] plot_2d_one() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] plot_2d_with_grid() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] plot_multi_element_multi_file() (pytoughreact.plotting.plot_multiple_files_routine.PlotMultiFiles method), [1] plot_multi_file_distance() (pytoughreact.plotting.plot_multiple_files_routine.PlotMultiFiles method), [1] plot_multi_param_single_plot() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method), [1] plot_multi_per_panel() (pytoughreact.plotting.plot_multiple_files_routine.PlotMultiFiles method), [1] plot_param_with_layer() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] (pytoughreact.results.result_multiple.FileReadMultiple method), [1] (pytoughreact.results.result_single.FileReadSingle method), [1] plot_param_with_param() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] (pytoughreact.results.result_single.FileReadSingle method), [1] plot_param_with_time() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] plot_param_with_time_restart() (pytoughreact.plotting.plot_tough_routine.PlotTough method), [1] plot_time() (pytoughreact.results.result_multiple.FileReadMultiple method), [1] (pytoughreact.results.result_single.FileReadSingle method), [1] plot_time_per_panel() (pytoughreact.results.result_multiple.FileReadMultiple method), [1] PlotMultiFiles (class in pytoughreact.plotting.plot_multiple_files_routine), [1] PlotMultiTough (class in pytoughreact.plotting.plot_multiple_tough_routine), [1] PlotTough (class in pytoughreact.plotting.plot_tough_routine), [1] Precipitation (class in pytoughreact.chemical.kinetic_properties), [1] present_sections (pytoughreact.writers.bio_writing.T2Bio property), [1] (pytoughreact.writers.chemical_writing.T2Chemical property), [1] (pytoughreact.writers.react_writing.T2React property), [1] (pytoughreact.writers.solute_writing.T2Solute property), [1] PrimarySpecies (class in pytoughreact.chemical.chemical_composition), [1] Process (class in pytoughreact.chemical.bio_process_description), [1] pytoughreact module pytoughreact.chemical module pytoughreact.chemical.bio_process_description module pytoughreact.chemical.biomass_composition module pytoughreact.chemical.chemical_composition module pytoughreact.chemical.kinetic_properties module pytoughreact.chemical.mineral_composition module pytoughreact.chemical.mineral_description module pytoughreact.chemical.mineral_zone module pytoughreact.chemical.perm_poro_zone module pytoughreact.constants module pytoughreact.constants.cap_pressure_constants module, [1]

pytoughreact.constants.default_minerals module, [1] pytoughreact.constants.defaults_constants module pytoughreact.constants.format_specifications module, [1] pytoughreact.constants.generalconstants module, [1] pytoughreact.constants.grid_constants module, [1] pytoughreact.constants.plotconstants module, [1] pytoughreact.constants.reactionconstants module, [1] pytoughreact.constants.rel_perm_constants module, [1] pytoughreact.constants.sections module, [1] pytoughreact.exceptions module pytoughreact.exceptions.custom_error module pytoughreact.plotting module pytoughreact.plotting.plot_multiple_files_routine module pytoughreact.plotting.plot_multiple_tough_routine module pytoughreact.plotting.plot_tough_routine module pytoughreact.results module pytoughreact.results.multi_result_tough_3 module pytoughreact.results.multi_result_tough_react module pytoughreact.results.result_multiple module pytoughreact.results.result_single module pytoughreact.results.result_tough_3 module pytoughreact.results.result_tough_react module pytoughreact.results.simple_experiment_data module pytoughreact.utilities module pytoughreact.version module pytoughreact.writers module pytoughreact.writers.bio_writing module pytoughreact.writers.chemical_writing module pytoughreact.writers.react_writing module pytoughreact.writers.solute_writing module

R

ReactData (class in pytoughreact.wrapper.react_data) ReactGas (class in pytoughreact.chemical.chemical_composition), [1] ReactiveConstraintsError ReactiveOptionsError read() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] read_adsorption_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_aqueous_complexes() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_aqueous_kinetics() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_aqueous_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_biodg() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_blocks() (pytoughreact.wrapper.react_data.ReactData method) (pytoughreact.writers.react_writing.T2React method), [1] read_cation_exchange() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_chem() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_chemical_zones() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_chemical_zones_to_nodes() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_connections() (pytoughreact.writers.react_writing.T2React method), [1] read_constraints() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_decay_species() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_exchange_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_exchangeable_cations() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_file() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method) (pytoughreact.results.result_tough_3.ResultTough3 method), [1] (pytoughreact.results.simple_experiment_data.Experiment method), [1] read_file_multi() (pytoughreact.plotting.plot_multiple_tough_routine.PlotMultiTough method) read_gas() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_gases() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_ib_waters() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_ij_gas() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_linear_equilibrium() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_mineral_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_minerals() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1]

read_more_options() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_multi() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_multi_value_line() (pytoughreact.writers.bio_writing.T2BioParser method), [1] read_nodes() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_options() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_parameters() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.react_writing.T2React method), [1] read_params_value_line() (pytoughreact.writers.bio_writing.T2BioParser method), [1] read_perm_poro() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_primary_aqueous() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_primary_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_printout() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_react() (pytoughreact.writers.react_writing.T2React method) read_readio() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_rocktypes() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.react_writing.T2React method), [1] read_solids() (pytoughreact.writers.bio_writing.T2Bio method), [1] read_surface_adsorption() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_surface_complexes() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] read_tolerance() (pytoughreact.writers.solute_writing.T2Solute method), [1] read_weight_diffu() (pytoughreact.writers.solute_writing.T2Solute method), [1] RelativePermeabilityTypeError remove_non_increasing() (pytoughreact.results.result_tough_3.ResultTough3 method), [1] remove_repetiting() (pytoughreact.utilities.t2_utilities.T2Utilities method) RequiredInputError reset_bio_dicta() (pytoughreact.writers.bio_writing.T2Bio method), [1] RestrictionError ResultReact (class in pytoughreact.results.result_tough_react), [1] ResultTough3 (class in pytoughreact.results.result_tough_3), [1] retrieve_data_multi_file_fixed_time() (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] retrieve_data_multi_file_fixed_time_layer() (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] retrieve_data_multi_timeseries() (pytoughreact.results.multi_result_tough_3.MultiResultTough3 method), [1] (pytoughreact.results.multi_result_tough_react.MultiResultReact method), [1] run() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.react_writing.T2React method), [1]

S

search_for_node_index() (pytoughreact.writers.chemical_writing.T2ChemicalData method), [1] (pytoughreact.writers.solute_writing.T2SoluteParser method), [1] section_insertion_index() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1]

set_echo_extra_precision() (pytoughreact.writers.bio_writing.T2Bio method) slice_off_file() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) slice_off_line() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) Solids (class in pytoughreact.chemical.biomass_composition), [1]

T

T2Bio (class in pytoughreact.writers.bio_writing), [1] T2BioParser (class in pytoughreact.writers.bio_writing), [1] T2Block (class in pytoughreact.wrapper.reactblock) T2Chemical (class in pytoughreact.writers.chemical_writing), [1] T2ChemicalData (class in pytoughreact.writers.chemical_writing), [1] T2ExtraPrecisionDataParser (class in pytoughreact.writers.react_writing), [1] T2React (class in pytoughreact.writers.react_writing), [1]

T2ReactGrid (class in pytoughreact.wrapper.reactgrid) T2ReactParser (class in pytoughreact.writers.react_writing), [1] T2Solute (class in pytoughreact.writers.solute_writing), [1] T2SoluteParser (class in pytoughreact.writers.solute_writing), [1] T2Utilities (class in pytoughreact.utilities.t2_utilities) T2UtilitiesToughReact (class in pytoughreact.utilities.t2_tough_react_utilities) T2Zone (class in pytoughreact.wrapper.reactzone) trim_data_points() (pytoughreact.utilities.t2_utilities.T2Utilities method)

U

update_read_write_functions() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1]

V

validate_file() (pytoughreact.results.result_single.FileReadSingle method), [1]

W

Water (class in pytoughreact.chemical.chemical_composition), [1] WaterBio (class in pytoughreact.chemical.biomass_composition) WaterComp (class in pytoughreact.chemical.chemical_composition), [1] write() (pytoughreact.writers.bio_writing.T2Bio method), [1] (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.react_writing.T2React method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] write_adsorption_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_aqueous_complexes() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_aqueous_kinetics() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_aqueous_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_biodg() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_cation_exchange() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_chem() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_chemical_zones() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_chemical_zones_to_nodes() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_constraints() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_decay_species() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_dissolution_precipitation() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_equilibrium() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_exchange_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_exchangeable_cations() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_gas() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_gases() (pytoughreact.writers.chemical_writing.T2Chemical method), [1]

write_ib_waters() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_ij_gas() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_linear_equilibrium() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_mineral_zones() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_minerals() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] write_nodes() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_options() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_parameters() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_perm_poro() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_primary_aqueous() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_primary_species() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_printout() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_react() (pytoughreact.writers.react_writing.T2React method), [1] write_readio() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_solids() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_start() (pytoughreact.writers.bio_writing.T2Bio method), [1] write_surface_adsorption() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_surface_complexes() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] write_title() (pytoughreact.writers.chemical_writing.T2Chemical method), [1] (pytoughreact.writers.solute_writing.T2Solute method), [1] write_to_file() (pytoughreact.utilities.t2_tough_react_utilities.T2UtilitiesToughReact method) write_tolerance() (pytoughreact.writers.solute_writing.T2Solute method), [1] write_weight_diffu() (pytoughreact.writers.solute_writing.T2Solute method), [1]