Index

A

add_charge_flag_to_species_in_solution() (in module mf6rtm.utils.utils)

add_m0_to_config() (mf6rtm.io.externalio.Regenerator method) add_new_configuration() (mf6rtm.config.config.MF6RTMConfig method)

B

Block (class in mf6rtm.mup3d.base)

C

cells (mf6rtm.mup3d.base.ChemStress attribute) charge_offset (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) check_config_file() (in module mf6rtm.simulation.solver) check_nam_files() (in module mf6rtm.simulation.solver) check_phreeqcrm_status() (in module mf6rtm.utils.utils) ChemStress (class in mf6rtm.mup3d.base)

components (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) concentration_l_to_m3() (in module mf6rtm.utils.utils) concentration_m3_to_l() (in module mf6rtm.utils.utils) concentration_to_massrate() (in module mf6rtm.utils.utils) concentration_volbulk_to_volwater() (in module mf6rtm.utils.utils) ConfigSchema (class in mf6rtm.config.config)

D

data (mf6rtm.mup3d.base.Block attribute)

database (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

E

eq_solutions (mf6rtm.mup3d.base.Block attribute) equilibrium_phases (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

EquilibriumPhases (class in mf6rtm.mup3d.base) exchange_phases (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) ExchangePhases (class in mf6rtm.mup3d.base)

F

feat_var (mf6rtm.Mf6RTM.selected_output attribute) (mf6rtm.simulation.Mf6RTM.selected_output attribute) (mf6rtm.simulation.solver.Mf6RTM.selected_output attribute) fill_missing_minerals() (in module mf6rtm.utils.utils) fixed_components (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

flatten_list() (in module mf6rtm.utils.utils) from_dict() (mf6rtm.config.config.MF6RTMConfig class method) from_mf6() (mf6rtm.mup3d.base.Mup3d class method) (mf6rtm.mup3d.Mup3d class method) from_toml_file() (mf6rtm.config.config.MF6RTMConfig class method)

G

GasPhase (class in mf6rtm.mup3d.base) generate_equ_phases_block() (in module mf6rtm.utils.utils) generate_equilibrium_phases_blocks() (mf6rtm.io.externalio.Regenerator method) generate_exchange_block() (in module mf6rtm.utils.utils) generate_exchange_phases_blocks() (mf6rtm.io.externalio.Regenerator method) generate_kinetic_phases_blocks() (mf6rtm.io.externalio.Regenerator method) generate_kinetics_block() (in module mf6rtm.utils.utils) generate_new_script() (mf6rtm.io.externalio.Regenerator method) generate_phreeqc_script() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) generate_solution_block() (in module mf6rtm.utils.utils) generate_surface_block() (in module mf6rtm.utils.utils) get_componenth2o() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) get_compound_names() (in module mf6rtm.utils.utils) get_conc_change_mask() (in module mf6rtm.simulation.solver) get_config() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) get_grid_to_map() (mf6rtm.PhreeqcBMI method) (mf6rtm.simulation.PhreeqcBMI method) (mf6rtm.simulation.phreeqcbmi.PhreeqcBMI method)

get_inactive_idx() (in module mf6rtm.simulation.solver) get_indices() (in module mf6rtm.utils.utils) get_less_than_zero_idx() (in module mf6rtm.simulation.solver) get_names() (mf6rtm.mup3d.base.Block method) get_saturation_from_mf6() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) get_time_units_from_mf6() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) get_tsteps_for_period() (mf6rtm.config.config.MF6RTMConfig method) grid_dimensions() (in module mf6rtm.simulation.discretization) grid_shape (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) grid_type (mf6rtm.Mf6API property) (mf6rtm.simulation.Mf6API property) (mf6rtm.simulation.mf6api.Mf6API property) group (mf6rtm.config.config.ConfigSchema attribute)

H

handle_block() (in module mf6rtm.utils.utils)

I

ic (mf6rtm.mup3d.base.Block attribute), [1] init_conc_array_phreeqc (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) init_temp (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) initialize() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method)

initialize_chem_stress() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) initialize_interfaces() (in module mf6rtm.simulation.solver) is_reaction_tstep() (mf6rtm.config.config.MF6RTMConfig method) is_reactive_tstep() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method)

K

kinetic_phases (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

KineticPhases (class in mf6rtm.mup3d.base)

L

load_mup3d() (mf6rtm.mup3d.base.Mup3d class method) (mf6rtm.mup3d.Mup3d class method)

load_yaml_to_phreeqcrm() (in module mf6rtm.config.yaml_reader) longest_common_substring() (in module mf6rtm.simulation.solver)

M

map_species_property_to_grid() (in module mf6rtm.utils.utils) Mf6API (class in mf6rtm) (class in mf6rtm.simulation) (class in mf6rtm.simulation.mf6api) mf6rtm module Mf6RTM (class in mf6rtm) (class in mf6rtm.simulation) (class in mf6rtm.simulation.solver) mf6rtm.assets module mf6rtm.config.config module mf6rtm.config.yaml_reader module mf6rtm.io module mf6rtm.io.externalio module mf6rtm.mup3d module mf6rtm.mup3d.base module mf6rtm.simulation module mf6rtm.simulation.discretization module mf6rtm.simulation.mf6api module mf6rtm.simulation.phreeqcbmi module

mf6rtm.simulation.solver module mf6rtm.utils module mf6rtm.utils.utils module MF6RTMConfig (class in mf6rtm.config.config) ml_output (mf6rtm.Mf6RTM attribute) (mf6rtm.simulation.Mf6RTM attribute) (mf6rtm.simulation.solver.Mf6RTM attribute) module mf6rtm mf6rtm.assets mf6rtm.config.config mf6rtm.config.yaml_reader mf6rtm.io mf6rtm.io.externalio mf6rtm.mup3d mf6rtm.mup3d.base mf6rtm.simulation mf6rtm.simulation.discretization mf6rtm.simulation.mf6api mf6rtm.simulation.phreeqcbmi mf6rtm.simulation.solver mf6rtm.utils mf6rtm.utils.utils mrbeaker() (in module mf6rtm.simulation.solver) mrbeaker_path() (in module mf6rtm.assets) Mup3d (class in mf6rtm.mup3d) (class in mf6rtm.mup3d.base)

N

name (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) names (mf6rtm.mup3d.base.Block attribute) ncol (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

nlay (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) nrow (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) nxyz (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

O

options (mf6rtm.mup3d.base.Block attribute)

P

packnme (mf6rtm.mup3d.base.ChemStress attribute) parameters (mf6rtm.mup3d.base.EquilibriumPhases attribute) (mf6rtm.mup3d.base.ExchangePhases attribute) (mf6rtm.mup3d.base.GasPhase attribute) (mf6rtm.mup3d.base.KineticPhases attribute) (mf6rtm.mup3d.base.Solutions attribute) (mf6rtm.mup3d.base.Surfaces attribute) parse_equilibriums_dataframe() (in module mf6rtm.utils.utils) parse_kinetics_dataframe() (in module mf6rtm.utils.utils) phinp (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

phreeqc_rm (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) PhreeqcBMI (class in mf6rtm) (class in mf6rtm.simulation) (class in mf6rtm.simulation.phreeqcbmi) postfix (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) prep_bins() (in module mf6rtm.utils.utils) prep_to_run() (in module mf6rtm.simulation.solver) print_warning_user_active() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method)

R

reaction_timing (mf6rtm.config.config.MF6RTMConfig attribute) read_external_files() (mf6rtm.io.externalio.Regenerator method) read_phinp() (mf6rtm.io.externalio.Regenerator method) rearrange_copy_blocks() (in module mf6rtm.utils.utils) regenerate_from_external_files() (mf6rtm.io.externalio.Regenerator class method)

Regenerator (class in mf6rtm.io.externalio) run() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) run_cmd() (in module mf6rtm) (in module mf6rtm.simulation) (in module mf6rtm.simulation.solver)

S

save_config() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) save_mup3d() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) save_to_file() (mf6rtm.config.config.MF6RTMConfig method) sconc (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) SelectedOutput (class in mf6rtm.io.externalio) set_cells() (mf6rtm.mup3d.base.ChemStress method) set_charge_offset() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_chem_stress() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_componenth2o() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_config() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_database() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_diffusion_coeff() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_emulator_output_add_variables() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) set_emulator_training() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) set_equilibrate_solutions() (mf6rtm.mup3d.base.Block method) set_equilibrium_phases() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_exchange_phases() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_fixed_components() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_ic() (mf6rtm.mup3d.base.Block method) set_initial_temp() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_kiter() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method)

set_min_concentration() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) set_nthread_yaml() (in module mf6rtm.simulation.solver) set_options() (mf6rtm.mup3d.base.Block method) set_parameters() (mf6rtm.mup3d.base.KineticPhases method) set_phases() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_postfix() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_reaction_temp() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) set_scalar() (mf6rtm.PhreeqcBMI method) (mf6rtm.simulation.PhreeqcBMI method) (mf6rtm.simulation.phreeqcbmi.PhreeqcBMI method) set_spd() (mf6rtm.mup3d.base.ChemStress method) set_time_conversion() (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) set_type() (mf6rtm.mup3d.base.ChemStress method) set_wd() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) sol_spd (mf6rtm.mup3d.base.ChemStress attribute) solution_csv_to_dict() (in module mf6rtm.utils.utils) solution_df_to_dict() (in module mf6rtm.utils.utils) Solutions (class in mf6rtm.mup3d.base) solutions (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) solve() (in module mf6rtm) (in module mf6rtm.simulation) (in module mf6rtm.simulation.solver) (mf6rtm.Mf6RTM method) (mf6rtm.simulation.Mf6RTM method) (mf6rtm.simulation.solver.Mf6RTM method) Surfaces (class in mf6rtm.mup3d.base) surfaces_csv_to_dict() (in module mf6rtm.utils.utils) surfaces_phases (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute)

T

target_var (mf6rtm.Mf6RTM.selected_output attribute) (mf6rtm.simulation.Mf6RTM.selected_output attribute) (mf6rtm.simulation.solver.Mf6RTM.selected_output attribute) to_dict() (mf6rtm.config.config.MF6RTMConfig method)

toml_name (mf6rtm.config.config.ConfigSchema attribute) total_cells_in_grid() (in module mf6rtm.simulation.discretization) tsteps (mf6rtm.config.config.MF6RTMConfig attribute) type (mf6rtm.mup3d.base.ChemStress attribute)

U

update_yaml() (mf6rtm.io.externalio.Regenerator method)

V

validate_external_files() (mf6rtm.io.externalio.Regenerator method)

W

wd (mf6rtm.mup3d.base.Mup3d attribute) (mf6rtm.mup3d.Mup3d attribute) working_dir() (in module mf6rtm.mup3d.base) write_external_files_layered() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method)

write_internal_parameters() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method) write_ml_arrays() (mf6rtm.io.externalio.SelectedOutput method) write_new_script() (mf6rtm.io.externalio.Regenerator method) write_simulation() (mf6rtm.mup3d.base.Mup3d method) (mf6rtm.mup3d.Mup3d method)