Chemical Class

Biodegradation Processes

class pytoughreact.chemical.bio_process_description.BIODG(imonod, bfac, sw1, sw2, wea, wsub, processes, biomass, icflag=0)

Process specification

__init__(imonod, bfac, sw1, sw2, wea, wsub, processes, biomass, icflag=0)

Initialization of Parameters

Parameters:

• imonod (int) – Selects between multiplicative and minimum Monod model for the substrate degradation rate equation

• bfac (float) – Reduction factor criterion for local Newton-Raphson iteration in BIOREACT subroutine to reduce substrate residual

• sw1 (float) – Lower limit of aqueous phase saturation considered in the saturation inhibition function (if =0, the default value is 0.02)

• sw2 (float) – Upper limit of aqueous phase saturation considered in the saturation inhibition function (SW1 < SW2 ≤ 1)

• wea (float) – Weighting factor for the linear interpolation of electron acceptor and nutrients concentrations to be used in the substrate degradation rate equation (0 < WEA ≤ 1). Default value is WEA = 0.5. WEA = 1 corresponds to using the concentration evaluated at the end of the time step

• wsub (float) – weighting factor for the linear interpolation of substrate concentration to be used in the substrate degradation rate equation (0 < WSUB ≤ 1). Default value is WSUB = 0.5. WSUB=1 corresponds to using the concentration evaluated at the end of the time step

• processes (Process) – List of Processes making use of this biodegradation configuration

• biomass (Biomass) – Biomass class list with all properties of the biomass

• icflag (int) – Selects how to consider the competitive and Haldane inhibition terms in the Monod model

__weakref__

list of weak references to the object (if defined)

get_base_parameter_and_index(process)

Function that retrieves base parameter and index

Parameters:

process (bio.Process) – the particular process of investigation

Returns:

index – Index and Base Parameter

Return type:

int

get_first_set()

Function that gets the first line of information

Returns:

bio_numerical_parameters – List of numerical parameters for biodegradation

Return type:

list

get_number_of_biomasses()

Function that gets the number of biomasses

Returns:

biomass_number – Number of biomasses

Return type:

int

class pytoughreact.chemical.bio_process_description.Process(biomass, number_of_components, mumax, yield_mass, enthalpy, total_component=0, number_of_haldane=0, number_of_non_competiting=0, number_competiting=0, component_params=None, gas_params=None, water_params=None)

Process specification

__init__(biomass, number_of_components, mumax, yield_mass, enthalpy, total_component=0, number_of_haldane=0, number_of_non_competiting=0, number_competiting=0, component_params=None, gas_params=None, water_params=None)

Initialization of Parameters

Parameters:

• biomass (Biomass) – Biomass class with all properties of the biomass

• number_of_components (int) – Number of mass components responsible for competitive inhibition in process

• mumax (float) – Maximum specific substrate degradation rate

• yield_max (float) – Yield coefficient for the growth of biomass due to the degradation of unit mass of substrate in process IP (kg biomass / kg substrate)

• enthalpy (float) – Heat of reaction for the degradation of substrate in process (J/kg substrate)

• total_component (int) – Number of mass components controlling the substrate degradation rate in process

• number_of_haldane (int) – Number of mass components responsible for Haldane inhibition in process

• number_of_non_competiting (int) – Number of mass components responsible for non-competitive inhibition in process

• component_params (list) – List of chemical components involved in the process

• water_params (list) – List of water components involved in the process

• gas_params (list) – List of gas components involved in the process

__weakref__

list of weak references to the object (if defined)

get_kc()

Function that retrieves competitive inhibition information

Returns:

output – list of competitive inhibition parameters

Return type:

list

get_kh()

Function that retrieves haldane inhibition information

Returns:

output – list of haldane inhibition parameters

Return type:

list

get_knc()

Function that retrieves non competitive inhibition information

Returns:

output – list of non competitive inhibition parameters

Return type:

list

get_ks()

Function that retrieves Ks information

Returns:

output – list of Ks parameters

Return type:

list

get_number_of_competiting()

Function that retrieves number of competiting specie

Returns:

num_of_competiting – Number of Competiting species

Return type:

int

get_uptake()

Function that retrieves uptake information

Returns:

output – list of uptake parameters

Return type:

list

Biomass Composition

class pytoughreact.chemical.biomass_composition.Biomass(index, name, init_conc, min_conc, max_temp, death_rate, inhibition_constant)

Biomass type

__init__(index, name, init_conc, min_conc, max_temp, death_rate, inhibition_constant)

Initialization of Parameters

Parameters:

• index (int) – Serial index of biomass

• name (string) – Name of biomass

• init_conc (float) – Initial concentration (valid for the entire simulation grid) in the aqueous phase of microbial population (kg biomass / kg aqueous phase)

• min_conc (float) – Minimum concentration in the aqueous phase of microbial population enforced during the simulation (kg biomass / kg aqueous phase)

• max_temp (float) – Maximum temperature for the calculation of temperature inhibition function in the substrate degradation rate equation (°C)

• death_rate (float) – Death rate constant, or maintenance constant, for the microbial population (s-1)

• inhibition_constant (float) – Inhibition constant for biomass growth of microbial population # IB (kg biomass kg aqueous phase).

class pytoughreact.chemical.biomass_composition.Gas(name, index)

Rock type

__init__(name, index)

Initialization of Parameters

Parameters:

• index (int) – Serial index of gas

• name (string) – Name of gas

add_to_process(process, uptake, ks=None, kc=None, knc=None, kh=None)

Add gas component to the process

Parameters:

• process (Process) – This should be a Process class with all properties of the process

• uptake (int) – uptake coefficient of gas component in particular process with respect to 1 mole of degraded primary substrate (mole component / mole substrate).

• ks (float) – Substrate degradation rate

• kc (float) – Competitive inhibition rate

• knc (float) – Non Competitive inhibition rate

• kh (float) – Haldane inhibition rate

Returns:

• output (dict) – Dictionary of all parameters

• process (Process) – Updated Process with new parameters

class pytoughreact.chemical.biomass_composition.BaseComponent(name=None, critical_temperature=None, critical_pressure=None, critical_compressibility=None, acentric_factor=None, dipole_moment=None, boiling_point=None, vapor_pressure_a=None, vapor_pressure_b=None, vapor_pressure_c=None, vapor_pressure_d=None, molecular_weight=None, heat_capacity_constant_a=None, heat_capacity_constant_b=None, heat_capacity_constant_c=None, heat_capacity_constant_d=None, liquid_density=None, reference_temp_for_density=None, reference_binary_diffusivity=None, reference_temperature_for_diffusivity=None, exponent_chemical_diffusivity=None, liquid_viscosity_constant_a=None, liquid_viscosity_constant_b=None, liquid_viscosity_constant_c=None, liquid_viscosity_constant_d=None, liquid_critical_volume=None, liquid_chemical_solubility_a=None, liquid_chemical_solubility_b=None, liquid_chemical_solubility_c=None, liquid_chemical_solubility_d=None, carbon_partition_coefficient=None, fractional_organic_carbon=None, decay_constant=None)

Rock type

__init__(name=None, critical_temperature=None, critical_pressure=None, critical_compressibility=None, acentric_factor=None, dipole_moment=None, boiling_point=None, vapor_pressure_a=None, vapor_pressure_b=None, vapor_pressure_c=None, vapor_pressure_d=None, molecular_weight=None, heat_capacity_constant_a=None, heat_capacity_constant_b=None, heat_capacity_constant_c=None, heat_capacity_constant_d=None, liquid_density=None, reference_temp_for_density=None, reference_binary_diffusivity=None, reference_temperature_for_diffusivity=None, exponent_chemical_diffusivity=None, liquid_viscosity_constant_a=None, liquid_viscosity_constant_b=None, liquid_viscosity_constant_c=None, liquid_viscosity_constant_d=None, liquid_critical_volume=None, liquid_chemical_solubility_a=None, liquid_chemical_solubility_b=None, liquid_chemical_solubility_c=None, liquid_chemical_solubility_d=None, carbon_partition_coefficient=None, fractional_organic_carbon=None, decay_constant=None)

Initialization of Parameters

Parameters:

• name (string) – Name of component

• critical_temperature (float) – Chemical critical temperature, K

• critical_pressure (float) – Chemical critical pressure, bar (1 bar = 105 Pa)

• critical_compressibility (float) – Chemical critical compressibility

• acentric_factor (float) – Pitzer’s acentric factor for the chemical.

• dipole_moment (float) – Chemical dipole moment, debyes.

• boiling_point (float) – Chemical normal boiling point, K.

• vapor_pressure_a (float) – Chemical vapor pressure constant from Reid et al. (1987)

• vapor_pressure_b (float) – Chemical vapor pressure constant from Reid et al. (1987)

• vapor_pressure_c (float) – Chemical vapor pressure constant from Reid et al. (1987)

• vapor_pressure_d (float) – Chemical vapor pressure constant from Reid et al. (1987)

• molecular_weight (float) – Chemical molecular weight, g/mole.

• heat_capacity_constant_a (float) – Chemical ideal gas heat capacity constant from Reid et al. (1987).

• heat_capacity_constant_b (float) – Chemical ideal gas heat capacity constant from Reid et al. (1987).

• heat_capacity_constant_c (float) – Chemical ideal gas heat capacity constant from Reid et al. (1987).

• heat_capacity_constant_d (float) – Chemical ideal gas heat capacity constant from Reid et al. (1987).

• liquid_density (float) – Reference NAPL (liquid) density, kg/m3.

• reference_temp_for_density (float) – Reference temperature for NAPL density, K.

• reference_binary_diffusivity (float) – Reference binary diffusivity of VOC in air, m2/s.

• reference_temperature_for_diffusivity (float) – Reference temperature for gas diffusivity, K..

• exponent_chemical_diffusivity (float) – Exponent for calculation of chemical diffusivity.

• liquid_viscosity_constant_a (float) – Liquid NAPL viscosity constant from Reid et al. (1987).

• liquid_viscosity_constant_b (float) – Liquid NAPL viscosity constant from Reid et al. (1987).

• liquid_viscosity_constant_c (float) – Liquid NAPL viscosity constant from Reid et al. (1987).

• liquid_viscosity_constant_d (float) – Liquid NAPL viscosity constant from Reid et al. (1987).

• liquid_critical_volume (float) – Chemical critical volume, cm3/mole.

• liquid_chemical_solubility_a (float) – Constant for chemical solubility in water, mole fraction.

• liquid_chemical_solubility_b (float) – Constant for chemical solubility in water, mole fraction/K.

• liquid_chemical_solubility_c (float) – Constant for chemical solubility in water, mole fraction/K2.

• liquid_chemical_solubility_d (float) – Constant for chemical solubility in water, mole fraction/K3.

• carbon_partition_coefficient (float) – chemical organic carbon partition coefficient Koc, m3/kg.

• fractional_organic_carbon (float) – Default value for fraction of organic carbon in soil.

• decay_constant (float) – decay constant for biodegradation of VOC, s-1.

add_to_process(process, uptake, ks=None, kc=None, knc=None, kh=None)

Add bio component to the process

Parameters:

• process (Process) – This should be a Process class with all properties of the process

• uptake (int) – uptake coefficient of bio component in particular process with respect to 1 mole of degraded primary substrate (mole component / mole substrate).

• ks (float) – Substrate degradation rate

• kc (float) – Competitive inhibition rate

• knc (float) – Non Competitive inhibition rate

• kh (float) – Haldane inhibition rate

Returns:

• output (dict) – Dictionary of all parameters

• process (Process) – Updated Process with new parameters

default_benzene()

Function that provides default parameters for Benzene component (can be modified)

Returns:

benzene – List of default parameters for benzene for biodegradation

Return type:

BaseComponent

default_n_decane()

Function that provides default parameters for Decane component (can be modified)

Returns:

decane – List of default parameters for decane for biodegradation

Return type:

BaseComponent

default_n_pentane()

Function that provides default parameters for N Pentane component (can be modified)

Returns:

component – List of default parameters for N Pentane for biodegradation

Return type:

BaseComponent

default_n_propyl_benzene()

Function that provides default parameters for N Propyl Benzene component (can be modified)

Returns:

component – List of default parameters for N Propyl Benzene for biodegradation

Return type:

BaseComponent

default_p_xylene()

Function that provides default parameters for P-Xylene component (can be modified)

Returns:

component – List of default parameters for p-xylene for biodegradation

Return type:

BaseComponent

default_toluene()

Function that provides default parameters for Toluene component (can be modified)

Returns:

toluene – List of default parameters for Toluene for biodegradation

Return type:

BaseComponent

get_fifth_set()

Function that gets the fifth line of information in INFILE Component Section

Returns:

parameters – List of parameters (Liquid Viscosity) for biodegradation

Return type:

list

get_first_set()

Function that gets the first line of information in INFILE Component Section

Returns:

parameters – List of parameters (Critical Temperature, Critical Pressure, Acentric Factor, Dipole Moment) for biodegradation

Return type:

list

get_fourth_set()

Function that gets the fourth line of information in INFILE Component Section

Returns:

parameters – List of parameters (Liquid density, Reference Temperature for density, Diffusion) for biodegradation

Return type:

list

get_second_set()

Function that gets the second line of information in INFILE Component Section

Returns:

parameters – List of parameters (Boiling Point, Vapor Pressure) for biodegradation

Return type:

list

get_seventh_set()

Function that gets the seventh line of information in INFILE Component Section

Returns:

parameters – List of parameters (carbon Coefficient, Decay Constant) for biodegradation

Return type:

list

get_sixth_set()

Function that gets the sixth line of information in INFILE Component Section

Returns:

parameters – List of parameters (Liquid Chemical Solubility) for biodegradation

Return type:

list

get_third_set()

Function that gets the third line of information in INFILE Component Section

Returns:

parameters – List of parameters (Molecular Weight, heat Capacity Constant) for biodegradation

Return type:

list

class pytoughreact.chemical.biomass_composition.Component(index)

__init__(index)

Initialization of Parameters

Parameters:

index (int) – Serial index of component

class pytoughreact.chemical.biomass_composition.Solids(name, molecular_weight, carbon_partition_coefficient, decay_constant)

__init__(name, molecular_weight, carbon_partition_coefficient, decay_constant)

Initialization of Parameters

Parameters:

• name (string) – Name of dissolved solid

• molecular_weight (float) – Dissolved solid molecular weight, g/mole

• carbon_partition_coefficient (float) – Dissolved solid organic carbon partition coefficient KOC, m3/kg

• decay_constant (float) – decay constant for dissolved solid, s-1.

get_first_set()

Function that gets the first line of information in INFILE Solids Section

Returns:

parameters – List of parameters (Name, Molecular Weight, Decay Constant, Carbon Coefficient) for biodegradation

Return type:

list

Chemical Composition

class pytoughreact.chemical.chemical_composition.Water(primary_species, temperature, pressure)

__init__(primary_species, temperature, pressure)

Initialization of Parameters (Water composition)

Parameters:

• primary_species (PrimarySpecies) – Primary specie present in the water composition

• temperature (float) – Temperature of the solution (°C). Note that this temperature is used only for initial speciation calculations for this water, before the water composition is assigned to different grid block

• pressure (float) – Pressure of the solution (bar). This value can be omitted, in which case PT is assumed 1 bar

class pytoughreact.chemical.chemical_composition.ReactGas(name, fugacity_flag, partial_pressure)

__init__(name, fugacity_flag, partial_pressure)

Initialization of Parameters (React Gas)

Parameters:

• name (string) – Name of the gaseous species present in the system

• partial_pressure (float) – Initial partial pressure of the gaseous species (in bars)

• fugacity_flag (int) – Flag depicting if fugacity is enabled or not

class pytoughreact.chemical.chemical_composition.WaterComp(primary_species, icon, nrguess, ctot, nameq='*', qksat=0.0, naads_min=None, sdens=None, imod=None, capac=None)

__init__(primary_species, icon, nrguess, ctot, nameq='*', qksat=0.0, naads_min=None, sdens=None, imod=None, capac=None)

Initialization of Parameters (Water composition)

Parameters:

• primary_species (PrimarySpecies) – Primary specie present in the water composition

• icon (int) – Flag indicating the type of constraint controlling the input concentration of the aqueous species 1: input values of CTOT represent total amounts (in moles) for aqueous species, and total kilogram s for liquid H2O 2: the total concentration of the species will be computed such that the saturation index of mineral or gas equals qksat at temperature and pressure TC2 and PT, respectively. 3: input values of ctot represent the known activity of the specific species (i.e., not total concentration) at temperature and pressure TC2 and PT, respectively. 4: the total concentration of the species is adjusted to yield charge balance. Use only with a charged species

• nrguess (float) – initial guess (trial) value for the concentration of the individual primary species (not total concentration), in moles/kg H2O (molal) for species other than H2O and in kg for H2O.

• ctot (float) – If icon=1, CTOT is total moles of aqueous species, and total amount (in kg) of liquid water for H2O

• nameq (string) – Name of mineral or gas (in quotes) to use with option ICON=2. Names must match exactly those previously listed as minerals or gases in the definition of the chemical system

• qksat (float) – desired value of mineral log(Q/K) or gas log(fugacity) when option icon=2 is used

• sdens (float) – Sorption site density in molsites/m2mineral for this surface species

• imod (int) – Adsorption model type 0 surface complexation without electrostatic terms 1 constant capacitance model 2 double diffuse layer model, linear 3 double diffuse layer model, Gouy-Chapman (most common)

• capac (float) – Capacitance in F m–2. Must be entered only if imod=1

class pytoughreact.chemical.chemical_composition.PrimarySpecies(name, notrans)

__init__(name, notrans)

Initialization of Parameters

Parameters:

• name (string) – Name of the primary species,

• notrans (int) – Flag for transport and surface complexation options; 0 species (component) will be transported, 1 no transport for this species (component)

get_name_trans()

Function that retrieves the name of primary species and flag for transport and surface complexation options

Returns:

parameter – List containing name of primary species and flag for transport and surface complexation options

Return type:

list

Chemical Kinetic Properties

class pytoughreact.chemical.kinetic_properties.Kinetic(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a=0, coef_b=0, coef_c=0)

__init__(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a=0, coef_b=0, coef_c=0)

Initialization of Parameters

Parameters:

• rate_constant (float) – Rate constant (in mol/m2/sec) at 25°C

• rate_ph (int) – Flag for rate constant dependence on pH

• exponent_n (float) – exponent eta in rate equation

• exponent_theta (float) – exponent theta in rate equation

• activation_energy (float) – Activation energy in kJ/mol

• coef_a (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desired

• coef_b (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

• coef_c (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

class pytoughreact.chemical.kinetic_properties.Dissolution(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a=0, coef_b=0, coef_c=0)

__init__(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a=0, coef_b=0, coef_c=0)

Initialization of Parameters

Parameters:

• rate_constant (float) – Rate constant (in mol/m2/sec) at 25°C

• rate_ph (int) – Flag for rate constant dependence on pH

• exponent_n (float) – exponent eta in rate equation

• exponent_theta (float) – exponent theta in rate equation

• activation_energy (float) – Activation energy in kJ/mol

• coef_a (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desired

• coef_b (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

• coef_c (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

class pytoughreact.chemical.kinetic_properties.Precipitation(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a, coef_b, coef_c, initial_volume_fraction, precipitation_law_index, log_qk_gap, temperature_gap_1, temperature_gap_2)

__init__(rate_constant, rate_ph, exponent_n, exponent_theta, activation_energy, coef_a, coef_b, coef_c, initial_volume_fraction, precipitation_law_index, log_qk_gap, temperature_gap_1, temperature_gap_2)

Initialization of Parameters

Parameters:

• rate_constant (float) – Rate constant (in mol/m2/sec) at 25°C

• rate_ph (int) – Flag for rate constant dependence on pH

• exponent_n (float) – exponent eta in rate equation

• exponent_theta (float) – exponent theta in rate equation

• activation_energy (float) – Activation energy in kJ/mol

• coef_a (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desired

• coef_b (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

• coef_c (float) – Coefficient that shows the rate constant dependence on temperature. Defaulted to zero unless a different form of rate constant dependence with temperature is desire

• initial_volume_fraction (float) – The initial volume fraction (Vmineral/Vsolid) to be assumed for calculating initial effective surface are a if the mineral is not present at the start of a simulation but precipitates as a new reaction product

• precipitation_law_index (int) – Precipitation law index (See user guide for more)

• log_qk_gap (float) – Log (Q/K) gap (supersaturation window). A zero value represents no gap (See user guide for more).

• temperature_gap_1 (float) – Temperature (in °C) at which to begin reducing gap

• temperature_gap_2 (float) – Temperature (in °C) endpoint at which the gap has diminished to nearly zero (1% of original value). The gap decreases exponentially from the first (temperature_gap_1) to the second (temperature_gap_2) temperature, and temperature_gap_2 must always be greater than temperature_gap_1

class pytoughreact.chemical.kinetic_properties.Equilibrium(log_qk, temperature_gap_1, temperature_gap_2)

__init__(log_qk, temperature_gap_1, temperature_gap_2)

Initialization of Parameters

Parameters:

• log_qk (float) – Log (Q/K) gap (supersaturation window). A zero value represents no gap (See user guide for more).

• temperature_gap_1 (float) – Temperature (in °C) at which to begin reducing gap

• temperature_gap_2 (float) – Temperature (in °C) endpoint at which the gap has diminished to nearly zero (1% of original value). The gap decreases exponentially from the first (tempGap1) to the second (tempGap2) temperature, and tempGap2 must always be greater than tempGap1

Chemical Mineral Composition

class pytoughreact.chemical.mineral_composition.MineralComp(mineral, init_volume_fraction, reaction_type, radius=None, reactive_surface_area=None, unit=None)

__init__(mineral, init_volume_fraction, reaction_type, radius=None, reactive_surface_area=None, unit=None)

Initialization of Parameters

Parameters:

• mineral (Mineral) – Mineral phase with all its properties,

• init_volume_fraction (float) – initial volume fraction of the mineral, excluding liquid (mineral volume divided by total volume of solids). The sum of VOL’s need not add up to 1. If the sum is less than 1, the remaining solid volume fraction is considered nonreactive.

• reaction_type (int) – Flag for the mineral type ; 0 for minerals at equilibrium, for minerals under kinetic constraints and 2 to suppress reaction for either kinetic and/or equilibrium minerals

• radius (float) – Radius of mineral grain (in m) used to calculate surface area

• reactive_surface_area (float) – Specific reactive surface area (See user guide for more)

• unit (int) – Flag to specify the units of input reactive_surface_area values. 0 for cm2mineral/gmineral, 1 for m2mineral/m3mineral, 2 for m2rock/m3medium (total), 3 for m2rock/m3medium (solids), 3 and radius=0, the input surface area will remain constant, 4 (constant rate is input in mol/sec; surface area is not used)

Chemical Mineral Description

class pytoughreact.chemical.mineral_description.Mineral(name, type_of_mineral, type_of_kinetic_constraint, index_solid_solution, dry_grid_block)

__init__(name, type_of_mineral, type_of_kinetic_constraint, index_solid_solution, dry_grid_block)

Initialization of Parameters

Parameters:

• name (string) – Name of the mineral phase,

• type_of_mineral (int) – Flag for the type of mineral: 0 for minerals at equilibrium, and 1 for those under kinetic constraints

• type_of_kinetic_constraint (int) – Flag for the type of kinetic constraint: 1 for dissolution only, 2 for precipitation only, and 3 for both (mineral can either precipitate or dissolve

• index_solid_solution (int) – Index for a solid solution mineral end member. All end members for a specified phase are given the same ISS value: ISS = 1 for each end member of the first solid solution, ISS = 2 for each end member of the second solid solution

• dry_grid_block (int) – Flag to indicate that the mineral may precipitate in a dry grid block as a result of complete evaporation (See user guide for more)

get_dissolution_parameters()

Function that gets Dissolution parameters

Returns:

parameters – List of parameters (rate constant, rate pH, activation energy) for dissolution

Return type:

list

get_equilibrium_data()

Function that gets Equilibrium parameters

Returns:

parameters – List of parameters for equilibrium

Return type:

list

get_first_row()

Function that gets the first line of information in Minerals Section

Returns:

parameters – List of parameters (name, Mineral Type, Dry Grid) for mineral reactions

Return type:

list

get_number_of_ph_dependence()

Function that gets number of pH dependencies

Returns:

parameter – number of pH dependencies

Return type:

int

get_ph_dependency_2(ph_dependency)

Function that gets pH Dependency parameters

Returns:

parameters – List of parameters (rate constant, activation Energy, number of Species) for pH Dependency

Return type:

list

get_precipitation_parameters()

Function that gets Precipitation parameters

Returns:

parameters – List of parameters (rate constant, rate pH, activation energy etc) for Precipitation

Return type:

list

get_precipitation_parameters_2()

Function that gets Precipitation parameters

Returns:

parameters – List of parameters () for Precipitation

Return type:

list

Chemical Mineral Zone

class pytoughreact.chemical.mineral_zone.MineralZone(minerals)

__init__(minerals)

Initialization of Parameters

Parameters:

minerals (list[MineralComp]) – List of all mineral compositions

Chemical Permeability Porosity Zone

class pytoughreact.chemical.perm_poro_zone.PermPoroZone(permporo)

__init__(permporo)

Initialization of Parameters (Permeability Porosity)

Parameters:

permporo (PermPoro) – List of permeability porosity equations

class pytoughreact.chemical.perm_poro_zone.PermPoro(law_type, a_param, b_param)

__init__(law_type, a_param, b_param)

Initialization of Parameters (Permeability Porosity)

Parameters:

• law_type (int) – Index for the permeability law. 0: no change in permeability. Can be used to turn off permeability changes in specific zones 1: simplified Carman-Kozeny (See user guide for more). The parameter values (a_param and b_param) are not used and may be set to 0.0 or any real number. 2: Modified Hagen-Poiseulle Model. Permeability calculated from pore throat diameter, number of throats per pore, and number of pores per area using the Hagen-Poiseulle equation. The parameters are: a_param - number of effective throats per pore (typically about 2 to 3). b_param - number of pores per m2 area 3: cubic law (See user guide for more). The parameter values a_param and b_param are not used and may be set to 0.0 or any real number. 4: modified Cubic Law (See user guide for more). The parameters are: a_param - fracture porosity / fracture-matrix area (analogous to fracture aperture) (m3/m2) and b_param - fracture spacing (m). 5: Verma-Pruess permeability-porosity relation (See user guide for more). The parameters are: a_param - the value of “critical” porosity at which permeability goes to zero and b_param - a power law exponent.

• a_param (float) – Parameter A based on the permeability law selected

• b_param (float) – Parameter B based on the permeability law selected