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CHEMISTRY

Specifies geochemistry details for multicomponent transport.

Required Cards:

PRIMARY_SPECIES

List of primary aqueous or basis species for which concentrations will be solved.

Optional Cards:

Basic Settings

ACTIVE_GAS_SPECIES

List of gas species where the gas phase mass is included in the mass conservation equations.

ACTIVITY_COEFFICIENTS <algorithm string> <frequency string>

Specifies algorithms for calculating activity coefficients. (default = LAG TIMESTEP)

  • Algorithm:

  • OFF:

    Disables the calculation of activity coefficients. All activity coefficients are assume to be 1.

  • LAG:

    The update of activity coefficients is lagged by a TIMESTEP or NEWTON_ITERATION.

  • NEWTON

    Ionic strength and activity coefficient calculation iterates to convergence. Computationally expensive.

  • Update Frequency:

  • TIMESTEP

    Update after every time step

  • NEWTON_ITERATION

    Update after every Newton iteration

ACTIVITY_H2O, ACTIVITY_WATER

Calculate activity of water. (default = False)

AQUEOUS_DIFFUSION_COEFFICIENTS

List of primary species and diffusion coefficients for which the default aqueous diffusion coefficient will be overwritten. Species-dependent diffusion is not supported for simulations with aqueous complexation. (default units [m2/s])

CALCULATE_INITIAL_POROSITY

Calculate the initial porosity as the sum of the initial mineral volume fractions.

DATABASE <string>

Path/filename for reaction database. For descriptions of the database format, see the brief Geochemical Database, or Thermodynamic Database, a more indepth description from the theory guide.

DECOUPLED_EQUILIBRIUM_REACTIONS

List of equilibrium reaction species from the database to be decoupled, likely so that the associated primary and secondary species in the database can be used in kinetic reactions.

GAS_DIFFUSION_COEFFICIENTS

List of gas species and diffusion coefficients for which the default gas diffusion coefficient will be overwritten. (default units [m2/s])

GENERAL_REACTION

Parameters for general forward/reverse kinetic reactions.

IMMOBILE_DECAY_REACTION

Parameters for decay of immobile species (e.g. biomass).

IMMOBILE_SPECIES

List of immobile species that are included as primary dependent variables (e.g. biomass, NAPL, customization in the reaction sandbox).

LOG_FORMULATION

Flag for solving Newton-Raphson equations with derivatives computed with respect to the logarithm (base 10) of the concentrations. Should not be used for linear equations (e.g. conservative tracers).

MAX_DLNC <float>

Specifies maximum change in log concentration for a Newton Raphson iteration. Changes in concentration larger than this value will be truncated to this value. (default = 5)

MAX_RELATIVE_CHANGE_TOLERANCE <float>

Specifies the maximum relative change in free ion concentration allowed for convergence (i.e. ||(c^k+1-c^k)/c^k||_inf). (default = 1.e-12)

MAX_RESIDUAL_TOLERANCE <float>

Specified the maximum residual allowed for a primary species for convergence (i.e. ||f(c^k+1)||_inf). (default = 1.e-12)

MICROBIAL_REACTION

Parameters for microbially-mediated reactions.

MINERAL_KINETICS

Parameters for kinetic mineral precipitation/dissolution reactions.

MINERALS

List of minerals.

MINIMUM_POROSITY <float>

Float specifies minimum porosity to which porosity is truncated if below that value. (default = 0)

MOLAL, MOLALITY

Print concentrations as molalities instead of molarities.

NO_BDOT

Use Debye-Huckel formulation without B-dot.

NO_CHECKPOINT_ACT_COEFS

Disables checkpointing of activity coefficients. Since activity coefficients are a function of the solution ionic strength from the previous time step, the original and restarted solutions will not match identically if such checkpointing is disabled.

NO_RESTART_MINERAL_VOL_FRAC

Disables the reading of mineral volume fractions on restart. Mineral volume fractions specified in the input file will be used instead.

OUTPUT (CHEMISTRY)

Specifies parameters for output.

OVERRIDE_MINERAL_MASS_ACTION

Specifies reaction expressions and log Ks that will override what is defined in the database.

PASSIVE_GAS_SPECIES

List of gas species used as reference species (e.g. reaction database, transport constraints, basis swapping, etc.).

RADIOACTIVE_DECAY_REACTION

Parameters for kinetic radioactive decay reactions.

REACTION_SANDBOX

Reaction sandbox for custom, user-defined reactions.

SECONDARY_SPECIES

List of secondary aqueous species or complexes.

SORPTION

Sorption reactions.

TRUNCATE_CONCENTRATION <float>

Specify a minimum concentration below which free-ion concentration may not fall. (Due to the molality/molarity conversion, the concentration may fall slightly below the prescribed value when the water density is less than 1000 kg/m3)

UPDATE_MINERAL_SURFACE_AREA

Update mineral surface area after every time step. See Changes in Material Properties in the Theory Guide.

UPDATE_MNRL_SURF_AREA_WITH_POR

Update mineral surface area as a function of porosity after every time step. See Eq. (34). See Changes in Material Properties in the Theory Guide.

UPDATE_PERMEABILITY

Update permeabilty after every time step. See Changes in Material Properties in the Theory Guide.

UPDATE_POROSITY

Update porosity after every time step. The default minimum porosity is 0, and one can make minimum porosity non-zero using MINIMUM_POROSITY. The initial porosity is calculated as a function of initial mineral volume fractions. See Changes in Material Properties in the Theory Guide.

UPDATE_TORTUOSITY

Update tortuosity after every time step. See Changes in Material Properties in the Theory Guide.

USE_FULL_GEOCHEMISTRY

Forces full geochemistry calculation even if only tracers are specified.

Expert Settings

GEOTHERMAL_HPT

Turns on the geothermal high pressure-temperature capability.

NO_CHECK_UPDATE

Disables (pre)check on solution update.

Examples

CHEMISTRY
  PRIMARY_SPECIES
    H+
    HCO3-
    Ca++
  /
  SECONDARY_SPECIES
    OH-
    CO3--
    CO2(aq)
    CaOH+
    CaHCO3+
    CaCO3(aq)
  /
  MINERALS
    Calcite
  /
  MINERAL_KINETICS
    Calcite
      RATE_CONSTANT 1.d-13
    /
  /
  DATABASE ./calcite.dat
  LOG_FORMULATION
  ACTIVITY_COEFFICIENTS TIMESTEP
END

CHEMISTRY
  PRIMARY_SPECIES
    H+
    Ca++
    Cu++
    Mg++
    UO2++
    K+
    Na+
    HCO3-
    Cl-
    F-
    HPO4--
    NO3-
    SO4--
    Tracer
    Tracer2
  /
  SECONDARY_SPECIES
    OH-
    CO3--
    CO2(aq)
    CaCO3(aq)
    CaHCO3+
    CaSO4(aq)
    CaCl+
    CaCl2(aq)
    CaF+
    CaH2PO4+
    CaHPO4(aq)
    CaNO3+
    CaPO4-
    MgCO3(aq)
    MgHCO3+
    MgSO4(aq)
    MgCl+
    MgF+
    UO2(H2PO4)(H3PO4)+
    UO2(H2PO4)2(aq)
    UO2HPO4(aq)
    UO2H2PO4+
    UO2H3PO4++
    UO2PO4-
  /
  GAS_SPECIES
    CO2(g)
  /
  MINERALS
    Calcite
    Magnesite
    Dolomite
    Dolomite-dis
    Dolomite-ord
    Brucite
    Nesquehonite
    Gypsum
    Schoepite
    UO2CO3
    UO2(PO3)2
    (UO2)3(PO4)2
    (UO2)3(PO4)2.4H2O
    CaUO4
    UO2SO4
    UOF4
    UO3.2H2O
    UO3.0.9H2O(alpha)
    Saleeite
    Sylvite
    Metatorbernite
    Whitlockite
    Chalcanthite
    Brochantite
    Tenorite
    Malachite
    Fluorapatite
    Fluorite
    Hydroxylapatite
    Torbernite
  /
:
  MINERAL_KINETICS
    Calcite
      RATE_CONSTANT 1.e-12 mol/cm^2-sec
    /
    Metatorbernite
      RATE_CONSTANT 2.e-17 mol/cm^2-sec
    /
  /
  SORPTION
    JUMPSTART_KINETIC_SORPTION
    SURFACE_COMPLEXATION_RXN
      MINERAL Calcite
      SITE >SOH 15.264 ! 20 m^2/g, por = 0.25
      COMPLEXES
        >SOUO2OH
        >SOHUO2CO3
      /
    /
  /
  DATABASE ../../../hanford.dat
  LOG_FORMULATION
  MAX_RELATIVE_CHANGE_TOLERANCE 1.d-10
  ACTIVITY_COEFFICIENTS NEWTON_ITERATION
  OUTPUT
    UO2++
    Tracer
  /
END