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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:

SECONDARY_SPECIES
List of secondary aqueous species or complexes.
RADIOACTIVE_DECAY_REACTION
Parameters for kinetic radioactive decay reactions.
GENERAL_REACTION
Parameters for general forward/reverse kinetic reactions.
IMMOBILE_DECAY_REACTION
Parameters for decay of immobile species (e.g. biomass).
MICROBIAL_REACTION
Parameters for microbially-mediated reactions.
MINERALS
List of minerals.
MINERAL_KINETICS
Parameters for kinetic mineral precipitation/dissolution reactions.
SORPTION
Sorption reactions.
REACTION_SANDBOX
Reaction sandbox for custom, user-defined reactions.
DATABASE <string>
Path/filename for reaction database. Description of Geochemical Database.
LOG_FORMULATION
Flag for solving Newton-Raphson equations with derivatives computed with respect to the logarithm (base 10) of the concentrations.
ACTIVITY_COEFFICIENTS <string> <string>

Specifies algorithms for calculating activity coefficients

  • Algorithms:
  • LAG:

    Single pass update to activity coefficients

  • NEWTON

    Iterative Newton-based updated (iterates until convergence tolerance is satisfied)

  • Update Frequency:
  • TIMESTEP

    Update after every time step

  • NEWTON_ITERATION

    Update after every newton iteration

NO_CHECKPOINT_ACT_COEFS
Do not store activity coefficients when checkpointing simulations.
NO_BDOT
Do not use bdot form of activity coefficient equation.
UPDATE_POROSITY <optional float>
Update porosity after every time step. Optional float specifies minimum porosity to which porosity is truncated if below that value (default = 0.).
UPDATE_PERMEABILITY
Update permeabilty after every time step.
UPDATE_TORTUOSITY
Update tortuosity after every time step.
UPDATE_MINERAL_SURFACE_AREA
Update mineral surface area after every time step.
MOLAL, MOLALITY
Print concentrations as molalities.
ACTIVITY_H2O, ACTIVITY_WATER
Calculate activity of water.
(CHEMISTRY) OUTPUT
Specifies parameters for output.
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.
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)
USE_FULL_GEOCHEMISTRY
Forces full geochemistry calculation even if only tracers are specified.

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