TOUGH4 User Manual
  • Quick Entry to Keywords for Data Input
  • 1️⃣INTRODUCTION
    • About TOUGH
    • TOUGH Development History
    • TOUGH4 Implementation
    • Scope and Methodology
  • 2️⃣WHAT IS NEW IN TOUGH4
  • 3️⃣CODE COMPILATION AND INSTALLATION
    • Setup for Compilation
    • Code Compilation
      • 1. Compilation of TOUGH4 using Visual Studio
      • 2. Compilation of TOUGH4 on Linux-like platform
    • Installation
    • Running the Executable for Simulations
  • 4️⃣GOVERNING EQUATIONS
    • Mass-Balance Equation
    • Accumulation Terms
    • Flux Terms
    • Sink and Source Terms
    • Virtual Node Well Treatment
    • Semi-Analytical Conductive Heat Exchange
    • Drift Model
    • Non-Darcy Flow
  • 5️⃣NUMERICAL METHOD
    • Space and Time Discretization
    • Interface Weighting Schemes
    • Initial and Boundary Conditions
      • Initial Conditions and Restarting
      • Neumann Boundary Conditions
      • Dirichlet Boundary Conditions
      • Atmospheric Boundary Conditions
      • Constant Temperature Boundary Conditions
    • Parallel computing schemes
    • Linear Solvers
    • Python Functions
      • Relative Permeability
      • Capillary Pressure
      • Initial Condition Calculation
      • Fetching Output Data
      • Fetching Thermophysical Property Data From NIST Webbook
      • Coupling With Third-Party Software
  • 6️⃣SOFTWARE ARCHITECTURE
    • Program Design
    • Data Structure
    • Linear Equation Setup
  • 7️⃣PROCESS MODELING
    • EOS1
    • EOS2
    • EOS3
    • EOS4
    • EOS6
    • EOS7
    • EOS9
    • ECO2
    • EWASG
    • TMVOC
    • Tracers/Decay Chain
    • Biodegradation Reaction
    • Wellbore Flow
    • Non-Darcy Flow
    • Enhanced Coal Bed Methane
  • 8️⃣PREPARATION OF MODEL INPUT
    • Input Formatting
    • Keywords and Input Data
      • TITLE
      • BIODG
      • CBMDA
      • CHEMP
      • COFT
      • CONNE
      • COUPL
      • DIFFU
      • ELEME
      • ENDCY
      • ENDFI
      • FLAC
      • FNIST
      • FOFT
      • FORCH
      • GASES
      • GENER
      • GOFT
      • HYSTE
      • INCON
      • INDOM
      • MESHM
      • MODDE
      • MOMOP
      • MULTI
      • OUTPU
      • PARAM
      • ROCKS
      • ROFT
      • RPCAP
      • SELEC
      • SOLVR
      • SPAVA
      • TIMBC
      • TIMES
      • TRACR
      • WELLB
    • Inputs for Initial Conditions
      • EOS1
      • EOS2
      • EOS3
      • EOS4
      • EOS6
      • EOS7
      • EOS9
      • ECO2
      • EWASG
      • TMVOC
    • Geometry Data
      • General Concepts
      • MESHMaker
      • Multiple-continuum processing
    • Inputs for MESHMaker
      • Generation of radially symmetric grids
        • RADII
        • EQUID
        • LOGAR
        • LAYER
      • Generation of rectilinear grids
      • MINC processing for fractured media
    • Adjustment of Computing Parameters at Run-time
  • 9️⃣OUTPUTS
  • 🔟VALIDATION AND APPLICATION EXAMPLES
    • EOS1
      • Problem 1 - Code Demonstration
      • Problem 2 - Heat Sweep in a Vertical Fracture (rvf)
      • Problem 3 - Five-spot Geothermal Production/Injection (rfp)
      • Problem 4 - Coupled Wellbore Flow (r1q)
      • Problem 5 - Five-Spot Geothermal Production/Injection under extremely high temperature
    • EOS2
      • Problem 1 -Five-spot Geothermal Production/Injection (rfp)
    • EOS3
      • Problem 1 - Code Demonstration (eos3p1)
      • Problem 2 - 1D TH Problem with Heating and Gas Source (by Guanlong Guo)
      • Problem 3 - Heat Pipe in Cylindrical Geometry (rhp)
      • Problem 4 - 3D Thermal Consolidation Test, Coupling with FLAC3D Simulator (by Guanlong Guo)
    • EOS4
      • Problem 1 - Code Demonstration （eos4p1)
      • Problem 2 - Heat Pipe in Cylindrical Geometry (rhp)
    • EOS6
      • Problem 1-Validation with EOS2
      • Problem 2-Noble Gas Transport
    • EOS7
      • Problem 1-Multiphase and Nonisothermal Processes in a System with Variable Salinity (rf1)
      • Problem 2-Thermal and Tracer Diffusion (EOS7R/rdif7)
      • Problem 3-Contamination of an Aquifer from VOC Vapors in the Vadose Zone (EOS7R/rdica)
      • Problem 4-Density, Viscosity, Solubility, and Enthalpy of Real Gas Mixtures (EOS7C/SAM7C1)
      • Problem 5-CO2 Injection into a Depleted Gas Reservoir (EOS7C2/SAM7C2)
      • Problem 6- CO2 Injection into a Saturated System (EOS7C/SAM7C3)
      • Problem 7-Density, Viscosity, and Enthalpy of Real Gas Mixtures (EOS7CA/SAM7CA1)
      • Problem 8-CO2 Injection into a Shallow Vadose Zone (EOS7CA/SAM7CA2)
      • Problem 9-Non-Isothermal Compressed Air Energy Storage in Reservoir (by Julien Mouli-Castillo)
    • EOS9
      • Page 1
    • ECO2
      • Problem 1-Demonstration of Initialization Options (ECO2N/rtab)
      • Problem 2-Radial Flow from a CO2 Injection Well (ECO2N/rcc3)
      • Problem 3-CO2 Discharge Along a Fault Zone (ECO2N/r1dv)
      • Problem 4-CO2 Injection into a 2-D Layered Brine Formation (ECO2N/rtp7)
      • Problem 5-Upflow of CO2 along a Deep Fault Zone (ECO2M/r1d)
      • Problem 6-Migration of a CO2 Plume in a Sloping Aquifer, Intersected by a Fault (ECO2M/rwaf)
      • Problem 7-GCS/GHE with a double-porosity reservoir (Case6_50kg_DP/ECO2NV2)
    • EWASG
      • Problem 1 - Brine Density Calculation (dnh)
      • Problem 2 - Production from a Geothermal Reservoir with Hypersaline Brine and CO2 (rhbc)
    • TMVOC
      • Problem 1-Initialization of Different Phase Conditions (r7c)
      • Problem 2-1-D Buckley-Leverett Flow (rblm)
      • Problem 3-Diffusion of components (rdif2)
      • Problem 4-Steam Displacement of a NAPL in a Laboratory Column (rtcem)
      • Problem 5-Steam Displacement of a Benzene-Toluene Mixture in a Laboratory Column (rbt)
      • Problem 6 -Air Displacement of a NAPL from a Laboratory Column (rad)
      • Problem 7-NAPL Spill in the Unsaturated Zone (r2dl)
    • T4.Well
      • Problem 1-Steady-state two-phase flow upward
      • Problem 2-Non-isothermal CO2 flow through a wellbore initially full of water
  • CONCLUSION REMARKS
  • REFERENCES
  • ACKNOWLEDGEMENT
  • Appendix
    • ☑️A: RELATIVE PERMEABILITY FUNCTIONS
      • IRP=1 Linear function
      • IRP=2 Power function
      • IRP=3 Corey's curves
      • IRP=4 Grant's curve
      • IRP=5 Perfectly mobile
      • IRP=6 Fatt and Klikoff function
      • IRP=7 van Genuchten-Mualem Model
      • IRP=8 Verma function
      • IRP=10 Modified Brooks-Corey Model
      • IRP=11 Modified van Genuchten Model
      • IRP=12 Regular hysteresis
      • IRP=13 Simple hysteresis
      • IRP=31 Three phase perfectly mobile
      • IRP=32 Modified Stone's first 3-phase method
      • IRP=33 Three-phase Parker's function
      • IRP=34 Alternative Stone 3-phase
      • IRP=35 Power-law function
      • IRP=36 Faust for two-phase Buckley-Leverett problem
      • IRP=37 Another alternative to Stone function
      • IRP=40 Table lookup
      • IRP=41 User-Defined relative permeability function
    • ☑️B: CAPILLARY PRESSURE FUNCTIONS
      • ICP=1 Linear function
      • ICP=2 Function of Pickens
      • ICP=3 TRUST capillary pressure
      • ICP=4 Milly’s function
      • ICP=6 Leverett’s function
      • ICP=7 van Genuchten function
      • ICP=8 No capillary pressure
      • ICP=10 Modified Brooks-Corey Model
      • ICP=11 Modified van Genuchten Model
      • ICP=12 Regular hysteresis
      • ICP=13 Simple hysteresis
      • ICP=31 Parker et al 3-phase function
      • ICP=32 Parker 3-phase function, alternative 1
      • ICP=33 Parker 3-phase function, alternative 2
      • ICP=34 Parker 3-phase function, alternative 3
      • ICP=40 Table lookup
      • ICP=41 User-Defined capillary pressure function
    • ☑️C: ADDITIONAL PROGRAM OPTIONS
    • ☑️D: DESCRIPTION OF FRACTURED FLOW
      • Multiple Continuum Approaches
      • Active Fracture Modle
Powered by GitBook
On this page
  1. PREPARATION OF MODEL INPUT
  2. Keywords and Input Data

BIODG

BIODG input data block introducing parameters needed to simulate the biodegradation processes.

Record BIODG.1

Free format for 7 parameters, or Format (I5,I5,E10.4,10X,4E10.4)

IMONOD, ICFLAG, BFAC, SW1, SW2, WEA, WSUB

IMONOD selects between multiplicative and minimum Monod model for the substrate degradation rate equation.

0 : multiplicative Monod model (default).

>0 : minimum Monod model.

ICFLAG selects how to consider the competitive and Haldane inhibition terms in the Monod model.

=0: competitive and Haldane inhibition factors are applied to all Monod terms in the substrate degradation rate equation, including the electron acceptor and nutrients terms as in the BIOMOC code formulation (default).

>0: competitive and Haldane inhibition factors are applied only to the substrate Monod term, as in conventional formulations of cometabolic degradation processes modelled using competitive inhibition effects.

BFAC reduction factor criterion for local Newton-Raphson iteration to reduce substrate residual. Nonlinearity of the reaction is handled by local Newton-Raphson iteration for the primary substrate. BFAC is the factor by which the residual must be reduced before convergence.

SW1 lower limit of aqueous phase saturation considered in the saturation inhibition function (if =0, the default value 0.02 will be applied.).

SW2 upper limit of aqueous phase saturation considered in the saturation inhibition function (SW1 < SW2 ≤ 1).

WEA 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 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.

Record BIODG.2

Free format for 1 parameter, or Format (I5)

NPROC

NPROC number of biodegradation processes in the simulation (NPROC ≤ 20).

Record BIODG.3

Free format for 8 parameters, or Format (2(5X, I5), 2E10.4, 3(5X, I5), E10.4)

NSPROC(IP), IBIO(IP), AMUMAX(IP), YIELD(IP), NCOMP(IP), NNC(IP), NHAL(IP), ENTB(IP)

NSPROC(IP) number of mass components controlling the substrate degradation rate in process IP.

IBIO(IP) index of microbial population involved in process IP.

AMUMAX(IP) maximum specific substrate degradation rate in process IP (kg substrate/ (s kg biomass) ).

YIELD(IP) yield coefficient for the growth of biomass due to the degradation of unit mass of substrate in process IP (kg biomass / kg substrate).

NCOMP(IP) number of mass components responsible for competitive inhibition in process IP.

NNC(IP) number of mass components responsible for non-competitive inhibition in process IP.

NHAL(IP) number of mass components responsible for Haldane inhibition in process IP.

ENTB(IP) heat of reaction for the degradation of substrate in process IP (J/kg substrate).

Record BIODG.4

Free format for as more as 12 parameters, or Format ( 6(5X, I5, E10.4) )

KSPROC(IP,NC), AKS(IP,NC) ; NC=1, NSPROC(IP)

KSPROC(IP,NC) index of mass component # NC controlling the substrate degradation rate in process IP. By convention, the first (NC=1) must refer to the primary substrate of process IP.

AKS(IP,NC) half saturation constant of mass component # NC in the Monod term of substrate degradation rate in process IP (kg substrate / kg aqueous phase). If specified, must be >0.

Record BIODG.5

Free format for as more as 12 parameters, or Format ( 6(5X, I5, E10.4) )

KSCOMP(IP,NC), AKCOMP(IP,NC) ; NC=1, NCOMP(IP)

KSCOMP(IP,NC) index of mass component # NC responsible for competitive inhibition in process IP.

AKCOMP(IP,NC) competitive inhibition coefficient for mass component # NC in process IP (kg solute / kg aqueous phase).

Record BIODG.6

Free format for as more as 12 parameters, or Format ( 6(5X, I5, E10.4) )

KSNC(IP,NC), AKNC(IP,NC) ; NC=1, NNC(IP)

KSNC(IP,NC) index of mass component # NC responsible for non-competitive inhibition in process IP.

AKNC(IP,NC) non-competitive inhibition coefficient for mass component # NC in process IP (kg solute / kg aqueous phase).

Record BIODG.7

Free format for as more as 12 parameters, or Format ( 6(5X, I5, E10.4) )

KSHAL(IP,NC), AKHAL(IP,NC) ; NC=1, NHAL(IP)

KSHAL(IP,NC) index of mass component # NC responsible for Haldane inhibition in process IP.

AKHAL(IP,NC) Haldane inhibition coefficient for mass component # NC in process IP (kg solute /kg aqueous phase).

Record BIODG.8

Free format for as more as 20 parameters, or Format (8E10.4)

UPTAKE(IP,L) ; L=1,NumCom

UPTAKE(IP,L) uptake coefficient of component # L in process IP with respect to 1 mole of degraded primary substrate (mole component / mole substrate).

Repeat records BIODG.3 through BIODG.8 for a total of NPROC (up to 20) different biodegradation processes (IP= 1, NPROC).

Record BIODG.9

Free format for 2 parameters, or Format (2I5)

NPOP, IBFLAG

NPOP number of microbial populations (NPOP ≤ 20).

IBFLAG specifies if initial conditions for biomass concentration are supplied through input blocks INDOM, INCON, or through an INCON file.

0: constant biomass concentrations are given as initial conditions through block BIODG.10.

>0: variable biomass concentrations are supplied as initial conditions through blocks INDOM, INCON or through an INCON file.

Record BIODG.10

Free format for 5 parameters, or Format (5E10.4)

BAI(IB), BA0(IB), TMAX(IB), DEATH(IB), AKBIO(IB)

BAI(IB) initial concentration (valid for the entire simulation grid) in the aqueous phase of microbial population # IB (kg biomass / kg aqueous phase).

BA0(IB) minimum concentration in the aqueous phase of microbial population # IB enforced during the simulation (kg biomass / kg aqueous phase).

TMAX(IB) maximum temperature for the calculation of temperature inhibition function in the substrate degradation rate equation (°C).

DEATH(IB) death rate constant, or maintenance constant, for the microbial population # IB (s-1).

AKBIO(IB) inhibition constant for biomass growth of microbial population # IB (kg biomass kg aqueous phase).

Repeat record BIODG.10 for a total of NPOP (up to 20) different microbial populations (IB= 1, NPOP).

Used in: All EOS modules

Example:

BIODG----1--------2--------3--------4--------5--------6--------7----*----8

0, 1.e-10, , 0.0 , .2, 0.9, 0.9 //BIODG.1

2 //BIODG.2

2, 1, 1.2732e-5, 1.0, 0, 0, 0, 0.0 //BIODG.3 for process 1

4, 2.e-6, 2, 1.e-6 //BIODG.4 for process 1

0 //BIODG.5 for process 1

0 //BIODG.6 for process 1

0 //BIODG.7 for process 1

-4.0, 9.0, 0.0, 1.0 //BIODG.8 for process 1

2, 1, 1.1574e-5, 0.8, 0, 0, 0, 0.0 //BIODG.3 for process 2

3, 1.e-6, 2, 0.5e-6 //BIODG.4 for process 2

0 //BIODG.5 for process 2

0 //BIODG.6 for process 2

0 //BIODG.7 for process 2

-3.0, 7.5, 1.0, 0.0 //BIODG.8 for process 2

1 // BIODG.9

1.530e-6, 1.00e-6, 40., 2.3148e-7, 0.0 //BIODG.10

PreviousTITLENextCBMDA

Last updated 7 months ago

8️⃣