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PHAST—A Program for Simulating Ground-Water Flow, Solute Transport, and Multicomponent Geochemical Reactions

U.S. Geological Survey Techniques and Methods 6–A8

ONLINE ONLY

 

By David L. Parkhurst, Kenneth L. Kipp, Peter Engesgaard, and Scott R. Charlton


This report is available in pdf.

Abstract

The computer program PHAST simulates multi-component, reactive solute transport in three-dimensional saturated ground-water flow systems. PHAST is a versatile ground-water flow and solute-transport simulator with capabilities to model a wide range of equilibrium and kinetic geochemical reactions. The flow and transport calculations are based on a modified version of HST3D that is restricted to constant fluid density and constant temperature. The geochemical reactions are simulated with the geochemical model PHREEQC, which is embedded in PHAST.

PHAST is applicable to the study of natural and contaminated ground-water systems at a variety of scales ranging from laboratory experiments to local and regional field scales. PHAST can be used in studies of migration of nutrients, inorganic and organic contaminants, and radionuclides; in projects such as aquifer storage and recovery or engineered remediation; and in investigations of the natural rock-water interactions in aquifers. PHAST is not appropriate for unsaturated-zone flow, multiphase flow, density-dependent flow, or waters with high ionic strengths.

A variety of boundary conditions are available in PHAST to simulate flow and transport, including specified-head, flux, and leaky conditions, as well as the special cases of rivers and wells. Chemical reactions in PHAST include (1) homogeneous equilibria using an ion-association thermodynamic model; (2) heterogeneous equilibria between the aqueous solution and minerals, gases, surface complexation sites, ion exchange sites, and solid solutions; and (3) kinetic reactions with rates that are a function of solution composition. The aqueous model (elements, chemical reactions, and equilibrium constants), minerals, gases, exchangers, surfaces, and rate expressions may be defined or modified by the user.

A number of options are available to save results of simulations to output files. The data may be saved in three formats: a format suitable for viewing with a text editor; a format suitable for exporting to spreadsheets and post-processing programs; or in Hierarchical Data Format (HDF), which is a compressed binary format. Data in the HDF file can be visualized on Windows computers with the program Model Viewer and extracted with the utility program PHASTHDF; both programs are distributed with PHAST.

Operator splitting of the flow, transport, and geochemical equations is used to separate the three processes into three sequential calculations. No iterations between transport and reaction calculations are implemented. A three-dimensional Cartesian coordinate system and finite-difference techniques are used for the spatial and temporal discretization of the flow and transport equations. The non-linear chemical equilibrium equations are solved by a Newton-Raphson method, and the kinetic reaction equations are solved by a Runge-Kutta or an implicit method for integrating ordinary differential equations.

The PHAST simulator may require large amounts of memory and long Central Processing Unit (CPU) times. To reduce the long CPU times, a parallel version of PHAST has been developed that runs on a multiprocessor computer or on a collection of computers that are networked. The parallel version requires Message Passing Interface, which is currently (2004) freely available. The parallel version is effective in reducing simulation times.

This report documents the use of the PHAST simulator, including running the simulator, preparing the input files, selecting the output files, and visualizing the results. It also presents four examples that verify the numerical method and demonstrate the capabilities of the simulator. PHAST requires three input files. Only the flow and transport file is described in detail in this report. The other two files, the chemistry data file and the database file, are identical to PHREEQC files and the detailed description of these files is found in the PHREEQC documentation.

Contents

Abstract

Chapter 1. Introduction

1.1. Applicability

1.2. Simulator Capabilities

1.3. Simulator Results

1.4. Numerical Implementation

1.5. Computer Resources

1.6. Purpose and Scope

1.7. Acknowledgments

Chapter 2. Running the Simulator

2.1. Input Files

2.2. Output Files

2.3. Program Execution

Chapter 3. Thermodynamic Database and Chemistry Data Files

3.1. Thermodynamic Database File

3.2. Chemistry Data File

3.2.1. Chemical Initial and Boundary Conditions for Reactive Transport

3.2.2. Output of Chemical Data

Chapter 4. Flow and Transport Data File

4.1. Organization of the Flow and Transport Data File

4.2. Spatial Data

4.2.1. Zones

4.2.1.1. Use of Zones for Defining Porous-Media Properties

4.2.1.2. Use of Zones for Defining Initial- and Boundary-Condition Properties

4.2.1.3. Property Definitions

4.2.2. Rivers and Wells

4.3. Transient Data

4.4. Description of Keyword Data Blocks

CHEMISTRY_IC

Example

Explanation

Notes

Example Problems

END

Example Problems

FLUX_BC

Example

Explanation

Notes

Example Problems

FREE_SURFACE_BC

Example

Explanation

Notes

Example Problems

GRID

Example

Explanation

Notes

Example Problems

HEAD_IC

Example 1

Explanation 1

Example 2

Explanation 2

Notes

Example Problems

LEAKY_BC

Example

Explanation

Notes

Example Problems

MEDIA

Example

Explanation

Notes

Example Problems

PRINT_FREQUENCY

Example

Explanation

Notes

Example Problems

PRINT_INITIAL

Example

Explanation

Notes

Example Problems

PRINT_LOCATIONS

Example

Explanation

Notes

Example Problems

RIVER

Example

Explanation

Notes

Example Problems

SOLUTE_TRANSPORT

Example

Explanation

Notes

Example Problems

SOLUTION_METHOD

Example 1

Explanation 1

Notes 1

Example 2

Explanation 2

Notes 2

Example Problems

SPECIFIED_HEAD_BC

Example

Explanation

Notes

Example Problems

STEADY_FLOW

Example

Explanation

Notes

Example Problems

TIME_CONTROL

Example

Explanation

Notes

Example Problems

TITLE

Example

Explanation

Notes

Example Problems

UNITS

Example

Explanation

Notes

Example Problems

WELL

Example

Explanation

Notes

Example Problems

Chapter 5. Output Files

5.1. Content of Output Files

5.2. Selection of Data for Chemical Output Files

5.3. Output Files for Post-Processing

5.4. Diagnostic Output Files

Chapter 6. Examples

6.1. Verification Examples

6.2. Example 1: Pulse Source of Chemical Constituent that Undergoes Sorption and Decay

6.3. Example 2: Chain of Four Kinetically Decaying Reactants

6.4. Example 3: Aerobic Consumption of a Substrate with Biomass Growth

6.5. Example 4: Simulation of Regional-Scale Transport and Reactions in the Central Oklahoma Aquifer

6.5.1. Initial Conditions

6.5.2. Chemistry Data File

6.5.3. Flow and Transport Data File

6.5.4. Results

Chapter 7. Notation

7.1. Roman Characters

7.2. Greek Characters

7.3. Mathematical Operators and Special Functions

References Cited

Appendix A. Three-Dimensional Visualization of PHAST Simulation Results

Appendix B. Using PHASTHDF to Extract Data from the HDF Output File

Appendix C. Parallel-Processing Version of PHAST

C.1. Parallelization of PHAST

C.2. Running the Parallel Version

Appendix D. Theory and Numerical Implementation

D.1. Flow and Transport Equations

D.1.1. Components

D.1.2. Spatial Discretization

D.1.3. Temporal Discretization

D.1.4. Automatic Time-Step Algorithm for Steady-State Flow Simulation

D.2. Chemical-Reaction Equations

D.2.1. Equilibrium Reactions

D.2.2. Component Mole Balance

D.2.3. Kinetic Reactions

D.3. Property Functions and Transport Coefficients

D.4. Well-Source Conditions

D.5. Boundary Conditions

D.5.1. Specified-Head Boundary with Associated Solution Composition

D.5.2. Specified-Head Boundary with Specified Solution Composition

D.5.3. Specified-Flux Boundary

D.5.4. Leakage Boundary

D.5.5. River-Leakage Boundary

D.5.6. Free-Surface Boundary

D.5.7. Boundary-Condition Compatibility

D.6. Initial Conditions

D.7. Method of Solution

D.7.1. Operator Splitting and Sequential Solution

D.7.2. Linear-Equation Solvers for Flow and Transport Finite-Difference Equations

D.7.3. Solving Equilibrium and Kinetic Chemical Equations

D.8. Accuracy from Spatial and Temporal Discretization

D.9. Global Mass-Balance Calculations

D.10. Nodal Velocity Calculation

 

Suggested citation: Parkhurst, D.L., Kipp, K.L., Engesgaard, Peter, and Charlton, S.R., 2004, PHAST—A program for simulating ground-water flow, solute transport, and multicomponent geochemical reactions: U.S. Geological Survey Techniques and Methods 6–A8, 154 p.

 


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