Package: toughio
TOUGH(Transport Of Unsaturated Groundwater and Heat) is a general purpose numerical simulation software designed for fluid and heat flows of multiphase, multicomponent fluid mixtures in porous and fractured media developed at Lawrence Berkeley National Laboratory. It solves mass and energy balance equations that describe fluid and heat flow in multiphase and multicomponent systems. TOUGH handles all types of multiphase and multicomponent flow systems since the governing equations for fluid and heat flow have the same mathematical form. The nature and properties of fluid mixtures are described by thermophysical variables (e.g., density, viscosity, enthalpy) which are provided by an equation-of-state (EOS) module.toughiois an open-source library that provides tools to facilitate pre- and post-processing for TOUGH using the latest Python standards. It aims to make setting up of a TOUGH simulation user-friendly by relying on existing well-established Python packages:numpy: vectorized calculation of N-dimensional arrays,meshio: input/output for many mesh formats,pyvista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK).Note that the results of a TOUGH simulation are sensitive to the quality of the mesh (ideally, it should satisfy the orthogonality condition). A mesh that contains too many ill-shaped cells can potentially lead to unexpected results although the simulation converged successfully.toughiodoes not verify the quality of the mesh which is left to the discretion of the user.Simulation of CO2leakage along a fault. Mesh generated with Gmsh and animation exported by PyVista.FeaturesMeshing:Create simple 2D cylindric or 2D/3D structured meshes similarly to TOUGH’s built-inMESHMAKER,Import mesh generated by external softwares (e.g.,Abaqus,FLAC3D,Gmsh,LaGriT),Export imported or generated mesh to aMESHfile for TOUGH assumingconformity(and optionally write initial condition fileINCON).Pre-processing:Easily add initial conditions, boundary conditions or other physical properties (e.g., porosity, permeability) using the convenient classtoughio.Mesh,Import previous TOUGH simulation input file into Python or define simulation parameters in a human-readable andJSONable dictionary,Export simulation parameters dictionary to a TOUGH input file.Post-processing:Import outputs of a TOUGH simulation into Python,Visualize results directly in Python usingpyvistaor export the results to another format supported bymeshio(e.g., VTK, Tecplot…),Create animations (GIF or MP4) or export results for all time steps to a XDMF file to be visualized in ParaView.InstallationThe recommended way to installtoughioand all its dependencies is through the Python Package Index:pipinstalltoughio[full]--userOtherwise, clone and extract the package, then run from the package location:pipinstall.[full]--userTo test the integrity of the installed package, check out this repository and run:gitlfspullpytestDocumentationRefer to the onlinedocumentationfor detailed description of the API and examples.Alternatively, the documentation can be built usingSphinx:pipinstall-rdoc/requirements.txtsphinx-build-bhtmldoc/sourcedoc/buildNote that some sample files are stored with LFS, so you may have to run the following command beforehand:gitlfspullUsageIn Python, to read a mesh and write the corresponding TOUGHMESHfile (without any pre-processing), simply doimporttoughiomesh=toughio.read_mesh(filename,file_format="flac3d",# Optional, inferred from file extension otherwise)mesh.write_tough()# Write MESH fileParameters of a TOUGH simulation can be defined as a dictionary with specific keywords following the JSON standard, for instanceparameters={"title":"Sample title","eos":"eco2n","isothermal":False,"default":{# Default rock properties"density":2600.0,"porosity":0.1,# "permeability", "conductivity", "specific_heat"...},"rocks":{"shale":{# To overwrite default rock properties"capillarity":{"id":1,"parameters":[0.0,0.0,1.0],},# same keywords as in "default"},# other materials},"options":{"n_cycle":100,"t_max":3.0*365.25*24.0*3600.0,# "t_ini", "t_steps", "t_step_max", "gravity", "eps1", "eps2"...},# "extra_options", "selections", "solver", "generators"...}toughio.write_input("INFILE",parameters)TOUGH simulation output can also be imported into Python as a list ofnamedtuple(type,format,time,labels,data)output=toughio.read_output(filename)toughiois mainly intended to be used as a Python scripting library for TOUGH. Nevertheless, several utility command line scripts are available for users who are not familiar with Python. From a console or terminal, the user can execute the following scripts:toughio-co2tab: copy fileCO2TABto the target directory,toughio-export: export TOUGH simulation results to a file for visualization (VTK, VTU, Tecplot or XDMF),toughio-extract: extract results from TOUGH main output file and reformat as a TOUGH3 element or connection output file (mostly useful for TOUGH2 outputbeforecallingtoughio-export),toughio-merge: merge input file, GENER and/or MESH and/or INCON into a single file,toughio-save2incon: convert aSAVEfile to anINCONfile (mostly useful to automatically restart a simulation and reset the counters).ContributingPlease refer to theContributing
Guidelinesto see how you can help. This project is released with aCode of Conductwhich you agree to abide by when contributing.Noticetoughio Copyright (c) 2022, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab’s Intellectual Property Office atIPO@lbl.gov.This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.