Technical Details of PyTOUGHREACT
Why PyTOUGHREACT
PyTOUGHREACT was borne out of the need to automatically undertake a lot of simulations with the TOUGHREACT, TMVOC and TMVOC-BIO softwares developed by the Lawrence Berkeley National Laboratory (LBNL). It was noticed at the time that to carry out multiple simulations for uncertainty quantifications involved storing multiple files on ones local system and attempting to name them descriptively. This was time consuming and importantly was subject to human errors and mistakes.
A similar tool exists for TOUGH3 with PyTOUGH and PyTOUGHREACT extends its capability to TOUGHREACT with additional capabilities for plotting. Details of how PyTOUGH works can be found here https://pytough.readthedocs.io/_/downloads/en/latest/pdf/ and is essential to understand how it works before using PyTOUGHREACT.
What is TOUGHREACT / TMVOC and TMVOC-BIO
TOUGHREACT
TOUGHREACT is a multiphase, multicomponent non-isothermal simulator that utilizes coupled numerical modeling methods to the solution of fluid, heat, solute and chemical reaction equations. It has wide applicability in many subsurface problems such as waste disposal and acid mine drainage remediation. Full information on how the software functions can be found here https://www.osti.gov/servlets/purl/834237
TMVOC
TMVOC is another multicomponent nonisothermal simulator by LBNL designed for the simulation of flow of volatile organic chemicals in variably saturated media. It involves additional processes such as diffusion, sorption, advection and phase-partitioning. Details on how the software works can be found in https://tough.lbl.gov/assets/docs/TMVOC_Users_Guide.pdf
TMVOC-BIO
TMVOC-BIO possess exact features as the TMVOC with an additional capbility for the modeling of biodegradation reactions. Details can be found here https://www.osti.gov/servlets/purl/1377850
What is PyTOUGHREACT
Simply put, PyTOUGHREACT is a python Library for automating reaction simulations using TOUGHREACT, TMVOC and TMVOC-BIO. In addition to this capability, it also posesses the ability to make different kinds of 2D line and surface plots for different kinds of visualizations.
PyTOUGHREACT Software Architecture
General Architecture
The software uses object-oriented programming principles to structure the code. The software can be thought of as composed of two main segments; the processing segment and the output segment. The processing segment contains three main sections, IO processing, BIO and REACT. The IO processing is responsible for most of the input and output processing such as reading, writing. The BIO section is responsible for the TMVOC section of the package where it contains classes for storing biomass and degradation information and processing it before passing to IO processing for read/write. Similarly, the react section assists in processing reaction parameters such as mineral, chemical, and solute information before passing to the IO processing segment for read/write. After the files have been written to or read from the appropriate file types, the executable is called from within PyTOUGHREACT and the simulation is performed using the executable. Thereafter, the output segment is called which can read the results of the simulations and contains methods and functions which assist the user in creating 2D or 3D plots through the plotting module.
BIO Architecture
The BIO section is responsible for processing the TMVOC inputs. It makes use of two subsections to achieve this. The first subsection is responsible for aggregating the unique constituents of a biodegradation simulation for TMVOC; these constituents include water, gas, biomass, solids, and components. The second subsection is responsible for unique biodegradation processes in the simulation. This is done via two classes Process class and the BIODG class. The process class defines the constituents for any biodegradation process and BIODG class combines all processes together with numerical parameters for that process.
REACT Architecture
The react component consists of two main subcomponents: the chemical subcomponent and the solute subcomponent. The chemical subcomponent is responsible for defining the chemical constituents of the simulation such as the primary species, water, mineral, gas while the solute sub component is responsible for mapping each of the defined chemical constituents to the grid of the simulation and other functions such as what grids to write to output etc. This component contains information stored in the solute.inp file for TOUGHREACT simulations.
Result and Plotting Architecture
Though separate, the result and plotting architecture have very similar structures. The two sections are subdivided into single and multiple file processing. As the name suggests, the single file enables the processing of a single file. While the results section enables to process simulation output further in python, the plotting sections uses the output from the results section to make line and 2D plots. Similarly, the multiple file processing of the results section makes use of multiple files to output results which are then used in the plotting section for line and 2D plots. The multiple file processing provides efficiency when multiple files are required to be processed or in the plotting section to see variations from one simulation to another in a single plot.
