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https://github.com/ptsolvers/pseudotransienthmc.jl

Iterative hydro-mechanical-chemical solvers
https://github.com/ptsolvers/pseudotransienthmc.jl

geosciences gpu hpc multi-physics

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Iterative hydro-mechanical-chemical solvers

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README 

        
# Pseudo-transient Hydro-Mechanical-Chemical



[![Build Status](https://github.com/PTsolvers/PseudoTransientHMC.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/PTsolvers/PseudoTransientHMC.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![DOI](https://zenodo.org/badge/299357364.svg)](https://zenodo.org/badge/latestdoi/299357364)



This repository contains Pseudo-Transient (PT) routines resolving chemical reactions coupled to fluid flow in viscously defroming solid pourous matrix, so-called Hydro-Mechanical-Chemical (HMC) coupling. Example of such multi-physical processes to understand, e.g, the formation of olivine veins by dehydration of ductile serpentinite ([Schmalholz et al., 2023](https://doi.org/10.1029/2023JB026985)), or the brucite-periclase reactions ([Schmalholz et al., 2020](https://doi.org/10.1029/2020GC009351)).



![Serpentinite dehydration and olivine vein formation during ductile shearing](docs/viz_dehy.png)

> Serpentinite dehydration and olivine vein formation during ductile shearing



Pseudo-Transient approach relies in using physics-motivated transient terms within differential equations in order to iteratively converge to an accurate solution. The PT HMC routines are written using the [Julia programming language](https://julialang.org) and build upon the high-performance [ParallelStencil.jl](https://github.com/omlins/ParallelStencil.jl) package to enable for optimal execution on graphics processing units (GPUs) and multi-threaded CPUs.



## Script list

The Julia scripts are located in the [scripts](scripts) folder which contains the routines for the [(Schmalholz et al., 2023)](https://doi.org/10.1029/2023JB026985) study.

- The main script is [`DeHy.jl`](scripts/DeHy.jl);

- The visualisation script is [`vizme_DeHy.jl`](scripts/vizme_DeHy.jl).



## Usage

All the routines are written in Julia and can be executed from the [Julia REPL], or from the terminal for improved performance. Output is produced using [Makie.jl] (using the `CairoMakie` backend).



The either multi-threaded CPU or GPU backend can be selected by adding the appropriate flag to the `USE_GPU` constant, modifying either the default behaviour in the top-most lines of the codes

```julia

const USE_GPU  = haskey(ENV, "USE_GPU" ) ? parse(Bool, ENV["USE_GPU"] ) : false

```

or by setting/exporting the desired environment variable.



- Selecting `false` will use the `Base.threads` backend. Multi-threading can be enabled by defining and exporting the `JULIA_NUM_THREADS` environment variable (e.g. `export JULIA_NUM_THREADS=2` prior to launching Julia will enable the code to run on 2 CPU threads).

- Selecting `true` will use the [CUDA.jl] GPU backend and will succeed if a CUDA-capable GPU is available.



### Example running the routine from the REPL



1. Launch Julia

```sh

% julia --project

```

2. Activate and instantiate the environment to download all required dependencies:

```julia-repl

julia> ]



(PseudoTransientHMC) pkg> activate .



(PseudoTransientHMC) pkg> instantiate

```

3. Run the script

```julia-repl

julia> include("DeHy.jl")

```



### Example running the routine from the terminal



Launch the Julia executable using the project's dependencies `--project`:

```sh

julia --project DeHy.jl

```



## References

Schmalholz, S. M., Moulas, E., Plümper, O., Myasnikov, A. V., & Podladchikov, Y. Y. (2020). **2D hydro‐mechanical‐chemical modeling of (De)hydration reactions in deforming heterogeneous rock: The periclase‐brucite model reaction**. Geochemistry, Geophysics, Geosystems, 21, 2020GC009351. [https://doi.org/10.1029/2020GC009351](https://doi.org/10.1029/2020GC009351)



Schmalholz, S. M., Moulas, E., Räss, L., & Müntener, O. (2023). **Shear-driven formation of olivine veins by dehydration of ductile serpentinite: a numerical study with implications for porosity production and transient weakening.** [https://doi.org/10.1029/2023JB026985](https://doi.org/10.1029/2023JB026985)



[CUDA.jl]: https://github.com/JuliaGPU/CUDA.jl

[Makie.jl]: https://docs.makie.org/stable/

[Julia REPL]: https://docs.julialang.org/en/v1/stdlib/REPL/