pyGoFEM

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A python front-end for the GoFEM modelling and inversion code

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# Motivation

Python front-end for the **GoFEM** package.

See jupyter notebooks for examples on how to setup GoFEM with python and process the results.

It invokes [MTPy-v2](https://mtpy-v2.readthedocs.io/en/latest/index.html) for handling MT data.

To generate and work with **GoFEM** mesh and model files, we use the [Python interface](https://github.com/dealii/dealii/blob/master/contrib/python-bindings/notebooks/tutorial-1.ipynb) of the [deal.II](https://www.dealii.org/) library. It is available in deal.II since version 9.2, see the [Release](https://www.degruyter.com/document/doi/10.1515/jnma-2020-0043/html) co-authored by me.

# MT Impedance Helper

`gofem.data_utils.calculate_MT_impedance()` supports Cartesian and spherical field-component conventions through its `coordinate_system` argument.

Use `coordinate_system='cartesian'` when the input field components are already local `X, Y, Z`. Use `coordinate_system='spherical'` when the input field components are ordered as `phi, theta, r`; in that case the local MT components are formed as `X = -theta`, `Y = phi`, and `Z = -r`. The default is `spherical` to preserve the historical behavior of pyGoFEM.

# Contributing

If you implement some functions that you think may be of general use, please feel free to create a [Pull Request](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) and contribute your code.

# Installation

### Linux

It is easiest to setup the pyGoFEM via [conda](https://docs.conda.io/en/latest/). Just deploy the environment using the environment file *pyGoFEM.yml* as:

```
conda env create -f pyGoFEM.yml
conda activate pygofem
```

After deploying the environment, we need to compile the deal.II library with the Python-interface enabled. To this end, first download the deal.II, for instance by doing *git clone https://github.com/dealii/dealii.git* or go directly for a release tarball, e.g. *wget https://dealii.org/downloads/dealii-9.6.2.tar.gz*. Go to the deal.II directory, configure and compile the library with the Python bindings enabled:

```
mkdir build; cd build
cmake -DCMAKE_BUILD_TYPE=DebugRelease -DCMAKE_INSTALL_PREFIX=/path/to/lib/deal.II -DDEAL_II_STATIC_EXECUTABLE=OFF -DEAL_II_WITH_UMFPACK=OFF -DDEAL_II_COMPONENT_EXAMPLES=OFF -DDEAL_II_FORCE_BUNDLED_BOOST=OFF -DDEAL_II_COMPONENT_PYTHON_BINDINGS=ON ../
make
```

That is it! You should now be able to run the tutorial notebooks.

### Windows

On Windows, you have to use [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl) and follow instructions for **Linux** above. *Note* that WSL version **2** or newer is required.

### macOS

The process is identical to the **Linux**. However, you may need to replace linux compiler packages in the *pyGoFEM.yml* files. Specifically, these

- gcc_linux-64
- gxx_linux-64
- gfortran_linux-64

should be replaced by

- clang_osx-64
- clangxx_osx-64
- gfortran_osx-64

For more details check [this](https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html).

# Referencing

Please acknowledge GoFEM and deal.II by citing one or more of the following publications:

> Grayver A.V., 2015, *Parallel 3D magnetotelluric inversion using adaptive finite-element method. Part I: theory and synthetic study*, Geophysical Journal International, 202(1), pp. 584-603, doi: 10.1093/gji/ggv165

> Grayver A.V., and Kolev, T. V., 2015, *Large-scale 3D geo-electromagnetic modeling using parallel adaptive high-order finite element method*, Geophysics, 80(6), pp. 277-291, doi: 10.1190/GEO2015-0013.1

> Arndt, D., Bangerth, W., Blais, B., Clevenger, T. C., Fehling, M., Grayver, A. V., ... & Wells, D. (2020). The deal. II library, version 9.2. Journal of Numerical Mathematics, 28(3), 131-146.

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