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timlichtenberg merged 1 commit into from
Mar 24, 2026
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Add FastChem installation step to docs #662

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46 changes: 40 additions & 6 deletions docs/How-to/installation.md
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Expand Up @@ -189,7 +189,41 @@ cd ../

Use this `get_agni.sh` script to keep AGNI and its data files up to date. AGNI must be available at `./AGNI/` inside your PROTEUS folder (either a symbolic link or the true location).

## 9. Install submodules as editable
## 9. Install FastChem (equilibrium chemistry solver)

FastChem is used by AGNI for equilibrium chemistry calculations. It must be compiled from source inside the AGNI directory:

!!! note
This step requires `cmake` and `make`. Check with:

```console
which cmake
which make
```

```console
cd AGNI
bash src/get_fastchem.sh
cd ../
```

The environment variable `FC_DIR` must always point to the FastChem installation path. Add it to your shell config file:

=== "bash"

```console
echo "export FC_DIR=$PWD/AGNI/fastchem/" >> "$HOME/.bashrc"
source "$HOME/.bashrc"
```

=== "zsh"

```console
echo "export FC_DIR=$PWD/AGNI/fastchem/" >> "$HOME/.zshrc"
source "$HOME/.zshrc"
```

## 10. Install submodules as editable

Clone and install each submodule in editable mode.

Expand Down Expand Up @@ -259,7 +293,7 @@ bash src/get_zalmoxis.sh
cd ../
```

## 10. Setup PETSc (numerical computing library)
## 11. Setup PETSc (numerical computing library)

!!! warning
PETSc requires Python <= 3.12. Make sure your active environment uses a compatible version.
Expand All @@ -281,25 +315,25 @@ cd ../

The script automatically detects Apple Silicon vs Intel, uses Homebrew's MPI, and applies the necessary compiler/linker workarounds. If you encounter issues, see [Troubleshooting: PETSc on Apple Silicon](troubleshooting.md#petsc-compilation-fails-on-apple-silicon).

## 11. Setup SPIDER (interior evolution model)
## 12. Setup SPIDER (interior evolution model)

```console
./tools/get_spider.sh
```

## 12. Install PROTEUS framework
## 13. Install PROTEUS framework

```console
python -m pip install -e ".[develop]"
```

## 13. Enable pre-commit hooks
## 14. Enable pre-commit hooks

```console
pre-commit install -f
```

## 14. Done!
## 15. Done!

Any remaining dependencies will be downloaded when the model is first run.

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