Installation

GenSec is written in Python 3 and is currently used from source.

Requirements

  • Python 3

  • Git

  • ASE-compatible calculator backend for geometry optimization (for example, an ASE calculator script configured in your input file)

Core dependencies

Install the core Python dependencies:

pip install numpy ase scipy networkx timeout-decorator

Optional dependencies

Install these only if you use FPS/descriptor-based structure selection:

pip install featomic metatensor scikit-matter

Install from source

Clone the repository and move into it:

git clone https://github.com/sabia-group/gensec.git
cd gensec

Create and activate a virtual environment (recommended):

python3 -m venv .venv
source .venv/bin/activate

Add the repository root to PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:$PWD

Test

From the repository root, run:

python gensec.py inputs/parameters_generate.json

If the run starts and creates output folders/databases, GenSec is installed correctly.