ElectronDensity2

Setup

We recommend running Electrondensity in conda environment. The following command creates conda environment with necessary dependencies.

conda env create -f environment.yaml

File env.sh contains environmental variables that can be modified to suit your configuration:

DATA_DIR is the path for storing datasets LOG_DIR is the path for storing log files MODEL_DIR is a path for storing and saving models CPU_COUNT specifies number of cpus used for parallel processing of datasets default -1 means all available CPUs.

It also downloads and installs orbkit package which cannot be installed using conda. To finish installation and activate electrondensity environmet run:

source env.sh

Generating training data

python bin/generate_dataset.py QM9

This command will download and generate electron densities for QM9 dataset (it requires 256GB od harddisk space) using number of CPUs specified in CPU_COUNT.

Training the model

Generating new electron densities