By Seongsu Kim, Feb, 2024 [arxiv] [PDF]

🌟 This repository contains an implementation of the ICML 2024 paper Gaussian plane-wave neural operator for electron density estimation. The code implementation of the model is mainly inspired by the InfGCN by Chaoran Cheng.

All codes are run with python 3.9 and CUDA 12.0. A similar environment should also work, as this project does not rely on some rapidly changing packages.

conda create -n GPWNO python==3.9
conda activate GPWNO

pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117
pip install pyg-lib torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cu117.html
pip install numpy==1.23.4 scipy==1.9.3 matplotlib==3.7 tqdm
pip install hydra-core lightning wandb omegaconf
pip install lz4 pymatgen mp-api python-dotenv PyYAML easydict
pip install e3nn

.
├── conf                        # Training configurations
├── source                      # Source files 
│   ├── baseline (optional)             
│   ├── common                 
│   ├── datamodule             
│   ├── datasets               
│   └── models (✈)              # Models are here
│       └── GPWNO.py (⭐)       # Our Architecture
├── scripts                     # Shorts snippets
├── run.py                      # Main file for running the files
└── README.md

Datasets QM9, MP, and MD are not included in the repository since the size of the datasets is too large.

The QM9 dataset contains 133885 small molecules consisting of C, H, O, N, and F. The QM9 electron density dataset was built by Jørgensen et al. (paper) and was publicly available via Figshare. Each tarball needs to be extracted, but the inner lz4 compression should be kept. We provided code to read the compressed lz4 file.

For convenience, we provide the list of the scripts\qm9_url.txt that splits url list of the QM9 files. After download aria2c, You can use the below command

aria2c --input-file scripts\qm9_url.txt -d ../dataset_qm9

You can additionally use the -x keywords to set the multiple connections. See aria2 for more information.

The MD dataset contains 6 small molecules (ethanol, benzene, phenol, resorcinol, ethane, malonaldehyde) with different geometries sampled from molecular dynamics (MD). The dataset was curated from here by Bogojeski et al. and here by Brockherde et al. The dataset is publicly available at the Quantum Machine website.

We assume the data is stored in the ../dataset/<mol_name>/<mol_name>_<split>/ directory, where mol_name should be one of the molecules mentioned above and split should be either train or test. The directory should contain the following files:

• structures.npy contains the coordinates of the atoms.
• dft_densities.npy contains the voxelized electron charge density data.

This is the format for the latter four molecules (you can safely ignore other files). For the former two molecules, run python generate_dataset.py to generate the correctly formatted data. You can also specify the data directory with --root and the output directory with --out.

All MD datasets assume a cubic box with a side length of 20 Bohr and 50 grids per side. The densities are stored as Fourier coefficients, and we provided code to convert them.

The MP dataset curated from here is the dataset of the inorganic crystalline materials. We newly conduct a benchmark from the MP by categorizing the 117,535 molecules into seven crystal families: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, and cubic. We also providied the list of the materials on our experiments in the code.

MP does not have an official download site, it needs to be downloaded by handed query by API. To download the full dataset, you can use the download code we provide. You need to register your API key in scirpts/MP/download_mp.py from Materials project.

You can download all the MP datasets with this code

python scripts/MP/download_mp.py

Note that the size of the MP dataset is about 10T. We assume the data is stored in the ../dataset_mp with the data split we attach. FYI, it took about 7 days to download all for me.

[⚠️Note] Before running the code, you have to modify the .env files as a proper directory in your system. And also you have to fix the path of the configure in the conf/data. Other scripts that is used for running code are in scripts directory.

# can specify the molecular name
python run.py --config-name=md \
    model=GPWNO_MD \
    data.num_workers=32 \
    logging=draw \
    data.mol_name=benzene

python run.py --config-name=qm9 \
    model=GPWNO_QM9

# default is mixed
python run.py --config-name=mp \
    model=GPWNO_pbc

# specify the lattice type
python run.py --config-name=mp \
    model=GPWNO_pbc \
    data=mp_tetragonal

If you find this code useful, please cite our paper

@misc{kim2024gaussian,
      title={Gaussian Plane-Wave Neural Operator for Electron Density Estimation}, 
      author={Seongsu Kim and Sungsoo Ahn},
      year={2024},
      eprint={2402.04278},
      archivePrefix={arXiv},
      primaryClass={physics.chem-ph}
}

We implemented these baselines in our repo:

DeepDFT

InfGCN

charge3net