thu-wangz17 / hermnet

Heterogeneous relational message passing networks (HermNet)

HermNet

Heterogeneous relational message passing networks (HermNet)

Note: The code of HermNet is refactored from DGL-based to PYG-based because of the efficiency. Some codes are still unfinished and the related codes have not been tested.

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Table of Contents

• HermNet
  • Table of Contents
  • Architecture
  • Requirements
  • Citation

Architecture

Three kinds of HermNet are proposed, i.e. Heterogeneous Vertex Networks (HVNet), Heterogeneous Pair Networks (HPNet), Heterogeneous Triadic Networks (HTNet). HermNet is inspired by LAMMPS, whose pair_style could be set as hybrid, which is self-consistent with heterogeneous. The entire architecture of HermNet is displayed as follows,

The subgraphs are extracted with the following operations,

The sub-network used in the manuscript is a modified and simplified PAINN, which is shown as follows,

Requirements

The following libraries are required:

PyTorch
Numpy
Torch_Scatter
Torch_Geometric
Ase

The code has been tested with the libraries whose versions could be found in requirements.txt.

Citation

@article{wang2022heterogeneous,
  title={Heterogeneous relational message passing networks for molecular dynamics simulations},
  author={Wang, Zun and Wang, Chong and Zhao, Sibo and Xu, Yong and Hao, Shaogang and Hsieh, Chang Yu and Gu, Bing-Lin and Duan, Wenhui},
  journal={npj Computational Materials},
  volume={8},
  number={1},
  pages={1--9},
  year={2022},
  publisher={Nature Publishing Group}
}

hermnet's Issues

When do I use QM9Dataset v2?

Hi, thanks a lot for the great research and code sharing.

I'm now trying to implement your code to QM9-like dataset.

I found two data-creating classes; QM9Dataset and QM9Dataset_v2, and I found that in your QM9 example, only v1 was used.

I'm wondering what are the differences of v1 and v2, and what is the purpose of the version 2.

Thanks again for sharing the source code of the amazing work! :)

I wonder know how to implement the code

Hello, i'm the student who are studying molecular dynamics.
I wonder know set up the module HermNet.
When I download the code and implement hvnet_main.py, there is no module named HermNet.
Thanks.