Skip to content

Latest commit

 

History

History
106 lines (76 loc) · 4.07 KB

README.md

File metadata and controls

106 lines (76 loc) · 4.07 KB
Raw

AIMNet2: a general-purpose neural network potential for organic and element-organic molecules.

The repository contains AIMNet2 ensemble models only and a convince method to load the models via python, see the original repository for all models.

AIMNet2: A Neural Network Potential to Meet your Neutral, Charged, Organic, and Elemental-Organic Needs Dylan Anstine ,Roman Zubatyuk ,Olexandr Isayev 10.26434/chemrxiv-2023-296ch

Models

The models are applicable for systems containing the following set of chemical elements: {H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, I}, both neutral and charged. The models aim to reproduce RKS B97-3c and wB97M-D3 energies.

The models are in the form of JIT-compiled PyTorch-2.0 files and could be loaded in Python or C++ code.

Note, that at present models have O(N^2) compute and memory complexity w.r.t. number of atoms. They could be applied to systems up to a few 100's of atoms.

In Python, the models could be loaded with the torch.jit.load function. As an input, they accept single argument of type Dict[str, Tensor] with the following data:

coords: shape (m, n, 3) - atomic coordinates in Angstrom 
numbers: shape (m, n) - atomic numbers
charge: shape (m, ) - total charge

Output is a dictionary with the following keys:

energy: shape (m, ) - energy in eV
charges: shape (m, n) - partial atomic charges

Installation

To make accessing the models simpler this package can be installed into a python environment. It is recommended that you create a new conda environment with the required dependencies to run the AIMNET2 model and provided calculator interfaces. You can create the environment using the following command

mamba create -n aimnet2 -c conda-forge 'pytorch=2' numpy ase

you should then activate the environment using

conda activate aimnet2

to use the pysisyphus calculator you will need to install the package from PyPI using pip

pip install pysisyphus

you should then clone this package and install from source via

git clone https://github.com/isayevlab/AIMNet2.git
cd AIMNet2
pip install .

Loading models via python

The aimnet2 package provides a convenience function to load the ensemble models

from pyaimnet2 import load_model

model = load_model("wb97m-d3")  # can also load b973c

the model can then be used by providing the inputs as described in Models or used with one of the provided calculators like ASE

from pyaimnet2.calculators.aimnet2ase import AIMNet2Calculator

calculator = AIMNet2Calculator(model=model)

Calculators

We provide example code for AIMNet2 calculators for ASE and pysisyphus Python libraries. The code shows an example use of the AIMNet2 models.

We also provide example geometry optimization scripts with ASE and Pysisyphus, and pysis_mod script which is a drop-in replacement for Pysisyphus pysis command-line utility, with AIMNet2 calculator enabled.

Docker image

We provide an example Dockerfile to build a CPU docker image.

The commands for building docker image:

cd /path/to/AIMNet2 
docker build --platform linux/amd64 --pull --rm -f "docker/Dockerfile_cpu" -t aimnet-box "."

You might skip the --platform flag if you are building on Linux.

The image exposes aimnet2_ase_opt.py script as entrypoint.

Example command to run geometry optimization with docker image:

docker run -it --rm -v $(pwd):/app/ aimnet-box models/aimnet2_wb97m-d3_ens.jpt input.sdf output.sdf --charge 0 --traj output.traj

Use ase convert output.traj output.xyz for conversion to e.g. xyz file format.

=======

Feedback

We would appreciate it if you could share feedback about model accuracy and performance. This would be important not only for us, to guide further developments of the model, but for the broad community as well. Please share your thoughts and experience, either positive or negative, by opening an issue in this repo.