mace-torch 0.3.4

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MACE

Table of contents

• About MACE
• Documentation
• Installation
• Usage
  • Training
  • Evaluation
• Tutorial
• Weights and Biases
• Development
• Pretrained foundation models
  • MACE-MP: Materials Project Force Fields
  • MACE-OFF: Transferable Organic Force Fields
• References
• Contact
• License

About MACE

MACE provides fast and accurate machine learning interatomic potentials with higher order equivariant message passing.

This repository contains the MACE reference implementation developed by Ilyes Batatia, Gregor Simm, and David Kovacs.

Also available:

• MACE in JAX, currently about 2x times faster at evaluation, but training is recommended in Pytorch for optimal performances.
• MACE layers for constructing higher order equivariant graph neural networks for arbitrary 3D point clouds.

Documentation

A partial documentation is available at: https://mace-docs.readthedocs.io

Installation

Requirements:

• Python >= 3.7
• PyTorch >= 1.12

(for openMM, use Python = 3.9)

pip installation

To install via pip, follow the steps below:

pip install --upgrade pip
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
pip install mace-torch

For CPU or MPS (Apple Silicon) installation, use pip install torch torchvision torchaudio instead.

conda installation

If you do not have CUDA pre-installed, it is recommended to follow the conda installation process:

# Create a virtual environment and activate it
conda create --name mace_env
conda activate mace_env

# Install PyTorch
conda install pytorch torchvision torchaudio pytorch-cuda=11.6 -c pytorch -c nvidia

# (optional) Install MACE's dependencies from Conda as well
conda install numpy scipy matplotlib ase opt_einsum prettytable pandas e3nn

# Clone and install MACE (and all required packages)
git clone https://github.com/ACEsuit/mace.git
pip install ./mace

pip installation from source

To install via pip, follow the steps below:

# Create a virtual environment and activate it
python -m venv mace-venv
source mace-venv/bin/activate

# Install PyTorch (for example, for CUDA 11.6 [cu116])
pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu116

# Clone and install MACE (and all required packages)
git clone https://github.com/ACEsuit/mace.git
pip install ./mace

Note: The homonymous package on PyPI has nothing to do with this one.

Usage

Training

To train a MACE model, you can use the mace_run_train script, which should be in the usual place that pip places binaries (or you can explicitly run python3 <path_to_cloned_dir>/mace/cli/run_train.py)

mace_run_train \
    --name="MACE_model" \
    --train_file="train.xyz" \
    --valid_fraction=0.05 \
    --test_file="test.xyz" \
    --config_type_weights='{"Default":1.0}' \
    --E0s='{1:-13.663181292231226, 6:-1029.2809654211628, 7:-1484.1187695035828, 8:-2042.0330099956639}' \
    --model="MACE" \
    --hidden_irreps='128x0e + 128x1o' \
    --r_max=5.0 \
    --batch_size=10 \
    --max_num_epochs=1500 \
    --swa \
    --start_swa=1200 \
    --ema \
    --ema_decay=0.99 \
    --amsgrad \
    --restart_latest \
    --device=cuda \

To give a specific validation set, use the argument --valid_file. To set a larger batch size for evaluating the validation set, specify --valid_batch_size.

To control the model's size, you need to change --hidden_irreps. For most applications, the recommended default model size is --hidden_irreps='256x0e' (meaning 256 invariant messages) or --hidden_irreps='128x0e + 128x1o'. If the model is not accurate enough, you can include higher order features, e.g., 128x0e + 128x1o + 128x2e, or increase the number of channels to 256.

It is usually preferred to add the isolated atoms to the training set, rather than reading in their energies through the command line like in the example above. To label them in the training set, set config_type=IsolatedAtom in their info fields. If you prefer not to use or do not know the energies of the isolated atoms, you can use the option --E0s="average" which estimates the atomic energies using least squares regression.

If the keyword --swa is enabled, the energy weight of the loss is increased for the last ~20% of the training epochs (from --start_swa epochs). This setting usually helps lower the energy errors.

The precision can be changed using the keyword --default_dtype, the default is float64 but float32 gives a significant speed-up (usually a factor of x2 in training).

The keywords --batch_size and --max_num_epochs should be adapted based on the size of the training set. The batch size should be increased when the number of training data increases, and the number of epochs should be decreased. An heuristic for initial settings, is to consider the number of gradient update constant to 200 000, which can be computed as $\text{max-num-epochs}*\frac{\text{num-configs-training}}{\text{batch-size}}$.

The code can handle training set with heterogeneous labels, for example containing both bulk structures with stress and isolated molecules. In this example, to make the code ignore stress on molecules, append to your molecules configuration a config_stress_weight = 0.0.

To use Apple Silicon GPU acceleration make sure to install the latest PyTorch version and specify --device=mps.

Evaluation

To evaluate your MACE model on an XYZ file, run the mace_eval_configs:

mace_eval_configs \
    --configs="your_configs.xyz" \
    --model="your_model.model" \
    --output="./your_output.xyz"

Tutorial

You can run our Colab tutorial to quickly get started with MACE.

We also have a more detailed user and developer tutorial at https://github.com/ilyes319/mace-tutorials

Weights and Biases for experiment tracking

If you would like to use MACE with Weights and Biases to log your experiments simply install with

pip install ./mace[wandb]

And specify the necessary keyword arguments (--wandb, --wandb_project, --wandb_entity, --wandb_name, --wandb_log_hypers)

Pretrained Foundation Models

MACE-MP: Materials Project Force Fields

We have collaborated with the Materials Project (MP) to train a universal MACE potential covering 89 elements on 1.6 M bulk crystals in the MPTrj dataset selected from MP relaxation trajectories. The models are releaed on GitHub at https://github.com/ACEsuit/mace-mp. If you use them please cite our paper which also contains an large range of example applications and benchmarks.

Example usage in ASE

from mace.calculators import mace_mp
from ase import build

atoms = build.molecule('H2O')
calc = mace_mp(model="medium", dispersion=False, default_dtype="float32", device='cuda')
atoms.calc = calc
print(atoms.get_potential_energy())

MACE-OFF: Transferable Organic Force Fields

There is a series (small, medium, large) transferable organic force fields. These can be used for the simulation of organic molecules, crystals and molecular liquids, or as a starting point for fine-tuning on a new dataset. The models are released under the ASL license. The models are releaed on GitHub at https://github.com/ACEsuit/mace-off. If you use them please cite our paper which also contains detailed benchmarks and example applications.

Example usage in ASE

from mace.calculators import mace_off
from ase import build

atoms = build.molecule('H2O')
calc = mace_off(model="medium", device='cuda')
atoms.calc = calc
print(atoms.get_potential_energy())

Development

We use black, isort, pylint, and mypy. Run the following to format and check your code:

bash ./scripts/run_checks.sh

We have CI set up to check this, but we highly recommend that you run those commands before you commit (and push) to avoid accidentally committing bad code.

We are happy to accept pull requests under an MIT license. Please copy/paste the license text as a comment into your pull request.

References

If you use this code, please cite our papers:

@inproceedings{Batatia2022mace,
  title={{MACE}: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields},
  author={Ilyes Batatia and David Peter Kovacs and Gregor N. C. Simm and Christoph Ortner and Gabor Csanyi},
  booktitle={Advances in Neural Information Processing Systems},
  editor={Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho},
  year={2022},
  url={https://openreview.net/forum?id=YPpSngE-ZU}
}

@misc{Batatia2022Design,
  title = {The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials},
  author = {Batatia, Ilyes and Batzner, Simon and Kov{\'a}cs, D{\'a}vid P{\'e}ter and Musaelian, Albert and Simm, Gregor N. C. and Drautz, Ralf and Ortner, Christoph and Kozinsky, Boris and Cs{\'a}nyi, G{\'a}bor},
  year = {2022},
  number = {arXiv:2205.06643},
  eprint = {2205.06643},
  eprinttype = {arxiv},
  doi = {10.48550/arXiv.2205.06643},
  archiveprefix = {arXiv}
 }

Contact

If you have any questions, please contact us at [e-mail].

For bugs or feature requests, please use GitHub Issues.

License

MACE is published and distributed under the MIT License.