m3gnet 0.0.2

Materials Graph with Three-body Interactions

m3gnet

A universal material graph interatomic potential with three-body interactions

Table of Contents

• Introduction
• System requirements
• Installation
• Demo
• Model training
• Datasets
• References

Introduction

This repository contains the M3GNet interatomic potential for the periodic table. The model has been developed for inorganic crystals using the Materials Project relaxation trajectory as training data.

System requirements

Hardware requirements

Inferences using the pre-trained models can be ran on any standard computer. For model training, the GPU memory needs to be > 18 Gb for a batch size of 32 using the crystal training data. In our work, we used single RTX 3090 GPU for model training.

Software requirements

The package has been tested on the following systems:

• macOS: Monterey 12.1
• Linux: Ubuntu 18.04 (with tensorflow==2.7.0)
• Windows: 11

Installation

The following dependencies are needed

pymatgen==2022.2.10
pandas==1.4.1
tensorflow==2.7.0
numpy==1.22.2
monty==2022.3.12
sympy==1.9
ase==3.22.0
cython==0.29.26

m3gnet can be installed via source code installation by cloning the code from github

git clone https://github.com/materialsvirtuallab/m3gnet.git
cd m3gnet
pip install -r requirements.txt
python setup.py install

The installation time should be less than 1 minute.

Demo

Structure relaxation

Here is an example of how to run m3gnet relaxation of any crystals.

from pymatgen.core import Structure, Lattice
from m3gnet.models import Relaxer

# Init a Mo structure with stretched lattice (DFT lattice constant ~ 3.168)
mo = Structure(Lattice.cubic(3.3), 
               ["Mo", "Mo"], [[0., 0., 0.], [0.5, 0.5, 0.5]])

relaxer = Relaxer()  # this loads the default model

relax_results = relaxer.relax(mo)

final_structure = relax_results['final_structure']
final_energy = relax_results['trajectory'].energies[-1] / 2

print(f"Relaxed lattice parameter is {final_structure.lattice.abc[0]: .3f} Å")
print(f"Final energy is {final_energy.item(): .3f} eV/atom")

We will see output

Relaxed lattice parameter is  3.169 Å
Final energy is -10.859 eV/atom

The original lattice parameter of 3.3 Å was successfully relaxed to 3.169 Å, close to the DFT value of 3.168 Å.

The final energy -10.859 eV/atom is also close to DFT value of -10.8456 eV/atom.

The relaxation takes less than 20 seconds.

Molecular dynamics

Molecular dynamics simulations can be easily performed as well.

from pymatgen.core import Structure, Lattice
from m3gnet.models import MolecularDynamics

# Init a Mo structure with stretched lattice (DFT lattice constant ~ 3.168)
mo = Structure(Lattice.cubic(3.3), 
               ["Mo", "Mo"], [[0., 0., 0.], [0.5, 0.5, 0.5]])

md = MolecularDynamics(
    atoms=mo,
    temperature=1000,  # 1000 K
    ensemble='nvt',  # NVT ensemble
    timestep=1, # 1fs,
    trajectory="mo.traj",  # save trajectory to mo.traj
    logfile="mo.log",  # log file for MD
    loginterval=100,  # interval for record the log
)

md.run(steps=1000)

After the run, mo.log contains thermodynamic information similar to the following

Time[ps]      Etot[eV]     Epot[eV]     Ekin[eV]    T[K]
0.0000         -21.3307     -21.3307       0.0000     0.0
0.1000         -21.3307     -21.3307       0.0000     0.0
0.2000         -21.2441     -21.3087       0.0645   249.7
0.3000         -21.0466     -21.2358       0.1891   731.6
0.4000         -20.9702     -21.1149       0.1447   559.6
0.5000         -20.9380     -21.1093       0.1713   662.6
0.6000         -20.9176     -21.1376       0.2200   850.9
0.7000         -20.9016     -21.1789       0.2773  1072.8
0.8000         -20.8804     -21.1638       0.2835  1096.4
0.9000         -20.8770     -21.0695       0.1925   744.5
1.0000         -20.8908     -21.0772       0.1864   721.2

The MD run takes less than 1 minute.

Model training

The potential model can be trained using the PotentialTrainer in m3gnet.trainers. The training dataset can be

• structures, a list of pymatgen Structures
• energies, a list of energy floats
• forces, a list of nx3 force matrix, where n is the number of atom in each structure. n does not need to be the same for all structures.
• stresses, a list of 3x3 stress matrix.

where the stresses is optional.

For the stresses, we use the convention that compressive stress gives negative values. VASP stress should change signs to work directly with the model.

We use validation dataset to select the stopping epoch number. The dataset has similar format as the training dataset.

A minimal example of model training is shown below.

from m3gnet.models import M3GNet, Potential
from m3gnet.trainers import PotentialTrainer

import tensorflow as tf

m3gnet = M3GNet(is_intensive=False)
potential = Potential(model=m3gnet)

trainer = PotentialTrainer(
    potential=potential, optimizer=tf.keras.optimizers.Adam(1e-3)
)


trainer.train(
    structures,
    energies,
    forces,
    stresses,
    validation_graphs_or_structures=val_structures,
    val_energies=val_energies,
    val_forces=val_forces,
    val_stresses=val_stresses,
    epochs=100,
    fit_per_element_offset=True,
    save_checkpoint=False,
)

Datasets

The training data MPF.2021.2.8 is hosted on figshare with DOI 10.6084/m9.figshare.19470599.

Reference

This package is the result from our recent paper

Chi Chen, and Shyue Ping Ong. "A Universal Graph Deep Learning Interatomic Potential for the Periodic Table." arXiv preprint arXiv:2202.02450 (2022).