developer.md

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Developer Guide

This is a developer's guide to writing new models in matgl. It is still a work in progress.

MatGL is based on the Deep Graph Library (DGL). Most of the questions relating to how to implement graph deep learning models, etc. is already covered in the extensive documentation for DGL. You are encouraged to read those. Here, we will focus our discussion on improvements / additions / design elements specifically for matgl.

Modular components

To maintain maximum flexibility, we have implemented the steps of using graph deep learning for materials in separate, reusable modular components. These steps include:

• Converting materials to DGL graphs from pymatgen, ase and other materials science codes (matgl.ext).
• Dataset loading (matgl.graphs).
• Actual graph model implementations (matgl.models) and their internal components (matgl.layers).
• Special use cases of models, e.g., for interatomic potentials (matgl.apps).

Controlled API exposure

The exposed API is controlled to allow for code refactoring and development. Any module that is preceded by an underscore is a "private" implementation by convention and there are no guarantees as to backwards compatibility. For example, the MEGNet and M3GNet models are exposed via matgl.models in the __init__.py while the actual implementations are in _megnet.py and _m3gnet.py, respectively. This is similar to the convention adopted by scikit-learn. As far as possible, do imports only from exposed APIs.

Nested Models

Often, a simple input->output model architecture is often insufficient. For instance, one might want to fit a model on a scaled or transformed version of the target. For instance, the current best practice is to fit models to the log of the bulk modulus as it spans several orders of magnitude. Similarly, an interatomic potential has to compute derivatives such as forces and stresses from the energies. This presents a difficulty when the model is actually being used for end predictions as the user has to remember to invert the scaling or transformation or perform additional steps.

To make matgl models much more friendly for end users, we implement a nested model concept. Examples include matgl.apps.pes.Potential, which is an interatomic potential model that wraps around a graph model (e.g. M3GNet), and the matgl.models.TransformedTargetModel, which is modelled after scikit-learn's TransformedTargetRegressor. The goal is for users to be able to use such models directly without having to worry about the internal transformations.

Model IO

All models subclass the matgl.utils.io.IOMixIn class, which is basically a wrapper around PyTorch's mechanisms for loading and saving model state but with additional metadata to make it simpler to load models. To use this class properly, models should subclass torch.nn.Module and IOMixIn. In addition, the save_args method should be called after the super class call. A simpel example is as follows:

import torch
from matgl.utils.io import IOMixIn

class MyModel(torch.nn.Module, IOMixIn):

    __version__ = 1

    def __init__(self, *args, **kwargs):
        super().__init__()
        self.save_args(locals(), kwargs)

Models implementing this protocol can be saved and loaded using model.save(path), Model.load(path) and the convenience matgl.load_model(path) methods.

Model versioning

The IOMixIn supports optional model versioning. To enable this, the model class should have an integer __version__ class variable. The goal is to increment this variable when architectural changes occur and saved pre-trained models need to be invalidated. If not specified, the model is not versioned at all.

Testing

All code contributions must be accompanied by comprehensive unittests. These tests should be added to the appropriate mirror directory in the tests folder.

We use pytest. Useful fixtures have been written in the conftest.py file in the tests directory, which provides crystals, molecules, and pre-generated graphs for reuse in tests.

Documentation

We use Google doc style.