Exporting a model

This tutorial shows how to define and export an atomistic model following metatensor’s interface.

Model export in metatensor is based on PyTorch and TorchScript, so make sure you are familiar with both before reading this tutorial!

Let’s start by importing things we’ll need: typing for the model type annotations, torch itself, the main metatensor types and classes specific to metatensor atomistic models:

import glob
from typing import Dict, List, Optional

import torch

from metatensor.torch import Labels, TensorBlock, TensorMap
from metatensor.torch.atomistic import (
    MetatensorAtomisticModel,
    ModelCapabilities,
    ModelMetadata,
    ModelOutput,
    System,
)

Defining the model

The model is defined as a class, inheriting from torch.nn.Module, and with a very specific signature for the forward() function:

class MyCustomModel(torch.nn.Module):
    def forward(
        self,
        systems: List[System],
        outputs: Dict[str, ModelOutput],
        selected_atoms: Optional[Labels],
    ) -> Dict[str, TensorMap]:
        pass

Here systems will be the list of System (sometimes also called structures, or frames) for which the model should make a prediction. outputs defines what properties should be included in the model output (in case where the model supports computing more than one property), as well as some options regarding how the properties should be computed in ModelOutput. outputs will be provided by whoever is using the model: a simulation engine, yourself later, a coworker, etc.

Finally, selected_atoms is also set by whoever is using the model, and is either None, meaning all atoms should be included in the calculation, or a metatensor.torch.Labels object containing two dimensions: "system" and "atom", with values corresponding to the structure/atoms indexes to include in the calculation. For example when working with additive atom-centered models, only atoms in selected_atoms will be used as atomic centers, but all atoms will be considered when looking for neighbors of the central atoms.

Let’s define a model that predict the energy of a system as a sum of single atom energy (for example some isolated atom energy computed with DFT), and completely ignores the interactions between atoms. Such model can be useful as a baseline model on top of which more refined models can be trained.

class SingleAtomEnergy(torch.nn.Module):
    def __init__(self, energy_by_atom_type: Dict[int, float]):
        super().__init__()
        self.energy_by_atom_type = energy_by_atom_type

    def forward(
        self,
        systems: List[System],
        outputs: Dict[str, ModelOutput],
        selected_atoms: Optional[Labels] = None,
    ) -> Dict[str, TensorMap]:
        # if the model user did not request an energy calculation, we have nothing to do
        if "energy" not in outputs:
            return {}

        # we don't want to worry about selected_atoms yet
        if selected_atoms is not None:
            raise NotImplementedError("selected_atoms is not implemented")

        if outputs["energy"].per_atom:
            raise NotImplementedError("per atom energy is not implemented")

        # compute the energy for each system by adding together the energy for each atom
        energy = torch.zeros((len(systems), 1), dtype=systems[0].positions.dtype)
        for i, system in enumerate(systems):
            for atom_type in system.types:
                energy[i] += self.energy_by_atom_type[int(atom_type)]

        # add metadata to the output
        block = TensorBlock(
            values=energy,
            samples=Labels("system", torch.arange(len(systems)).reshape(-1, 1)),
            components=[],
            properties=Labels("energy", torch.tensor([[0]])),
        )
        return {
            "energy": TensorMap(keys=Labels("_", torch.tensor([[0]])), blocks=[block])
        }

With the class defined, we can now create an instance of the model, specifying the per-atom energies we want to use. When dealing with more complex models, this is also where you would actually train your model to reproduce some target energies, using standard PyTorch tools.

model = SingleAtomEnergy(
    energy_by_atom_type={
        1: -6.492647589968434,
        6: -38.054950840332474,
        8: -83.97955098636527,
    }
)

We don’t need to train this model since there are no trainable parameters inside. If you are adapting this example to your own models, this is where you would train them for example like:

optimizer = ...
for epoch in range(...):
    optimizer.zero_grad()
    loss = ...
    optimizer.step()

Exporting the model

Once your model has been trained, we can export it to a model file, that can be used to run simulations or make predictions on new systems. This is done with the MetatensorAtomisticModel class, which takes your model and make sure it follows the required interface.

When exporting the model, we can define some metadata about this model, so when the model is shared with others, they still know what this model is and where it comes from.

metadata = ModelMetadata(
    name="single-atom-energy",
    description="a long form description of this specific model",
    authors=["You the Reader <[email protected]>"],
    references={
        # you can add references that should be cited when using this model here,
        # check the documentation for more information
    },
)

A big part of exporting a model is the definition of the model capabilities, i.e. what are the things that this model can do? First we’ll need to define which outputs our model can handle: there is only one, called "energy", which correspond to the physical quantity of energies (quantity="energy"). This energy is returned in electronvolt (units="eV"); and with the code above it can not be computed per-atom, only for the full structure (per_atom=False).

outputs = {
    "energy": ModelOutput(quantity="energy", unit="eV", per_atom=False),
}

In addition to the set of outputs a model can compute, the capabilities also include:

  • the set of atomic_types the model can handle;

  • the interaction_range of the model, i.e. how far away from one particle the model needs to know about other particles. This is mainly relevant for domain decomposition, and running simulations on multiple nodes;

  • the length_unit the model expects as input. This applies to the interaction_range, any neighbors list cutoff, the atoms positions and the system cell. If this is set to a non empty string, MetatensorAtomisticModel will handle the necessary unit conversions for you;

  • the set of supported_devices on which the model can run. These should be ordered according to the model preference.

  • the dtype (“float32” or “float64”) that the model uses for its inputs and outputs

capabilities = ModelCapabilities(
    outputs=outputs,
    atomic_types=[1, 6, 8],
    interaction_range=0.0,
    length_unit="Angstrom",
    supported_devices=["cpu"],
    dtype="float64",
)

With the model metadata and capabilities defined, we can now create a wrapper around the model, and export it to a file:

wrapper = MetatensorAtomisticModel(model.eval(), metadata, capabilities)
wrapper.save("exported-model.pt")

# the file was created in the current directory
print(glob.glob("*.pt"))
['exported-model.pt']

Now that we have an exported model, the next tutorial will show how you can use such a model to run Molecular Dynamics simulation using the Atomic Simulating Environment (ASE).

Total running time of the script: (0 minutes 0.065 seconds)

Gallery generated by Sphinx-Gallery