Overview

In recent years, there has been an explosion in the use of machine learning for atomistic applications, in particular using ML models as interatomic potentials for molecular simulations (i.e. molecular dynamics, Monte Carlo, …). This, in turn, creates a lot of redundant work integrating new ML models with simulation engines (such as ASE, LAMMPS, i-PI, GROMACS, and many more!). Each new ML model needs to write code to integrate each relevant engine one by one.

Our goal with metatensor atomistic models is to define a very clear boundary between the model and the engines, such that models following the metatensor interface can be used with any simulation engine (provided they know how to use the interface); and that simulation engine only need to implement code to use to ML models once, and get access to all machine learning models following this interface.

Different steps in the workflow of running simulations with metatensor. Defining a model, training a model and running simulations with it can be done by different users; and the same metatensor-based model can be used with multiple simulation engines.

This atomistic models interface is based on metatensor data format, and make extensive use of data format ability to express sparsity (for example when storing neighbor lists) and self-describing properties (to communicate what exactly a model output contains in a generic manner). Using metatensor rich data types (Labels, TensorBlock, and TensorMap) in the atomistic interface is what allows us to make the interface smaller and with fewer special cases. The same interface can be used to communicate about both complex (e.g. electron density, Hamiltonian matrix elements) and simple (e.g. energy, atomic charges) predictions of the models; and support multiple pathways for the prediction of gradients of properties.

See also

We have a couple of tutorials to learn how to define, export, and use metatensor atomistic models.

Why use metatensor for atomistic models

The reason for using metatensor atomistic models will depend on which kind of user you are (the same user can fall into multiple categories at different points in time!):

Creating new machine learning architectures

You are working to define new ML architectures, incorporating the latest ML research and coming up with new ideas to make ML models better.

By using metatensor, you’ll get to make your architecture available to everyone immediately and with fewer efforts. You’ll also potentially get to delegate the work on the simulation engine interface to other developers, by sharing a single metatensor-based implementation with them.

Training existing architectures on new datasets

You are taking existing architectures, and training them on your own dataset.

By using metatensor, you’ll get the ability to immediately test your model inside a Python environment (with Python-based simulation engines) and once you are confident with it, scale your simulations to larger scales while keeping the exact same model. You can also more easily integrate various architectures in your workflow (or even combine multiple models) and compare them for your own data.

Running simulations to study specific systems

You want to study a specific system, and machine learning is only one of the tools in your toolbox. You might be training your own models, or using pre-trained models from someone else.

By using metatensor, you’ll get too use simulation software you are already familiar with, instead of having to install and learn new software just to use one specific ML model. You’ll also get an easy way to try and compare existing models: just load them in your simulation engine and hit the floor running!

Developing of simulation engines

You are working on software for molecular simulations, including algorithms to sample different thermodynamic ensembles, or high performance simulation code.

By using metatensor, you’ll get access to the whole space of machine learning potentials at once! You’ll also get to use models for more than predicting the energy of a system (for example using ML models for charge transfers, predicting polarizability along a trajectory, etc.).

How it works

Metatensor atomistic models are based on PyTorch, and more particularly TorchScript. TorchScript is a programming language which is mainly a subset of Python, and PyTorch contains a compiler from Python to TorchScript code. After doing this translation, the model no longer depends on Python and can be executed directly inside simulation engines implemented in C, C++, Fortran, … This approach allow to define and tweak models as Python code, and then once they are working as intended, export them to a Python-independent representation to be used in simulations.

In practice, models should be defined as custom torch.nn.Module sub-class, following our ModelInterface. New models can be written using this interface directly, and pre-existing models can use a small wrapper to convert from this interface to the model’s existing input and output data. The models take as input a set of atomistic System (typically a single one during simulations, and multiple systems during training); a set of outputs requested by the engine, and should make prediction for all properties in the outputs. All predictions are then returned to the engine in a dictionary of metatensor.torch.TensorMap, one such tensor map for each property (i.e. energy, atomic charges, dipole, electronic density, chemical shielding, etc.)

Once a model is defined and trained, it should be exported by constructing a MetatensorAtomisticModel, and calling export on it. This class is a wrapper for the model that will handle unit conversions on input and outputs. It will also store metadata about the model (such as the authors, a list of references, …) and the model capabilities (what properties it can compute, which neighbors list the whole model requires, …). Optionally, this class can also check that both data provided by the engine and properties computed by the model follow the metatensor interface, which can be used to debug your code.

Finally, the exported model can be loaded by simulation engines and used to run simulations and make predictions.

Constrains on atomistic models

There are a couple of constrains on what a given model must do to be useable with metatensor, but apart from these you can do what you want inside the model!

The main constrain is that the model must be compatible with TorchScript, i.e. you must use either pure PyTorch code in the definition of your model, or implement a custom TorchScript extension for any operations where a pure PyTorch implementation is too slow or too much work. See the corresponding documentation <torch-extensions>_ for more information on custom TorchScript extensions.

Your model should also only take data from our System definition: atomic types and positions, simulation cell, and list of neighbors for different spherical cutoffs.

If you need additional data that you can not compute inside the model (such as atomic spins, non-spherical particle orientation, etc.) you can use System.get_data(), but this comes with significant caveats:

• anything going through System.get_data() is experimental with no stability guarantee;

• you must modify the engine code to use System.add_data() to add the required data to the systems;

If you need such data, please contact us (using email or GitHub issues) to formulate a plan to add it to metatensor interface!

Finally, your model can compute and output what it wants, and organize the data and metadata of the outputs as it pleases, except for a set of standardized outputs (identified by the corresponding key in the output dictionary). These standardized outputs are documented in this page.

Data flow between the model and engine

The sequence of operations to use a metatensor atomistic model from a simulation engine follows the same high level sequence of operations, illustrated and explained below.

Illustration of the flow of data between the engine and the model.

1. the engine loads an exported model from a file;

   Tip

   The engine should use check_atomistic_model() or metatensor_torch::load_atomistic_model() to also perform checks before loading the model.

2. the engine requests and gets its capabilities from the model;

   Tip

   This can be done by calling MetatensorAtomisticModel.capabilities(). This function is also exported to TorchScript and can be called from C++ with torch::jit::Module::run_method().

3. the engine creates the ModelEvaluationOptions based on the model’s capabilities and user input;

4. the engine creates a list of System (typically the list only contains one system) matching its own internal data representation;

   Tip

   The positions and cell should have their respective requires_grad parameters set if the engine wants to run backward propagation at step 10.

5. the engine asks the model for the required neighbor lists;

   Tip

   This can be done by calling MetatensorAtomisticModel.requested_neighbor_lists(). This function is also exported to TorchScript and can be called from C++ with torch::jit::Module::run_method().

6. the engine computes the neighbor lists corresponding to the model requests, and register them with all systems;

   Tip

   If the engine does not use torch to compute the neighbor lists (using instead some other neighbors list implementation), the neighbors list should be registered with torch’s automatic differentiation framework by using register_neighbors_autograd() before adding the neighbors lists to the systems.

   We provide a set of regression tests for neighbors lists in metatensor-torch/tests/neighbor-checks. The data in these files can be used to validate that a specific engine is computing the expected set of pairs for integration with metatensor models.

7. the engine calls the model forward() function with all the systems, the evaluations options and selected atoms, if any;

8. the model runs and executes its calculations;

9. the model returns all the requested outputs to the engine;

10. if needed, the engine runs backward() on the outputs to get gradients of some outputs with backward propagation;

    Tip

    The API for metatensor atomistic models also supports gradients computed during the forward pass with ModelOutput.explicit_gradients. Most models will not support this option though, and as such it is better to try to rely on backward differentiation gradients where possible.