metatrain 2025.7

Training and evaluating machine learning models for atomistic systems.

metatrain is a command line interface (cli) to train and evaluate atomistic models of various architectures. It features a common yaml option inputs to configure training and evaluation. Trained models are exported as standalone files that can be used directly in various molecular dynamics (MD) engines (e.g. LAMMPS, i-PI, ASE …) using the metatensor atomistic interface.

The idea behind metatrain is to have a general hub that provide an homogeneous environment and user interface transforms every ML architecture in an end-to-end model that can be connected to an MD engine. Any custom architecture compatible with TorchScript can be integrated in metatrain, gaining automatic access to a training and evaluation interface, as well as compatibility with various MD engines.

Note: metatrain does not provide mathematical functionalities per se but relies on external models that implement the various architectures.

List of Implemented Architectures

Currently metatrain supports the following architectures for building an atomistic model.

Name	Description
GAP	Sparse Gaussian Approximation Potential (GAP) using Smooth Overlap of Atomic Positions (SOAP).
PET	Point Edge Transformer (PET), interatomic machine learning potential
NanoPET (experimental)	re-implementation of the original PET with slightly improved training and evaluation speed
PET (deprecated)	Original implementation of the PET model used for prototyping, now deprecated in favor of the native metatrain PET implementation.
SOAP BPNN	A Behler-Parrinello neural network with SOAP features

Documentation

For details, tutorials, and examples, please have a look at our documentation.

Installation

You can install metatrain with pip:

pip install metatrain

In addition, specific models must be installed by specifying the model name. For example, to install the SOAP-BPNN model, you can run:

pip install metatrain[soap-bpnn]

We also offer a conda installation:

conda install -c conda-forge metatrain

The conda installation does not install model specific dependencies and will therefore only work for architectures without optional dependencies such as NanoPET or PET.

After installation you can then use mtt from the command line to train your models!

Quickstart

To train a model, you can use the following command:

mtt train options.yaml

Where options.yaml is a configuration file that specifies the training options. For example, the following configuration file trains a SOAP-BPNN model on the QM9 dataset:

# architecture used to train the model
architecture:
  name: soap_bpnn
  training:
    num_epochs: 5 # a very short training run

# Mandatory section defining the parameters for system and target data of the
# training set
training_set:
  systems: "qm9_reduced_100.xyz" # file where the positions are stored
  targets:
    energy:
      key: "U0" # name of the target value
      unit: "eV" # unit of the target value

test_set: 0.1 # 10 % of the training_set are randomly split and taken for test set
validation_set: 0.1 # 10 % of the training_set are randomly split and for validation set

Shell Completion

metatrain comes with completion definitions for its commands for bash and zsh. Since it is difficult to automatically configure shell completions in a robust manner, you must manually configure your shell to enable its completion support.

To make the completions available, source the definitions as part of your shell’s startup. Add the following to your ~/.bash_profile, ~/.zshrc (or, if they don’t exist, ~/.profile):

source $(mtt --shell-completion)

Having problems or ideas?

Having a problem with metatrain? Please let us know by submitting an issue.

Submit new features or bug fixes through a pull request.

Contributors

Thanks goes to all people that make metatrain possible: