Metatomic

Overview

This module implements the interface between PLUMED and metatomic, allowing to use arbitrary machine learning models as collective variables. These machine learning models are defined using custom Python code — following the metatomic interface — and then exported to TorchScript. The exported model is then loaded inside PLUMED and executed during the simulation.

Installation

This module requires two main dependencies: the C++ torch library (i.e. libtorch); and the C++ metatomic_torch library. There are multiple ways of installing both libraries, which are discussed below.

Getting the dependnecies

Using Python's package manager (pip)

The easiest way to get all dependencies on your system is to download the pre-built Python wheels with pip. This is the same set of wheels you will need to define custom models.

pip install "metatomic-torch ==0.1.0"  # change this version to get newer releases
 
# you can then get the compiler and linker flags using the script at
# src/metatomic/flags-from-python.py
CPPFLAGS=$(python src/metatomic/flags-from-python.py --cppflags)
LDFLAGS=$(python src/metatomic/flags-from-python.py --ldflags)

That's it, you can now jump to the last part of the installation instructions.

Using conda

You can also use conda with the conda-forge channel to install all dependencies:

conda install -c conda-forge libmetatomic-torch
 
# setup compiler flags:
CPPFLAGS="-I$CONDA_PREFIX/include $CPPFLAGS"
CPPFLAGS="-I$CONDA_PREFIX/include/torch/csrc/api/include $CPPFLAGS"
 
LDFLAGS="-L$CONDA_PREFIX/lib $LDFLAGS"
LDFLAGS="-Wl,-rpath,$CONDA_PREFIX/lib $LDFLAGS"
 
# if you are using linux, force the use of rpath instead of runpath
# (we rely on the rpath to find dependencies of dependencies)
LDFLAGS="-Wl,--disable-new-dtags"

That's it, you can now jump to the last part of the installation instructions.

From sources

You can also compile all required libraries from source. To this end, please follow the corresponding instructions:

• torch: https://pytorch.org/get-started/locally/, for the C++ language
• metatensor: https://docs.metatensor.org/latest/installation.html#install-c
• metatensor-torch: https://docs.metatensor.org/latest/installation.html#install-torch-cxx
• metatomic-torch: https://docs.metatensor.org/metatomic/latest/installation.html#install-torch-cxx

Once everything is compiled and installed, you should set the corresponding preprocessor flags in CPPFLAGS and the corresponding linker flags in LDFLAGS.

Building plumed with metatensor

Once you installed all dependencies with one of the methods above, you can now configure PLUMED:

./configure --enable-libtorch --enable-libmetatomic --enable-modules=+metatomic LDFLAGS="$LDFLAGS" CPPFLAGS="$CPPFLAGS"

Note

Pay close attention to the output, it should contain both a line about checking libtorch and a line about checking libmetatomic, both ending with ...yes. If this is not the case, you'll get a warning about cannot enable __PLUMED_HAS_LIBTORCH or cannot enable __PLUMED_HAS_LIBMETATOMIC.

If you get any of these warnings, you should check config.log to know more about what's going on and why these libraries can't be found.

Module Contents

This module defines the following actions:

METATOMIC

Use arbitrary machine learning models as collective variables.