Add GROMACS simulation engine

docs/src/_prolog.rst

@@ -68,6 +68,11 @@
     :align: middle
     :alt: eOn
 
+.. |gromacs-logo| image:: /../static/images/logo-gromacs-large.*
+    :height: 60px
+    :align: middle
+    :alt: GROMACS
+
 .. |ipi-logo| image:: /../static/images/logo-ipi.*
     :height: 60px
     :align: middle

docs/src/engines/gromacs.rst

@@ -0,0 +1,232 @@
+.. _engine-gromacs:
+
+GROMACS
+=======
+
+.. list-table::
+    :header-rows: 1
+
+    * - Official website
+      - How is metatomic supported?
+    * - https://www.gromacs.org
+      - In a separate `fork <https://github.com/metatensor/gromacs>`_
+
+Supported model outputs
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The :ref:`energy <energy-output>` is supported in the custom metatomic module in
+GROMACS. The module allows running molecular dynamics simulations on the full system or
+on a subgroup (ML/MM) with interatomic potentials in the metatomic format.
+
+How to install the code
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Building from sources
+---------------------
+
+The code is available in a custom fork of GROMACS, and you can get it with
+
+.. code-block:: bash
+
+    git clone https://github.com/metatensor/gromacs gromacs-metatomic
+    cd gromacs-metatomic
+
+You'll need to provide some of the code dependencies yourself. There are
+multiple ways to go about it, here we detail a fully manual installation, an
+installation using ``conda`` and an installation using ``pip``.
+
+Option 1: dependencies from ``conda``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+All the dependencies of the code are available on ``conda``, you can install
+them with
+
+.. code-block:: bash
+
+    # create an environment (you can also re-use an existing one)
+    conda create -n gromacs-metatomic
+    conda activate gromacs-metatomic
+
+    conda install -c metatensor -c conda-forge libmetatomic-torch
+
+    # Store this information to configure cmake down the line
+    CMAKE_PREFIX_PATH="$CONDA_PREFIX"
+
+
+Option 2: dependencies from ``pip``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+All the dependencies of the code are also available on ``PyPI``, you can install
+them with
+
+.. code-block:: bash
+
+    # (optional) create an environment with your preferred method
+    ...
+
+    python -m pip install metatomic-torch
+
+    # on linux, if you don't have a GPU available, you should force the use of
+    # CPU-only torch instead
+    python -m pip install --extra-index-url=https://download.pytorch.org/whl/cpu metatomic-torch
+
+    # Get the information to configure cmake down the line
+    TORCH_PREFIX=$(python -c "import torch; print(torch.utils.cmake_prefix_path)")
+    MTS_PREFIX=$(python -c "import metatensor; print(metatensor.utils.cmake_prefix_path)")
+    MTS_TORCH_PREFIX=$(python -c "import metatensor.torch; print(metatensor.torch.utils.cmake_prefix_path)")
+    MTA_TORCH_PREFIX=$(python -c "import metatomic.torch; print(metatomic.torch.utils.cmake_prefix_path)")
+
+    CMAKE_PREFIX_PATH="$TORCH_PREFIX;$MTS_PREFIX;$MTS_TORCH_PREFIX;$MTA_TORCH_PREFIX"
+
+
+Option 3: manual dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You'll need to build or download the the C++ version of ``libtorch``. You can
+download it from https://pytorch.org/get-started/locally/, using the C++
+language selector. Once you have it downloaded, extract the archive somewhere,
+and record the path:
+
+.. code-block:: bash
+
+    # point this to the path where you extracted the C++ libtorch
+    TORCH_PREFIX=<path/to/torch/installation>
+
+For the other dependencies, you'll either need to install them yourself
+following the links below, or let ``cmake`` download and build the latest
+compatible versions:
+
+- :external+metatensor:ref:`metatensor <install-c>`
+- :external+metatensor:ref:`metatensor-torch <install-torch-cxx>`
+- :ref:`metatomic-torch <install-torch-cxx>`
+
+If you want to provide these yourself, you'll need to also record the
+corresponding installation paths:
+
+.. code-block:: bash
+
+    MTS_PREFIX=<path/to/metatensor/installation>
+    MTS_TORCH_PREFIX=<path/to/metatensor/torch/installation>
+    MTA_TORCH_PREFIX=<path/to/metatomic/torch/installation>
+
+And finally you can store this information to configure cmake down the line:
+
+.. code-block:: bash
+
+    CMAKE_PREFIX_PATH="$TORCH_PREFIX;$MTS_PREFIX;$MTS_TORCH_PREFIX;$MTA_TORCH_PREFIX"
+
+Building the code
+~~~~~~~~~~~~~~~~~
+
+After installing the dependencies with one of the options above, you can
+configure the build with:
+
+.. code-block:: bash
+
+    mkdir build && cd build
+
+    # you can add more options here.
+    cmake .. \
+        -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" \
+        -DTorch_DIR=$TORCH_PREFIX \
+        -DGMX_METATOMIC=AUTO
+
+    cmake --build . --parallel 4 # or `make -jX`
+
+    # optionally install the code on your machine. You can also directly use
+    # the `gmx` binary in `gromacs-metatomic/build/bin/gmx` without installation
+    cmake --build . --target install # or `make install`
+
+By default, ``cmake`` will try to find the ``metatensor`` and ``metatomic``
+libraries on your system and use them. If it can not find the libraries, it will
+download and build them as part of the main GROMACS build. You can control this
+behavior by adding ``-DDOWNLOAD_METATENSOR=ON`` and ``-DDOWNLOAD_METATOMIC=ON``
+to the ``cmake`` options to always force a download; or prevent any download by
+setting these options to ``OFF``.
+
+How to use the code
+^^^^^^^^^^^^^^^^^^^
+
+.. note::
+
+    Here we assume you already have an exported model that you want to use in
+    your simulations. Please see :ref:`this tutorial
+    <atomistic-tutorial-export>` to learn how to manually create and export a
+    model; or use a tool like `metatrain`_ to create a model based on existing
+    architectures and your own dataset.
+
+    .. _metatrain: https://github.com/metatensor/metatrain
+
+After building and optionally installing the code, you can now use metatomic
+module in your GROMACS molecular dynamics parameter (MDP) files! Below are the
+reference options
+
+  .. parsed-literal::
+
+      **metatomic-active** yes or no
+        set this to yes to activate the metatomic potential, or no to disable it.
+      **metatomic-input-group**
+        name of the input group to use for the metatomic potential. To couple the whole
+        system use "System".
+      **metatomic-model**
+        path to the file containing the exported metatomic model.
+      **metatomic-extensions**
+        path to a directory containing TorchScript extensions as shared libraries. If
+        the model uses extensions, we will try to load them from this directory first
+      **metatomic-device** cpu or cuda
+        device to use to run the model. If not given, the best available device will be
+        used.
+      **metatomic-check-consistency** yes or no
+        if yes, the code will check that the model is consistent with the system
+        topology at the start of the simulation. This can help catch errors due to
+        mismatched atom ordering between the model and the system, but it comes at a
+        performance cost.
+      **metatomic-variant** no or <variant>
+        specifies which variant of the model outputs should be uses for making
+        predictions. Defaults to no variant.
+
+.. note::
+
+    The device can also be overridden at runtime by setting the environment
+    variable ``GMX_METATOMIC_DEVICE`` to a value.
+
+Sample input file
+-----------------
+
+Below is a example input file for an ML/MM simulation of an alanin dipeptide in water,
+using a metatomic model for the peptide and a classical force field for the water
+molecules. For a detailed example we refer to the `chapter in the atomistic cookbook
+<TODO>`_.
+
+.. code-block:: ini
+
+    ; Run control
+    integrator              = md
+    dt                      = 0.0005
+    nsteps                  = 500
+
+    ; Output control
+    nstxout                 = 10
+    nstvout                 = 10
+    nstenergy               = 10
+    nstcalcenergy           = 10
+    nstlog                  = 10
+
+    ; Neighborsearching
+    cutoff-scheme           = Verlet
+    pbc                     = xyz
+
+    ; Electrostatics
+    coulombtype             = PME
+
+    ; Temperature coupling
+    tcoupl                  = v-rescale
+    tc-grps                 = water protein ; two coupling groups - more accurate
+    tau-t                   = 2.0   2.0 ; time constant, in ps
+    ref-t                   = 300   300
+
+    ; Metatomic interface
+    metatomic-active        = yes
+    metatomic-input-group   = protein  ; the group on which ML forces are applied
+    metatomic-modelfile     = model.pt  ; path to the model file
+    metatomic-device        = cpu  ; device to run the model on (cpu or cuda)

docs/src/engines/index.rst

@@ -46,6 +46,14 @@ add it here!
         :width: 150px
         :align: center
 
+    .. grid-item-card:: GROMACS
+      :link: engine-gromacs
+      :link-type: ref
+
+      .. image:: /../static/images/logo-gromacs.*
+        :width: 150px
+        :align: center
+
     .. grid-item-card:: i-PI
       :link: engine-ipi
       :link-type: ref
@@ -86,6 +94,7 @@ add it here!
   ase
   chemiscope
   eon
+  gromacs
   ipi
   lammps
   plumed

docs/src/index.rst

@@ -6,12 +6,12 @@
    :class: only-dark sd-mb-4
    :width: 600px
 
-``metatomic`` is a library that defines a common interface between atomistic
-machine learning models, and atomistic simulation engines. Our main goal is to
-define and train models once, and then be able to re-use them across many
-different simulation engines (such as LAMMPS, PLUMED, *etc.*). We strive to
-achieve this goal without imposing any structure on the model itself, and to
-allow any model architecture to be used.
+``metatomic`` is a library that defines a common interface between atomistic machine
+learning models, and atomistic simulation engines. Our main goal is to define and train
+models once, and then be able to re-use them across many different simulation engines
+(such as LAMMPS, GROMACS, PLUMED, *etc.*). We strive to achieve this goal without
+imposing any structure on the model itself, and to allow any model architecture to be
+used.
 
 This library focuses on exporting and importing fully working, already trained
 models. If you want to train existing architectures with new data or re-use

docs/src/outputs/energy.rst

@@ -55,19 +55,27 @@ The following simulation engines can use the ``"energy"`` output:
   .. grid-item-card::
     :text-align: center
     :padding: 1
-    :link: engine-ipi
+    :link: engine-eon
     :link-type: ref
 
-    |ipi-logo|
+    |eon-logo|
+    |eon-logo-dark|
 
   .. grid-item-card::
     :text-align: center
     :padding: 1
-    :link: engine-eon
+    :link: engine-gromacs
     :link-type: ref
 
-    |eon-logo|
-    |eon-logo-dark|
+    |gromacs-logo|
+
+  .. grid-item-card::
+    :text-align: center
+    :padding: 1
+    :link: engine-ipi
+    :link-type: ref
+
+    |ipi-logo|
 
   .. grid-item-card::
     :text-align: center

docs/src/outputs/variants.rst

@@ -40,10 +40,19 @@ The following simulation engines can use variants for all their supported output
   .. grid-item-card::
     :text-align: center
     :padding: 1
-    :link: engine-lammps
+    :link: engine-eon
     :link-type: ref
 
-    |lammps-logo|
+    |eon-logo|
+    |eon-logo-dark|
+
+  .. grid-item-card::
+    :text-align: center
+    :padding: 1
+    :link: engine-gromacs
+    :link-type: ref
+
+    |gromacs-logo|
 
   .. grid-item-card::
     :text-align: center
@@ -56,8 +65,7 @@ The following simulation engines can use variants for all their supported output
   .. grid-item-card::
     :text-align: center
     :padding: 1
-    :link: engine-eon
+    :link: engine-lammps
     :link-type: ref
 
-    |eon-logo|
-    |eon-logo-dark|
+    |lammps-logo|