.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/atomistic/3-atomistic-model-with-nl.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_atomistic_3-atomistic-model-with-nl.py: .. _atomistic-tutorial-nl-md: Creating models that use neighbor lists ======================================= .. py:currentmodule:: metatensor.torch.atomistic This tutorial demonstrates how to create an atomistic model that requires a neighbor list, and use it to run MD simulations. This tutorial assumes knowledge of how to export an atomistic model and run it with the ASE calculator. If you haven't read the corresponding examples, please refer to :ref:`atomistic-tutorial-export` and :ref:`atomistic-tutorial-md`. As depicted below, one or more neighbor lists will be requested by the model, computed by the simulation engine and attached to the :py:class:`Systems`. The :py:class:`Systems` with the neighbor list is then passed to the model. .. figure:: ../../../static/images/nl-dataflow.* :width: 600px :align: center The simulation engine computes the neighbor lists for the model, which then uses them to predict outputs. This figure is a subset of the figure in :ref:`model-dataflow`. As example, we will run a 1 ps short molecular dynamics simulation of 125 already equilibrated liquid argon atoms interacting via Lennard-Jones within a cutoff of 5 Å. The system will be simulated at a temperature of 94.4 K and a mass density of 1.374 g/cm³. In the end, we will obtain the pair-correlation function :math:`g(r)` of the liquid. .. GENERATED FROM PYTHON SOURCE LINES 33-66 .. code-block:: Python from typing import Dict, List, Optional # tools for analysis import ase.geometry.rdf # tools to run the simulation and visualization import ase.io import ase.md import ase.neighborlist import ase.visualize.plot import chemiscope import matplotlib.pyplot as plt # the usual suspects import numpy as np import torch from metatensor.torch import Labels, TensorBlock, TensorMap from metatensor.torch.atomistic import ( MetatensorAtomisticModel, ModelCapabilities, ModelMetadata, ModelOutput, NeighborListOptions, System, ) # Integration with ASE calculator for metatensor atomistic models from metatensor.torch.atomistic.ase_calculator import MetatensorCalculator .. GENERATED FROM PYTHON SOURCE LINES 68-73 The simulation system ---------------------- We load the pre-equilibrated :download:`liquid argon system from a file`. .. GENERATED FROM PYTHON SOURCE LINES 74-77 .. code-block:: Python atoms = ase.io.read("liquid-argon.xyz") .. GENERATED FROM PYTHON SOURCE LINES 78-82 The system was generated based on a 5x5x5 supercell of a simple cubic (sc) cell with a lattice constant of a = 3.641 Å. After initialization of the velocities, the system was run for 100 ps with the same parameters we will use below and the final state can be visualized as .. GENERATED FROM PYTHON SOURCE LINES 83-89 .. code-block:: Python ax = ase.visualize.plot.plot_atoms(atoms, radii=0.5) ax.set_xlabel("$\\AA$") ax.set_ylabel("$\\AA$") plt.show() .. image-sg:: /examples/atomistic/images/sphx_glr_3-atomistic-model-with-nl_001.png :alt: 3 atomistic model with nl :srcset: /examples/atomistic/images/sphx_glr_3-atomistic-model-with-nl_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 90-91 The system already has velocities and the expected density of 1.374 g/cm³. .. GENERATED FROM PYTHON SOURCE LINES 92-100 .. code-block:: Python u_to_g = 1.66053906660e-24 Å_to_cm = 1e-08 mass_density = sum(atoms.get_masses()) / atoms.cell.volume * u_to_g / Å_to_cm**3 print(f"ρ_m = {mass_density:.3f} g/cm³") .. rst-class:: sphx-glr-script-out .. code-block:: none ρ_m = 1.374 g/cm³ .. GENERATED FROM PYTHON SOURCE LINES 101-115 Metatensor's neighbor lists --------------------------- .. note:: The steps below of creating a neighbor list, wrapping it inside a :py:class:`TensorBlock ` and attaching it to a system will be done by the simulation engine and must not be handled by the model developer. How to request a neighbor list will be presented below when the actual model is defined. Before implementing the actual model, let's take a look at how metatensor stores neighbor lists inside a :py:class:`System` object. We start by computing the neighbor list for our argon systen using ASE. .. GENERATED FROM PYTHON SOURCE LINES 116-119 .. code-block:: Python i, j, S, D = ase.neighborlist.neighbor_list(quantities="ijSD", a=atoms, cutoff=5.0) .. GENERATED FROM PYTHON SOURCE LINES 120-124 The :py:func:`ase.neighborlist.neighbor_list` function returns the neighbor indices: quantities ``"i"`` and ``"j"``, the neighbor shifts ``"S"``, and the distance vectors ``"D"``. We now stack these together and convert them into the suitable types. .. GENERATED FROM PYTHON SOURCE LINES 125-134 .. code-block:: Python i = torch.from_numpy(i.astype(int)) j = torch.from_numpy(j.astype(int)) neighbor_indices = torch.stack([i, j], dim=1) neighbor_shifts = torch.from_numpy(S.astype(int)) print("neighbor_indices:", neighbor_indices) print("neighbor_shifts:", neighbor_shifts) .. rst-class:: sphx-glr-script-out .. code-block:: none neighbor_indices: tensor([[ 0, 6], [ 0, 1], [ 0, 20], ..., [124, 104], [124, 78], [124, 98]]) neighbor_shifts: tensor([[ 1, 0, 0], [ 0, 0, 0], [ 1, -1, -1], ..., [ 0, 0, 0], [ 0, 0, 0], [ 0, 0, 0]]) .. GENERATED FROM PYTHON SOURCE LINES 135-141 Creating a neighbor list ^^^^^^^^^^^^^^^^^^^^^^^^ We now assemble the neighbor list following metatensor conventions. First, we create the ``samples`` metadata for the :py:class:`TensorBlock ` which will hold the neighbor list. .. GENERATED FROM PYTHON SOURCE LINES 141-163 .. code-block:: Python sample_values = torch.hstack([neighbor_indices, neighbor_shifts]) samples = Labels( names=[ "first_atom", "second_atom", "cell_shift_a", "cell_shift_b", "cell_shift_c", ], values=sample_values, ) neighbors = TensorBlock( values=torch.from_numpy(D).reshape(-1, 3, 1), samples=samples, components=[Labels.range("xyz", 3)], properties=Labels.range("distance", 1), ) print(neighbors) .. rst-class:: sphx-glr-script-out .. code-block:: none TensorBlock samples (1356): ['first_atom', 'second_atom', 'cell_shift_a', 'cell_shift_b', 'cell_shift_c'] components (3): ['xyz'] properties (1): ['distance'] gradients: None .. GENERATED FROM PYTHON SOURCE LINES 164-168 The data and metadata inside the ``neighbors`` object do not contain information about the ``cutoff`` and whether this is a full or half neighbor list. To account for this, metatensor neighbor lists are always stored together with :py:class:`NeighborListOptions`. For our system, these options can be saved as .. GENERATED FROM PYTHON SOURCE LINES 169-172 .. code-block:: Python options = NeighborListOptions(cutoff=5.0, full_list=True) .. GENERATED FROM PYTHON SOURCE LINES 173-188 We set ``full_list=True`` because ASE computes a “full” list (as opposed to a half list) where each `i, j` pair appears twice, stored once as `i, j` and once as `j, i`. Now we can, in principle, attach the neighbor list to a metatensor system using .. code:: python system.add_neighbor_list(options=options, neighbors=neighbors) Accessing data in neighbor lists ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Now that we have a neighbor list, we can access the data and metadata. First, we can extract the ``distances`` vectors between the neighboring pairs within the cutoff, which we can then use in our models. .. GENERATED FROM PYTHON SOURCE LINES 189-194 .. code-block:: Python distances = neighbors.values print(distances.shape) .. rst-class:: sphx-glr-script-out .. code-block:: none torch.Size([1356, 3, 1]) .. GENERATED FROM PYTHON SOURCE LINES 195-198 We can also get the metadata values like *neighbor indices* or the *neighbor shifts* using the :py:meth:`Labels.column ` and :py:meth:`Labels.view ` methods. .. GENERATED FROM PYTHON SOURCE LINES 199-208 .. code-block:: Python i = neighbors.samples.column("first_atom") j = neighbors.samples.column("second_atom") neighbor_indices = neighbors.samples.view(["first_atom", "second_atom"]).values neighbor_shifts = neighbors.samples.view( ["cell_shift_a", "cell_shift_b", "cell_shift_c"] ).values .. GENERATED FROM PYTHON SOURCE LINES 209-222 As mentioned above, in practical use cases you will not have to compute neighbor lists yourself, but instead the simulation engine will compute it for you and you'll just need to get the right list for a given :py:class:`System` using the corresponding ``options``: .. code:: python neighbors = system.get_neighbor_list(options) You can also loop over all attached lists of a :py:class:`System` using :py:meth:`System.known_neighbor_lists` to find a suitable one based on :py:class:`NeighborListOptions` attributes like ``cutoff``, ``full_list``, and ``requestors``. .. GENERATED FROM PYTHON SOURCE LINES 226-259 A Lennard-Jones model --------------------- Now that we know how the neighbor data is stored and can be accessed, and know how to use it we can construct our Lennard-Jones model with a fixed cutoff. The Lennard-Jones potential is a mathematical basis to approximate the interaction between a pair of neutral atoms or molecules. It is given by the equation: .. math:: V(r) = 4\epsilon \left[ \left( \frac{\sigma}{r} \right)^{12} - \left( \frac{\sigma}{r} \right)^{6} \right] where :math:`\epsilon` is the depth of the potential well, :math:`\sigma` is the finite distance at which the inter-particle potential is zero, and :math:`r` is the distance between the particles. The 12-6 form is chosen because the :math:`r^{12}` term approximates the Pauli repulsion at short ranges, while the :math:`r^6` term represents the attractive van der Waals forces. The :math:`r^{12}` is chosen because it is just the *square* of the :math:`r^6` and therefore allows fast evaluation. A Lennard-Jones potential is well-suited for argon because it accurately represents the van der Waals forces that dominate the interactions between argon atoms, as for all noble gases. This potential was used in one of the first MD simulations: "Correlation in the motions of atoms in liquid Argon" by A. Rahman (`Phys. Rev. 136, A405-A411, 1964 `_), which demonstrated the effectiveness of continuous potentials in molecular dynamics. The model below is a simplified version of a `more complex Lennard-Jones model `_. The linked version also implements ``per_atom`` energies as well as atom selection using the ``selected_atoms`` parameter of the ``forward()`` method. In this model, we shift the energy by its value at the ``cutoff``. This will break the conservativeness of the potential, which is unproblematic in here because we use a large cutoff and therefore the potential already almost decayed to zero. For more sophisticated methods like a polynomial switching potential like XPLOR, we refer to the literature. .. GENERATED FROM PYTHON SOURCE LINES 260-335 .. code-block:: Python class LennardJonesModel(torch.nn.Module): """Implementation of a single particle type Lennard-Jones potential.""" def __init__(self, cutoff, sigma, epsilon): super().__init__() # define neighbor list options to request the right set of neighbors self._nl_options = NeighborListOptions(cutoff=cutoff, full_list=False) self._sigma = sigma self._epsilon = epsilon # shift the energy to 0 at the cutoff self._shift = 4 * epsilon * ((sigma / cutoff) ** 12 - (sigma / cutoff) ** 6) def requested_neighbor_lists(self) -> List[NeighborListOptions]: """Method declaring which neighbors lists this model desires. The method is required to tell an simulation engine (here ase) to compute and attach the requested neighbor list to a system which will be passed to the ``forward`` method defined below Note that a model can request as many neighbor lists as it wants """ return [self._nl_options] def forward( self, systems: List[System], outputs: Dict[str, ModelOutput], selected_atoms: Optional[Labels], ) -> Dict[str, TensorMap]: if list(outputs.keys()) != ["energy"]: raise ValueError( "this model can only compute 'energy', but `outputs` contains other " f"keys: {', '.join(outputs.keys())}" ) # 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") # Initialize device so we can access it outside of the for loop device = torch.device("cpu") for system in systems: device = system.device neighbors = system.get_neighbor_list(self._nl_options) distances = neighbors.values.reshape(-1, 3) sigma_r_6 = (self._sigma / torch.linalg.vector_norm(distances, dim=1)) ** 6 sigma_r_12 = sigma_r_6 * sigma_r_6 e = 4.0 * self._epsilon * (sigma_r_12 - sigma_r_6) - self._shift samples = Labels( ["system"], torch.arange(len(systems), device=device).reshape(-1, 1) ) block = TensorBlock( values=torch.sum(e).reshape(-1, 1), samples=samples, components=torch.jit.annotate(List[Labels], []), properties=Labels(["energy"], torch.tensor([[0]], device=device)), ) return { "energy": TensorMap( Labels("_", torch.tensor([[0]], device=device)), [block] ), } .. GENERATED FROM PYTHON SOURCE LINES 336-355 In the model above, in addition to the required ``__init__()`` and :py:meth:`ModelInterface.forward` methods, we also implemented the :py:meth:`ModelInterface.requested_neighbor_lists` method, which declares the neighbor list our model requires. Running the simulation ---------------------- We now define and wrap the model, using the initial positions and the Lennard-Jones parameters taken from `Méndez-Bermúdez et.al, Phys. Commun. 2022 `_. .. note:: The **units** of the Lennard Jones parameters from the reference are in ``"Angstrom"`` and ``"kJ/mol"``. We declare the (energy) ``unit`` and ``length_unit`` accordiningly when defining the :py:class:`ModelCapabilities` object below. From then on, metatensor is taking care of the correct unit conversion when the energies and forces are passed to the simulation engine. .. GENERATED FROM PYTHON SOURCE LINES 356-382 .. code-block:: Python sigma = 3.3646 # Å epsilon = 0.94191 # kJ / mol model = LennardJonesModel( cutoff=5.0, sigma=sigma, epsilon=epsilon, ) capabilities = ModelCapabilities( outputs={ "energy": ModelOutput(quantity="energy", unit="kJ/mol", per_atom=False), }, atomic_types=[18], interaction_range=5.0, length_unit="Angstrom", supported_devices=["cpu"], dtype="float32", ) wrapper = MetatensorAtomisticModel(model.eval(), ModelMetadata(), capabilities) # Use the wrapped model as the calculator for these atoms atoms.calc = MetatensorCalculator(wrapper) .. GENERATED FROM PYTHON SOURCE LINES 383-387 We'll run the simulation in the constant volume/temperature thermodynamic ensemble (NVT or Canonical ensemble), using a Langevin thermostat for time integration. Please refer to the corresponding documentation (:py:class:`ase.md.langevin.Langevin`) for more information! .. GENERATED FROM PYTHON SOURCE LINES 388-405 .. code-block:: Python integrator = ase.md.Langevin( atoms, timestep=2.0 * ase.units.fs, temperature_K=94.4, friction=0.1 / ase.units.fs, ) trajectory = [] for _ in range(50): # run a single simulation for 10 steps integrator.run(10) # collect data about the simulation trajectory.append(atoms.copy()) .. GENERATED FROM PYTHON SOURCE LINES 406-407 We can use `chemiscope `_ to visualize the trajectory .. GENERATED FROM PYTHON SOURCE LINES 408-411 .. code-block:: Python viewer_settings = {"bonds": False, "playbackDelay": 70} chemiscope.show(trajectory, mode="structure", settings={"structure": [viewer_settings]}) .. chemiscope:: _datasets/fig_3-atomistic-model-with-nl_002.json.gz :mode: structure .. raw:: html


.. GENERATED FROM PYTHON SOURCE LINES 412-414 We finally compute and plot the avaregae pair-correlation function :math:`g(r)` of the recorded ``trajectory``. .. GENERATED FROM PYTHON SOURCE LINES 415-432 .. code-block:: Python rdf = [] for atoms in trajectory: rdf_step, rdf_dists = ase.geometry.rdf.get_rdf(atoms, rmax=9.0, nbins=100) rdf.append(rdf_step) fig, ax = plt.subplots() ax.plot(rdf_dists, np.mean(rdf, axis=0)) ax.set_xlabel("distance / Å") ax.set_ylabel("$g(r)$") ax.minorticks_on() fig.tight_layout() fig.show() .. image-sg:: /examples/atomistic/images/sphx_glr_3-atomistic-model-with-nl_002.png :alt: 3 atomistic model with nl :srcset: /examples/atomistic/images/sphx_glr_3-atomistic-model-with-nl_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 433-435 The pair-correlation function shows the usual structure for a liquid and we find the expected first narrow peak at 3.7 Å and a second broader peak at 7.0 Å. .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 13.215 seconds) .. _sphx_glr_download_examples_atomistic_3-atomistic-model-with-nl.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: 3-atomistic-model-with-nl.ipynb <3-atomistic-model-with-nl.ipynb>` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: 3-atomistic-model-with-nl.py <3-atomistic-model-with-nl.py>` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: 3-atomistic-model-with-nl.zip <3-atomistic-model-with-nl.zip>` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_