.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "generated_examples/1-ase-simulations/plot_md_nvt.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_generated_examples_1-ase-simulations_plot_md_nvt.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_generated_examples_1-ase-simulations_plot_md_nvt.py:


NVT molecular dynamics
======================

Canonical (constant temperature) molecular dynamics of bulk silicon with
the :py:class:`ase.md.langevin.Langevin` thermostat at 300 K. The
instantaneous temperature fluctuates around the target and its running
average converges there after a short equilibration.

.. GENERATED FROM PYTHON SOURCE LINES 10-67



.. image-sg:: /generated_examples/1-ase-simulations/images/sphx_glr_plot_md_nvt_001.png
   :alt: Langevin NVT — bulk Si at 300 K
   :srcset: /generated_examples/1-ase-simulations/images/sphx_glr_plot_md_nvt_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/runner/work/upet/upet/.tox/docs/lib/python3.13/site-packages/ase/md/langevin.py:110: FutureWarning: The implementation of `fixcm=True` in `Langevin` does not strictly sample the correct NVT distributions. The deviations are typically small for large systems but can be more pronounced for small systems. Use `fixcm=False` together with `ase.constraints.FixCom`. `fixcm` is deprecated since ASE 3.28.0 and will be removed in a future release.
      warnings.warn(msg, FutureWarning)
    /home/runner/work/upet/upet/.tox/docs/lib/python3.13/site-packages/metatomic_ase/_neighbors.py:78: UserWarning: `compute_requested_neighbors_from_options` is deprecated and will be removed in a future version. Please use `neighbor_lists_for_model` to get the calculators and call them directly.
      vesin.metatomic.compute_requested_neighbors_from_options(






|

.. code-block:: Python


    import matplotlib.pyplot as plt
    import numpy as np
    from ase import units
    from ase.build import bulk
    from ase.md.langevin import Langevin
    from ase.md.velocitydistribution import MaxwellBoltzmannDistribution

    from upet.calculator import UPETCalculator


    T_TARGET = 300.0  # K

    atoms = bulk("Si", cubic=True, a=5.43, crystalstructure="diamond")
    atoms.calc = UPETCalculator(model="pet-mad-xs", version="1.5.0", device="cpu")

    MaxwellBoltzmannDistribution(
        atoms, temperature_K=T_TARGET, rng=np.random.default_rng(0)
    )

    dyn = Langevin(
        atoms,
        timestep=1.0 * units.fs,
        temperature_K=T_TARGET,
        friction=0.01 / units.fs,
        rng=np.random.default_rng(1),
    )

    n_steps = 200
    times, temperatures = [], []  # type: ignore


    def log():
        times.append(len(times) * 1.0)
        temperatures.append(atoms.get_temperature())


    log()
    for _ in range(n_steps):
        dyn.run(1)
        log()

    times = np.asarray(times)
    temperatures = np.asarray(temperatures)
    running_avg = np.cumsum(temperatures) / np.arange(1, len(temperatures) + 1)

    fig, ax = plt.subplots(figsize=(6, 3.5))
    ax.plot(times, temperatures, alpha=0.5, label="instantaneous")
    ax.plot(times, running_avg, lw=2, label="running average")
    ax.axhline(T_TARGET, color="k", ls="--", lw=0.8, label=f"target ({T_TARGET:.0f} K)")
    ax.set_xlabel("time [fs]")
    ax.set_ylabel("temperature [K]")
    ax.set_title("Langevin NVT — bulk Si at 300 K")
    ax.legend()

    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_generated_examples_1-ase-simulations_plot_md_nvt.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_md_nvt.ipynb <plot_md_nvt.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_md_nvt.py <plot_md_nvt.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_md_nvt.zip <plot_md_nvt.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_