.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "generated_examples/1-ase/run_ase_basics.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_run_ase_basics.py>`
        to download the full example code.

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

.. _sphx_glr_generated_examples_1-ase_run_ase_basics.py:


Basics: single-structure evaluation
===================================

Single-point evaluation of a bulk silicon cell with the smallest PET-MAD
model (``pet-mad-xs``). Two atoms are displaced off their equilibrium
positions so the predicted forces are non-trivial; we then attach a
:py:class:`~upet.ase.UPETCalculator`, read energy and forces via
the standard ASE API, and render the unit cell with the forces drawn as
arrows on top of the atoms.

.. GENERATED FROM PYTHON SOURCE LINES 12-46



.. image-sg:: /generated_examples/1-ase/images/sphx_glr_run_ase_basics_001.png
   :alt: run ase basics
   :srcset: /generated_examples/1-ase/images/sphx_glr_run_ase_basics_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    Number of atoms:        8
    Total energy:           -46.8499 eV
    Energy per atom:        -5.8562 eV
    Max |force| component:  1.7096e+00 eV/Å
    Stress (Voigt, eV/ų):  [-0.0079 -0.0047 -0.0059 -0.0008  0.0164  0.0048]






|

.. code-block:: Python


    import matplotlib.pyplot as plt
    import numpy as np
    from ase.build import bulk
    from ase.visualize.plot import plot_atoms

    from upet.ase import UPETCalculator


    atoms = bulk("Si", cubic=True, a=5.43, crystalstructure="diamond")

    # perturb every atom by a small random displacement so the predicted
    # forces on every site are non-zero and of comparable magnitude

    atoms.rattle(0.05, seed=0)  # ASE's built-in random displacement method

    calculator = UPETCalculator(model="pet-mad-xs", version="1.6.0", device="cpu")
    atoms.calc = calculator

    energy = atoms.get_potential_energy()
    forces = atoms.get_forces()
    stress = atoms.get_stress()

    print(f"Number of atoms:        {len(atoms)}")
    print(f"Total energy:           {energy:.4f} eV")
    print(f"Energy per atom:        {energy / len(atoms):.4f} eV")
    print(f"Max |force| component:  {np.abs(forces).max():.4e} eV/Å")
    print(f"Stress (Voigt, eV/ų):  {np.array2string(stress, precision=4)}")

    # Visualize the cell projected along z and overlay the in-plane force
    # components as red arrows. A matplotlib quiver key acts as a scale bar.
    fig, ax = plt.subplots(figsize=(5.5, 5.5))
    plot_atoms(atoms, ax, radii=0.6, show_unit_cell=2)
    plt.show()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 11.722 seconds)


.. _sphx_glr_download_generated_examples_1-ase_run_ase_basics.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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