:orphan:

Examples
========

Runnable tutorials covering UPET workflows. Each example can be downloaded as
a Python script or Jupyter notebook from the link at the bottom of its page.


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ASE simulations
---------------

Runnable end-to-end ASE workflows: single-point evaluation, geometry
optimization, and molecular dynamics in the NVE / NVT / NPT ensembles.


.. raw:: html

  <div id='sg-tag-list' class='sphx-glr-tag-list'></div>


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    <div class="sphx-glr-thumbcontainer" tooltip="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~upet.calculator.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.">

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  .. image:: /generated_examples/1-ase-simulations/images/thumb/sphx_glr_plot_energy_forces_thumb.png
    :alt:

  :doc:`/generated_examples/1-ase-simulations/plot_energy_forces`

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      <div class="sphx-glr-thumbnail-title">Energy and forces</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Two-stage geometry optimization of a slightly perturbed silicon unit cell. First, positions are relaxed at fixed cell with :pyase.optimize.LBFGS. Then the cell itself is relaxed jointly with the atomic positions by wrapping the Atoms in :pyase.filters.FrechetCellFilter.">

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  .. image:: /generated_examples/1-ase-simulations/images/thumb/sphx_glr_plot_geometry_optimization_thumb.png
    :alt:

  :doc:`/generated_examples/1-ase-simulations/plot_geometry_optimization`

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      <div class="sphx-glr-thumbnail-title">Geometry optimization (LBFGS)</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Isobaric–isothermal (constant pressure, constant temperature) MD of bulk silicon with the :pyase.md.npt.NPT integrator (Parrinello–Rahman barostat coupled to a Nosé–Hoover thermostat) at 300 K and 1 bar. Both the cell and the atomic coordinates evolve; we monitor temperature, cell volume and instantaneous pressure.">

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  .. image:: /generated_examples/1-ase-simulations/images/thumb/sphx_glr_plot_md_npt_thumb.png
    :alt:

  :doc:`/generated_examples/1-ase-simulations/plot_md_npt`

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      <div class="sphx-glr-thumbnail-title">NPT molecular dynamics</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Microcanonical (constant energy) molecular dynamics of bulk silicon using :pyase.md.verlet.VelocityVerlet. Velocities are initialized from a Maxwell–Boltzmann distribution at 300 K; total energy should stay flat up to integration noise.">

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  .. image:: /generated_examples/1-ase-simulations/images/thumb/sphx_glr_plot_md_nve_thumb.png
    :alt:

  :doc:`/generated_examples/1-ase-simulations/plot_md_nve`

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      <div class="sphx-glr-thumbnail-title">NVE molecular dynamics</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Canonical (constant temperature) molecular dynamics of bulk silicon with the :pyase.md.langevin.Langevin thermostat at 300 K. The instantaneous temperature fluctuates around the target and its running average converges there after a short equilibration.">

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  .. image:: /generated_examples/1-ase-simulations/images/thumb/sphx_glr_plot_md_nvt_thumb.png
    :alt:

  :doc:`/generated_examples/1-ase-simulations/plot_md_nvt`

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      <div class="sphx-glr-thumbnail-title">NVT molecular dynamics</div>
    </div>


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    </div>


.. toctree::
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   :includehidden:


   /generated_examples/1-ase-simulations/index.rst


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  .. container:: sphx-glr-footer sphx-glr-footer-gallery

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

      :download:`Download all examples in Python source code: generated_examples_python.zip </generated_examples/generated_examples_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: generated_examples_jupyter.zip </generated_examples/generated_examples_jupyter.zip>`


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