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

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_tutorials_make_effqh.py>`
        to download the full example code.

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

.. _sphx_glr_tutorials_make_effqh.py:


Effective quasi-harmonic potential
==================================

This example shows how to fit the effective quasi-harmonic potential
as a function of volume and temperature.

.. GENERATED FROM PYTHON SOURCE LINES 8-18

.. code-block:: Python


    import numpy as np
    from ase.build import bulk
    from tensorpotential.calculator import grace_fm

    from directupsampling.calculators.emt import EMT
    from directupsampling.effqh.effqh import EffQH
    from directupsampling.plot_tools import plot
    from directupsampling.sampling import GridSampler





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

 .. code-block:: none

    [tensorpotential] Info: Environment variable TF_USE_LEGACY_KERAS is automatically set to '1'.
    WARNING:tensorflow:UserWarning: enabling the new type promotion must happen at the beginning of the program. Please ensure no TF APIs have been used yet.
    WARNING:tensorflow:UserWarning: enabling the new type promotion must happen at the beginning of the program. Please ensure no TF APIs have been used yet.
    WARNING:tensorflow:UserWarning: enabling the new type promotion must happen at the beginning of the program. Please ensure no TF APIs have been used yet.
    WARNING:tensorflow:UserWarning: enabling the new type promotion must happen at the beginning of the program. Please ensure no TF APIs have been used yet.
    WARNING:tensorflow:UserWarning: enabling the new type promotion must happen at the beginning of the program. Please ensure no TF APIs have been used yet.




.. GENERATED FROM PYTHON SOURCE LINES 19-20

Make the initial ASE Atoms object.

.. GENERATED FROM PYTHON SOURCE LINES 20-22

.. code-block:: Python

    atoms = bulk("Al", "fcc", cubic=True) * 3








.. GENERATED FROM PYTHON SOURCE LINES 23-28

Make two calculators.
The first one is a light-weight calculator to sample MD trajectories.
The second one is an accurate calculator to compute forces on atoms.
The accurate calculator is typically a DFT calculator.
In this example, we intead use a GRACE foundation model.

.. GENERATED FROM PYTHON SOURCE LINES 28-31

.. code-block:: Python

    atoms.calc = EMT()
    calc_dft = grace_fm("GRACE-1L-OMAT")





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

 .. code-block:: none

    Using cached GRACE model from /root/.cache/grace/GRACE-1L-OMAT
    Model license: Academic Software License




.. GENERATED FROM PYTHON SOURCE LINES 32-33

Define a volume-temperature grid using a GridSampler.

.. GENERATED FROM PYTHON SOURCE LINES 33-37

.. code-block:: Python

    temperature = 20.0  # in K
    grid_fqh = [(v, temperature) for v in np.linspace(15.0, 18.0, 7)]
    effqh_sampler = GridSampler(atoms, grid_fqh)








.. GENERATED FROM PYTHON SOURCE LINES 38-43

Run MD calculations.
For a relatively light-weight calculator, we can run directly ``calculate_with``.
For a DFT calculator, it may be more convenient to first make input files using
``write_folders``, run DFT calculations in these folders, and then collect
the results using ``read_folders``.

.. GENERATED FROM PYTHON SOURCE LINES 43-53

.. code-block:: Python

    effqh_sampler.sample_snapshots(30)
    snapshots_for_effqh = effqh_sampler.calculate_with(calc_dft)
    # effqh_sampler.write_folders(
    #     root_path="./calcs",
    #     joblist_file="./jobList",
    #     calc=std_dft,
    # )
    # Run DFT calculations in the folders.
    # snapshots_for_effqh = GridSampler.read_folders("./calcs").snapshot_container





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

 .. code-block:: none

    /usr/local/lib/python3.12/site-packages/ase/md/velocitydistribution.py:147: FutureWarning: `communicator` has been deprecated since ASE 3.26.0 and will be removed in ASE 3.27.0. Use `comm` instead.
      warnings.warn(msg, FutureWarning)
    /usr/local/lib/python3.12/site-packages/ase/md/velocitydistribution.py:154: FutureWarning: `comm=="serial"` has been deprecated since ASE 3.26.0 and will be removed in ASE 3.27.0. Use `comm=DummyMPI()` instead.
      warnings.warn(msg, FutureWarning)




.. GENERATED FROM PYTHON SOURCE LINES 54-55

Fit the effective harmonic potential as a function of volume and temperature.

.. GENERATED FROM PYTHON SOURCE LINES 55-58

.. code-block:: Python

    effqh = EffQH(atoms, fit_order=3)
    effqh.fit_snapshots(snapshots_for_effqh, method="least-squares")
    effqh.write_fc_fit("effqh_force_constants_fit.hdf5")







.. GENERATED FROM PYTHON SOURCE LINES 59-60

Check the quasi-harmonic frequencies.

.. GENERATED FROM PYTHON SOURCE LINES 60-61

.. code-block:: Python

    plot(effqh.exact_phonons).show()



.. image-sg:: /tutorials/images/sphx_glr_make_effqh_001.png
   :alt: make effqh
   :srcset: /tutorials/images/sphx_glr_make_effqh_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (5 minutes 44.360 seconds)


.. _sphx_glr_download_tutorials_make_effqh.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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