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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_flow_gallery_run_relax.py>`
        to download the full example code or to run this example in your browser via Binder

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

.. _sphx_glr_flow_gallery_run_relax.py:


Relaxation Flow
===============

This script shows how to perform a structural relaxation in two steps:

    1) Relaxation of atomic positions with unit cell parameters fixed.
    2) Full relaxation (atoms + cell) with the initial configuration read from step 1)

.. GENERATED FROM PYTHON SOURCE LINES 11-116



.. image:: /flow_gallery/images/sphx_glr_run_relax_001.png
    :alt: run relax
    :class: sphx-glr-single-img





.. code-block:: default


    import sys
    import os
    import abipy.data as abidata
    import abipy.abilab as abilab
    import abipy.flowtk as flowtk


    def make_ion_ioncell_inputs(paral_kgb=0):

        structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))

        # Perturb the structure (random perturbation of 0.1 Angstrom)
        # then compress the volume to trigger dilatmx.
        structure.perturb(distance=0.1)
        structure.scale_lattice(structure.volume * 0.6)

        global_vars = dict(
            ecut=4,
            ngkpt=[4, 4, 4],
            shiftk=[0, 0, 0],
            nshiftk=1,
            chksymbreak=0,
            paral_kgb=paral_kgb,
            iomode=3,
            #prtwf=0,
        )

        multi = abilab.MultiDataset(structure, pseudos=abidata.pseudos("14si.pspnc"), ndtset=2)

        # Global variables
        multi.set_vars(global_vars)

        # Dataset 1 (Atom Relaxation)
        multi[0].set_vars(
            optcell=0,
            ionmov=2,
            tolrff=0.02,
            tolmxf=5.0e-5,
            #ntime=50,
            ntime=3,  #To test the restart
            #dilatmx=1.1, # FIXME: abinit crashes if I don't use this
        )

        # Dataset 2 (Atom + Cell Relaxation)
        multi[1].set_vars(
            optcell=1,
            ionmov=2,
            ecutsm=0.5,
            dilatmx=1.02,
            tolrff=0.02,
            tolmxf=5.0e-5,
            strfact=100,
            #ntime=50,
            ntime=3,  # To test the restart
            )

        #print(multi)

        ion_inp, ioncell_inp = multi.split_datasets()
        return ion_inp, ioncell_inp


    def build_flow(options):
        # Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
        if not options.workdir:
            options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_", "flow_")

        # Create the flow
        flow = flowtk.Flow(options.workdir, manager=options.manager)

        # Create a relaxation work and add it to the flow.
        ion_inp, ioncell_inp = make_ion_ioncell_inputs()

        relax_work = flowtk.RelaxWork(ion_inp, ioncell_inp)
        flow.register_work(relax_work)

        #bands_work = flowtk.BandStructureWork(scf_input, nscf_input)
        bands_work = flowtk.Work()
        deps = {relax_work[-1]: "@structure"}
        deps = {relax_work[-1]: ["DEN", "@structure"]}  # --> This is not possible because the file ext is changed!
        #deps = {relax_work[-1]: ["WFK", "@structure"]} # --> This triggers an infamous bug in abinit

        bands_work.register_relax_task(ioncell_inp, deps=deps)
        flow.register_work(bands_work)

        return flow


    # This block generates the thumbnails in the AbiPy gallery.
    # You can safely REMOVE this part if you are using this script for production runs.
    if os.getenv("READTHEDOCS", False):
        __name__ = None
        import tempfile
        options = flowtk.build_flow_main_parser().parse_args(["-w", tempfile.mkdtemp()])
        build_flow(options).graphviz_imshow()


    @flowtk.flow_main
    def main(options):
        return build_flow(options)


    if __name__ == "__main__":
        sys.exit(main())


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

   **Total running time of the script:** ( 0 minutes  0.345 seconds)


.. _sphx_glr_download_flow_gallery_run_relax.py:


.. only :: html

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


  .. container:: binder-badge

    .. image:: images/binder_badge_logo.svg
      :target: https://mybinder.org/v2/gh/abinit/abipy/gh-pages?filepath=notebooks/flow_gallery/run_relax.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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