.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "flow_gallery/run_sic_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_sic_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_sic_relax.py:


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

This example shows how to build a very simple Flow for the structural relaxation of SiC.
One could use a similar logic to perform multiple relaxations with different input parameters...

.. GENERATED FROM PYTHON SOURCE LINES 9-86

.. code-block:: default


    import sys
    import os

    import abipy.abilab as abilab
    import abipy.data as data
    import abipy.flowtk as flowtk


    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_")

        pseudos = data.pseudos("14si.pspnc", "6c.pspnc")
        structure = data.structure_from_ucell("SiC")

        # Initialize the input
        relax_inp = abilab.AbinitInput(structure, pseudos=pseudos)

        # Set variables
        relax_inp.set_vars(
            ecut=20,
            paral_kgb=1,
            iomode=3,
            # Relaxation part
            ionmov=2,
            optcell=1,
            strfact=100,
            ecutsm=0.5,       # Important!
            dilatmx=1.15,     # Important!
            toldff=1e-6,
            tolmxf=1e-5,
            ntime=100,
        )

        # K-points sampling
        shiftk = [
            [0.5,0.5,0.5],
            [0.5,0.0,0.0],
            [0.0,0.5,0.0],
            [0.0,0.0,0.5]
        ]
        relax_inp.set_kmesh(ngkpt=[4, 4, 4], shiftk=shiftk)

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

        # Register the task.
        flow.register_relax_task(relax_inp)

        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):
        """
        This is our main function that will be invoked by the script.
        flow_main is a decorator implementing the command line interface.
        Command line args are stored in `options`.
        """
        return build_flow(options)


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





.. image:: /flow_gallery/images/sphx_glr_run_sic_relax_001.png
    :alt: run sic relax
    :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 87-126

Run the script with:

    run_sic_relax.py -s

then use:

   abirun.py flow_sic_relax structures

to compare the input and output structures of the tasks:

.. code-block:: bash

   Lattice parameters:
             formula  natom  angle0  angle1  angle2      a      b      c  volume  \
   w0_t0_in   Si1 C1      2    60.0    60.0    60.0  3.065  3.065  3.065  20.351
   w0_t0_out  Si1 C1      2    60.0    60.0    60.0  3.065  3.065  3.065  20.355

             abispg_num  P [GPa]  Max|F| eV/ang task_class              status
   w0_t0_in        None      NaN            NaN  RelaxTask  Completed
   w0_t0_out       None   -0.001            0.0  RelaxTask  Completed

   Use `--verbose` to print atoms.

As you can see, the pressure at the end of the RelaxTask is very small (forces are zero by symmetry):

To visualize the evolution of the lattice parameters during the structura relaxation use:

   abiopen.py flow_sic_relax/w0/t0/outdata/out_HIST.nc

and then inside the ipython terminal, type:

.. code-block:: ipython

   In [1]: %matplotlib
   In [2]: abifile.plot()

.. image:: https://github.com/abinit/abipy_assets/blob/master/run_sic_relax.png?raw=true
   :alt: Structural relaxation of SiC.



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

   **Total running time of the script:** ( 0 minutes  0.281 seconds)


.. _sphx_glr_download_flow_gallery_run_sic_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_sic_relax.ipynb
      :alt: Launch binder
      :width: 150 px


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

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



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

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


.. only:: html

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

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