.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "flow_gallery/run_phonons.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note Click :ref:`here ` 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_phonons.py: Flow for phonons with DFPT ========================== This example shows how to compute the phonon band structure of AlAs with AbiPy flows. Symmetries are taken into account: only q-points in the IBZ are generated and for each q-point only the independent atomic perturbations are computed. The final results (out_DDB, out_DVDB) will be produced automatically at the end of the run and saved in ``flow_phonons/outdata/``. .. GENERATED FROM PYTHON SOURCE LINES 12-99 .. code-block:: default import sys import os import abipy.abilab as abilab import abipy.data as abidata from abipy import flowtk def make_scf_input(paral_kgb=0): """ This function constructs the input file for the GS calculation: """ # Crystalline AlAs: computation of the second derivative of the total energy structure = abidata.structure_from_ucell("AlAs") pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc") gs_inp = abilab.AbinitInput(structure, pseudos=pseudos) gs_inp.set_vars( nband=4, ecut=2.0, ngkpt=[4, 4, 4], nshiftk=4, shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid 0.0, 0.5, 0.0, 0.5, 0.0, 0.0, 0.5, 0.5, 0.5], #shiftk=[0, 0, 0], paral_kgb=paral_kgb, tolvrs=1.0e-10, ixc=1, diemac=9.0, #iomode=3, ) return gs_inp def build_flow(options): """ Create a `Flow` for phonon calculations. The flow has two works. The first work contains a single GS task that produces the WFK file used in DFPT Then we have multiple Works that are generated automatically in order to compute the dynamical matrix on a [4, 4, 4] mesh. Symmetries are taken into account: only q-points in the IBZ are generated and for each q-point only the independent atomic perturbations are computed. """ # 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_") # Build input for GS calculation scf_input = make_scf_input() # Create flow to compute all the independent atomic perturbations # corresponding to a [4, 4, 4] q-mesh. # Electric field and Born effective charges are also computed. flow = flowtk.PhononFlow.from_scf_input(options.workdir, scf_input, ph_ngqpt=(4, 4, 4), with_becs=True) 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_phonons_001.png :alt: run phonons :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 100-134 Run the script with: run_phonons.py -s then use: abirun.py flow_phonons history to get the list of actions perfomed by AbiPy to complete the flow. Note how the ``PhononWork`` has merged all the partial DDB files produced by the PhononTasks .. code-block:: bash =================================================================================================================================== ====================================== =============================== =================================================================================================================================== [Thu Dec 7 22:55:02 2017] Finalized set to True [Thu Dec 7 22:55:02 2017] Will call mrgddb to merge [ .... ] Now open the final DDB file with: abiopen.py flow_phonons/outdata/out_DDB and invoke anaddb to compute the phonon band structure and the phonon DOS with: .. code-block:: ipython In [1]: phbst_file, phdos_file = abifile.anaget_phbst_and_phdos_files() In [2]: %matplotlib In [3]: phbst_file.plot_phbands() .. image:: https://github.com/abinit/abipy_assets/blob/master/run_phonons.png?raw=true :alt: Phonon band structure of AlAs. .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 2.008 seconds) .. _sphx_glr_download_flow_gallery_run_phonons.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_phonons.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: run_phonons.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: run_phonons.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_