Flow to compute e-ph matrix elements along a q-pathΒΆ

This example shows how to compute the e-ph matrix elements in AlAs along a q-path with AbiPy flows. The final results are stored in the GKQ.nc file (one file for q-point) in the outdata of each task.

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

from abipy import flowtk


def make_scf_input(ngkpt):
    """
    This function constructs the input file for the GS calculation:
    """
    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=6,
        ecut=6.0,
        ngkpt=ngkpt,
        nshiftk=1,
        shiftk=[0, 0, 0],
        tolvrs=1.0e-10,
    )

    return gs_inp


def build_flow(options):
    """
    Create a `Flow` for the computation of e-ph matrix elements
    """
    # 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_")

    # Use 2x2x2 both for k-mesh.
    # Build input for GS calculation
    scf_input = make_scf_input(ngkpt=(2, 2, 2))

    # corresponding to a [2, 2, 2] q-mesh.
    ngqpt = (2, 2, 2)

    # Create flow to compute all the independent atomic perturbations
    # Use ndivsm = 0 to pass an explicit list of q-points.
    # If ndivsm > 0, qpath_list is interpreted as a list of boundaries for the q-path
    qpath_list = [[0.0, 0.0, 0.0], [0.01, 0, 0], [0.1, 0, 0],
                  [0.24, 0, 0], [0.3, 0, 0], [0.45, 0, 0], [0.5, 0.0, 0.0]]

    from abipy.flowtk.eph_flows import GkqPathFlow
    flow = GkqPathFlow.from_scf_input(options.workdir, scf_input,
                                      ngqpt, qpath_list, ndivsm=0, with_becs=True,
                                      ddk_tolerance={"tolwfr": 1e-8})

    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())
../_images/sphx_glr_run_gkq_001.png

Out:

/Users/gmatteo/git_repos/pymatgen/pymatgen/util/plotting.py:550: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
  plt.show()

Run the script with:

run_gkq.py -s

then use:

abirun.py flow_phonons history

Total running time of the script: ( 0 minutes 2.924 seconds)

Gallery generated by Sphinx-Gallery