Flow for E-PH calculationsΒΆ

This flow computes the phonon linewidths and the Eliashberg function in Al.

../_images/sphx_glr_run_eph_al_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()

import sys
import os
import abipy.data as abidata
import abipy.abilab as abilab
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_")

    # Preparatory run for E-PH calculations.
    # The sequence of datasets makes the ground states and
    # all of the independent perturbations of the single Al atom
    # for the irreducible qpoints in a 4x4x4 grid.
    # Note that the q-point grid must be a sub-grid of the k-point grid (here 8x8x8)
    pseudos = abidata.pseudos("Al.oncvpsp")

    structure = abilab.Structure.from_abivars(
        acell=3 * [7.5],
        rprim=[0.0, 0.5, 0.5,
               0.5, 0.0, 0.5,
               0.5, 0.5, 0.0],
        typat=1,
        xred=[0.0, 0.0, 0.0],
        ntypat=1,
        znucl=13,
    )

    same_structure = abilab.Structure.fcc(a=7.5, species=["Al"], units="bohr")
    assert same_structure == structure

    gs_inp = abilab.AbinitInput(structure, pseudos)

    gs_inp.set_vars(
        ecut=8.0,
        nband=5,
        occopt=7,    # include metallic occupation function with a small smearing
        tsmear=0.04,
        tolvrs=1e-7,
    )

    # The kpoint grid is minimalistic to keep the calculation manageable.
    gs_inp.set_kmesh(
        ngkpt=[8, 8, 8],
        shiftk=[0.0, 0.0, 0.0],
    )

    # Phonon calculation with 4x4x4
    ddb_ngqpt = [4, 4, 4]
    qpoints = gs_inp.abiget_ibz(ngkpt=ddb_ngqpt, shiftk=[0, 0, 0], kptopt=1).points

    flow = flowtk.Flow(options.workdir, manager=options.manager)
    work0 = flow.register_scf_task(gs_inp)

    ph_work = flowtk.PhononWork.from_scf_task(work0[0], qpoints)
    flow.register_work(ph_work)

    eph_work = flow.register_work(flowtk.Work())
    eph_deps = {work0[0]: "WFK", ph_work: ["DDB", "DVDB"]}

    for eph_ngqpt_fine in [(4, 4, 4,), (8, 8, 8)]:
        # Build input file for E-PH run.
        eph_inp = gs_inp.new_with_vars(
            optdriver=7,
            ddb_ngqpt=ddb_ngqpt,           # q-mesh used to produce the DDB file (must be consistent with DDB data)
            eph_intmeth=2,                 # Tetra method
            eph_fsewin="0.8 eV",           # Energy window around Ef
            eph_mustar=0.12,               # mustar parameter
            eph_ngqpt_fine=eph_ngqpt_fine, # Interpolate DFPT potentials if != ddb_ngqpt
        )

        # Set q-path for phonons and phonon linewidths.
        eph_inp.set_qpath(20)

        # TODO: Define wstep and smear
        # Set q-mesh for phonons DOS and a2F(w)
        eph_inp.set_phdos_qmesh(nqsmall=16, method="tetra")
        eph_work.register_eph_task(eph_inp, deps=eph_deps)

    flow.allocate(use_smartio=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())

Total running time of the script: ( 0 minutes 2.279 seconds)

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