Phonons + dynamical quadrupoles

This example shows how to compute the dynamical matrix of GaP on a user-defined q-mesh including Born effective charges, the macroscopic dielectric matric and the dynamical quadrupoles Q*. The final results (out_DDB, out_DVDB) will be produced automatically at the end of the run and saved in flow_phonons_with_quad/outdata/.

The Q* tensor may be needed to improve the accuracy of the Fourier interpolation of the phonon frequencies, especially in the long-wavelength limit |q| –> 0.

This example is based on <https://docs.abinit.org/tests/tutorespfn/Input/tlw_4.abi> Note that only selected features are compatible with dynamical quadrupoles. Please consult <https://docs.abinit.org/topics/longwave/>

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

from abipy import flowtk


def build_flow(options):
    """
    Create a `Flow` for phonon calculations including
    eps_inf, Born effective charges and  dynamical quadrupoles
    """
    # 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 = abidata.pseudos("31-Ga.LDA.fhi", "15-P.LDA.fhi")

    # Initialize the structure from an abinit string
    # Other approaches (e.g. from cif files) are available as well.
    structure = abilab.Structure.from_abistring("""
 acell 1.0 1.0 1.0
 rprim 0.0 5.023016083002 5.023016083002
       5.023016083002 0.0 5.023016083002
       5.023016083002 5.023016083002 0.0

 # Definition of the atom types and positions
 # ******************************************
 ntypat 2
 znucl  31 15
 natom 2
 typat 1 2
 xred
         0.0000000      0.0000000      0.0000000
         0.2500000      0.2500000      0.2500000
""")

    # Build input for GS calculation
    scf_input = abilab.AbinitInput(structure, pseudos=pseudos)

    # We use parameters similar to the ones in https://docs.abinit.org/tests/tutorespfn/Input/tlw_4.abi
    scf_input.set_vars(
        nband=4,
        ecut=5.0,
        ngkpt=[4, 4, 4],
        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],
        ],
        diemac=12.0,
        nstep=100,
        tolvrs=1.0e-10,
        #tolvrs=1.0e-18,  # This is the value used in tlw_4.abi
                          # but it is not always possible to reach this precision in more complex systems.
        #useylm=1,
        #ixc=7
        #iomode=3,
        #paral_kgb=1,
    )

    # At the time of writing, Q* calculations are implemented only for
    # NC scalar-relativistic pseudos without non-linear core correction.
    # This section shows how to use the Pseudo API to perform this kind of check
    # before runnnig the calculation.
    for pseudo in scf_input.pseudos:
        # print(pseudo)
        if not pseudo.isnc:
            raise RuntimeError("Only NC pseudos are compatible with Q*")
        if pseudo.has_nlcc:
            raise RuntimeError("NLCC is not compatible with Q*")

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

    # Compute phonons on the ddb_ngqpt q-mesh.
    # Include Born effective charges and dynamical quadrupoles via `with_quad=True`.
    #
    #ddb_ngqpt = [1, 1, 1]
    ddb_ngqpt = [2, 2, 2]
    ph_work = flowtk.PhononWork.from_scf_input(scf_input, qpoints=ddb_ngqpt, is_ngqpt=True,
                                               with_becs=True, with_quad=True, ndivsm=5)

    # Add the phonon work to the flow
    flow.register_work(ph_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):
    """
    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())