Raman Flow with independent-particle approximation (optic)ΒΆ

This script shows how to perform a Raman calculation with excitonic effects included with the BSE formalism.

../_images/sphx_glr_run_raman_optic_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 numpy as np

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


def build_flow(options):
    # Get the unperturbed structure.
    pseudos = abidata.pseudos("14si.pspnc")
    base_structure = abidata.structure_from_ucell("Si")

    ngkpt = [6, 6, 6]

    etas = [-.001, 0, +.001]
    ph_displ = np.reshape(np.zeros(3*len(base_structure)), (-1,3))
    ph_displ[0,:] = [+1, 0, 0]
    ph_displ[1,:] = [-1, 0, 0]

    # Build new structures by displacing atoms according to the phonon displacement
    # ph_displ (in cartesian coordinates). The Displacement is normalized so that
    # the maximum atomic diplacement is 1 Angstrom and then multiplied by eta.
    modifier = abilab.StructureModifier(base_structure)

    displaced_structures = modifier.displace(ph_displ, etas, frac_coords=False)

    # Initialize flow. Each workflow in the flow defines a complete BSE calculation for given eta.
    if not options.workdir:
        options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_", "flow_")

    flow = flowtk.Flow(options.workdir, manager=options.manager)

    # Generate the different shifts to average
    ndiv = 1
    shift1D = np.arange(1, 2*ndiv+1, 2) / (2 * ndiv)
    all_shifts = [[x, y, z] for x in shift1D for y in shift1D for z in shift1D]

    for structure, eta in zip(displaced_structures, etas):
        for ishift,shift in enumerate(all_shifts):
            flow.register_work(raman_work(structure, pseudos, ngkpt, shift),
                               workdir="eta_" + str(eta) + "shift_" + str(ishift))

    return flow


def raman_work(structure, pseudos, ngkpt, shiftk):
    # Generate 3 different input files for computing optical properties with Optic.

    global_vars = dict(
        istwfk="*1",
        paral_kgb=0,
        ecut=8,
        nstep=200,
        diemac=12,
        ixc=7,
        chksymbreak=0,
        #accesswff=3
    )

    multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=5)
    multi.set_vars(global_vars)
    multi.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)

    # GS run
    multi[0].set_vars(
        tolvrs=1e-8,
        nband=20,
        nbdbuf=2,
    )

    # Note kptopt 2 in NSCF and DDK
    # In principle kptopt 2 is needed only in DDK.
    # one could do a first NSCF run with kptopt 1, reread with kptopt 2 and enter DDK...

    # NSCF run
    multi[1].set_vars(
       iscf=-2,
       nband=40,
       nbdbuf=5,
       kptopt=2,
       tolwfr=1.e-12,
    )

    # DDK along 3 directions
    # Third dataset : ddk response function along axis 1
    # Fourth dataset : ddk response function along axis 2
    # Fifth dataset : ddk response function along axis 3
    for idir in range(3):
        rfdir = 3 * [0]
        rfdir[idir] = 1

        multi[2 + idir].set_vars(
           iscf=-3,
           nband=40,
           nbdbuf=5,
           nstep=1,
           nline=0,
           prtwf=3,
           kptopt=2,
           nqpt=1,
           qpt=[0.0, 0.0, 0.0],
           rfdir=rfdir,
           rfelfd=2,
           tolwfr=1.e-12,
        )

    scf_inp, nscf_inp, ddk1, ddk2, ddk3 = multi.split_datasets()
    ddk_inputs = [ddk1, ddk2, ddk3]

    work = flowtk.Work()
    scf_t = work.register_scf_task(scf_inp)
    nscf_t = work.register_nscf_task(nscf_inp, deps={scf_t: "DEN"})

    ddk_nodes = []
    for inp in ddk_inputs:
        ddk_t = work.register_ddk_task(inp, deps={nscf_t: "WFK"})
        ddk_nodes.append(ddk_t)

    optic_input = abilab.OpticInput(
        broadening=0.002,     # Value of the smearing factor, in Hartree
        domega=0.0003,        # Frequency mesh.
        maxomega=0.3,
        scissor=0.000,        # Scissor shift if needed, in Hartree
        tolerance=0.002,      # Tolerance on closeness of singularities (in Hartree)
        num_lin_comp=6,       # Number of components of linear optic tensor to be computed
        lin_comp=(11, 12, 13, 22, 23, 33), # Linear coefficients to be computed (x=1, y=2, z=3)
        num_nonlin_comp=0     # Number of components of nonlinear optic tensor to be computed
        #nonlin_comp=(123, 222),
    )

    optic_t = flowtk.OpticTask(optic_input, nscf_node=nscf_t, ddk_nodes=ddk_nodes)
    work.register(optic_t)

    return work


# 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 0.908 seconds)

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