Flow for Relaxation + BandsΒΆ

This script shows how to perform a structural relaxation and a band structure calculation

WARNING: The API could change!

../_images/sphx_glr_run_relax_and_ebands_001.png

Out:

<ScfTask, node_id=196436, workdir=../../../../../../../var/folders/nc/k69spyd12qv2tk3stk2xrxg40000gr/T/tmpjsql7nix/w1/t0>: setting prtwf to -1
/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 make_ion_ioncell_inputs(paral_kgb=0):
    pseudos = abidata.pseudos("14si.pspnc")
    structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))

    # Perturb the structure (random perturbation of 0.1 Angstrom)
    # then compress the volume to trigger dilatmx.
    #structure.perturb(distance=0.1)
    #structure.scale_lattice(structure.volume * 0.6)

    global_vars = dict(
        ecut=28,
        ngkpt=[4,4,4],
        shiftk=[0,0,0],
        nshiftk=1,
        chksymbreak=0,
        paral_kgb=paral_kgb,
        #prtwf=0,
    )

    multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=2)

    # Global variables
    multi.set_vars(global_vars)

    # Dataset 1 (Atom Relaxation)
    multi[0].set_vars(
        optcell=0,
        ionmov=2,
        tolrff=0.02,
        tolmxf=5.0e-5,
        ntime=50,
        #ntime=3,  #To test the restart
        #dilatmx=1.1, # FIXME: abinit crashes if I don't use this
    )

    # Dataset 2 (Atom + Cell Relaxation)
    multi[1].set_vars(
        optcell=1,
        ionmov=2,
        ecutsm=0.5,
        dilatmx=1.02,
        tolrff=0.02,
        tolmxf=5.0e-5,
        strfact=100,
        ntime=50,
        #ntime=3,  # To test the restart
        )

    ion_inp, ioncell_inp = multi.split_datasets()
    return ion_inp, ioncell_inp


def make_scf_nscf_inputs(paral_kgb=1):
    """Returns two input files: GS run and NSCF on a high symmetry k-mesh."""
    pseudos = abidata.pseudos("14si.pspnc")
    #pseudos = data.pseudos("Si.GGA_PBE-JTH-paw.xml")

    multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"), pseudos=pseudos, ndtset=2)

    # Global variables
    ecut = 28
    global_vars = dict(ecut=ecut,
                       nband=8,
                       timopt=-1,
                       istwfk="*1",
                       nstep=15,
                       paral_kgb=paral_kgb,
                    )

    if multi.ispaw:
        global_vars.update(pawecutdg=2*ecut)

    multi.set_vars(global_vars)

    # Dataset 1 (GS run)
    multi[0].set_kmesh(ngkpt=[8,8,8], shiftk=[0,0,0])
    multi[0].set_vars(tolvrs=1e-6)

    # Dataset 2 (NSCF run)
    kptbounds = [
        [0.5, 0.0, 0.0], # L point
        [0.0, 0.0, 0.0], # Gamma point
        [0.0, 0.5, 0.5], # X point
    ]

    multi[1].set_kpath(ndivsm=6, kptbounds=kptbounds)
    multi[1].set_vars(tolwfr=1e-12)

    # Generate two input files for the GS and the NSCF run
    scf_input, nscf_input = multi.split_datasets()
    return scf_input, nscf_input


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_")

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

    paral_kgb = 1
    #paral_kgb = 0  # This one is OK

    # Create a relaxation work and add it to the flow.
    ion_inp, ioncell_inp = make_ion_ioncell_inputs(paral_kgb=paral_kgb)

    relax_work = flowtk.RelaxWork(ion_inp, ioncell_inp)
    flow.register_work(relax_work)

    scf_inp, nscf_inp = make_scf_nscf_inputs(paral_kgb=paral_kgb)

    bands_work = flowtk.BandStructureWork(scf_inp, nscf_inp)

    # The scf task in bands work restarts from the DEN file of the last task in relax_work
    if paral_kgb == 0:
        # cg works fine if we restart from the WFK
        bands_work.scf_task.add_deps({relax_work[-1]: "WFK"})
    else:
        # --> This triggers an infamous bug in abinit
        bands_work.scf_task.add_deps({relax_work[-1]: "WFK"})

        # --> This is ok if we used fourier_interp to change the FFT mesh.
        #bands_work.scf_task.add_deps({relax_work[-1]: "DEN"})

    # All task in bands_work will fetch the relaxed structure from the last task in relax_work
    for task in bands_work:
        task.add_deps({relax_work[-1]: "@structure"})

    flow.register_work(bands_work)
    flow.allocate()
    flow.use_smartio()
    flow.set_garbage_collector()

    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 0.558 seconds)

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