Starting a Flow from external filesΒΆ

This example shows how to build a flow for Nscf calculations in which the dependency is given by an external density file.

../_images/sphx_glr_run_from_files_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 make_scf_nscf_inputs(paral_kgb=1):
    """Returns two input files: GS run and NSCF on a high symmetry k-mesh."""
    multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
                                pseudos=abidata.pseudos("14si.pspnc"), ndtset=2)

    # Global variables
    ecut = 6
    global_vars = dict(
        ecut=ecut,
        nband=8,
        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_")

    # Get the SCF and the NSCF input.
    scf_input, nscf_input = make_scf_nscf_inputs()

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

    # Create a Work, all tasks in work will start from the DEN file.
    # Note that the file must exist when the work is created
    # Use the standard approach based on tasks and works if
    # there's a node who needs a file produced in the future.
    work = flowtk.Work()
    den_filepath = abidata.ref_file("si_DEN.nc")
    work.register_nscf_task(nscf_input, deps={den_filepath: "DEN"})
    flow.register_work(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())

Total running time of the script: ( 0 minutes 0.475 seconds)

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