Relaxation FlowΒΆ

This script shows how to perform a structural relaxation in two steps:

  1. Relaxation of atomic positions with unit cell parameters fixed.

  2. Full relaxation (atoms + cell) with the initial configuration read from step 1)

../_images/sphx_glr_run_relax_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_ion_ioncell_inputs(paral_kgb=0):

    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=4,
        ngkpt=[4,4,4],
        shiftk=[0,0,0],
        nshiftk=1,
        chksymbreak=0,
        paral_kgb=paral_kgb,
        iomode=3,
        #prtwf=0,
    )

    multi = abilab.MultiDataset(structure, pseudos=abidata.pseudos("14si.pspnc"), 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 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)

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

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

    #bands_work = flowtk.BandStructureWork(scf_input, nscf_input)
    bands_work = flowtk.Work()
    deps = {relax_work[-1]: "@structure"}
    deps = {relax_work[-1]: ["DEN", "@structure"]}  # --> This is not possible because the file ext is changed!
    #deps = {relax_work[-1]: ["WFK", "@structure"]} # --> This triggers an infamous bug in abinit

    bands_work.register_relax_task(ioncell_inp, deps=deps)
    flow.register_work(bands_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):
    return build_flow(options)


if __name__ == "__main__":
    sys.exit(main())

Total running time of the script: ( 0 minutes 0.578 seconds)

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