def get_hirshfeld(self, structure, all_el_dens_paths=None, fhi_all_el_path=None, workdir=None):
"""
Runs cut3d to get the Hirshfeld charges. Requires all-electron density files, so at least one source
should be specified (all_el_dens_paths or fhi_all_el_path)
Args:
structure: a Structure object representing the structure used to generate the density
all_el_dens_paths: a list of paths to the all-electron density files correspinding to the elements defined
in the abinit input.
fhi_all_el_path: path to the folder containing the fhi all-electron density files that will be used
to automatically determine the path of the required densities.
workdir: directory where cut3d is executed.
Returns:
(HirshfeldCharges) the calculated Hirshfeld charges.
"""
if all_el_dens_paths is None and fhi_all_el_path is None:
raise ValueError("At least one source of all electron densities should be provided.")
if all_el_dens_paths is not None and fhi_all_el_path is not None:
raise ValueError("all_el_dens_paths and fhi_all_el_path are mutually exclusive.")
if all_el_dens_paths is not None:
cut3d_input = Cut3DInput.hirshfeld(self.filepath, all_el_dens_paths)
else:
cut3d_input = Cut3DInput.hirshfeld_from_fhi_path(self.filepath, structure, fhi_all_el_path)
workdir = os.path.abspath(tempfile.mkdtemp() if workdir is None else workdir)
cut3d = Cut3D()
outfile, converted_file = cut3d.cut3d(cut3d_input, workdir)
from abipy.electrons.charges import HirshfeldCharges
return HirshfeldCharges.from_cut3d_outfile(structure=structure, filepath=cut3d.stdout_fname)
def _convert(self, cut3d_input, workdir=None):
"""
Internal function to run a conversion using cut3d.
"""
workdir = os.path.abspath(tempfile.mkdtemp() if workdir is None else workdir)
outfile, converted_file = Cut3D().cut3d(cut3d_input, workdir)
return converted_file
def _convert(self, cut3d_input, workdir=None):
"""
Internal function to run a conversion using cut3d.
"""
workdir = tempfile.mkdtemp() if workdir is None else workdir
# local import to avoid circular references
from abipy.flowtk import Cut3D
outfile, converted_file = Cut3D().cut3d(cut3d_input, workdir)
return converted_file
def get_density(self, workdir=None):
"""
Invoke cut3d to produce a netcdf file with the density, read the file and return Density object.
Args:
workdir: directory in which cut3d is executed.
"""
workdir = os.path.abspath(tempfile.mkdtemp() if workdir is None else workdir)
output_filepath = os.path.join(workdir, "field_CUT3DDENPOT.nc")
# FIXME Converters with nspden > 1 won't work since cut3d asks for the ispden index.
cut3d_input = Cut3DInput(infile_path=self.filepath, output_filepath=output_filepath,
options=[15, output_filepath, 0, 0])
outfile, _ = Cut3D().cut3d(cut3d_input, workdir)
with Cut3dDenPotNcFile(output_filepath) as nc:
assert nc.field.is_density_like and nc.field.netcdf_name == "density"
return nc.field