def structure_from_etsf_file(ncdata, site_properties=None):
"""
Reads and returns a pymatgen structure from a NetCDF file
containing crystallographic data in the ETSF-IO format.
Args:
ncdata:
filename or NetcdfReader instance.
site_properties:
Dictionary with site properties.
"""
ncdata, closeit = as_ncreader(ncdata)
# TODO check whether atomic units are used
lattice = ArrayWithUnit(ncdata.read_value("primitive_vectors"),
"bohr").to("ang")
red_coords = ncdata.read_value("reduced_atom_positions")
natom = len(red_coords)
znucl_type = ncdata.read_value("atomic_numbers")
# type_atom[0:natom] --> index Between 1 and number of atom species
type_atom = ncdata.read_value("atom_species")
# Fortran to C index and float --> int conversion.
species = natom * [None]
for atom in range(natom):
type_idx = type_atom[atom] - 1
species[atom] = int(znucl_type[type_idx])
d = {}
if site_properties is not None:
for prop in site_properties:
d[property] = ncdata.read_value(prop)
structure = Structure(lattice, species, red_coords, site_properties=d)
# Quick and dirty hack.
# I need an abipy structure since I need to_abivars and other methods.
#from pymatgen.io.abinitio.abiobjects import AbiStructure
#structure.__class__ = AbiStructure
try:
from abipy.core.structure import Structure as AbipyStructure
structure.__class__ = AbipyStructure
except ImportError:
pass
if closeit:
ncdata.close()
return structure
def structure_from_etsf_file(ncdata, site_properties=None):
"""
Reads and returns a pymatgen structure from a NetCDF file
containing crystallographic data in the ETSF-IO format.
Args:
ncdata:
filename or NetcdfReader instance.
site_properties:
Dictionary with site properties.
"""
ncdata, closeit = as_ncreader(ncdata)
# TODO check whether atomic units are used
lattice = ArrayWithUnit(ncdata.read_value("primitive_vectors"),
"bohr").to("ang")
red_coords = ncdata.read_value("reduced_atom_positions")
natom = len(red_coords)
znucl_type = ncdata.read_value("atomic_numbers")
# type_atom[0:natom] --> index Between 1 and number of atom species
type_atom = ncdata.read_value("atom_species")
# Fortran to C index and float --> int conversion.
species = natom * [None]
for atom in range(natom):
type_idx = type_atom[atom] - 1
species[atom] = int(znucl_type[type_idx])
d = {}
if site_properties is not None:
for prop in site_properties:
d[property] = ncdata.read_value(prop)
structure = Structure(lattice, species, red_coords, site_properties=d)
# Quick and dirty hack.
# I need an abipy structure since I need to_abivars and other methods.
#from pymatgen.io.abinitio.abiobjects import AbiStructure
#structure.__class__ = AbiStructure
try:
from abipy.core.structure import Structure as AbipyStructure
structure.__class__ = AbipyStructure
except ImportError:
pass
if closeit:
ncdata.close()
return structure
