def from_file(cls, filepath):
"""
Return a new Structure instance from a NetCDF file
Args:
filename:
netcdf file with crystallographic data in the ETSF-IO format.
or any other file format supported by `pymatgen.io.smartio`.
"""
if filepath.endswith(".nc"):
file, closeit = as_etsfreader(filepath)
new = file.read_structure()
# Change the class of new.
new.__class__ = cls
new.set_spacegroup(SpaceGroup.from_file(file))
if closeit:
file.close()
else:
# TODO: Spacegroup is missing here.
#from pymatgen.io.smartio import read_structure
#new = read_structure(filepath)
new = super(Structure, cls).from_file(filepath)
# Change the class of new.
new.__class__ = cls
return new
def from_file(cls, filepath, primitive=True, sort=False):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR, Netcdf and pymatgen's JSON serialized structures.
Args:
filename (str): The filename to read from.
primitive (bool): Whether to convert to a primitive cell
Only available for cifs, POSCAR, CSSR, JSON, YAML
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
:class:`Structure` object
"""
if filepath.endswith(".nc"):
from pymatgen.io.abinitio.netcdf import as_etsfreader
file, closeit = as_etsfreader(filepath)
new = file.read_structure(cls=cls)
new.set_spacegroup(SpaceGroup.from_file(file))
if closeit: file.close()
else:
# TODO: Spacegroup is missing here.
new = super(Structure, cls).from_file(filepath, primitive=primitive, sort=sort)
# Change the class of new.
if new.__class__ != cls: new.__class__ = cls
return new
def __init__(self, filepath):
super(DdbFile, self).__init__(filepath)
self._header = self._parse_header()
self._structure = Structure.from_abivars(**self.header)
# Add Spacegroup (needed in guessed_ngkpt)
# FIXME: has_timerev is always True
spgid, has_timerev, h = 0, True, self.header
self._structure.set_spacegroup(SpaceGroup(spgid, h.symrel, h.tnons, h.symafm, has_timerev))
frac_coords = self._read_qpoints()
self._qpoints = KpointList(self.structure.reciprocal_lattice, frac_coords, weights=None, names=None)
# Guess q-mesh
self._guessed_ngqpt = self._guess_ngqpt()
def from_file(cls, filepath, primitive=True, sort=False):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR, Netcdf and pymatgen's JSON serialized structures.
Netcdf files supported:
All files produced by ABINIT with info of the crystalline geometry
HIST_FILEs, in this case the last structure of the history is returned.
Args:
filename (str): The filename to read from.
primitive (bool): Whether to convert to a primitive cell
Only available for cifs, POSCAR, CSSR, JSON, YAML
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
:class:`Structure` object
"""
if filepath.endswith(".nc"):
from pymatgen.io.abinitio.netcdf import as_etsfreader
file, closeit = as_etsfreader(filepath)
new = file.read_structure(cls=cls)
new.set_spacegroup(SpaceGroup.from_file(file))
if closeit: file.close()
elif filepath.endswith("_HIST") or filepath.endswith("_HIST.nc"):
# Abinit history file. In this case we return the last structure!
from abipy.dynamics.hist import HistFile
with HistFile(filepath) as hist:
return hist.structures[-1]
else:
# TODO: Spacegroup is missing here.
new = super(Structure, cls).from_file(filepath,
primitive=primitive,
sort=sort)
# Change the class of new.
if new.__class__ != cls: new.__class__ = cls
return new
def from_file(cls, filepath, primitive=True, sort=False):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR, Netcdf and pymatgen's JSON serialized structures.
Netcdf files supported:
All files produced by ABINIT with info of the crystalline geometry
HIST_FILEs, in this case the last structure of the history is returned.
Args:
filename (str): The filename to read from.
primitive (bool): Whether to convert to a primitive cell
Only available for cifs, POSCAR, CSSR, JSON, YAML
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
:class:`Structure` object
"""
if filepath.endswith("_HIST") or filepath.endswith("_HIST.nc"):
# Abinit history file. In this case we return the last structure!
# Note that HIST does not follow the etsf-io conventions.
from abipy.dynamics.hist import HistFile
with HistFile(filepath) as hist:
return hist.structures[-1]
elif filepath.endswith(".nc"):
from pymatgen.io.abinit.netcdf import as_etsfreader
file, closeit = as_etsfreader(filepath)
new = file.read_structure(cls=cls)
new.set_spacegroup(SpaceGroup.from_file(file))
if closeit: file.close()
else:
# TODO: Spacegroup is missing here.
new = super(Structure, cls).from_file(filepath, primitive=primitive, sort=sort)
# Change the class of new.
if new.__class__ != cls: new.__class__ = cls
return new
