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 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, file, inord="F"):
"""Initialize the object from a Netcdf file."""
file, closeit = as_etsfreader(file)
new = cls(spgid=file.read_value("space_group"),
symrel=file.read_value("reduced_symmetry_matrices"),
tnons=file.read_value("reduced_symmetry_translations"),
symafm=file.read_value("symafm"),
has_timerev=True, # FIXME not treated by ETSF-IO.
inord=inord,
)
if closeit:
file.close()
return new
def from_file(cls, ncfile, inord="F"):
"""Initialize the object from a Netcdf file."""
r, closeit = as_etsfreader(ncfile)
kptopt = int(r.read_value("kptopt", default=1))
new = cls(spgid=r.read_value("space_group"),
symrel=r.read_value("reduced_symmetry_matrices"),
tnons=r.read_value("reduced_symmetry_translations"),
symafm=r.read_value("symafm"),
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
if closeit:
file.close()
return new
def from_file(cls, ncfile, inord="F"):
"""Initialize the object from a Netcdf file."""
r, closeit = as_etsfreader(ncfile)
kptopt = int(r.read_value("kptopt", default=1))
new = cls(spgid=r.read_value("space_group"),
symrel=r.read_value("reduced_symmetry_matrices"),
tnons=r.read_value("reduced_symmetry_translations"),
symafm=r.read_value("symafm"),
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
if closeit:
file.close()
return new
def from_file(cls, filepath):
"""
Initialize the object from a Netcdf file with data
saved in the ETSF-IO format.
"""
file, closeit = as_etsfreader(filepath)
d = {}
for k in cls.KNOWN_KEYS:
try:
d[k] = file.read_value(k)
except file.Error:
pass
if closeit:
file.close()
return cls(**d)
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
def from_file(cls, file, inord="F"):
"""Initialize the object from a Netcdf file."""
#is_ncfile = is_string(file) and file.endswith(".nc")
#if not is_ncfile
#structure = Structure.from_file(file):
#return cls.from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5)
file, closeit = as_etsfreader(file)
new = cls(spgid=file.read_value("space_group"),
symrel=file.read_value("reduced_symmetry_matrices"),
tnons=file.read_value("reduced_symmetry_translations"),
symafm=file.read_value("symafm"),
has_timerev=True, # FIXME not treated by ETSF-IO.
inord=inord)
if closeit:
file.close()
return new
def from_file(cls, file, inord="F"):
"""Initialize the object from a Netcdf file."""
#is_ncfile = is_string(file) and file.endswith(".nc")
#if not is_ncfile
#structure = Structure.from_file(file):
#return cls.from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5)
file, closeit = as_etsfreader(file)
new = cls(
spgid=file.read_value("space_group"),
symrel=file.read_value("reduced_symmetry_matrices"),
tnons=file.read_value("reduced_symmetry_translations"),
symafm=file.read_value("symafm"),
has_timerev=True, # FIXME not treated by ETSF-IO.
inord=inord)
if closeit:
file.close()
return new
def kpoints_factory(filepath):
"""
Factory function: returns an instance of [Kpath, IrredZone]
from a netcdf file written according to the ETSF-IO specifications.
"""
file, closeit = as_etsfreader(filepath)
structure = file.read_structure()
kinfo = KpointsInfo.from_file(filepath)
if kinfo.is_sampling:
obj = IrredZone(structure.reciprocal_lattice, kinfo.frac_coords, kinfo)
elif kinfo.is_path:
obj = Kpath(structure.reciprocal_lattice, kinfo.frac_coords, kinfo)
else:
raise ValueError("Only path or sampling modes are supported!")
if closeit:
file.close()
return obj
