def test_structure(self):
bise_poscar = Structure.from_file("POSCAR.BiSe")
self.assertTrue(bise_poscar.matches(self.ctrl_bise.structure))
self.assertEqual(
self.ctrl_bise,
LMTOCtrl(self.ctrl_bise.structure, header="Bi6Se6, hexagonal"),
)
def test_read_write(self):
self.ctrl_bise.write_file(filename="CTRL.tmp")
ctrl_tmp = LMTOCtrl.from_file(filename="CTRL.tmp")
self.assertTrue(self.ctrl_bise.structure.matches(ctrl_tmp.structure))
os.remove("CTRL.tmp")
def test_dict(self):
self.assertEqual(self.ctrl_bise,
LMTOCtrl.from_dict(self.ctrl_bise.as_dict()))
def setUp(self):
os.chdir(test_dir)
self.ctrl_bise = LMTOCtrl.from_file(filename="CTRL.BiSe")
self.ctrl_fe = LMTOCtrl.from_file()
def test_read_write(self):
self.ctrl_bise.write_file(filename="CTRL.tmp")
ctrl_tmp = LMTOCtrl.from_file(filename="CTRL.tmp")
self.assertTrue(self.ctrl_bise.structure.matches(ctrl_tmp.structure))
os.remove("CTRL.tmp")
def test_dict(self):
self.assertEqual(self.ctrl_bise,
LMTOCtrl.from_dict(self.ctrl_bise.as_dict()))
def setUp(self):
os.chdir(test_dir)
self.ctrl_bise = LMTOCtrl.from_file(filename="CTRL.BiSe")
self.ctrl_fe = LMTOCtrl.from_file()
def from_file(cls, filename, primitive=False, sort=False, merge_tol=0.0):
"""
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. Defaults to False.
sort (bool): Whether to sort sites. Default to False.
merge_tol (float): If this is some positive number, sites that
are within merge_tol from each other will be merged. Usually
0.01 should be enough to deal with common numerical issues.
Returns:
Structure.
"""
filename = str(filename)
if filename.endswith(".nc"):
# Read Structure from a netcdf file.
from pymatgen.io.abinit.netcdf import structure_from_ncdata
s = structure_from_ncdata(filename, cls=cls)
if sort:
s = s.get_sorted_structure()
return s
from pymatgen.io.lmto import LMTOCtrl
from pymatgen.io.vasp import Vasprun, Chgcar
from pymatgen.io.exciting import ExcitingInput
from monty.io import zopen
fname = os.path.basename(filename)
with zopen(filename, "rt") as f:
contents = f.read()
if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
return cls.from_str(contents, fmt="cif",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
s = cls.from_str(contents, fmt="poscar",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
s = Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
s = Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
return cls.from_str(contents, fmt="cssr",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
return cls.from_str(contents, fmt="json",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.yaml*"):
return cls.from_str(contents, fmt="yaml",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.xsf"):
return cls.from_str(contents, fmt="xsf",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "input*.xml"):
return ExcitingInput.from_file(fname).structure
elif fnmatch(fname, "*rndstr.in*") \
or fnmatch(fname, "*lat.in*") \
or fnmatch(fname, "*bestsqs*"):
return cls.from_str(contents, fmt="mcsqs",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "CTRL*"):
return LMTOCtrl.from_file(filename=filename).structure
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
if merge_tol:
s.merge_sites(merge_tol)
s.__class__ = cls
return s