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 setUp(self): os.chdir(test_dir) self.ctrl_bise = LMTOCtrl.from_file(filename="CTRL.BiSe") self.ctrl_fe = LMTOCtrl.from_file()
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 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