def write_structure(structure, filename):
"""
Write a structure to a file based on file extension. For example, anything
ending in a "cif" is assumed to be a Crystallographic Information Format
file. Supported formats include CIF, POSCAR, CSSR and pymatgen's JSON
serialized structures.
Args:
structure (Structure/IStructure): Structure to write
filename (str): A filename to write to.
"""
fname = os.path.basename(filename)
if fnmatch(fname, "*.cif*"):
writer = CifWriter(structure)
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
writer = Poscar(structure)
elif fnmatch(fname.lower(), "*.cssr*"):
writer = Cssr(structure)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename, "wt") as f:
f.write(str2unicode(json.dumps(structure, cls=MontyEncoder)))
return
else:
raise ValueError("Unrecognized file extension!")
writer.write_file(filename)
def convert_fmt(args):
iformat = args.input_format[0]
oformat = args.output_format[0]
filename = args.input_filename[0]
out_filename = args.output_filename[0]
try:
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CONVENTIONAL_CIF":
r = CifParser(filename)
structure = r.get_structures(primitive=False)[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
else:
structure = Structure.from_file(filename)
if oformat == "smart":
structure.to(filename=out_filename)
elif oformat == "POSCAR":
p = Poscar(structure)
p.write_file(out_filename)
elif oformat == "CIF":
w = CifWriter(structure)
w.write_file(out_filename)
elif oformat == "CSSR":
c = Cssr(structure)
c.write_file(out_filename)
elif oformat == "VASP":
ts = TransformedStructure(
structure, [],
history=[{"source": "file",
"datetime": str(datetime.datetime.now()),
"original_file": open(filename).read()}])
ts.write_vasp_input(MPRelaxSet, output_dir=out_filename)
elif oformat == "MITVASP":
ts = TransformedStructure(
structure, [],
history=[{"source": "file",
"datetime": str(datetime.datetime.now()),
"original_file": open(filename).read()}])
ts.write_vasp_input(MITRelaxSet, output_dir=out_filename)
except Exception as ex:
print("Error converting file. Are they in the right format?")
print(str(ex))
def setUp(self):
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR")
p = Poscar.from_file(filepath)
self.cssr = Cssr(p.structure)
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.cssr = Cssr(p.structure)
