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 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 parse(self, options, *args, **kwargs):
path = self.raw_value
if exists(path):
if isfile(path):
filename = basename(path)
if filename.lower().endswith('.cif'):
from pymatgen.io.cif import CifParser
try:
result = CifParser(path).get_structures()[0]
except:
self.write_message(
'Could not parse CIF file: "{0}"'.format(path))
raise InvalidOption
elif filename.lower().endswith('.cssr'):
from pymatgen.io.cssr import Cssr
try:
result = Cssr.from_file(path).structure
except:
self.write_message(
'Could not parse CSSR file: "{0}"'.format(path))
raise InvalidOption
elif filename.lower().endswith('.xml'):
from pymatgen.io.exciting import ExcitingInput
try:
result = ExcitingInput.from_file(path).structure
except:
self.write_message(
'Could not parse Exciting input file: "{0}"'.
format(path))
raise InvalidOption
else:
from pymatgen.io.vasp import Poscar
try:
result = Poscar.from_file(path).structure
except:
self.write_message(
'Could not parse POSCAR file "{0}"'.format(path))
raise InvalidOption
if not 'result' in locals():
write_message('File format not supported')
raise InvalidOption
else:
return result
else:
self.write_message('"{0}" is a directory!'.format(path))
raise InvalidOption
else:
self.write_message('Cannot locate file "{0}"'.format(path))
raise InvalidOption
def read_structure(filename, primitive=True, sort=False):
"""
Reads a structure 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/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename (str): A filename to read from.
primitive (bool): Whether to convert to a primitive cell for cifs.
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
s = parser.get_structures(primitive=primitive)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
s = Poscar.from_file(filename, False).structure
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*"):
cssr = Cssr.from_file(filename)
s = cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=MontyDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
return s
def read_structure(filename, primitive=True, sort=False):
"""
Reads a structure 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/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename (str): A filename to read from.
primitive (bool): Whether to convert to a primitive cell for cifs.
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
s = parser.get_structures(primitive=primitive)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
s = Poscar.from_file(filename, False).structure
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*"):
cssr = Cssr.from_file(filename)
s = cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=MontyDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
return s
def get_structure(f):
name = f.name
content = f.read()
content = content.decode("utf-8")
if "POSCAR" in name or "CONTCAR" in name:
s = Poscar.from_string(content, False).structure
elif ".cif" in name.lower():
parser = CifParser.from_string(content)
s = parser.get_structures(False)[0]
elif ".cssr" in name.lower():
cssr = Cssr.from_string(content)
s = cssr.structure
elif ".mson" in name.lower():
s = json.loads(content, cls=MontyDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError(name + " is an invalid file format. Only "
"POSCAR, CIF, CSSR and MSON (Materials "
"Project JSON) are supported right now.")
return name, s
def test_from_file(self):
filename = os.path.join(test_dir, "Si.cssr")
cssr = Cssr.from_file(filename)
self.assertIsInstance(cssr.structure, Structure)
def test_from_file(self):
filename = os.path.join(PymatgenTest.TEST_FILES_DIR, "Si.cssr")
cssr = Cssr.from_file(filename)
self.assertIsInstance(cssr.structure, Structure)
def setUp(self):
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR")
p = Poscar.from_file(filepath)
self.cssr = Cssr(p.structure)
def test_from_file(self):
filename = os.path.join(test_dir, "Si.cssr")
cssr = Cssr.from_file(filename)
self.assertIsInstance(cssr.structure, Structure)
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.cssr = Cssr(p.structure)