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 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, "w") as f:
json.dump(structure, f, cls=PMGJSONEncoder)
return
else:
raise ValueError("Unrecognized file extension!")
writer.write_file(filename)
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 to write
filename:
A filename to write to.
"""
lower_filename = os.path.basename(filename).lower()
if re.search("\.cif", lower_filename):
writer = CifWriter(structure)
elif lower_filename.startswith("poscar") \
or lower_filename.startswith("contcar"):
writer = Poscar(structure)
elif re.search("\.cssr", lower_filename):
writer = Cssr(structure)
elif re.search("\.[mj]son", lower_filename):
with zopen(lower_filename, "w") as f:
json.dump(structure, f, cls=PMGJSONEncoder)
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 == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, 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":
input_set = MPVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
elif oformat == "MITVASP":
input_set = MITVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)
def cif(src="POSCAR"):
"""
cifファイルを作成
"""
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure)
std = finder.get_conventional_standard_structure()
cif = CifWriter(std, find_spacegroup=True, symprec=0.1)
cif.write_file("poscar.cif")
def prim_cif(self, dst):
"""
primitive cellでのcifフォーマットをgetする
"""
finder = SpacegroupAnalyzer(self.structure)
structure = finder.get_primitive_standard_structure()
structure = finder.get_conventional_standard_structure()
cif = CifWriter(structure, find_spacegroup=True, symprec=0.1)
cif.write_file(dst)
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 == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, 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":
input_set = MPVaspInputSet()
ts = TransformedStructure(
structure,
[],
history=[
{"source": "file", "datetime": str(datetime.datetime.now()), "original_file": open(filename).read()}
],
)
ts.write_vasp_input(input_set, output_dir=out_filename)
elif oformat == "MITVASP":
input_set = MITVaspInputSet()
ts = TransformedStructure(
structure,
[],
history=[
{"source": "file", "datetime": str(datetime.datetime.now()), "original_file": open(filename).read()}
],
)
ts.write_vasp_input(input_set, output_dir=out_filename)
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)
def batch_write_vasp_input(structures,
vasp_input_set,
output_dir,
make_dir_if_not_present=True,
subfolder=None,
sanitize=False,
include_cif=False):
"""
Batch write vasp input for a sequence of structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
structures:
Sequence of Structures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
make_dir_if_not_present:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from structure.
Defaults to simply "formula_count".
sanitize:
Boolean indicating whether to sanitize the structure before
writing the VASP input files. Sanitized output are generally easier
for viewing and certain forms of analysis. Defaults to False.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(structures):
formula = re.sub("\s+", "", s.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir)
else:
dirname = os.path.join(output_dir, '{}_{}'.format(formula, i))
if sanitize:
s = s.copy(sanitize=True)
vasp_input_set.write_input(
s, dirname, make_dir_if_not_present=make_dir_if_not_present)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s)
writer.write_file(
os.path.join(dirname, "{}_{}.cif".format(formula, i)))
def batch_write_vasp_input(structures, vasp_input_set, output_dir,
make_dir_if_not_present=True, subfolder=None,
sanitize=False, include_cif=False):
"""
Batch write vasp input for a sequence of structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
structures:
Sequence of Structures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
make_dir_if_not_present:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from structure.
Defaults to simply "formula_count".
sanitize:
Boolean indicating whether to sanitize the structure before
writing the VASP input files. Sanitized output are generally easier
for viewing and certain forms of analysis. Defaults to False.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(structures):
formula = re.sub("\s+", "", s.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir)
else:
dirname = os.path.join(output_dir, '{}_{}'.format(formula, i))
if sanitize:
s = s.copy(sanitize=True)
vasp_input_set.write_input(
s, dirname, make_dir_if_not_present=make_dir_if_not_present
)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s)
writer.write_file(os.path.join(dirname,
"{}_{}.cif".format(formula, i)))
def batch_write_vasp_input(transformed_structures,
vasp_input_set,
output_dir,
create_directory=True,
subfolder=None,
include_cif=False):
"""
Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
transformed_structures:
Sequence of TransformedStructures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
create_directory:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from transformed_structure.
eg. lambda x: x.other_parameters["tags"][0] to use the first tag.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(transformed_structures):
formula = re.sub("\s+", "", s.final_structure.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir,
"{}_{}".format(formula, i))
else:
dirname = os.path.join(output_dir, "{}_{}".format(formula, i))
s.write_vasp_input(vasp_input_set,
dirname,
create_directory=create_directory)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s.final_structure)
writer.write_file(os.path.join(dirname, "{}.cif".format(formula)))
def batch_write_vasp_input(transformed_structures, vasp_input_set, output_dir,
create_directory=True, subfolder=None,
include_cif=False):
"""
Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
transformed_structures:
Sequence of TransformedStructures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
create_directory:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from transformed_structure.
eg. lambda x: x.other_parameters["tags"][0] to use the first tag.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(transformed_structures):
formula = re.sub("\s+", "", s.final_structure.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir,
"{}_{}".format(formula, i))
else:
dirname = os.path.join(output_dir, "{}_{}".format(formula, i))
s.write_vasp_input(vasp_input_set, dirname,
create_directory=create_directory)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s.final_structure)
writer.write_file(os.path.join(dirname, "{}.cif".format(formula)))
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 == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, 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":
input_set = MaterialsProjectVaspInputSet()
transmuter = StandardTransmuter.from_structures([structure], [])
transmuter.write_vasp_input(input_set, 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.
Args:
structure:
Structure to write
filename:
A filename to write to.
"""
lower_filename = os.path.basename(filename).lower()
if re.search("\.cif", lower_filename):
writer = CifWriter(structure)
elif lower_filename.startswith("poscar") \
or lower_filename.startswith("contcar"):
writer = Poscar(structure)
elif re.search("\.cssr", lower_filename):
writer = Cssr(structure)
else:
raise ValueError("Unrecognized file extension!")
writer.write_file(filename)
def move_atom(input_cif, output_cif, atom_idx, displacement_vec):
"""
Reads input cif (as file name), moves atom by displacement vector (in
angstroms), and writes to output_cif (as file name).
Currently, doesn't take into account the symmetry operations. This is
theoretically possible with PyMatGen, although I found it to be buggy so
decided it might not be worth it.
Useful things to look up for implementing this:
pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_symmetrized_structure
and its resulting method
find_equivalent_sites()
"""
parser = CifParser(input_cif)
struct = parser.get_structures()[0]
lat_const = np.array(struct.lattice.abc)
frac_pos = struct[atom_idx].frac_coords
new_pos = frac_pos + displacement_vec / lat_const
struct[atom_idx] = struct[atom_idx].species_and_occu.elements[0], new_pos
writer = CifWriter(struct)
writer.write_file(output_cif)
def move_atom(input_cif, output_cif, atom_idx, displacement_vec): """ Reads input cif (as file name), moves atom by displacement vector (in angstroms), and writes to output_cif (as file name). Currently, doesn't take into account the symmetry operations. This is theoretically possible with PyMatGen, although I found it to be buggy so decided it might not be worth it. Useful things to look up for implementing this: pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_symmetrized_structure and its resulting method find_equivalent_sites() """ parser = CifParser(input_cif) struct = parser.get_structures()[0] lat_const = np.array(struct.lattice.abc) frac_pos = struct[atom_idx].frac_coords new_pos = frac_pos + displacement_vec/lat_const struct[atom_idx] = struct[atom_idx].species_and_occu.elements[0], new_pos writer = CifWriter(struct) writer.write_file(output_cif)
__email__ = "*****@*****.**"
__date__ = "Nov 14, 2011"
import argparse
from pymatgen.io.vaspio import Poscar
from pymatgen.io.cifio import CifParser, CifWriter
parser = argparse.ArgumentParser(description='''Convenient file format convertor.
Author: Shyue Ping Ong
Version: 1.0
Last updated: Oct 26 2011''')
parser.add_argument('input_file', metavar='input file', type=str, nargs = 1, help='input file')
parser.add_argument('output_file', metavar='output file', type=str, nargs = 1, help='output file')
parser.add_argument('-c', '--conversion', dest='conversion', type=str, nargs = 1, choices=['poscar2cif','cif2poscar'], default='poscar2cif', help='Format conversion desired. ')
args = parser.parse_args()
try:
if args.conversion[0] == 'poscar2cif':
p = Poscar.from_file(args.input_file[0])
w = CifWriter(p.struct)
w.write_file(args.output_file[0])
else:
r = CifParser(args.input_file[0])
p = Poscar(r.get_structures()[0])
p.write_file(args.output_file[0])
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)
