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 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)
parser.add_argument('-n',
type=int,
default=8,
help='number of interpolated images')
parser.add_argument('-chg', type=str, help='CHGCAR for pathFinder')
arg = parser.parse_args()
s1 = Poscar.from_file(arg.s1).structure
s2 = Poscar.from_file(arg.s2).structure
chg = Chgcar.from_file(arg.chg)
relax_sites = []
for i, site in enumerate(s1.sites):
if site.specie == Element(arg.e):
relax_sites.append(i)
pf = NEBPathfinder(s1,
s2,
relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(),
n_images=(3 * arg.n))
images = pf.images
for i, image in enumerate(images):
if i % 3 == 0:
p = Poscar(image)
directory = "0" + str(i / 3)
if not os.path.exists(directory):
os.makedirs(directory)
p.write_file("{}/POSCAR".format(directory))
def main(api="", queryid=""):
"""Get VASP inputs for Materials Project structure
Args:
api <str>: Materials Project API key
queryid <str>: Materials Project ID of the structure
Returns:
creates a folder named with that mpid, and including
some VASP input files.
"""
if api == "":
print "Must have an API key from materialsproject.org"
return None
if queryid == "":
print "No MP structure ID given. Exiting."
return None
rest_adapter = MPRester(api)
entries = list()
proplist = list()
proplist.append('pretty_formula')
proplist.append('structure')
proplist.append('potcar')
proplist.append('material_id')
myentry = rest_adapter.mpquery(criteria={'material_id': queryid},
properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s as material_id. Trying entry_id." % queryid
myentry = rest_adapter.mpquery(criteria={'entry_id': queryid},
properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s" % queryid
return None
entries.extend(myentry)
workdir = os.getcwd()
from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet
for entry in entries:
mpvis = MPVaspInputSet()
myname = str(entry['pretty_formula'])
#print entry['structure'].composition
#print entry['structure'].formula
#myname = entry['pretty_formula']
myname = myname.replace("(", "_").replace(")", "_")
myname = myname + "_" + entry['material_id']
os.mkdir(myname)
os.chdir(myname)
mystructure = entry['structure']
if mystructure.num_sites <= 10:
mystructure.make_supercell([2, 2, 2])
#mystructure.perturb(0.01)
incar = mpvis.get_incar(mystructure)
incar.write_file("INCAR")
potcar = mpvis.get_potcar(mystructure)
potcar.write_file("POTCAR")
#potcar_symbols = mpvis.get_potcar_symbols(mystructure)
myposcar = Poscar(mystructure)
mykpoints = mpvis.get_kpoints(mystructure)
mykpoints.write_file("KPOINTS")
myposcar.write_file("POSCAR")
os.chdir(workdir)