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)
def _vasp_poscar_setup(self):
"""Set up the POSCAR file for a single VASP run.
"""
name = self.keywords['name']
pospath = os.path.join(name, "POSCAR")
if os.path.isfile(pospath):
my_poscar = Poscar.from_file(pospath)
#parent should have given a structure
else: #this is an originating run; mast should give it a structure
if self.keywords['structure'] is not None:
my_poscar = Poscar(self.keywords['structure'])
else:
pf = os.path.join(os.path.dirname(name),'POSCAR_%s'%os.path.basename(name))
if os.path.isfile(pf):
my_poscar = Poscar.from_file(pf)
workdir=os.path.dirname(name)
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
mystr=my_poscar.structure
manname="manifest___"
myatomindex=AtomIndex(structure_index_directory=sdir)
newstr=myatomindex.graft_new_coordinates_from_manifest(mystr, manname, "")
self.logger.info("Getting original coordinates from manifest.")
new_pos=Poscar(newstr)
my_poscar=new_pos
self.logger.info("No POSCAR found from a parent; base structure used for %s" % self.keywords['name'])
if 'mast_coordinates' in self.keywords['program_keys'].keys():
sxtend = StructureExtensions(struc_work1=my_poscar.structure, name=self.keywords['name'])
coordstrucs=self.get_coordinates_only_structure_from_input()
newstruc = sxtend.graft_coordinates_onto_structure(coordstrucs[0])
my_poscar.structure=newstruc.copy()
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
return my_poscar
def forward_final_structure_file(self, childpath, newname="POSCAR"):
"""Forward the final structure.
For VASP, this is the CONTCAR.
Args:
childpath <str>: Path of child ingredient
newname <str>: new name (default 'POSCAR')
"""
proceed=False
workdir=os.path.dirname(self.keywords['name'])
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
proceed=True
if not proceed:
return self.copy_a_file(childpath, "CONTCAR", newname)
childmeta=Metadata(metafile="%s/metadata.txt" % childpath)
child_program=childmeta.read_data("program")
if not "vasp" in child_program: #madelung utility or another folder
return self.copy_a_file(childpath, "CONTCAR", newname)
child_scaling_label=childmeta.read_data("scaling_label")
child_defect_label=childmeta.read_data("defect_label")
child_neb_label=childmeta.read_data("neb_label")
child_phonon_label=childmeta.read_data("phonon_label")
if child_scaling_label == None:
child_scaling_label = ""
if child_defect_label == None:
child_defect_label = ""
if child_neb_label == None:
child_neb_label = ""
if child_phonon_label == None:
child_phonon_label = ""
parentmeta=Metadata(metafile="%s/metadata.txt" % self.keywords['name'])
parent_defect_label=parentmeta.read_data("defect_label")
parent_neb_label=parentmeta.read_data("neb_label")
if parent_defect_label == None:
parent_defect_label = ""
if parent_neb_label == None:
parent_neb_label = ""
if (not (child_neb_label == "")) and (not (parent_defect_label == "")):
child_defect_label = parent_defect_label
if (not (child_phonon_label == "")):
if (not (parent_defect_label == "")):
child_defect_label = parent_defect_label
if (not (parent_neb_label == "")):
child_neb_label = parent_neb_label
child_defect_label = parent_neb_label.split('-')[0].strip() # always define phonons from first endpoint
#get child manifest
childmanifest="manifest_%s_%s_%s" % (child_scaling_label, child_defect_label, child_neb_label)
#build structure from atom indices using parent name_frac_coords
ing_label=os.path.basename(self.keywords['name'])
childmeta.write_data("parent",ing_label)
mystr=Poscar.from_file("%s/CONTCAR" % self.keywords['name']).structure
myatomindex=AtomIndex(structure_index_directory=sdir)
if "inducescaling" in childpath: #initial scaled coords have no parent
ing_label="original"
newstr=myatomindex.graft_new_coordinates_from_manifest(mystr, childmanifest,ing_label)
newposcar=Poscar(newstr)
newposcar.write_file(os.path.join(childpath,newname))
return
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 standard(src="POSCAR"):
"""
standardに変換
"""
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure)
std = finder.get_conventional_standard_structure()
dstpos = Poscar(std)
dst = "POSCAR_std"
Cabinet.reserve_file(dst)
dstpos.write_file(dst)
def primitive(src="POSCAR"):
"""
primitiveに変換
"""
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure)
prim = finder.get_primitive_standard_structure()
dstpos = Poscar(prim)
dst = "POSCAR_prim"
Cabinet.reserve_file(dst)
dstpos.write_file(dst)
def refined(src="POSCAR"):
"""
refined poscar を 作成する
"""
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure, symprec=5e-1, angle_tolerance=8)
std = finder.get_refined_structure()
dstpos = Poscar(std)
dst = "POSCAR_refined"
Cabinet.reserve_file(dst)
dstpos.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 set_up_neb_folders(self, image_structures):
"""Set up NEB folders.
Args:
image_structures <list of Structure>: List
of image structures
"""
imct=0
myname = self.keywords['name']
if 'mast_coordinates' in self.keywords['program_keys'].keys():
coordstrucs=self.get_coordinates_only_structure_from_input()
newstrucs=list()
sidx = 0 #ex. coordstrucs 0, 1, 2 for 3 images
while sidx < self.keywords['program_keys']['mast_neb_settings']['images']:
sxtend = StructureExtensions(struc_work1=image_structures[sidx+1].copy(), name=self.keywords['name'])
newstrucs.append(sxtend.graft_coordinates_onto_structure(coordstrucs[sidx]))
sidx = sidx + 1
while imct < len(image_structures):
imposcar = Poscar(image_structures[imct])
num_str = str(imct).zfill(2)
impath = os.path.join(myname, num_str)
impospath = os.path.join(myname, "POSCAR_" + num_str)
if 'mast_coordinates' in self.keywords['program_keys'].keys():
if imct == 0: #skip endpoint
pass
elif imct == len(image_structures)-1: #skip other endpt
pass
else:
imposcar.structure=newstrucs[imct-1].copy()
dirutil.lock_directory(myname)
imposcar.write_file(impospath)
dirutil.unlock_directory(myname)
try:
os.makedirs(impath)
except OSError:
self.logger.warning("Directory at %s already exists." % impath)
return None
dirutil.lock_directory(impath)
imposcar.write_file(os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
def produce(irreps):
os.makedirs('irrep')
for i, irrep in enumerate(irreps):
poscar = Poscar(irrep)
symbols = poscar.site_symbols
natoms = poscar.natoms
name_dict = {'Al': 'A', 'Ti': 'B'}
tmp = ["{0}{1}".format(name_dict[x], y)
for x, y in zip(symbols, natoms)]
finder = SymmetryFinder(irrep)
spg_num = finder.get_spacegroup_number()
spg = "_".join(finder.get_spacegroup_symbol().split('/'))
dirname = "No." + "{0:03d}".format(i) + "_" + spg + "_" + "".join(tmp)
poscar.comment += " (#" + str(spg_num) + ": " + spg + ")"
standard = finder.get_conventional_standard_structure()
stand_pos = Poscar(standard)
stand_pos.comment += " (#" + str(spg_num) + ": " + spg + ")"
os.makedirs(os.path.join('irrep', dirname))
poscar.write_file(os.path.join('irrep', dirname, 'POSCAR.prim'))
stand_pos.write_file(os.path.join('irrep', dirname, 'POSCAR.std'))
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 scaleCell(path,volume):
poscar = os.path.join(path,'POSCAR')
refcar = os.path.join(path,'REFCAR')
potcar = Potcar()
assert os.path.isfile(poscar)
struct = read_structure(poscar)
struct.scale_lattice(volume)
species = [ pot.element for pot in potcar.from_file('POTCAR') ]
reprule = { old:new for old,new in zip(struct.composition.elements,species) }
struct.replace_species(reprule)
p = Poscar(struct)
with open(poscar) as f:
poscomment = f.readline().strip()
p.comment = poscomment
p.write_file(poscar,vasp4_compatible=True)
if os.path.isfile(refcar):
tmp = os.path.join(path,'POSCARtmp')
# copy Poscar to temporary file and refcar to poscar
copyfile(poscar,tmp)
copyfile(refcar,poscar)
struct = read_structure(poscar)
struct.scale_lattice(volume)
species = [ pot.element for pot in potcar.from_file('POTCAR') ]
reprule = { old:new for old,new in zip(struct.composition.elements,species) }
struct.replace_species(reprule)
r = Poscar(struct)
with open(poscar) as f:
poscomment = f.readline().strip()
r.comment = poscomment
r.write_file(poscar,vasp4_compatible=True)
with open(refcar) as f:
poscomment = f.readline().strip()
r.comment = poscomment
r.write_file(refcar,vasp4_compatible=True)
# replace poscar with its original
move(tmp,poscar)
else:
print 'No REFCAR found.'
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)
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 write_final_structure_file(self, mystruc):
"""Write the final structure to a file.
For VASP, this is CONTCAR.
"""
mycontcar = Poscar(mystruc)
mycontcar.write_file(os.path.join(self.keywords['name'],'CONTCAR'))
__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)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-s1', type=str, help='starting point CONTCAR')
parser.add_argument('-s2', type=str, help='ending point CONTCAR')
parser.add_argument('-e', type=str, help='diffusing cation')
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))
