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 main():
s1name = "geometry/BCC_to_FCC/POSCAR_BCC"
s2name = "geometry/BCC_to_FCC/POSCAR_FCC"
s1 = Poscar.from_file(s1name).structure
s2 = Poscar.from_file(s2name).structure
# print s1,s2
smatcher = StructureMatcher(primitive_cell=False)
res = smatcher.get_transformation(s1, s2)
print res
def checkrelax_single(path, src_ini="posfinal", src_fin="posfinal3"):
dirc = path
initial = Poscar.from_file(os.path.join(dirc, src_ini)).structure.as_dict()["lattice"]
final = Poscar.from_file(os.path.join(dirc, src_fin)).structure.as_dict()["lattice"]
length_a = final[u"a"] / initial[u"a"]
length_b = final[u"b"] / initial[u"b"]
length_c = final[u"c"] / initial[u"c"]
delta_length = ((length_b / length_a - 1) ** 2 + (length_c / length_a - 1) ** 2) ** 0.5
# print(delta_length)
angle_a = final["alpha"] / initial["alpha"] - 1
angle_b = final["beta"] / initial["beta"] - 1
angle_c = final["gamma"] / initial["gamma"] - 1
delta_angle = (angle_a ** 2 + angle_b ** 2 + angle_c ** 2) ** 0.5
# print(delta_angle)
return delta_length, delta_angle
def five(src="POSCAR"):
"""
ver5 に変換
"""
srcpos = Poscar.from_file(src)
dst = "POSCAR_five"
srcpos.write_file(dst)
def test_init_from_structure(self):
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
struct = poscar.struct
xyz = XYZ(struct)
ans = """24
Fe4 P4 O16
Fe 2.277347 4.550379 2.260125
Fe 2.928536 1.516793 4.639870
Fe 7.483231 4.550379 0.119620
Fe 8.134420 1.516793 2.499364
P 0.985089 1.516793 1.990624
P 4.220794 4.550379 4.370369
P 6.190973 1.516793 0.389120
P 9.426677 4.550379 2.768865
O 0.451582 4.550379 3.365614
O 1.006219 1.516793 3.528306
O 1.725331 0.279529 1.358282
O 1.725331 2.754057 1.358282
O 3.480552 3.313115 3.738027
O 3.480552 5.787643 3.738027
O 4.199665 4.550379 1.148562
O 4.754301 1.516793 0.985870
O 5.657466 4.550379 3.773620
O 6.212102 1.516793 3.610928
O 6.931215 0.279529 1.021463
O 6.931215 2.754057 1.021463
O 8.686436 3.313115 3.401208
O 8.686436 5.787643 3.401208
O 9.405548 4.550379 1.231183
O 9.960184 1.516793 1.393875"""
self.assertEqual(str(xyz), ans)
def set_structure_from_inputs(self, input_options):
"""Make a pymatgen structure and update the
structure key.
Args:
input_options <InputOptions>
"""
strposfile = input_options.get_item('structure','posfile')
if strposfile is None:
iopscoords=input_options.get_item('structure','coordinates')
iopslatt=input_options.get_item('structure','lattice')
iopsatoms=input_options.get_item('structure','atom_list')
iopsctype=input_options.get_item('structure','coord_type')
structure = MAST2Structure(lattice=iopslatt,
coordinates=iopscoords, atom_list=iopsatoms,
coord_type=iopsctype)
elif ('poscar' in strposfile.lower()):
from pymatgen.io.vaspio import Poscar
structure = Poscar.from_file(strposfile).structure
elif ('cif' in strposfile.lower()):
from pymatgen.io.cifio import CifParser
structure = CifParser(strposfile).get_structures()[0]
else:
error = 'Cannot build structure from file %s' % strposfile
raise MASTError(self.__class__.__name__, error)
input_options.update_item('structure','structure',structure)
if input_options.get_item('structure','use_structure_index') in ['True','true','T','t']:
self.do_structure_indexing(input_options)
return
def set_structure_from_inputs(self, input_options):
"""Make a pymatgen structure and update the
structure key.
Args:
input_options <InputOptions>
"""
strposfile = input_options.get_item('structure', 'posfile')
if strposfile is None:
iopscoords = input_options.get_item('structure', 'coordinates')
iopslatt = input_options.get_item('structure', 'lattice')
iopsatoms = input_options.get_item('structure', 'atom_list')
iopsctype = input_options.get_item('structure', 'coord_type')
structure = MAST2Structure(lattice=iopslatt,
coordinates=iopscoords,
atom_list=iopsatoms,
coord_type=iopsctype)
elif ('poscar' in strposfile.lower()):
from pymatgen.io.vaspio import Poscar
structure = Poscar.from_file(strposfile).structure
elif ('cif' in strposfile.lower()):
from pymatgen.io.cifio import CifParser
structure = CifParser(strposfile).get_structures()[0]
else:
error = 'Cannot build structure from file %s' % strposfile
raise MASTError(self.__class__.__name__, error)
input_options.update_item('structure', 'structure', structure)
if input_options.get_item('structure', 'use_structure_index') in [
'True', 'true', 'T', 't'
]:
self.do_structure_indexing(input_options)
return
def print_spg(src="POSCAR"):
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure, symprec=5e-2, angle_tolerance=8)
spg = finder.get_spacegroup_symbol()
spg_num = finder.get_spacegroup_number()
print(spg)
print(spg_num)
def read_structure(filename):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Args:
filename:
A filename to read from.
Returns:
A Structure object.
"""
lower_filename = os.path.basename(filename).lower()
if re.search("\.cif", lower_filename):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif lower_filename.startswith("poscar") \
or lower_filename.startswith("contcar"):
return Poscar.from_file(filename, False).structure
elif lower_filename.startswith("chgcar") \
or lower_filename.startswith("locpot"):
return Chgcar.from_file(filename).structure
elif re.search("vasprun", lower_filename) \
and re.search("xml", lower_filename):
return Vasprun(filename).final_structure
elif re.search("\.cssr", lower_filename):
cssr = Cssr.from_file(filename)
return cssr.structure
raise ValueError("Unrecognized file extension!")
def get_structure_from_file(self, myfilepath=""):
"""Get the structure from a specified file path.
For VASP, this is a POSCAR-type file.
Args:
myfilepath <str>: File path for structure.
"""
return Poscar.from_file(myfilepath).structure
def supercell(poscar,scale,outFile=None,replace=False):
'''Reads in a structure in VASP POSCAR format and returns one with a supercell
of that structure
Args:
-------------------------------------
poscar: location of POSCAR file to find supercell of
scale: iterable of integer scaling factors with length 3.
kwargs:
-------------------------------------
outFile: location for new poscar file with
modifies:
-------------------------------------
outFile: if replace=True
poscar: if replace=False
'''
assert os.path.isfile(poscar)
assert replace==True or not outFile is None
p = Poscar.from_file(poscar,False)
# with open(poscar) as f:
# poscomment = f.readline().strip()
#
# p.comment = poscomment
p.structure.make_supercell(scale)
if replace==True:
p.write_file(poscar,vasp4_compatible=True)
else:
p.write_file(outFile,vasp4_compatible=True)
def read_structure(filename):
"""
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.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
return Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
return Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
return Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
return cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
return s
raise ValueError("Unrecognized file extension!")
def read_structure(filename):
"""
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:
A filename to read from.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
return Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
return Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
return Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
return cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
return s
raise ValueError("Unrecognized file extension!")
def get_elements(src):
"""
組成比を得るための method
"""
srcpos = Poscar.from_file(src)
elements = [x.symbol for x in srcpos.structure.species]
elem_counter = Counter(elements)
return elem_counter
def get_primitive(fname):
poscar = Poscar.from_file(fname)
finder = SymmetryFinder(poscar.structure)
spg_num = finder.get_spacegroup_number()
primitive = finder.get_primitive_standard_structure()
return spg_num, primitive
def test_to_from_dict(self):
json_str = json.dumps(PartialRemoveSpecieTransformation("Li+", 0.5, PartialRemoveSpecieTransformation.ALGO_BEST_FIRST).to_dict)
t = transformation_from_json(json_str)
module_dir = os.path.dirname(os.path.abspath(__file__))
p = Poscar.from_file(os.path.join(module_dir, 'POSCAR.LiFePO4'))
t1 = OxidationStateDecorationTransformation({"Li":1, "Fe":2, "P":5, "O":-2})
s = t1.apply_transformation(p.struct)
self.assertEqual(len(t.apply_transformation(s)), 26)
def test_apply_transformations_complete_ranking(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
p = Poscar.from_file(os.path.join(module_dir, 'POSCAR.LiFePO4'))
t1 = OxidationStateDecorationTransformation({"Li":1, "Fe":2, "P":5, "O":-2})
s = t1.apply_transformation(p.struct)
t = PartialRemoveSpecieTransformation("Li+", 0.5, PartialRemoveSpecieTransformation.ALGO_COMPLETE)
self.assertEqual(len(t.apply_transformation(s, 10)), 6)
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.struct
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MaterialsProjectVaspInputSet()
def test_get_atoms(self):
if not aio.ase_loaded:
raise SkipTest("ASE not present. Skipping...")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
structure = p.struct
atoms = aio.AseAtomsAdaptor.get_atoms(structure)
ase_composition = Composition.from_formula(atoms.get_name())
self.assertEqual(ase_composition, structure.composition)
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 update_atom_index_for_complete(self):
"""Update atom index files with positions for the
completed ingredient.
"""
proceed=False
mydir = self.keywords['name']
workdir=os.path.dirname(mydir)
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
proceed=True
if not proceed:
self.logger.warning("Called update atom index for ingredient %s, but no atom indices exist." % self.keywords['name'])
return
mymeta=Metadata(metafile="%s/metadata.txt" % mydir)
phonon_label = mymeta.read_data("phonon_label")
if not (phonon_label == None): #Don't update atom indices for phonons
self.logger.debug("Skipping atom index update for phonon calculation %s" % self.keywords['name'])
return
scaling_label=mymeta.read_data("scaling_label")
defect_label=mymeta.read_data("defect_label")
neb_label=mymeta.read_data("neb_label")
if scaling_label == None:
scaling_label = ""
if defect_label == None:
defect_label = ""
if neb_label == None:
neb_label = ""
if neb_label == "":
mystr=Poscar.from_file("%s/CONTCAR" % self.keywords["name"]).structure
ing_label=os.path.basename(mydir)
manname="manifest_%s_%s_%s" % (scaling_label, defect_label, neb_label)
myatomindex=AtomIndex(structure_index_directory=sdir)
myatomindex.update_atom_indices_from_structure(mystr, ing_label, manname)
else:
nebdirs = dirutil.immediate_subdirs(self.keywords["name"])
for mysubdir in nebdirs:
if os.path.isfile("%s/%s/CONTCAR" % (self.keywords["name"],mysubdir)):
mystr=Poscar.from_file("%s/%s/CONTCAR" % (self.keywords["name"], mysubdir)).structure
ing_label=os.path.join(os.path.basename(mydir), mysubdir)
for defect_label in neb_label.split("-"):
manname="manifest_%s_%s_%s" % (scaling_label, defect_label, neb_label)
myatomindex=AtomIndex(structure_index_directory=sdir)
myatomindex.update_atom_indices_from_structure(mystr, ing_label, manname)
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 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 _phon_inphon_get_masses(self):
"""Get the ntypes and masses line for INPHON.
Returns:
nline, massline
nline <str>: NYTPES = <number of atomic types in POSCAR>
massline <str>: MASS = <mass1> <mass2> ...
"""
name=self.keywords['name']
if os.path.isfile(name + "/POSCAR_prePHON"):
mypos = Poscar.from_file(name + "/POSCAR_prePHON")
else: #not yet modified to strip out the species line.
mypos = Poscar.from_file(name + "/POSCAR")
sitesym = mypos.site_symbols
nline="NTYPES=" + str(len(sitesym))
massline="MASS="
for sym in sitesym:
el = pymatgen.core.periodic_table.Element(sym)
massline = massline + str(float(el.atomic_mass)) + " "
return [nline, massline]
def print_spg(src='POSCAR'):
"""
space group を return
"""
srcpos = Poscar.from_file(src)
finder = SpacegroupAnalyzer(srcpos.structure,
symprec=5e-2, angle_tolerance=8)
spg = finder.get_spacegroup_symbol()
spg_num = finder.get_spacegroup_number()
return spg, spg_num
def _phon_inphon_get_masses(self):
"""Get the ntypes and masses line for INPHON.
Returns:
nline, massline
nline <str>: NYTPES = <number of atomic types in POSCAR>
massline <str>: MASS = <mass1> <mass2> ...
"""
name = self.keywords['name']
if os.path.isfile(name + "/POSCAR_prePHON"):
mypos = Poscar.from_file(name + "/POSCAR_prePHON")
else: #not yet modified to strip out the species line.
mypos = Poscar.from_file(name + "/POSCAR")
sitesym = mypos.site_symbols
nline = "NTYPES=" + str(len(sitesym))
massline = "MASS="
for sym in sitesym:
el = pymatgen.core.periodic_table.Element(sym)
massline = massline + str(float(el.atomic_mass)) + " "
return [nline, massline]
def alt_volume(func, src="POSCAR"):
"""
体積を変更した POSCAR を作成
"""
srcpos = Poscar.from_file(src)
elem = get_elements(src)
ideal_v = func(elem)
srcpos.structure.scale_lattice(ideal_v)
dst = "POSCAR_newvol"
srcpos.write_file(dst)
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 get_final_structure_from_directory(self, mydir=""):
"""Get the final structure.
For VASP, this is the CONTCAR file.
Args:
mydir <str>: Directory. If no directory is given,
use current ingredient directory given
as keyword 'name'
"""
if mydir == "":
mydir = self.keywords['name']
return Poscar.from_file("%s/CONTCAR" % mydir).structure
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 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 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 setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.struct
self.sg = SymmetryFinder(self.structure, 0.001)
parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif'))
self.disordered_structure = parser.get_structures()[0]
self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001)
s = p.struct
editor = StructureEditor(p.struct)
site = s[0]
editor.delete_site(0)
editor.append_site(site.species_and_occu, site.frac_coords)
self.sg3 = SymmetryFinder(editor.modified_structure, 0.001)
def read_xyz(fileobj,n=-1,data=False):
"""
Function to read multi-atom xyz file with data
Inputs:
fileobj = String containing file name or file object
n = Integer indicating number for structure from xyz file
to read. Default is last structure in file.
Or String=='All' which will output all structures in file
data = True/False boolean indicating whether or not to output
any data strings read from xyz file
Outputs:
atmslist = ASE Atoms class object containing structure from file
or list of Atoms objects if n=='All'
datalist(Optional) = String of data read from xyz file or list
of data strings read from xyz file
"""
try:
from pymatgen.io.vaspio import Poscar
mystructure = Poscar.from_file(fileobj).structure
from pymatgen.io.aseio import AseAtomsAdaptor
myatoms = AseAtomsAdaptor.get_atoms(mystructure)
return myatoms
except:
if isinstance(fileobj, str):
fileobj = open(fileobj,'r')
lines = fileobj.readlines()
atmslist = []
datalist = []
while len(lines)>0:
natoms = int(lines[0])
datalist.append(lines[1])
atm1 = Atoms()
i =- 1
for i in range(natoms):
a = lines[i+2].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atm1.append(Atom(symbol=sym,position=position))
atmslist.append(atm1)
lines = lines[i+3::]
if n == 'All':
if data == True:
return atmslist, datalist
else:
return atmslist
else:
if data == True:
return atmslist[n],datalist[n]
else:
return atmslist[n]
def test_check_correct(self):
#NOTE: the vasprun here has had projected and partial eigenvalues removed
subdir = os.path.join(test_dir, "max_force")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("POSCAR", "POSCAR.orig")
h = MaxForceErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['MaxForce'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
incar = Incar.from_file('INCAR')
poscar = Poscar.from_file('POSCAR')
contcar = Poscar.from_file('CONTCAR')
shutil.move("INCAR.orig", "INCAR")
shutil.move("POSCAR.orig", "POSCAR")
self.assertEqual(poscar.structure, contcar.structure)
self.assertAlmostEqual(incar['EDIFF'], 0.00075)
def get_coordinates_only_structure_from_input(self):
"""Get coordinates-only structures from mast_coordinates
ingredient keyword
Args:
keywords <dict>: ingredient keywords
Returns:
coordstrucs <list>: list of Structure objects
"""
coordposlist = self.keywords['program_keys']['mast_coordinates']
coordstrucs = list()
coordstruc = None
for coordpositem in coordposlist:
if ('poscar' in os.path.basename(coordpositem).lower()):
coordstruc = Poscar.from_file(coordpositem).structure
elif ('cif' in os.path.basename(coordpositem).lower()):
coordstruc = CifParser(coordpositem).get_structures()[0]
else:
error = 'Cannot build structure from file %s' % coordpositem
raise MASTError(self.__class__.__name__, error)
coordstrucs.append(coordstruc)
return coordstrucs
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 False.
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=PMGJSONDecoder)
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 _phon_poscar_setup(self):
"""Set up a PHON POSCAR file. Strip out the "elements" line (that is,
use VASP version 4 format. Also strip out anything beneath the atoms
line.
"""
name = self.keywords['name']
pospath = os.path.join(name, "POSCAR")
prepath = os.path.join(name, "POSCAR_prePHON")
if os.path.isfile(pospath): #Already done. Return.
return
my_poscar = Poscar.from_file(prepath)
my_poscar.selective_dynamics=None #unset SD if it is set
my_poscar.velocities=None #unset velocities
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
#pick up a copy and strip out the elements line.
mypfile = MASTFile(pospath)
myline6=mypfile.get_line_number(6)
if myline6.strip().split()[0].isalpha:
mypfile.modify_file_by_line_number(6,"D")
mypfile.to_file(pospath)
return
""" Get input data first """
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", help="file with calculation variables",
required=True, metavar="FILE")
parser.add_argument("-p", "--parent", help="parent file in vasp POSCAR format",
required=True, metavar="FILE")
args = parser.parse_args()
invars = Conf(args.input)
''' Import initial parent structure '''
poscar = Poscar.from_file(args.parent)
parent_struct = poscar.structure
os.chdir(invars.run_dir)
if invars.restart == ".FALSE.":
with open("ORDERING_OUTPUT.txt", 'a') as file:
file.write("Input Structure Info:\n\n")
file.write("-------------------------------------------------------------------------------------\n\n")
file.write("{}\n\n".format(parent_struct))
file.write("-------------------------------------------------------------------------------------\n\n")
def end_status(status):
if status == 'success':
with open("ORDERING_OUTPUT.txt", 'a') as file:
file.write("Yor job has ended sucessfully\n")
from PathFinder.pathFinder import NEBPathfinder, ChgcarPotential
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
]
if len(structures_list) == 0:
print('no structures found')
pass
else:
file_format = 'cif'
else:
file_format = 'poscar'
isomer_count = {'cis': 0, 'trans': 0, 'fac': 0, 'mer': 0, 'mixed': 0}
for entry in structures_list:
struct_name = entry.replace("{}-".format(dictionary), '')
struct_name = struct_name.replace('.vasp', '')
#print struct_name
if file_format == 'poscar':
poscar = Poscar.from_file(entry)
struct = poscar.structure
elif file_format == 'cif':
parser = CifParser(entry)
struct = parser.get_structures()[0]
#cations_indx = [0,3,5,6]
if len(cations_indx) == 0:
cations_indx = struct.indices_from_symbol(cati)
anions_indx = struct.indices_from_symbol(ani)
cation_neighs = dict()
ordering_rank = []
for cation in cations_indx:
myneigh = []
for anion in anions_indx:
def process_killed_run(cls, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
filename = os.path.join(dir_name, f)
if fnmatch(f, "INCAR*"):
try:
incar = Incar.from_file(filename)
d["incar"] = incar.to_dict
d["is_hubbard"] = incar.get("LDAU", False)
if d["is_hubbard"]:
us = incar.get("LDAUU", [])
js = incar.get("LDAUJ", [])
if sum(us) == 0 and sum(js) == 0:
d["is_hubbard"] = False
d["hubbards"] = {}
else:
d["hubbards"] = {}
if d["is_hubbard"]:
d["run_type"] = "GGA+U"
elif incar.get("LHFCALC", False):
d["run_type"] = "HF"
else:
d["run_type"] = "GGA"
except Exception as ex:
print str(ex)
logger.error(
"Unable to parse INCAR for killed run {}.".format(
dir_name))
elif fnmatch(f, "KPOINTS*"):
try:
kpoints = Kpoints.from_file(filename)
d["kpoints"] = kpoints.to_dict
except:
logger.error(
"Unable to parse KPOINTS for killed run {}.".format(
dir_name))
elif fnmatch(f, "POSCAR*"):
try:
s = Poscar.from_file(filename).structure
comp = s.composition
el_amt = s.composition.get_el_amt_dict()
d.update({
"unit_cell_formula": comp.to_dict,
"reduced_cell_formula": comp.to_reduced_dict,
"elements": list(el_amt.keys()),
"nelements": len(el_amt),
"pretty_formula": comp.reduced_formula,
"anonymous_formula": comp.anonymized_formula,
"nsites": comp.num_atoms,
"chemsys": "-".join(sorted(el_amt.keys()))
})
d["poscar"] = s.to_dict
except:
logger.error(
"Unable to parse POSCAR for killed run {}.".format(
dir_name))
elif fnmatch(f, "POTCAR*"):
try:
potcar = Potcar.from_file(filename)
d["pseudo_potential"] = {
"functional": "pbe",
"pot_type": "paw",
"labels": potcar.symbols
}
except:
logger.error(
"Unable to parse POTCAR for killed run in {}.".format(
dir_name))
elif fnmatch(f, "OSZICAR"):
try:
d["oszicar"]["root"] = \
Oszicar(os.path.join(dir_name, f)).to_dict
except:
logger.error(
"Unable to parse OSZICAR for killed run in {}.".format(
dir_name))
elif re.match("relax\d", f):
if os.path.exists(os.path.join(dir_name, f, "OSZICAR")):
try:
d["oszicar"][f] = Oszicar(
os.path.join(dir_name, f, "OSZICAR")).to_dict
except:
logger.error("Unable to parse OSZICAR for killed "
"run in {}.".format(dir_name))
return d
#!/usr/bin/env python
from pymatgen.io.vaspio import Poscar
import cProfile
import pstats
import os
import logging
logging.basicConfig(level=logging.DEBUG)
p = Poscar.from_file("../test_files/POSCAR.LiFePO4", check_for_POTCAR=False)
s = p.structure
def test():
nn = s.get_all_neighbors(20)
print len(nn)
def chgcar_test():
from pymatgen.io.vaspio import Chgcar
c = Chgcar.from_file("../test_files/CHGCAR.noncubic")
print c.get_integrated_diff(1, 2.5, 3)
def vasprun_test():
from pymatgen.io.vaspio import Vasprun
v = Vasprun("../test_files/vasprun.xml")
print v.final_energy
def matcher_test():
p = Poscar.from_file("../test_files/POSCAR.Li2O")
s = p.structure
from pymatgen.analysis.structure_matcher import StructureMatcher
def matcher_test():
p = Poscar.from_file("../test_files/POSCAR.Li2O")
s = p.structure
from pymatgen.analysis.structure_matcher import StructureMatcher
print StructureMatcher().fit(s, s)
