def write_undefected_atom_indices(self):
"""Write undefected atom indices, including scaled indices.
Also write an undefected manifest file.
"""
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE=SE(struc_work1=self.startstr.copy())
mystruc=mySE.keywords['struc_work1']
else:
mySE=SE(struc_work1=self.startstr.copy(), scaling_size=self.scaling[scaling_label]["mast_size"])
mystruc=mySE.scale_structure()
alist=list()
manname=os.path.join(self.sdir,"manifest_%s__" % scaling_label)
for site in mystruc:
akey=self.get_new_key()
aname="atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index",akey)
ameta.write_data("original_frac_coords", site.frac_coords)
ameta.write_data("element", site.species_string)
ameta.write_data("scaling_label", scaling_label)
alist.append(akey)
self.write_manifest_file(alist,manname)
return
def test_scale_defect(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=size)
scaled = sxtend.scale_structure()
sxtend2 = StructureExtensions(struc_work1=scaled, scaling_size=size)
vac1 = {
'symbol': 'O',
'type': 'vacancy',
'coordinates': np.array([0.25, 0.75, 0.25])
}
defected = sxtend2.scale_defect(vac1, 'fractional', 0.0001)
int1 = {
'symbol': 'Ni',
'type': 'interstitial',
'coordinates': np.array([0.3, 0.3, 0.3])
}
sxtend3 = StructureExtensions(struc_work1=defected, scaling_size=size)
defected2 = sxtend3.scale_defect(int1, 'fractional', 0.0001)
sub1 = {
'symbol': 'Fe',
'type': 'substitution',
'coordinates': np.array([0.25, 0.25, 0.75])
}
sxtend4 = StructureExtensions(struc_work1=defected2, scaling_size=size)
defected3 = sxtend4.scale_defect(sub1, 'fractional', 0.0001)
self.assertEqual(
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled_defected").structure, defected3)
def test_scale_structure_nine(self):
hcp = pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP").structure
sxtend = StructureExtensions(struc_work1=hcp, scaling_size="2 0 0,0 2 0,0 0 2", name=testdir)
scaled = sxtend.scale_structure()
self.assertEqual(scaled, pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure)
self.assertEqual(scaled.lattice, pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure.lattice)
self.assertEqual(scaled.sites.sort(), pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure.sites.sort())
def write_undefected_atom_indices(self):
"""Write undefected atom indices, including scaled indices.
Also write an undefected manifest file.
"""
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE = SE(struc_work1=self.startstr.copy())
mystruc = mySE.keywords['struc_work1']
else:
mySE = SE(
struc_work1=self.startstr.copy(),
scaling_size=self.scaling[scaling_label]["mast_size"])
mystruc = mySE.scale_structure()
alist = list()
manname = os.path.join(self.sdir, "manifest_%s__" % scaling_label)
for site in mystruc:
akey = self.get_new_key()
aname = "atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index", akey)
ameta.write_data("original_frac_coords", site.frac_coords)
ameta.write_data("element", site.species_string)
ameta.write_data("scaling_label", scaling_label)
alist.append(akey)
self.write_manifest_file(alist, manname)
return
def test_scale_structure(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect,scaling_size=size)
scaled = sxtend.scale_structure()
self.assertEqual(scaled, pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure)
self.assertEqual(scaled.lattice, pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure.lattice)
self.assertEqual(scaled.sites.sort(), pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure.sites.sort())
def test_scale_defect(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
scalingsize = "2,2,2"
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=scalingsize, name=testdir)
scaled = sxtend.scale_structure()
sxtend2 = StructureExtensions(struc_work1=scaled, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
vac1={'symbol':'O', 'type': 'vacancy', 'coordinates': np.array([0.25, 0.75, 0.25])}
defected = sxtend2.scale_defect(vac1,'fractional',0.0001)
int1={'symbol':'Ni', 'type': 'interstitial', 'coordinates': np.array([0.3, 0.3, 0.3])}
sxtend3 = StructureExtensions(struc_work1=defected, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
defected2 = sxtend3.scale_defect(int1,'fractional',0.0001)
sub1={'symbol':'Fe', 'type': 'substitution','coordinates':np.array([0.25, 0.25,0.75])}
sxtend4 = StructureExtensions(struc_work1=defected2, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
defected3 = sxtend4.scale_defect(sub1,'fractional',0.0001)
self.assertEqual(pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled_defected").structure, defected3)
def test_scale_structure(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=size)
scaled = sxtend.scale_structure()
self.assertEqual(
scaled,
pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure)
self.assertEqual(
scaled.lattice,
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled").structure.lattice)
self.assertEqual(
scaled.sites.sort(),
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled").structure.sites.sort())
