def test_init(self):
if not enumlib_present:
raise SkipTest("enumlib not present. Skipping...")
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
parser = CifParser(os.path.join(test_dir, "LiFePO4.cif"))
struct = parser.get_structures(False)[0]
subtrans = SubstitutionTransformation({'Li': {'Li': 0.5}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 86)
for s in structures:
self.assertAlmostEqual(s.composition
.get_atomic_fraction(Element("Li")),
0.5 / 6.5)
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2,
refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 52)
subtrans = SubstitutionTransformation({'Li': {'Li': 0.25}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 1,
refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 1)
for s in structures:
self.assertAlmostEqual(s.composition
.get_atomic_fraction(Element("Li")),
0.25 / 6.25)
#Make sure it works for completely disordered structures.
struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{'Fe':0.5}],
[[0, 0, 0]])
adaptor = EnumlibAdaptor(struct, 1, 2)
adaptor.run()
self.assertEqual(len(adaptor.structures), 3)
#Make sure it works properly when symmetry is broken by ordered sites.
parser = CifParser(os.path.join(test_dir, "LiFePO4.cif"))
struct = parser.get_structures(False)[0]
subtrans = SubstitutionTransformation({'Li': {'Li': 0.25}})
s = subtrans.apply_transformation(struct)
#REmove some ordered sites to break symmetry.
removetrans = RemoveSitesTransformation([4, 7])
s = removetrans.apply_transformation(s)
adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 4)
struct = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
[{"Si": 0.5}] * 2, [[0, 0, 0], [0.5, 0.5, 0.5]])
adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 10)
def test_init(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({"Li": {"Li": 0.5}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 86)
for s in structures:
self.assertAlmostEqual(s.composition.get_atomic_fraction(Element("Li")), 0.5 / 6.5)
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2, refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 52)
subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 1, refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 1)
for s in structures:
self.assertAlmostEqual(s.composition.get_atomic_fraction(Element("Li")), 0.25 / 6.25)
# Make sure it works for completely disordered structures.
struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{"Fe": 0.5}], [[0, 0, 0]])
adaptor = EnumlibAdaptor(struct, 1, 2)
adaptor.run()
self.assertEqual(len(adaptor.structures), 3)
# Make sure it works properly when symmetry is broken by ordered sites.
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
s = subtrans.apply_transformation(struct)
# REmove some ordered sites to break symmetry.
removetrans = RemoveSitesTransformation([4, 7])
s = removetrans.apply_transformation(s)
adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 4)
struct = Structure(
[[3, 0, 0], [0, 3, 0], [0, 0, 3]],
[{"Si": 0.5}] * 2,
[[0, 0, 0], [0.5, 0.5, 0.5]],
)
adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 10)
struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "EnumerateTest.json"))
adaptor = EnumlibAdaptor(struct, 1, 1)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 2)
def test_init(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({"Li": {"Li": 0.5}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 86)
for s in structures:
self.assertAlmostEqual(s.composition.get_atomic_fraction(Element("Li")), 0.5 / 6.5)
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2, refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 52)
subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 1, refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 1)
for s in structures:
self.assertAlmostEqual(s.composition.get_atomic_fraction(Element("Li")), 0.25 / 6.25)
# Make sure it works for completely disordered structures.
struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{"Fe": 0.5}], [[0, 0, 0]])
adaptor = EnumlibAdaptor(struct, 1, 2)
adaptor.run()
self.assertEqual(len(adaptor.structures), 3)
# Make sure it works properly when symmetry is broken by ordered sites.
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
s = subtrans.apply_transformation(struct)
# REmove some ordered sites to break symmetry.
removetrans = RemoveSitesTransformation([4, 7])
s = removetrans.apply_transformation(s)
adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 4)
struct = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]], [{"Si": 0.5}] * 2, [[0, 0, 0], [0.5, 0.5, 0.5]])
adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 10)
struct = Structure.from_file(os.path.join(test_dir, "EnumerateTest.json"))
adaptor = EnumlibAdaptor(struct, 1, 1)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 2)
def test_init(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
structs = []
for i, j in itertools.combinations(xrange(4, 8), 2):
trans = RemoveSitesTransformation([i, j])
structs.append(trans.apply_transformation(struct))
sg = SymmetryFinder(struct, 0.1).get_spacegroup()
fitter = SymmetryFitter(structs, sg, 0.1)
self.assertEqual(len(fitter.unique_groups), 3)
structs = []
for i in xrange(4, 8):
trans = RemoveSitesTransformation([i])
structs.append(trans.apply_transformation(struct))
fitter = SymmetryFitter(structs, sg, 0.1)
self.assertEqual(len(fitter.unique_groups), 1)
def remove_atom(prev_dir, this_dir, atom_nums, optional_files=None):
Poscar.get_string = get_string_more_sigfig
vasp = VaspInput.from_directory(prev_dir, optional_files, )
transformation = RemoveSitesTransformation(atom_nums)
# Modifying POSCAR
sd = vasp['POSCAR'].selective_dynamics
if 'MAGMOM' in vasp['INCAR']:
mm = vasp["INCAR"]['MAGMOM']
else:
mm = False
atom_nums.sort(reverse=True)
if sd:
for i in atom_nums:
sd.pop(i)
if mm:
for i in atom_nums:
mm.pop(i)
vasp['POSCAR'] = Poscar(transformation.apply_transformation(vasp['POSCAR'].structure),selective_dynamics=sd)
vasp['POSCAR'].comment = ' '.join(vasp['POSCAR'].site_symbols)
if sd:
vasp['POSCAR'].selective_dynamics = sd
# Creating new POTCAR
symbols = vasp['POSCAR'].site_symbols
for i in range(len(symbols)):
if symbols[i] in ['Fe', 'Ti', 'V', 'Cr', 'Mn', 'Co', 'Ni', 'Cu']:
symbols[i] += '_pv'
elif symbols[i] in ['Sc']:
symbols[i] += '_sv'
# Modifying INCAR
#update_incar(vasp['POSCAR'].structure, vasp['INCAR'])
if mm:
vasp["INCAR"]['MAGMOM'] = mm
vasp.write_input(this_dir)
return
def test_to_from_dict(self):
d = RemoveSitesTransformation(range(2)).as_dict()
t = RemoveSitesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Li2 O4")
def test_apply_transformation(self):
t = RemoveSitesTransformation(range(2))
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Li2 O4")
str(t)
def test_to_from_dict(self):
d = RemoveSitesTransformation(range(2)).as_dict()
t = RemoveSitesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Li2 O4")
def test_apply_transformation(self):
t = RemoveSitesTransformation(range(2))
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Li2 O4")
str(t)
def test_init(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({'Li': {'Li': 0.5}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 86)
for s in structures:
self.assertAlmostEqual(
s.composition.get_atomic_fraction(Element("Li")), 0.5 / 6.5)
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct),
1,
2,
refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 52)
subtrans = SubstitutionTransformation({'Li': {'Li': 0.25}})
adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct),
1,
1,
refine_structure=True)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 1)
for s in structures:
self.assertAlmostEqual(
s.composition.get_atomic_fraction(Element("Li")), 0.25 / 6.25)
#Make sure it works for completely disordered structures.
struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{
'Fe': 0.5
}], [[0, 0, 0]])
adaptor = EnumlibAdaptor(struct, 1, 2)
adaptor.run()
self.assertEqual(len(adaptor.structures), 3)
#Make sure it works properly when symmetry is broken by ordered sites.
struct = self.get_structure("LiFePO4")
subtrans = SubstitutionTransformation({'Li': {'Li': 0.25}})
s = subtrans.apply_transformation(struct)
#REmove some ordered sites to break symmetry.
removetrans = RemoveSitesTransformation([4, 7])
s = removetrans.apply_transformation(s)
adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 4)
struct = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]], [{
"Si": 0.5
}] * 2, [[0, 0, 0], [0.5, 0.5, 0.5]])
adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 10)
struct = Structure.from_file(
os.path.join(test_dir, "EnumerateTest.json"))
adaptor = EnumlibAdaptor(struct, 1, 1)
adaptor.run()
structures = adaptor.structures
self.assertEqual(len(structures), 2)
def test_to_from_dict(self):
d = InsertSitesTransformation(["Fe", "Mn"],
[[0.1, 0, 0], [0.1, 0.2, 0.2]]).to_dict
t = RemoveSitesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Li4 Mn1 Fe1 O4")
def create_SNL(dirbase, molecules, atoms, spc_present, num_each_spc, struct,
s):
layers = len(molecules)
with MPRester("sm5RbuEp83T9Wo7P") as m:
first_mol = struct[0]
mono_or_homo = 0
#if system is a monolayer or homogeneous use its proper .cif file, else use generic WTe2 for heterostructures
if (layers == 1) or all(x == first_mol for x in struct):
mono_or_homo = 1
if (first_mol == molec[0]):
structure = m.get_structure_by_material_id("mp-2815") #MoS2
ref = m.get_materials_id_references("mp-2815")
r1 = np.array([0, 2, 4])
elif (first_mol == molec[1]):
structure = m.get_structure_by_material_id("mp-1634") #MoSe2
ref = m.get_materials_id_references("mp-1634")
r1 = np.array([0, 2, 4])
elif (first_mol == molec[2]):
structure = m.get_structure_by_material_id("mp-602") #MoTe2
ref = m.get_materials_id_references("mp-602")
r1 = np.array([1, 2, 5])
elif (first_mol == molec[3]):
structure = m.get_structure_by_material_id("mp-224") #WS2
ref = m.get_materials_id_references("mp-224")
r1 = np.array([0, 3, 5])
elif (first_mol == molec[4]):
structure = m.get_structure_by_material_id("mp-1821") #WSe2
ref = m.get_materials_id_references("mp-1821")
r1 = np.array([0, 2, 4])
elif (first_mol == molec[5]):
structure = m.get_structure_by_material_id("mp-1019322") #WTe2
ref = m.get_materials_id_references("mp-1019322")
r1 = np.array([0, 3, 5])
else:
structure = m.get_structure_by_material_id("mp-1019322") #WTe2
ref = m.get_materials_id_references("mp-1019322")
r1 = np.array([0, 3, 5])
# initialize history
history = []
#half the height of original unit cell...to be used for vacuum length calculation later
halfz = (structure.lattice.c) / 2
#make supercell if necessary
levels = layers
if (levels % 2 == 1): levels = levels + 1
tsuper = SupercellTransformation([[1, 0, 0], [0, 1, 0],
[0, 0, (levels) / 2]])
history.append(history_node(tsuper))
supercell = tsuper.apply_transformation(structure)
#make species replacements for heterostructures with more than one layer
levels = layers
if (levels % 2 == 1): levels = levels + 1
#if heterostructure has more than one layer:
if (mono_or_homo == 0):
for i in range(0, len(molecules)):
if (molecules[i] == 5):
continue
else:
TMspc = elems[atoms[2 * i]]
TMloc = (levels * 2) + (i % 2) * (levels / 2) + int(
np.floor((i) / 2))
DCspc = elems[atoms[2 * i + 1]]
DCloc1 = (levels -
(levels / 2)) - i % 2 * (levels / 2) + int(
np.floor((i) / 2))
DCloc2 = levels + i % 2 * (levels / 2) + int(
np.floor((i) / 2))
t1 = ReplaceSiteSpeciesTransformation({TMloc: TMspc})
t2 = ReplaceSiteSpeciesTransformation({DCloc1: DCspc})
t3 = ReplaceSiteSpeciesTransformation({DCloc2: DCspc})
history.append(history_node(t1))
history.append(history_node(t2))
history.append(history_node(t3))
supercell = t1.apply_transformation(supercell)
supercell = t2.apply_transformation(supercell)
supercell = t3.apply_transformation(supercell)
#remove top layer of atom if necessary
mult_factor = (layers + 1) / 2 - 1
r = r1 + (r1 + 1) * mult_factor
tremove = RemoveSitesTransformation(r)
if (layers % 2 == 1):
supercell = tremove.apply_transformation(supercell)
history.append(history_node(tremove))
#sort structure
supercell = supercell.get_sorted_structure()
#extend z-axis cell vector to add vaccuum to supercell
vacuum = 10.0
old_lattice = supercell.lattice
if (layers % 2 == 1):
new_c = old_lattice.c - halfz + vacuum
else:
new_c = old_lattice.c + vacuum
new_lattice = Lattice.from_parameters(old_lattice.a, old_lattice.b,
new_c, old_lattice.alpha,
old_lattice.beta,
old_lattice.gamma)
final_structure = Structure(
new_lattice,
supercell.species,
supercell.frac_coords *
np.array([1., 1., (old_lattice.c / new_lattice.c)]),
coords_are_cartesian=False)
hnode = {
'name': 'add vaccuum',
'url': '',
'description': 'increase z-direction cell vector by 10 angstroms'
}
history.append(hnode)
#creat final SNL
authors = [{"name": "Lindsay Bassman", "email": "*****@*****.**"}]
projects = ["TMDC-Heterostructures"]
remarks = [
"MAGICS calculation of band structures of 2D TMDC stacked heterostructures"
]
final_snl = StructureNL(final_structure,
authors,
projects=projects,
remarks=remarks,
references=ref,
history=history)
#optionally write POSCAR file
poscar = Poscar(final_structure, s)
poscar.write_file(dirbase + "POSCAR", direct=False)
