def apply_defect(self,
number: int,
defect_type: str = 'vac',
supercell: List[int] = [1, 1, 1],
element: str = '') -> Structure:
'''
Apply the defects, i.e. make changes to the structure including
removing, substitution and etc.
@in
- defect_type, str:
- vac: randomly remove some sites with given number of atoms
- subs: randomly substitute some sites with given element
a number of substitution operations is need.
- inte: not implemented yet
- vint: not implemented yet
- supercell, [int, int, int]
- element, str, must be a valid element symbol
@out
- Structure
'''
assert number >= 0, f"Number of defects should be non-negative"
assert len(supercell) == 3, f"Length of supercell list must be 3"
sc = self.old_structure.copy()
sc.make_supercell(supercell)
indices = random.sample(range(len(sc)),
number) # Select the apply site
if 'vac' == defect_type:
rest_id = [i for i in range(len(sc)) if i not in indices]
new_structure = sc[rest_id].copy()
self.operations.append({'vacancy': number})
return new_structure
elif 'subs' == defect_type:
assert is_valid_symbol(
element), f'Invalid element input: "{element}"'
ops = {i: element for i in indices}
trans = ReplaceSiteSpeciesTransformation(ops)
new_structure = trans.apply_transformation(sc)
new_structure.sort()
self.operations.append({'substitution': number})
return new_structure
elif 'inte' == defect_type:
raise Exception(
f'This type of defect ({defect_type}) is still in developing')
elif 'vint' == defect_type:
raise Exception(
f'This type of defect ({defect_type}) is still in developing')
else:
raise Exception(f'Invalid defect type input: "{defect_type}"')
def replace_atom_NEB(prev_NEB_dir, this_NEB_dir, atom_nums, new_atom):
NEB = VaspNEBInput.from_directory(prev_NEB_dir, True)
atom_mapping = {k-1:new_atom for k in atom_nums}
transformation = ReplaceSiteSpeciesTransformation(atom_mapping)
for i in range(len(NEB['POSCARs'])):
sd = NEB['POSCARs'][i].selective_dynamics
NEB['POSCARs'][i].structure = transformation.apply_transformation(NEB['POSCARs'][i].structure)
NEB['POSCARs'][i].comment = ' '.join(NEB['POSCARs'][i].site_symbols)
NEB['POSCARs'][i].selective_dynamics = sd
NEB['POTCAR'] = Potcar(NEB['POSCARs'][i].site_symbols)
update_incar(vasp['POSCAR'].structure, vasp['INCAR'])
NEB.write_input(this_NEB_dir)
return
def replace_atom(prev_dir, this_dir, atom_nums, new_atom, optional_files=None, spin=0):
Poscar.get_string = get_string_more_sigfig
vasp = VaspInput.from_directory(prev_dir, optional_files)
atom_mapping = {k-1:new_atom for k in atom_nums}
transformation = ReplaceSiteSpeciesTransformation(atom_mapping)
# Modifying POSCAR
sd = vasp['POSCAR'].selective_dynamics
if 'MAGMOM' in vasp['INCAR']:
mm = vasp["INCAR"]['MAGMOM']
else:
mm = None
vasp['POSCAR'].structure = transformation.apply_transformation(vasp['POSCAR'].structure)
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'
for atom in atom_nums:
mm[atom-1] = spin
vasp['POTCAR'] = Potcar(symbols)
# Modifying INCAR
update_incar(vasp['POSCAR'].structure, vasp['INCAR'])
if 'MAGMOM' in vasp['INCAR']:
vasp['INCAR']['MAGMOM'] = mm
vasp.write_input(this_dir)
return
def test_to_from_dict(self):
d = ReplaceSiteSpeciesTransformation({0: "Na"}).as_dict()
t = ReplaceSiteSpeciesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Na1 Li3 O4")
def test_apply_transformation(self):
t = ReplaceSiteSpeciesTransformation({0: "Na"})
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Na1 Li3 O4")
str(t)
def test_to_from_dict(self):
d = ReplaceSiteSpeciesTransformation({0: "Na"}).as_dict()
t = ReplaceSiteSpeciesTransformation.from_dict(d)
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Na1 Li3 O4")
def test_apply_transformation(self):
t = ReplaceSiteSpeciesTransformation({0: "Na"})
s = t.apply_transformation(self.struct)
self.assertEqual(s.formula, "Na1 Li3 O4")
str(t)
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)