def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one vacancy in each structure.
"""
if not return_ranked_list:
raise ValueError(
"VacancyTransformation has no single best structure"
" output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
vac = Vacancy(structure, self.valences, self.radii)
scs = vac.make_supercells_with_defects(self.supercell_dim,
self.species, num_to_return)
#if num_to_return < len(scs)-1:
# raise ValueError("VacancyTransformation has no ordering of best "
# "structure. Must increase return_ranked_list.")
structures = []
for sc in scs[1:]:
structures.append({'structure': sc})
return structures
def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one vacancy in each structure.
"""
if not return_ranked_list:
raise ValueError("VacancyTransformation has no single best structure"
" output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
vac = Vacancy(structure,self.valences,self.radii)
scs = vac.make_supercells_with_defects(
self.supercell_dim,self.species, num_to_return)
#if num_to_return < len(scs)-1:
# raise ValueError("VacancyTransformation has no ordering of best "
# "structure. Must increase return_ranked_list.")
structures = []
for sc in scs[1:]:
structures.append({'structure':sc})
return structures
def vac_intl(cellmax=2, mpid='', struct=None):
"""
Vacancy and interstitial generator
Args:
cellmax: maximum cell size
struct: Structure object
Returns:
def_str: defect structures
"""
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print("Provide structure")
sg_mat = SpacegroupAnalyzer(struct)
struct = sg_mat.get_conventional_standard_structure()
def_str = []
count = 0
cell_arr = [cellmax, cellmax, cellmax]
vac = Vacancy(struct, {}, {})
for el in list(struct.symbol_set):
scs = vac.make_supercells_with_defects(cell_arr, el)
for i in range(len(scs)):
if i == 0:
pos = Poscar(scs[i])
pos.comment = str('bulk') + str('.') + str('cellmax') + str(
cellmax)
if count == 0:
def_str.append(pos)
count = count + 1
else:
pos = Poscar(scs[i])
pos.comment = str('vac') + str('cellmax') + str(cellmax) + str(
'@') + str(vac.get_defectsite_multiplicity(i)) + str(
'Element') + str(el)
if pos not in def_str:
def_str.append(pos)
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
intl = Interstitial(struct, val, rad)
for el in struct.composition.elements:
scs = intl.make_supercells_with_defects(cell_arr, el)
for i in range(1, len(scs)):
pos = Poscar(scs[i])
pos.comment = str('intl') + str('cellmax') + str(cellmax) + str(
'@') + str(intl.get_defectsite_coordination_number(
i - 1)) + str('Element') + str(el)
if pos not in def_str:
def_str.append(pos)
print(len(def_str))
return def_str
def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one substitution defect in each structure.
"""
if not return_ranked_list:
raise ValueError(
"SubstitutionDefectTransformation has no single"
"best structure output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
species = self._species_map.keys()
vac = Vacancy(structure, self.valences, self.radii)
scs = vac.make_supercells_with_defects(self.supercell_dim, species,
num_to_return)
blk_sc = scs[0]
sub_scs = []
for i in range(1, len(scs)):
vac_sc = scs[i]
vac_site = list(set(blk_sc.sites) - set(vac_sc.sites))[0]
if isinstance(vac_site.specie, Specie):
site_specie = vac_site.specie.element.symbol
elif isinstance(vac_site.specie, Element):
site_specie = vac_site.specie.symbol
if site_specie in self._species_map.keys():
substitute_specie = self._species_map[site_specie]
vac_sc.append(substitute_specie, vac_site.frac_coords)
sub_scs.append(vac_sc.get_sorted_structure())
#if num_to_return < len(sub_scs)-1:
# raise ValueError("SubstitutionDefectTransformation has no ordering"
# " of best structure. Must increase return_ranked_list.")
num_to_return = min(num_to_return, len(sub_scs))
structures = []
if num_to_return:
for sc in sub_scs[0:num_to_return]:
structures.append({'structure': sc})
else:
structures.append({'structure': scs[0]})
return structures
def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one substitution defect in each structure.
"""
if not return_ranked_list:
raise ValueError("SubstitutionDefectTransformation has no single"
"best structure output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
species = self._species_map.keys()
vac = Vacancy(structure,self.valences,self.radii)
scs = vac.make_supercells_with_defects(
self.supercell_dim,species,num_to_return)
blk_sc = scs[0]
sub_scs = []
for i in range(1,len(scs)):
vac_sc = scs[i]
vac_site = list(set(blk_sc.sites) - set(vac_sc.sites))[0]
if isinstance(vac_site.specie,Specie):
site_specie = vac_site.specie.element.symbol
elif isinstance(vac_site.specie,Element):
site_specie = vac_site.specie.symbol
if site_specie in self._species_map.keys():
substitute_specie = self._species_map[site_specie]
vac_sc.append(substitute_specie, vac_site.frac_coords)
sub_scs.append(vac_sc.get_sorted_structure())
#if num_to_return < len(sub_scs)-1:
# raise ValueError("SubstitutionDefectTransformation has no ordering"
# " of best structure. Must increase return_ranked_list.")
num_to_return = min(num_to_return, len(sub_scs))
structures = []
if num_to_return:
for sc in sub_scs[0:num_to_return]:
structures.append({'structure':sc})
else:
structures.append({'structure':scs[0]})
return structures
def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one antisite defect in each structure.
"""
if not return_ranked_list:
raise ValueError("AntisiteDefectTransformation has no single best"
"structure output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
vac = Vacancy(structure, self.valences, self.radii)
scs = vac.make_supercells_with_defects(self.supercell_dim)
blk_sc = scs[0]
as_scs = []
struct_species = blk_sc.types_of_specie
for i in range(1, len(scs)):
vac_sc = scs[i]
vac_site = list(set(blk_sc.sites) - set(vac_sc.sites))[0]
for specie in set(struct_species) - set([vac_site.specie]):
anti_struct = vac_sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
as_scs.append(anti_struct.get_sorted_structure())
#if num_to_return < len(as_scs)-1:
# raise ValueError("AntisiteDefectTransformation has no ordering "
# "of best structures. Must increase return_ranked_list.")
num_to_return = min(num_to_return, len(as_scs))
structures = []
for sc in as_scs[0:num_to_return]:
structures.append({'structure': sc})
return structures
def apply_transformation(self, structure, return_ranked_list=False):
"""
:param structure:
:param return_ranked_list (Logical or integer): Use big enough
number to return all defect structures
:return:
scs: Supercells with one antisite defect in each structure.
"""
if not return_ranked_list:
raise ValueError("AntisiteDefectTransformation has no single best"
"structure output. Must use return_ranked_list.")
try:
num_to_return = int(return_ranked_list)
except ValueError:
num_to_return = 1
vac = Vacancy(structure,self.valences,self.radii)
scs = vac.make_supercells_with_defects(self.supercell_dim)
blk_sc = scs[0]
as_scs = []
struct_species = blk_sc.types_of_specie
for i in range(1,len(scs)):
vac_sc = scs[i]
vac_site = list(set(blk_sc.sites) - set(vac_sc.sites))[0]
for specie in set(struct_species) - set([vac_site.specie]):
anti_struct = vac_sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
as_scs.append(anti_struct.get_sorted_structure())
#if num_to_return < len(as_scs)-1:
# raise ValueError("AntisiteDefectTransformation has no ordering "
# "of best structures. Must increase return_ranked_list.")
num_to_return = min(num_to_return,len(as_scs))
structures = []
for sc in as_scs[0:num_to_return]:
structures.append({'structure':sc})
return structures
def vac_antisite_def_struct_gen(c_size=15, mpid='', struct=None):
def_str = []
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print("Provide structure")
dim1 = int((float(c_size) / float(max(abs(struct.lattice.matrix[0]))))) + 1
dim2 = int(float(c_size) / float(max(abs(struct.lattice.matrix[1])))) + 1
dim3 = int(float(c_size) / float(max(abs(struct.lattice.matrix[2])))) + 1
cellmax = max(dim1, dim2, dim3)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = 1 + int(conv_struct_sites / prim_struct_sites)
sc_scale = [dim1, dim2, dim3]
print("sc_scale", sc_scale)
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
#print ('scssssss',scs[0].make_supercell([1,1,1]))
for i in range(len(scs)):
sc = scs[i]
mpvis = MPRelaxSet(sc) #VaspInputSet(struct)
#print ('sccccc',sc,type(sc[0]))
tmp = struct.copy()
poscar = mpvis.poscar
#kpoints = Kpoints.automatic_density(sc,kpoint_den)
#incar = mpvis.get_incar(sc)
#print ('big pos',poscar)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
poscar.comment = str('bulk') + str('@') + str('cellmax') + str(
cellmax)
def_str.append(poscar)
poscar.write_file('POSCAR-' + str('bulk') + str(".vasp"))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
poscar.comment = str(vac_dir) + str('@') + str(
'cellmax') + str(cellmax)
except:
pass
pos = poscar
def_str.append(pos)
poscar.write_file('POSCAR-' + str(vac_dir) + str(".vasp"))
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
mpvis = MPRelaxSet(anti_struct) #VaspInputSet(struct)
print('anti_struct', anti_struct)
poscar = mpvis.poscar
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
poscar.comment = str(as_dir) + str('@') + str('cellmax') + str(
cellmax)
pos = poscar
def_str.append(pos)
poscar.write_file('POSCAR-' + str(as_dir) + str(".vasp"))
return def_str
def vac_antisite_def_struct_gen(c_size=15,
mpid='',
struct=None,
write_file=True):
"""
Vacancy, antisite generator
Args:
c_size: cell size
struct: Structure object or
mpid: materials project id
Returns:
def_str: defect structures in Poscar object format
"""
def_str = []
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print("Provide structure")
c_size = c_size
dim1 = int((float(c_size) / float(max(abs(struct.lattice.matrix[0]))))) + 1
dim2 = int(float(c_size) / float(max(abs(struct.lattice.matrix[1])))) + 1
dim3 = int(float(c_size) / float(max(abs(struct.lattice.matrix[2])))) + 1
cellmax = max(dim1, dim2, dim3)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = [dim1, dim2, dim3]
print("sc_scale", sc_scale)
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = Poscar(sc) #mpvis.get_poscar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
poscar.comment = str('bulk') + str('@') + str('cellmax') + str(
cellmax)
def_str.append(poscar)
if write_file == True:
poscar.write_file('POSCAR-' + str('bulk') + str(".vasp"))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
poscar.comment = str(vac_dir) + str('@') + str(
'cellmax') + str(cellmax)
except:
pass
pos = poscar
def_str.append(pos)
if write_file == True:
poscar.write_file('POSCAR-' + str(vac_dir) + str(".vasp"))
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = Poscar(anti_struct)
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
poscar.comment = str(as_dir) + str('@') + str('cellmax') + str(
cellmax)
pos = poscar
def_str.append(pos)
if write_file == True:
poscar.write_file('POSCAR-' + str(as_dir) + str(".vasp"))
return def_str
def vac_antisite_def_struct_gen(mpid, mapi_key, cellmax):
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
sc_scale = get_sc_scale(struct,cellmax)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc,kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir,'INCAR'))
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
def substitute_def_struct_gen(args):
mpid = args.mpid
solute = args.solute
mapi_key = args.mapi_key
cellmax = args.cellmax
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not solute:
print ("============\nERROR: Provide solute atom\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
mpvis = MPRelaxSet(struct, user_incar_settings={"LDAU": False})
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.potcar
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct,cellmax)
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1,len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
mpvis = MPRelaxSet(solute_struct, user_incar_settings={"LDAU": False})
incar = mpvis.incar
incar.update(def_vasp_incar_param)
poscar = mpvis.poscar
kpoints = Kpoints.automatic_density(solute_struct,kpoint_den)
if ptcr_flag:
potcar = mpvis.potcar
sub_def_dir ='solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir,sub_def_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
def vac_antisite_def_struct_gen(c_size=15,mpid='',struct=None):
"""
Vacancy, antisite generator
Args:
c_size: cell size
struct: Structure object or
mpid: materials project id
Returns:
def_str: defect structures in Poscar object format
"""
def_str=[]
if struct ==None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print ("Provide structure")
c_size=c_size
dim1=int((float(c_size)/float( max(abs(struct.lattice.matrix[0])))))+1
dim2=int(float(c_size)/float( max(abs(struct.lattice.matrix[1]))))+1
dim3=int(float(c_size)/float( max(abs(struct.lattice.matrix[2]))))+1
cellmax=max(dim1,dim2,dim3)
#print ("in vac_def cellmax=",cell
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
#sc_scale = get_sc_scale(struct,cellmax)
sc_scale=[dim1,dim2,dim3]
#sc_scale=[cellmax,cellmax,cellmax]
print ("sc_scale",sc_scale)
#mpvis = MITRelaxSet #MPGGAVaspInputSet()
# Begin defaults: All default settings.
#blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
#def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
# 'EDIFFG':0.001,'NSW':40,}
#kpoint_den = 6000
# End defaults
#ptcr_flag = True
#try:
# potcar = mpvis.get_potcar(struct)
#except:
# print ("VASP POTCAR folder not detected.\n" \
# "Only INCAR, POSCAR, KPOINTS are generated.\n" \
# "If you have VASP installed on this system, \n" \
# "refer to pymatgen documentation for configuring the settings.")
# ptcr_flag = False
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
#site_no = scs[0].num_sites
#if site_no > cellmax:
# max_sc_dim = max(sc_scale)
# i = sc_scale.index(max_sc_dim)
# sc_scale[i] -= 1
# scs = vac.make_supercells_with_defects(sc_scale)
#print ('struct',scs)
for i in range(len(scs)):
sc = scs[i]
#print (type(sc))
poscar = Poscar(sc) #mpvis.get_poscar(sc)
#kpoints = Kpoints.automatic_density(sc,kpoint_den)
#incar = mpvis.get_incar(sc)
#if ptcr_flag:
# potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
#try:
# os.makedirs(fin_dir)
#except:
# pass
#incar.update(blk_vasp_incar_param)
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.comment=str('bulk')+str('@')+str('cellmax')+str(cellmax)
def_str.append(poscar)
poscar.write_file('POSCAR-'+str('bulk')+str(".vasp"))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
#try:
# site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
#except:
# site_mult=1
# pass
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
#try:
# os.makedirs(fin_dir)
#except:
# pass
#incar.update(def_vasp_incar_param)
try:
poscar.comment=str(vac_dir)+str('@')+str('cellmax')+str(cellmax)
except:
pass
pos=poscar
#pos=poscar.structure
def_str.append(pos)
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.write_file('POSCAR-'+str(vac_dir)+str(".vasp"))
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = Poscar(anti_struct)
#incar = mpvis.get_incar(anti_struct)
#incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
#try:
# os.makedirs(fin_dir)
#except:
# pass
poscar.comment=str(as_dir)+str('@')+str('cellmax')+str(cellmax)
pos=poscar
#pos=poscar.structure
def_str.append(pos)
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.write_file('POSCAR-'+str(as_dir)+str(".vasp"))
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
#try:
# struct.make_supercell(sc_scale)
# intl = Interstitial(struct, val, rad)
# cell_arr=sc_scale
# for el in struct.composition.elements:
# scs = intl.make_supercells_with_defects(1,el)
# #scs = intl.make_supercells_with_defects(cell_arr,el)
# for i in range(1,len(scs)):
# pos=Poscar(scs[i])
# pos.comment=str('intl_')+str('cellmax')+str(cellmax)+str('@')+str(intl.get_defectsite_coordination_number(i-1))+str('Element')+str(el)
# def_str.append(pos)
# pos.write_file('POSCAR-'+str('intl_')+str('cellmax')+str(cellmax)+str('@')+str(intl.get_defectsite_coordination_number(i-1))+str('Element')+str(el))
#except:
# pass
return def_str
def vac_antisite_def_struct_gen(mpid, mapi_key, cellmax):
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = get_sc_scale(struct, cellmax)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {
'IBRION': -1,
'EDIFF': 1e-4,
'EDIFFG': 0.001,
'NSW': 0,
}
def_vasp_incar_param = {
'ISIF': 2,
'NELM': 99,
'IBRION': 2,
'EDIFF': 1e-6,
'EDIFFG': 0.001,
'NSW': 40,
}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc, kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir, 'INCAR'))
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
incar.update(def_vasp_incar_param)
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
def substitute_def_struct_gen(args):
mpid = args.mpid
solute = args.solute
mapi_key = args.mapi_key
cellmax = args.cellmax
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not solute:
print("============\nERROR: Provide solute atom\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
mpvis = MPRelaxSet(struct, user_incar_settings={"LDAU": False})
# Begin defaults: All default settings.
blk_vasp_incar_param = {
'IBRION': -1,
'EDIFF': 1e-4,
'EDIFFG': 0.001,
'NSW': 0,
}
def_vasp_incar_param = {
'ISIF': 2,
'NELM': 99,
'IBRION': 2,
'EDIFF': 1e-6,
'EDIFFG': 0.001,
'NSW': 40,
}
kpoint_den = 6000
# End defaults
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.potcar
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct, cellmax)
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1, len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
mpvis = MPRelaxSet(solute_struct, user_incar_settings={"LDAU": False})
incar = mpvis.incar
incar.update(def_vasp_incar_param)
poscar = mpvis.poscar
kpoints = Kpoints.automatic_density(solute_struct, kpoint_den)
if ptcr_flag:
potcar = mpvis.potcar
sub_def_dir = 'solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir, sub_def_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))