def getInterstitials(ase_in,inter,spinpol):
pmg_init = AseAtomsAdaptor.get_structure(ase_in)
pmg_init2 = SpacegroupAnalyzer(pmg_init).get_conventional_standard_structure()
interstitial = Interstitial(pmg_init2,None,covalent_radii) #accuracy=high breaks...
os.system('cls' if os.name == 'nt' else 'clear')
output = []
for i,site in enumerate(interstitial.enumerate_defectsites()):
coordination = int(round(interstitial.get_defectsite_coordination_number(i)))
mult = 0 # interstitial.get_defectsite_multiplicity(i) -- broken ???
insert = InsertSitesTransformation([inter],[site.coords],coords_are_cartesian=True)
try:
pmg_new = insert.apply_transformation(pmg_init2.copy())
ase_new = AseAtomsAdaptor.get_atoms(pmg_new)
if coordination == 4: siteName='T'
elif coordination == 6: siteName='O'
else: siteName = '%d-fold'%coordination
strname = '_%s-%s'%(inter,siteName)
if spinpol:
new_magmoms = [3 if e in misc.magElems else 0 for e in ase_new.get_chemical_symbols()]
ase_new.set_initial_magnetic_moments(new_magmoms)
output.append((ase_new,strname))
except ValueError: pass #ValueError: New site is too close to an existing site!
return output
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
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_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)
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)
tmp = struct.copy()
tmp.make_supercell(sc_scale)
sc_tmp = tmp # Poscar(tmp).structure .make_supercell(list(sc_scale))
scs = list(VacancyGenerator(struct))
supercell = Poscar(sc_tmp)
supercell.comment = str("bulk") + str("@") + str("cellmax") + str(cellmax)
def_str.append(supercell)
if write_file == True:
supercell.write_file("POSCAR-" + str("bulk") + str(".vasp"))
for i in range(len(scs)):
sc = scs[i].generate_defect_structure(sc_scale)
poscar = Poscar(sc) # mpvis.get_poscar(sc)
pmg_name = str(scs[i].name).split("_")
sitespecie = pmg_name[1]
mult = pmg_name[2].split("mult")[1]
name = (str("vacancy_") + str(i + 1) + str("_mult-") + str(mult) +
str("_sitespecie-") + str(sitespecie) + str("@cellmax") +
str(cellmax))
poscar.comment = str(name)
def_str.append(poscar)
if write_file == True:
filename = (str("POSCAR-") + str("vacancy_") + str(i + 1) +
str("_mult-") + str(mult) + str("_sitespecie-") +
str(sitespecie) + str(".vasp"))
poscar.write_file(filename)
return def_str
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 main():
jIDs = [x[0] for x in plotQuery(['jobid'], CONSTRAINTS)]
question = "Going to add an %s interstitial to %d bulk objects.\n(y/n)--> " % (
inter, len(jIDs))
if raw_input(question).lower() in ['y', 'yes']:
for j in jIDs:
aseinitID = query1('aseid', 'jobid', j)
aseinit = asedb.get_atoms(id=aseinitID)
# Access information about previous Job / Atoms object
jobinit = db2object(j)
xc, pw, kptden = jobinit.xc, jobinit.pw, jobinit.kptden
psp, xtol, strain = jobinit.psp, jobinit.xtol, jobinit.strain
precalc, dftcode = jobinit.precalc, jobinit.dftcode
nameinit = jobinit.name()
structure = jobinit.structure()
vacancies = jobinit.vacancies()
# Create conventional PyMatGen Object
pmg_init = AseAtomsAdaptor.get_structure(aseinit)
pmg_init2 = SpacegroupAnalyzer(
pmg_init).get_conventional_standard_structure()
interstitial = Interstitial(
pmg_init2, None, covalent_radii) #accuracy=high breaks...
os.system('cls' if os.name == 'nt' else 'clear')
for i, site in enumerate(interstitial.enumerate_defectsites()):
coordination = int(
round(interstitial.get_defectsite_coordination_number(i)))
mult = 0 # interstitial.get_defectsite_multiplicity(i) -- broken ???
insert = InsertSitesTransformation([inter], [site.coords],
coords_are_cartesian=True)
pmg_new = insert.apply_transformation(pmg_init2.copy())
ase_new = AseAtomsAdaptor.get_atoms(pmg_new)
ase_new.set_calculator(EMT())
emt = ase_new.get_potential_energy()
if coordination == 4: siteName = 'T'
elif coordination == 6: siteName = 'O'
else: siteName = '%d-fold' % coordination
question = ('site: %s\ncoordination: %s\nmultiplicity: %s' %
(site.coords, coordination, mult) +
'\ninitial ase id: %d \nxc: %s \npw: %d ' %
(aseinitID, xc, pw) +
'\nkptden: %f \npsp: %s\nxtol: %f\nstrain: %f' %
(kptden, psp, xtol, strain) +
'\nprecalc: %s \ndftcode: %s' %
(precalc, dftcode) +
'\n\nDoes this structure look good?\n(y/n)--> ')
view(ase_new)
if raw_input(question).lower() in ['y', 'yes']:
if checkForDuplicates(ase_new, structure, emt):
newquestion = 'What structure does this have?\n(leave blank for general triclinic case)\n--> '
structure = raw_input(newquestion)
if structure is '': structure = 'triclinic'
info = {
'name': nameinit + '_%s-%s' % (inter, siteName),
'emt':
emt # EMT for relaxed structures useless, only relevant for deciding when to relax something
,
'relaxed':
False # Could always doing this be a problem?
,
'comments': 'Generated from initializeHydride.py',
'parent': aseinitID,
'kind': 'bulk',
'structure': structure,
'interstitial': siteName
}
if vacancies is not None: info['vacancies'] = vacancies
newaseid = asedb.write(ase_new, key_value_pairs=info)
newjob = Job(None, 'bulkrelax', newaseid, None, None,
xc, pw, kptden, psp, xtol, strain,
2 if xc == 'mBEEF' else 1, precalc,
dftcode, None, None, 'initialized')
insertObject(newjob)
