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 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)