def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
abs_path_perf = '%s/%s/' % (self.directory, perf_dir)
abs_path_def = '%s/%s/' % (self.directory, def_dir)
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
pa = PotentialAlignment()
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
return pa.get_potential_alignment(perfect_info, defect_info)
def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
abs_path_perf = '%s/%s/' % (self.directory, perf_dir)
abs_path_def = '%s/%s/' % (self.directory, def_dir)
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
pa = PotentialAlignment()
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
#ifndef VERSION1
#else /* VERSION1 */
#endif /* VERSION1 */
return pa.get_potential_alignment(perfect_info, defect_info)
def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
abs_path_perf = '%s/%s/' % (self.recdir, perf_dir)
abs_path_def = '%s/%s/' % (self.recdir, def_dir)
pa = PotentialAlignment()
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
print "TTM DEBUG: Perfect PA info: ", perfect_info
print "TTM DEBUG: Defected PA info: ", defect_info
pa_output = pa.get_potential_alignment(perfect_info, defect_info)
print "TTM DEBUG: PA output: ", defect_info
return pa_output
def get_potential_alignment(self, perf_dir, def_dir):
"""Returns the potential alignment correction used in charge defects"""
abs_path_perf = '%s/%s/' % (self.recdir, perf_dir)
abs_path_def = '%s/%s/' % (self.recdir, def_dir)
pa = PotentialAlignment()
if ('OUTCAR' in os.listdir(abs_path_perf)):
perfect_info = pa.read_outcar('%s/%s' % (abs_path_perf, 'OUTCAR'))
defect_info = pa.read_outcar('%s/%s' % (abs_path_def, 'OUTCAR'))
print "TTM DEBUG: Perfect PA info: ", perfect_info
print "TTM DEBUG: Defected PA info: ", defect_info
pa_output = pa.get_potential_alignment(perfect_info, defect_info)
print "TTM DEBUG: PA output: ", defect_info
return pa_output
def __init__(self):
self.inputs = ParseInput().read_input()
self.pa = PotentialAlignment()
class DefectFormationEnergy:
def __init__(self):
self.inputs = ParseInput().read_input()
self.pa = PotentialAlignment()
def read_CARs(self,GGA,HSE):
perfect = defaultdict(defaultdict)
defect = defaultdict(lambda:defaultdict(defaultdict))
PA = dict()
CARs = os.listdir('.')
perfect_tag = self.inputs['perfect']
defect_tag = self.inputs['defect']
for i in range(len(CARs)):
keywords = CARs[i].split('_')
if not 'CAR' in CARs[i]: continue
if 'HSE' in CARs[i]:
size = keywords[1]+'_HSE'
elif keywords[1] in ' '.join(HSE['size']):
size = keywords[1]+'_GGA'
else: size = keywords[1]
if keywords[0]==perfect_tag and keywords[-1]=='OSZICAR':
perfect[size]['energy'] = float(open(CARs[i]).readlines()[-1].split('E0=')[1].split()[0])
elif keywords[0]==defect_tag and keywords[-1]=='OSZICAR':
defect[keywords[2]][keywords[3]][size] = float(open(CARs[i]).readlines()[-1].split('E0=')[1].split()[0])
elif keywords[0]==perfect_tag and keywords[-1]=='OUTCAR':
PA[size] = self.pa.read_outcar(CARs[i])
elif keywords[0]==defect_tag and keywords[-1]=='OUTCAR':
PA['%s_%s_%s'%(keywords[2],keywords[3],size)] = self.pa.read_outcar(CARs[i])
elif keywords[0]==perfect_tag and (keywords[-1]=='POSCAR' or keywords[-1]=='CONTCAR'):
shutil.copy(CARs[i],'POSCAR')
Ele = pmg.read_structure('POSCAR').species
ele = dict()
for k in range(len(Ele)):
if not Ele[k] in ele.keys():
ele[Ele[k]] = 1
else: ele[Ele[k]] += 1
perfect[size]['ele'] = ele
elif keywords[0]==defect_tag and (keywords[-1]=='POSCAR' or keywords[-1]=='CONTCAR'):
shutil.copy(CARs[i],'POSCAR')
Ele = pmg.read_structure('POSCAR').species
ele = dict()
os.system('rm POSCAR')
for k in range(len(Ele)):
if not Ele[k] in ele.keys():
ele[Ele[k]] = 1
else: ele[Ele[k]] += 1
defect[keywords[2]]['ele'][size] = ele
return [perfect,defect,PA]
def calculate_dfe(self,GGA,HSE):
[perfect,defect,PA] = self.read_CARs(GGA,HSE)
Eform = defaultdict(lambda:defaultdict(lambda:defaultdict(lambda:defaultdict(defaultdict))))
for N in defect.keys():
for Q in defect[N].keys():
if Q=='ele': continue
if Q[-2]=='p': charge = float(Q[-1])
elif Q[-2]=='n': charge = -float(Q[-1])
for S in defect[N][Q].keys():
eshift = self.pa.get_potential_alignment(PA[S],PA['%s_%s_%s'%(N,Q,S)])
if not 'HSE' in S: xc = GGA
else: xc = HSE
if not '_' in S: X = 'GGA'
else: X = 'HSE'
for C in xc['chem_pot'].keys():
chempot = xc['chem_pot'][C]
Eform[X][C][N][Q][S] = defect[N][Q][S]-perfect[S]['energy']+charge*(xc['gap']['efermi']+eshift)
for pe in perfect[S]['ele']:
Eform[X][C][N][Q][S] += perfect[S]['ele'][pe]*chempot[str(pe)]
for de in defect[N]['ele'][S].keys():
Eform[X][C][N][Q][S] -= defect[N]['ele'][S][de]*chempot[str(de)]
return Eform
def main(self,GGA,HSE):
Eform = self.calculate_dfe(GGA,HSE)
for X in Eform.keys():
for C in Eform[X].keys():
fp = open('%s_%s.txt'%(C,X),'w')
for N in Eform[X][C].keys():
fp.write(N+'\n')
dfe = []
charge = Eform[X][C][N].keys()
for i in range(len(charge)):
if charge[i][-2]=='p': charge[i]=int(charge[i][-1])
elif charge[i][-2]=='n': charge[i]=-int(charge[i][-1])
charge.sort()
for i in range(len(charge)):
if charge[i]<0: charge[i]='q=n'+str(abs(charge[i]))
else: charge[i]='q=p'+str(charge[i])
dfe = []
for q in range(len(charge)):
Q = charge[q]
string = ''
if X=='GGA':
if len(Eform.keys())==2:
size=GGA['size']+['delta_E']
else: size=GGA['size']
elif X=='HSE': size=HSE['size']
for S in size:
if S=='delta_E':
for i in HSE['size']:
if 'HSE' in i: hse = i
else: gga = i
try: string += '%.4f '%(Eform['HSE'][C][N][Q][hse]-Eform['HSE'][C][N][Q][gga])
except KeyError: string += 'NaN '
else:
try: string += '%.4f '%(Eform[X][C][N][Q][S])
except KeyError: string += 'NaN '
charge[q] += ':'
dfe.append(string.split())
fp.write(pandas.DataFrame(dfe,charge,size).to_string()+'\n\n')