def totalenfit(indiv, Optimizer):
"""Function to calculate total energy fitness of individual.
Input:
indiv = structopt Individual class object to be evaluated
Optimizer = structopt Optimizer class object
Output:
indiv = structopt Individual class object with new fitness.
"""
#logger = initialize_logger(Optimizer.loggername)
logger = logging.getLogger(Optimizer.loggername)
starting = indiv.duplicate()
cwd = os.getcwd()
try:
outs = eval_energy(Optimizer,indiv)
except Exception, e:
logger.warn('Error in energy evaluation: {0}'.format(e), exc_info=True)
stro = 'ERROR: Problem in Energy Evaluation'
print stro
print e
stro += '\n' + repr(e)
os.chdir(cwd)
f=open('problem-structures.xyz','a')
totalsol = indiv[0].copy()
#totalsol.extend(indiv.bulki)
write_xyz(f,totalsol,data='Starting structure hindex={0}'.format(indiv.history_index))
indiv.energy = 10000
f.close()
print ' Writing structure to problemstructures.xyz file. Structure (hindex) : '+indiv.history_index
print ' Setting individual energy to 50000.'
#outs = [10000, starting.bulki, starting, stro]
outs = [10000, starting, starting, stro]
def sibias2(indiv, Optimizer):
"""Function to calculate total energy fitness of individual and bias away
from Si-Interstitials.
Input:
indiv = structopt Individual class object to be evaluated
Optimizer = structopt Optimizer class object
Output:
indiv = structopt Individual class object with new fitness.
"""
#logger = initialize_logger(Optimizer.loggername)
logger = logging.getLogger(Optimizer.loggername)
starting = indiv.duplicate()
cwd = os.getcwd()
try:
outs = eval_energy(Optimizer, indiv)
except Exception, e:
logger.warn('Error in energy evaluation: {0}'.format(e), exc_info=True)
stro = 'ERROR: Problem in Energy Evaluation'
print stro
print e
stro += '\n' + repr(e)
os.chdir(cwd)
f = open('problem-structures.xyz', 'a')
totalsol = indiv[0].copy()
totalsol.extend(indiv.bulki)
write_xyz(f,
totalsol,
data='Starting structure hindex={0}'.format(
indiv.history_index))
indiv.energy = 10000
f.close()
print ' Writing structure to problemstructures.xyz file. Structure (hindex) : ' + indiv.history_index
print ' Setting individual energy to 50000.'
outs = [10000, starting.bulki, starting, stro]
def find_stem_coeff(Optimizer, indiv):
from MAST.structopt.tools.eval_energy import eval_energy
outs = eval_energy([Optimizer, indiv])
indiv.energy = outs[0]
stro = outs[3]
if Optimizer.structure == 'Defect' or Optimizer.structure == 'Surface':
indiv.bulki = outs[1]
chisq = Optimizer.stemcalc.run(indiv[0])
aflag = True
alpha = 1.0
while True:
value = alpha * chisq
div = abs(indiv.energy) / value
if div < 1:
alpha *= 0.1
elif div > 10:
alpha *= 10
else:
break
indiv.fitness = indiv.energy + alpha * chisq
return alpha, indiv
def find_stem_coeff(Optimizer, indiv):
from MAST.structopt.tools.eval_energy import eval_energy
outs = eval_energy([Optimizer,indiv])
indiv.energy = outs[0]
stro=outs[3]
if Optimizer.structure == 'Defect' or Optimizer.structure=='Surface':
indiv.bulki = outs[1]
chisq = Optimizer.stemcalc.run(indiv[0])
aflag=True
alpha = 1.0
while True:
value=alpha*chisq
div=abs(indiv.energy)/value
if div <1:
alpha*=0.1
elif div >10:
alpha*=10
else:
break
indiv.fitness=indiv.energy/indiv[0].get_number_of_atoms()+alpha*chisq
return alpha, indiv
