def chempotswap(indiv, Optimzier):
"""Fitness function to evaluate fitness of energy in which swaps are allowed
Inputs:
indiv = Individual class object to be evaluated
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Evaluated Individual class object
"""
#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 stem_cost(indiv, Optimizer):
'''Function to calculate STEM_Cost fitness of individual.
Input:
indiv = structopt_stem Individual class object to be evaluated
Optimizer = structopt_stem Optimizer class object
Must have STEM Calc function attached
Output:
indiv = structopt_stem 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 enpafit(indiv,Optimizer):
"""Fitness function to evaluate the energy per atom of an individual structure.
Inputs:
indiv = Individual class object to be evaluated
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Evaluated Individual class object
"""
#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 stem_cost_rotation(indiv, Optimizer):
'''Function to calculate STEM_Cost fitness of individual.
Input:
indiv = structopt_stem Individual class object to be evaluated
Optimizer = structopt_stem Optimizer class object
Must have STEM Calc function attached
Output:
indiv = structopt_stem Individual class object with new fitness.
'''
if 'FIT' in Optimizer.debug:
debug=True
else:
debug=False
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 formationenergy(indiv, Optimizer):
"""Function to calculate formation energy fitness of individual.
Input:
indiv = structopt_stem Individual class object to be evaluated
Optimizer = structopt_stem Optimizer class object
Output:
indiv = structopt_stem Individual class object with new fitness.
"""
if Optimizer.structure != 'Defect':
if Optimizer.generation < 1:
print 'WARNING: Formation Energy fitness calculator only available for Defect structure simulation.'
print ' Using total energy fitness calculator instead'
indiv = totalenfit(indiv, Optimizer)
stro = ''
else:
logger = logging.getLogger(Optimizer.loggername)
#logger = initialize_logger(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]
indiv.energy = outs[0]
stro = outs[3]
indiv.bulki = outs[1]
#fit = (indiv.purebulkenpa*(indiv[0].get_number_of_atoms()+indiv.bulki.get_number_of_atoms()) - indiv.energy)/(indiv[0].get_number_of_atoms()+indiv.bulki.get_number_of_atoms()-indiv.natomsbulk)
solid = Atoms()
solid.extend(indiv[0])
solid.extend(indiv.bulki)
fit = indiv.energy
passflag = True
if abs(fit) > Optimizer.energy_cutoff_factor * (len(indiv[0]) +
len(indiv.bulki)):
fit = 10000
message = 'Warning: Found oddly large energy from Lammps in structure HI={0}'.format(
indiv.history_index)
logger.warn(message)
print message
print ' Setting fitness to 10000'
passflag = False
if math.isnan(fit):
logger.warn('Found NAN energy structure HI={0}'.format(
indiv.history_index))
fit = 10000
passflag = False
indiv.energy = 10000
if passflag:
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in solid if atm.symbol == sym])
fit -= float(nc) * float(u)
indiv.fitness = fit
def formationenergy(indiv, Optimizer):
"""Function to calculate formation energy fitness of individual.
Input:
indiv = structopt_stem Individual class object to be evaluated
Optimizer = structopt_stem Optimizer class object
Output:
indiv = structopt_stem Individual class object with new fitness.
"""
if Optimizer.structure != 'Defect':
if Optimizer.generation <1:
print 'WARNING: Formation Energy fitness calculator only available for Defect structure simulation.'
print ' Using total energy fitness calculator instead'
indiv = totalenfit(indiv,Optimizer)
stro = ''
else:
logger = logging.getLogger(Optimizer.loggername)
#logger = initialize_logger(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]
indiv.energy = outs[0]
stro=outs[3]
indiv.bulki = outs[1]
#fit = (indiv.purebulkenpa*(indiv[0].get_number_of_atoms()+indiv.bulki.get_number_of_atoms()) - indiv.energy)/(indiv[0].get_number_of_atoms()+indiv.bulki.get_number_of_atoms()-indiv.natomsbulk)
solid=Atoms()
solid.extend(indiv[0])
solid.extend(indiv.bulki)
fit=indiv.energy
passflag = True
if abs(fit) > Optimizer.energy_cutoff_factor*(len(indiv[0])+len(indiv.bulki)):
fit=10000
message = 'Warning: Found oddly large energy from Lammps in structure HI={0}'.format(indiv.history_index)
logger.warn(message)
print message
print ' Setting fitness to 10000'
passflag=False
if math.isnan(fit):
logger.warn('Found NAN energy structure HI={0}'.format(indiv.history_index))
fit=10000
passflag=False
indiv.energy = 10000
if passflag:
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in solid if atm.symbol==sym])
fit-= float(nc)*float(u)
indiv.fitness=fit