def algorithm_par_mp(self):
"""Subprogram for running parallel version of GA
Requires MPI4PY"""
global logger
comm = MPI.COMM_WORLD
rank = MPI.COMM_WORLD.Get_rank()
if rank==0:
if 'MA' in self.debug:
debug = True
else:
debug = False
self.algorithm_initialize()
self.convergence = False
convergence = False
while not convergence:
if rank==0:
pop = self.population
offspring = self.generation_set(self,pop)
# Identify the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if ind.energy==0]
#Evaluate the individuals with invalid fitness
self.output.write('\n--Evaluate Structures--\n')
else:
invalid_ind=[]
for i in range(len(invalid_ind)):
if self.fitness_scheme=='STEM_Cost':
if self.stem_coeff==None:
ind = invalid_ind.pop()
from MAST.structopt.tools.StemCalc import find_stem_coeff
outs = find_stem_coeff(self,ind)
ind = outs[1]
self.stem_coeff = outs[0]
self.output.write('stem_coeff Calculated to be: '+repr(self.stem_coeff)+'\n')
pop.append(ind)
ind=invalid_ind[i]
if 'MA' in self.debug: write_xyz(self.debugfile,ind[0],'Individual to fitness_switch')
outs = switches.fitness_switch([self,ind])
self.output.write(outs[1])
invalid_ind[i]=outs[0]
self.output.flush()
if rank==0:
pop.extend(invalid_ind)
pop = self.generation_eval(pop)
self.write()
convergence = comm.bcast(self.convergence, root=0)
if rank==0:
end_signal = self.algorithm_stats(self.population)
else:
end_signal = None
end_signal = comm.bcast(end_signal, root=0)
return end_signal
def mutation_dups_adapt_stem(pop, Optimizer):
"""Predator function that removes individuals based on fitness and mutates replacements
"""
fitlist = [one.fitness for one in pop]
nfitlist, nindices = remove_duplicates(fitlist, Optimizer.demin)
STR = ''
newpop = []
if len(nfitlist) != len(fitlist):
STR+='Predator: Removed total of '+repr(len(fitlist)-len(nfitlist))+' from population\n'
otherlist = []
for i in range(len(pop)):
if i not in nindices:
STR+='Predator: Removed '+repr(pop[i].history_index)+'\n'
otherlist.append(pop[i])
else:
newpop.append(pop[i])
while len(newpop) < Optimizer.nindiv:
indiv = random.choice(otherlist).duplicate()
indiv, scheme = moves_switch(indiv,Optimizer)
indiv.energy = 1000
indiv.fitness = 1000
newpop.append(indiv)
STR+='Predator: Adding mutated duplicates to new pop history='+indiv.history_index+'\n'
nindices.append(indiv.index)
nindices.sort()
if Optimizer.natural_selection_scheme=='fussf':
for ind in newpop:
if ind.fingerprint == 0:
ind.fingerprint = get_fingerprint(Optimizer,ind,Optimizer.fpbin,Optimizer.fpcutoff)
if 'lambda,mu' in Optimizer.algorithm_type:
try:
mark = [ index for index,n in enumerate(nindices) if n > Optimizer.nindiv-1][0]
except:
mark = Optimizer.nindiv
Optimizer.mark = mark
pop, str1 = lambdacommamu.lambdacommamu(newpop, Optimizer)
STR+=str1
else:
pop = selection_switch(newpop, Optimizer.nindiv, Optimizer.natural_selection_scheme, Optimizer)
pop = get_best(pop,len(pop))
indiv = pop[0]
if (indiv.fitness/indiv.energy <2.0):
from MAST.structopt.tools.StemCalc import find_stem_coeff
outs = find_stem_coeff(Optimizer,indiv)
ind = outs[1]
Optimizer.stem_coeff = outs[0]
STR+='Readjusting STEM Coeff = {0}'.format(Optimizer.stem_coeff))
return pop, STR
def generation_set(self,pop):
global logger
self.calc = tools.setup_calculator(self) #Set up calculator for atomic structures
#Set up calculator for fixed region calculations
if self.fixed_region:
self.static_calc = self.calc #May need to copy this
self.calc = tools.setup_fixed_region_calculator(self)
self.output.write('\n-------- Generation '+repr(self.generation)+' --------\n')
self.files[self.nindiv].write('Generation '+str(self.generation)+'\n')
if len(pop) == 0:
logger.info('Initializing structures')
offspring = self.initialize_structures()
self.population = offspring
else:
for i in range(len(pop)):
# Reset History index
pop[i].history_index=repr(pop[i].index)
# Select the next generation individuals
offspring = switches.selection_switch(pop, self.nindiv,
self.selection_scheme, self)
# Clone the selected individuals
offspring=[off1.duplicate() for off1 in offspring]
# Apply crossover to the offspring
self.output.write('\n--Applying Crossover--\n')
cxattempts = 0
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < self.cxpb:
child1,child2 = switches.crossover_switch(child1, child2, self)
cxattempts+=2
self.cxattempts=cxattempts
#DEBUG: Write first child
if 'MA' in self.debug:
inp_out.write_xyz(self.debugfile,offspring[0][0],'First Child '+
repr(offspring[0].history_index))
# Apply mutation to the offspring
self.output.write('\n--Applying Mutation--\n')
mutattempts = []
muts = []
for mutant in offspring:
if random.random() < self.mutpb:
if self.mutant_add:
mutant = mutant.duplicate()
mutant, optsel = switches.moves_switch(mutant,self)
mutattempts.append([mutant.history_index,optsel])
if self.mutant_add:
muts.append(mutant)
if self.mutant_add:
offspring.extend(muts)
self.mutattempts=mutattempts
#DEBUG: Write first offspring
if 'MA' in self.debug:
inp_out.write_xyz(self.debugfile,muts[0][0],'First Mutant '+\
repr(muts[0].history_index))
if 'stem' in self.fitness_scheme:
if self.stem_coeff==None:
logger.info('Setting STEM coeff (alpha)')
ind = offspring.pop()
from MAST.structopt.tools.StemCalc import find_stem_coeff
outs = find_stem_coeff(self,ind)
ind = outs[1]
ind.fitness = 0
ind.energy = 0
self.stem_coeff = outs[0]
logger.info('STEM Coeff = {0}'.format(self.stem_coeff))
self.output.write('stem_coeff Calculated to be: '+repr(self.stem_coeff)+'\n')
offspring.append(ind)
return offspring
def algorithm_par_mp1(self):
"""Subprogram for running parallel version of GA
Requires MPI4PY"""
comm = MPI.COMM_WORLD
rank = MPI.COMM_WORLD.Get_rank()
if rank==0:
if 'MA' in self.debug:
debug = True
else:
debug = False
self.algorithm_initialize()
self.convergence = False
convergence = False
while not convergence:
if rank==0:
self.calc = tools.setup_calculator(self) #Set up calculator for atomic structures
#Set up calculator for fixed region calculations
if self.fixed_region:
self.static_calc = self.calc #May need to copy this
self.calc = tools.setup_fixed_region_calculator(self)
pop = self.population
offspring = self.generation_set(self,pop)
# Identify the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if ind.energy==0]
#Evaluate the individuals with invalid fitness
self.output.write('\n--Evaluate Structures--\n')
proc_dist = int(comm.Get_size()/self.n_proc_eval)
ntimes=int(math.ceil(float(len(invalid_ind))/float(proc_dist)))
nadd=int(ntimes*proc_dist-len(invalid_ind))
maplist=[[] for n in range(ntimes)]
strt=0
for i in range(len(maplist)):
maplist[i]=[[self,indi] for indi in invalid_ind[strt:proc_dist+strt]]
strt+=proc_dist
for i in range(nadd):
maplist[len(maplist)-1].append([None,None])
masterlist = [i*self.n_proc_eval for i in range(proc_dist)]
else:
ntimes=None
masterlist = None
ntimes = comm.bcast(ntimes,root=0)
outs=[]
for i in range(ntimes):
if rank==0:
one=maplist[i]
for j in range(len(one)):
comm.send(ind, dest=1, tag=11)
elif rank == 1:
ind = comm.recv(source=0, tag=11)
else:
one=None
ind =comm.scatter(one,root=0)
out = switches.fitness_switch(ind)
else:
invalid_ind=[]
poorlist = []
for i in range(len(invalid_ind)):
if self.fitness_scheme=='STEM_Cost':
if self.stem_coeff==None:
ind = invalid_ind.pop()
from MAST.structopt.tools.StemCalc import find_stem_coeff
outs = find_stem_coeff(self,ind)
ind = outs[1]
self.stem_coeff = outs[0]
self.output.write('stem_coeff Calculated to be: '+repr(self.stem_coeff)+'\n')
pop.append(ind)
ind=invalid_ind[i]
if 'MA' in self.debug: write_xyz(self.debugfile,ind[0],'Individual to fitness_switch')
outs = switches.fitness_switch([self,ind])
self.output.write(outs[1])
invalid_ind[i]=outs[0]
if invalid_ind[i].energy == float('inf'):
poorlist.append(i)
self.output.write('Removing infinite energy individual '+repr(ind.history_index)+'\n')
elif invalid_ind[i].energy == float('nan'):
poorlist.append(i)
self.output.write('Removing nan energy individual '+repr(ind.history_index)+'\n')
self.output.flush()
if len(poorlist) != 0:
poorlist.sort(reverse=True)
for one in poorlist:
del invalid_ind[one]
if rank==0:
pop.extend(invalid_ind)
pop = self.generation_eval(pop)
convergence = comm.bcast(self.convergence, root=0)
if rank==0:
end_signal = self.algorithm_stats(self.population)
else:
end_signal = None
end_signal = comm.bcast(end_signal, root=0)
return end_signal