def gen_solid(solidfile, solidcell, outfilename, calc=False, calcmeth=None):
"""Function to load a bulk solid from a file for use in Defect structure optimization
Inputs:
solidfile=String of filename to load
solidcell=List/Matrix of cell parameters for ASE Atoms class
outfilename=String of filename to write solid
calc=False/calculator object for evaluating energy of solid
calcmeth='VASP' or other method for calculating the energy of the solid
Outputs:
solid as ASE Atoms class
energy and string if calc is not false
"""
try:
sol = read_xyz(solidfile)
except Exception as e1:
try:
sol = read(solidfile)
except Exception as e2:
raise RuntimeError('Encountered errror:' + repr(e1) + ' ' +
repr(e2) +
' While trying to read solid file given as:' +
repr(solidfile))
cell = solidcell
sol.set_cell(cell)
sol.set_pbc(True)
#Evaluate pure Bulk structure
if calc:
cwd = os.getcwd()
sol.set_calculator(calc)
stro = ''
try:
if calcmeth == 'VASP':
en = sol.get_potential_energy()
calcb = Vasp(restart=True)
sol = calcb.get_atoms()
PureBulkEnpa = en / sol.get_number_of_atoms()
else:
OUT = sol.calc.calculate(sol)
PureBulkEnpa = OUT['thermo'][-1][
'pe'] / sol.get_number_of_atoms()
sol = OUT['atoms']
sol.set_pbc(True)
except:
stro = 'WARNING: Unable to calculate energy of pure bulk solid'
PureBulkEnpa = 0
os.chdir(cwd)
# Write bulk file to directory
write_xyz(outfilename, sol, PureBulkEnpa)
return sol, PureBulkEnpa, stro
else:
# Write bulk file to directory
write_xyz(outfilename, sol, 'Pure Bulk')
return sol
def gen_solid(solidfile,solidcell,outfilename,calc=False,calcmeth=None):
"""Function to load a bulk solid from a file for use in Defect structure optimization
Inputs:
solidfile=String of filename to load
solidcell=List/Matrix of cell parameters for ASE Atoms class
outfilename=String of filename to write solid
calc=False/calculator object for evaluating energy of solid
calcmeth='VASP' or other method for calculating the energy of the solid
Outputs:
solid as ASE Atoms class
energy and string if calc is not false
"""
try:
sol = read_xyz(solidfile)
except Exception as e1:
try:
sol = read(solidfile)
except Exception as e2:
raise RuntimeError('Encountered errror:'+repr(e1)+' '+repr(e2)+
' While trying to read solid file given as:'+repr(solidfile))
cell = solidcell
sol.set_cell(cell)
sol.set_pbc(True)
#Evaluate pure Bulk structure
if calc:
cwd = os.getcwd()
sol.set_calculator(calc)
stro = ''
try:
if calcmeth == 'VASP':
en = sol.get_potential_energy()
calcb = Vasp(restart=True)
sol = calcb.get_atoms()
PureBulkEnpa = en/sol.get_number_of_atoms()
else:
OUT = sol.calc.calculate(sol)
PureBulkEnpa = OUT['thermo'][-1]['pe']/sol.get_number_of_atoms()
sol = OUT['atoms']
sol.set_pbc(True)
except:
stro = 'WARNING: Unable to calculate energy of pure bulk solid'
PureBulkEnpa = 0
os.chdir(cwd)
# Write bulk file to directory
write_xyz(outfilename,sol,PureBulkEnpa)
return sol, PureBulkEnpa, stro
else:
# Write bulk file to directory
write_xyz(outfilename,sol,'Pure Bulk')
return sol
def initialize_structures(self):
global logger
self.output.write('\n----Initialize Structures----\n')
#self.logger.info('Initializing Structures')
# Initialize Population - Generate a list of ncluster individuals
# Set bulk and index atributes
if self.restart:
logger.info('Loading previous population')
pop = generate.get_restart_population(self)
else:
logger.info('Generating new population')
pop = generate.get_population(self)
if 'MA' in self.debug:
inp_out.write_xyz(self.debugfile,pop[0][0],'First Generated Individual')
#Use if concentration of interstitials is unknown
if self.swaplist:
mutlist=self.mutation_options
self.mutation_options=['IntSwapLocal']
for i in range(len(pop)):
one = pop[i]
one.swaplist=copy.deepcopy(swaplist)
if random.random() < 0.25:
pop[i], opt = switches.moves_switch(one,self)
self.mutation_options=mutlist
# Write Initial structures to files
self.output.write('\n---Starting Structures---\n')
inp_out.write_pop(self, pop)
#Print number of atoms to Summary file
if self.structure=='Defect' or self.structure=='Surface':
natstart=len(pop[0][0])+len(pop[0].bulki)
else:
natstart=len(pop[0][0])
if not self.restart:
if self.structure=='Defect':
self.summary.write('Defect Run Pure Bulk Energy per Atom : '+repr(self.purebulkenpa)+'\n')
else:
self.summary.write(self.structure+' Run : '+repr(0)+'\n')
self.summary.write('Natoms '+repr(natstart)+ '\n')
#Print data headers to summary file
self.summary.write('Generation Fitmin Fitavg Fitmedium Fitmax std time \n')
offspring=pop
#pop=[]
#BESTS=[]
return offspring
def algorithm_serial(self):
"""Subprogram to run the optimizer in serial"""
global logger
self.algorithm_initialize()
logger.info('Beginning main algorithm loop')
#Begin main algorithm loop
while not self.convergence:
logger.info('Setup calculator for generation {0}'.format(self.generation))
pop = self.population
logger.info('Setup population')
offspring = self.generation_set(pop)
# Identify the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if ind.energy==0]
#DEBUG: Write first invalid ind
if 'MA' in self.debug:
logger.info('Identified {0} structures with energy=0'.format(len(invalid_ind)))
inp_out.write_xyz(self.debugfile,invalid_ind[0][0],\
'First from Invalid_ind list '+repr(invalid_ind[0].energy))
#DEBUG: Write first invalid ind in solid
if self.structure=='Defect' or self.structure=='Surface':
sols = invalid_ind[0][0].copy()
sols.extend(invalid_ind[0].bulki)
inp_out.write_xyz(self.debugfile,sols,'First from Invalid-ind + Bulki')
sols = invalid_ind[0][0].copy()
sols.extend(invalid_ind[0].bulko)
inp_out.write_xyz(self.debugfile,sols,'First from Invalid-ind + Bulko')
self.output.write('\n--Evaluate Structures--\n')
logger.info('Evaluating fitness of structures')
for i in range(len(invalid_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]
pop.extend(invalid_ind)
logger.info('Eval Population')
pop = self.generation_eval(pop)
self.write()
logger.info('Run algorithm stats')
end_signal = self.algorithm_stats(self.population)
return end_signal
def newclus(ind1, ind2, Optimizer):
"""Select a box in the cluster configuration"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Box Cluster Cx between individual ' +
repr(ind1.index) + ' and individual ' +
repr(ind2.index) + '\n')
#Perserve starting conditions of individual
solid1 = ind1[0].copy()
solid2 = ind2[0].copy()
cello1 = ind1[0].get_cell()
cello2 = ind2[0].get_cell()
cell1 = numpy.maximum.reduce(solid1.get_positions())
cell1m = numpy.minimum.reduce(solid1.get_positions())
cell2 = numpy.maximum.reduce(solid2.get_positions())
cell2m = numpy.minimum.reduce(solid2.get_positions())
cell = numpy.minimum(cell1, cell2)
pbc1 = solid1.get_pbc()
pbc2 = solid2.get_pbc()
#Get starting concentrations and number of atoms
nat1 = len(solid1)
nat2 = len(solid2)
# Pick a origin point for box in the cell
pt1 = random.choice(solid1)
pt1f = [(pt1.position[i] - cell1m[i]) / cell1[i] for i in range(3)]
pt2 = [pt1f[i] * cell2[i] + cell2m[i] for i in range(3)]
solid2.append(Atom(position=pt2))
pt2 = solid2[len(solid2) - 1]
#Find max neighborsize of circle cut
r = random.uniform(0, min(nat1, nat2) / 5.0)
if debug:
print 'DEBUG CX: Point one =', pt1.position
print 'DEBUG CX: Point two =', pt2.position
#Find atoms within sphere of neighborsize r for both individuals
#Make sure that crossover is only selection of atoms not all
while True:
ctoff = [r for on in solid1]
nl = NeighborList(ctoff, bothways=True, self_interaction=False)
nl.update(solid1)
indices1, offsets = nl.get_neighbors(pt1.index)
if len(indices1) == 0:
r = r * 1.2
elif len(indices1) < nat1 * .75:
break
else:
r = r * 0.8
if debug:
print 'Neighborsize of box = ' + repr(
r) + '\nPosition in solid1 = ' + repr(
pt1.position) + '\nPosition in solid2 = ' + repr(pt2.position)
group1 = Atoms(cell=solid1.get_cell(), pbc=solid1.get_pbc())
group1.append(pt1)
indices1a = [pt1.index]
for index, d in zip(indices1, offsets):
if index not in indices1a:
index = int(index)
pos = solid1[index].position + numpy.dot(d, solid1.get_cell())
group1.append(Atom(symbol=solid1[index].symbol, position=pos))
indices1a.append(index)
indices1 = indices1a
ctoff = [r for on in solid2]
nl = NeighborList(ctoff, bothways=True, self_interaction=False)
nl.update(solid2)
indices2, offsets = nl.get_neighbors(pt2.index)
group2 = Atoms(cell=solid2.get_cell(), pbc=solid2.get_pbc())
indices2a = []
for index, d in zip(indices2, offsets):
if index not in indices2a:
index = int(index)
pos = solid2[index].position + numpy.dot(d, solid2.get_cell())
group2.append(Atom(symbol=solid2[index].symbol, position=pos))
indices2a.append(index)
indices2 = indices2a
if len(indices2) == 0:
for one in group1:
while True:
sel = random.choice(solid2)
if sel.symbol == one.symbol:
if sel.index not in indices2:
group2.append(sel)
indices2.append(sel.index)
break
if Optimizer.forcing == 'Concentration':
symlist = list(set(group1.get_chemical_symbols()))
seplist = [[atm for atm in group2 if atm.symbol == sym]
for sym in symlist]
group2n = Atoms(cell=group2.get_cell(), pbc=group2.get_pbc())
indices2n = []
dellist = []
for one in group1:
sym1 = one.symbol
listpos = [i for i, s in enumerate(symlist) if s == sym1][0]
if len(seplist[listpos]) > 0:
pos = random.choice(range(len(seplist[listpos])))
group2n.append(seplist[listpos][pos])
indices2n.append(indices2[seplist[listpos][pos].index])
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
indices2n.append(pt2.index)
indices2 = indices2n
group2 = group2n.copy()
else:
dellist = []
while len(group2) < len(group1) - len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2) - len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other2 = Atoms(cell=solid2.get_cell(), pbc=solid2.get_pbc())
for one in solid2:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=solid1.get_cell(), pbc=solid1.get_pbc())
for one in solid1:
if one.index not in indices1:
other1.append(one)
#Exchange atoms in sphere and build new solids
nsolid1 = other1.copy()
nsolid1.extend(group2.copy())
nsolid2 = other2.copy()
nsolid2.extend(group1.copy())
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1, 'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2, 'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym, c, m, u in Optimizer.atomlist:
if Optimizer.structure == 'Defect':
nc = len([atm for atm in nsolid1 if atm.symbol == sym])
nc += len([atm for atm in ind1.bulki if atm.symbol == sym])
oc = len([atm for atm in solid1 if atm.symbol == sym])
oc += len([atm for atm in ind1.bulki if atm.symbol == sym])
else:
nc = len([atm for atm in nsolid1 if atm.symbol == sym])
oc = len([atm for atm in solid1 if atm.symbol == sym])
Optimizer.output.write('CX(clustbx):New solid1 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
if debug:
print 'DEBUG CX: New solid1 contains ' + repr(nc) + ' ' + repr(
sym) + ' atoms'
if oc != nc:
#pdb.set_trace()
print 'CX: Issue in maintaining atom concentration\n Dropping new individual'
Optimizer.output.write(
'CX: Issue in maintaining atom concentration\n Dropping new individual 1\n'
)
nsolid1 = solid1
for sym, c, m, u in Optimizer.atomlist:
if Optimizer.structure == 'Defect':
nc = len([atm for atm in nsolid2 if atm.symbol == sym])
nc += len([atm for atm in ind2.bulki if atm.symbol == sym])
oc = len([atm for atm in solid2 if atm.symbol == sym])
oc += len([atm for atm in ind2.bulki if atm.symbol == sym])
else:
nc = len([atm for atm in nsolid2 if atm.symbol == sym])
oc = len([atm for atm in solid2 if atm.symbol == sym])
Optimizer.output.write('CX(clustbx):New solid2 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
if debug:
print 'DEBUG CX: New solid2 contains ' + repr(nc) + ' ' + repr(
sym) + ' atoms'
if oc != nc:
#pdb.set_trace()
print 'CX: Issue in maintaining atom concentration\n Dropping new individual'
Optimizer.output.write(
'CX: Issue in maintaining atom concentration\n Dropping new individual 2\n'
)
solid2.pop()
nsolid2 = solid2
if Optimizer.forcing != 'Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in nsolid1
if inds.symbol == Optimizer.atomlist[i][0]
]
atms2 = [
inds for inds in nsolid2
if inds.symbol == Optimizer.atomlist[i][0]
]
if len(atms1) == 0:
if len(atms2) == 0:
nsolid1[random.randint(
0,
len(indi1) - 1)].symbol == Optimizer.atomlist[i][0]
nsolid2[random.randint(
0,
len(indi2) - 1)].symbol == Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0, len(atms2) - 1)])
nsolid1.pop(random.randint(0, len(nsolid1) - 2))
else:
if len(atms2) == 0:
nsolid2.append(atms1[random.randint(0, len(atms1) - 1)])
nsolid2.pop(random.randint(0, len(nsolid2) - 2))
nsolid1.set_cell(cello1)
nsolid2.set_cell(cello2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
ind1[0] = nsolid1.copy()
ind2[0] = nsolid2.copy()
return ind1, ind2
def rotct_rand_clus(ind1, ind2, Optimizer):
"""Rotate atoms cut and splice
Rotates atoms randomly around center of mass and cuts with xy plane
Maintains number of atoms
Maintains concentration of atoms
Returns individuals to standard positions at end (un-rotates)
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
if Optimizer.structure != 'Defect':
Optimizer.output.write('Rotate-Cut Random Cluster Cx attempted on Non Defect structure. SKIPPING CX.\n')
else:
Optimizer.output.write('Rotate-Cut Random Cluster Cx between individual '+repr(ind1.index)+' and individual '+repr(ind2.index)+'\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 =ind2[0].copy()
indi1c,indi1b,vacant1,swap1,stro1 = find_defects(indi1,Optimizer.solidbulk,0)
indi2c,indi2b,vacant2,swap2,stro2 = find_defects(indi2,Optimizer.solidbulk,0)
if len(indi1c) !=0 and len(indi2c) != 0:
#Translate individuals so COM is at (0,0,0)
com1 = indi1c.get_center_of_mass()
indi1c.translate(-1*com1)
com2 = indi2c.get_center_of_mass()
indi2c.translate(-1*com2)
#Select random axis, random angle, and random position and rotate individuals
cmax = [min(numpy.maximum.reduce(indi1c.get_positions())[i],numpy.maximum.reduce(indi2c.get_positions())[i]) for i in range(3)]
cmin = [min(numpy.minimum.reduce(indi1c.get_positions())[i],numpy.minimum.reduce(indi2c.get_positions())[i]) for i in range(3)]
n=0
while n<10:
rax = random.choice(['x', '-x','y','-y','z','-z'])
rang = random.random()*90
rpos = [random.uniform(cmin[i]*0.8,cmax[i]*0.8) for i in range(3)]
indi1c.rotate(rax,a=rang,center=rpos,rotate_cell=False)
#Search for atoms in individual 1 that are above the xy plane
group1 = Atoms(cell=ind1[0].get_cell(),pbc=ind1[0].get_pbc())
indices1=[]
for one in indi1c:
if one.position[2] >= 0:
group1.append(one)
indices1.append(one.index)
if len(group1) > 2 and len(group1) < len(indi1):
break
else:
n+=1
indi1c.rotate(rax,a=-1*rang,center=rpos, rotate_cell=False)
indi2c.rotate(rax,a=rang,center=rpos,rotate_cell=False)
if debug:
print 'Group1 size = ', len(group1)
print 'Position = ', rpos
print 'Angle = ', rang
print 'Axis = ', rax
print 'Number of tries = ', n
if len(group1) != 0:
#Apply concentration forcing if needed
group2 = Atoms(cell=ind2[0].get_cell(),pbc=ind2[0].get_pbc())
indices2 = []
dellist = []
for one in indi2c:
if one.position[2] >= 0:
group2.append(one)
indices2.append(one.index)
if Optimizer.forcing=='Concentration':
symlist = list(set(indi1c.get_chemical_symbols()))
seplist = [[atm for atm in group2 if atm.symbol == sym] for sym in symlist]
group2n=Atoms(cell=group2.get_cell(),pbc=group2.get_pbc())
indices2n = []
dellist = []
for one in group1:
sym1=one.symbol
listpos=[i for i,s in enumerate(symlist) if s==sym1][0]
if len(seplist[listpos]) > 0:
pos = random.choice(range(len(seplist[listpos])))
group2n.append(seplist[listpos][pos])
indices2n.append(indices2[seplist[listpos][pos].index])
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
indices2=indices2n
group2=group2n.copy()
else:
dellist = []
while len(group2) < len(group1)-len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2)-len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other2 = Atoms(cell=ind2[0].get_cell(),pbc=ind2[0].get_pbc())
for one in indi2c:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=ind1[0].get_cell(),pbc=ind1[0].get_pbc())
for one in indi1c:
if one.index not in indices1:
other1.append(one)
group1.rotate(rax,a=-1*rang,center=rpos, rotate_cell=False)
group1.translate(com1)
other1.rotate(rax,a=-1*rang,center=rpos, rotate_cell=False)
other1.translate(com1)
group2.rotate(rax,a=-1*rang,center=rpos, rotate_cell=False)
group2.translate(com2)
other2.rotate(rax,a=-1*rang,center=rpos, rotate_cell=False)
other2.translate(com2)
indi1 = group2.copy()
indi1.extend(other1)
indi1.extend(indi1b)
indi2 = group1.copy()
indi2.extend(other2)
indi2.extend(indi2b)
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, group1,'group1')
write_xyz(Optimizer.debugfile, other1,'other1')
write_xyz(Optimizer.debugfile, group2,'group2')
write_xyz(Optimizer.debugfile, other2,'other2')
print 'Length of group1 = ',len(group1),'Length of group2',len(group2)
#DEBUG: Check structure of atoms exchanged
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in indi1 if atm.symbol==sym])
Optimizer.output.write('CX RANDROTCT: Individual 1 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc=len([atm for atm in indi2 if atm.symbol==sym])
Optimizer.output.write('CX RANDROTCT: Individual 2 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if Optimizer.forcing !='Concentration':
for i in range(len(Optimizer.atomlist)):
atms1=[inds for inds in indi1 if inds.symbol==Optimizer.atomlist[i][0]]
atms2=[inds for inds in indi2 if inds.symbol==Optimizer.atomlist[i][0]]
if len(atms1)==0:
if len(atms2)==0:
indi1[random.randint(0,len(indi1)-1)].symbol==Optimizer.atomlist[i][0]
indi2[random.randint(0,len(indi2)-1)].symbol==Optimizer.atomlist[i][0]
else:
indi1.append(atms2[random.randint(0,len(atms2)-1)])
indi1.pop(random.randint(0,len(indi1)-2))
else:
if len(atms2)==0:
indi2.append(atms1[random.randint(0,len(atms1)-1)])
indi2.pop(random.randint(0,len(indi2)-2))
#DEBUG: Check structure and number of atoms in crystal
if Optimizer.structure=='Defect':
solid1=Atoms()
solid1.extend(indi1)
solid1.extend(ind1.bulki)
solid2=Atoms()
solid2.extend(indi2)
solid2.extend(ind2.bulki)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in solid1 if atm.symbol==sym])
Optimizer.output.write('CX RANDROTCT: Defect 1 configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc=len([atm for atm in solid2 if atm.symbol==sym])
Optimizer.output.write('CX RANDROTCT: Defect 2 configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if debug: Optimizer.output.flush()
#pdb.set_trace()
else:
Optimizer.output.write(' Warning: failed to identify a cluster:\n')
Optimizer.output.write(' Individual '+repr(ind1.index)+' length = '+repr(len(indi1c))+'\n')
Optimizer.output.write(' Individual '+repr(ind2.index)+' length = '+repr(len(indi2c))+'\n')
ind1[0]=indi1
ind2[0]=indi2
return ind1, ind2
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_stem.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 generation_eval(self, pop):
global logger
emx = max(ind.energy for ind in pop)
emn = min(ind.energy for ind in pop)
for ind in pop:
ind.tenergymx = emx
ind.tenergymin = emn
#DEBUG: Write relaxed individual
if 'MA' in self.debug:
if self.generation > 0:
inp_out.write_xyz(self.debugfile,pop[self.nindiv][0],\
'First Relaxed Offspring '+repr(pop[self.nindiv-1].energy))
#DEBUG: Write relaxed ind in solid
if self.structure=='Defect' or self.structure=='Surface':
inp_out.write_xyz(self.debugfile,pop[self.nindiv].bulki,\
'First Relaxed bulki '+repr(pop[self.nindiv-1].energy))
sols = pop[self.nindiv][0].copy()
sols.extend(pop[self.nindiv].bulki)
inp_out.write_xyz(self.debugfile,sols,'First from Invalid-ind + Bulki '+\
repr(pop[self.nindiv].energy))
sols = pop[self.nindiv][0].copy()
sols.extend(pop[self.nindiv].bulko)
inp_out.write_xyz(self.debugfile,sols,\
'First from Invalid-ind + Bulko '+repr(pop[self.nindiv].energy))
if self.generation==0:
logger.info('Initializing Bests list')
self.BESTS = list()
if self.best_inds_list:
self.BESTS = tools.BestInds(pop,self.BESTS,self,writefile=True)
# Determine survival based on fitness predator
if 'lambda,mu' not in self.algorithm_type:
pop = tools.get_best(pop, len(pop))
if self.fingerprinting:
logger.info('Writing fingerprint files')
for one in pop:
self.fpfile.write(repr(fingerprinting.fingerprint_dist(
pop[0].fingerprint,one.fingerprint))+' '+repr(one.energy)+' ')
self.fpfile.write('\n')
self.fpminfile.write(repr(pop[0].fingerprint)+'\n')
self.fpminfile.write(repr(pop[0].energy)+'\n')
nevals = len(pop)/2
if self.generation !=0:
logger.info('Applying predator')
pop = predator_switch(pop,self)
else:
self.genrep = 0
self.minfit = 0
# Evaluate population
logger.info('Checking population for convergence')
self.check_pop(pop)
#Update general output tracking
if self.generation !=0:
histlist = []
for ind in pop:
histlist.append(ind.history_index)
self.Runtimes.append(time.time())
self.Evaluations.append(nevals)
cxsuccess = 0
mutsuccess = []
for one in histlist:
if '+' in one:
cxsuccess +=1
if 'm' in one:
mutsuccess.append(one)
self.CXs.append((self.cxattempts,cxsuccess))
mutslist = [[0,0] for one in self.mutation_options]
for one in mutsuccess:
for two, opt in self.mutattempts:
if one==two:
index = [ind for ind,value in enumerate(
self.mutation_options) if value==opt][0]
mutslist[index][1]+=1
for one,opt in self.mutattempts:
index = [ind for ind,value in enumerate(
self.mutation_options) if value==opt][0]
mutslist[index][0]+=1
self.Muts.append(mutslist)
self.output.write('\n----- Generation Stats -----\n')
self.output.write('Attempted Crossovers: ' + repr(self.cxattempts)+'\n')
self.output.write('Successful Crossovers: ' + repr(cxsuccess)+'\n')
self.output.write('Mutations:\n')
i=0
for opt in self.mutation_options:
self.output.write(' Attempted ' + opt + ' : ' + repr(mutslist[i][0]) + '\n')
self.output.write(' Successful ' + opt + ' : ' + repr(mutslist[i][1]) + '\n')
i+=1
self.generation += 1
# Set new index values
index1 = 0
for ind in pop:
ind.index = index1
index1+=1
index1 = 0
if not self.convergence:
try:
self.calc.clean()
if self.fixed_region:
self.static_calc.clean()
except:
pass
if self.lammps_keep_files:
try:
if self.parallel and ('Island_Method' not in self.algorithm_type):
nproc = MPI.COMM_WORLD.Get_size()
lmpfilepath = os.path.dirname(self.calc.tmp_dir)
for proc in range(nproc):
pth = os.path.join(lmpfilepath,'rank-{0}'.format(proc))
fls = [fl for fl in os.listdir(pth) if '.' not in fl]
for one in fls:
os.remove(pth+'/'+one)
else:
fls = [fl for fl in os.listdir(self.calc.tmp_dir) if '.' not in fl]
for one in fls:
os.remove(self.calc.tmp_dir+'/'+one)
except Exception, e:
logger.error('Print issue in removing files {0}.'.format(e),exc_info=True)
print str(e)
pass
def clustbx(ind1, ind2, Optimizer):
"""Select a box in the cluster configuration
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Box Cluster Cx between individual ' +
repr(ind1.index) + ' and individual ' +
repr(ind2.index) + '\n')
#Perserve starting conditions of individual
solid1 = ind1[0].copy()
solid2 = ind2[0].copy()
cello1 = ind1[0].get_cell()
cello2 = ind2[0].get_cell()
cell1 = numpy.maximum.reduce(
solid1.get_positions()) #-numpy.minimum.reduce(solid1.get_positions())
cell2 = numpy.maximum.reduce(
solid2.get_positions()) #-numpy.minimum.reduce(solid2.get_positions())
cell = numpy.minimum(cell1, cell2)
pbc1 = solid1.get_pbc()
pbc2 = solid2.get_pbc()
#Get starting concentrations and number of atoms
nat1 = len(solid1)
nat2 = len(solid2)
if Optimizer.alloy == False:
#Atomlist-based
concent1 = [c for sym, c, m, u in Optimizer.atomlist]
concent2 = [c for sym, c, m, u in Optimizer.atomlist]
symlist = [sym for sym, c, m, u in Optimizer.atomlist]
else:
symlist = list(set(solid1.get_chemical_symbols()))
#Assumes same types of atoms in both solid1 and solid2
concent1 = []
for one in symlist:
atmss = [atm for atm in solid1 if atm.symbol == one]
concent1.append(len(atmss))
concent2 = []
for one in symlist:
atmss = [atm for atm in solid2 if atm.symbol == one]
concent2.append(len(atmss))
# Pick a origin point for box in the cell
#pt=[random.uniform(0,cell[0]),random.uniform(0,cell[1]),random.uniform(0,cell[2])]
pt1 = random.choice(solid1).position
pt2 = random.choice(solid2).position
#Find max radius of circle cut
r1 = min([
min(cell1[0] - pt1[0], pt1[0]),
min(cell1[1] - pt1[1], pt1[1]),
min(cell1[2] - pt1[2], pt1[2])
])
r2 = min([
min(cell2[0] - pt2[0], pt2[0]),
min(cell2[1] - pt2[1], pt2[1]),
min(cell2[2] - pt2[2], pt2[2])
])
r = min(r1, r2)
mcell = min(cell)
if r > mcell * 0.125:
r = mcell * 0.125
elif r == 0.0:
r = 1.0
if debug:
print 'Radius of box = ' + repr(r) + '\nPosition in solid1 = ' + repr(
pt1) + '\nPosition in solid2 = ' + repr(pt2)
#Find atoms within sphere of radius r
solid1.append(Atom(position=pt1))
dist1 = []
blist1 = []
for i in range(len(solid1) - 1):
d = solid1.get_distance(i, len(solid1) - 1)
if d < r:
dist1.append((d, solid1[i]))
else:
blist1.append((d, solid1[i]))
solid1.pop()
solid2.append(Atom(position=pt2))
dist2 = []
blist2 = []
for i in range(len(solid2) - 1):
d = solid2.get_distance(i, len(solid2) - 1)
if d < r:
dist2.append((d, solid2[i]))
else:
blist2.append((d, solid2[i]))
solid2.pop()
#Translate spheres to opposite location
dats1 = Atoms()
for d, atm in dist1:
dats1.append(atm)
dats1.translate(-pt1)
dats1.translate(pt2)
dats2 = Atoms()
for d, atm in dist2:
dats2.append(atm)
dats2.translate(-pt2)
dats2.translate(pt1)
#Exchange atoms in sphere and build new solids
nsolid1 = dats2.copy()
for d, atm in blist1:
nsolid1.append(atm)
nsolid2 = dats1.copy()
for d, atm in blist2:
nsolid2.append(atm)
#Identify new number of atoms
nnat1 = len(nsolid1)
nnat2 = len(nsolid2)
if nnat1 > nat1:
ds = []
#More atoms in new solid1 means solid2 has less atoms
#Need to transfer atoms from solid1 to solid2
#Find atoms that are too close
for i in range(len(dist2)):
for j in range(len(dist2), len(nsolid1)):
ds.append((nsolid1.get_distance(i, j), i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one: one[0])
diff = nnat1 - nat1
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid1 = Atoms()
for i in range(len(nsolid1)):
if i not in exchangeindices:
nnsolid1.append(nsolid1[i])
nnsolid2 = nsolid2.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [
random.uniform(pt2[0] - r / (2**0.5), pt2[0] + r / (2**0.5)),
random.uniform(pt2[1] - r / (2**0.5), pt2[1] + r / (2**0.5)),
random.uniform(pt2[2] - r / (2**0.5), pt2[2] + r / (2**0.5))
]
nnsolid2.append(Atom(symbol=nsolid1[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
elif nnat1 < nat1:
ds = []
#More atoms in new solid2 means solid1 has less atoms
#Need to transfer atoms from solid2 to solid1
#Find atoms that are too close
for i in range(len(dist1)):
for j in range(len(dist1), len(nsolid2)):
ds.append((nsolid2.get_distance(i, j), i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one: one[0])
diff = nnat2 - nat2
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid2 = Atoms()
for i in range(len(nsolid2)):
if i not in exchangeindices:
nnsolid2.append(nsolid2[i])
nnsolid1 = nsolid1.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [
random.uniform(pt1[0] - r / (2**0.5), pt1[0] + r / (2**0.5)),
random.uniform(pt1[1] - r / (2**0.5), pt1[1] + r / (2**0.5)),
random.uniform(pt1[2] - r / (2**0.5), pt1[2] + r / (2**0.5))
]
nnsolid1.append(Atom(symbol=nsolid2[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
#Number of atoms in each individual should now be preserved
try:
if Optimizer.forcing == 'Concentration':
#Need to check concentrations
nconcent1 = []
for one in symlist:
atmss = [atm for atm in nsolid1 if atm.symbol == one]
nconcent1.append(len(atmss))
nconcent2 = []
for one in symlist:
atmss = [atm for atm in nsolid2 if atm.symbol == one]
nconcent2.append(len(atmss))
#Let's assume a random perturbation to concentration in order to correct this issue
posd = []
negd = []
for i in range(len(nconcent1)):
diff = nconcent1[i] - concent1[i]
if diff > 0:
posd.append((diff, symlist[i]))
elif diff < 0:
negd.append((diff, symlist[i]))
for c, sym in negd:
while c != 0:
symr = posd[0][1]
rlist = [
atm.index for atm in nsolid1 if atm.symbol == symr
]
index1 = random.choice(rlist)
nsolid1[index1].symbol = sym
c += 1
posd[0] = (posd[0][0] - 1, posd[0][1])
if posd[0][0] == 0:
posd = posd[1::]
#Do the same for solid2
posd = []
negd = []
for i in range(len(nconcent2)):
diff = nconcent2[i] - concent2[i]
if diff > 0:
posd.append((diff, symlist[i]))
elif diff < 0:
negd.append((diff, symlist[i]))
for c, sym in negd:
while c != 0:
symr = posd[0][1]
rlist = [
atm.index for atm in nsolid2 if atm.symbol == symr
]
index1 = random.choice(rlist)
nsolid2[index1].symbol = sym
c += 1
posd[0] = (posd[0][0] - 1, posd[0][1])
if posd[0][0] == 0:
posd = posd[1::]
except:
f = open('problem-structures.xyz', 'a')
write_xyz(f,
nsolid1,
data='Failed - CX(randalloybx):nsolid1 ' +
ind1.history_index)
write_xyz(f,
nsolid2,
data='Failed - CX(randalloybx):nsolid2 ' +
ind2.history_index)
nsolid1 = ind1[0].copy()
nsolid2 = ind2[0].copy()
f.close()
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1, 'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2, 'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in nsolid1 if atm.symbol == sym])
Optimizer.output.write('CX(clustbx):New solid1 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in nsolid2 if atm.symbol == sym])
Optimizer.output.write('CX(clustbx):New solid2 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
if Optimizer.forcing != 'Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in nsolid1
if inds.symbol == Optimizer.atomlist[i][0]
]
atms2 = [
inds for inds in nsolid2
if inds.symbol == Optimizer.atomlist[i][0]
]
if len(atms1) == 0:
if len(atms2) == 0:
nsolid1[random.randint(
0,
len(indi1) - 1)].symbol == Optimizer.atomlist[i][0]
nsolid2[random.randint(
0,
len(indi2) - 1)].symbol == Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0, len(atms2) - 1)])
nsolid1.pop(random.randint(0, len(nsolid1) - 2))
else:
if len(atms2) == 0:
nsolid2.append(atms1[random.randint(0, len(atms1) - 1)])
nsolid2.pop(random.randint(0, len(nsolid2) - 2))
nsolid1.set_cell(cello1)
nsolid2.set_cell(cello2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
ind1[0] = nsolid1.copy()
ind2[0] = nsolid2.copy()
return ind1, ind2
def rotct_rand_defect(ind1, ind2, Optimizer):
"""Rotate atoms cut and splice
Translates atoms to center of positions first
Rotates atoms randomly around center of mass and cuts with xy plane
Maintains number of atoms
Maintains concentration of atoms
Returns individuals to standard positions at end (un-rotates)
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write(
'Random Rotate Cut/Splice Cx for defects between individual ' +
repr(ind1.index) + ' and individual ' + repr(ind2.index) + '\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 = ind2[0].copy()
#Translate individuals so COP is at (0,0,0)
if Optimizer.structure == 'Defect':
#Identify center of positions for defect structure
indi1c, indi1b, vacant1, swap1, stro1 = find_defects(
indi1, Optimizer.solidbulk, 0)
com1 = position_average(indi1c)
indi1 = shift_atoms(indi1, com1)
#Do the same for second individual
indi2c, indi2b, vacant2, swap2, stro2 = find_defects(
indi2, Optimizer.solidbulk, 0)
com2 = position_average(indi2c)
indi2 = shift_atoms(indi2, com2)
else:
com1 = indi1.get_center_of_mass()
indi1.translate(-1 * com1)
com2 = indi2.get_center_of_mass()
indi2.translate(-1 * com2)
#Select random axis, random angle, and random position and rotate individuals
cmax = [
min(
numpy.maximum.reduce(indi1.get_positions())[i],
numpy.maximum.reduce(indi2.get_positions())[i]) for i in range(3)
]
cmin = [
min(
numpy.minimum.reduce(indi1.get_positions())[i],
numpy.minimum.reduce(indi2.get_positions())[i]) for i in range(3)
]
n = 0
while n < 10:
rax = random.choice(['x', '-x', 'y', '-y', 'z', '-z'])
rang = random.random() * 90
rpos = [random.uniform(cmin[i] * 0.8, cmax[i] * 0.8) for i in range(3)]
indi1.rotate(rax, a=rang, center=rpos, rotate_cell=False)
#Search for atoms in individual 1 that are above the xy plane
group1 = Atoms(cell=ind1[0].get_cell(), pbc=ind1[0].get_pbc())
indices1 = []
for one in indi1:
if one.position[2] >= 0:
group1.append(one)
indices1.append(one.index)
if len(group1) > 2 and len(group1) < len(indi1):
break
else:
n += 1
indi1.rotate(rax, a=-1 * rang, center=rpos, rotate_cell=False)
indi2.rotate(rax, a=rang, center=rpos, rotate_cell=False)
if debug:
print 'Group1 size = ', len(group1)
print 'Position = ', rpos
print 'Angle = ', rang
print 'Axis = ', rax
print 'Number of tries = ', n
if len(group1) != 0:
#Apply concentration forcing if needed
group2 = Atoms(cell=ind2[0].get_cell(), pbc=ind2[0].get_pbc())
indices2 = []
dellist = []
for one in indi2:
if one.position[2] >= 0:
group2.append(one)
indices2.append(one.index)
if Optimizer.forcing == 'Concentration':
symlist = list(set(indi1.get_chemical_symbols()))
seplist = [[atm for atm in group2 if atm.symbol == sym]
for sym in symlist]
group2n = Atoms(cell=group2.get_cell(), pbc=group2.get_pbc())
indices2n = []
dellist = []
for one in group1:
sym1 = one.symbol
listpos = [i for i, s in enumerate(symlist) if s == sym1][0]
if len(seplist[listpos]) > 0:
pos = random.choice(range(len(seplist[listpos])))
group2n.append(seplist[listpos][pos])
indices2n.append(indices2[seplist[listpos][pos].index])
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
indices2 = indices2n
group2 = group2n.copy()
else:
dellist = []
while len(group2) < len(group1) - len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2) - len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other2 = Atoms(cell=ind2[0].get_cell(), pbc=ind2[0].get_pbc())
for one in indi2:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=ind1[0].get_cell(), pbc=ind1[0].get_pbc())
for one in indi1:
if one.index not in indices1:
other1.append(one)
indi1 = group2.copy()
indi1.extend(other1)
indi2 = group1.copy()
indi2.extend(other2)
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, group1, 'group1')
write_xyz(Optimizer.debugfile, other1, 'other1')
write_xyz(Optimizer.debugfile, group2, 'group2')
write_xyz(Optimizer.debugfile, other2, 'other2')
print 'Length of group1 = ', len(group1), 'Length of group2', len(
group2)
#DEBUG: Check structure of atoms exchanged
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in indi1 if atm.symbol == sym])
Optimizer.output.write(
'CX RANDROTCT_Defect: Individual 1 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in indi2 if atm.symbol == sym])
Optimizer.output.write(
'CX RANDROTCT_Defect: Individual 2 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
if Optimizer.forcing != 'Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in indi1
if inds.symbol == Optimizer.atomlist[i][0]
]
atms2 = [
inds for inds in indi2
if inds.symbol == Optimizer.atomlist[i][0]
]
if len(atms1) == 0:
if len(atms2) == 0:
indi1[random.randint(
0,
len(indi1) - 1)].symbol == Optimizer.atomlist[i][0]
indi2[random.randint(
0,
len(indi2) - 1)].symbol == Optimizer.atomlist[i][0]
else:
indi1.append(atms2[random.randint(0, len(atms2) - 1)])
indi1.pop(random.randint(0, len(indi1) - 2))
else:
if len(atms2) == 0:
indi2.append(atms1[random.randint(0, len(atms1) - 1)])
indi2.pop(random.randint(0, len(indi2) - 2))
indi1.rotate(rax, a=-1 * rang, center=rpos, rotate_cell=False)
indi2.rotate(rax, a=-1 * rang, center=rpos, rotate_cell=False)
if Optimizer.structure == 'Defect':
indi1 = shift_atoms(indi1, [-p for p in com1])
indi2 = shift_atoms(indi2, [-p for p in com2])
else:
indi1.translate(com1)
indi2.translate(com2)
#DEBUG: Check structure and number of atoms in crystal
if Optimizer.structure == 'Defect':
solid1 = Atoms()
solid1.extend(indi1)
solid1.extend(ind1.bulki)
solid2 = Atoms()
solid2.extend(indi2)
solid2.extend(ind2.bulki)
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in solid1 if atm.symbol == sym])
Optimizer.output.write(
'CX RANDROTCT_Defect: Defect 1 configuration contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in solid2 if atm.symbol == sym])
Optimizer.output.write(
'CX RANDROTCT_Defect: Defect 2 configuration contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
if debug: Optimizer.output.flush()
#pdb.set_trace()
ind1[0] = indi1
ind2[0] = indi2
return ind1, ind2
def clustbx(ind1, ind2, Optimizer):
"""Select a box in the cluster configuration
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Box Cluster Cx between individual '+repr(ind1.index)+' and individual '+repr(ind2.index)+'\n')
#Perserve starting conditions of individual
solid1=ind1[0].copy()
solid2=ind2[0].copy()
cello1=ind1[0].get_cell()
cello2=ind2[0].get_cell()
cell1=numpy.maximum.reduce(solid1.get_positions())#-numpy.minimum.reduce(solid1.get_positions())
cell2=numpy.maximum.reduce(solid2.get_positions())#-numpy.minimum.reduce(solid2.get_positions())
cell=numpy.minimum(cell1,cell2)
pbc1=solid1.get_pbc()
pbc2=solid2.get_pbc()
#Get starting concentrations and number of atoms
nat1=len(solid1)
nat2=len(solid2)
if Optimizer.alloy==False:
#Atomlist-based
concent1=[c for sym,c,m,u in Optimizer.atomlist]
concent2=[c for sym,c,m,u in Optimizer.atomlist]
symlist=[sym for sym,c,m,u in Optimizer.atomlist]
else:
symlist=list(set(solid1.get_chemical_symbols()))
#Assumes same types of atoms in both solid1 and solid2
concent1=[]
for one in symlist:
atmss=[atm for atm in solid1 if atm.symbol==one]
concent1.append(len(atmss))
concent2=[]
for one in symlist:
atmss=[atm for atm in solid2 if atm.symbol==one]
concent2.append(len(atmss))
# Pick a origin point for box in the cell
#pt=[random.uniform(0,cell[0]),random.uniform(0,cell[1]),random.uniform(0,cell[2])]
pt1=random.choice(solid1).position
pt2=random.choice(solid2).position
#Find max radius of circle cut
r1=min([min(cell1[0]-pt1[0],pt1[0]),min(cell1[1]-pt1[1],pt1[1]),min(cell1[2]-pt1[2],pt1[2])])
r2=min([min(cell2[0]-pt2[0],pt2[0]),min(cell2[1]-pt2[1],pt2[1]),min(cell2[2]-pt2[2],pt2[2])])
r=min(r1,r2)
mcell=min(cell)
if r > mcell*0.125:
r=mcell*0.125
elif r==0.0:
r=1.0
if debug:
print 'Radius of box = '+repr(r)+'\nPosition in solid1 = '+repr(pt1)+'\nPosition in solid2 = '+repr(pt2)
#Find atoms within sphere of radius r
solid1.append(Atom(position=pt1))
dist1=[]
blist1=[]
for i in range(len(solid1)-1):
d=solid1.get_distance(i,len(solid1)-1)
if d < r:
dist1.append((d,solid1[i]))
else:
blist1.append((d,solid1[i]))
solid1.pop()
solid2.append(Atom(position=pt2))
dist2=[]
blist2=[]
for i in range(len(solid2)-1):
d=solid2.get_distance(i,len(solid2)-1)
if d < r:
dist2.append((d,solid2[i]))
else:
blist2.append((d,solid2[i]))
solid2.pop()
#Translate spheres to opposite location
dats1=Atoms()
for d,atm in dist1:
dats1.append(atm)
dats1.translate(-pt1)
dats1.translate(pt2)
dats2=Atoms()
for d,atm in dist2:
dats2.append(atm)
dats2.translate(-pt2)
dats2.translate(pt1)
#Exchange atoms in sphere and build new solids
nsolid1=dats2.copy()
for d,atm in blist1:
nsolid1.append(atm)
nsolid2=dats1.copy()
for d,atm in blist2:
nsolid2.append(atm)
#Identify new number of atoms
nnat1=len(nsolid1)
nnat2=len(nsolid2)
if nnat1 > nat1:
ds=[]
#More atoms in new solid1 means solid2 has less atoms
#Need to transfer atoms from solid1 to solid2
#Find atoms that are too close
for i in range(len(dist2)):
for j in range(len(dist2),len(nsolid1)):
ds.append((nsolid1.get_distance(i,j),i))
#Sort distances by longest to shortest
ds=sorted(ds, key=lambda one:one[0])
diff=nnat1-nat1
exchangeindices=[]
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index=ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid1=Atoms()
for i in range(len(nsolid1)):
if i not in exchangeindices:
nnsolid1.append(nsolid1[i])
nnsolid2=nsolid2.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position=[random.uniform(pt2[0]-r/(2**0.5),pt2[0]+r/(2**0.5)),random.uniform(pt2[1]-r/(2**0.5),pt2[1]+r/(2**0.5)),random.uniform(pt2[2]-r/(2**0.5),pt2[2]+r/(2**0.5))]
nnsolid2.append(Atom(symbol=nsolid1[i].symbol, position=position))
nsolid1=nnsolid1.copy()
nsolid2=nnsolid2.copy()
elif nnat1 < nat1:
ds=[]
#More atoms in new solid2 means solid1 has less atoms
#Need to transfer atoms from solid2 to solid1
#Find atoms that are too close
for i in range(len(dist1)):
for j in range(len(dist1),len(nsolid2)):
ds.append((nsolid2.get_distance(i,j),i))
#Sort distances by longest to shortest
ds=sorted(ds, key=lambda one:one[0])
diff=nnat2-nat2
exchangeindices=[]
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index=ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid2=Atoms()
for i in range(len(nsolid2)):
if i not in exchangeindices:
nnsolid2.append(nsolid2[i])
nnsolid1=nsolid1.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position=[random.uniform(pt1[0]-r/(2**0.5),pt1[0]+r/(2**0.5)),random.uniform(pt1[1]-r/(2**0.5),pt1[1]+r/(2**0.5)),random.uniform(pt1[2]-r/(2**0.5),pt1[2]+r/(2**0.5))]
nnsolid1.append(Atom(symbol=nsolid2[i].symbol, position=position))
nsolid1=nnsolid1.copy()
nsolid2=nnsolid2.copy()
#Number of atoms in each individual should now be preserved
try:
if Optimizer.forcing=='Concentration':
#Need to check concentrations
nconcent1=[]
for one in symlist:
atmss=[atm for atm in nsolid1 if atm.symbol==one]
nconcent1.append(len(atmss))
nconcent2=[]
for one in symlist:
atmss=[atm for atm in nsolid2 if atm.symbol==one]
nconcent2.append(len(atmss))
#Let's assume a random perturbation to concentration in order to correct this issue
posd=[]
negd=[]
for i in range(len(nconcent1)):
diff=nconcent1[i]-concent1[i]
if diff >0:
posd.append((diff,symlist[i]))
elif diff<0:
negd.append((diff,symlist[i]))
for c,sym in negd:
while c !=0:
symr=posd[0][1]
rlist=[atm.index for atm in nsolid1 if atm.symbol==symr]
index1=random.choice(rlist)
nsolid1[index1].symbol=sym
c+=1
posd[0]=(posd[0][0]-1,posd[0][1])
if posd[0][0]==0:
posd=posd[1::]
#Do the same for solid2
posd=[]
negd=[]
for i in range(len(nconcent2)):
diff=nconcent2[i]-concent2[i]
if diff >0:
posd.append((diff,symlist[i]))
elif diff<0:
negd.append((diff,symlist[i]))
for c,sym in negd:
while c !=0:
symr=posd[0][1]
rlist=[atm.index for atm in nsolid2 if atm.symbol==symr]
index1=random.choice(rlist)
nsolid2[index1].symbol=sym
c+=1
posd[0]=(posd[0][0]-1,posd[0][1])
if posd[0][0]==0:
posd=posd[1::]
except:
f=open('problem-structures.xyz','a')
write_xyz(f,nsolid1,data='Failed - CX(randalloybx):nsolid1 '+ind1.history_index)
write_xyz(f,nsolid2,data='Failed - CX(randalloybx):nsolid2 '+ind2.history_index)
nsolid1=ind1[0].copy()
nsolid2=ind2[0].copy()
f.close()
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1,'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2,'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in nsolid1 if atm.symbol==sym])
Optimizer.output.write('CX(clustbx):New solid1 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc=len([atm for atm in nsolid2 if atm.symbol==sym])
Optimizer.output.write('CX(clustbx):New solid2 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if Optimizer.forcing !='Concentration':
for i in range(len(Optimizer.atomlist)):
atms1=[inds for inds in nsolid1 if inds.symbol==Optimizer.atomlist[i][0]]
atms2=[inds for inds in nsolid2 if inds.symbol==Optimizer.atomlist[i][0]]
if len(atms1)==0:
if len(atms2)==0:
nsolid1[random.randint(0,len(indi1)-1)].symbol==Optimizer.atomlist[i][0]
nsolid2[random.randint(0,len(indi2)-1)].symbol==Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0,len(atms2)-1)])
nsolid1.pop(random.randint(0,len(nsolid1)-2))
else:
if len(atms2)==0:
nsolid2.append(atms1[random.randint(0,len(atms1)-1)])
nsolid2.pop(random.randint(0,len(nsolid2)-2))
nsolid1.set_cell(cello1)
nsolid2.set_cell(cello2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
ind1[0]=nsolid1.copy()
ind2[0]=nsolid2.copy()
return ind1, ind2
def randalloybox(ind1, ind2, Optimizer):
"""Select a box in the alloy configuration
*** Note: CX may be obsolete. In development ***
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
if Optimizer.structure != 'Defect':
Optimizer.output.write('WARNING: Box Random alloy Cx attempted on nondefect structure. SKIPPING CX.\n')
else:
Optimizer.output.write('Box Random alloy Cx between individual '+repr(ind1.index)+' and individual '+repr(ind2.index)+'\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 = ind2[0].copy()
cell1 = numpy.maximum.reduce(indi1.get_cell())
cell2 = numpy.maximum.reduce(indi2.get_cell())
cell = numpy.minimum(cell1,cell2)
pbc1 = indi1.get_pbc()
pbc2 = indi2.get_pbc()
#Build solids
solid1 = indi1.copy()
solid1.extend(ind1.bulki.copy())
solid2 = indi2.copy()
solid2.extend(ind2.bulki.copy())
#Get starting concentrations and number of atoms
nat1 = len(solid1)
nat2 = len(solid2)
symlist = list(set(solid1.get_chemical_symbols()))
#Assumes same types of atoms in both solid1 and solid2
concent1 = []
concent2 = []
for one in symlist:
atmss = [atm for atm in solid1 if atm.symbol==one]
concent1.append(len(atmss))
atmss = [atm for atm in solid2 if atm.symbol==one]
concent2.append(len(atmss))
# Pick a origin point for box in the cell
#pt=[random.uniform(0,cell[0]),random.uniform(0,cell[1]),random.uniform(0,cell[2])]
pt1 = solid1[0].position
pt2 = solid2[0].position
#Find max radius of circle cut
r1 = min([min(cell1[0]-pt1[0],pt1[0]),min(cell1[1]-pt1[1],pt1[1]),min(cell1[2]-pt1[2],pt1[2])])
r2 = min([min(cell2[0]-pt2[0],pt2[0]),min(cell2[1]-pt2[1],pt2[1]),min(cell2[2]-pt2[2],pt2[2])])
r = min(r1,r2)
mcell = min(cell)
if r > mcell*0.125:
r = mcell*0.125
if debug:
Optimizer.output.write('Radius of box = '+repr(r)+'\nPosition in solid1 = '+repr(pt1)+'\nPosition in solid2 = '+repr(pt2)+'\n')
#Find atoms within sphere of radius r
solid1.append(Atom(position=pt1))
dist1 = []
blist1 = []
for i in range(len(solid1)-1):
d = solid1.get_distance(i,len(solid1)-1)
if d < r:
dist1.append((d,solid1[i]))
else:
blist1.append((d,solid1[i]))
solid1.pop()
solid2.append(Atom(position=pt2))
dist2 = []
blist2 = []
for i in range(len(solid2)-1):
d = solid2.get_distance(i,len(solid2)-1)
if d < r:
dist2.append((d,solid2[i]))
else:
blist2.append((d,solid2[i]))
solid2.pop()
#Translate spheres to opposite location
dats1 = Atoms()
for d,atm in dist1:
dats1.append(atm)
dats1.translate(-pt1)
dats1.translate(pt2)
dats2 = Atoms()
for d,atm in dist2:
dats2.append(atm)
dats2.translate(-pt2)
dats2.translate(pt1)
#Exchange atoms in sphere and build new solids
nsolid1 = dats2.copy()
for d,atm in blist1:
nsolid1.append(atm)
nsolid2 = dats1.copy()
for d,atm in blist2:
nsolid2.append(atm)
#Identify new number of atoms
nnat1 = len(nsolid1)
nnat2 = len(nsolid2)
if nnat1 > nat1:
ds = []
#More atoms in new solid1 means solid2 has less atoms
#Need to transfer atoms from solid1 to solid2
#Find atoms that are too close
for i in range(len(dist2)):
for j in range(len(dist2),len(nsolid1)):
ds.append((nsolid1.get_distance(i,j),i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one:one[0])
diff = nnat1-nat1
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid1 = Atoms()
for i in range(len(nsolid1)):
if i not in exchangeindices:
nnsolid1.append(nsolid1[i])
nnsolid2 = nsolid2.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [random.uniform(pt2[0]-r/(2**0.5),pt2[0]+r/(2**0.5)),random.uniform(pt2[1]-r/(2**0.5),pt2[1]+r/(2**0.5)),random.uniform(pt2[2]-r/(2**0.5),pt2[2]+r/(2**0.5))]
nnsolid2.append(Atom(symbol=nsolid1[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
elif nnat1 < nat1:
ds = []
#More atoms in new solid2 means solid1 has less atoms
#Need to transfer atoms from solid2 to solid1
#Find atoms that are too close
for i in range(len(dist1)):
for j in range(len(dist1),len(nsolid2)):
ds.append((nsolid2.get_distance(i,j),i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one:one[0])
diff = nnat2-nat2
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid2 = Atoms()
for i in range(len(nsolid2)):
if i not in exchangeindices:
nnsolid2.append(nsolid2[i])
nnsolid1 = nsolid1.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [random.uniform(pt1[0]-r/(2**0.5),pt1[0]+r/(2**0.5)),random.uniform(pt1[1]-r/(2**0.5),pt1[1]+r/(2**0.5)),random.uniform(pt1[2]-r/(2**0.5),pt1[2]+r/(2**0.5))]
nnsolid1.append(Atom(symbol=nsolid2[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
#Number of atoms in each individual should now be preserved
if Optimizer.forcing=='Concentration':
#Need to check concentrations
nconcent1 = []
for one in symlist:
atmss = [atm for atm in nsolid1 if atm.symbol==one]
nconcent1.append(len(atmss))
nconcent2 = []
for one in symlist:
atmss = [atm for atm in nsolid2 if atm.symbol==one]
nconcent2.append(len(atmss))
#Let's assume a random perturbation to concentration in order to correct this issue
posd = []
negd = []
for i in range(len(nconcent1)):
diff = nconcent1[i]-concent1[i]
if diff >0:
posd.append((diff,symlist[i]))
elif diff<0:
negd.append((diff,symlist[i]))
for c,sym in negd:
while c !=0:
symr = posd[0][1]
rlist = [atm.index for atm in nsolid1 if atm.symbol==symr]
index1 = random.choice(rlist)
nsolid1[index1].symbol=sym
c += 1
posd[0] = (posd[0][0]-1,posd[0][1])
if posd[0][0]==0:
posd = posd[1::]
#Do the same for solid2
posd = []
negd = []
for i in range(len(nconcent2)):
diff = nconcent2[i]-concent2[i]
if diff >0:
posd.append((diff,symlist[i]))
elif diff<0:
negd.append((diff,symlist[i]))
for c,sym in negd:
while c !=0:
symr = posd[0][1]
rlist = [atm.index for atm in nsolid2 if atm.symbol==symr]
index1 = random.choice(rlist)
nsolid2[index1].symbol=sym
c += 1
posd[0] = (posd[0][0]-1,posd[0][1])
if posd[0][0]==0:
posd = posd[1::]
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1,'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2,'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym,c,m,u in Optimizer.atomlist:
nc = len([atm for atm in nsolid1 if atm.symbol==sym])
Optimizer.output.write('CX(randalloybx):New solid1 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc = len([atm for atm in nsolid2 if atm.symbol==sym])
Optimizer.output.write('CX(randalloybx):New solid2 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if Optimizer.forcing !='Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [inds for inds in nsolid1 if inds.symbol==Optimizer.atomlist[i][0]]
atms2 = [inds for inds in nsolid2 if inds.symbol==Optimizer.atomlist[i][0]]
if len(atms1)==0:
if len(atms2)==0:
nsolid1[random.randint(0,len(indi1)-1)].symbol = Optimizer.atomlist[i][0]
nsolid2[random.randint(0,len(indi2)-1)].symbol = Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0,len(atms2)-1)])
nsolid1.pop(random.randint(0,len(nsolid1)-2))
else:
if len(atms2)==0:
nsolid2.append(atms1[random.randint(0,len(atms1)-1)])
nsolid2.pop(random.randint(0,len(nsolid2)-2))
nsolid1.set_cell(cell1)
nsolid2.set_cell(cell2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
outs = find_defects(nsolid1,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False)
ind1[0] = outs[0].copy()
ind1.bulki = outs[1].copy()
ind1.vacancies = outs[2].copy()
ind1.swaps = outs[3].copy()
outs = find_defects(nsolid2,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False)
ind2[0] = outs[0].copy()
ind2.bulki = outs[1].copy()
ind2.vacancies = outs[2].copy()
ind2.swaps = outs[3].copy()
return ind1, ind2
def rotct(ind1, ind2, Optimizer):
"""Rotate atoms cut and splice
Rotates atoms randomly around center of mass and cuts with xy plane
Maintains number of atoms
Maintains concentration of atoms
Returns individuals to standard positions at end (un-rotates)
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Rotate Cut/Splice Cx between individual ' +
repr(ind1.index) + ' and individual ' +
repr(ind2.index) + '\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 = ind2[0].copy()
#Translate individuals so COM is at (0,0,0)
com1 = indi1.get_center_of_mass()
indi1.translate(-1 * com1)
com2 = indi2.get_center_of_mass()
indi2.translate(-1 * com2)
#Select random axis and random angle and rotate individuals
n = 0
while n < 10:
rax = random.choice(['x', '-x', 'y', '-y', 'z', '-z'])
rang = random.random() * 90
indi1.rotate(rax, a=rang, center='COM', rotate_cell=False)
#Search for atoms in individual 1 that are above the xy plane
group1 = Atoms(cell=ind1[0].get_cell(), pbc=ind1[0].get_pbc())
indices1 = []
for one in indi1:
if one.position[2] >= 0:
group1.append(one)
indices1.append(one.index)
if len(group1) > 2 and len(group1) < len(indi1):
break
else:
indi1.rotate(rax, a=-1 * rang, center='COM', rotate_cell=False)
n += 1
indi2.rotate(rax, a=rang, center='COM', rotate_cell=False)
if debug:
print 'Group1 size = ', len(group1)
print 'Position = ', [0, 0, 0]
print 'Angle = ', rang
print 'Axis = ', rax
print 'Number of tries = ', n + 1
#Apply concentration forcing if needed
group2 = Atoms(cell=ind2[0].get_cell(), pbc=ind2[0].get_pbc())
indices2 = []
dellist = []
if Optimizer.forcing == 'Concentration':
symlist = list(set(group1.get_chemical_symbols()))
seplist = [[atm for atm in indi2 if atm.symbol == sym]
for sym, count in symlist]
for one in group1:
sym1 = one.symbol
listpos = [i for i, s in enumerate(symlist) if s == sym1][0]
if len(seplist[listpos]) > 0:
dist = [
z
for x, y, z in [one.position for one in seplist[listpos]]
]
pos = [
i for i, value in enumerate(dist) if value == max(dist)
][0]
group2.append(seplist[listpos][pos])
indices2.append(seplist[listpos][pos].index)
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
#indices2.append(pt2.index)
else:
for one in indi2:
if one.position[2] >= 0:
group2.append(one)
indices2.append(one.index)
while len(group2) < len(group1) - len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2) - len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other1 = Atoms()
other2 = Atoms()
other2 = Atoms(cell=ind2[0].get_cell(), pbc=ind2[0].get_pbc())
for one in indi2:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=ind1[0].get_cell(), pbc=ind1[0].get_pbc())
for one in indi1:
if one.index not in indices1:
other1.append(one)
indi1 = group2.copy()
indi1.extend(other1)
indi2 = group1.copy()
indi2.extend(other2)
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, group1, 'group1')
write_xyz(Optimizer.debugfile, other1, 'other1')
write_xyz(Optimizer.debugfile, group2, 'group2')
write_xyz(Optimizer.debugfile, other2, 'other2')
print 'Length of group1 = ', len(group1), 'Length of group2', len(
group2)
#DEBUG: Check structure of atoms exchanged
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in indi1 if atm.symbol == sym])
Optimizer.output.write('CX ROTCT: Individual 1 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in indi2 if atm.symbol == sym])
Optimizer.output.write('CX ROTCT: Individual 2 contains ' + repr(nc) +
' ' + repr(sym) + ' atoms\n')
#Need to have at least one atom of each structure in atomlist to prevent Lammps for erroring
if Optimizer.forcing != 'Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in indi1
if inds.symbol == Optimizer.atomlist[i][0]
]
atms2 = [
inds for inds in indi2
if inds.symbol == Optimizer.atomlist[i][0]
]
if len(atms1) == 0:
if len(atms2) == 0:
indi1[random.randint(0,
len(indi1) -
1)].symbol == Optimizer.atomlist[i][0]
indi2[random.randint(0,
len(indi2) -
1)].symbol == Optimizer.atomlist[i][0]
else:
indi1.append(atms2[random.randint(0, len(atms2) - 1)])
indi1.pop(random.randint(0, len(indi1) - 2))
else:
if len(atms2) == 0:
indi2.append(atms1[random.randint(0, len(atms1) - 1)])
indi2.pop(random.randint(0, len(indi2) - 2))
indi1.rotate(rax, a=-1 * rang, center='COM', rotate_cell=False)
indi2.rotate(rax, a=-1 * rang, center='COM', rotate_cell=False)
indi1.translate(com1)
indi2.translate(com2)
if Optimizer.structure != 'Defect':
cm = indi1.get_center_of_mass()
cell = numpy.maximum.reduce(indi1.get_cell())
cop = [cell[0] / float(2), cell[1] / float(2), cell[2] / float(2)]
indi1.translate(-1 * cm)
indi1.translate(cop)
cm = indi2.get_center_of_mass()
cell = numpy.maximum.reduce(indi2.get_cell())
cop = [cell[0] / float(2), cell[1] / float(2), cell[2] / float(2)]
indi2.translate(-1 * cm)
indi2.translate(cop)
ind1[0] = indi1
ind2[0] = indi2
#Check structure and number of atoms in crystal
if Optimizer.structure == 'Defect':
solid1 = Atoms()
solid1.extend(ind1[0])
solid1.extend(ind1.bulki)
solid2 = Atoms()
solid2.extend(ind1[0])
solid2.extend(ind2.bulki)
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in solid1 if atm.symbol == sym])
Optimizer.output.write('CX ROTCT: CIBS 1 configuration contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in solid2 if atm.symbol == sym])
Optimizer.output.write('CX ROTCT: CIBS 2 configuration contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
return ind1, ind2
def rotct(ind1, ind2, Optimizer):
"""Rotate atoms cut and splice
Rotates atoms randomly around center of mass and cuts with xy plane
Maintains number of atoms
Maintains concentration of atoms
Returns individuals to standard positions at end (un-rotates)
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Rotate Cut/Splice Cx between individual '+repr(ind1.index)+' and individual '+repr(ind2.index)+'\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 = ind2[0].copy()
#Translate individuals so COM is at (0,0,0)
com1 = indi1.get_center_of_mass()
indi1.translate(-1*com1)
com2 = indi2.get_center_of_mass()
indi2.translate(-1*com2)
#Select random axis and random angle and rotate individuals
n=0
while n<10:
rax = random.choice(['x', '-x','y','-y','z','-z'])
rang = random.random()*90
indi1.rotate(rax,a=rang,center='COM',rotate_cell=False)
#Search for atoms in individual 1 that are above the xy plane
group1 = Atoms(cell=ind1[0].get_cell(),pbc=ind1[0].get_pbc())
indices1=[]
for one in indi1:
if one.position[2] >= 0:
group1.append(one)
indices1.append(one.index)
if len(group1) > 2 and len(group1) < len(indi1):
break
else:
indi1.rotate(rax,a=-1*rang,center='COM', rotate_cell=False)
n+=1
indi2.rotate(rax,a=rang,center='COM', rotate_cell=False)
if debug:
print 'Group1 size = ', len(group1)
print 'Position = ', [0,0,0]
print 'Angle = ', rang
print 'Axis = ', rax
print 'Number of tries = ', n+1
#Apply concentration forcing if needed
group2 = Atoms(cell=ind2[0].get_cell(),pbc=ind2[0].get_pbc())
indices2 = []
dellist = []
if Optimizer.forcing=='Concentration':
symlist = list(set(group1.get_chemical_symbols()))
seplist = [[atm for atm in indi2 if atm.symbol == sym] for sym, count in symlist]
for one in group1:
sym1=one.symbol
listpos=[i for i,s in enumerate(symlist) if s==sym1][0]
if len(seplist[listpos]) > 0:
dist=[z for x,y,z in [one.position for one in seplist[listpos]]]
pos = [i for i,value in enumerate(dist) if value==max(dist)][0]
group2.append(seplist[listpos][pos])
indices2.append(seplist[listpos][pos].index)
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
#indices2.append(pt2.index)
else:
for one in indi2:
if one.position[2] >= 0:
group2.append(one)
indices2.append(one.index)
while len(group2) < len(group1)-len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2)-len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other1 = Atoms()
other2 = Atoms()
other2 = Atoms(cell=ind2[0].get_cell(),pbc=ind2[0].get_pbc())
for one in indi2:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=ind1[0].get_cell(),pbc=ind1[0].get_pbc())
for one in indi1:
if one.index not in indices1:
other1.append(one)
indi1 = group2.copy()
indi1.extend(other1)
indi2 = group1.copy()
indi2.extend(other2)
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, group1,'group1')
write_xyz(Optimizer.debugfile, other1,'other1')
write_xyz(Optimizer.debugfile, group2,'group2')
write_xyz(Optimizer.debugfile, other2,'other2')
print 'Length of group1 = ',len(group1),'Length of group2',len(group2)
#DEBUG: Check structure of atoms exchanged
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in indi1 if atm.symbol==sym])
Optimizer.output.write('CX ROTCT: Individual 1 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc=len([atm for atm in indi2 if atm.symbol==sym])
Optimizer.output.write('CX ROTCT: Individual 2 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
#Need to have at least one atom of each structure in atomlist to prevent Lammps for erroring
if Optimizer.forcing !='Concentration':
for i in range(len(Optimizer.atomlist)):
atms1=[inds for inds in indi1 if inds.symbol==Optimizer.atomlist[i][0]]
atms2=[inds for inds in indi2 if inds.symbol==Optimizer.atomlist[i][0]]
if len(atms1)==0:
if len(atms2)==0:
indi1[random.randint(0,len(indi1)-1)].symbol==Optimizer.atomlist[i][0]
indi2[random.randint(0,len(indi2)-1)].symbol==Optimizer.atomlist[i][0]
else:
indi1.append(atms2[random.randint(0,len(atms2)-1)])
indi1.pop(random.randint(0,len(indi1)-2))
else:
if len(atms2)==0:
indi2.append(atms1[random.randint(0,len(atms1)-1)])
indi2.pop(random.randint(0,len(indi2)-2))
indi1.rotate(rax,a=-1*rang,center='COM', rotate_cell=False)
indi2.rotate(rax,a=-1*rang,center='COM', rotate_cell=False)
indi1.translate(com1)
indi2.translate(com2)
if Optimizer.structure != 'Defect':
cm = indi1.get_center_of_mass()
cell = numpy.maximum.reduce(indi1.get_cell())
cop = [cell[0]/float(2), cell[1]/float(2), cell[2]/float(2)]
indi1.translate(-1*cm)
indi1.translate(cop)
cm = indi2.get_center_of_mass()
cell = numpy.maximum.reduce(indi2.get_cell())
cop = [cell[0]/float(2), cell[1]/float(2), cell[2]/float(2)]
indi2.translate(-1*cm)
indi2.translate(cop)
ind1[0]=indi1
ind2[0]=indi2
#Check structure and number of atoms in crystal
if Optimizer.structure=='Defect':
solid1=Atoms()
solid1.extend(ind1[0])
solid1.extend(ind1.bulki)
solid2=Atoms()
solid2.extend(ind1[0])
solid2.extend(ind2.bulki)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in solid1 if atm.symbol==sym])
Optimizer.output.write('CX ROTCT: CIBS 1 configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n')
nc=len([atm for atm in solid2 if atm.symbol==sym])
Optimizer.output.write('CX ROTCT: CIBS 2 configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n')
return ind1, ind2
def randalloybox(ind1, ind2, Optimizer):
"""Select a box in the alloy configuration
*** Note: CX may be obsolete. In development ***
"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
if Optimizer.structure != 'Defect':
Optimizer.output.write(
'WARNING: Box Random alloy Cx attempted on nondefect structure. SKIPPING CX.\n'
)
else:
Optimizer.output.write('Box Random alloy Cx between individual ' +
repr(ind1.index) + ' and individual ' +
repr(ind2.index) + '\n')
#Perserve starting conditions of individual
indi1 = ind1[0].copy()
indi2 = ind2[0].copy()
cell1 = numpy.maximum.reduce(indi1.get_cell())
cell2 = numpy.maximum.reduce(indi2.get_cell())
cell = numpy.minimum(cell1, cell2)
pbc1 = indi1.get_pbc()
pbc2 = indi2.get_pbc()
#Build solids
solid1 = indi1.copy()
solid1.extend(ind1.bulki.copy())
solid2 = indi2.copy()
solid2.extend(ind2.bulki.copy())
#Get starting concentrations and number of atoms
nat1 = len(solid1)
nat2 = len(solid2)
symlist = list(set(solid1.get_chemical_symbols()))
#Assumes same types of atoms in both solid1 and solid2
concent1 = []
concent2 = []
for one in symlist:
atmss = [atm for atm in solid1 if atm.symbol == one]
concent1.append(len(atmss))
atmss = [atm for atm in solid2 if atm.symbol == one]
concent2.append(len(atmss))
# Pick a origin point for box in the cell
#pt=[random.uniform(0,cell[0]),random.uniform(0,cell[1]),random.uniform(0,cell[2])]
pt1 = solid1[0].position
pt2 = solid2[0].position
#Find max radius of circle cut
r1 = min([
min(cell1[0] - pt1[0], pt1[0]),
min(cell1[1] - pt1[1], pt1[1]),
min(cell1[2] - pt1[2], pt1[2])
])
r2 = min([
min(cell2[0] - pt2[0], pt2[0]),
min(cell2[1] - pt2[1], pt2[1]),
min(cell2[2] - pt2[2], pt2[2])
])
r = min(r1, r2)
mcell = min(cell)
if r > mcell * 0.125:
r = mcell * 0.125
if debug:
Optimizer.output.write('Radius of box = ' + repr(r) +
'\nPosition in solid1 = ' + repr(pt1) +
'\nPosition in solid2 = ' + repr(pt2) +
'\n')
#Find atoms within sphere of radius r
solid1.append(Atom(position=pt1))
dist1 = []
blist1 = []
for i in range(len(solid1) - 1):
d = solid1.get_distance(i, len(solid1) - 1)
if d < r:
dist1.append((d, solid1[i]))
else:
blist1.append((d, solid1[i]))
solid1.pop()
solid2.append(Atom(position=pt2))
dist2 = []
blist2 = []
for i in range(len(solid2) - 1):
d = solid2.get_distance(i, len(solid2) - 1)
if d < r:
dist2.append((d, solid2[i]))
else:
blist2.append((d, solid2[i]))
solid2.pop()
#Translate spheres to opposite location
dats1 = Atoms()
for d, atm in dist1:
dats1.append(atm)
dats1.translate(-pt1)
dats1.translate(pt2)
dats2 = Atoms()
for d, atm in dist2:
dats2.append(atm)
dats2.translate(-pt2)
dats2.translate(pt1)
#Exchange atoms in sphere and build new solids
nsolid1 = dats2.copy()
for d, atm in blist1:
nsolid1.append(atm)
nsolid2 = dats1.copy()
for d, atm in blist2:
nsolid2.append(atm)
#Identify new number of atoms
nnat1 = len(nsolid1)
nnat2 = len(nsolid2)
if nnat1 > nat1:
ds = []
#More atoms in new solid1 means solid2 has less atoms
#Need to transfer atoms from solid1 to solid2
#Find atoms that are too close
for i in range(len(dist2)):
for j in range(len(dist2), len(nsolid1)):
ds.append((nsolid1.get_distance(i, j), i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one: one[0])
diff = nnat1 - nat1
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid1 = Atoms()
for i in range(len(nsolid1)):
if i not in exchangeindices:
nnsolid1.append(nsolid1[i])
nnsolid2 = nsolid2.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [
random.uniform(pt2[0] - r / (2**0.5),
pt2[0] + r / (2**0.5)),
random.uniform(pt2[1] - r / (2**0.5),
pt2[1] + r / (2**0.5)),
random.uniform(pt2[2] - r / (2**0.5),
pt2[2] + r / (2**0.5))
]
nnsolid2.append(
Atom(symbol=nsolid1[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
elif nnat1 < nat1:
ds = []
#More atoms in new solid2 means solid1 has less atoms
#Need to transfer atoms from solid2 to solid1
#Find atoms that are too close
for i in range(len(dist1)):
for j in range(len(dist1), len(nsolid2)):
ds.append((nsolid2.get_distance(i, j), i))
#Sort distances by longest to shortest
ds = sorted(ds, key=lambda one: one[0])
diff = nnat2 - nat2
exchangeindices = []
while len(exchangeindices) < diff:
#Grab shortest distance in ds list
d, index = ds.pop()
if index not in exchangeindices:
exchangeindices.append(index)
nnsolid2 = Atoms()
for i in range(len(nsolid2)):
if i not in exchangeindices:
nnsolid2.append(nsolid2[i])
nnsolid1 = nsolid1.copy()
for i in exchangeindices:
#for j in range(3):
# position[j]=nsolid2[i].position[j]-pt1[j]+pt2[j]
position = [
random.uniform(pt1[0] - r / (2**0.5),
pt1[0] + r / (2**0.5)),
random.uniform(pt1[1] - r / (2**0.5),
pt1[1] + r / (2**0.5)),
random.uniform(pt1[2] - r / (2**0.5),
pt1[2] + r / (2**0.5))
]
nnsolid1.append(
Atom(symbol=nsolid2[i].symbol, position=position))
nsolid1 = nnsolid1.copy()
nsolid2 = nnsolid2.copy()
#Number of atoms in each individual should now be preserved
if Optimizer.forcing == 'Concentration':
#Need to check concentrations
nconcent1 = []
for one in symlist:
atmss = [atm for atm in nsolid1 if atm.symbol == one]
nconcent1.append(len(atmss))
nconcent2 = []
for one in symlist:
atmss = [atm for atm in nsolid2 if atm.symbol == one]
nconcent2.append(len(atmss))
#Let's assume a random perturbation to concentration in order to correct this issue
posd = []
negd = []
for i in range(len(nconcent1)):
diff = nconcent1[i] - concent1[i]
if diff > 0:
posd.append((diff, symlist[i]))
elif diff < 0:
negd.append((diff, symlist[i]))
for c, sym in negd:
while c != 0:
symr = posd[0][1]
rlist = [
atm.index for atm in nsolid1 if atm.symbol == symr
]
index1 = random.choice(rlist)
nsolid1[index1].symbol = sym
c += 1
posd[0] = (posd[0][0] - 1, posd[0][1])
if posd[0][0] == 0:
posd = posd[1::]
#Do the same for solid2
posd = []
negd = []
for i in range(len(nconcent2)):
diff = nconcent2[i] - concent2[i]
if diff > 0:
posd.append((diff, symlist[i]))
elif diff < 0:
negd.append((diff, symlist[i]))
for c, sym in negd:
while c != 0:
symr = posd[0][1]
rlist = [
atm.index for atm in nsolid2 if atm.symbol == symr
]
index1 = random.choice(rlist)
nsolid2[index1].symbol = sym
c += 1
posd[0] = (posd[0][0] - 1, posd[0][1])
if posd[0][0] == 0:
posd = posd[1::]
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1, 'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2, 'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym, c, m, u in Optimizer.atomlist:
nc = len([atm for atm in nsolid1 if atm.symbol == sym])
Optimizer.output.write('CX(randalloybx):New solid1 contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
nc = len([atm for atm in nsolid2 if atm.symbol == sym])
Optimizer.output.write('CX(randalloybx):New solid2 contains ' +
repr(nc) + ' ' + repr(sym) + ' atoms\n')
if Optimizer.forcing != 'Concentration':
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in nsolid1
if inds.symbol == Optimizer.atomlist[i][0]
]
atms2 = [
inds for inds in nsolid2
if inds.symbol == Optimizer.atomlist[i][0]
]
if len(atms1) == 0:
if len(atms2) == 0:
nsolid1[random.randint(
0,
len(indi1) - 1)].symbol = Optimizer.atomlist[i][0]
nsolid2[random.randint(
0,
len(indi2) - 1)].symbol = Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0,
len(atms2) - 1)])
nsolid1.pop(random.randint(0, len(nsolid1) - 2))
else:
if len(atms2) == 0:
nsolid2.append(atms1[random.randint(0,
len(atms1) - 1)])
nsolid2.pop(random.randint(0, len(nsolid2) - 2))
nsolid1.set_cell(cell1)
nsolid2.set_cell(cell2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
outs = find_defects(nsolid1,
Optimizer.solidbulk,
Optimizer.sf,
atomlistcheck=Optimizer.atomlist,
trackvacs=Optimizer.trackvacs,
trackswaps=Optimizer.trackswaps,
debug=False)
ind1[0] = outs[0].copy()
ind1.bulki = outs[1].copy()
ind1.vacancies = outs[2].copy()
ind1.swaps = outs[3].copy()
outs = find_defects(nsolid2,
Optimizer.solidbulk,
Optimizer.sf,
atomlistcheck=Optimizer.atomlist,
trackvacs=Optimizer.trackvacs,
trackswaps=Optimizer.trackswaps,
debug=False)
ind2[0] = outs[0].copy()
ind2.bulki = outs[1].copy()
ind2.vacancies = outs[2].copy()
ind2.swaps = outs[3].copy()
return ind1, ind2
def newclus(ind1, ind2, Optimizer):
"""Select a box in the cluster configuration"""
if 'CX' in Optimizer.debug:
debug = True
else:
debug = False
Optimizer.output.write('Box Cluster Cx between individual '+repr(ind1.index)+' and individual '+repr(ind2.index)+'\n')
#Perserve starting conditions of individual
solid1 = ind1[0].copy()
solid2 = ind2[0].copy()
cello1 = ind1[0].get_cell()
cello2 = ind2[0].get_cell()
cell1 = numpy.maximum.reduce(solid1.get_positions())
cell1m = numpy.minimum.reduce(solid1.get_positions())
cell2 = numpy.maximum.reduce(solid2.get_positions())
cell2m = numpy.minimum.reduce(solid2.get_positions())
cell = numpy.minimum(cell1,cell2)
pbc1 = solid1.get_pbc()
pbc2 = solid2.get_pbc()
#Get starting concentrations and number of atoms
nat1 = len(solid1)
nat2 = len(solid2)
# Pick a origin point for box in the cell
pt1 = random.choice(solid1)
pt1f = [(pt1.position[i]-cell1m[i])/cell1[i] for i in range(3)]
pt2 = [pt1f[i]*cell2[i]+cell2m[i] for i in range(3)]
solid2.append(Atom(position=pt2))
pt2=solid2[len(solid2)-1]
#Find max neighborsize of circle cut
r = random.uniform(0,min(nat1,nat2)/5.0)
if debug:
print 'DEBUG CX: Point one =', pt1.position
print 'DEBUG CX: Point two =', pt2.position
#Find atoms within sphere of neighborsize r for both individuals
#Make sure that crossover is only selection of atoms not all
while True:
ctoff = [r for on in solid1]
nl = NeighborList(ctoff, bothways=True, self_interaction=False)
nl.update(solid1)
indices1, offsets = nl.get_neighbors(pt1.index)
if len(indices1)==0:
r = r*1.2
elif len(indices1) < nat1*.75:
break
else:
r = r*0.8
if debug:
print 'Neighborsize of box = '+repr(r)+'\nPosition in solid1 = '+repr(pt1.position)+'\nPosition in solid2 = '+repr(pt2.position)
group1 = Atoms(cell=solid1.get_cell(),pbc=solid1.get_pbc())
group1.append(pt1)
indices1a=[pt1.index]
for index, d in zip(indices1,offsets):
if index not in indices1a:
index = int(index)
pos = solid1[index].position + numpy.dot(d,solid1.get_cell())
group1.append(Atom(symbol=solid1[index].symbol,position=pos))
indices1a.append(index)
indices1=indices1a
ctoff = [r for on in solid2]
nl = NeighborList(ctoff, bothways=True, self_interaction=False)
nl.update(solid2)
indices2, offsets = nl.get_neighbors(pt2.index)
group2 = Atoms(cell=solid2.get_cell(),pbc=solid2.get_pbc())
indices2a = []
for index, d in zip(indices2,offsets):
if index not in indices2a:
index = int(index)
pos = solid2[index].position + numpy.dot(d,solid2.get_cell())
group2.append(Atom(symbol=solid2[index].symbol,position=pos))
indices2a.append(index)
indices2=indices2a
if len(indices2)==0:
for one in group1:
while True:
sel = random.choice(solid2)
if sel.symbol==one.symbol:
if sel.index not in indices2:
group2.append(sel)
indices2.append(sel.index)
break
if Optimizer.forcing=='Concentration':
symlist = list(set(group1.get_chemical_symbols()))
seplist = [[atm for atm in group2 if atm.symbol == sym] for sym in symlist]
group2n=Atoms(cell=group2.get_cell(),pbc=group2.get_pbc())
indices2n = []
dellist = []
for one in group1:
sym1=one.symbol
listpos=[i for i,s in enumerate(symlist) if s==sym1][0]
if len(seplist[listpos]) > 0:
pos = random.choice(range(len(seplist[listpos])))
group2n.append(seplist[listpos][pos])
indices2n.append(indices2[seplist[listpos][pos].index])
del seplist[listpos][pos]
else:
dellist.append(one.index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
indices2n.append(pt2.index)
indices2=indices2n
group2=group2n.copy()
else:
dellist = []
while len(group2) < len(group1)-len(dellist):
#Too many atoms in group 1
dellist.append(random.choice(group1).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group1[one]
del indices1[one]
dellist = []
while len(group1) < len(group2)-len(dellist):
#Too many atoms in group 2
dellist.append(random.choice(group2).index)
if len(dellist) != 0:
dellist.sort(reverse=True)
for one in dellist:
del group2[one]
del indices2[one]
other2 = Atoms(cell=solid2.get_cell(),pbc=solid2.get_pbc())
for one in solid2:
if one.index not in indices2:
other2.append(one)
other1 = Atoms(cell=solid1.get_cell(),pbc=solid1.get_pbc())
for one in solid1:
if one.index not in indices1:
other1.append(one)
#Exchange atoms in sphere and build new solids
nsolid1 = other1.copy()
nsolid1.extend(group2.copy())
nsolid2 = other2.copy()
nsolid2.extend(group1.copy())
#DEBUG: Write crossover to file
if debug:
write_xyz(Optimizer.debugfile, nsolid1,'CX(randalloybx):nsolid1')
write_xyz(Optimizer.debugfile, nsolid2,'CX(randalloybx):nsolid2')
#DEBUG: Check structure of atoms exchanged
for sym,c,m,u in Optimizer.atomlist:
if Optimizer.structure=='Defect':
nc=len([atm for atm in nsolid1 if atm.symbol==sym])
nc+=len([atm for atm in ind1.bulki if atm.symbol==sym])
oc=len([atm for atm in solid1 if atm.symbol==sym])
oc+=len([atm for atm in ind1.bulki if atm.symbol==sym])
else:
nc=len([atm for atm in nsolid1 if atm.symbol==sym])
oc=len([atm for atm in solid1 if atm.symbol==sym])
Optimizer.output.write('CX(clustbx):New solid1 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if debug: print 'DEBUG CX: New solid1 contains '+repr(nc)+' '+repr(sym)+' atoms'
if oc != nc:
#pdb.set_trace()
print 'CX: Issue in maintaining atom concentration\n Dropping new individual'
Optimizer.output.write('CX: Issue in maintaining atom concentration\n Dropping new individual 1\n')
nsolid1 = solid1
for sym,c,m,u in Optimizer.atomlist:
if Optimizer.structure=='Defect':
nc=len([atm for atm in nsolid2 if atm.symbol==sym])
nc+=len([atm for atm in ind2.bulki if atm.symbol==sym])
oc=len([atm for atm in solid2 if atm.symbol==sym])
oc+=len([atm for atm in ind2.bulki if atm.symbol==sym])
else:
nc=len([atm for atm in nsolid2 if atm.symbol==sym])
oc=len([atm for atm in solid2 if atm.symbol==sym])
Optimizer.output.write('CX(clustbx):New solid2 contains '+repr(nc)+' '+repr(sym)+' atoms\n')
if debug: print 'DEBUG CX: New solid2 contains '+repr(nc)+' '+repr(sym)+' atoms'
if oc != nc:
#pdb.set_trace()
print 'CX: Issue in maintaining atom concentration\n Dropping new individual'
Optimizer.output.write('CX: Issue in maintaining atom concentration\n Dropping new individual 2\n')
solid2.pop()
nsolid2 = solid2
if Optimizer.forcing !='Concentration':
for i in range(len(Optimizer.atomlist)):
atms1=[inds for inds in nsolid1 if inds.symbol==Optimizer.atomlist[i][0]]
atms2=[inds for inds in nsolid2 if inds.symbol==Optimizer.atomlist[i][0]]
if len(atms1)==0:
if len(atms2)==0:
nsolid1[random.randint(0,len(indi1)-1)].symbol==Optimizer.atomlist[i][0]
nsolid2[random.randint(0,len(indi2)-1)].symbol==Optimizer.atomlist[i][0]
else:
nsolid1.append(atms2[random.randint(0,len(atms2)-1)])
nsolid1.pop(random.randint(0,len(nsolid1)-2))
else:
if len(atms2)==0:
nsolid2.append(atms1[random.randint(0,len(atms1)-1)])
nsolid2.pop(random.randint(0,len(nsolid2)-2))
nsolid1.set_cell(cello1)
nsolid2.set_cell(cello2)
nsolid1.set_pbc(pbc1)
nsolid2.set_pbc(pbc2)
ind1[0]=nsolid1.copy()
ind2[0]=nsolid2.copy()
return ind1, ind2