def get_population(Optimizer):
"""
Function to generate a population of structures.
Inputs:
Optimizer = structopt Optimizer class object
Outputs:
pop = List of structopt Individual class objects containing new structures.
"""
index1 = 0
pop = []
for i in range(Optimizer.nindiv):
if Optimizer.structure == 'Defect':
individ = get_defect_indiv(Optimizer)
elif Optimizer.structure == 'Surface':
individ = get_surface_indiv(Optimizer)
elif Optimizer.structure == 'Crystal':
individ = get_crystal_indiv(Optimizer)
else:
if 'sphere' in Optimizer.generate_flag:
ind = gen_pop_sphere(Optimizer.atomlist,Optimizer.size)
else:
ind = gen_pop_box(Optimizer.atomlist,Optimizer.size)
individ = Individual(ind)
individ.index = index1
if Optimizer.genealogy:
individ.history_index = repr(index1)
Optimizer.output.write('Generated cluster individual with natoms = '+
repr(individ[0].get_number_of_atoms())+'\n')
pop.append(individ)
index1=index1+1
# Generate new atomlist concentrations based on cluster+box
if Optimizer.structure == 'Defect':
if Optimizer.alloy:
concents=[]
for ind in pop:
cs=[]
for sym,c,u,m in Optimizer.atomlist:
sylen=[atm for atm in ind[0] if atm.symbol==sym]
cs.append(len(sylen))
concents.append(cs)
natmlist=[0]*len(Optimizer.atomlist)
for i in range(len(concents[0])):
alls=[cs[i] for cs in concents]
avgall=int(sum(alls)/len(alls))
if avgall>=Optimizer.atomlist[i][1]:
natmlist[i]=(Optimizer.atomlist[i][0], avgall,
Optimizer.atomlist[i][2],Optimizer.atomlist[i][3])
else:
natmlist[i]=(Optimizer.atomlist[i][0], Optimizer.atomlist[i][1],
Optimizer.atomlist[i][2],Optimizer.atomlist[i][3])
else:
natmlist=[0]*len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
atms1=[inds for inds in pop[0][0] if inds.symbol==Optimizer.atomlist[i][0]]
natmlist[i]=(Optimizer.atomlist[i][0], len(atms1),Optimizer.atomlist[i][2],
Optimizer.atomlist[i][3])
Optimizer.atomlist=natmlist
Optimizer.output.write('\n\nNew atomlist concentrations based on cluster+box = '+
repr(Optimizer.atomlist)+'\n')
return pop
Optimizer.output.flush()
Optimizer.nindiv-=1
if successflag:
Optimizer.output.write('Found good individual = {0}\n'.format(indiv))
if Optimizer.structure == 'Defect':
individ = get_defect_restart_indiv(Optimizer,indiv)
elif Optimizer.structure == 'Surface':
individ = get_surface_restart_indiv(Optimizer, indiv)
else:
cell = indiv.get_cell()
if cell[0][0] == 1.0:
indiv.set_cell([Optimizer.size,Optimizer.size,Optimizer.size])
individ = Individual(indiv)
individ.index = index1
if Optimizer.genealogy:
individ.history_index = repr(index1)
pop.append(individ)
index1 = index1+1
if len(pop) == 0:
raise RuntimeError('Unable to load any structures for Restart')
# Generate new atomlist concentrations based on cluster+box
if Optimizer.structure == 'Defect':
if Optimizer.alloy:
concents=[]
for ind in pop:
cs=[]
for sym,c,u,m in Optimizer.atomlist:
sylen=[atm for atm in ind[0] if atm.symbol==sym]
cs.append(len(sylen))
concents.append(cs)
natmlist=[0]*len(Optimizer.atomlist)
Optimizer.output.flush()
Optimizer.nindiv -= 1
if successflag:
Optimizer.output.write(
'Found good individual = {0}\n'.format(indiv))
if Optimizer.structure == 'Defect':
individ = get_defect_restart_indiv(Optimizer, indiv)
elif Optimizer.structure == 'Surface':
individ = get_surface_restart_indiv(Optimizer, indiv)
else:
indiv.set_cell(
[Optimizer.size, Optimizer.size, Optimizer.size])
individ = Individual(indiv)
individ.index = index1
if Optimizer.genealogy:
individ.history_index = repr(index1)
pop.append(individ)
index1 = index1 + 1
if len(pop) == 0:
raise RuntimeError('Unable to load any structures for Restart')
# Generate new atomlist concentrations based on cluster+box
if Optimizer.structure == 'Defect':
if Optimizer.alloy:
concents = []
for ind in pop:
cs = []
for sym, c, u, m in Optimizer.atomlist:
sylen = [atm for atm in ind[0] if atm.symbol == sym]
cs.append(len(sylen))
concents.append(cs)
natmlist = [0] * len(Optimizer.atomlist)
def read_individual(indivfile, n=-1):
"""Function to write the data of an individual class object to a flat file
Input:
indivfile = String or fileobject for file to be read from
n = which individual from file to return. Default is last individual written.
optional All
Output:
returns an individual class object or list of individual class objects depending on value of n
"""
if isinstance(indivfile, str):
indivfile = open(indivfile, 'r')
all_lines = indivfile.readlines()
indivfile.close()
linen = 0
all_indivs = []
while linen < len(all_lines):
if '----------' in all_lines[linen]:
individ = Individual(Atoms())
elif 'Structure information' in all_lines[linen]:
natomstruct = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natomstruct):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ = Individual(atomstruct)
linen += 2 + natomstruct
elif 'structure cell' in all_lines[linen]:
cell_line = all_lines[linen].split('=')
structcell = eval(cell_line[1])
individ[0].set_cell(structcell)
elif 'fitness' in all_lines[linen]:
fitline = all_lines[linen].split('=')
individ.fitness = float(fitline[1])
elif 'history_index' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.history_index = line[1].strip()
elif 'index' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.index = float(line[1])
elif 'tenergymx' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.tenergymx = float(line[1])
elif 'tenergymin' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.tenergymin = float(line[1])
elif 'energy' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.energy = float(line[1])
elif 'pressure' in all_lines[linen]:
line = all_lines[linen].split('=')
# HKK 05-21-2015:: Occassionally found 'Null' pressure during VASP-GA. Need investigation, but setting to 0 pressure for now.
if line[1] and line[1].strip():
individ.pressure = float(line[1])
else:
individ.pressure = 0.0
elif 'volume' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.volume = float(line[1])
elif 'force' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.force = float(line[1])
elif 'purebulkenpa' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.purebulkenpa = float(line[1])
elif 'natomsbulk' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.natomsbulk = float(line[1])
elif 'fingerprint' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.fingerprint = eval(line[1])
elif 'swpalist' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.swaplist = eval(line[1])
elif 'bulki cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.bulki.set_cell(cell)
elif 'bulki' in all_lines[linen]:
natoms = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ.bulki = atomstruct.copy()
linen += 2 + natoms
elif 'bulko cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.bulko.set_cell(cell)
elif 'bulko' in all_lines[linen]:
natoms = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ.bulko = atomstruct.copy()
linen += 2 + natoms
elif 'box cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.box.set_cell(cell)
elif 'box' in all_lines[linen]:
natoms = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ.box = atomstruct.copy()
linen += 2 + natoms
elif 'vacancies cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.vacancies.set_cell(cell)
elif 'vacancies' in all_lines[linen]:
natoms = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ.vacancies = atomstruct.copy()
linen += 2 + natoms
elif 'swaps cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.swaps.set_cell(cell)
elif 'swaps' in all_lines[linen]:
natoms = int(all_lines[linen + 1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen + i + 3].split()
sym = a[0]
position = [float(a[1]), float(a[2]), float(a[3])]
atomstruct.append(Atom(symbol=sym, position=position))
individ.swaps = atomstruct.copy()
linen += 2 + natoms
elif 'Finish' in all_lines[linen]:
all_indivs.append(individ.duplicate())
linen += 1
if n == 'All':
return all_indivs
else:
return all_indivs[n]
def get_population(Optimizer):
"""
Function to generate a population of structures.
Inputs:
Optimizer = structopt Optimizer class object
Outputs:
pop = List of structopt Individual class objects containing new structures.
"""
index1 = 0
pop = []
for i in range(Optimizer.nindiv):
if Optimizer.structure == 'Defect':
individ = get_defect_indiv(Optimizer)
elif Optimizer.structure == 'Surface':
individ = get_surface_indiv(Optimizer)
elif Optimizer.structure == 'Crystal':
individ = get_crystal_indiv(Optimizer)
else:
if 'sphere' in Optimizer.generate_flag:
ind = gen_pop_sphere(Optimizer.atomlist, Optimizer.size)
else:
ind = gen_pop_box(Optimizer.atomlist, Optimizer.size)
individ = Individual(ind)
individ.index = index1
if Optimizer.genealogy:
individ.history_index = repr(index1)
Optimizer.output.write('Generated cluster individual with natoms = ' +
repr(individ[0].get_number_of_atoms()) + '\n')
pop.append(individ)
index1 = index1 + 1
# Generate new atomlist concentrations based on cluster+box
if Optimizer.structure == 'Defect':
if Optimizer.alloy:
concents = []
for ind in pop:
cs = []
for sym, c, u, m in Optimizer.atomlist:
sylen = [atm for atm in ind[0] if atm.symbol == sym]
cs.append(len(sylen))
concents.append(cs)
natmlist = [0] * len(Optimizer.atomlist)
for i in range(len(concents[0])):
alls = [cs[i] for cs in concents]
avgall = int(sum(alls) / len(alls))
if avgall >= Optimizer.atomlist[i][1]:
natmlist[i] = (Optimizer.atomlist[i][0], avgall,
Optimizer.atomlist[i][2],
Optimizer.atomlist[i][3])
else:
natmlist[i] = (Optimizer.atomlist[i][0],
Optimizer.atomlist[i][1],
Optimizer.atomlist[i][2],
Optimizer.atomlist[i][3])
else:
natmlist = [0] * len(Optimizer.atomlist)
for i in range(len(Optimizer.atomlist)):
atms1 = [
inds for inds in pop[0][0]
if inds.symbol == Optimizer.atomlist[i][0]
]
natmlist[i] = (Optimizer.atomlist[i][0], len(atms1),
Optimizer.atomlist[i][2],
Optimizer.atomlist[i][3])
Optimizer.atomlist = natmlist
Optimizer.output.write(
'\n\nNew atomlist concentrations based on cluster+box = ' +
repr(Optimizer.atomlist) + '\n')
return pop
def read_individual(indivfile, n=-1):
"""Function to write the data of an individual class object to a flat file
Input:
indivfile = String or fileobject for file to be read from
n = which individual from file to return. Default is last individual written.
optional All
Output:
returns an individual class object or list of individual class objects depending on value of n
"""
if isinstance(indivfile, str):
indivfile=open(indivfile, 'r')
all_lines = indivfile.readlines()
indivfile.close()
linen = 0
all_indivs = []
while linen < len(all_lines):
if '----------' in all_lines[linen]:
individ = Individual(Atoms())
elif 'Structure information' in all_lines[linen]:
natomstruct = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natomstruct):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ = Individual(atomstruct)
linen += 2+natomstruct
elif 'structure cell' in all_lines[linen]:
cell_line = all_lines[linen].split('=')
structcell = eval(cell_line[1])
individ[0].set_cell(structcell)
elif 'fitness' in all_lines[linen]:
fitline = all_lines[linen].split('=')
individ.fitness = float(fitline[1])
elif 'history_index' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.history_index = line[1].strip()
elif 'index' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.index = float(line[1])
elif 'tenergymx' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.tenergymx = float(line[1])
elif 'tenergymin' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.tenergymin = float(line[1])
elif 'energy' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.energy = float(line[1])
elif 'pressure' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.pressure = float(line[1])
elif 'volume' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.volume = float(line[1])
elif 'force' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.force = float(line[1])
elif 'purebulkenpa' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.purebulkenpa = float(line[1])
elif 'natomsbulk' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.natomsbulk = float(line[1])
elif 'fingerprint' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.fingerprint = eval(line[1])
elif 'swpalist' in all_lines[linen]:
line = all_lines[linen].split('=')
individ.swaplist = eval(line[1])
elif 'bulki cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.bulki.set_cell(cell)
elif 'bulki' in all_lines[linen]:
natoms = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ.bulki = atomstruct.copy()
linen += 2+natoms
elif 'bulko cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.bulko.set_cell(cell)
elif 'bulko' in all_lines[linen]:
natoms = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ.bulko = atomstruct.copy()
linen += 2+natoms
elif 'box cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.box.set_cell(cell)
elif 'box' in all_lines[linen]:
natoms = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ.box = atomstruct.copy()
linen += 2+natoms
elif 'vacancies cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.vacancies.set_cell(cell)
elif 'vacancies' in all_lines[linen]:
natoms = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ.vacancies = atomstruct.copy()
linen += 2+natoms
elif 'swaps cell' in all_lines[linen]:
line = all_lines[linen].split('=')
cell = eval(line[1])
individ.swaps.set_cell(cell)
elif 'swaps' in all_lines[linen]:
natoms = int(all_lines[linen+1])
atomstruct = Atoms()
for i in range(natoms):
a = all_lines[linen+i+3].split()
sym = a[0]
position = [float(a[1]),float(a[2]),float(a[3])]
atomstruct.append(Atom(symbol=sym,position=position))
individ.swaps = atomstruct.copy()
linen += 2+natoms
elif 'Finish' in all_lines[linen]:
all_indivs.append(individ.duplicate())
linen+=1
if n=='All':
return all_indivs
else:
return all_indivs[n]