def mate(parent1, parent2, fit1, fit2, surfGA=False):
"""
Randomly selected clusters from tournament selection are passed:
1. If gas-phase, rotate randomly the clusters.
2. Weighted cut of the clusters in a plane
perpendicular to the surface.
3. Join parts and repare overlaps.
"""
compositionWrong = True
clus1 = parent1
clus2 = parent2
while compositionWrong:
if surfGA == False:
angle = ran.randint(1, 180)
axis = ran.choice(['x', 'y', 'z'])
clus1.rotate(angle, axis, center='COM')
clus1 = fixOverlap(clus1)
clus2.rotate(angle, axis, center='COM')
clus2 = fixOverlap(clus2)
child = []
eleNames, eleNums, natoms, _, _ = get_data(clus1)
cut = int(natoms * (fit1 / (fit1 + fit2)))
if cut == 0:
cut = 1
elif cut == natoms:
cut = natoms - 1
for i in range(cut):
child.append(clus1[i])
for j in range(cut, len(clus2)):
child.append(clus2[j])
CheckEle = []
for ele in eleNames:
eleCount = 0
for atom in child:
if atom.symbol == ele:
eleCount += 1
CheckEle.append(eleCount)
if CheckEle == eleNums:
compositionWrong = False
final_child = Atoms(child[0].symbol, positions=[child[0].position])
for i in range(1, len(child)):
c = Atoms(child[i].symbol, positions=[child[i].position])
final_child += c
final_child = fixOverlap(final_child)
parent1 = final_child
parent2 = parent2
return [parent1, parent2]
def partialInversion(parent):
'''
Choose a fragment with 30% of the cluster atoms
nearest to a randomly chosen atom and invert the
structure with respect to its geometrical center
'''
clus = parent
natoms = len(clus)
CoM(clus)
nInvert = int(round(0.3 * natoms))
mAtom = ran.randrange(natoms)
R0 = clus.get_positions()[mAtom]
clus = sortR0(clus, R0)
fc = np.array([0.0, 0.0, 0.0])
for i in range(nInvert):
r = clus.get_positions()[i]
fc += r / nInvert
new_pos = []
for i in range(nInvert):
ele, x, y, z = clus.get_chemical_symbols()[i], clus.get_positions(
)[i][0], clus.get_positions()[i][1], clus.get_positions()[i][2]
r = np.array([x, y, z])
ri = 2 * fc - r
clus[i].x = ri[0]
clus[i].y = ri[1]
clus[i].z = ri[2]
new_coord = (ri[0], ri[1], ri[2])
clus = fixOverlap(clus)
return clus
def changeCore(parent):
'''
Modify the core
'''
clus = parent
eleNames, eleNums, natoms, stride, eleRadii = get_data(clus)
CoM(clus)
inout = ran.choice(
[1, 2]) #inout = 1 muttpe: + core; inout = 2 muttype: - core
if inout == 1:
nout = int(0.2 * natoms)
if nout < 1:
nout = 1
icenter = ran.randrange(nout) + 1
R0 = [0.0, 0.0, 0.0]
clus = sortR0(clus, R0)
clus[-icenter].position = [0.1, 0.0, 0.0]
clus = fixOverlap(clus)
elif inout == 2:
ncore = int(0.1 * natoms)
if ncore < 1:
ncore = 1
iout = ran.randrange(ncore)
R0 = [0.0, 0.0, 0.0]
clus = sortR0(clus, R0)
del clus[iout]
clus = addAtoms(clus, eleNames, eleNums, eleRadii)
return clus
def tunnel(parent):
'''
Tunnel one of the atoms farthest from the center to
the other side of the cluster
'''
clus = parent
natoms = len(clus)
CoM(clus)
w = []
for atom in clus:
ele = atom.symbol
x, y, z = atom.position
r = np.sqrt(x * x + y * y + z * z)
w.append([r, ele, x, y, z])
w.sort()
for i in range(natoms):
clus[i].symbol = w[i][1]
clus[i].x = w[i][2]
clus[i].y = w[i][3]
clus[i].z = w[i][4]
nat = int(round(0.75 * natoms))
atomNum = ran.randrange(nat, natoms)
x, y, z = clus[atomNum].x, clus[atomNum].y, clus[atomNum].z
clus[atomNum].x, clus[atomNum].y, clus[atomNum].z = -x, -y, -z
clus = fixOverlap(clus)
return clus
def twist(parent):
'''
Twist the cluster
'''
clus = parent
CoM(clus)
clus.rotate('y', 'z', center='COM')
clus = fixOverlap(clus)
return clus
def rotate_mut(parent):
'''
Rotate the cluster by a randomly selected angle over a randomly selected axis
'''
clus = parent
CoM(clus)
angle = ran.randint(1, 180)
axis = ran.choice(['x', 'y', 'z'])
clus.rotate(angle, axis, center='COM')
clus = fixOverlap(clus)
return clus
def rattle_mut(parent):
'''
Fix a third of the atoms, then rattle the rest with a std deviation of 0.01
'''
clus = parent
CoM(clus)
indices = ran.sample(range(len(clus)), int(len(clus) / 3))
const = FixAtoms(indices=indices)
clus.set_constraint(const)
clus.rattle(stdev=0.1)
del clus.constraints
clus = fixOverlap(clus)
return clus
def homotop(parent):
'''
Choose pair of different elements to swap
'''
clus = parent
CoM(clus)
eleNames, eleNums, natoms, stride, eleRadii = get_data(clus)
eles = ran.sample(eleNames, 2)
ele1_index = []
ele2_index = []
for i in clus:
if i.symbol == eles[0]:
ele1_index.append(i.index)
if i.symbol == eles[1]:
ele2_index.append(i.index)
ele1_position = ran.choice(ele1_index)
ele2_position = ran.choice(ele2_index)
clus.positions[[ele1_position, ele2_position
]] = clus.positions[[ele2_position, ele1_position]]
clus = fixOverlap(clus)
return clus