def new_by_switch_atoms_on_substrate(ind_in: Individual):
# returns individual made by switch of two random atoms on particular substrate
struct = ind_in.get_relaxed_structure().copy()
substrate = read_vasp("POSCAR.substrate")
s = surface(substrate, (0, 0, 1), 1, vacuum=0., tol=1e-10)
cell = s.get_cell()
cell[2][2] = 25.
s.set_cell(cell)
z_max = -100.
positions = s.get_positions()
for pos in positions:
z = pos[2]
if z > z_max:
z_max = z
# print("z_max", z_max)
chem_sym = struct.get_chemical_symbols()
Nat = len(chem_sym)
flag = 0
while flag == 0:
indx1 = randrange(Nat)
indx2 = randrange(Nat)
z1 = struct.get_positions()[indx1][2]
z2 = struct.get_positions()[indx2][2]
# print(z1,z2)
if indx2 != indx1 and chem_sym[indx1] != chem_sym[
indx2] and z1 > z_max and z2 > z_max:
# print(indx1,indx2)
chem_sym_new = swap_positions(chem_sym, indx1, indx2)
struct.set_chemical_symbols(chem_sym_new)
flag = 1
ind = Individual(struct, -1)
return ind
def new_by_shift_coordinate(ind_in: Individual):
# returns individual made by random change of one coordinate
struct = ind_in.get_relaxed_structure().copy()
Nat = len(struct.get_chemical_symbols())
positions = struct.get_scaled_positions()
delta = uniform(-0.1, 0.1)
indx_at = randrange(Nat)
indx_coord = randrange(3)
positions[indx_at][indx_coord] = positions[indx_at][indx_coord] + delta
struct.set_scaled_positions(positions)
ind = Individual(struct)
return ind
def init_population_random_on_substrate(self):
print("generating initial population on substrate randomly ...")
population = []
i = 1
while i <= self.Npop:
struct = random_structure_on_substrate(self.chem_form, self.amin,
self.amax, self.dmin,
self.model_file)
individual = Individual(struct)
individual.origin = "new ind. random on substrate from scratch"
population.append(individual)
i = i + 1
return population
def get_population_db(dbfile, ngen):
population = []
conn = sqlite3.connect(dbfile)
cur = conn.cursor()
cur.execute("SELECT * FROM individuals WHERE ngen=?", [ngen])
rows = cur.fetchall()
for row in rows:
struct = pickle.loads(row[4])
ind = Individual(struct)
population.append(ind)
return population
def get_best_individual(population):
e_tot_min = 0.
for ind in population:
try:
e_tot = ind.e_tot
struct = ind.get_relaxed_structure()
except:
e_tot = 1000.
if e_tot < e_tot_min:
struct_best = struct
e_tot_min = e_tot
print("e_tot_min: " + str(e_tot_min))
individual = Individual(struct_best)
return individual
def new_by_switch_atoms(ind_in: Individual):
# returns individual made by switch of two random atoms
struct = ind_in.get_relaxed_structure().copy()
chem_sym = struct.get_chemical_symbols()
Nat = len(chem_sym)
if Nat > 2:
indx1 = randrange(Nat)
flag = 0
while flag == 0:
indx2 = randrange(Nat)
if indx2 != indx1 and chem_sym[indx1] != chem_sym[indx2]:
chem_sym_new = swap_positions(chem_sym, indx1, indx2)
struct.set_chemical_symbols(chem_sym_new)
flag = 1
ind = Individual(struct, -1)
return ind
def new_by_shift_coordinates(ind_in: Individual):
# returns individual made by random change of x,y coordinates by random delta
struct = ind_in.get_relaxed_structure().copy()
Nat = len(struct.get_chemical_symbols())
positions = struct.get_scaled_positions()
delx = uniform(0., 0.2)
dely = uniform(0., 0.2)
indx1 = randrange(Nat)
indx2 = indx1
while indx2 == indx1:
indx2 = randrange(Nat)
positions[indx1][0] = positions[indx1][0] + delx
positions[indx1][1] = positions[indx1][1] + dely
positions[indx2][0] = positions[indx2][0] - delx
positions[indx2][1] = positions[indx2][1] - dely
struct.set_scaled_positions(positions)
ind = Individual(struct, -1)
return ind
def init_population_random(self, model=1):
# inits random population with model verification, returns list of individuals
# verification regards "bad" struxtures
print("generating initial population randomly ...")
population = []
i = 1
while i <= self.Npop:
if model == 0:
struct = random_structure(self.chem_form, self.amin, self.amax,
self.dmin)
if model == 1:
struct = random_structure_model(self.chem_form, self.amin,
self.amax, self.dmin,
self.model_file)
individual = Individual(struct)
individual.origin = "new ind. random from scratch"
population.append(individual)
i = i + 1
return population
def new_by_random_coordinates(ind_in: Individual):
# returns individual made by changing all coordinates randomly (cell is intact)
struct = ind_in.get_relaxed_structure().copy()
Nat = len(struct.get_chemical_symbols())
flag = 0
while flag == 0:
positions = []
#
for i in range(Nat):
pos = [uniform(0., 0.90), uniform(0., 0.90), uniform(-0.1, 0.1)]
positions.append(pos)
#
struct.set_scaled_positions(positions)
positions_ang = struct.get_positions()
# print(positions_ang)
flag = check_dist(Nat, positions_ang, dmin=1.4)
# print(flag)
# print(struct)
ind = Individual(struct, -1)
return ind
def init_population_random_group(self):
# inits pyxtal random population with model verification, returns list of individuals
print(
"generating initial population randomly but using group theory ..."
)
population = []
i = 1
while i <= self.Npop:
struct = random_structure_group(self.chem_sym,
self.stoichio,
thickness=3.0,
tol_factor=0.9,
model_file=self.model_file,
dmin=self.dmin,
Natt=100)
individual = Individual(struct)
individual.origin = "new ind. random from scratch"
population.append(individual)
i = i + 1
return population
def get_c2db_prototypes(dbfile,
prototype,
stability=False,
smagstate=False,
sgap=0):
# returns list of Individuals from c2db
# Connect to the database - ase interface
db = ase.db.connect(dbfile)
# Connect to the database - sqlite3 interface
conn = sqlite3.connect(dbfile)
cur = conn.cursor()
cur.execute('SELECT SQLITE_VERSION()')
data = cur.fetchone()
print("SQLite version: " + str(format(data)))
# nstruct = 0
# magstate = 'FM'
dyn_key = 'dynamic_stability_level'
th_key = 'thermodynamic_stability_level'
# gap_key = 'gap'
# rows = db.select('magstate=FM')
if prototype != "":
query = 'class=' + prototype
# print(query)
rows = db.select(query)
if prototype == "":
# rows = db.select('calculator=gpaw')
rows = db.select('gap>-1')
print(rows)
individuals = []
for row in rows:
id = row.get("id")
e_tot = row.get("energy")
label = row.get('formula')
gap = row.get('gap')
#print(gap)
magstate = row.get('magstate')
magmom = row.get('magmom')
positions = row.get('positions')
cell = row.get('cell')
hform = row.get('hform')
e_tot = row.get('energy')
# Stability info - not implemented is ase interface
cur.execute(
"SELECT * FROM number_key_values WHERE id=:id AND key=:dyn_key", {
"id": id,
"dyn_key": dyn_key
})
data = cur.fetchone()
if data is not None:
stability_dyn = data[1]
else:
stability_dyn = 0.
cur.execute(
"SELECT * FROM number_key_values WHERE id=:id AND key=:th_key", {
"id": id,
"th_key": th_key
})
data = cur.fetchone()
if data is not None:
stability_th = data[1]
else:
stability_th = 0.
if stability == False:
struct_ase = Atoms(label,
positions=positions,
cell=cell,
pbc=np.array([True, True, True], dtype=bool))
Nat = len(struct_ase.get_chemical_symbols())
ind = Individual(struct_ase)
ind.set_e_tot(e_tot / float(Nat))
ind.set_mmtot(magmom)
ind.set_hform(hform)
individuals.append(ind)
if stability == True and smagstate == False and sgap == 0:
if stability_th == 3.0:
struct_ase = Atoms(label,
positions=positions,
cell=cell,
pbc=np.array([True, True, True],
dtype=bool))
Nat = len(struct_ase.get_chemical_symbols())
ind = Individual(struct_ase)
ind.set_e_tot(e_tot / float(Nat))
ind.set_mmtot(magmom)
ind.set_hform(hform)
individuals.append(ind)
if stability == True and smagstate == False and sgap > 0:
if stability_th == 3.0 and gap > 0.:
struct_ase = Atoms(label,
positions=positions,
cell=cell,
pbc=np.array([True, True, True],
dtype=bool))
Nat = len(struct_ase.get_chemical_symbols())
ind = Individual(struct_ase)
ind.set_e_tot(e_tot / float(Nat))
ind.set_mmtot(magmom)
ind.set_hform(hform)
individuals.append(ind)
if stability == True and smagstate == True and smagstate == "FM":
if stability_dyn == 3.0 and stability_th == 3.0 and abs(
float(magmom)) > 0.1:
struct_ase = Atoms(label,
positions=positions,
cell=cell,
pbc=np.array([True, True, True],
dtype=bool))
Nat = len(struct_ase.get_chemical_symbols())
ind = Individual(struct_ase)
ind.set_e_tot(e_tot / float(Nat))
ind.set_mmtot(magmom)
ind.set_hform(hform)
individuals.append(ind)
return individuals
def new_by_switch_layers(ind_in: Individual):
# returns individual made by switch of two random layers
struct = ind_in.get_relaxed_structure().copy()
write(filename="POSCAR.in.in", images=struct, format="espresso-in")
layers = get_layers(struct)
nlay = len(layers)
if nlay > 1:
# random indexes
indx1 = randrange(nlay)
flag = 0
while flag == 0:
indx2 = randrange(nlay)
if indx2 != indx1:
flag = 1
layer1 = layers[indx1]
layer2 = layers[indx2]
print("switching layers " + str(indx1 + 1) + " and " + str(indx2 + 1))
pos = struct.get_positions()
chem = struct.get_chemical_symbols()
cell = struct.get_cell()
new_pos = []
new_chem = []
# 1 - setting all other atoms
n = len(chem)
for i in range(n):
if i not in layer1 and i not in layer2:
# print(i)
new_pos.append(pos[i])
new_chem.append(chem[i])
# 2 - calculate shift between layers
z1 = []
z2 = []
for i in layer1:
z = pos[i][2]
z1.append(z)
for i in layer2:
z = pos[i][2]
z2.append(z)
min1 = max(z1)
min2 = max(z2)
zshift = min1 - min2
# 3 - setting layer1 and layer2 atoms with shift
for i in range(n):
if i in layer1:
# print(i)
if min1 > min2:
pos[i][2] = pos[i][2] + zshift
if min1 < min2:
pos[i][2] = pos[i][2] - zshift
new_pos.append(pos[i])
new_chem.append(chem[i])
if i in layer2:
# print(i)
if min1 > min2:
pos[i][2] = pos[i][2] - zshift
if min1 < min2:
pos[i][2] = pos[i][2] + zshift
new_pos.append(pos[i])
new_chem.append(chem[i])
st = ""
for chem in new_chem:
st = st + chem
new_struct = Atoms(st)
new_struct.set_cell(cell)
new_pos2 = np.asarray(new_pos)
new_struct.set_positions(new_pos2)
ind = Individual(new_struct)
write(filename="POSCAR.out.in",
images=new_struct,
format="espresso-in")
else:
ind = Individual(struct)
print("warning: only one layer, no change in structure!")
return ind
def generate_new_population_alg2_substrate(self, population):
# generates new population using algorithm no. 2
print("")
print("generating new population with softmutation ...")
print("")
new_population = []
population.sort()
Npop = self.Npop
adapt = AseAtomsAdaptor()
model = MEGNetModel.from_file(self.model_file)
for i in range(int(Npop / 4)): # 1/4 of population by atoms switch
indx = randrange(Npop /
4) # +1 # using only best 25% of population
print("-------------------------------")
print("new ind. from no. " + str(indx) + " by atoms switch")
individual = new_by_switch_atoms_on_substrate(population[indx])
individual.origin = "new ind. from no. " + str(
indx) + " by atoms switch"
new_population.append(individual)
for i in range(int(Npop /
4)): # 1/4 of population by kind of softmutation
indx = randrange(Npop /
4) # +1 # using only best 25% of population
print("-------------------------------")
print("new ind. from no. " + str(indx) + " by softmutation")
ind_in = population[indx]
structure_ase = ind_in.get_relaxed_structure().copy()
structure_pymatgen = adapt.get_structure(structure_ase)
e_tot_in = model.predict_structure(structure_pymatgen)
e_tot_min = e_tot_in
flag = 0
for i in range(100):
individual = new_by_shift_coordinate(population[indx])
structure_ase = individual.get_init_structure().copy()
structure_pymatgen = adapt.get_structure(structure_ase)
try:
e_tot = model.predict_structure(structure_pymatgen)
except:
e_tot = 0.
print("isolated molecule exception handled")
if e_tot < e_tot_min:
flag = 1
e_tot_min = e_tot
ind_out = individual
ind_out.origin = "new ind. from no. " + str(
indx) + " by softmutation"
if flag == 1:
new_population.append(ind_out)
print("softmutate energy gain: " + str(e_tot_min - e_tot_in))
if flag == 0:
new_population.append(ind_in)
for i in range(int((Npop / 2) - 1)):
# 1/2 of population (minus one) by new random structures, pyxtal+model
# indx = randrange(Npop/2)+1
print("-------------------------------")
print("new ind. random from scratch")
struct = random_structure_group(self.chem_sym,
self.stoichio,
thickness=3.0,
tol_factor=0.9,
model_file=self.model_file,
dmin=self.dmin,
Natt=RANDOM_ATTEMPTS)
individual = Individual(struct)
individual.origin = "new ind. random from scratch"
new_population.append(individual)
best_ind = get_best_individual(
population) # last one is the best in the current population
best_ind.origin = "kept best"
new_population.append(best_ind)
return new_population