def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
entry_id = None
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
comp = self.composition.composition.copy()
#print("Initial composition: %s" % comp)
#print(Composition(comp))
#print(Composition(comp).symbols)
for i in comp:
comp[i] *= factor
new_comp = Composition(comp)
while True:
rnd = random.random()
condition = {
'structure.nspecies': new_comp.nspecies,
'structure.natom': new_comp.natom
}
if self.pcdb_source is None:
rnd = 0
elif len(self.sources[factor]) == 0:
rnd = 0
if self.pcdb_source is None or rnd < random_probability:
pcm_log.debug('Random Structure')
structure = Structure.random_cell(new_comp,
method='stretching',
stabilization_number=5,
nparal=5,
periodic=True)
break
else:
pcm_log.debug('From source')
entry_id = self.sources[factor][np.random.randint(
0, len(self.sources[factor]))]
structure = self.pcdb_source.get_structure(entry_id)
print("chosen structure from database =", structure)
sym = CrystalSymmetry(structure)
scale_factor = float(
np.max(covalent_radius(new_comp.species)) /
np.max(covalent_radius(structure.species)))
reduce_scale = scale_factor**(1. / 3) # WIH
msg = 'Mult: %d natom: %d From source: %s Spacegroup: %d Scaling: %7.3f'
print(msg % (factor, structure.natom, structure.formula,
sym.number(), scale_factor))
# structure.set_cell(np.dot(scale_factor * np.eye(3), structure.cell)) # WIH
structure.set_cell(
np.dot(reduce_scale * np.eye(3), structure.cell)) # WIH
print("symbols before change = ", structure.symbols)
structure.symbols = new_comp.symbols
print("symbols after change = ", structure.symbols)
self.sources[factor].remove(entry_id)
break
return self.new_entry(structure), entry_id
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
comp = self.composition.composition.copy()
rnd = random.random()
natom_limit = self.max_comp_mult * self.composition.natom / self.composition.gcd
condition = {
'structure.nspecies': self.composition.nspecies,
'structure.natom': {
'$lte': natom_limit
}
}
if self.pcdb_source is None or self.pcdb_source.entries.find(
condition).count() <= len(self.source_blacklist):
rnd = 0
origin = None
if self.pcdb_source is None or rnd < random_probability or self.composition.nspecies > 1:
pcm_log.debug('Random Structure')
factor = np.random.randint(self.min_comp_mult,
self.max_comp_mult + 1)
for i in comp:
comp[i] *= factor
structure = Structure.random_cell(comp,
method='stretching',
stabilization_number=5,
nparal=5,
periodic=True)
else:
pcm_log.debug('From source')
while True:
entry = None
condition['properties.spacegroup'] = random.randint(1, 230)
print('Trying', condition['properties.spacegroup'])
for ientry in self.pcdb_source.entries.find(condition):
if ientry['_id'] not in self.source_blacklist:
entry = ientry
break
if entry is not None:
origin = entry['_id']
structure = self.pcdb_source.get_structure(entry['_id'])
factor = covalent_radius(
self.composition.species[0]) / covalent_radius(
structure.species[0])
print('From source: %s Spacegroup: %d Scaling: %7.3f' %
(structure.formula,
entry['properties']['spacegroup'], factor))
structure.set_cell(
np.dot(factor * np.eye(3), structure.cell))
structure.symbols = structure.natom * self.composition.species
self.source_blacklist.append(entry['_id'])
break
return self.new_entry(structure), origin
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
entry_id = None
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
comp = self.composition.composition.copy()
# print("Initial composition: %s" % comp)
# print(Composition(comp))
# print(Composition(comp).symbols)
for i in comp:
comp[i] *= factor
new_comp = Composition(comp)
while True:
rnd = random.random()
condition = {'structure.nspecies': new_comp.nspecies,
'structure.natom': new_comp.natom}
if self.pcdb_source is None:
rnd = 0
elif len(self.sources[factor]) == 0:
rnd = 0
if self.pcdb_source is None or rnd < random_probability:
pcm_log.debug('Random Structure')
structure = Structure.random_cell(new_comp, method='stretching', stabilization_number=5, nparal=5,
periodic=True)
break
else:
pcm_log.debug('From source')
entry_id = self.sources[factor][np.random.randint(0, len(self.sources[factor]))]
structure = self.pcdb_source.get_structure(entry_id)
print("chosen structure from database =", structure)
sym = CrystalSymmetry(structure)
scale_factor = float(np.max(covalent_radius(new_comp.species)) /
np.max(covalent_radius(structure.species)))
reduce_scale = scale_factor ** (1. / 3) # WIH
msg = 'Mult: %d natom: %d From source: %s Spacegroup: %d Scaling: %7.3f'
print(msg % (factor, structure.natom, structure.formula, sym.number(), scale_factor))
# structure.set_cell(np.dot(scale_factor * np.eye(3), structure.cell)) # WIH
structure.set_cell(np.dot(reduce_scale * np.eye(3), structure.cell)) # WIH
print("symbols before change = ", structure.symbols)
structure.symbols = new_comp.symbols
print("symbols after change = ", structure.symbols)
self.sources[factor].remove(entry_id)
break
return self.new_entry(structure), entry_id
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
comp = self.composition.composition.copy()
rnd = random.random()
natom_limit = self.max_comp_mult * self.composition.natom / self.composition.gcd
condition = {'structure.nspecies': self.composition.nspecies,
'structure.natom': {'$lte': natom_limit}}
if self.pcdb_source is None or self.pcdb_source.entries.find(condition).count() <= len(self.source_blacklist):
rnd = 0
origin = None
if self.pcdb_source is None or rnd < random_probability or self.composition.nspecies > 1:
pcm_log.debug('Random Structure')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
for i in comp:
comp[i] *= factor
structure = Structure.random_cell(comp, method='stretching', stabilization_number=5, nparal=5,
periodic=True)
else:
pcm_log.debug('From source')
while True:
entry = None
condition['properties.spacegroup'] = random.randint(1, 230)
print('Trying', condition['properties.spacegroup'])
for ientry in self.pcdb_source.entries.find(condition):
if ientry['_id'] not in self.source_blacklist:
entry = ientry
break
if entry is not None:
origin = entry['_id']
structure = self.pcdb_source.get_structure(entry['_id'])
factor = covalent_radius(self.composition.species[0]) / covalent_radius(structure.species[0])
print('From source: %s Spacegroup: %d Scaling: %7.3f' % (structure.formula,
entry['properties']['spacegroup'],
factor))
structure.set_cell(np.dot(factor * np.eye(3), structure.cell))
structure.symbols = structure.natom * self.composition.species
self.source_blacklist.append(entry['_id'])
break
return self.new_entry(structure), origin
