def get_atoms(self, geometry=True):
"""Return an ASE Atoms object with additional
information such as coverage and Turn-over-frequencies
attached."""
if geometry:
ase = import_ase()
atoms = ase.atoms.Atoms()
for i in xrange(lattice.system_size[0]):
for j in xrange(lattice.system_size[1]):
for k in xrange(lattice.system_size[2]):
for n in xrange(1, 1 + lattice.spuck):
species = lattice.get_species([i, j, k, n])
if self.species_representation[species]:
atom = deepcopy(
self.species_representation[species])
atom.translate(np.dot(lattice.unit_cell_size,
np.array([i, j, k]) \
+ lattice.site_positions[n - 1]))
atoms += atom
lattice_repr = deepcopy(self.lattice_representation)
lattice_repr.translate(
np.dot(lattice.unit_cell_size, np.array([i, j,
k])))
atoms += lattice_repr
atoms.set_cell(self.cell_size)
else:
class Expando():
pass
atoms = Expando()
atoms.calc = None
atoms.kmc_time = base.get_kmc_time()
atoms.kmc_step = base.get_kmc_step()
# calculate TOF since last call
atoms.procstat = np.zeros((proclist.nr_of_proc, ))
atoms.occupation = proclist.get_occupation()
for i in range(proclist.nr_of_proc):
atoms.procstat[i] = base.get_procstat(i + 1)
delta_t = (atoms.kmc_time - self.time)
size = self.size**lattice.model_dimension
if delta_t == 0. and atoms.kmc_time > 0:
print(
"Warning: numerical precision too low, to resolve time-steps")
print(' Will reset kMC for next step')
base.set_kmc_time(0.0)
atoms.tof_data = np.zeros_like(self.tof_matrix[:, 0])
else:
atoms.tof_data = np.dot(self.tof_matrix,
(atoms.procstat - self.procstat) /
delta_t / size)
# update trackers for next call
self.procstat[:] = atoms.procstat
self.time = atoms.kmc_time
return atoms
def get_atoms(self, geometry=True):
"""Return an ASE Atoms object with additional
information such as coverage and Turn-over-frequencies
attached."""
if geometry:
ase = import_ase()
atoms = ase.atoms.Atoms()
for i in xrange(lattice.system_size[0]):
for j in xrange(lattice.system_size[1]):
for k in xrange(lattice.system_size[2]):
for n in xrange(1, 1 + lattice.spuck):
species = lattice.get_species([i, j, k, n])
if self.species_representation[species]:
atom = deepcopy(
self.species_representation[species])
atom.translate(np.dot(lattice.unit_cell_size,
np.array([i, j, k]) \
+ lattice.site_positions[n - 1]))
atoms += atom
lattice_repr = deepcopy(self.lattice_representation)
lattice_repr.translate(np.dot(lattice.unit_cell_size,
np.array([i, j, k])))
atoms += lattice_repr
atoms.set_cell(self.cell_size)
else:
class Expando():
pass
atoms = Expando()
atoms.calc = None
atoms.kmc_time = base.get_kmc_time()
atoms.kmc_step = base.get_kmc_step()
# calculate TOF since last call
atoms.procstat = np.zeros((proclist.nr_of_proc,))
atoms.occupation = proclist.get_occupation()
for i in range(proclist.nr_of_proc):
atoms.procstat[i] = base.get_procstat(i + 1)
delta_t = (atoms.kmc_time - self.time)
size = self.size ** lattice.model_dimension
if delta_t == 0. and atoms.kmc_time > 0:
print(
"Warning: numerical precision too low, to resolve time-steps")
print(' Will reset kMC for next step')
base.set_kmc_time(0.0)
atoms.tof_data = np.zeros_like(self.tof_matrix[:, 0])
else:
atoms.tof_data = np.dot(self.tof_matrix,
(atoms.procstat - self.procstat) / delta_t / size)
# update trackers for next call
self.procstat[:] = atoms.procstat
self.time = atoms.kmc_time
return atoms
def put(self, site, species):
"""Puts a certain species at a certain site.
(Not implemented)
"""
species = species.lower()
cell, name = np.array(site[:3]), site[3].lower()
site_nr = eval('lattice.%s' % name)
site = np.array(list(cell) + [site_nr])
species = lattice.get_species(site)
if species:
pass
def put(self, site, species):
"""Puts a certain species at a certain site.
(Not implemented)
"""
species = species.lower()
cell, name = np.array(site[:3]), site[3].lower()
site_nr = eval('lattice.%s' % name)
site = np.array(list(cell) + [site_nr])
species = lattice.get_species(site)
if species:
pass
def get_atoms(self, geometry=True):
"""Return an ASE Atoms object with additional
information such as coverage and Turn-over-frequencies
attached."""
if geometry:
kmos_tags = {}
ase = import_ase()
atoms = ase.atoms.Atoms()
for i in xrange(lattice.system_size[0]):
for j in xrange(lattice.system_size[1]):
for k in xrange(lattice.system_size[2]):
for n in xrange(1, 1 + lattice.spuck):
species = lattice.get_species([i, j, k, n])
if self.species_representation[species]:
# create the ad_atoms
ad_atoms = deepcopy(
self.species_representation[species])
# move to the correct location
ad_atoms.translate(
np.dot(
np.array([i, j, k]) +
lattice.site_positions[n - 1],
lattice.unit_cell_size))
# add to existing slab
atoms += ad_atoms
if self.species_tags:
for atom in range(
len(atoms) - len(ad_atoms),
len(atoms)):
kmos_tags[
atom] = self.species_tags.values(
)[species]
lattice_repr = deepcopy(self.lattice_representation)
lattice_repr.translate(
np.dot(np.array([i, j, k]),
lattice.unit_cell_size))
atoms += lattice_repr
atoms.set_cell(self.cell_size)
# workaround for older ASE < 3.6
if not hasattr(atoms, 'info'):
atoms.info = {}
atoms.info['kmos_tags'] = kmos_tags
else:
class Expando():
pass
atoms = Expando()
atoms.calc = None
atoms.kmc_time = base.get_kmc_time()
atoms.kmc_step = base.get_kmc_step()
# calculate TOF since last call
atoms.procstat = np.zeros((proclist.nr_of_proc, ))
atoms.occupation = proclist.get_occupation()
for i in range(proclist.nr_of_proc):
atoms.procstat[i] = base.get_procstat(i + 1)
delta_t = (atoms.kmc_time - self.time)
size = self.size**lattice.model_dimension
if delta_t == 0. and atoms.kmc_time > 0:
print(
"Warning: numerical precision too low, to resolve time-steps")
print(' Will reset kMC time to 0s.')
base.set_kmc_time(0.0)
atoms.tof_data = np.zeros_like(self.tof_matrix[:, 0])
else:
atoms.tof_data = np.dot(self.tof_matrix,
(atoms.procstat - self.procstat) /
delta_t / size)
atoms.delta_t = delta_t
# update trackers for next call
self.procstat[:] = atoms.procstat
self.time = atoms.kmc_time
return atoms
def get_atoms(self, geometry=True):
"""Return an ASE Atoms object with additional
information such as coverage and Turn-over-frequencies
attached."""
if geometry:
kmos_tags = {}
ase = import_ase()
atoms = ase.atoms.Atoms()
for i in xrange(lattice.system_size[0]):
for j in xrange(lattice.system_size[1]):
for k in xrange(lattice.system_size[2]):
for n in xrange(1, 1 + lattice.spuck):
species = lattice.get_species([i, j, k, n])
if self.species_representation[species]:
# create the ad_atoms
ad_atoms = deepcopy(
self.species_representation[species])
# move to the correct location
ad_atoms.translate(
np.dot(
np.array([i, j, k]) +
lattice.site_positions[n - 1],
lattice.unit_cell_size))
# add to existing slab
atoms += ad_atoms
if self.species_tags:
for atom in range(len(atoms) - len(ad_atoms), len(atoms)):
kmos_tags[atom] = self.species_tags.values()[species]
lattice_repr = deepcopy(self.lattice_representation)
lattice_repr.translate(np.dot(np.array([i, j, k]),
lattice.unit_cell_size))
atoms += lattice_repr
atoms.set_cell(self.cell_size)
# workaround for older ASE < 3.6
if not hasattr(atoms, 'info'):
atoms.info = {}
atoms.info['kmos_tags'] = kmos_tags
else:
class Expando():
pass
atoms = Expando()
atoms.calc = None
atoms.kmc_time = base.get_kmc_time()
atoms.kmc_step = base.get_kmc_step()
# calculate TOF since last call
atoms.procstat = np.zeros((proclist.nr_of_proc,))
atoms.occupation = proclist.get_occupation()
for i in range(proclist.nr_of_proc):
atoms.procstat[i] = base.get_procstat(i + 1)
delta_t = (atoms.kmc_time - self.time)
size = self.size ** lattice.model_dimension
if delta_t == 0. and atoms.kmc_time > 0:
print(
"Warning: numerical precision too low, to resolve time-steps")
print(' Will reset kMC time to 0s.')
base.set_kmc_time(0.0)
atoms.tof_data = np.zeros_like(self.tof_matrix[:, 0])
else:
atoms.tof_data = np.dot(self.tof_matrix,
(atoms.procstat - self.procstat) / delta_t / size)
atoms.delta_t = delta_t
# update trackers for next call
self.procstat[:] = atoms.procstat
self.time = atoms.kmc_time
return atoms