def analyse_ovito_cna_adaptive(atoms, mode="total"):
"""
Use Ovito's common neighbor analysis binding.
Args:
atoms (pyrion.structure.atoms.Atoms): The structure to analyze.
mode ("total"/"numeric"/"str"): Controls the style and level of detail of the output. (Default is "total", only
return a summary of the values in the structure.)
Returns:
(depends on `mode`)
"""
s.publication_add(publication())
if not mode in ["total", "numeric", "str"]:
raise ValueError("Unsupported mode")
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(
CommonNeighborAnalysisModifier(
mode=CommonNeighborAnalysisModifier.Mode.AdaptiveCutoff))
output = node.compute()
if mode == "total":
return output.attributes
else:
atoms_output = output.to_ase_atoms()
if mode == "numeric":
return atoms_output.get_array("Structure Type")
elif mode == "str":
cna_property = output.particle_properties.structure_type
return np.array([
cna_property.get_type_by_id(cnatype).name
for cnatype in atoms_output.get_array("Structure Type")
])
def atoms_to_data(atoms):
data = DataCollection()
cell_matrix = np.zeros((3,4))
cell_matrix[:, :3] = atoms.get_cell()
cell_matrix[:, 3] = atoms.info.get('cell_origin',
[0., 0., 0.])
cell = SimulationCell(matrix=cell_matrix,
pbc=atoms.get_pbc())
data.addObject(cell)
position = ParticleProperty(name='Position',
type=Particles.ParticleProperty.Type.Position,
array=atoms.get_positions())
data.addObject(position)
return data
def analyse_ovito_cna_adaptive(atoms, mode='total'):
"""
Args:
atoms:
mode:
Returns:
"""
if not mode in ['total', 'numeric', 'str']:
raise ValueError('Unsupported mode')
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(CommonNeighborAnalysisModifier(mode=CommonNeighborAnalysisModifier.Mode.AdaptiveCutoff))
output = node.compute()
if mode == 'total':
return output.attributes
else:
atoms_output = output.to_ase_atoms()
if mode == 'numeric':
return atoms_output.get_array("Structure Type")
elif mode == 'str':
cna_property = output.particle_properties.structure_type
return np.array([cna_property.get_type_by_id(cnatype).name
for cnatype in atoms_output.get_array("Structure Type")])
def analyse_ovito_voronoi_volume(atoms):
"""
Args:
mode (str): ['total', 'numeric', 'str']
"""
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(VoronoiAnalysisModifier())
output = node.compute()
return output.particle_properties['Atomic Volume'].array
def analyse_ovito_centro_symmetry(atoms, num_neighbors=12):
"""
Args:
mode (str): ['total', 'numeric', 'str']
"""
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(CentroSymmetryModifier(num_neighbors = num_neighbors))
output = node.compute()
return output.particle_properties['Centrosymmetry'].array
def analyse_ovito_voronoi_volume(atoms):
"""
Args:
atoms:
Returns:
"""
s.publication_add(publication())
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(VoronoiAnalysisModifier())
output = node.compute()
return output.particle_properties["Atomic Volume"].array
def analyse_ovito_centro_symmetry(atoms, num_neighbors=12):
"""
Args:
atoms:
num_neighbors:
Returns:
"""
s.publication_add(publication())
data = DataCollection.create_from_ase_atoms(atoms.copy())
node = ObjectNode()
node.source = data
node.modifiers.append(CentroSymmetryModifier(num_neighbors=num_neighbors))
output = node.compute()
return output.particle_properties["Centrosymmetry"].array