def wrap_cc(cell1, pts):
"""
Function finds the indices of atoms making tetrahedrons
Parameters
-------------
cell1 :
The simulation cell ( a 3*4 numpy array where the first 3 columns are the
cell vectors and the last column is the box origin)
pts :
Position of atoms in initial cell, the atoms within an rCut of the initial cell.
Returns
------------
pts1 :
Position of atoms in initial cell, the atoms within an rCut of the initial cell,
and the Voronoi coordinates as the new set of atoms.
"""
data = ovd.DataCollection()
data.objects.append(cell1)
particles = ovd.Particles()
particles.create_property('Position', data=pts)
data.objects.append(particles)
# Create a new Pipeline with a StaticSource as data source:
pipeline = Pipeline(source=StaticSource(data=data))
pipeline.modifiers.append(ovm.WrapPeriodicImagesModifier())
data1 = pipeline.compute()
pts1 = np.array(data1.particle_properties['Position'][...])
return pts1
def ovito_dxa(atoms, replicate_z=3):
from ovito.io.ase import ase_to_ovito
from ovito.modifiers import ReplicateModifier, DislocationAnalysisModifier
from ovito.pipeline import StaticSource, Pipeline
data = ase_to_ovito(atoms)
pipeline = Pipeline(source=StaticSource(data=data))
pipeline.modifiers.append(ReplicateModifier(num_z=replicate_z))
dxa = DislocationAnalysisModifier(
input_crystal_structure=DislocationAnalysisModifier.Lattice.BCC)
pipeline.modifiers.append(dxa)
data = pipeline.compute()
return (np.array(data.dislocations.segments[0].true_burgers_vector),
data.dislocations.segments[0].length / replicate_z,
data.dislocations.segments[0])
# pass
#else:
# atoms = atoms*(2, 2, 2)
data = ase_to_ovito(atoms)
node = Pipeline(source=StaticSource(data=data))
node.modifiers.append(modifier)
#node.modifiers.append(CommonNeighborAnalysisModifier(mode=CommonNeighborAnalysisModifier.Mode.FixedCutoff))
# node.modifiers.append(CommonNeighborAnalysisModifier(mode=CommonNeighborAnalysisModifier.Mode.AdaptiveCutoff))
#node.modifiers.append(AcklandJonesModifier())
# node.modifiers.append(BondAngleAnalysisModifier())
# node.modifiers.append(PolyhedralTemplateMatchingModifier(rmsd_cutoff=0.0))
# Let OVITO's data pipeline do the heavy work.
node.compute()
# A two-dimensional array containing the three CNA indices
# computed for each bond in the system.
atom_classes = list(node.output.particle_properties['Structure Type'].array)
#AcklandJonesModifier.Type.OTHER(0)
#AcklandJonesModifier.Type.FCC(1)
#AcklandJonesModifier.Type.HCP(2)
#AcklandJonesModifier.Type.BCC(3)
#AcklandJonesModifier.Type.ICO(4)
# CommonNeighborAnalysisModifier.Type.OTHER(0)
# CommonNeighborAnalysisModifier.Type.FCC(1)
# CommonNeighborAnalysisModifier.Type.HCP(2)