Example B2: Computing CNA bond indices — OVITO Python Reference 3.15.3-dev-HEAD-b1e9512d documentation

# Example B2: Computing CNA bond indices

The following script demonstrates how to use the `CreateBondsModifier` to create bonds between particles. The structural environment of each created bond is then characterized with the help of the `CommonNeighborAnalysisModifier`, which computes a triplet of indices for each bond from the topology of the surrounding bond network. The script accesses the computed CNA bond indices in the output `DataCollection` of the modification pipeline and exports them to a text file. The script enumerates the bonds of each particle using the `BondsEnumerator` helper class.

The generated text file has the following format:

    Atom    CNA_pair_type:Number_of_such_pairs ...

    1       [4 2 1]:2  [4 2 2]:1 [5 4 3]:1
    2       ...
    ...

Python script:

    # Import OVITO modules.
    from ovito.io import *
    from ovito.modifiers import *
    from ovito.data import *

    # Import standard Python and NumPy modules.
    import sys
    import numpy

    # Load the simulation dataset to be analyzed.
    pipeline = import_file("input/simulation.0.dump")

    # Create bonds.
    pipeline.modifiers.append(CreateBondsModifier(cutoff = 3.5))

    # Compute CNA indices on the basis of the created bonds.
    pipeline.modifiers.append(CommonNeighborAnalysisModifier(
        mode = CommonNeighborAnalysisModifier.Mode.BondBased))

    # Let OVITO's data pipeline do the heavy work.
    data = pipeline.compute()

    # The 'CNA Indices' bond property is a two-dimensional array
    # containing the three CNA indices computed for each bond in the system.
    cna_indices = data.particles.bonds['CNA Indices']

    # This helper function takes a two-dimensional array and computes the frequency
    # histogram of the data rows using some NumPy magic.
    # It returns two arrays (of same length):
    #    1. The list of unique data rows from the input array
    #    2. The number of occurrences of each unique row
    def row_histogram(a):
        ca = numpy.ascontiguousarray(a).view([('', a.dtype)] * a.shape[1])
        unique, indices, inverse = numpy.unique(ca, return_index=True, return_inverse=True)
        counts = numpy.bincount(numpy.reshape(inverse, (inverse.shape[0],)))
        return (a[indices], counts)

    # Used below for enumerating the bonds of each particle:
    bond_enumerator = BondsEnumerator(data.particles.bonds)

    # Loop over particles and print their CNA indices.
    for particle_index in range(data.particles.count):

        # Print particle index (1-based).
        sys.stdout.write("%i " % (particle_index+1))

        # Create local list with CNA indices of the bonds of the current particle.
        bond_index_list = list(bond_enumerator.bonds_of_particle(particle_index))
        local_cna_indices = cna_indices[bond_index_list]

        # Count how often each type of CNA triplet occurred.
        unique_triplets, triplet_counts = row_histogram(local_cna_indices)

        # Print list of triplets with their respective counts.
        for triplet, count in zip(unique_triplets, triplet_counts):
            sys.stdout.write("%s:%i " % (triplet, count))

        # End of particle line
        sys.stdout.write("\n")