How to use ovito - 10 common examples

def analyse_ovito_cna_adaptive(atoms, mode='total'):
    """

    Args:
        atoms:
        mode:

    Returns:

    """
    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 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 pyiron_to_ovito(atoms):
    """
    
    Args:
        atoms: 

    Returns:

    """
    try:
        from ovito.data import DataCollection
        return DataCollection.create_from_ase_atoms(atoms)
    except ImportError:
        raise ValueError('ovito package not yet installed')

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

def pyiron_to_ovito(atoms):
    """
    
    Args:
        atoms: 

    Returns:

    """
    try:
        from ovito.data import DataCollection
        return DataCollection.create_from_ase_atoms(atoms)
    except ImportError:
        raise ValueError('ovito package not yet installed')

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:

    """
    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 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

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

"""

    Args:
        atoms:
        mode:

    Returns:

    """
    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")])