ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
The vtkAtoms class plots atoms during simulations, extracting the relevant information from the list of
atoms. It is created using the list of atoms as an argument to the constructor. Then one or more visualization
modules can be attached using add_module(name, module).
Example:
>>> va = vtkAtoms(atoms)
>>> va.add_forces()
>>> va.add_axes()
>>> XXX va.add_to_renderer(vtk_ren)
Construct a fundamental VTK-representation of atoms.
atoms: Atoms object or list of Atoms objects The atoms to be plotted.
scale = 1: float or int Relative scaling of all Atoms-specific visualization.
add_axes()
Add an orientation indicator for the cartesian axes. An appropriate vtkAxesModule is added to the
module anchor under axes.
add_cell()
Add a box outline of the cell using atoms.get_cell(). The existing vtkUnitCellModule is added
to the module anchor under cell.
add_forces()
Add force vectors for the atoms using atoms.get_forces(). A vtkGlyphModule is added to the
module anchor under force.
add_velocities()
Add velocity vectors for the atoms using atoms.get_velocities(). A vtkGlyphModule is added to
the module anchor under velocity.
Atom-centered data
The superclass vtkAtomicPositions implements the basic concepts for representing atomic-centered data
in VTK.
class ase.visualize.vtk.grid.vtkAtomicPositions(pos, cell)
Provides an interface for adding Atoms-centered data to VTK modules. Atomic positions, e.g. obtained
using atoms.get_positions(), constitute an unstructured grid in VTK, to which scalar and vector can be added
as point data sets.
Just like Atoms, instances of vtkAtomicPositions can be divided into subsets, which makes it easy
to select atoms and add properties.
Example:
>>> cell = vtkUnitCellModule(atoms)
>>> apos = vtkAtomicPositions(atoms.get_positions(), cell)
>>> apos.add_scalar_property(atoms.get_charges(), ’charges’)
>>> apos.add_vector_property(atoms.get_forces(), ’forces’)
Construct basic VTK-representation of a set of atomic positions.
pos: NumPy array of dtype float and shape (n,3) Cartesian positions of the atoms.
cell: Instance of vtkUnitCellModule of subclass thereof Holds information equivalent to that of
atoms.get_cell().
add_scalar_property(data, name=None, active=True)
Add VTK-representation of scalar data at the atomic positions.
data: NumPy array of dtype float and shape (n,) Scalar values corresponding to the atomic positions.
name=None: str Unique identifier for the scalar data.
108 Chapter 7. Documentation for modules in ASE