ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
‘data’: Autoscale using the data on visible atoms. The range goes from the lowest to the highest
value present on the atoms. If only a few atoms have extreme values, the entire color range may
not be used on the plot, as many values may be averaged on each point in the plot.
‘plot’: Autoscale using the data on the plot. Unlike ‘data’ this guarantees that the entire color
range is used.
min, max: Use the range [min, max]
set_dimensions(dims)
Set the size of the canvas (a 2-tuple).
set_invisibility_function(invfunc)
Set an invisibility function.
set_invisible(inv)
Choose invisible atoms.
set_log(log)
Sets a file for logging.
log may be an open file or a filename.
set_plot_plane(plane)
Set the plotting plane to xy, xz or yz (default: xy)
set_radii(radii)
Set the atomic radii. Give an array or a single number.
set_red_yellow_colors(reverse=False)
Set colors to Black-Red-Yellow-White (a.k.a. STM colors)
set_rotation(rotation)
Set the rotation angles (in degrees).
update(newatoms=None)
Cause a plot (respecting the interval setting).
update causes a plot to be made. If the interval variable was specified when the plotter was create, it
will only produce a plot with that interval. update takes an optional argument, newatoms, which can
be used to replace the list of atoms with a new one.
7.13 ASE-VTK
For ASE, the vtk interface consists of Python modules for automatic visualization of positions, bonds, forces and
volume data (e.g. wave functions) from an Atoms object, provided such data is made available by the calculator.
Note: The Python modules in ASE are intended to wrap lower-level functionality of the VTK object models
in small and easy-to-comprehend classes. To be able to distinguish between build-in VTK objects and their
wrappers, and because VTK uses the CamelCase naming convention whereas ASE uses lower-case cf. our coding
conventions, all variables referring to VTK built-in types are prefixed by vtk_. However, both VTK and wrapper
classes are named according to the standard vtkFooBar.
7.13.1 Representing atoms
class ase.visualize.vtk.atoms.vtkAtoms(atoms, scale=1)
Bases: ase.visualize.vtk.module.vtkModuleAnchor, ase.visualize.vtk.grid.vtkAtomicPositi
Provides fundamental representation for Atoms-specific data in VTK.
7.13. ASE-VTK 107