OVITO Python script modifier database

Collection of python script modifiers for OVITO Pro. Each script is designed to be used on a data collection from the graphical user interface using the python script modifier. The OVITO version used for testing can be found in each individual script.

Installation

To make these modifiers available from the 'Add modification...' dropdown menu the *.py files can be copied to ovito-pro-root-dir/share/ovito/scripts/modifiers/

Modifiers

AddParticle.py

Adds a single particle of type symbol (integer or string) at position x, y, z to the data collection.

AddParticles.py

Adds multiple particles defined by the particle type array symbol and the position arrays x, y, z to the data collection.

ApplyDefaultParticleTypes.py

Reads the species names, e.g. Cu, from the types property and applies the corresponding default settings stored in OVITO.

CreateNeighborLists.py

Create neighbor lists for each atom and store them in a particle property
num_neighors should contain a list of neighbors per shell, e.g., [12, 8] to find the first 12 neighbors for the first shell and the subsequent 8 for the second neighbor shell.
only_selected calculate the neighbor lists only for selected elements, note that neighboring atoms are still found, even if they are not selected.
use_particle_identifier toggles the usage of particle identifiers or particle indicies in the neighbor list

FixParticleIdentifier.py

Replaces the current Particle Identifer array with a new continuous one, starting at init_val. This can be necessary after particles were inserted or deleted.

GenerateRandomSolution.py

Replaces the current atomic configurations with a new random arrangement. The concentrations per species are given in the conc array (sum conc == 1).
only_selected applies the modifier only to selected atoms.

JiggleAtoms.py

Randomly displaces all atoms.
mode can be either "uniform" or "normal". Depending on the mode, random displacements are either drawn from a uniform or normal distribution.
amp gives the displacement magnitude (mode: uniform) or standard deviation (mode: normal)
seed sets the starting value of the random number generator.

SelectSphere.py

Select a spherical region of a given radius around a center point.
add_to_selection toggle can be used to add to the current selection or create a new one.

SelectCylinder.py

Select a cylindrical region of a given radius from point p1 to point p2.
add_to_selection toggle can be used to add to the current selection or create a new one.

hitergelei/OVITO_python_modifier_db