Modifiers

Modifiers are the basic building blocks for creating a data pipeline in OVITO. Like tools in a toolbox, each modifier implements a very specific, well-defined type of operation or computation, and typically you will need to combine several modifiers to accomplish more complex tasks.

List of modifiers available in OVITO:

Analysis
Atomic strain	Calculates local strain tensors based on the relative motion of neighboring particles.
Bond analysis pro	Computes bond angle and bond length distributions.
Cluster analysis	Decomposes a particle system into clusters of particles.
Coordination analysis	Determines the number of neighbors of each particle and computes the radial distribution function for the system.
Dislocation analysis (DXA)	Identifies dislocation defects in a crystal.
Displacement vectors	Calculates the displacements of particles based on an initial and a deformed configuration.
Elastic strain calculation	Calculates the atomic-level elastic strain tensors in crystalline systems.
Grain segmentation	Determines the grain structure in a polycrystalline microstructure.
Histogram	Computes the histogram of a property.
Scatter plot	Generates a scatter plot of two properties.
Spatial binning pro	Aggregates a particle property over a one-, two- or three-dimensional bin grid.
Spatial correlation function	Calculates the spatial cross-correlation function between two particle properties.
Time averaging pro	Computes the average of some time-dependent input quantity over the entire trajectory.
Time series pro	Plots the value of a global attribute as function of simulation time.
Voronoi analysis	Computes the coordination number, atomic volume, and Voronoi index of particles from their Voronoi polyhedra.
Wigner-Seitz defect analysis	Identifies point defects (vacancies and interstitials) in a crystal lattice.

Coloring
Ambient occlusion	Performs an ambient occlusion calculation to shade particles.
Assign color	Assigns a color to all selected elements.
Color by type pro	Colors particles or bonds according to a typed (discrete) property.
Color coding	Colors particles or bonds based on the value of a scalar (continuous) property.

Modification
Affine transformation	Applies an affine transformation to the system.
Combine datasets	Merges the particles and bonds from two separate input files into one dataset.
Compute property	Assigns property values to particles or bonds according to a user-defined formula.
Delete selected	Removes the selected elements from the visualization.
Freeze property	Freezes the values of a dynamic particle property at a given animation time to make them available at other times.
Load trajectory	Loads time-dependent atomic positions from a separate trajectory file.
Python script pro	Lets you write your own modifier function in Python.
Replicate	Duplicates particles and other data elements to visualize periodic images of the system.
Slice	Cuts the structure along an infinite plane.
Smooth trajectory	Computes time-averaged particle positions using a sliding window or generates intermediate sub-frames using linear interpolation.
Unwrap trajectories	Computes unwrapped particle coordinates in order to generate continuous trajectories at periodic cell boundaries.
Wrap at periodic boundaries	Folds particles located outside of the periodic simulation box back into the box.

Selection
Clear selection	Resets the selection state of all elements.
Expand selection	Selects particles that are neighbors of already selected particles.
Expression selection	Selects particles and other elements based on a user-defined criterion.
Manual selection	Lets you select individual particles or bonds with the mouse.
Invert selection	Inverts the selection state of each element.
Select type	Selects all elements of a particular type, e.g. all atoms of a chemical species.

Structure identification
Ackland-Jones analysis	Identifies common crystal structures by an analysis of the bond-angle distribution.
Centrosymmetry parameter	Calculates the centrosymmetry parameter for every particle.
Chill+	Identifies hexagonal ice, cubic ice, hydrate and other arrangements of water molecules.
Common neighbor analysis	Performs the common neighbor analysis (CNA) to determine local crystal structures.
Identify diamond structure	Identifies atoms that are arranged in a cubic or hexagonal diamond lattice.
Polyhedral template matching	Identifies common crystal structures using the PTM method and computes local crystal orientations.
VoroTop analysis	Identifies local structure of particles using the topology of their Voronoi polyhedra.

Visualization
Construct surface mesh	Constructs a triangle mesh representing the surface of a solid.
Create bonds	Creates bonds between particles.
Create isosurface	Generates an isosurface from a scalar field.
Coordination polyhedra	Shows coordination polyhedra.
Generate trajectory lines	Generates trajectory lines from the time-dependent particle positions.
Interactive molecular dynamics (IMD)	Visualize live atomic trajectories from a running MD simulation as they are being calculated.

Python-based modifiers
Calculate local entropy pro	Computes local pair entropy fingerprints of particles.
Identify fcc planar faults pro	Discerns between stacking fault and twin boundary crystal defects.
Render LAMMPS regions pro	Visualize LAMMPS regions as surface meshes.
Shrink-wrap simulation box pro	Resets the simulation cell to tightly fit all particles.