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# 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.

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.

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.

Computes the average of some time-dependent input quantity over the entire trajectory.

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.

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.

Loads time-dependent atomic positions from a separate trajectory file.

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

Computes local pair entropy fingerprints of particles.

Discerns between stacking fault and twin boundary crystal defects.

Visualize LAMMPS regions as surface meshes.

Resets the simulation cell to tightly fit all particles.