OVITO

OVITO (Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data. It is the primary tool used in the SWZ for inspecting and analyzing MD simulation results.

Key Features

• Load simulation data: supports LAMMPS dump files, XYZ, CFG, POSCAR, NetCDF, and many more formats

• Built-in analysis modifiers: Common Neighbor Analysis (CNA), Dislocation Extraction Algorithm (DXA), Voronoi analysis, coordination analysis, Wigner-Seitz defect analysis, surface mesh construction

• Rendering: high-quality ray-traced images and animations for publications

• Python scripting: automate analysis pipelines using the OVITO Python module (ovito package)

Common Workflows

Visualizing a LAMMPS Trajectory

1. Open OVITO and load your LAMMPS dump file (File > Load File)

2. Navigate through timesteps using the timeline slider

3. Apply modifiers from the pipeline editor (e.g., "Color Coding" to map per-atom properties)

Structural Analysis

• CNA (Common Neighbor Analysis): identify crystal structures (FCC, BCC, HCP) in your system

• DXA (Dislocation Extraction Algorithm): extract dislocation lines and compute Burgers vectors

• Voronoi Analysis: compute atomic volumes and coordination numbers

Python Scripting

OVITO provides a Python module for batch processing:

from ovito.io import import_file
from ovito.modifiers import CommonNeighborAnalysisModifier

pipeline = import_file("trajectory.dump")
pipeline.modifiers.append(CommonNeighborAnalysisModifier())
data = pipeline.compute()

Installation

• OVITO Basic: free for academic and commercial use, available from ovito.org

• OVITO Pro: additional features (Python scripting IDE, advanced modifiers), requires a license

• Python module: install via pip install ovito

Resources

• OVITO documentation

• OVITO Python reference

• OVITO forum