from ovito.io import import_file, export_file
from ovito.modifiers import CoordinationAnalysisModifier, ClusterAnalysisModifier
pipeline = import_file("trajectory.dump")
pipeline.modifiers.append(CoordinationAnalysisModifier(cutoff=3.0))
pipeline.modifiers.append(ClusterAnalysisModifier(cutoff=3.0, sort_by_size=True))
data = pipeline.compute()
# access per-atom properties: data.particles['Coordination']
export_file(pipeline, "processed.dump", "lammps/data")
One of OVITO’s flagship features is the Construct Surface Mesh modifier. Historically, identifying surface atoms was done via simple coordination number cut-offs (e.g., "if an atom has fewer than 8 neighbors, it is a surface atom"). While functional, this method is crude and often misidentifies internal defects as surface atoms.
OVITO employs the Alpha Shape method (a generalization of the convex hull) to generate a triangulated mesh around clusters of atoms. This allows researchers to:
Beyond PTM, OVITO includes the Identify Diamond Structure modifier, specifically tailored for carbon systems. Whether analyzing the transition from graphite to diamond or studying amorphous carbon films, this modifier categorizes atoms into diamond, lonsdaleite, or sp2/sp3 hybridizations. This high-level classification is essential for materials scientists designing hard coatings.
In nanotechnology and surface science, the interface between a material and its environment dictates its properties. OVITO excels at isolating and analyzing these "top" layers.
Even with the best hardware and software, a poor workflow kills productivity. Here is how the top 1% of OVITO users operate:
Order of operations is critical. A "top" pipeline sequence is:
Source Data → Wrap Around Periodic Image (essential for boundaries) → Select Type (filter solvent) → Compute Property (e.g., coordination number) → Color Coding → Render.
Never put Generate Trajectory Lines before Wrap Around Periodic Images—you will get chaotic spaghetti lines.
If you have ever opened a 500MB trajectory file in OVITO only for your computer to freeze, or if you have stared at a sea of colored atoms wondering "How do I actually measure this dislocation?" — this post is for you.
Here are the top 5 OVITO features you need to master to go from "pretty pictures" to publishable data.
from ovito.io import import_file, export_file
from ovito.modifiers import CoordinationAnalysisModifier, ClusterAnalysisModifier
pipeline = import_file("trajectory.dump")
pipeline.modifiers.append(CoordinationAnalysisModifier(cutoff=3.0))
pipeline.modifiers.append(ClusterAnalysisModifier(cutoff=3.0, sort_by_size=True))
data = pipeline.compute()
# access per-atom properties: data.particles['Coordination']
export_file(pipeline, "processed.dump", "lammps/data")
One of OVITO’s flagship features is the Construct Surface Mesh modifier. Historically, identifying surface atoms was done via simple coordination number cut-offs (e.g., "if an atom has fewer than 8 neighbors, it is a surface atom"). While functional, this method is crude and often misidentifies internal defects as surface atoms.
OVITO employs the Alpha Shape method (a generalization of the convex hull) to generate a triangulated mesh around clusters of atoms. This allows researchers to:
Beyond PTM, OVITO includes the Identify Diamond Structure modifier, specifically tailored for carbon systems. Whether analyzing the transition from graphite to diamond or studying amorphous carbon films, this modifier categorizes atoms into diamond, lonsdaleite, or sp2/sp3 hybridizations. This high-level classification is essential for materials scientists designing hard coatings. ovito top
In nanotechnology and surface science, the interface between a material and its environment dictates its properties. OVITO excels at isolating and analyzing these "top" layers.
Even with the best hardware and software, a poor workflow kills productivity. Here is how the top 1% of OVITO users operate: Color coding: assign colors by property (CSP, CNA
Order of operations is critical. A "top" pipeline sequence is:
Source Data → Wrap Around Periodic Image (essential for boundaries) → Select Type (filter solvent) → Compute Property (e.g., coordination number) → Color Coding → Render.
Never put Generate Trajectory Lines before Wrap Around Periodic Images—you will get chaotic spaghetti lines. from ovito
If you have ever opened a 500MB trajectory file in OVITO only for your computer to freeze, or if you have stared at a sea of colored atoms wondering "How do I actually measure this dislocation?" — this post is for you.
Here are the top 5 OVITO features you need to master to go from "pretty pictures" to publishable data.