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Questions tagged [ovito]

Questions about or related to the OVITO software or its Python interface.

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3 votes
1 answer

Colour coding modifier in Ovito

I have what is probably a silly question about the colour coding modifier. I am using it to begin the analysis of my LAMMPS trajectory files by colour coding the potential energy per atom and entropy ...
4 votes
0 answers

How to extract Lindemann Index from LAMMPS dump files?

I used a python code to extract Lindemann index from dump files. But the problem is the code works fine with dump files with little amount of data and atoms. When I use large files if shows overflow ...
4 votes
1 answer

How to get displacements along VASP NEB trajectory?

I am performing an NEB calculation with VASP and VTST. I would like to visualize the atoms along the path and to calculate their displacements. When I have a single relaxation's XDATCAR, I can unwrap ...
5 votes
2 answers

How to visualize a slice of the unit cell?

I have a cell that contains a sphere of organic molecules in a cube of water. What tool and how could I visualize the central cut (slice) of the unit cell? Similar to the one visualized in packmol ...
1 vote
0 answers

Analyzing ELECTRO -ELECTROLYTE MD trajectories for calculating bulk density in a simulation box [closed]

I am simulating electrode electrolyte simulation and my professor told me to calculate the density of bulk in simulation box, I am clueless about the how to calculate ,also I want to know if charges ...
3 votes
1 answer

Ovito dislocation analysis

How can I append my pipeline in Ovito? I tried to append DislocationAnalysisModifier with Selected atom: ...
6 votes
0 answers

LAMMPS fix print function [closed]

First of all, I'm very new to LAMMPS so I'm sorry if my question is trivial. I'm trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-...
5 votes
0 answers

How to get the coordination number from RDF in python ovito? [closed]

Basically, I am trying to get the running coordination number (CN), but the result isn't correct? I am multiplying the Radial Distribution Function (RDF) with ...