Questions tagged [ovito]
Questions about or related to the OVITO software or its Python interface.
7
questions
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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
59
views
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 ...
- 139
5
votes
2
answers
317
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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 ...
- 1,658
1
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30
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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
148
views
Ovito dislocation analysis
How can I append my pipeline in Ovito?
I tried to append DislocationAnalysisModifier with Selected atom:
...
- 31
6
votes
0
answers
477
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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-...
- 61
5
votes
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605
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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 ...
- 949