What is the most efficient method to store trajectory files?
I run custom simulations on a remote computer. At the moment, the trajectory files are stored in the .xyz format. However, at each time step, only a few atoms are added to or removed from the system. It seems to be a waste of disk space to write out the atomic positions of every atom in the simulation cell. I looked through the supported file formats listed here Exporting data — OVITO User Manual 3.10.0 documentation. I’m not sure which one would be suitable for my goal. Can someone help?
It’s not entirely clear from your question, but it sounds like atoms don’t move in your simulation. Once they are added to the simulation, they keep their initial positions. Is that correct?
I don’t know of any standard file format that is made for this particular type of scenario. So it might be necessary to develop your own file format to optimally compress this kind of simulation trajectory. Then you could write your own file reader for OVITO to load this format into the program.
Yes. It is correct. Deposited atoms do not move, or move very little. And the substrate consists of tens of thousands of atoms. Basically, on-lattice atomistic PVD simulation.
Are some of the Pro features, in this case supporting a customized file format, available in the python library?