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topology (data bond) lost after loading trajectory (dump txt) - Ovito version 2.9

Hello,

By following the user manual, I use file->load file to open a Lammps data. The process is done successfully and I can see the correct topology. The I use input->external file->pick new file and load the trajectory into the topology. The process is successfully done but I lost the topology information. Here are more information that maybe be useful to help me resolve the issue:

  1. I used version 2.9 installed by nix on a cluster and I cannot update it to the most recent version.
  2. I changed the data file name to be similar to the trajectory file name: XXXX.data and XXXX.lammpstrj. But it did not change the situation.
  3. The simulation box info in the data file had been changed by change_box command in the LAMMPS script. Consequently, the cell size in data file is different from the one in the trajectory file loaded on top of that.
  4. There are two types of particle in data file with 1 bond type whereas the trajectory file has 1 particle type and 1 bond type. P article type 1 and the bond type 1 compose a polymeric chain together whereas Particle type 2 are free particles and they are present or absent in the simulations based on the input data.
  5. The idea for use one data file for all trajectory files is that the topology of the chain is the same in all the simulations however the simulation box and the number of particle type 2 change from one simulation to other.

Please find attached a copy of data file and a copy of trajectory file containing 2 snapshots.

Thank you in advance for your help.

Amir

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Dear Amir,

I can point you only to information for OVITO 3.x, but the general steps to load a combination of topology and trajectory files has not changed since OVITO 2.9.

  1. Import the topology file (LAMMPS data file) using the File->Load File menu function.
  2. Insert the Load Trajectory modifier into the data pipeline.
  3. Pick the trajectory file (the LAMMPS dump file). Make sure you do this in the file panel belonging to the Load Trajectory modifier (which has no file selected yet) and not in the original file source panel (which has already the LAMMPS data file loaded).

Note that the last step is important. If you used the External file->Pick new file function in the original file panel, you would simply replace the currently loaded dataset (the topology) with a different dataset (now coming from the trajectory dump file).

It's the Load Trajectory modifier that takes care of merging the static information from the topology file with the time-varying data from the trajectory file. It overwrites the atomic positions with the coordinates it finds in the LAMMSP dump file, and retains the static topological information loaded from the LAMMPS data file (e.g. atom types, bonds list, etc.).