Dear Users and Axel
I am having some issues with my CNT system visualization where box is not orthogonal, one of the angles is 120. I am not sure if it is VMD or msi2lmp or topotools.
I have a periodic (non-orthogonal system) (9,5) CNT in .mdf and .car format (attached) that I generated using Material Studio (PCFF forcefield). Then, I used new version (after Axel modified it back in August) to convert to lammps data file. Older version could not handle non-orthogonal boxes if I remember correctly, so Axel’s version is only choice (Thanks)
msi2lmp.exe runs fine and output a data file (attached).
When I visualize .car and .data (using topotools) file of the same system in VMD, I see differences.
.car file look as it should be in VMD.
For .data file, the CNT appears to be breaking in almost half followed by some shifting (1/2 the box length) in non-orthogonal direction (see the screenshot). Bond connectivity seems fine but due to this shifting, some of the bonds look to be extremely streched.
For your reference, I am attaching the appropriate files as well. Please have a look at them when you get a chance if you get same issue in VMD visualization. If so, what might be causing it.
Thanks in advance.
09-05-10.data (294 KB)
09-05-10.car (48.5 KB)
09-05-10.mdf (61.1 KB)