Load and visualize a xyz trajectory frame by frame

Luis

Luis

Hello,

SAMSON (last version) is crashing when I tried to load a multi-frame xyz file. I haven't tried to visualize trajectories in xyz format for a while, so I don't know if something has changed in the last versions. Could someone please tell me if this is no longer supported. Has the format changed maybe?

Thanks in advance.

Luis

DmitriyMarin

Hi @Luis ,

This is still supported and will be supported. Would it be possible for you to share with us the XYZ file that causes the issue (you can send it to contact@samson-connect.net) so that we can check what might be the problem?

Please note that there are several flavors of XYZ format that vary slightly. While we try to support as many of them as possible, the main format follows the following format:

NUMBER_OF_ATOMS
COMMENT_LINE
ELEMENT_TYPE POS_X POS_Y POS_Z

For example:

3
 STEP:           1
 H      0.967485      6.687080      5.821420
 H      2.507099      7.320300      6.535832
 H      2.819131      8.163311      3.557150
3
 STEP:         2
 H      0.987382      6.755653      5.887846
 H      2.528730      7.288068      6.545012
 H      2.899837      8.187620      3.675997

Luis

Hi @DmitriyMarin ,

Thanks for the quick reply. I used the example from your answer, and it crashed the application as shown in the image below

DmitriyMarin

That's strange since it should work. We received your crash report and will check what might be the issue.
Are you able to open other file formats?

Luis

I am able to open XYZ files with a single frame. LAMMPS data and trajectory files are also loaded without problem. As a workaround I can transform the XYZ trajectory files to LAMMPS data and lammpstrj to visualize them (the bonds are not generated automatically), but it requires to use external tools (or scripting something).

DmitriyMarin

Thanks for checking! We will try to see what might be an issue here. I will let you know once it is resolved.

DmitriyMarin

Dear @Luis ,

We fixed the issue with the XYZ importer for loading trajectories. The module should be updated automatically once you restart SAMSON. Could you please try and check if it works for you now?

Luis

Dear @DmitriyMarin ,

Thank you very much. It works!

With kind regards,

Luis

DmitriyMarin

Dear @Luis ,

Great! Thanks for checking and for reporting the issue in the first place!