From: Ali Sheikholeslam (
Date: Tue Jan 25 2022 - 13:34:14 CST


I was seeking utilities that could visualize combinations of spheres during
my code running and I found VMD is a powerful tool.

I am working on movements of spheres for dense packing of them in a box in
an iteration scheme. So, my particles (spheres) are moving a little during
the solution steps. steps (loops) could be at least 100000 to perhaps
1000000 or more (it is not limited) and spheres could be 50000 to 500000 or
1000000 numbers with various specified radii. In each loop I will get numpy
arrays of positions and radii of the all spheres which could be used for
further usages.
I don't know, VMD is an appropriate tool for visualizing the movements
during the running time of my code (visualizing such as an animation). I
would like to see what is happening during my running code to sphere
positions. Could I use numpy arrays to put all data in a moment (one-step)
in each step, or it needs just to loop?
If it could, how could I do this in python? Is there any prepared codes
anywhere to use for showing spheres' movements (with their radii) during
the execution?

I would be very grateful if any one would help doing this or referring to a
python code to do so.

best regards,