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sntioudis / papreca

PAPRECA hybrid off-lattice kinetic Monte Carlo/molecular dynamics (kMC/MD) simulator
GNU General Public License v2.0
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Example 2: comments and possible improvements #18

Closed jfaraudo closed 3 months ago

jfaraudo commented 3 months ago

Comments about example 2

jfaraudo commented 3 months ago

I like Example 2, adsorption is a classical example in MC. My only comment is about the trajectory file .xyz geneated by LAMMPS. Apparently the file only contains the particles in the substrate but not the adsorbed atoms. I am showing here typical snapshots that I got by representing the xyz file with VMD.

jfaraudo commented 3 months ago

snapshot

jfaraudo commented 3 months ago

vmdscene2

jfaraudo commented 3 months ago

However the simulation run seems to be executed correctly. This is a typical result for the adsorption

jfaraudo commented 3 months ago

comparison_plot_ra3 0_rd5 0

jfaraudo commented 3 months ago

I expected to be able to generate visualizations similar to the ones shown in the documentation , with the adsorbed atoms and the substrate. Apparently the dump in LAMMPS indicates to dump everything, so I do not know what may be wrong here.

sntioudis commented 3 months ago

I like Example 2, adsorption is a classical example in MC. My only comment is about the trajectory file .xyz geneated by LAMMPS. Apparently the file only contains the particles in the substrate but not the adsorbed atoms. I am showing here typical snapshots that I got by representing the xyz file with VMD.

Thank you for your comment. I think this is an issue with VMD. For some reason, VMD cannot handle .xyz files whose number of atoms changes from timestep to timestep. This is exactly the case for this example, since we add/remove (i.e., adsorb/desorb) atoms.

However, OVITO draws all the particles (as depicted in the gif in the documentation). You probably faced the same issue in the Phosphates example (i.e., VMD didn't draw the film).

sntioudis commented 3 months ago

I reckon I should mention that somewhere in the documentation.

jfaraudo commented 3 months ago

I see, you are right. It is worth mentioning in the documentation. This is a problem in VMD that I always forget, it requires constant number of atoms.

sntioudis commented 3 months ago

@jfaraudo I added a comment at the beginning of the examples section. Feel free to close the issue whenever you are satisfied with Example #2.

jfaraudo commented 3 months ago

Perfect! I know that a major new release of VMD (2.0) is coming. Maybe the new release is able to cope with variable number of particles. Let us keep an eye on that.

jfaraudo commented 3 months ago

Perfect! I know that a major new release of VMD (2.0) is coming. Maybe the new release is able to cope with variable number of particles. Let us keep an eye on that.