I was wondering how to compute the temperature and velocity of and impinging nitrogen molecule onto a substrate? I am doing so using the fix deposit command.
The nitrogen molecule has been defined through the molecule command. Now I want to get the temperature of the nitrogen molecule as a whole, not on the individual atoms.
Does this mean I can define the nitrogen molecule as an atom with mass 28.013? Will this give me the same results?
I looked through the documentation of fix rigid/small but I find it a little bit confusing. there is a note which says
With fix rigid/small, which requires bodystyle molecule, you can define a system that has no rigid bodies initially. This is useful when you are using the mol keyword in conjunction with another fix that is adding rigid bodies on-the-fly, such as fix deposit or fix pour.
How do I define body style as molecule? I only have a molecule ‘template’ ID and no molecule ID. Is there a way to assign molecule IDs to molecule templates?
- I also looked through the compute temp/chunk option, but again I am not sure how to define the group ID for a molecule command defined molecule.
Secondly, in one of my previous emails http://sourceforge.net/p/lammps/mailman/message/34782282/
you had mentioned ‘you write out your trajectory in .xyz format (with dump_modify elements) and can then use the readvarxyz function of the topotools plugin to convert it into a fake trajectory with a constant number of atoms on-the-fly and label the visibility of those atoms via the user field.’
After running the simulation, I added two random atoms in the dump file for the ‘timestep 0’. I opened the file on vmd command line using topo readvarxyz filename. I can see the movement in the substrate, but no movement of the nitrogen molecule through all the frames. It is present in the simulation box but doesn’t move at all.
I don’t really understand what you mean by ‘label the visibility via user field’. Is there an example that I can see to get a clearer picture?