Temperature calculation and trajectory visualization

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1

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.

  1. Does this mean I can define the nitrogen molecule as an atom with mass 28.013? Will this give me the same results?

  2. 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?

  1. 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?

Thank you.

2

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.

temperature is a bulk property and is not well defined or makes much
sense for individual molecules, especially very small ones.

1) Does this mean I can define the nitrogen molecule as an atom with mass
28.013? Will this give me the same results?

that is nonsense.

2) 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?

re-read the documentation with *much* more care. your confusion is due
to your sloppiness in reading docs and making unfounded speculations
all the time.
you are definitely exhausting my patience quickly in this regard.

3) 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.

you really have to work to get rid of your fixation on the molecule
command. once atoms are created LAMMPS doesn't care, with the notable
exception of the rigid fixes for reasons that are explained in the
corresponding documentation.

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.

the latter has nothing to do with VMD.

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?

LAMMPS with a whole folder of examples, including one for fix deposit.

axel.