velocity

Dear lammps users

i am depositing molecules on a surface using fix deposit in a loop. initial system is comprised of oxygen molecules and Ni atoms. initial velocity for this system is chosen from a gaussian distribution. each time that 1 oxygen molecule is adsorbed on the surface i use fix deposit for inserting new one. i think i should define velocity for this new molecule but i do not know how can i do this without disrupting dynamics of system? is a bad idea to reset velocities of all oxygens in gas phase every step that i insert new particle?

Best Regard.

Dear lammps users

i am depositing molecules on a surface using fix deposit in a loop

why a loop?

. initial system is comprised of oxygen molecules and Ni atoms. initial velocity for this system is chosen from a gaussian distribution. each time that 1 oxygen molecule is adsorbed on the surface i use fix deposit for inserting new one.

i don't understand what you mean by this statement. and also, why you
would need to wait until a molecule is absorbed. this seems rather
unrealistic.

i think i should define velocity for this new molecule but i do not know how can i do this without disrupting dynamics of system?

it is a new molecule that (ideally) would not (yet) interact with any
other molecule, so what does it matter. then initial velocity can be
chosen from a range in fix deposit itself.

is a bad idea to reset velocities of all oxygens in gas phase every step that i insert new particle?

yes, absolutely. it makes no sense at all.

axel.

Dear Axel
thanks for your reply.you are right. i paste here a part of reference that i am trying to do:
The oxidation of the Fe surfaces is initiated by introducing
O2 molecules in the vacuum with their radial positions chosen
randomly, The pressure is adjusted based on the
ratio of number of metal surface atoms and the oxygen gas
phase molecules, The velocities of the O2 are chosen from a
Maxwell‚ąíBoltzmann distribution corresponding to the re-
quired temperature, The gas pressure is maintained constant
during the simulation by introducing a new O2 molecule only
when the previous molecule dissociates and forms bonds with
the metal atoms, The
simulations were carried out using the Large-scale Atomic/
Molecular Massively Parallel Simulator (LAMPPS).
here is my input file:
dimension 3
units real
boundary p p f
atom_style charge

Dear Axel
thanks for your reply.you are right. i paste here a part of reference that i am trying to do:

the fact that something get published doesn't automatically mean, that
is is a smart or realistic model.

there are essentially two possible cases to consider:

1) low oxygen density where molecules are aimed at the surface. there
the insertion rate would be constant and the velocity wouldn't matter
so much.

2) high gas density. then is is simply a matter of making the gas
volume large enough so that the amount of oxygen molecules that reacts
with the surface is irrelevant.

the reasoning of "keeping the pressure constant" is laughable,
considering the typical fluctuations that you have with the length
scales available for MD. in any case, it would be easy to make some
estimates of the absorption/reaction rate and then adjust the
deposition rate accordingly. also, you are most welcome to prove me
wrong by means of a sensitivity study.

[...]

i think inserted particle with v=0 is not a good choice and setting velocity with fix deposit is not what i want.i want that maxwel-boltzman distribution of velocity in every step.

considering the discussion of the two scenarios, i consider this
desire a waste of time and effort. however, *if* you insist, you
always have the option to program a modified fix deposit yourself that
does what you want. that is the benefit of open source software.

thanks for your useful solution.

Best Regard.