Using the fix deposit command, I’m trying to deposit carbon atoms on the amorphous silica substrate. The velocity of these atoms should be -353.55 as it is equal to 75 eV of each atom which is the recommended value to obtain DLC properties according to many articles. The problem is this high velocity causes the substrate to sputter instead of the intended deposition. When I tried to lower the velocity to -10, deposition occurred correctly.
How can I solve this issue?
Secondly, I need to perform a relaxation process with a time interval of 1 ps between two sequential impacts across 100 steps to ensure that the system is at equilibrium before the deposition of subsequent carbon atoms. I am guessing that this can be done via the minimize command. However, in the last paragraph of the fix deposit command documentation, it is written that " This fix is not invoked during energy minimization."
How can I perform this relaxation process? deposit.in (2.5 KB) amorphous.data (1.5 MB)
Thank you so much for your time!
In which units? How did you compare this to 75 eV?
You are guessing wrong. Minimization is not equilibration. Minimization will try to move the system to the next potential energy minimum, so that is equivalent to reducing its temperature to 0K (it won’t show, because the assigned velocities will remain unchanged, but the minimization procedure will ignore those). Instead equilibration means that you continue running your system, ideally with a thermostat to remove excess kinetic energy and return to a state that is consistent with the desired temperature.
It would not make sense to deposit atoms during minimization since minimization does not have a “timeline”.
You should discuss equilbration versus minimization with your adviser/tutor. This is a fundamental part of doing correct MD simulations and thus there should be no questions about it. There should also be useful information about this in (proper) MD text books.