A problem with integration during deposition

      1. 오후 3:30에 “Axel Kohlmeyer” <[email protected]>님이 작성:

From your description of the symptom, either the created atom has zero

velocity, or it is not being included in the MD integrator (usually fx
nve). To check the first case, every time you execute the command:

    velocity g_temp set \{vx\} {vy} ${vz} units box

the values of vz that is used will be echoed to screen and log file.
For the second case, you could print out the value of count(group_id),
where group_id is the group id of the atoms that are supposed to move.


Thank you.
As you mentioned, I used following script and check that every time the created atom had velocity in negative z direction.

group g_temp id {id1} velocity g_temp set {vx} {vy} {vz} units box

variable vz equal -126.73999999999999488
variable vx equal 0
variable vy equal 0

But at some point, the create atom moved in “positive z direction” even though the printed velocity was in “negative z direction”. It was the start of the problem and i don’t know why!

After the problematic atom (if the atom id was 10) leaved the simulation box, an atom created right after had atom id 10 too (i set the id =11), so it was not included in any group and couldn’t be integrated.