Please reply to the list, not to me.
I do think the 3x volume is added by pppm slab,
you do not need to preserve a box 3x as large.
However, having a wall to keep your particles from
evaporating may be artificial. I can’t think why
that would cause a problem for pppm, but Stan
will know better. If your simulation is running
fine (conserving energy), then it’s likely ok.
Steve
Thank you very much for your reply. I have now reduced the box dimension by removing the empty space. Thanks to it, the simulations are running must faster now!!
please note, that it doesn’t matter whether you have free space above or below your slab, as this calculation is still performed periodically. to recover the electrostatics for a slab configuration, a poisson solver is then used to compute the periodic interactions in z-direction and subtract those from the periodic result.
this solver is also the reason, why you must not use a reflecting wall on the edge of the cell. atoms must stay outside this additional space added or else the result for the periodic correction will be incorrect. one alternative way to deal with this, is to define a region above the adsorbed species where you use fix oneway instead. this works similar to a reflecting wall, but can be used in places where fix wall/reflect cannot be applied.
axel.
Thank you very much for your reply. I have understood your point regarding the fix reflect position wrt to the slab. However, I could not understand how to apply fix oneway to my case. I am studying droplet wetting on a substrate. The reflective wall prevents the atoms from crossing the top of the domain. The fix oneway seems to enforce particles to move in a particular direction. How to employ this fix in my case? I simply wish to prevent the atoms from crossing zhi, but not move them in a specific direction.
Regards,
Manash
Thank you very much for your reply. I have understood your point regarding the fix reflect position wrt to the slab. However, I could not understand how to apply fix oneway to my case. I am studying droplet wetting on a substrate. The reflective wall prevents the atoms from crossing the top of the domain. The fix oneway seems to enforce particles to move in a particular direction. How to employ this fix in my case? I simply wish to prevent the atoms from crossing zhi, but not move them in a specific direction.
fix oneway operates pretty much the same as fix wall/reflect: if an atom enters the region it applies on (i.e. crosses the wall), the fix will reverse the corresponding velocity component. so all you have to do is to define a sufficiently thick region (so that an atom cannot pass through it within a single time step) near the original (before expansion due to kspace_modify slab) boundary, and you have your fix preventing atoms from escaping and moving through the “forbidden zone”.
axel.
Thank you very much. That makes everything clear!!
Regards,
Manash