LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] Insertion of empty volume with kspace_modify slab and fix wall/reflect
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] Insertion of empty volume with kspace_modify slab and fix wall/reflect


From: Manash Pratim Borthakur <manash.pborthakur@...24...>
Date: Thu, 23 Aug 2018 19:44:37 +0530

Thank you very much. That makes everything clear!!

Regards,
Manash

On Thu, Aug 23, 2018 at 7:27 PM Axel Kohlmeyer <akohlmey@...24...> wrote:


On Thu, Aug 23, 2018 at 9:52 AM Manash Pratim Borthakur <manash.pborthakur@...24...> wrote:
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.

 

Regards,
Manash

On Tue, Aug 21, 2018 at 7:19 PM Axel Kohlmeyer <akohlmey@...24...> wrote:
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.

On Tue, Aug 21, 2018 at 8:08 AM Manash Pratim Borthakur <manash.pborthakur@...24...> wrote:
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!!

On Sun, Aug 19, 2018 at 4:01 AM Steve Plimpton <sjplimp@...24...> wrote:
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

On Sat, Aug 18, 2018 at 2:14 AM, Manash Pratim Borthakur <manash.pborthakur@...24...> wrote:
Thank you for your reply. I am simulating wetting of a droplet on a substrate. To prevent losing atoms from the top non-periodic surface, I am using wall/reflect. So, if the box dimension does not have to be increased and the reflective walls are given at "zhi EDGE", does that mean the actual reflective wall is at a larger zhi distance due to kspace slab value of 3.0? 

Regards,
Manash

On Sat, Aug 18, 2018 at 3:53 AM Steve Plimpton <sjplimp@...24...> wrote:
Stan can answer these (CCd), though he may not be checking email for a while.

I don't think people generally use fix wall/reflect with slab-PPPM.  Rather they
just define a free surface, e.g. shrink-wrap boundary conditions.  I don't believe
you need to make the box bigger than the non-periodic dim.

Steve

On Tue, Aug 14, 2018 at 11:47 PM, Manash Pratim Borthakur <manash.pborthakur@...24...> wrote:
Hi,

I am simulating a water droplet on a solid substrate. The domain is periodic in x and y and empty space is provided in z direction with kspace_modify slab and fix wall/reflect. After going through a recent thread on kspace slab and fix wall/reflect (https://lammps.sandia.gov/threads/msg70495.html), I have some confusions which I wanted to clarify :

1. While using the kspace slab 3.0 option, should I manually insert empty space (in the z direction) in the input data file by changing the box dimensions? Since the droplet is sitting on the solid, I need empty space mostly on TOP of the droplet, not under the solid substrate. Thus, I need to extend only zhi, not zlo. Should I increase zhi (by about ~3 times) and apply the slab command or is it not necessary at all?

2. The fix wall/reflect boundary is applied at the zhi EDGE (far from the droplet) so that its influence is less. While using the slab command, what should be the zhi value for wall/reflect if empty space is not required to be manually inserted?

Kindly advise.

Regards,
Manash

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
lammps-users mailing list
lammps-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users



------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
lammps-users mailing list
lammps-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users


--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
lammps-users mailing list
lammps-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users


--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.