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[lammps-users] How to set up the box size for mono-layer graphene
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[lammps-users] How to set up the box size for mono-layer graphene

From: JWG <w.g.jiang@...127...>
Date: Sun, 11 Jun 2017 19:52:59 +0800 (CST)

Dear all,

I am simulating nanoindentation of mono-layer graphene. We modeled the mono-layer graphene in Lammps. 

boundary f f s
units metal
# create geometry
lattice       custom 1.0 a1 2.46 0.0 0.0 a2 0.0 4.26 0.0 a3 0.0 0.0 3.4 &
                         basis 0.0 0.0 0.0 &
                         basis 0.5 0.16666666667 0.0 &  
                         basis 0.5 0.5 0.0 &
                         basis 0.0 0.66666666667 0.0 
region        graphene block 0 364.14 0 364.14 77.52 80.92 units box
create_box 1 graphene
create_atoms 1 region graphene
mass          1 12.01
group         graphene region graphene
pair_style  airebo 2.5 0 0
#pair_style  rebo
pair_coeff * * ../CH.airebo  C  
timestep 0.001 
minimize 2.3e-16 1.0e-3 200000 200000

but we got an error message: Cannot use neighbor bins - box size << cutoff (../neighbor.cpp:1803).
If I change the region command:
region        graphene block 0 364.14 0 364.14 67.52 80.92 units box,
that is ok. But we cannot get a single-layer graphene.
What mistakes in our input codes? How to correct the codes for get a single-layer graphene?
thanks very much.


在 2017-06-11 08:39:41,"Axel Kohlmeyer" <akohlmey@...24...> 写道:

On Sat, Jun 10, 2017 at 6:02 PM, 严锐 <r-yan14@...61...> wrote:
Dear All, 

I'm using lammps to simulate Al2O3 single crystal and pure Al single crystal. My dump file contatins id, type, x, y, z. When I use VMD to visualize my dump file, I found that there were some isolated atoms on the surface of the box as shown in picuture_1, making the surface rough. My understandings is that this is because the coordinates of these atoms are out of the boundary of the box. If we check the dump file, we can see that the coordiantes of some atoms are less than xlo or greater than xhi.I want to know how to move these atoms back to the simulation box so that VMD can give a better visualization of the surface, with the surface of a crystal being as flat as a inner plane, which is shown in picture_2? To do this, what should be included in dump file?

try dumping xu, yu, zu instead of x, y, z.

you don't want to wrap them "back into the box"; that is already happening, but rather you don't want them to be wrapped back.

another issue could be, that you are creating atoms exactly on the box boundary. move the box by a small fraction of the lattice constant, say 20%, and these atoms may not be coming close to the box boundaries at all, so this all will become a non-issue.



Thanks and look forward to your reply.


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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.