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Re: [lammps-users] MD simulations in hexagon prism unit cell

# Re: [lammps-users] MD simulations in hexagon prism unit cell

 From: Axel Kohlmeyer Date: Tue, 19 Sep 2017 09:20:56 -0400

```surendra,

please note that you are about to set yourself up for public
embarrassment and ridicule.

a) the kind of changes you would need to do to LAMMPS to support a
different kind of cell representation are **substantial**.
it is not just a couple of subroutines. it is all over the place.
check out the changes required for a triclinic cell. i counted over
1000 places where this is tested for and where special subroutines are
implemented. ...and a lot of the triclinic code can utilize the
orthogonal cell code by switching between fractional coordinate
representation (which is orthogonal) and conventional coordinates.
specifically the parallel communication for setting up the domain
decomposition and communication of ghost atom information (forward and
reverse) and the border communication for particle exchange with
neighboring cells is a major effort. major effort meaning of the order
of years of your time spent programming and debugging.

b) on top of that, what you claim you need to do is _not at all_ needed.
you can **easily** represent your hexagonal system with a triclinic
cell that is tilted in the xy plane, and if you build a supercell from
two primitive triclinic cells, you can even use an orthogonal cell. i
recommend the latter, as it makes many things easier.

since this is essentially a 2d problem, i suggest you pick up a piece
of quad-ruled paper, draw it out, and you'll see.  draw four hexagons
(one over two over one) and connect the centers, you will get a
rhombus, that covers the same area as one hexagon. add more hexagons
and more rhombi you will see clearly that you cover the same volume
with hexagons and rhombi and that both are a space-filling lattice.

and you'll see.

or google it for a bit, and you'll see.

axel.

On Tue, Sep 19, 2017 at 12:08 AM, surendra jain <jainsk.iitkgp@...24...> wrote:
> Dear Andrew,
>
>   I am using hexagon prism unit cell. The boundaries of the simulation
> cell is below :
>
>
>                                        5
>                                2              1
>
>                                        0
>
>                                 3             4
>
>                                        6
>
> Thus 1 to 6 marks the corners of my simulation cell.. The PBC in this
> system is different than orthogonal or hexagonal system. I have to
> change the neighbors calculation routine and PBC routine.

>
> Best Regards,
> Surendra
>
>

--
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.

```