IBI of periodic molecules

[Pragati Sharma]

Dear all,

Can the coarse grain potentials using IBI for graphene sheet which is periodic along xy direction be performed in votca.

I am trying to do it and it's throwing an error saying the "bead is bigger than half of the box".

Any ideas on this.

Thanks

[Christoph Junghans]

On Sat, Jan 16, 2021 at 1:40 AM Pragati Sharma <praga...@gmail.com> wrote:
>
> Dear all,
>
> Can the coarse grain potentials using IBI for graphene sheet which is periodic along xy direction be performed in votca.
>
> I am trying to do it and it's throwing an error saying the "bead is bigger than half of the box".

This check is in there to avoid non-unique mapping of the position in
case of periodic boundary conditions.
You could certainly modify the code to disable it and see what
happens, but my guess is your setup of the sheet has a very small box
length in z.
As that is mainly empty space, just try to increase the box size by a
factor 10 in z or so.

Above the error message VOTCA prints out two vectors, the first 3
numbers are the position of the reference point for the pbc
calculations r0 and the next 3 numbers are the positions of the atoms
that are too far away from r0. Can you post these numbers?

Christoph

> Any ideas on this.
>
> Thanks
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Pragati Sharma]

Hi Christoph,

I tried increasing the box length in z direction, but the error still persists. Its two layers of graphene each have 96 atoms.

The errors is:

"I have 192 beads in 2 molecules
I have 48 beads in 2 molecules for the coarse graining
Reading frame       0 time    0.000  
1.128
1.587
2.668 0.338
1.141
1.688
an error occurred:
coarse-grained bead is bigger than half the box
 (atoms C (id 1), C (id 21) , molecule 1)"

Is there an issue with the atomistic simulation?

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5Gy7wZSdt6ALR9r4gWb79vf8nzeGX0ZrzbSwgFBXZvtQ%40mail.gmail.com.

[Christoph Junghans]

On Thu, Feb 4, 2021 at 4:01 AM Pragati Sharma <praga...@gmail.com> wrote:
>
> Hi Christoph,
>
> I tried increasing the box length in z direction, but the error still persists. Its two layers of graphene each have 96 atoms.
>
> The errors is:
>
> "I have 192 beads in 2 molecules
> I have 48 beads in 2 molecules for the coarse graining
> Reading frame 0 time 0.000
> 1.128
> 1.587
> 2.668 0.338
> 1.141
> 1.688
> an error occurred:
> coarse-grained bead is bigger than half the box
> (atoms C (id 1), C (id 21) , molecule 1)"
>
>
> Is there an issue with the atomistic simulation?

There is nothing wrong, it is just that if a molecule is bigger that
1/2 box length the mapping is unique and hence VOTCA won't do it.
Imagine the following toy example in 1D: in a periodic box of length L
with one particle at L/4 and one at L*3/4 and you try to map these two
particles together, then the mapped particle could be at position L/2
or 0.

From the six numbers above, you can calculate 3 distances:
|1.128-2.668|, |1.587-1.141| and |0.338-1.688| which you can compare
to the 3 box lengths to know which box length you need to increase.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAMpF9Q3rBGmNYzPpiv7eH6MQJ2Zkwqr1BzDTAC0HoqXXOT_bow%40mail.gmail.com.