On Thu, Feb 4, 2021 at 4:01 AM Pragati Sharma <[email protected]> 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 > > > On Sat, Jan 16, 2021 at 7:44 PM Christoph Junghans <[email protected]> wrote: >> >> On Sat, Jan 16, 2021 at 1:40 AM Pragati Sharma <[email protected]> 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 >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/CAMpF9Q3hL857_shxbt-bCSZ7Kf6vrbkGt%3D1DFVUE1CBYSd7qCA%40mail.gmail.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5Gy7wZSdt6ALR9r4gWb79vf8nzeGX0ZrzbSwgFBXZvtQ%40mail.gmail.com. > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAMpF9Q3rBGmNYzPpiv7eH6MQJ2Zkwqr1BzDTAC0HoqXXOT_bow%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4Xjc9bz6yu%3D3W7VqQww4AudwJmyNp2tjxJd%3DwgjoWH6A%40mail.gmail.com.
