Matt McGrath obfis... at gmail.com
Wed Aug 24 03:08:15 UTC 2011

When you say "import coordinates of a crystal", do you mean as a swap
move?  As in, you want to have gas molecules and crystal molecules
come into the box, or that you put crystal coordinates into the box at
the beginning, treat the whole box as QM, and then swap gas molecules
into the box (also treated as QM)?  The latter option should be
possible if the test I described above worked (since the force_env of
each box can be specified separately), and is what I assumed you
wanted to do in the first post.  If you also want to swap in crystal
nuclei, you could do that by making it a new molecule type (and
creating a psf file for it), but then it would swap into the QM box in
a completely random position, and would still be treated as a molecule
from CP2K's standpoint (rotated and translated together).  I don't
know if that's what you want or not.

                      Cheers, Matt

On Aug 23, 9:23 pm, Isaak Daniels <isaakdan... at gmail.com> wrote:
> Can I also have it so that in the non-vapor box, gas molecules can
> enter that box and one can also import coordinates of a crystal, with
> this box having QM?
> Thank you
> On Aug 23, 3:21 am, Matt McGrath <obfis... at gmail.com> wrote:
> > Hmm.  I was thinking about that, and I didn't think it would work
> > before I responded to your original question.  But now, I'm not so
> > sure.  If you set all the MM interactions in the vapor box to have
> > epsilon=0 and no charges (so you don't need Ewald sums), then you have
> > an ideal gas, so...maybe.
> > A quick way to check would be to try it with MM in both boxes, but set
> > all the LJ parameters and charges equal to zero in the vapor box.
> > Choose it to be large enough that the density doesn't really change
> > over the course of the simulation, don't do any molecule displacements
> > in the vapor box, and compare it against GCMC with a different code.
> > One concern I have is that, on swap moves, the code is going to check
> > for overlaps in the vapor box, which it should do for true GCMC.  If
> > you try this test and get an answer that is close, and you feel
> > comfortable changing the source code, I can let you know which lines
> > to change to remove those checks so we can see if it works.  I know of
> > codes that do GCMC as basically GEMC with a box that has no
> > interactions in it (and is big...500 molecules or more), so this
> > doesn't seem so different.
> >                                               Cheers, Matt
> > On Aug 22, 10:57 pm, Isaak Daniels <isaakdan... at gmail.com>
> > wrote:
> > > Can one do it so that the box not of interest (representing the
> > > environment) is MM while the other is done with QM, so one can avoid
> > > the pitfalls of enlarging the box?
> > > Thank you
> > > On Aug 21, 7:42 pm, Matt McGrath <obfis... at gmail.com> wrote:
> > > > Hi Isaak.  Unfortunately, this isn't really possible at the moment,
> > > > unless you do Gibbs ensemble Monte Carlo and make the second box huge,
> > > > i.e. essentially a reservoir.  Of course, if you're using any grid-
> > > > based method to compute the energy (Quickstep, Ewald) this adds a
> > > > whole lot of expense to the simulation as well, and probably isn't
> > > > worth it.
> > > > GCMC has been in the pipeline for a while (there have been issues with
> > > > the choice of reference state for QS calculations with GCMC), and is
> > > > the next big project on my list.  I'm about 30% done with the current
> > > > project (making the MC routines more streamlined), so it might get
> > > > implemented in the next year...but that's just a guess.  Could be six
> > > > months, could be a couple years, so if you're working on a major
> > > > project, it's probably best to use a different code.  Sorry!
> > > >                                 Cheers, Matt
> > > > On Aug 21, 2:51 am, Isaak Daniels <isaakdan... at gmail.com> wrote:
> > > > > Is there a way to run a sort of GCMC on Cp2k?
> > > > > Thank you

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