[ase-users] Constrained center of mass (Elsebeth Schr?der)

[Jens Jørgen Mortensen]

On Mon, 2011-03-07 at 11:19 +0000, Felix Hanke wrote:
> Hi,
> > Dear ASE users,
> >
> > I am looking at adsorbed molecules on a surface (at the moment using gpaw). I would like to include a constraint that fixes position of the center of mass of the molecule relative to the surface, or at least the center of mass of two of the atoms in the molecule.
> I wrote such a script fairly recently, the code and an example is 
> attached. The example takes a Cu slab with H2 in a very unphysical 
> position and forces the slab to rearrange around the H-atoms such as to 
> keep their CM constant. This should be a reasonably rigorous test for 
> such a constraint. To explicitly make sure that the constraint is 
> working, you need to run the example and open the trajectory output in 
> ag. Plotting the following should confirm that the CM is conserved to 
> within 1E-14 or so Angstrom in the y-direction:
> i, 0.5*(R[65][1] + R[64][1])
> and likewise for the other directions.
> 
> Hope this helps
> Cheers,
> Felix
> 
> > The (very) old dacapo version that had atomic position optimization imbedded in the dacapo code (i.e., before the optimization was lifted out into ASE) was able to do the latter

Elsebeth: What exactly did Dacapo do?  I don't think it could fix COM
for a molecule on a surface.

Jens Jørgen

>  and I wonder if this has also been included in ASE, or if anybody could help me how to write such a constraint. I have browsed the ASE documentation but didn't find anything that seemed useful.
> >
> > Elsebeth
> >
> > =====================================================================
> > Elsebeth Schr?der, prof.
> > Dept. of Microtechnology and         tel.:   +46 31 772 8424
> > Nanoscience (MC2)                    fax:    +46 31 772 3471
> > Chalmers Univ. of Technology         e-mail: schroder at chalmers.se
> > SE-412 96 Gothenburg, Sweden         http://fy.chalmers.se/~schroder
> > =====================================================================
> >
> 
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