Thanks!
This is exactly what I needed.
On Sat, Dec 17, 2016 at 4:31 AM, Joseph Weston <joseph.westo...@gmail.com>
wrote:
> Hi,
>
> > I'm doing a self consistent calculation and I need the matrix element
> for a
> > site when setting the coupling.
> > I got it working but I wanted to know if there was a correct way.
> > Here is my code which uses scipy.spatial.
> >
> > def onsite(site, Delta=None, coords=None):
> > if (Delta is None and coords is None):
> > Delta_r = Delta_0
> > else:
> > _, i = spatial.KDTree(coords).query(site.pos)
> > Delta_r = Delta[i]
> > return -mu * tau_z + Delta_r * tau_x
>
> Ok, so you essentially need to map from site -> site_index in order to
> index into your array, right? I guess the solution will depend on
> whether your sites are moving around or not during your self-consistent
> loop. My guess is "no", as you appear to be self-consistently
> determining some superconducting order parameter, and I guess your sites
> correspond to a discretisation of the continuous problem.
>
> In this case I would say that the simplest thing to do would be to use
> a `dict` data structure to do the mapping site -> site_index. The reason
> is that lookups in a dict have O(1) complexity, unlike a KDTree. In
> addition, this mapping can be constructed once, when the system is
> finalized, and then passed to the `onsite` function as a parameter.
>
> In Kwant 1.3 systems will have an attribute `id_by_site`, which stores
> this dictionary, but constructing it is also trivial:
>
> id_by_site = {site: i for i, site in enumerate(syst.sites)}
>
>
> So a full example would look like:
>
> def onsite(site, id_by_site, Delta=None):
> Delta_r = Delta_0 if Delta is None else Delta[id_by_site[site]]
> return -mu * tau_z + Delta_r * tau_x
>
> builder = kwant.Builder(...)
> builder[...] = onsite
> ...
>
> syst = builder.finalize()
>
> id_by_site = {site: i for i, site in enumerate(syst.sites)}
> Delta = [0.1] * len(syst.sites) # trivial example
> ...
> syst.smatrix(syst, args=(id_by_site, Delta))
>
>
> Hope that helps,
>
> Joe
>
