How do I get the index for a given site?
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 where coords is obtained by sites = kwant.plotter.sys_leads_sites(syst, 0)[0] coords = kwant.plotter.sys_leads_pos(syst, sites) I feel like this may be a roundabout solution but it is working. Any help would be appreciated. Thanks, Eric
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
Thanks! This is exactly what I needed. On Sat, Dec 17, 2016 at 4:31 AM, Joseph Weston <joseph.weston08@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
participants (2)
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Eric Mascot -
Joseph Weston