Dear Xavier, It's still not obvious to me, how to extract site coordinates in an easy way. The sys.sites is a long tuple with entries like Site(kwant.lattice.Monatomic([[1.0, 0.0, 0.0], [0.5, 0.8660254037844386, 0.0], [0.0, 0.0, 1.0]], [0.0, 0.0, 0.0], '0'), array([-4, 3, 0])) and "Site" is an unknown object. Best wishes, Sergey On 15/04/15 08:09, Xavier Waintal wrote:
Dear Sergey,
First you get the wave function through a call of wf = kwant.wave_function(finalized_sys, energy) Second your finalized sytem contains a list of the sites of the system finalized_sys.sites And each site contains its positions.
Best regards, Xavier
Le 15 avr. 2015 à 02:15, Sergey
a écrit : Dear Xavier, Thank you for rapid and useful reply! I am using a 3D embedding route, so, I cannot use the map function to plot the wave-function density. So, I need to find a way to get positions for the array returned by wave_function. I tried the command
coords=[kwant.plotter.sys_leads_pos(sys,site) for site in kwant.plotter.sys_leads_sites(sys, num_lead_cells=0)[0]]
but this does not work for some reason. Is there a more obvious way to get an array of site coordinates for finalized system?
Thank you, Sergey