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First of all, let me express my greatest admiration for the package.. It is really useful!
Specially I would like to express my profound gratitude for implementing the KPM stuff!
So I have been playing around with the package. The current problem I am investigating is a 3D lattice with two orbitals on a single site and I have came up on a small bug.
Let me illustrate it with the following small bit of code
Thanks for reporting the bug and for the nice reproducible code example! Looks like the Hamiltonian builder was mistakenly ignoring the onsite matrix if the diagonal elements were all zero. This should be fixed now in 9d511b6.
I'll release v0.9.4 with the bug fix later this week. If you need the fix sooner, you can get it by installing the latest dev version as described here: compiling from source.