Merge branch 'fixup/kpm' into 'stable'

fix kpm.conductivity in the case where 'norbs' is not set

See merge request kwant/kwant!321

kwant/kpm.py

@@ -778,6 +778,8 @@ def conductivity(hamiltonian, alpha='x', beta='x', positions=None, **kwargs):
 
     Parameters
     ----------
+    hamiltonian : `~kwant.system.FiniteSystem` or matrix Hamiltonian
+        If a system is passed, it should contain no leads.
     alpha, beta : str, or operators
         If ``hamiltonian`` is a kwant system, or if the ``positions``
         are provided, ``alpha`` and ``beta`` can be the directions of the
@@ -1049,10 +1051,11 @@ def _velocity(hamiltonian, params, op_type, positions):
     elif isinstance(op_type, str):
         direction = directions[op_type]
         if isinstance(hamiltonian, system.System):
-            operator = hamiltonian.hamiltonian_submatrix(params=params,
-                                                         sparse=True)
-            positions = np.array([site.pos for site in hamiltonian.sites
-                                  for iorb in range(site.family.norbs)])
+            operator, norbs, norbs = hamiltonian.hamiltonian_submatrix(
+                params=params, sparse=True, return_norb=True
+            )
+            positions = np.vstack([[hamiltonian.pos(i)] * norb
+                                   for i, norb in enumerate(norbs)])
         elif positions is not None:
             operator = coo_matrix(hamiltonian, copy=True)
         displacements = positions[operator.col] - positions[operator.row]

kwant/tests/test_kpm.py

@@ -80,6 +80,13 @@ def test_conductivity():
         cond = kwant.kpm.conductivity(syst, alpha=alpha, beta=beta,
                                         positions=None, **kpm_params)
 
+    # test when 'norbs' not provided
+    n = lat.norbs
+    lat.norbs = None
+    cond = kwant.kpm.conductivity(syst, alpha=alpha, beta=beta,
+                                  positions=None, **kpm_params)
+    lat.norbs = n
+
     # test system or hamiltonian, no positions, but velocity operators
     cond_xx = kwant.kpm.conductivity(syst, alpha='x', beta='x',
                                      positions=None, **kpm_params)