Merge pull request #519 from juijan/read-basis-fix

Fix reading of basis

sisl/io/siesta/orb_indx.py

@@ -83,11 +83,11 @@ def crt_atom(i_s, spec, orbs):
         orbs = []
         specs = []
         ia = 1
+        i_s = 0
         for _ in range(no):
             line = self.readline().split()
 
             i_a = int(line[1])
-            i_s = int(line[2]) - 1
             spec = line[3]
             if i_a != ia:
                 if i_s not in specs:
@@ -96,6 +96,8 @@ def crt_atom(i_s, spec, orbs):
                 ia = i_a
                 orbs = []
 
+            i_s = int(line[2]) - 1
+
             if i_s in specs:
                 continue
             nlmz = list(map(int, line[5:9]))

sisl/io/siesta/tests/test_orb_indx.py

@@ -18,5 +18,18 @@ def test_si_pdos_kgrid_orb_indx(sisl_files):
     atoms = orbindxSileSiesta(f).read_basis()
 
     assert len(atoms) == 2
+    assert atoms.nspecie == 1
     assert len(atoms[0]) == 13
     assert len(atoms[1]) == 13
+
+
+def test_sih_orb_indx(sisl_files):
+    f = sisl_files(_dir, 'sih.ORB_INDX')
+    nsc = orbindxSileSiesta(f).read_supercell_nsc()
+    assert np.all(nsc == 1)
+    atoms = orbindxSileSiesta(f).read_basis()
+
+    assert len(atoms) == 65
+    assert atoms.nspecie == 2
+    assert len(atoms[0]) == 4
+    assert len(atoms[-1]) == 1