Fix decontract_basis function when basis are missed on certain atoms. (…

…Fix pyscf#1711) (pyscf#1943)

* Fix decontract_basis when basis are missed on certain atoms. (Fix pyscf#1711)

pyscf/gto/mole.py

@@ -626,6 +626,9 @@ def _to_full_contraction(mol, bas_idx):
 
     aoslices = mol.aoslice_by_atom()
     for ia, (ib0, ib1) in enumerate(aoslices[:,:2]):
+        if ib0 == ib1: # No basis on atom ia
+            continue
+
         if atoms is not None:
             if isinstance(atoms, str):
                 to_apply = ((atoms == mol.atom_pure_symbol(ia)) or

pyscf/gto/test/test_mole.py

@@ -1033,6 +1033,11 @@ def test_decontract_basis(self):
         s = ctr_coeff.T.dot(pmol.intor('int1e_ovlp')).dot(ctr_coeff)
         self.assertAlmostEqual(abs(s - mol.intor('int1e_ovlp')).max(), 0, 12)
 
+        # discard basis on atom 2. (related to issue #1711)
+        mol._bas = mol._bas[:5]
+        pmol, c = mol.decontract_basis()
+        self.assertEqual(pmol.nbas, 14)
+
         mol = gto.M(atom='He',
                     basis=('ccpvdz', [[0, [5, 1]], [1, [3, 1]]]))
         pmol, contr_coeff = mol.decontract_basis()