Fix periodic PySCF calculations (#74)

* pass lattice vectors if pyscf object has them
* Add test case based on reported issue

python/dftd3/pyscf.py

@@ -220,9 +220,17 @@ def kernel(self) -> Tuple[float, np.ndarray]:
         """
         mol = self.mol
 
+        lattice = None
+        periodic = None
+        if hasattr(mol, 'lattice_vectors'):
+            lattice = mol.lattice_vectors()
+            periodic = np.array([True, True, True], dtype=bool)
+
         disp = DispersionModel(
             np.array([gto.charge(mol.atom_symbol(ia)) for ia in range(mol.natm)]),
             mol.atom_coords(),
+            lattice=lattice,
+            periodic=periodic,
         )
 
         if self.param is not None:

python/dftd3/test_pyscf.py

@@ -20,7 +20,7 @@
 
 try:
     import pyscf
-    from pyscf import lib, gto, scf
+    from pyscf import gto, scf, pbc
     import dftd3.pyscf as disp
 except ModuleNotFoundError:
     pyscf = None
@@ -225,3 +225,31 @@ def test_gradient_hf():
     )
     grad = disp.energy(scf.RHF(mol)).run().nuc_grad_method()
     assert grad.kernel() == approx(ref, abs=1.0e-7)
+
+
+def test_issue_gh73():
+    mol = gto.M(
+        atom="""
+             O  -1.6256  -0.0413   0.3705
+             H  -0.7061  -0.0938   0.0934
+             H  -2.0618  -0.7328  -0.1359
+             """,
+        basis="def2-tzvp",
+    )
+
+    pmol = pbc.gto.M(
+        atom="""
+             O  -1.6256  -0.0413   0.3705
+             H  -0.7061  -0.0938   0.0934
+             H  -2.0618  -0.7328  -0.1359
+             """,
+        basis="def2-tzvp",
+        a=[[3, 0, 0], [0, 3, 0], [0, 0, 3]],
+    )
+
+    xc = 'pbe'
+
+    e_mol_disp = disp.DFTD3Dispersion(mol, xc=xc, version="d3bj").kernel()[0]
+    e_pbc_disp = disp.DFTD3Dispersion(pmol, xc=xc, version="d3bj").kernel()[0]
+
+    assert e_mol_disp != e_pbc_disp