Recomputing MF when working with atom indices

examples/dmet.ipynb

@@ -84,9 +84,9 @@
     "from tangelo import SecondQuantizedMolecule\n",
     "\n",
     "# The minimal import for DMET.\n",
-    "from tangelo.problem_decomposition.dmet.dmet_problem_decomposition import DMETProblemDecomposition\n",
+    "from tangelo.problem_decomposition import DMETProblemDecomposition\n",
     "# Ability to change localization method.\n",
-    "from tangelo.problem_decomposition.dmet.dmet_problem_decomposition import Localization\n",
+    "from tangelo.problem_decomposition.dmet import Localization\n",
     "# Use for VQE ressources estimation vs DMET.\n",
     "from tangelo.algorithms import VQESolver\n",
     "# Use for comparison.\n",
@@ -103,9 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "butane = \"\"\"\n",
@@ -169,9 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -378,9 +374,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -502,9 +496,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",

examples/overview_endtoend.ipynb

@@ -308,7 +308,8 @@
     }
    ],
    "source": [
-    "from tangelo.problem_decomposition.dmet.dmet_problem_decomposition import DMETProblemDecomposition, Localization\n",
+    "from tangelo.problem_decomposition import DMETProblemDecomposition\n",
+    "from tangelo.problem_decomposition.dmet import Localization\n",
     "\n",
     "# DMET-VQE, 5 fragments of size 2 atoms each\n",
     "dmet_options = {\"molecule\": mol, \"verbose\": False,\n",
@@ -1257,9 +1258,9 @@
    "hash": "89fcd33a61ce1c8ae91bdb4eff5eb93c6c13a9486366ee1fefd22c672d14276a"
   },
   "kernelspec": {
-   "display_name": "tangelo_oct21",
+   "display_name": "qsdk",
    "language": "python",
-   "name": "tangelo_oct21"
+   "name": "qsdk"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1271,7 +1272,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.9"
   }
  },
  "nbformat": 4,

tangelo/problem_decomposition/dmet/__init__.py

@@ -11,3 +11,5 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+
+from .dmet_problem_decomposition import Localization

tangelo/problem_decomposition/dmet/dmet_problem_decomposition.py

@@ -17,7 +17,7 @@
 from enum import Enum
 from functools import reduce
 import numpy as np
-from pyscf import gto
+from pyscf import gto, scf
 import scipy
 import warnings
 
@@ -108,7 +108,7 @@ def __init__(self, opt_dict):
             if max(fragment_atoms_flatten) >= self.molecule.natm:
                 raise RuntimeError("An atom id is higher than the number of atom (indices start at 0).")
             elif len(fragment_atoms_flatten) != len(set(fragment_atoms_flatten)):
-                raise RuntimeError("Atom indexes must only appear once.")
+                raise RuntimeError("Atom indices must only appear once.")
 
             # Converting fragment_atoms to an expected list of number of atoms (not atom ids).
             new_fragment_atoms = [len(frag) for frag in self.fragment_atoms]
@@ -130,8 +130,10 @@ def __init__(self, opt_dict):
             self.fragment_atoms = new_fragment_atoms
 
             # Force recomputing the mean field if the atom ordering has been changed.
-            self.mean_field = None
             warnings.warn("The mean field will be recomputed even if one has been provided by the user.", RuntimeWarning)
+            self.mean_field = scf.RHF(self.molecule)
+            self.mean_field.verbose = 0
+            self.mean_field.scf()
 
         # Check if the number of fragment sites is equal to the number of atoms in the molecule
         if self.molecule.natm != sum(self.fragment_atoms):

tangelo/problem_decomposition/tests/dmet/test_dmet.py

@@ -16,7 +16,8 @@
 import numpy as np
 
 from tangelo.molecule_library import mol_H4_doublecation_minao, mol_H4_doublecation_321g, mol_H10_321g, mol_H10_minao
-from tangelo.problem_decomposition.dmet.dmet_problem_decomposition import Localization, DMETProblemDecomposition
+from tangelo.problem_decomposition import DMETProblemDecomposition
+from tangelo.problem_decomposition.dmet import Localization
 from tangelo.algorithms.variational import VQESolver
 from tangelo.toolboxes.molecular_computation.rdms import matricize_2rdm
 
@@ -159,6 +160,19 @@ def test_fragment_ids(self):
 
         self.assertEqual(solver.fragment_atoms, [1, 1, 1, 1])
 
+    def test_build_with_atom_indices(self):
+        """Tests if a mean field is recomputed when providing atom indices."""
+
+        opt_dmet = {"molecule": mol_H4_doublecation_321g,
+                    "fragment_atoms": [[0], [1], [2], [3]],
+                    "fragment_solvers": "ccsd",
+                    "electron_localization": Localization.iao,
+                    "verbose": False
+                    }
+
+        solver = DMETProblemDecomposition(opt_dmet)
+        solver.build()
+
     def test_fragment_ids_exceptions(self):
         """Tests exceptions if a bad nested list of atom ids is provided. Two
         cases: if an atom id is higher than the number of atoms and if an id is