New normalization energy + Fixes + Merge

src/openqdc/datasets/base.py

@@ -143,10 +143,18 @@ def _precompute_statistics(self, overwrite_local_cache: bool = False):
             logger.info("Loaded precomputed statistics")
         else:
             logger.info("Precomputing relevant statistics")
-            (formation_E_mean, formation_E_std, total_E_mean, total_E_std) = self._precompute_E()
+            (
+                inter_E_mean,
+                inter_E_std,
+                formation_E_mean,
+                formation_E_std,
+                total_E_mean,
+                total_E_std,
+            ) = self._precompute_E()
             forces_dict = self._precompute_F()
             stats = {
                 "formation": {"energy": {"mean": formation_E_mean, "std": formation_E_std}, "forces": forces_dict},
+                "inter": {"energy": {"mean": inter_E_mean, "std": inter_E_std}, "forces": forces_dict},
                 "total": {"energy": {"mean": total_E_mean, "std": total_E_std}, "forces": forces_dict},
             }
             with open(local_path, "wb") as f:
@@ -162,20 +170,24 @@ def _precompute_E(self):
         s = np.array(self.data["atomic_inputs"][:, :2], dtype=int)
         s[:, 1] += IsolatedAtomEnergyFactory.max_charge
         matrixs = [matrix[s[:, 0], s[:, 1]] for matrix in self.__isolated_atom_energies__]
-        converted_energy_data = self.convert_energy(self.data["energies"])
+        converted_energy_data = self.data["energies"]
         # calculation per molecule formation energy statistics
         E = []
         for i, matrix in enumerate(matrixs):
             c = np.cumsum(np.append([0], matrix))[splits_idx]
             c[1:] = c[1:] - c[:-1]
             E.append(converted_energy_data[:, i] - c)
         E = np.array(E).T
+        inter_E_mean = np.nanmean(E / self.data["n_atoms"][:, None], axis=0)
+        inter_E_std = np.nanstd(E / self.data["n_atoms"][:, None], axis=0)
         formation_E_mean = np.nanmean(E, axis=0)
         formation_E_std = np.nanstd(E, axis=0)
         total_E_mean = np.nanmean(converted_energy_data, axis=0)
         total_E_std = np.nanstd(converted_energy_data, axis=0)
 
         return (
+            np.atleast_2d(inter_E_mean),
+            np.atleast_2d(inter_E_std),
             np.atleast_2d(formation_E_mean),
             np.atleast_2d(formation_E_std),
             np.atleast_2d(total_E_mean),
@@ -265,10 +277,13 @@ def atoms_per_molecules(self):
 
     def _set_units(self, en, ds):
         old_en, old_ds = self.energy_unit, self.distance_unit
-        if en is not None:
-            self.set_energy_unit(en)
-        if ds is not None:
-            self.set_distance_unit(ds)
+        en = en if en is not None else old_en
+        ds = ds if ds is not None else old_ds
+
+        # if en is None:
+        self.set_energy_unit(en)
+        # if ds is not None:
+        self.set_distance_unit(ds)
         if self.__force_methods__:
             self.__forces_unit__ = self.energy_unit + "/" + self.distance_unit
             self.__class__.__fn_forces__ = get_conversion(old_en + "/" + old_ds, self.__forces_unit__)
@@ -566,7 +581,7 @@ def get_statistics(self, normalization: str = "formation", return_none: bool = T
         """
         Get the statistics of the dataset.
         normalization : str, optional
-            Type of energy, by default "formation", must be one of ["formation", "total"]
+            Type of energy, by default "formation", must be one of ["formation", "total", "inter"]
         return_none : bool, optional
             Whether to return None if the statistics for the forces are not available, by default True
             Otherwise, the statistics for the forces are set to 0.0

src/openqdc/utils/atomization_energies.py

@@ -606,6 +606,7 @@ def get_matrix(level_of_theory: str) -> np.ndarray:
     ("V", -3): -942.9562885518893,
     ("V", -2): -943.4308412125442,
     ("V", -1): -943.6771718004992,
+    ("V", 0): -943.5386343398394,
     ("V", 1): -943.4482869898394,
     ("V", 2): -942.9322435731367,
     ("V", 3): -941.7985542135455,

src/openqdc/utils/constants.py

@@ -6,7 +6,7 @@
 
 BOHR2ANG = 0.52917721092
 
-POSSIBLE_NORMALIZATION = ["formation", "total"]
+POSSIBLE_NORMALIZATION = ["formation", "total", "inter"]
 
 NOT_DEFINED = {
     "mean": None,