fixed freysoldt plotting (#116)

* fixed freysoldt plotting

* rename file

* typo

docs/source/content/defect-finder.ipynb

@@ -6,7 +6,7 @@
    "id": "22bb4abc-3e14-40c0-92af-6269729a4d3a",
    "metadata": {},
    "source": [
-    "# Finding the location of the point defect \n",
+    "# Defect Finder\n",
     "\n",
     "As you introduced a defect into a crystalline system, all of the atoms in the system will be subject to displacements\n",
     "during the atomic relaxation process. This can be especially problematic for native point defects, since the similar atoms in the simulation cell are technically fungible so split-vacancies and split-interstitials can be created with ill-defined positions.\n",

pymatgen/analysis/defects/corrections/freysoldt.py

@@ -340,8 +340,8 @@ def perform_pot_corr(
 
     C = np.mean(tmppot)
     _logger.debug("C = %f", C)
-    final_shift = [short[j] + C for j in range(len(v_R))]
-    v_R = [elmnt - C for elmnt in v_R]
+    short_range = short
+    v_R = [elmnt for elmnt in v_R]
 
     _logger.info("C value is averaged to be %f eV ", C)
     _logger.info("Potentital alignment energy correction (q * Delta):  %f (eV)", q * C)
@@ -352,7 +352,8 @@ def perform_pot_corr(
         "Vr": v_R,
         "x": axis_grid,
         "dft_diff": np.array(defavg) - np.array(pureavg),
-        "final_shift": final_shift,
+        "short_range": short_range,
+        "shift": C,
         "check": [mid - checkdis, mid + checkdis + 1],
     }
     # log uncertainty:
@@ -383,23 +384,26 @@ def plot_plnr_avg(plot_data, title=None, saved=False, ax=None):
     x = plot_data["pot_plot_data"]["x"]
     v_R = plot_data["pot_plot_data"]["Vr"]
     dft_diff = plot_data["pot_plot_data"]["dft_diff"]
-    final_shift = plot_data["pot_plot_data"]["final_shift"]
+    short_range = plot_data["pot_plot_data"]["short_range"]
     check = plot_data["pot_plot_data"]["check"]
+    C = plot_data["pot_plot_data"]["shift"]
 
     if ax is None:
         fig, ax = plt.subplots()
-    ax.plot(x, v_R, c="green", zorder=1, label="long range from model")
+    ax.plot(x, v_R, c="black", zorder=1, label="long range from model")
     ax.plot(x, dft_diff, c="red", label="DFT locpot diff")
-    ax.plot(x, final_shift, c="blue", label="short range (aligned)")
+    ax.plot(x, short_range, c="green", label="short range (not aligned)")
+    ax.axhline(C, color="k", linestyle="--")
+    ax.text(4, C, f"C={C:0.3f}", va="bottom")
 
     tmpx = [x[i] for i in range(check[0], check[1])]
     ax.fill_between(
         tmpx, -100, 100, facecolor="red", alpha=0.15, label="sampling region"
     )
 
     ax.set_xlim(round(x[0]), round(x[-1]))
-    ymin = min(min(v_R), min(dft_diff), min(final_shift))
-    ymax = max(max(v_R), max(dft_diff), max(final_shift))
+    ymin = min(min(v_R), min(dft_diff), min(short_range))
+    ymax = max(max(v_R), max(dft_diff), max(short_range))
     ax.set_ylim(-0.2 + ymin, 0.2 + ymax)
     ax.set_xlabel(r"distance along axis ($\AA$)", fontsize=15)
     ax.set_ylabel("Potential (V)", fontsize=15)

pymatgen/analysis/defects/generators.py

@@ -42,7 +42,9 @@ def _space_group_analyzer(self, structure: Structure) -> SpacegroupAnalyzer:
                 angle_tolerance=self.angle_tolerance,
             )
         else:  # pragma: no cover
-            raise ValueError("This generator does not have symprec and angle_tolerance")
+            raise ValueError(
+                "This generator is using the `SpaceGroupAnalyzer` and requires `symprec` and `angle_tolerance` to be set."
+            )
 
     def get_defects(self, *args, **kwargs) -> list[Defect]:
         """Call the generator and convert the results into a list."""
@@ -291,7 +293,7 @@ def generate(self, structure: Structure, insert_species: set[str] | list[str], *
             insert_species: The species to be inserted.
             **kwargs: Additional keyword arguments for the ``Interstitial`` constructor.
         """
-        if len(set(insert_species)) != len(insert_species):
+        if len(set(insert_species)) != len(insert_species):  # pragma: no cover
             raise ValueError("Insert species must be unique.")
         cand_sites_and_mul = [*self._get_candidate_sites(structure)]
         for species in insert_species:
@@ -368,7 +370,7 @@ def generate(self, chgcar: Chgcar, insert_species: set[str] | list[str], **kwarg
             insert_species: The species to be inserted.
             **kwargs: Additional keyword arguments for the ``Interstitial`` constructor.
         """
-        if len(set(insert_species)) != len(insert_species):
+        if len(set(insert_species)) != len(insert_species):  # pragma: no cover
             raise ValueError("Insert species must be unique.")
         cand_sites_and_mul = [*self._get_candidate_sites(chgcar)]
         for species in insert_species: