Merge pull request #29 from hentt30/develop

[feat]: One correction per orbital in minushalf execute

docs/source/execute.rst

@@ -220,10 +220,10 @@ on the values obtained in the optimization of the CUT and the resulting band ene
     .. code-block:: xml
 
             Valence correction cuts:
-                    (C):3.13 a.u
+                    (C,p):3.13 a.u
             ----------------------------------------------------------------
             Conduction correction cuts:
-                    (Si):2.77 a.u
+                    (Si,p):2.77 a.u
             ----------------------------------------------------------------
             GAP: 4.37eV
 

minushalf/corrections/vasp_correction.py

@@ -167,8 +167,9 @@ def execute(self) -> tuple:
         self.sum_correction_percentual = self._get_sum_correction_percentual()
 
         for symbol, orbitals in self.correction_indexes.items():
-            cut = self._find_best_correction(symbol, orbitals)
-            cuts_per_atom_orbital[symbol] = cut
+            for orbital in orbitals:
+                cut = self._find_best_correction(symbol, orbital)
+                cuts_per_atom_orbital[(symbol, orbital)] = cut
 
         gap = self._get_result_gap()
         return (cuts_per_atom_orbital, gap)
@@ -262,12 +263,11 @@ def _get_sum_correction_percentual(self) -> float:
 
         return total_sum
 
-    def _find_best_correction(self, symbol: str, orbitals: list) -> float:
+    def _find_best_correction(self, symbol: str, orbital: str) -> tuple:
         """
         Correct the potcar of the atom symbol in the
         orbital given. Then, find the best cut to the
         the correciton.
-
             Args:
                 symbol (str): Atom symbol
                 orbital (str): Orbital type (s,p,d,f)
@@ -276,7 +276,7 @@ def _find_best_correction(self, symbol: str, orbitals: list) -> float:
                 the optimum cut and the gap generated
                 by the correction.
         """
-        folder_name = "mkpotcar_{}".format(symbol.lower())
+        folder_name = f"mkpotcar_{symbol.lower()}_{orbital.lower()}"
         path = os.path.join(self.root_folder, folder_name)
         if os.path.exists(path):
             shutil.rmtree(path)
@@ -288,11 +288,12 @@ def _find_best_correction(self, symbol: str, orbitals: list) -> float:
         atoms_map = self.software_factory.get_atoms_map()
         number_equal_neighbors = self.software_factory.get_number_of_equal_neighbors(
             atoms_map=atoms_map, symbol=symbol)
-        for orbital in orbitals:
-            value = (100 / (1 + number_equal_neighbors)) * (
-                self.band_projection[orbital][symbol] /
-                self.sum_correction_percentual)
-            percentuals[orbital] = round(value)
+
+        value = (100 / (1 + number_equal_neighbors)) * (
+            self.band_projection[orbital][symbol] /
+            self.sum_correction_percentual)
+        percentuals[orbital] = round(value)
+
         self._generate_occupation_potential(path, percentuals)
 
         self.atom_potential = self._get_atom_potential_class(path, symbol)

minushalf/utils/fractionary_correction_indexes.py

@@ -31,6 +31,6 @@ def get_fractionary_correction_indexes(band_projection: pd.DataFrame,
 
     correction_indexes = defaultdict(list)
     for row, column in itertools.product(rows_name, columns_name):
-        if band_projection[column][row] >= treshold:
+        if band_projection[column][row] > treshold:
             correction_indexes[row].append(column)
     return correction_indexes

minushalf/utils/make_minushalf_results.py

@@ -32,19 +32,21 @@ def make_minushalf_results(
         if valence_cuts:
             file.write("Valence correction cuts:\n")
             for key, value in valence_cuts.items():
-                symbol = key
+                symbol, orbital = key
                 cut = value
-                file.write("\t({}):{:.2f} a.u\n".format(symbol, cut))
+                file.write("\t({},{}):{:.2f} a.u\n".format(
+                    symbol, orbital, cut))
             file.write(
                 "----------------------------------------------------------------\n"
             )
         ## Write conduction cuts
         if conduction_cuts:
             file.write("Conduction correction cuts:\n")
             for key, value in conduction_cuts.items():
-                symbol = key
+                symbol, orbital = key
                 cut = value
-                file.write("\t({}):{:.2f} a.u\n".format(symbol, cut))
+                file.write("\t({},{}):{:.2f} a.u\n".format(
+                    symbol, orbital, cut))
             file.write(
                 "----------------------------------------------------------------\n"
             )

tests/fixtures/minushalf_results/minushalf_results_conduction_cuts.dat

@@ -1,9 +1,9 @@
 Valence correction cuts:
-	(Ag):1.23 a.u
-	(Br):2.33 a.u
+	(Ag,d):1.23 a.u
+	(Br,f):2.33 a.u
 ----------------------------------------------------------------
 Conduction correction cuts:
-	(Ag):1.23 a.u
-	(Br):2.33 a.u
+	(Ag,s):1.23 a.u
+	(Br,p):2.33 a.u
 ----------------------------------------------------------------
 GAP: 2.33eV

tests/fixtures/minushalf_results/minushalf_results_only_valence_cuts.dat

@@ -1,5 +1,5 @@
 Valence correction cuts:
-	(Ag):1.23 a.u
-	(Br):2.33 a.u
+	(Ag,p):1.23 a.u
+	(Br,s):2.33 a.u
 ----------------------------------------------------------------
 GAP: 2.33eV

tests/unit/utils/test_get_fractionary_indexes.py

@@ -76,7 +76,7 @@ def test_aln_2d_cbm_treshold_29(file_path):
     cbm_projection = band_structure.cbm_projection()
     cbm_df = projection_to_df(cbm_projection)
     correction_indexes = get_fractionary_correction_indexes(cbm_df,
-                                                             treshold=29)
+                                                            treshold=28)
     assert correction_indexes["N"][0] == "s"
     assert correction_indexes["Al"][0] == "s"
 
@@ -102,7 +102,7 @@ def test_aln_2d_cbm_treshold_30(file_path):
     cbm_projection = band_structure.cbm_projection()
     cbm_df = projection_to_df(cbm_projection)
     correction_indexes = get_fractionary_correction_indexes(cbm_df,
-                                                             treshold=30)
+                                                            treshold=29)
     assert correction_indexes["N"][0] == "s"
     assert len(correction_indexes["Al"]) == 0
 
@@ -153,7 +153,7 @@ def test_gec_2d_vbm_changing_treshold_12(file_path):
     vbm_projection = band_structure.vbm_projection()
     vbm_df = projection_to_df(vbm_projection)
     correction_indexes = get_fractionary_correction_indexes(vbm_df,
-                                                             treshold=12)
+                                                            treshold=11)
     assert correction_indexes["C"][0] == "p"
     assert correction_indexes["Ge"][0] == "d"
 
@@ -179,7 +179,7 @@ def test_gec_2d_vbm_changing_treshold_13(file_path):
     vbm_projection = band_structure.vbm_projection()
     vbm_df = projection_to_df(vbm_projection)
     correction_indexes = get_fractionary_correction_indexes(vbm_df,
-                                                             treshold=13)
+                                                            treshold=12)
     assert correction_indexes["C"][0] == "p"
     assert len(correction_indexes["Ge"]) == 0
 
@@ -253,8 +253,7 @@ def test_bn_2d_vbm_without_treshold(file_path):
 
     vbm_projection = band_structure.vbm_projection()
     vbm_df = projection_to_df(vbm_projection)
-    correction_indexes = get_fractionary_correction_indexes(vbm_df,
-                                                             treshold=1)
+    correction_indexes = get_fractionary_correction_indexes(vbm_df, treshold=0)
     assert correction_indexes["N"][0] == "p"
     assert correction_indexes["B"][0] == "p"
 

tests/unit/utils/test_make_minushalf_results.py

@@ -13,8 +13,8 @@ def test_only_valence_cuts(file_path):
     expected_file_path = file_path(
         "/minushalf_results/minushalf_results_only_valence_cuts.dat")
     valence_cuts = {
-        "Ag": 1.23,
-        "Br": 2.33,
+        ("Ag", "p"): 1.23,
+        ("Br", "s"): 2.33,
     }
     gap = 2.334
     filename = "minushalf_results_only_valence_cuts.dat"
@@ -37,12 +37,12 @@ def test_conduction_cuts(file_path):
     expected_file_path = file_path(
         "/minushalf_results/minushalf_results_conduction_cuts.dat")
     valence_cuts = {
-        "Ag": 1.23,
-        "Br": 2.33,
+        ("Ag", "d"): 1.23,
+        ("Br", "f"): 2.33,
     }
     conduction_cuts = {
-        "Ag": 1.23,
-        "Br": 2.33,
+        ("Ag", "s"): 1.23,
+        ("Br", "p"): 2.33,
     }
     gap = 2.334
     filename = "minushalf_results_conduction_cuts.dat"