Bugfix for Vasprun reading with POTCAR for chemical shift calculations

pymatgen/apps/borg/tests/test_queen.py

@@ -30,7 +30,7 @@ def test_get_data(self):
         drone = VaspToComputedEntryDrone()
         self.queen = BorgQueen(drone, PymatgenTest.TEST_FILES_DIR, 1)
         data = self.queen.get_data()
-        assert len(data) == 15
+        assert len(data) == 16  # added new folder for testing of chemical shift vasprun.
 
     def test_load_data(self):
         drone = VaspToComputedEntryDrone()

pymatgen/io/vasp/inputs.py

@@ -2281,9 +2281,9 @@ def from_file(filename: str):
         potcar = Potcar()
 
         functionals = []
-        for p in fdata.split("End of Dataset"):
-            if p_strip := p.strip():
-                single = PotcarSingle(p_strip + "\nEnd of Dataset\n")
+        for p in fdata.split("End of Dataset\n"):
+            if p.strip():
+                single = PotcarSingle(p + "End of Dataset\n")
                 potcar.append(single)
                 functionals.append(single.functional)
         if len(set(functionals)) != 1:

pymatgen/io/vasp/outputs.py

@@ -1149,8 +1149,13 @@ def update_charge_from_potcar(self, path):
                 potcar_nelect = sum(ps.ZVAL * num for ps, num in zip(potcar, nums))
             charge = potcar_nelect - nelect
 
-            for s in self.structures:
-                s._charge = charge
+            # If we do a chemical shift calculation, there is only one ionic step really,
+            # but parsing the vasprun.xml file will result in len(self.ionic_steps) > 1
+            # only the first one contains a structure however, where we can update
+            # the charge.
+            if not self.incar.get("LCHIMAG"):
+                for s in self.structures:
+                    s._charge = charge
             if hasattr(self, "initial_structure"):
                 self.initial_structure._charge = charge
             if hasattr(self, "final_structure"):

pymatgen/io/vasp/tests/test_inputs.py

@@ -1019,15 +1019,13 @@ def test_verify_correct_potcar_with_hash(self):
     def test_multi_potcar_with_and_without_hash(self):
         filename = f"{PymatgenTest.TEST_FILES_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Fe_O.gz"
         cwd = os.path.abspath(os.path.dirname(__file__))
-        loadfn(os.path.join(cwd, "../vasp_potcar_file_hashes.json"))
-        Potcar.from_file(filename)
-        # Still need to test the if POTCAR can be read.
-        # No longer testing for hashes
-        # for psingle in potcars:
-        #     if hasattr(psingle, "hash_sha256_from_file"):
-        #         assert psingle.hash_sha256_computed == psingle.hash_sha256_from_file
-        # else:
-        #     assert psingle.file_hash in file_hash_db
+        file_hash_db = loadfn(os.path.join(cwd, "../vasp_potcar_file_hashes.json"))
+        potcars = Potcar.from_file(filename)
+        for psingle in potcars:
+            if hasattr(psingle, "hash_sha256_from_file"):
+                assert psingle.hash_sha256_computed == psingle.hash_sha256_from_file
+            else:
+                assert psingle.file_hash in file_hash_db
 
     # def test_default_functional(self):
     #     p = PotcarSingle.from_symbol_and_functional("Fe")

pymatgen/io/vasp/tests/test_outputs.py

@@ -665,6 +665,16 @@ def test_parsing_chemical_shift_calculations(self):
         assert n_estep == 10
         assert vasp_run.converged
 
+        # test another chemical shift calculation done with 6.4.1
+        # and also parsing the associated POTCAR file
+        filepath_wPOT = f"{self.TEST_FILES_DIR}/nmr/cs/with_POTCAR/vasprun.xml.gz"
+        vasp_run_wPOT = Vasprun(filepath_wPOT, parse_potcar_file=True)
+
+        n_estep_wPOT = len(vasp_run_wPOT.ionic_steps[-1]["electronic_steps"])
+        assert vasp_run_wPOT.converged
+        assert n_estep_wPOT == 4
+        assert vasp_run_wPOT.final_structure._charge == 0.0
+
     def test_parsing_efg_calcs(self):
         filepath = f"{self.TEST_FILES_DIR}/nmr/efg/AlPO4/vasprun.xml"
         vasp_run = Vasprun(filepath)