Merge pull request #1465 from pyiron/solvation_energy

parse ediel_sol from OUTCAR

pyiron_atomistics/vasp/output.py

@@ -150,6 +150,9 @@ def collect(self, directory=os.getcwd(), sorted_indices=None):
             self.generic_output.dft_log_dict["cbm_list"] = self.outcar.parse_dict[
                 "cbm_list"
             ]
+            self.generic_output.dft_log_dict["ediel_sol"] = self.outcar.parse_dict[
+                "ediel_sol"
+            ]
 
         if vasprun_working:
             log_dict["forces"] = self.vp_new.vasprun_dict["forces"]

pyiron_atomistics/vasp/parser/outcar.py

@@ -57,6 +57,7 @@ def from_file(self, filename="OUTCAR"):
         energies_int = self.get_energy_without_entropy(filename=filename, lines=lines)
         energies_zero = self.get_energy_sigma_0(filename=filename, lines=lines)
         scf_energies = self.get_all_total_energies(filename=filename, lines=lines)
+        ediel_sol = self.get_ediel_sol(filename=filename, lines=lines)
         n_atoms = self.get_number_of_atoms(filename=filename, lines=lines)
         forces = self.get_forces(filename=filename, lines=lines, n_atoms=n_atoms)
         positions = self.get_positions(filename=filename, lines=lines, n_atoms=n_atoms)
@@ -101,6 +102,7 @@ def from_file(self, filename="OUTCAR"):
         self.parse_dict["energies_int"] = energies_int
         self.parse_dict["energies_zero"] = energies_zero
         self.parse_dict["scf_energies"] = scf_energies
+        self.parse_dict["ediel_sol"] = ediel_sol
         self.parse_dict["forces"] = forces
         self.parse_dict["positions"] = positions
         self.parse_dict["cells"] = cells
@@ -484,6 +486,31 @@ def get_energy_sigma_0_from_line(line):
             [get_energy_sigma_0_from_line(lines[j + 4]) for j in trigger_indices]
         )
 
+    @staticmethod
+    def get_ediel_sol(filename="OUTCAR", lines=None):
+        """
+        Gets the ediel_sol for every ionic step from the OUTCAR file
+
+        Args:
+            filename (str): Filename of the OUTCAR file to parse
+            lines (list/None): lines read from the file
+
+        Returns:
+            numpy.ndarray: A 1xM array of the total energies in $eV$
+
+            where M is the number of time steps
+        """
+
+        def get_ediel_sol_from_line(line):
+            return float(_clean_line(line.strip()).split()[-1])
+
+        trigger_indices, lines = _get_trigger(
+            lines=lines,
+            filename=filename,
+            trigger="Solvation  Ediel_sol  = ",
+        )
+        return np.array([get_ediel_sol_from_line(lines[j]) for j in trigger_indices])
+
     @staticmethod
     def get_all_total_energies(filename="OUTCAR", lines=None):
         """

tests/vasp/test_outcar.py

@@ -575,6 +575,25 @@ def test_get_memory_used(self):
                 memory_usage_dict[int(filename.split("/OUTCAR_")[-1])]
             )
 
+    def test_get_ediel_sol(self):
+        ediel_sol_dict = {
+            1: [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
+            10: [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
+            2: [],
+            3: [],
+            4: [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
+            5: [],
+            6: [],
+            7: [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
+            8: [],
+            9: [0., 0., 0., 0.],
+        }
+        for filename in self.file_list:
+            self.assertTrue(np.all(np.isclose(
+                self.outcar_parser.get_ediel_sol(filename),
+                ediel_sol_dict[int(filename.split("/OUTCAR_")[-1])]
+            )))
+
     def test_get_cpu_time(self):
         cpu_time_dict = {
             1: 3.543,