Merge branch 'master' of github.com:materialsproject/pymatgen

Former-commit-id: dfacb43c24648c4eb1ef4f7b1f4b8aa38066194f [formerly ca4af68]
Former-commit-id: fcd5a869e5e023b1badab969f5233d35f434959f

Author: shyuep

pymatgen/io/qchemio.py

@@ -1207,7 +1207,7 @@ def _parse_job(cls, output):
         thermal_corr_pattern = re.compile("(?P<name>\S.*\S):\s+"
                                           "(?P<correction>\d+\.\d+)\s+"
                                           "k?cal/mol")
-        detailed_charge_pattern = re.compile("Ground-State (?P<method>\w+) Net"
+        detailed_charge_pattern = re.compile("(Ground-State )?(?P<method>\w+)( Net)?"
                                              " Atomic Charges")
         nbo_charge_pattern = re.compile("(?P<element>[A-Z][a-z]{0,2})\s+(?P<no>\d+)\s+(?P<charge>\-?\d\.\d+)"
                                         "\s+(?P<core>\-?\d+\.\d+)\s+(?P<valence>\-?\d+\.\d+)"
@@ -1278,6 +1278,7 @@ def _parse_job(cls, output):
         current_beta_homo = None
         homo_lumo = []
         bsse = None
+        hiershfiled_pop = False
         for line in output.split("\n"):
             for ep, message in error_defs:
                 if ep.search(line):
@@ -1517,8 +1518,13 @@ def _parse_job(cls, output):
                     parse_input = True
                 elif "Standard Nuclear Orientation (Angstroms)" in line:
                     parse_coords = True
-                elif "Cycle       Energy         DIIS Error" in line\
-                        or "Cycle       Energy        RMS Gradient" in line:
+                elif "Performing Hirshfeld population analysis" in line:
+                    hiershfiled_pop = True
+                elif "Hirshfeld: atomic densities completed" in line:
+                    hiershfiled_pop = False
+                elif ("Cycle       Energy         DIIS Error" in line\
+                        or "Cycle       Energy        RMS Gradient" in line)\
+                        and not hiershfiled_pop:
                     parse_scf_iter = True
                     scf_iters.append([])
                     scf_successful = False

pymatgen/io/tests/test_qchemio.py

@@ -1742,6 +1742,13 @@ def test_bsse(self):
         self.assertAlmostEqual(qcout.data[0]["bsse"], -0.164210762949, 5)
         self.assertEqual(qcout.data[0]["jobtype"], "bsse")
 
+    def test_hirshfeld_charge(self):
+        filename = os.path.join(test_dir, "hirshfeld_population.qcout")
+        qcout = QcOutput(filename)
+        self.assertEqual(qcout.data[0]["charges"]["hirshfeld"],
+                         [-0.286309, 0.143134, 0.143176])
+        self.assertFalse(qcout.data[0]["has_error"])
+
 
 if __name__ == "__main__":
     unittest.main()