Adapt parse_nd_scan_energies() to a slightly different Gaussian 2D sc…

…an format (#777) A test was added with a trimmed log file
ReactionMechanismGenerator · Dec 30, 2024 · 5518ed6 · 5518ed6
2 parents 6fda63e + 69bf820
commit 5518ed6
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Showing 3 changed files with 44,083 additions and 3 deletions.
diff --git a/arc/parser.py b/arc/parser.py
@@ -638,16 +638,17 @@ def parse_nd_scan_energies(path: str,
 
                 elif 'Summary of Optimized Potential Surface Scan' in line:
                     # ' Summary of Optimized Potential Surface Scan (add -264.0 to energies):'
-                    base_e = float(line.split('(add ')[1].split()[0])
+                    base_e = float(line.split('(add ')[1].split()[0]) if '(add' in line and 'to energies):' in line else 0.0
                     energies, dihedrals_dict = list(), dict()
                     dihedral_num = 0
-                    while 'Grad' not in line:
+                    while 'Grad' not in line and 'Largest change from initial coordinates' not in line:
                         line = f.readline()
                         splits = line.split()
+                        numbers = re.findall(r'-?\d+\.\d+', line)
                         if 'Eigenvalues --' in line:
                             # convert Hartree energy to kJ/mol
                             energies = [(base_e + float(e)) * 4.3597447222071e-18 * 6.02214179e23 * 1e-3
-                                        for e in splits[2:]]
+                                        for e in numbers]
                             min_es = min(energies)
                             min_e = min_es if min_e is None else min(min_e, min_es)
                             dihedral_num = 0

diff --git a/arc/parser_test.py b/arc/parser_test.py
@@ -561,6 +561,14 @@ def test_parse_nd_scan_energies(self):
         self.assertEqual(len(list(results[0]['directed_scan'].keys())), 36 * 36 + 1)  # 1297
         self.assertAlmostEqual(results[0]['directed_scan']['170.00', '40.00']['energy'], 26.09747088)
 
+        path2 = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'scan_2D_N3H5.out')
+        results = parser.parse_nd_scan_energies(path=path2, software='gaussian')
+        self.assertEqual(results[0]['directed_scan_type'], 'ess_gaussian')
+        self.assertEqual(results[0]['scans'], [(1, 2, 3, 7), (4, 1, 2, 3)])
+        self.assertEqual(len(list(results[0].keys())), 3)
+        self.assertEqual(len(list(results[0]['directed_scan'].keys())), 45 * 45)  # 2025
+        self.assertAlmostEqual(results[0]['directed_scan']['-38.33', '-65.67']['energy'], 27.01639591)
+
     def test_parse_dipole_moment(self):
         """Test parsing the dipole moment from an opt job output file"""
         path1 = os.path.join(ARC_PATH, 'arc', 'testing', 'composite', 'SO2OO_CBS-QB3.log')