Tests: Updated functional tests

Author: alongd

functional/functional_test.py

@@ -11,7 +11,6 @@
 
 from arc import ARC
 from arc.common import ARC_PATH
-from arc.exceptions import InputError
 from arc.imports import settings
 from arc.reaction import ARCReaction
 from arc.species import ARCSpecies
@@ -50,6 +49,7 @@ def setUpClass(cls):
                                job_types=cls.job_types,
                                conformer_level='gfn2',
                                level_of_theory='gfn2',
+                               arkane_level_of_theory='cbs-qb3',
                                freq_scale_factor=1.0,
                                n_confs=2,
                                bac_type=None,
@@ -69,6 +69,7 @@ def setUpClass(cls):
                                conformer_level='gfn2',
                                level_of_theory='gfn2',
                                ts_guess_level='gfn2',
+                               arkane_level_of_theory='cbs-qb3',
                                freq_scale_factor=1.0,
                                n_confs=2,
                                dont_gen_confs=["TS0"],
@@ -77,38 +78,51 @@ def setUpClass(cls):
                                compare_to_rmg=False,
                                )
 
-    def testThermo(self):
+    def test_thermo(self):
         """Test thermo"""
         self.arc_object_1.execute()
         summary = self.arc_object_1.summary()
         for _, ter in summary.items():
             self.assertTrue(ter)
-        self.assertTrue(os.path.exists(os.path.join(ARC_PATH, "functional", "test", "thermo", "output", "RMG libraries", "thermo")))
-        with open(file=os.path.join(ARC_PATH, "functional", "test", "thermo", "output", "RMG libraries", "thermo", "FunctionalThermoTest.py"), mode='r') as f:
-            entry = 0
+        self.assertTrue(os.path.isfile(os.path.join(ARC_PATH, "functional", "test", "thermo", "calcs", "statmech", "thermo", "arkane.log")))
+        species, thermo = 0, 0
+        with open(file=os.path.join(ARC_PATH, "functional", "test", "thermo", "calcs", "statmech", "thermo", "input.py"), mode='r') as f:
             for line in f.readlines():
-                if "entry" in line:
-                    entry += 1
-        self.assertEqual(entry, len(self.species_list_1))
+                if "species('" in line:
+                    species += 1
+                if "thermo('" in line:
+                    thermo += 1
+        self.assertEqual(species, len(self.species_list_1))
+        self.assertEqual(thermo, len(self.species_list_1))
 
-    def testKinetic(self):
+    def test_kinetic(self):
         """Test kinetics"""
-        try:
-            self.arc_object_2.execute()
-        except InputError as e:
-            self.skipTest(f"execution of ARC failed: {e}, skipping this test for now...")
+        self.arc_object_2.execute()
         summary = self.arc_object_2.summary()
         for _, ter in summary.items():
             self.assertTrue(ter)
-        self.assertTrue(os.path.exists(os.path.join(ARC_PATH, "functional", "test", "kinetic", "output", "RMG libraries", "kinetics")))
-        has_content = False
-        with open(file=os.path.join(ARC_PATH, "functional", "test", "kinetic", "output", "RMG libraries", "kinetics", "reactions.py"), mode='r') as f:
+        base_path = os.path.join(ARC_PATH, "functional", "test", "kinetic", "calcs", "statmech")
+        self.assertTrue(os.path.isfile(os.path.join(base_path, "thermo", "input.py")))
+        self.assertTrue(os.path.isfile(os.path.join(base_path, "kinetics", "input.py")))
+        self.assertTrue(os.path.isfile(os.path.join(base_path, "kinetics", "species", "iC3H7.py")))
+        self.assertTrue(os.path.isfile(os.path.join(base_path, "kinetics", "species", "nC3H7.py")))
+        self.assertTrue(os.path.isfile(os.path.join(base_path, "kinetics", "TSs", "TS0.py")))
+        species, thermo, kinetics, ts = 0, 0, 0, 0
+        with open(file=os.path.join(base_path, "kinetics", "input.py"), mode='r') as f:
             for line in f.readlines():
-                if "Arrhenius" in line:
-                    has_content = True
-                    break
-        self.assertTrue(has_content)
-    
+                if "species('" in line:
+                    species += 1
+                elif "thermo('" in line:
+                    thermo += 1
+                elif "kinetics(label='" in line:
+                    kinetics += 1
+                elif "transitionState" in line:
+                    ts += 1
+        self.assertEqual(species, 2)
+        self.assertEqual(thermo, 0)
+        self.assertEqual(kinetics, 1)
+        self.assertEqual(ts, 2)
+
     @classmethod
     def tearDownClass(cls):
         """

functional/restart_test.py

@@ -85,7 +85,7 @@ def test_restart_thermo(self):
                     spc = True
                 elif 'All jobs for species N2H3 successfully converged. Run time' in line:
                     rtm = True
-                elif 'Thermodynamics for H2O2' in line:
+                elif '   H2O2              -135.82          239.05' in line:
                     therm = True
                 elif 'Sources of thermodynamic properties determined by RMG for the parity plots:' in line:
                     src = True
@@ -108,15 +108,21 @@ def test_restart_thermo(self):
                          'Conformers optimized and compared at b3lyp/6-31g(d,p) empiricaldispersion=gd3bj; ')
         self.assertTrue(status['CH3CO2_rad']['job_types']['sp'])
 
-        with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'arkane', 'species_dictionary.txt'),
-                  'r') as f:
+        with open(os.path.join(project_directory, 'output', 'RMG libraries', 'thermo', 'species_dictionary.txt'), 'r') as f:
             lines = f.readlines()
-        adj_list = ''
+        species_name = 'H2O2'
+        adj_lines = list()
+        found = False
         for line in lines:
-            if 'H2O2' not in line:
-                adj_list += line
-            if line == '\n':
+            text = line.strip()
+            if not found:
+                if text == species_name:
+                    found = True
+                continue
+            if text == '':
                 break
+            adj_lines.append(line)
+        adj_list = ''.join(adj_lines)
         mol1 = Molecule().from_adjacency_list(adj_list)
         self.assertEqual(mol1.to_smiles(), 'OO')
 
@@ -135,7 +141,7 @@ def test_restart_rate_1(self):
         with open(kinetics_library_path, 'r') as f:
             got_rate = False
             for line in f.readlines():
-                if "kinetics = Arrhenius(A=(6.37e-02, '(cm^3/(mol*s))'), n=4.08, Ea=(57.55, 'kJ/mol')," in line:
+                if "kinetics = Arrhenius(A=(6.37e-02, 'cm^3/(mol*s)'), n=4.08, Ea=(57.55, 'kJ/mol')," in line:
                     got_rate = True
                     break
         self.assertTrue(got_rate)
@@ -179,8 +185,6 @@ def test_restart_bde(self):
             lines = f.readlines()
         self.assertIn(' BDE report for anilino_radical:\n', lines)
         self.assertIn(' (1, 9)            N - H           353.92\n', lines)
-        self.assertIn(' (3, 4)            C - H           454.12\n', lines)
-        self.assertIn(' (5, 10)           C - H           461.75\n', lines)
 
     def test_globalize_paths(self):
         """Test modifying a YAML file's contents to correct absolute file paths"""