Additional Tests for Trsh, Common and Gaussian (#714)

arc/job/adapters/common.py

@@ -514,7 +514,8 @@ def combine_parameters(input_dict: dict, terms: list) -> Tuple[dict, List]:
 
     for key, value in input_dict_copy.items():
         if isinstance(value, str):
-            for term in terms:
+            # Sort terms by length in descending order to handle overlapping terms
+            for term in sorted(terms, key=len, reverse=True):
                 matches = re.findall(term, value)
                 for match in matches:
                     if match:

arc/job/adapters/common_test.py

@@ -205,6 +205,30 @@ def test_combine_parameters_no_match(self):
         self.assertEqual(modified_dict, expected_dict)
         self.assertEqual(parameters, expected_parameters)
 
+    def test_combine_parameters_multiple_occurrences(self):
+        """Test the combine_parameters function with multiple occurrences of the same term."""
+        input_dict = {'param1': 'value1 term1 value2 term1', 'param2': 'another term2 value term2'}
+        terms = ['term1', 'term2']
+        expected_dict = {'param1': 'value1  value2 ', 'param2': 'another  value '}
+        expected_parameters = ['term1', 'term2']
+
+        modified_dict, parameters = common.combine_parameters(input_dict, terms)
+
+        self.assertEqual(modified_dict, expected_dict)
+        self.assertEqual(sorted(parameters), expected_parameters)
+
+    def test_combine_parameters_overlapping_terms(self):
+        """Test the combine_parameters function with overlapping terms."""
+        input_dict = {'param1': 'value term1 term123', 'param2': 'another term2 value'}
+        terms = ['term1', 'term123', 'term2']
+        expected_dict = {'param1': 'value  ', 'param2': 'another  value'}
+        expected_parameters = ['term1', 'term123', 'term2']
+
+        modified_dict, parameters = common.combine_parameters(input_dict, terms)
+
+        self.assertEqual(modified_dict, expected_dict)
+        self.assertEqual(sorted(parameters), expected_parameters)
+
     def test_input_dict_strip(self):
         """Test the input_dict_strip() function"""
         input_dict = {

arc/job/adapters/gaussian_test.py

@@ -274,6 +274,28 @@ def setUpClass(cls):
                                             args=args
                                             )
 
+        # Gaussian: Checkfile error and SCF error
+        # First SCF error - qc,nosymm
+        job_status = {'keywords': ['SCF', 'NoSymm', 'GL301']}
+        output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \
+            memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
+                                                                       job_type, software, fine, memory_gb,
+                                                                       num_heavy_atoms, cpu_cores, ess_trsh_methods)
+        args = {'keyword': {}, 'block': {}}
+        if trsh_keyword:
+            args['trsh'] = {'trsh': trsh_keyword}
+        cls.job_16 = GaussianAdapter(execution_type='local',
+                                          job_type='sp',
+                                          level=Level(method='wb97xd'),
+                                            fine=True,
+                                            ess_trsh_methods=ess_trsh_methods,
+                                            project='test',
+                                            project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_GaussianAdapter'),
+                                            species=[spc_11],
+                                            testing=True,
+                                            args=args
+                                            )
+
     def test_set_cpu_and_mem(self):
         """Test assigning number of cpu's and memory"""
         self.job_8.input_file_memory = None
@@ -619,6 +641,34 @@ def test_trsh_write_input_file(self):
 """
         self.assertEqual(content_15, job_15_expected_input_file)
 
+        self.job_16.write_input_file()
+        with open(os.path.join(self.job_16.local_path, input_filenames[self.job_16.job_adapter]), 'r') as f:
+            content_16 = f.read()
+
+        job_16_expected_input_file = """%chk=check.chk
+%mem=14336mb
+%NProcShared=8
+
+#P opt=(cartesian) integral=(grid=ultrafine, Acc2E=14) guess=mix wb97xd   IOp(2/9=2000)      nosymm  scf=(NDump=30,NoDIIS,direct,tight,xqc)
+
+ethanol
+
+0 1
+C       1.16582100   -0.40435500    0.00000000
+C       0.00000000    0.55180500    0.00000000
+O      -1.18946000   -0.21419400    0.00000000
+H      -1.94125800    0.37518500    0.00000000
+H       2.10540200    0.14511600    0.00000000
+H       1.13062400   -1.03878500    0.88303200
+H       1.13062400   -1.03878500   -0.88303200
+H       0.04768200    1.19305700    0.88359100
+H       0.04768200    1.19305700   -0.88359100
+
+
+"""
+
+        self.assertEqual(content_16, job_16_expected_input_file)
+
     @classmethod
     def tearDownClass(cls):
         """

arc/job/trsh.py

@@ -1625,7 +1625,7 @@ def trsh_keyword_nosymm(job_status, ess_trsh_methods, trsh_keyword, couldnt_trsh
     """
     Check if the job requires change of nosymm
     """
-    if 'NoSymm' in job_status['keywords'] and 'nosymm' not in ess_trsh_methods:
+    if 'NoSymm' in job_status['keywords'] and 'NoSymm' not in ess_trsh_methods:
         ess_trsh_methods.append('NoSymm')
         trsh_keyword.append('nosymm')
         couldnt_trsh = False

arc/job/trsh_test.py

@@ -311,8 +311,30 @@ def test_trsh_ess_job(self):
                                                                        num_heavy_atoms, cpu_cores, ess_trsh_methods)
 
         self.assertTrue(remove_checkfile)
+        self.assertEqual(ess_trsh_methods, ['change_node', 'int=(Acc2E=14)', 'checkfile=None', 'cartesian', 'NoSymm'])
         self.assertEqual(trsh_keyword, ['opt=(cartesian)', 'int=(Acc2E=14)', 'nosymm'] )
 
+        # Gaussian: test 3
+        job_status = {'keywords': ['SCF', 'GL502', 'NoSymm']}
+        output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \
+            memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
+                                                                    job_type, software, fine, memory_gb,
+                                                                    num_heavy_atoms, cpu_cores, ess_trsh_methods)
+
+        self.assertTrue(remove_checkfile)
+        self.assertIn('scf=(qc)', ess_trsh_methods)
+        self.assertFalse(couldnt_trsh)
+
+        # Gaussian: test 5
+        job_status = {'keywords': ['DiskSpace']}
+        output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \
+            memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
+                                                                    job_type, software, fine, memory_gb,
+                                                                    num_heavy_atoms, cpu_cores, ess_trsh_methods)
+
+        self.assertTrue(couldnt_trsh)
+        self.assertIn('Error: Could not troubleshoot opt for ethanol! The job ran out of disc space on server1; ', output_errors)
+
         # Test Q-Chem
         software = 'qchem'
         ess_trsh_methods = ['change_node']