Report electronic energy in an output file (#708)

1. Add the "report_e_elect" as the argument/attribute, and method
"save_e_elect" to decide whether electronic energy will be in the output
or not, after the single-point energy calculation.
2. A test case is also added for this purpose to check if
e_elect_summary.yml is created and have the electronic energy info

arc/main.py

@@ -155,6 +155,7 @@ class ARC(object):
                                  Only used for restarting.
         running_jobs (dict, optional): A dictionary of jobs submitted in a precious ARC instance, used for restarting.
         ts_adapters (list, optional): Entries represent different TS adapters.
+        report_e_elect (bool, optional): Whether to report electronic energy. Default is ``False``.
 
     Attributes:
         project (str): The project's name. Used for naming the working directory.
@@ -221,6 +222,8 @@ class ARC(object):
                              format (``True``) or classical two-parameter Arrhenius equation format (``False``).
         trsh_ess_jobs (bool): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
         ts_adapters (list): Entries represent different TS adapters.
+        report_e_elect (bool): Whether to report electronic energy.
+
     """
 
     def __init__(self,
@@ -269,6 +272,7 @@ def __init__(self,
                  ts_adapters: List[str] = None,
                  ts_guess_level: Optional[Union[str, dict, Level]] = None,
                  verbose=logging.INFO,
+                 report_e_elect: Optional[bool] = False,
                  ):
 
         if project is None:
@@ -320,6 +324,7 @@ def __init__(self,
         self.arkane_level_of_theory = Level(repr=arkane_level_of_theory) if arkane_level_of_theory is not None else None
         self.freq_scale_factor = freq_scale_factor
         self.ts_adapters = ts_adapters
+        self.report_e_elect = report_e_elect
         for ts_adapter in self.ts_adapters or list():
             if ts_adapter.lower() not in _registered_job_adapters.keys():
                 raise InputError(f'Unknown TS adapter: "{ts_adapter}"')
@@ -526,6 +531,8 @@ def as_dict(self) -> dict:
                 if not isinstance(self.ts_guess_level, (dict, str)) else self.ts_guess_level
         if self.verbose != logging.INFO:
             restart_dict['verbose'] = int(self.verbose)
+        if self.report_e_elect:
+            restart_dict['report_e_elect'] = self.report_e_elect
         return restart_dict
 
     def write_input_file(self, path=None):
@@ -592,6 +599,7 @@ def execute(self) -> dict:
                                    trsh_ess_jobs=self.trsh_ess_jobs,
                                    fine_only=self.fine_only,
                                    ts_adapters=self.ts_adapters,
+                                   report_e_elect=self.report_e_elect,
                                    )
 
         save_yaml_file(path=os.path.join(self.project_directory, 'output', 'status.yml'), content=self.scheduler.output)

arc/scheduler.py

@@ -23,6 +23,7 @@
                         get_logger,
                         get_number_with_ordinal_indicator,
                         is_angle_linear,
+                        read_yaml_file,
                         safe_copy_file,
                         save_yaml_file,
                         sort_two_lists_by_the_first,
@@ -160,6 +161,7 @@ class Scheduler(object):
         freq_scale_factor (float, optional): The harmonic frequencies scaling factor.
         trsh_ess_jobs (bool, optional): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
         ts_adapters (list, optional): Entries represent different TS adapters.
+        report_e_elect (bool, optional): Whether to report electronic energy. Default is ``False``.
 
     Attributes:
         project (str): The project's name. Used for naming the working directory.
@@ -214,6 +216,7 @@ class Scheduler(object):
         freq_scale_factor (float): The harmonic frequencies scaling factor.
         trsh_ess_jobs (bool): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
         ts_adapters (list): Entries represent different TS adapters.
+        report_e_elect (bool): Whether to report electronic energy.
     """
 
     def __init__(self,
@@ -248,6 +251,7 @@ def __init__(self,
                  kinetics_adapter: str = 'arkane',
                  freq_scale_factor: float = 1.0,
                  ts_adapters: List[str] = None,
+                 report_e_elect: Optional[bool] = False,
                  ) -> None:
 
         self.project = project
@@ -279,6 +283,7 @@ def __init__(self,
         self.ts_adapters = ts_adapters if ts_adapters is not None else default_ts_adapters
         self.ts_adapters = [ts_adapter.lower() for ts_adapter in self.ts_adapters]
         self.output = dict()
+        self.report_e_elect = report_e_elect
 
         self.species_dict, self.rxn_dict = dict(), dict()
         for species in self.species_list:
@@ -2552,6 +2557,9 @@ def post_sp_actions(self,
         if species_has_freq(self.output[label], self.species_dict[label].yml_path):
             self.check_rxn_e0_by_spc(label)
 
+        if self.report_e_elect:
+            self.save_e_elect(label)
+
         # set *at the end* to differentiate between sp jobs when using complex solvation corrections
         self.output[label]['job_types']['sp'] = True
 
@@ -3614,6 +3622,18 @@ def generate_final_ts_guess_report(self):
         if content:
             save_yaml_file(path=path, content=content)
 
+    def save_e_elect(self, label: str):
+        """
+        Save the electronic energy of the corresponding species.
+        It will append if the file already exists.
+        """
+        path = os.path.join(self.project_directory, 'output', 'e_elect_summary.yml')
+        content = dict()
+        if os.path.isfile(path):
+            content = read_yaml_file(path)
+        content[label] = self.species_dict[label].e_elect
+        save_yaml_file(path=path, content=content)
+
 
 def species_has_freq(species_output_dict: dict,
                      yml_path: Optional[str] = None,

arc/scheduler_test.py

@@ -12,7 +12,7 @@
 import arc.rmgdb as rmgdb
 import arc.parser as parser
 from arc.checks.ts import check_ts
-from arc.common import ARC_PATH, almost_equal_coords_lists, initialize_job_types
+from arc.common import ARC_PATH, almost_equal_coords_lists, initialize_job_types, read_yaml_file
 from arc.job.factory import job_factory
 from arc.level import Level
 from arc.plotter import save_conformers_file
@@ -701,6 +701,37 @@ def test_check_rxn_e0_by_spc(self):
         self.assertEqual(rxn.ts_species.ts_checks,
                          {'E0': True, 'e_elect': True, 'IRC': None, 'freq': True, 'normal_mode_displacement': True, 'warnings': ''})
 
+    def test_save_e_elect(self):
+        """Test the save_e_elect() method."""
+        project_directory = os.path.join(ARC_PATH, 'Projects', 'save_e_elect')
+        e_elect_summary_path = os.path.join(project_directory, 'output', 'e_elect_summary.yml')
+        self.assertFalse(os.path.isfile(os.path.join(project_directory, 'output', 'e_elect_summary.yml')))
+        sched = Scheduler(project='test_save_e_elect',
+                          ess_settings=self.ess_settings,
+                          project_directory=project_directory,
+                          species_list=[ARCSpecies(label='formaldehyde', smiles='C=O'),
+                                        ARCSpecies(label='mehylamine', smiles='CN')],
+                          freq_scale_factor=1.0,
+                          opt_level=Level(method='B3LYP', basis='6-31G(d,p)', software='gaussian'),
+                          sp_level=Level(method='B3LYP', basis='6-31G(d,p)', software='gaussian'),
+                          job_types={'opt': True, 'fine_grid': False, 'freq': False, 'sp': True, 'rotors': False,
+                                     'conformers': False, 'irc': False},
+                          report_e_elect=True,
+                          testing=True,
+                          )
+        sched.post_sp_actions(label='formaldehyde',
+                              sp_path=os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'formaldehyde_sp_terachem_output.out'))
+        self.assertTrue(os.path.isfile(e_elect_summary_path))
+        content = read_yaml_file(e_elect_summary_path)
+        self.assertEqual(content, {'formaldehyde': -300621.95378630824})
+
+        sched.post_sp_actions(label='mehylamine',
+                              sp_path=os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'mehylamine_CCSD(T).out'))
+        content = read_yaml_file(e_elect_summary_path)
+        self.assertEqual(content, {'formaldehyde': -300621.95378630824,
+                                    'mehylamine': -251377.49160993524})
+        shutil.rmtree(project_directory, ignore_errors=True)
+
     def test_species_has_geo_sp_freq(self):
         """Test the species_has_geo() / species_has_sp() / species_has_freq() functions."""
         for property_, species_has_property in zip(['geo', 'sp', 'freq'], [species_has_geo, species_has_sp, species_has_freq]):