Improves restart and TS guess handling #823
+241
−12
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||||
|---|---|---|---|---|---|---|---|---|
|
|
@@ -325,6 +325,8 @@ def __init__(self, | |||||||
| self.orbitals_level = orbitals_level | ||||||||
| self.unique_species_labels = list() | ||||||||
| self.save_restart = False | ||||||||
| if self.restart_dict is not None: | ||||||||
| self._sanitize_restart_output() | ||||||||
|
|
||||||||
| if len(self.rxn_list): | ||||||||
| rxn_info_path = self.make_reaction_labels_info_file() | ||||||||
|
|
@@ -2619,7 +2621,14 @@ def switch_ts(self, label: str): | |||||||
| logger.info(f'Switching a TS guess for {label}...') | ||||||||
| self.determine_most_likely_ts_conformer(label=label) # Look for a different TS guess. | ||||||||
| self.delete_all_species_jobs(label=label) # Delete other currently running jobs for this TS. | ||||||||
| if label in self.output: | ||||||||
| self.output[label]['convergence'] = False | ||||||||
| for key in ['opt', 'freq', 'sp', 'composite', 'fine']: | ||||||||
| if key in self.output[label]['job_types']: | ||||||||
| self.output[label]['job_types'][key] = False | ||||||||
| if 'paths' in self.output[label]: | ||||||||
| for key in self.output[label]['paths']: | ||||||||
| self.output[label]['paths'][key] = '' if key != 'irc' else list() | ||||||||
| freq_path = os.path.join(self.project_directory, 'output', 'rxns', label, 'geometry', 'freq.out') | ||||||||
| if os.path.isfile(freq_path): | ||||||||
| os.remove(freq_path) | ||||||||
|
|
@@ -3044,6 +3053,9 @@ def check_all_done(self, label: str): | |||||||
| logger.debug(f'Species {label} did not converge.') | ||||||||
| all_converged = False | ||||||||
| break | ||||||||
| if all_converged and self._missing_required_paths(label): | ||||||||
| logger.debug(f'Species {label} did not converge due to missing output paths.') | ||||||||
| all_converged = False | ||||||||
| if label in self.output and all_converged: | ||||||||
| self.output[label]['convergence'] = True | ||||||||
| if self.species_dict[label].is_ts: | ||||||||
|
|
@@ -3084,6 +3096,64 @@ def check_all_done(self, label: str): | |||||||
| # Update restart dictionary and save the yaml restart file: | ||||||||
| self.save_restart_dict() | ||||||||
|
|
||||||||
| def _missing_required_paths(self, label: str) -> bool: | ||||||||
| """ | ||||||||
| Check whether required output paths are missing for a species/TS. | ||||||||
|
|
||||||||
| Args: | ||||||||
| label (str): The species label. | ||||||||
|
|
||||||||
| Returns: | ||||||||
| bool: Whether required output paths are missing. | ||||||||
| """ | ||||||||
| if label not in self.output or 'paths' not in self.output[label]: | ||||||||
| return False | ||||||||
| path_map = { | ||||||||
| 'opt': 'geo', | ||||||||
| 'freq': 'freq', | ||||||||
| 'sp': 'sp', | ||||||||
| 'composite': 'composite', | ||||||||
| } | ||||||||
| for job_type, path_key in path_map.items(): | ||||||||
| if job_type == 'composite': | ||||||||
| required = self.composite_method is not None | ||||||||
| else: | ||||||||
| required = self.job_types.get(job_type, False) | ||||||||
| if not required: | ||||||||
| continue | ||||||||
| if self.species_dict[label].number_of_atoms == 1 and job_type in ['opt', 'freq']: | ||||||||
| continue | ||||||||
| if self.output[label]['job_types'].get(job_type, False) and not self.output[label]['paths'].get(path_key, ''): | ||||||||
| return True | ||||||||
| return False | ||||||||
|
|
||||||||
| def _sanitize_restart_output(self) -> None: | ||||||||
| """ | ||||||||
| Ensure restart output state is internally consistent (e.g., convergence without paths). | ||||||||
| """ | ||||||||
| path_map = { | ||||||||
| 'opt': 'geo', | ||||||||
| 'freq': 'freq', | ||||||||
| 'sp': 'sp', | ||||||||
| 'composite': 'composite', | ||||||||
| } | ||||||||
| for label in list(self.output.keys()): | ||||||||
| if label not in self.species_dict: | ||||||||
| continue | ||||||||
| if self.output[label].get('convergence') and self._missing_required_paths(label): | ||||||||
| self.output[label]['convergence'] = False | ||||||||
| for job_type, path_key in path_map.items(): | ||||||||
| if job_type == 'composite': | ||||||||
| required = self.composite_method is not None | ||||||||
| else: | ||||||||
| required = self.job_types.get(job_type, False) | ||||||||
| if not required: | ||||||||
| continue | ||||||||
| if self.species_dict[label].number_of_atoms == 1 and job_type in ['opt', 'freq']: | ||||||||
| continue | ||||||||
| if not self.output[label]['paths'].get(path_key, ''): | ||||||||
| self.output[label]['job_types'][job_type] = False | ||||||||
|
There was a problem hiding this comment. The _sanitize_restart_output method duplicates logic from _missing_required_paths. Lines 3145-3155 repeat the same path validation logic that's already in _missing_required_paths (lines 3117-3128). Consider refactoring to reuse the existing helper method or extracting the path validation into a shared utility function to improve maintainability and reduce duplication.
Member
There was a problem hiding this comment. if it's duplicated, maybe outsource it into a single external function? There was a problem hiding this comment. In the _sanitize_restart_output method, there's no check for the existence of 'job_types' key before accessing it at line 3155. While _missing_required_paths at line 3126 uses .get() with a default value to safely access job_types, this line directly accesses self.output[label]['job_types'][job_type]. If 'job_types' doesn't exist in self.output[label], this will raise a KeyError. Consider using safe dictionary access or add a check for the existence of 'job_types' key.
Suggested change
|
||||||||
|
|
||||||||
| def get_server_job_ids(self, specific_server: Optional[str] = None): | ||||||||
| """ | ||||||||
| Check job status on a specific server or on all active servers, get a list of relevant running job IDs. | ||||||||
|
|
@@ -3547,7 +3617,13 @@ def delete_all_species_jobs(self, label: str): | |||||||
| logger.info(f'Deleted job {job_name}') | ||||||||
| job.delete() | ||||||||
| self.running_jobs[label] = list() | ||||||||
| if label in self.output: | ||||||||
| self.output[label]['convergence'] = False | ||||||||
| for key in ['opt', 'freq', 'sp', 'composite', 'fine']: | ||||||||
| if key in self.output[label]['job_types']: | ||||||||
| self.output[label]['job_types'][key] = False | ||||||||
| self.output[label]['paths'] = {key: '' if key != 'irc' else list() | ||||||||
| for key in self.output[label]['paths'].keys()} | ||||||||
|
|
||||||||
| def restore_running_jobs(self): | ||||||||
| """ | ||||||||
|
|
||||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
|
|
@@ -1536,12 +1536,12 @@ def make_ts_report(self): | |||||
| self.ts_report += ':\n' | ||||||
| if self.successful_methods: | ||||||
| self.ts_report += 'Methods that successfully generated a TS guess:\n' | ||||||
| unique_successful_methods = list(dict.fromkeys(self.successful_methods)) | ||||||
| self.ts_report += ','.join(unique_successful_methods) | ||||||
| if self.unsuccessful_methods: | ||||||
| self.ts_report += '\nMethods that were unsuccessfully in generating a TS guess:\n' | ||||||
|
There was a problem hiding this comment. Grammatical error: "were unsuccessfully in generating" should be "were unsuccessful in generating" (remove the 'ly').
Suggested change
|
||||||
| unique_unsuccessful_methods = list(dict.fromkeys(self.unsuccessful_methods)) | ||||||
| self.ts_report += ','.join(unique_unsuccessful_methods) | ||||||
|
Comment on lines
+1539
to
+1544
There was a problem hiding this comment. The deduplication of TS methods in the report will cause an existing test to fail. The test in arc/species/species_test.py at line 1202-1206 expects the ts_report to contain duplicates (e.g., 'autotst,autotst,autotst,autotst,gcn,gcn,...'), but after this change, the report will show 'autotst,gcn,kinbot' instead. The test should be updated to match the new expected behavior. |
||||||
| if not self.ts_guesses_exhausted: | ||||||
| self.ts_report += f'\nThe method that generated the best TS guess and its output used for the ' \ | ||||||
| f'optimization: {self.chosen_ts_method}\n' | ||||||
|
|
||||||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
There is duplicated logic for resetting output between switch_ts (lines 2624-2631) and delete_all_species_jobs (lines 3620-3626). Both methods reset convergence, job_types, and paths in nearly identical ways. Since switch_ts calls delete_all_species_jobs at line 2623, consider removing the duplicate resetting logic from switch_ts and relying solely on delete_all_species_jobs to handle the output reset. This would improve maintainability and reduce the risk of the two implementations diverging.