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Report SA results per iteration #138

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Report SA results per iteration #138

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653a26b
Return YAML content when logging species & reactions based on SA
alongd Sep 11, 2023
4659206
Save SA yaml path per iterations
alongd Sep 11, 2023
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24 changes: 20 additions & 4 deletions t3/logger.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ def log_footer(self):

def log_species_to_calculate(self,
species_keys: List[int],
species_dict: Dict[int, dict]):
species_dict: Dict[int, dict]) -> Dict:
"""
Report the species to be calculated in the next iteration.
The 'QM label' is used for reporting, it is principally the
Expand All @@ -178,9 +178,10 @@ def log_species_to_calculate(self,
species_keys (List[int]): Entries are T3 species indices.
species_dict (dict): The T3 species dictionary.

Todo:
Log the reasons one by one with line breaks and enumerate
Returns:
Dict: SA content for the YAML file.
"""
yml_content = dict()
if len(species_keys):
self.info('\n\nSpecies to calculate thermodynamic data for:')
max_label_length = max([len(spc_dict['QM label'])
Expand All @@ -201,18 +202,27 @@ def log_species_to_calculate(self,
for j, reason in enumerate(spc_dict['reasons']):
if j:
self.info(f"{' ' * (max_label_length + max_smiles_length + 4)}{j + 1}. {spc_dict['reasons'][j]}")
yml_content[key] = {'SMILES': smiles,
'QM label': spc_dict['QM label'],
'reasons': spc_dict['reasons'],
}
return yml_content

def log_reactions_to_calculate(self,
reaction_keys: List[int],
reaction_dict: Dict[int, dict]):
reaction_dict: Dict[int, dict]) -> Dict:
"""
Report reaction rate coefficients to be calculated in the next iteration.
The reaction 'QM label' is used for reporting.

Args:
reaction_keys (List[int]): Entries are T3 reaction indices.
reaction_dict (dict): The T3 reaction dictionary.

Returns:
Dict: SA content for the YAML file.
"""
yml_content = dict()
if len(reaction_keys):
self.info('\n\nReactions to calculate high-pressure limit rate coefficients for:')
max_label_length = max([len(rxn_dict['QM label'])
Expand All @@ -228,10 +238,16 @@ def log_reactions_to_calculate(self,
space1 = ' ' * (max_label_length - len(rxn_dict['QM label']) + 1)
self.info(f"\n{rxn_dict['QM label']}{space1} {rxn_dict['reasons']}")
self.info(f"{rxn_dict['SMILES label']}\n")
yml_content[key] = {'SMILES label': rxn_dict['SMILES label'],
'QM label': rxn_dict['QM label'],
'reasons': rxn_dict['reasons'],
}
if hasattr(rxn_dict['object'], 'family') and rxn_dict['object'].family is not None:
label = rxn_dict['object'].family if isinstance(rxn_dict['object'].family, str) \
else rxn_dict['object'].family.label
self.info(f'RMG family: {label}\n')
yml_content[key]['RMG family'] = label
return yml_content

def log_species_summary(self, species_dict: Dict[int, dict]):
"""
Expand Down
8 changes: 4 additions & 4 deletions t3/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -370,6 +370,7 @@ def set_paths(self,
'chem annotated': os.path.join(iteration_path, 'RMG', 'chemkin', 'chem_annotated.inp'),
'species dict': os.path.join(iteration_path, 'RMG', 'chemkin', 'species_dictionary.txt'),
'SA': os.path.join(iteration_path, 'SA'),
'SA yaml': os.path.join(iteration_path, 'SA', 'SA.yml'),
'SA solver': os.path.join(iteration_path, 'SA', 'solver'),
'SA input': os.path.join(iteration_path, 'SA', 'input.py'),
'PDep SA': os.path.join(iteration_path, 'PDep_SA'),
Expand Down Expand Up @@ -729,10 +730,9 @@ def determine_species_and_reactions_to_calculate(self) -> bool:
or any(spc['converged'] is None for spc in self.species.values())

self.logger.info(f'Additional calculations required: {additional_calcs_required}\n')
if len(species_keys):
self.logger.log_species_to_calculate(species_keys, self.species)
if len(reaction_keys):
self.logger.log_reactions_to_calculate(reaction_keys, self.reactions)
spc_yml = self.logger.log_species_to_calculate(species_keys, self.species) if len(species_keys) else dict()
rxn_yml = self.logger.log_reactions_to_calculate(reaction_keys, self.reactions) if len(reaction_keys) else dict()
save_yaml_file(path=self.paths['SA yaml'], content={'Species': spc_yml, 'Reactions': rxn_yml})
Fixed Show fixed Hide fixed
Fixed Show fixed Hide fixed
return additional_calcs_required

def determine_species_based_on_sa(self) -> List[int]:
Expand Down
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