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Compute thermo #140

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7 changes: 3 additions & 4 deletions t3/logger.py
Original file line number Diff line number Diff line change
Expand Up @@ -177,11 +177,8 @@ def log_species_to_calculate(self,
Args:
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
"""
if len(species_keys):
if len(species_keys) and any(spc_dict['compute_thermo'] for spc_dict in species_dict.values()):
self.info('\n\nSpecies to calculate thermodynamic data for:')
max_label_length = max([len(spc_dict['QM label'])
for key, spc_dict in species_dict.items() if key in species_keys])
Expand All @@ -193,6 +190,8 @@ def log_species_to_calculate(self,
self.info(f'-----{space1} ------{space2} -----------------------------')
for key in species_keys:
spc_dict = species_dict[key]
if not spc_dict['compute_thermo']:
continue
smiles = spc_dict['object'].molecule[0].to_smiles()
space1 = ' ' * (max_label_length - len(spc_dict['QM label']) + 1)
space2 = ' ' * (max_smiles_length - len(smiles) + 1)
Expand Down
18 changes: 16 additions & 2 deletions t3/main.py
Original file line number Diff line number Diff line change
Expand Up @@ -321,7 +321,7 @@ def execute(self):
self.run_arc(arc_kwargs=self.qm)
self.process_arc_run()
if not additional_calcs_required and self.iteration >= len(self.rmg['model']['core_tolerance']):
# T3 iterated through all of the user requested tolerances, and there are no more calculations required
# T3 iterated through all the user requested tolerances, and there are no more calculations required
break

if self.check_overtime():
Expand Down Expand Up @@ -1231,6 +1231,7 @@ def load_species_and_reactions_from_chemkin_file(self) -> Tuple[List[Species], L
def add_species(self,
species: Species,
reasons: Union[List[str], str],
compute_thermo: bool = True,
) -> Optional[int]:
"""
Add a species to self.species and to self.qm['species'].
Expand All @@ -1239,6 +1240,7 @@ def add_species(self,
Args:
species (Species): The species to consider.
reasons (Union[List[str], str]): Reasons for calculating this species.
compute_thermo (bool, optional): Whether to compute thermo for this species (default: ``True``).

Returns:
Optional[int]: The T3 species index (the respective self.species key) if the species was just added,
Expand All @@ -1256,6 +1258,7 @@ def add_species(self,
'reasons': reasons,
'converged': None,
'iteration': self.iteration,
'compute_thermo': compute_thermo,
}

# Check whether T3 has xyz information for this species, if so process it.
Expand All @@ -1274,7 +1277,7 @@ def add_species(self,
xyzs.append(xyz_dict)
if len(xyzs):
if self.qm['adapter'] == 'ARC':
# Make qm_species and ARCSpecies instance to consider the xyz information
# Make qm_species an ARCSpecies instance to consider the xyz information
qm_species = ARCSpecies(label=qm_species.label,
rmg_species=qm_species,
xyz=xyzs,
Expand All @@ -1283,6 +1286,17 @@ def add_species(self,
else:
raise NotImplementedError(f"Passing XYZ information to {self.qm['adapter']} "
f"is not yet implemented.")
if not self.species_requires_refinement(qm_species):
if isinstance(qm_species, ARCSpecies):
qm_species.compute_thermo = False
qm_species.include_in_thermo_lib = False
else:
qm_species = ARCSpecies(label=qm_species.label,
rmg_species=qm_species,
xyz=None,
compute_thermo=False,
include_in_thermo_lib=False,
)
self.qm['species'].append(qm_species)
return key

Expand Down
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