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Fix combinations of concentration ranges for RMG SA #131

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Fix combinations of concentration ranges for RMG SA #131

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8a5e72e
Minor: Report missing path in SA solver error message
alongd May 2, 2024
d4dcb44
Fixed get_species_concentration_lists_from_ranged_params()
alongd Apr 17, 2024
179786b
Tests: get_species_concentration_lists_from_ranged_params() case 3
alongd Aug 13, 2023
f5ca766
Make `iteration` an optional arg for write_rmg_input_file()
alongd Aug 15, 2023
05f3881
Added a sensitivity block to the RMG input file
alongd Aug 15, 2023
1bc1772
Tests: SA as a subprocess
alongd May 2, 2024
03c87b7
Use the existing SA path in rmg_constantTP adatper
alongd May 2, 2024
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4 changes: 2 additions & 2 deletions t3/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -805,8 +805,8 @@ def determine_reactions_based_on_sa(self) -> List[int]:
"""
reaction_keys, pdep_rxns_to_explore = list(), list()
if not os.path.isdir(self.paths['SA solver']):
self.logger.error("Could not find the path to the SA solver output folder.\n"
"Not performing refinement based on sensitivity analysis!")
self.logger.error(f"Could not find the path to the SA solver output folder:\n{self.paths['SA solver']}\n"
f"Not performing refinement based on sensitivity analysis!")
return reaction_keys

sa_dict_max = dict()
Expand Down
36 changes: 17 additions & 19 deletions t3/simulate/rmg_constantTP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,6 @@ def set_up(self):
write_rmg_input_file(
rmg=self.generate_rmg_reactors_for_simulation(),
t3=self.t3,
iteration=1, # Does not matter for simulating or computing SA.
path=self.rmg_input_file,
walltime=self.t3['options']['max_RMG_walltime'],
)
Expand Down Expand Up @@ -236,17 +235,16 @@ def get_sa_coefficients(self) -> Optional[dict]:
sa_dict (Optional[dict]): An SA dictionary, structure is given in the docstring for T3/t3/main.py
"""
chem_to_rmg_rxn_index_map = get_chem_to_rmg_rxn_index_map(chem_annotated_path=self.paths['chem annotated'])
solver_path = os.path.join(self.paths['SA'], 'solver')
if not os.path.exists(solver_path):
self.logger.error("Could not find the path to RMG's SA solver output folder.")
if not os.path.exists(self.paths['SA solver']):
self.logger.error(f"Could not find the path to RMG's SA solver output folder:\n{self.paths['SA solver']}.")
return None
sa_files = list()
for file_ in os.listdir(solver_path):
for file_ in os.listdir(self.paths['SA solver']):
if 'sensitivity' in file_ and file_.endswith(".csv"):
sa_files.append(file_)
sa_dict = {'kinetics': dict(), 'thermo': dict(), 'time': list()}
for sa_file in sa_files:
df = pd.read_csv(os.path.join(solver_path, sa_file))
df = pd.read_csv(os.path.join(self.paths['SA solver'], sa_file))
for header in df.columns:
sa_type = None
if 'Time' in header:
Expand Down Expand Up @@ -320,7 +318,7 @@ def generate_rmg_reactors_for_simulation(self) -> dict:
v_vals = get_values_within_range(value_range=reactor['V'],
num=self.t3['options']['num_sa_per_volume_range'])
for t_val in t_vals:
for param in p_vals if ranged_p else v_vals:
for param in p_vals if (ranged_p or len(p_vals) == 1) else v_vals:
for species_list in species_lists:
new_reactor = {k: v for k, v in reactor.items() if k not in ['T', 'P', 'V']}
new_reactor['T'] = t_val
Expand All @@ -340,10 +338,10 @@ def get_species_concentration_lists_from_ranged_params(self) -> List[List[dict]]
species_lists = list()
spc_indices_w_ranges = [i for i, spc in enumerate(self.rmg['species'])
if isinstance(spc['concentration'], (list, tuple))]
species_list = [{'label': spc['label'], 'concentration': spc['concentration']} for spc in self.rmg['species']
if (isinstance(spc['concentration'], (float, int)) and spc['concentration'] > 0)
or spc['balance'] or not spc['reactive']]
species_vals = [get_values_within_range(value_range=self.rmg['species'][spc_indices_w_ranges.index(species_index)]['concentration'],
species_list_wo_ranges = [{'label': spc['label'], 'concentration': spc['concentration']} for spc in self.rmg['species']
if (isinstance(spc['concentration'], (float, int)) and spc['concentration'] > 0)
or (spc['balance'] and spc['concentration'] == 0)]
species_vals = [get_values_within_range(value_range=self.rmg['species'][species_index]['concentration'],
num=self.t3['options']['num_sa_per_concentration_range'])
for species_index in spc_indices_w_ranges]

Expand All @@ -353,13 +351,13 @@ def get_species_concentration_lists_from_ranged_params(self) -> List[List[dict]]
if spc['concentration'] > 0 or spc['balance'] or not spc['reactive']]]

# 2. Only two ranged concentrations and modify_concentration_ranges_in_reverse is True
if len(spc_indices_w_ranges) == 2 and self.t3['options']['modify_concentration_ranges_in_reverse']:
elif len(spc_indices_w_ranges) == 2 and self.t3['options']['modify_concentration_ranges_in_reverse']:
spc_0_vals = get_values_within_range(value_range=self.rmg['species'][spc_indices_w_ranges[0]]['concentration'],
num=self.t3['options']['num_sa_per_concentration_range'])
spc_1_vals = get_values_within_range(value_range=self.rmg['species'][spc_indices_w_ranges[1]]['concentration'],
num=self.t3['options']['num_sa_per_concentration_range'])
for val_0, val_1 in zip(spc_0_vals, spc_1_vals[::-1]):
new_species_list = species_list
new_species_list = species_list_wo_ranges
new_species_list.append({'label': self.rmg['species'][spc_indices_w_ranges[0]]['label'],
'concentration': val_0})
new_species_list.append({'label': self.rmg['species'][spc_indices_w_ranges[1]]['label'],
Expand All @@ -368,17 +366,17 @@ def get_species_concentration_lists_from_ranged_params(self) -> List[List[dict]]

# 3. No combinations, modify_concentration_ranges_together is True
elif self.t3['options']['modify_concentration_ranges_together']:
for point_number in range(self.t3['options']['num_sa_per_concentration_range']):
new_species_list = species_list
for i, spc_index in enumerate(spc_indices_w_ranges):
new_species_list.append({'label': self.rmg['species'][spc_index]['label'],
'concentration': species_vals[i][point_number]})
for point_number in range(self.t3['options']['num_sa_per_concentration_range']):
new_species_list = [entry for entry in species_list_wo_ranges]
for i, spc_index in enumerate(spc_indices_w_ranges):
new_species_list.append({'label': self.rmg['species'][spc_index]['label'],
'concentration': species_vals[i][point_number]})
species_lists.append(new_species_list)

# 4. Combinations (products)
else:
for vals in itertools.product(*species_vals):
new_species_list = species_list
new_species_list = species_list_wo_ranges
for i, val in enumerate(vals):
new_species_list.append({'label': self.rmg['species'][spc_indices_w_ranges[i]]['label'],
'concentration': val})
Expand Down
22 changes: 18 additions & 4 deletions t3/utils/writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,9 @@

def write_rmg_input_file(rmg: dict,
t3: dict,
iteration: int,
path: str,
iteration: int = 1,
run_sa: bool = False,
walltime: str = '00:00:00:00',
):
"""
Expand All @@ -29,8 +30,10 @@ def write_rmg_input_file(rmg: dict,
Args:
rmg (dict): The arguments to write in a keyword argument dictionary format.
t3 (dict): The T3 arguments in a keyword argument dictionary format. Includes atol and rtol for SA.
iteration (int): The T3 iteration, used to determine ``core_tolerance`` and ``tolerance_interrupt_simulation``.
path (str): The path where the RMG input file should be saved.
iteration (int, optional): The T3 iteration, used to determine ``core_tolerance`` and
``tolerance_interrupt_simulation``. Does not matter for simulating or computing SA.
run_sa (bool, optional): Whether to add sensitivity analysis information into the RMG input file.
walltime (str, optional): The time cap for an RMG run. Should pass here t3['options']['max_RMG_walltime']
"""
rmg = rmg.copy()
Expand Down Expand Up @@ -100,7 +103,7 @@ def write_rmg_input_file(rmg: dict,
pressure=${pressure},
initialMoleFractions={${concentrations()} },
${termination}
nSims=${conditions_per_iteration},${balance}${constant}
nSims=${conditions_per_iteration},${balance}${constant}${sensitivity}
)
<%def name="concentrations()">
% for spc in species_list:
Expand All @@ -118,7 +121,7 @@ def write_rmg_input_file(rmg: dict,
temperature=${temperature},
initialConcentrations={${concentrations()} },
${termination}
nSims=${conditions_per_iteration},${constant}
nSims=${conditions_per_iteration},${constant}${sensitivity}
)
<%def name="concentrations()">
% for spc in species_list:
Expand Down Expand Up @@ -166,6 +169,16 @@ def write_rmg_input_file(rmg: dict,
constant = '\n constantSpecies=['
constant += f"'{spc['label']}', "
constant += '],' if constant else ''
sensitivity = ''
observables = [spc['label'] for spc in species if spc['observable']]
if run_sa and len(observables):
sensitivity = '\n sensitivity=['
for i, observable in enumerate(observables):
sensitivity += f"'{observable}'"
if i < len(observables) - 1:
sensitivity += ', '
sensitivity += f"],\n sensitivityThreshold={t3['sensitivity']['SA_threshold']}"


if reactor['type'] == 'gas batch constant T P':
if isinstance(reactor['P'], float):
Expand All @@ -188,6 +201,7 @@ def write_rmg_input_file(rmg: dict,
conditions_per_iteration=reactor['conditions_per_iteration'],
balance=balance,
constant=constant,
sensitivity=sensitivity,
)

elif reactor['type'] == 'liquid batch constant T V':
Expand Down