Implemented get param and obs in simulate adapters

ReactionMechanismGenerator · Jul 7, 2024 · b525380 · b525380
1 parent 050fc2b
commit b525380
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Showing 2 changed files with 10 additions and 14 deletions.
diff --git a/t3/simulate/cantera_constantHP.py b/t3/simulate/cantera_constantHP.py
@@ -10,6 +10,7 @@
 from rmgpy.tools.canteramodel import generate_cantera_conditions
 from rmgpy.tools.data import GenericData
 
+from t3.common import get_observable_label_from_header, get_parameter_from_header
 from t3.logger import Logger
 from t3.simulate.adapter import SimulateAdapter
 from t3.simulate.factory import register_simulate_adapter
@@ -400,23 +401,19 @@ def get_sa_coefficients(self):
 
             # extract kinetic SA
             for rxn in reaction_sensitivity_data:
-                # for kinetics, get `ethane(1)` from `dln[ethane(1)]/dln[k8]: H(6)+ethane(1)=H2(12)+C2H5(5)`
-                observable_label = rxn.label.split('[')[1].split(']')[0]
+                observable_label = get_observable_label_from_header(rxn)
                 if observable_label not in sa_dict['kinetics']:
                     sa_dict['kinetics'][observable_label] = dict()
-                # for kinetics, get k8 from `dln[ethane(1)]/dln[k8]: H(6)+ethane(1)=H2(12)+C2H5(5)` then only extract 8
-                parameter = rxn.label.split('[')[2].split(']')[0]
+                parameter = get_parameter_from_header(rxn)
                 parameter = int(parameter[1:])
                 sa_dict['kinetics'][observable_label][parameter] = rxn.data
 
             # extract thermo SA
             for spc in thermodynamic_sensitivity_data:
-                # for thermo get 'C2H4(8)' from `dln[ethane(1)]/dH[C2H4(8)]`
-                observable_label = spc.label.split('[')[1].split(']')[0]
+                observable_label = get_observable_label_from_header(spc)
                 if observable_label not in sa_dict['thermo']:
                     sa_dict['thermo'][observable_label] = dict()
-                # for thermo get 'C2H4(8)' from `dln[ethane(1)]/dH[C2H4(8)]`
-                parameter = spc.label.split('[')[2].split(']')[0]
+                parameter = get_parameter_from_header(spc)
                 sa_dict['thermo'][observable_label][parameter] = spc.data
 
         return sa_dict

diff --git a/t3/simulate/rmg_constantTP.py b/t3/simulate/rmg_constantTP.py
@@ -7,6 +7,7 @@
 import itertools
 import os
 import pandas as pd
+import re
 import shutil
 from typing import List, Optional
 
@@ -18,7 +19,8 @@
 from rmgpy.tools.loader import load_rmg_py_job
 from rmgpy.tools.plot import plot_sensitivity
 
-from t3.common import get_chem_to_rmg_rxn_index_map, get_species_by_label, get_values_within_range, time_lapse
+from t3.common import get_chem_to_rmg_rxn_index_map, get_species_by_label, get_values_within_range, \
+    get_observable_label_from_header, get_parameter_from_header, time_lapse
 from t3.logger import Logger
 from t3.simulate.adapter import SimulateAdapter
 from t3.simulate.factory import register_simulate_adapter
@@ -256,17 +258,14 @@ def get_sa_coefficients(self) -> Optional[dict]:
                 elif '/dG[' in header:
                     sa_type = 'thermo'
                 if sa_type is not None:
-                    observable_label = header.split('[')[1].split(']')[0]
+                    observable_label = get_observable_label_from_header(header)
                     observable = get_species_by_label(observable_label, self.rmg_model.reaction_model.core.species)
                     if observable is None:
                         self.logger.error(f'Could not identify observable species for label: {observable_label}')
                     observable_label = observable.to_chemkin()
                     if observable_label not in sa_dict[sa_type].keys():
                         sa_dict[sa_type][observable_label] = dict()
-                    # parameter extraction examples:
-                    # for species get 'C2H4(8)' from `dln[ethane(1)]/dG[C2H4(8)]`
-                    # for reaction, get 8 from `dln[ethane(1)]/dln[k8]: H(6)+ethane(1)=H2(12)+C2H5(5)`
-                    parameter = header.split('[')[2].split(']')[0]
+                    parameter = get_parameter_from_header(header)
                     if sa_type == 'kinetics':
                         parameter = parameter[1:]
                         parameter = chem_to_rmg_rxn_index_map[int(parameter)] \