Added a sensitivity block to the RMG input file

Author: alongd

t3/utils/writer.py

@@ -20,6 +20,7 @@ def write_rmg_input_file(rmg: dict,
                          t3: dict,
                          path: str,
                          iteration: int = 1,
+                         run_sa: bool = False,
                          walltime: str = '00:00:00:00',
                          ):
     """
@@ -32,6 +33,7 @@ def write_rmg_input_file(rmg: dict,
         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()
@@ -101,7 +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:
@@ -119,7 +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:
@@ -167,6 +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):
@@ -189,6 +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':