Save sensitivity files for all species by specifying 'all'

ReactionMechanismGenerator · Oct 17, 2018 · 5dae781 · 5dae781
1 parent aaf3dce
commit 5dae781
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Showing 4 changed files with 14 additions and 4 deletions.
diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
@@ -193,9 +193,13 @@ def simpleReactor(temperature,
 
     sensitiveSpecies = []
     if sensitivity:
-        if isinstance(sensitivity, str): sensitivity = [sensitivity]
-        for spec in sensitivity:
-            sensitiveSpecies.append(speciesDict[spec])
+        if sensitivity != 'all':
+            if isinstance(sensitivity, str): sensitivity = [sensitivity]
+            for spec in sensitivity:
+                sensitiveSpecies.append(speciesDict[spec])
+
+        else:
+            sensitiveSpecies.append('all')
 
     if not isinstance(T,list):
         sensitivityTemperature = T

diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
@@ -896,6 +896,9 @@ def execute(self, **kwargs):
 
             if reactionSystem.sensitiveSpecies and reactionSystem.sensConditions:
                 logging.info('Conducting sensitivity analysis of reaction system %s...' % (index+1))
+
+                if reactionSystem.sensitiveSpecies == ['all']:
+                    reactionSystem.sensitiveSpecies = self.reactionModel.core.species
 
                 sensWorksheet = []
                 for spec in reactionSystem.sensitiveSpecies:

diff --git a/rmgpy/tools/loader.py b/rmgpy/tools/loader.py
@@ -108,7 +108,8 @@ def loadRMGPyJob(inputFile, chemkinFile=None, speciesDict=None, generateImages=T
         for t in reactionSystem.termination:
             if isinstance(t, TerminationConversion):
                 t.species = speciesDict[t.species]
-        reactionSystem.sensitiveSpecies = [speciesDict[spec] for spec in reactionSystem.sensitiveSpecies]
+        if reactionSystem.sensitiveSpecies != ['all']:
+            reactionSystem.sensitiveSpecies = [speciesDict[spec] for spec in reactionSystem.sensitiveSpecies]
 
     # Set reaction model to match model loaded from Chemkin file
     rmg.reactionModel.core.species = speciesList

diff --git a/rmgpy/tools/simulate.py b/rmgpy/tools/simulate.py
@@ -90,6 +90,8 @@ def simulate(rmg, diffusionLimited=True):
 
         if reactionSystem.sensitiveSpecies:
             logging.info('Conducting simulation and sensitivity analysis of reaction system %s...' % (index+1))
+            if reactionSystem.sensitiveSpecies == ['all']:
+                reactionSystem.sensitiveSpecies = rmg.reactionModel.core.species
 
         else:
             logging.info('Conducting simulation of reaction system %s...' % (index+1))