From 5dae781b574b6c09cc9a91c2e2f40812eabd4a37 Mon Sep 17 00:00:00 2001
From: Mark Payne <ampayne@mit.edu>
Date: Tue, 16 Oct 2018 18:54:04 -0400
Subject: [PATCH] Save sensitivity files for all species by specifying 'all'

---
 rmgpy/rmg/input.py      | 10 +++++++---
 rmgpy/rmg/main.py       |  3 +++
 rmgpy/tools/loader.py   |  3 ++-
 rmgpy/tools/simulate.py |  2 ++
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index 8f8c3ed26f..21e74b9363 100644
--- 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
index 75454cb32b..fdfcbaf752 100644
--- 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
index 2f0758fb26..7e15b1cdce 100644
--- 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
index 3da1b14d0a..1f47670ed9 100644
--- 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))