Adapt solver/reactor object syntax to deal with variable condition re…

…actors

Also adaption of conversion calculations and return type for simulate so that the time and conversion can be put into the RMG_Memory objects. Addition of sensConditions for specifying the conditions under, which to do sensitivity analysis.

rmgpy/rmg/input.py

@@ -133,47 +133,51 @@ def adjacencyList(string):
 def simpleReactor(temperature,
                   pressure,
                   initialMoleFractions,
+                  nSimsTerm=6,
                   terminationConversion=None,
                   terminationTime=None,
                   sensitivity=None,
-                  sensitivityThreshold=1e-3
+                  sensitivityThreshold=1e-3,
+                  sensitivityTemperature=None,
+                  sensitivityPressure=None,
+                  sensitivityMoleFractions=None,
                   ):
     logging.debug('Found SimpleReactor reaction system')
 
-    for value in initialMoleFractions.values():
-        if value < 0:
-            raise InputError('Initial mole fractions cannot be negative.')
-
-    for spec in initialMoleFractions:
-            initialMoleFractions[spec] = float(initialMoleFractions[spec])
-
-    totalInitialMoles = sum(initialMoleFractions.values())
-    if totalInitialMoles != 1:
-        logging.warning('Initial mole fractions do not sum to one; normalizing.')
-        logging.info('')
-        logging.info('Original composition:')
-        for spec, molfrac in initialMoleFractions.iteritems():
-            logging.info("{0} = {1}".format(spec,molfrac))
-        for spec in initialMoleFractions:
-            initialMoleFractions[spec] /= totalInitialMoles
-        logging.info('')
-        logging.info('Normalized mole fractions:')
-        for spec, molfrac in initialMoleFractions.iteritems():
-            logging.info("{0} = {1}".format(spec,molfrac))
-
-    if type(temperature) != list and type(pressure) != list:
+    for key,value in initialMoleFractions.iteritems():
+        if not isinstance(value,list):
+            initialMoleFractions[key] = float(value)
+            if value < 0:
+                raise InputError('Initial mole fractions cannot be negative.')
+        else:
+            if len(value) != 2:
+                raise InputError("Initial mole fraction values must either be a number or a list with 2 entries")
+            initialMoleFractions[key] = [float(value[0]),float(value[1])]
+            if len(value) > 2:
+                raise InputError('mole ranges can only have one or two entries')
+            elif value[0] < 0 or value[1] < 0:
+                raise InputError('Initial mole fractions cannot be negative.')
+            elif value[1] < value[0]:
+                raise InputError('Initial mole fraction range out of order: {0}'.format(key))
+
+    if not isinstance(temperature,list):
         T = Quantity(temperature)
-        P = Quantity(pressure)
     else:
-        if type(temperature) != list:
-            temperature = list(temperature)
-        if type(pressure) != list:
-            pressure = list(pressure)
+        if len(temperature) != 2:
+            raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
         T = [Quantity(t) for t in temperature]
+
+    if not isinstance(pressure,list):
+        P = Quantity(pressure)
+    else:
+        if len(pressure) > 2:
+            raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
         P = [Quantity(p) for p in pressure]
-        if len(T) > 2 or len(P) > 2:
-            raise InputError('Temperature and pressure ranges can only have one or two entries')
 
+
+    if not isinstance(temperature,list) and not isinstance(pressure,list) and all([not isinstance(x,list) for x in initialMoleFractions.values()]):
+        nSimsTerm=1
+
     termination = []
     if terminationConversion is not None:
         for spec, conv in terminationConversion.iteritems():
@@ -188,33 +192,59 @@ def simpleReactor(temperature,
         if isinstance(sensitivity, str): sensitivity = [sensitivity]
         for spec in sensitivity:
             sensitiveSpecies.append(speciesDict[spec])
-    system = SimpleReactor(T, P, initialMoleFractions, termination, sensitiveSpecies, sensitivityThreshold)
+
+    if not isinstance(T,list):
+        sensitivityTemperature = T
+    if not isinstance(P,list):
+        sensitivityPressure = P
+    if not any([isinstance(x,list) for x in initialMoleFractions.itervalues()]):
+        sensitivityMoleFractions = initialMoleFractions
+    if sensitivityMoleFractions is None or sensitivityTemperature is None or sensitivityPressure is None:
+        sensConditions = None
+    else:
+        sensConditions = sensitivityMoleFractions
+        sensConditions['T'] = Quantity(sensitivityTemperature)
+        sensConditions['P'] = Quantity(sensitivityPressure)
+
+    system = SimpleReactor(T, P, initialMoleFractions, nSimsTerm, termination, sensitiveSpecies, sensitivityThreshold,sensConditions)
     rmg.reactionSystems.append(system)
 
 
 # Reaction systems
 def liquidReactor(temperature,
                   initialConcentrations,
                   terminationConversion=None,
+                  nSimsTerm = 4,
                   terminationTime=None,
                   sensitivity=None,
                   sensitivityThreshold=1e-3,
+                  sensitivityTemperature=None,
+                  sensitivityConcentrations=None,
                   constantSpecies=None):
 
     logging.debug('Found LiquidReactor reaction system')
 
-    if type(temperature) != list:
+    if not isinstance(temperature,list):
         T = Quantity(temperature)
     else:
+        if len(temperature) != 2:
+            raise InputError('Temperature and pressure ranges can either be in the form of (number,units) or a list with 2 entries of the same format')
         T = [Quantity(t) for t in temperature]
-        if len(T) > 2:
-            raise InputError('Temperature ranges can only have one or two entries')
 
     for spec,conc in initialConcentrations.iteritems():
-        concentration = Quantity(conc)
-        # check the dimensions are ok
-        # convert to mol/m^3 (or something numerically nice? or must it be SI)
-        initialConcentrations[spec] = concentration.value_si
+        if not isinstance(conc,list):
+            concentration = Quantity(conc)
+            # check the dimensions are ok
+            # convert to mol/m^3 (or something numerically nice? or must it be SI)
+            initialConcentrations[spec] = concentration.value_si
+        else:
+            if len(conc) != 2:
+                raise InputError("Concentration values must either be in the form of (number,units) or a list with 2 entries of the same format")
+            initialConcentrations[spec] = [Quantity(conc[0]),Quantity(conc[1])]
+
+    if not isinstance(temperature,list) and all([not isinstance(x,list) for x in initialConcentrations.itervalues()]):
+        nSimsTerm=1
+
     termination = []
     if terminationConversion is not None:
         for spec, conv in terminationConversion.iteritems():
@@ -236,9 +266,18 @@ def liquidReactor(temperature,
             logging.debug("  {0}".format(constantSpecie))
             if not speciesDict.has_key(constantSpecie):
                 raise InputError('Species {0} not found in the input file'.format(constantSpecie))
-
-
-    system = LiquidReactor(T, initialConcentrations, termination, sensitiveSpecies, sensitivityThreshold,constantSpecies)
+
+    if not isinstance(T,list):
+        sensitivityTemperature = T
+    if not any([isinstance(x,list) for x in initialConcentrations.itervalues()]):
+        sensitivityConcentrations = initialConcentrations
+    if sensitivityConcentrations is None or sensitivityTemperature is None:
+        sensConditions = None
+    else:
+        sensConditions = Quantity(sensitivityConcentrations)
+        sensConditions['T'] = Quantity(sensitivityTemperature)
+
+    system = LiquidReactor(T, initialConcentrations, nSimsTerm, termination, sensitiveSpecies, sensitivityThreshold, sensConditions, constantSpecies)
     rmg.reactionSystems.append(system)
 
 def simulator(atol, rtol, sens_atol=1e-6, sens_rtol=1e-4):

rmgpy/rmg/main.py

@@ -647,7 +647,7 @@ def execute(self, **kwargs):
                         # Turn pruning off if we haven't reached minimum core size.
                         prune = False
 
-                    try: terminated,resurrected,obj,newSurfaceSpecies,newSurfaceReactions = reactionSystem.simulate(
+                    try: terminated,resurrected,obj,newSurfaceSpecies,newSurfaceReactions,t,x = reactionSystem.simulate(
                         coreSpecies = self.reactionModel.core.species,
                         coreReactions = self.reactionModel.core.reactions,
                         edgeSpecies = self.reactionModel.edge.species,
@@ -806,7 +806,7 @@ def execute(self, **kwargs):
         # Run sensitivity analysis post-model generation if sensitivity analysis is on
         for index, reactionSystem in enumerate(self.reactionSystems):
 
-            if reactionSystem.sensitiveSpecies:
+            if reactionSystem.sensitiveSpecies and reactionSystem.sensConditions:
                 logging.info('Conducting sensitivity analysis of reaction system %s...' % (index+1))
 
                 sensWorksheet = []
@@ -826,6 +826,7 @@ def execute(self, **kwargs):
                     sensWorksheet = sensWorksheet,
                     modelSettings = self.modelSettingsList[-1],
                     simulatorSettings = self.simulatorSettingsList[-1],
+                    conditions = reactionSystem.sensConditions,
                 )
 
                 plot_sensitivity(self.outputDirectory, index, reactionSystem.sensitiveSpecies)

rmgpy/solver/base.pxd

@@ -112,12 +112,13 @@ cdef class ReactionSystem(DASx):
 
     # methods
     cpdef initializeModel(self, list coreSpecies, list coreReactions, list edgeSpecies, list edgeReactions, list surfaceSpecies=?,
-        list surfaceReactions=?, list pdepNetworks=?, atol=?, rtol=?, sensitivity=?, sens_atol=?, sens_rtol=?, filterReactions=?)
+        list surfaceReactions=?, list pdepNetworks=?, atol=?, rtol=?, sensitivity=?, sens_atol=?, sens_rtol=?, filterReactions=?,
+        dict conditions=?)
 
     cpdef simulate(self, list coreSpecies, list coreReactions, list edgeSpecies, 
         list edgeReactions,list surfaceSpecies, list surfaceReactions,
         list pdepNetworks=?, bool prune=?, bool sensitivity=?, list sensWorksheet=?, object modelSettings=?,
-        object simulatorSettings=?)
+        object simulatorSettings=?, dict conditions=?)
 
     cpdef logRates(self, double charRate, object species, double speciesRate, double maxDifLnAccumNum, object network, double networkRate)
 

rmgpy/solver/base.pyx

@@ -188,7 +188,7 @@ cdef class ReactionSystem(DASx):
 
     cpdef initializeModel(self, list coreSpecies, list coreReactions, list edgeSpecies, list edgeReactions, list surfaceSpecies=None,
                           list surfaceReactions=None, list pdepNetworks=None, atol=1e-16, rtol=1e-8, sensitivity=False, 
-                          sens_atol=1e-6, sens_rtol=1e-4, filterReactions=False):
+                          sens_atol=1e-6, sens_rtol=1e-4, filterReactions=False, dict conditions=None):
         """
         Initialize a simulation of the reaction system using the provided
         kinetic model. You will probably want to create your own version of this
@@ -200,7 +200,21 @@ cdef class ReactionSystem(DASx):
         if surfaceReactions is None:
             surfaceReactions = []
 
-
+        if conditions:
+            isConc = hasattr(self,'initialConcentrations')
+            keys = conditions.keys()
+            if 'T' in keys and hasattr(self,'T'):
+                self.T = Quantity(conditions['T'],'K')
+            if 'P' in keys and hasattr(self,'P'):
+                self.P = Quantity(conditions['P'],'Pa')
+            for k in keys:
+                if isConc:
+                    if k in self.initialConcentrations.keys():
+                        self.initialConcentrations[k] = conditions[k] #already in SI units
+                else:
+                    if k in self.initialMoleFractions.keys():
+                        self.initialMoleFractions[k] = conditions[k]              
+
         self.numCoreSpecies = len(coreSpecies)
         self.numCoreReactions = len(coreReactions)
         self.numEdgeSpecies = len(edgeSpecies)
@@ -520,7 +534,7 @@ cdef class ReactionSystem(DASx):
     cpdef simulate(self, list coreSpecies, list coreReactions, list edgeSpecies, 
         list edgeReactions,list surfaceSpecies, list surfaceReactions,
         list pdepNetworks=None, bool prune=False, bool sensitivity=False, list sensWorksheet=None, object modelSettings=None,
-        object simulatorSettings=None):
+        object simulatorSettings=None, dict conditions=None):
         """
         Simulate the reaction system with the provided reaction model,
         consisting of lists of core species, core reactions, edge species, and
@@ -549,7 +563,7 @@ cdef class ReactionSystem(DASx):
         cdef bint terminated
         cdef object maxSpecies, maxNetwork
         cdef int i, j, k
-        cdef numpy.float64_t maxSurfaceDifLnAccumNum, maxSurfaceSpeciesRate 
+        cdef numpy.float64_t maxSurfaceDifLnAccumNum, maxSurfaceSpeciesRate, conversion
         cdef int maxSurfaceAccumReactionIndex, maxSurfaceSpeciesIndex
         cdef object maxSurfaceAccumReaction, maxSurfaceSpecies
         cdef numpy.ndarray[numpy.float64_t,ndim=1] surfaceSpeciesProduction, surfaceSpeciesConsumption
@@ -563,7 +577,7 @@ cdef class ReactionSystem(DASx):
         # cython declations for sensitivity analysis
         cdef numpy.ndarray[numpy.int_t, ndim=1] sensSpeciesIndices
         cdef numpy.ndarray[numpy.float64_t, ndim=1] moleSens, dVdk, normSens
-        cdef list time_array, normSens_array, newSurfaceReactions, newSurfaceReactionInds, newObjects, newObjectInds, conversions
+        cdef list time_array, normSens_array, newSurfaceReactions, newSurfaceReactionInds, newObjects, newObjectInds
 
         zeroProduction = False
         zeroConsumption = False
@@ -609,7 +623,7 @@ cdef class ReactionSystem(DASx):
 
         self.initializeModel(coreSpecies, coreReactions, edgeSpecies, edgeReactions, surfaceSpecies, surfaceReactions, 
                              pdepNetworks, absoluteTolerance, relativeTolerance, sensitivity, sensitivityAbsoluteTolerance, 
-                             sensitivityRelativeTolerance, filterReactions)
+                             sensitivityRelativeTolerance, filterReactions,conditions)
 
         prunableSpeciesIndices = self.prunableSpeciesIndices
         prunableNetworkIndices = self.prunableNetworkIndices
@@ -630,6 +644,7 @@ cdef class ReactionSystem(DASx):
         maxNetwork = None
         maxNetworkRate = 0.0
         iteration = 0
+        conversion = 0.0
 
         maxEdgeSpeciesRateRatios = self.maxEdgeSpeciesRateRatios
         maxNetworkLeakRateRatios = self.maxNetworkLeakRateRatios
@@ -667,12 +682,11 @@ cdef class ReactionSystem(DASx):
 
                     logging.info('Resurrecting Model...')
 
-                    conversions = []
-
+                    conversion = 0.0
                     for term in self.termination:
                         if isinstance(term, TerminationConversion):
                             index = speciesIndex[term.species]
-                            conversions.append(1-(y_coreSpecies[index] / y0[index]))
+                            conversion = 1-(y_coreSpecies[index] / y0[index])
 
                     if invalidObjects == []:
                         #species flux criterion
@@ -695,7 +709,7 @@ cdef class ReactionSystem(DASx):
                             invalidObjects.append(obj)
 
                     if invalidObjects != []:
-                        return False,True,invalidObjects,surfaceSpecies,surfaceReactions,self.t,conversions
+                        return False,True,invalidObjects,surfaceSpecies,surfaceReactions,self.t,conversion
                     else:
                         logging.error('Model Resurrection has failed')
                         logging.error("Core species names: {!r}".format([getSpeciesIdentifier(s) for s in coreSpecies]))
@@ -1031,7 +1045,6 @@ cdef class ReactionSystem(DASx):
                 logging.info('terminating simulation due to interrupt...')
                 break
 
-            conversions = []
             # Finish simulation if any of the termination criteria are satisfied
             for term in self.termination:
                 if isinstance(term, TerminationTime):
@@ -1042,7 +1055,7 @@ cdef class ReactionSystem(DASx):
                         break
                 elif isinstance(term, TerminationConversion):
                     index = speciesIndex[term.species]
-                    conversions.append(1-(y_coreSpecies[index] / y0[index]))
+                    conversion = 1-(y_coreSpecies[index] / y0[index])
                     if 1 - (y_coreSpecies[index] / y0[index]) > term.conversion:
                         terminated = True
                         logging.info('At time {0:10.4e} s, reached target termination conversion: {1:f} of {2}'.format(self.t,term.conversion,term.species))
@@ -1088,7 +1101,7 @@ cdef class ReactionSystem(DASx):
 
         # Return the invalid object (if the simulation was invalid) or None
         # (if the simulation was valid)
-        return terminated, False, invalidObjects, surfaceSpecies, surfaceReactions, self.t, conversions
+        return terminated, False, invalidObjects, surfaceSpecies, surfaceReactions, self.t, conversion
 
     cpdef logRates(self, double charRate, object species, double speciesRate, double maxDifLnAccumNum, object network, double networkRate):
         """