def sensitivityAnalysis(self, initialMoleFractions, sensitiveSpecies, T, P, terminationTime, sensitivityThreshold=1e-3, number=10, fileformat='.png'):
"""
Run sensitivity analysis using the RMG solver in a single ReactionSystem object
initialMoleFractions is a dictionary with Species objects as keys and mole fraction initial conditions
sensitiveSpecies is a list of sensitive Species objects
number is the number of top species thermo or reaction kinetics desired to be plotted
"""
from rmgpy.solver import SimpleReactor, TerminationTime
from rmgpy.quantity import Quantity
from rmgpy.tools.sensitivity import plotSensitivity
from rmgpy.rmg.listener import SimulationProfileWriter, SimulationProfilePlotter
from rmgpy.rmg.settings import ModelSettings, SimulatorSettings
T = Quantity(T)
P = Quantity(P)
termination=[TerminationTime(Quantity(terminationTime))]
reactionSystem = SimpleReactor(T, P, initialMoleFractions, termination, sensitiveSpecies, sensitivityThreshold)
# Create the csv worksheets for logging sensitivity
util.makeOutputSubdirectory(self.outputDirectory, 'solver')
sensWorksheet = []
reactionSystemIndex = 0
for spec in reactionSystem.sensitiveSpecies:
csvfilePath = os.path.join(self.outputDirectory, 'solver', 'sensitivity_{0}_SPC_{1}.csv'.format(reactionSystemIndex+1, spec.index))
sensWorksheet.append(csvfilePath)
reactionSystem.attach(SimulationProfileWriter(
self.outputDirectory, reactionSystemIndex, self.speciesList))
reactionSystem.attach(SimulationProfilePlotter(
self.outputDirectory, reactionSystemIndex, self.speciesList))
simulatorSettings = SimulatorSettings() #defaults
modelSettings = ModelSettings() #defaults
modelSettings.fluxToleranceMoveToCore = 0.1
modelSettings.fluxToleranceInterrupt = 1.0
modelSettings.fluxToleranceKeepInEdge = 0.0
reactionSystem.simulate(
coreSpecies = self.speciesList,
coreReactions = self.reactionList,
edgeSpecies = [],
edgeReactions = [],
surfaceSpecies = [],
surfaceReactions = [],
modelSettings = modelSettings,
simulatorSettings = simulatorSettings,
sensitivity = True,
sensWorksheet = sensWorksheet,
)
plotSensitivity(self.outputDirectory, reactionSystemIndex, reactionSystem.sensitiveSpecies, number=number, fileformat=fileformat)
def sensitivityAnalysis(self, initialMoleFractions, sensitiveSpecies, T, P, terminationTime, sensitivityThreshold=1e-3, number=10, fileformat='.png'):
"""
Run sensitivity analysis using the RMG solver in a single ReactionSystem object
initialMoleFractions is a dictionary with Species objects as keys and mole fraction initial conditions
sensitiveSpecies is a list of sensitive Species objects
number is the number of top species thermo or reaction kinetics desired to be plotted
"""
from rmgpy.solver import SimpleReactor, TerminationTime
from rmgpy.quantity import Quantity
from rmgpy.tools.sensitivity import plotSensitivity
from rmgpy.rmg.listener import SimulationProfileWriter, SimulationProfilePlotter
T = Quantity(T)
P = Quantity(P)
termination=[TerminationTime(Quantity(terminationTime))]
reactionSystem = SimpleReactor(T, P, initialMoleFractions, termination, sensitiveSpecies, sensitivityThreshold)
# Create the csv worksheets for logging sensitivity
util.makeOutputSubdirectory(self.outputDirectory, 'solver')
sensWorksheet = []
reactionSystemIndex = 0
for spec in reactionSystem.sensitiveSpecies:
csvfilePath = os.path.join(self.outputDirectory, 'solver', 'sensitivity_{0}_SPC_{1}.csv'.format(reactionSystemIndex+1, spec.index))
sensWorksheet.append(csvfilePath)
reactionSystem.attach(SimulationProfileWriter(
self.outputDirectory, reactionSystemIndex, self.speciesList))
reactionSystem.attach(SimulationProfilePlotter(
self.outputDirectory, reactionSystemIndex, self.speciesList))
reactionSystem.simulate(
coreSpecies = self.speciesList,
coreReactions = self.reactionList,
edgeSpecies = [],
edgeReactions = [],
toleranceKeepInEdge = 0,
toleranceMoveToCore = 1,
toleranceInterruptSimulation = 1,
sensitivity = True,
sensWorksheet = sensWorksheet,
)
plotSensitivity(self.outputDirectory, reactionSystemIndex, reactionSystem.sensitiveSpecies, number=number, fileformat=fileformat)