def testPropagateA(self, mockGetFunctToPropagate,
mockPropagateToNextTimeStep):
#Setup
functToPropagate = mock.Mock()
newMgConc, newOConc = self.mgStartConc + 10, self.oStartConc + 12
mockGetFunctToPropagate.side_effect = lambda *args, **kwargs: functToPropagate
# functToPropagate.side_effect = lambda *ags,**kwargs: [newMgConc,newOConc]
startInpReactants = copy.deepcopy(self.inputReactants)
mockPropagateToNextTimeStep.side_effect = lambda *args, **kwargs: [
newMgConc, newOConc
]
expOutReactants = [
coreHelp.ChemSpeciesStd("Mg", newMgConc),
coreHelp.ChemSpeciesStd("H", self.hStartConc),
coreHelp.ChemSpeciesStd("O", newOConc)
]
self.testObjA.propagate(self.inputReactants,
self.step,
temperature=self.temp,
potential=self.potential)
mockGetFunctToPropagate.assert_called_with(self.inputReactants,
self.temp, self.potential)
mockPropagateToNextTimeStep.assert_called_with(
[self.mgStartConc, self.oStartConc], self.step, functToPropagate)
self.assertEqual(
expOutReactants, self.inputReactants
) #self.inputReactants SHOULD have been updated with new concs
def testUpdateConcsStaysWithinLimits(self):
self.reactants = [
coreHelp.ChemSpeciesStd("Mg", 0.15),
coreHelp.ChemSpeciesStd("O", 0.9)
]
self.concChanges = {"Mg": -0.2, "O": 0.15}
self.testObjA._updateConcs(self.reactants, self.concChanges)
expUpdatedVals = [
coreHelp.ChemSpeciesStd("Mg", 0),
coreHelp.ChemSpeciesStd("O", 1)
]
self.assertEqual(expUpdatedVals, self.reactants)
def createTestObjs(self):
self.inputReactants = [
coreHelp.ChemSpeciesStd("Mg", self.mgStartConc),
coreHelp.ChemSpeciesStd("H", self.hStartConc),
coreHelp.ChemSpeciesStd("O", self.oStartConc)
]
self.mockRatesDictA = {
"Mg": 2,
"H": 3,
"O": 4
} #Return even fixed conc vals; propagator will figure out which need using/discarding
self.mockRateCalculator = mock.Mock()
self.mockRateCalculator.getRates.side_effect = lambda *args, **kwargs: self.mockRatesDictA
self.testObjA = tCode.ConcsPropagatorTemplate(self.mockRateCalculator,
self.variableConcSpecies)
def testGetFunctToPropagate_useNonInitialStartConcs(self):
""" Check our implementation doesnt rely on the integrator only propagating from starting concentrations. """
funct = self.testObjA.getFunctToPropagate(self.inputReactants,
self.temp, self.potential)
funct(self.step, [self.mgStartConc, self.oStartConc])
newMgConc, newOConc = self.mgStartConc + 2, self.oStartConc + 2
actOutVals = funct(self.step, [newMgConc, newOConc])
expOutVals = [self.mgRate, self.oRate]
expInputReactants = [
coreHelp.ChemSpeciesStd("Mg", newMgConc),
coreHelp.ChemSpeciesStd("H", self.hStartConc),
coreHelp.ChemSpeciesStd("O", newOConc)
]
self.mockRateCalculator.getRates.assert_called_with(
expInputReactants, temperature=self.temp, potential=self.potential)
for exp, act in it.zip_longest(expOutVals, actOutVals):
self.assertAlmostEqual(exp, act)
def createTestObjs(self):
self.chemA = coreHelp.ChemSpeciesStd(self.nameA, self.concA)
self.chemB = coreHelp.ChemSpeciesStd(self.nameB, self.concB)
self.inpReactants = {self.nameA: self.chemA, self.nameB: self.chemB}
self.reactionA, self.reactionB = mock.Mock(), mock.Mock()
reactionAReturnVals = {
self.nameA: self.reactionA_returnA,
self.nameB: self.reactionA_returnB
}
reactionBReturnVals = {
self.nameA: self.reactionB_returnA,
self.nameB: self.reactionB_returnB
}
self.reactionA.getChangesInReactants.side_effect = lambda *args, **kwargs: reactionAReturnVals
self.reactionB.getChangesInReactants.side_effect = lambda *args, **kwargs: reactionBReturnVals
self.testObjA = tCode.RateCalculatorStandard(
[self.reactionA, self.reactionB])
def testMoveForward(self):
#setup
def _propagate(inpReactants, *args, **kwargs):
for reactant in inpReactants:
if reactant.name == "Mg":
reactant.conc -= 10
self.propagator.propagate.side_effect = lambda inpReactants, *args, **kwargs: _propagate(
inpReactants, *args, **kwargs)
#test
timeStep = 10
expReactants = [coreHelp.ChemSpeciesStd("Mg", -8)]
self.testObjA.moveForwardByT(timeStep)
actReactants = self.testObjA.currentReactants
self.assertEqual(expReactants, actReactants)
def testExpectedUpdateA(self):
expReactants = [coreHelp.ChemSpeciesStd(self.nameA, 2 + 1 + 3 + 4)]
self._runTestFunct()
expRequestedTimeSteps = [1.5, 1.4, 1.0]
self.assertEqual(
len(expRequestedTimeSteps),
len(self.concChangesFinder.getConcChangesForNextTimeStep.
call_args_list))
for idx, callArgs in enumerate(
self.concChangesFinder.getConcChangesForNextTimeStep.
call_args_list):
args, kwargs = callArgs
expTimeStep, actTimeStep = expRequestedTimeSteps[idx], args[1]
self.assertAlmostEqual(expTimeStep, actTimeStep)
self.assertEqual(expReactants, self.inpReactants)
def testResetFunction(self):
expReactants = self.startReactants
self.testObjA.currentReactants = [coreHelp.ChemSpeciesStd("O", 4)]
self.assertNotEqual(expReactants, self.testObjA.currentReactants)
self.testObjA.reset()
self.assertEqual(expReactants, self.testObjA.currentReactants)
def createTestObjs(self):
self.inpReactants = [coreHelp.ChemSpeciesStd(self.nameA, self.concA)]
self.concChangesFinder = mock.Mock()
retVals = it.zip_longest(self.stepSizes, self.concChanges)
self.concChangesFinder.getConcChangesForNextTimeStep.side_effect = retVals
self.testObjA = tCode.ConcsPropagatorStandard(self.concChangesFinder)
def setUp(self):
self.startReactants = [coreHelp.ChemSpeciesStd("Mg", 2)]
self.temp = 25
self.pot = 4
self.createTestObjs()