def createTestObjs(self):
self.trajStepA = trajCoreHelp.TrajStepBase(unitCell=self.uCells[0],
step=self.steps[0])
self.trajStepB = trajCoreHelp.TrajStepBase(unitCell=self.uCells[1],
step=self.steps[1])
self.trajObjA = trajCoreHelp.TrajectoryInMemory(
[self.trajStepA, self.trajStepB])
def _getExpectedValsA(self):
expTrajA = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=step) for step in [0, 1]])
expTrajB = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=step) for step in [2, 3]])
expTrajC = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=step) for step in [4, 5]])
return [expTrajA, expTrajB, expTrajC]
def createTestObjs(self):
self.trajStepA = tCode.TrajStepBase(time=self.timeA,
step=self.stepA,
unitCell=self.unitCellA)
self.trajStepB = tCode.TrajStepBase(time=self.timeB,
step=self.stepB,
unitCell=self.unitCellA)
self.testObjA = tCode.TrajectoryInMemory(
[self.trajStepA, self.trajStepB])
def createTestObjs(self):
self._createCells()
self.trajStepA = trajHelp.TrajStepBase(unitCell=self.cellA,
step=self.stepA,
time=self.timeA)
self.trajStepB = trajHelp.TrajStepBase(unitCell=self.cellB,
step=self.stepB,
time=self.timeB)
trajSteps = [self.trajStepA, self.trajStepB]
self.testObjA = trajHelp.TrajectoryInMemory(trajSteps)
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellB = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords, self.cellB.cartCoords = self.coordsA, self.coordsB
self.trajStepA = trajHelp.TrajStepBase(unitCell=self.cellA)
self.trajStepB = trajHelp.TrajStepBase(unitCell=self.cellB)
self.fullTrajA = trajHelp.TrajectoryInMemory(
[self.trajStepA, self.trajStepB])
def createTestObjs(self):
self.trajA = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in self.stepsA])
self.trajB = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in self.stepsB])
self.trajC = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in self.stepsC])
self.trajListA = [self.trajA, self.trajB, self.trajC]
allSteps = self.stepsA + self.stepsB + self.stepsC
self.expTrajStd = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in allSteps])
def createTestObjs(self):
self.trajStepA = trajHelp.TrajStepBase(unitCell=self.unitCellA,
step=self.stepA,
time=self.timeA)
self.trajStepB = trajHelp.TrajStepBase(unitCell=self.unitCellB,
step=self.stepB,
time=self.timeB)
self.testTrajA = trajHelp.TrajectoryInMemory(
[self.trajStepA, self.trajStepB])
self.testRecord = {
self.folderKeyA: self.folderPathA,
self.fileKeyA: self.fileNameA
}
def testExpVals_step0InXyz(self, mockedParseCpout, mockedParseXyz):
#Modify the xyz output
stepZeroXyz = {"coords": self.initCoords, "step": 0, "time": 0}
self.parsedXyz.insert(0, stepZeroXyz)
#modify the expected dict
trajStepZero = trajHelp.TrajStepBase(unitCell=copy.deepcopy(
self.initMdCell),
step=0,
time=0)
self.expDict["trajectory"].trajSteps = [
trajStepZero
] + self.expDict["trajectory"].trajSteps
self.expDict["trajectory"].trajSteps[
0].unitCell.cartCoords = self.initCoords
for key in self.expDict["thermo_data"].dataDict.keys():
currVal = self.initThermoDict[key]
self.expDict["thermo_data"].dataDict[key].insert(0, currVal)
#Set mocks
expCpoutPath, expXyzPath = "fake_cpout_path", "fake_xyz_path"
mockedParseCpout.side_effect = lambda *args, **kwargs: self.parsedCpout
mockedParseXyz.side_effect = lambda *args, **kwargs: self.parsedXyz
#Run + test
actDict = tCode.parseFullMdInfoFromCpoutAndXyzFilePaths(
expCpoutPath, expXyzPath)
mockedParseCpout.assert_called_with(expCpoutPath)
mockedParseXyz.assert_called_with(expXyzPath)
self.assertEqual(self.expDict, actDict)
def createTestObjs(self):
kwargDict = {
"step": self.step,
"unitCell": self.unitCell,
"time": self.time
}
self.testObjA = tCode.TrajStepBase(**kwargDict)
def createTestObjs(self):
#Create thermo arrays + thermoDataObj
self.thermalArraysA = {
"step": self.steps,
"time": self.times,
"eKinetic": self.eKinetic
}
self.thermoDataA = thermoHelp.ThermoDataStandard(self.thermalArraysA)
#thngs to help mocking
trajSteps = [
trajHelp.TrajStepBase(unitCell=self.emptyCellA,
step=self.steps[0],
time=self.times[0]),
trajHelp.TrajStepBase(unitCell=self.emptyCellB,
step=self.steps[1],
time=self.times[1])
]
self.outTrajA = trajHelp.TrajectoryInMemory(trajSteps)
self.parsedCpout = {
"trajectory": self.outTrajA,
"thermo_data": self.thermoDataA,
"init_thermo_dict": self.initThermoDict,
"init_md_cell": self.initMdCell
}
self.parsedXyz = [{
"coords": self.coordsA,
"step": self.steps[0],
"time": self.times[0]
}, {
"coords": self.coordsB,
"step": self.steps[1],
"time": self.times[1]
}]
#Expected output
self.expCellA, self.expCellB = copy.deepcopy(
self.emptyCellA), copy.deepcopy(self.emptyCellB)
self.expCellA.cartCoords = self.coordsA
self.expCellB.cartCoords = self.coordsB
expTrajSteps = copy.deepcopy(trajSteps)
expTrajSteps[0].unitCell.cartCoords = self.coordsA
expTrajSteps[1].unitCell.cartCoords = self.coordsB
self.expDict = dict()
self.expDict["trajectory"] = trajHelp.TrajectoryInMemory(expTrajSteps)
self.expDict["thermo_data"] = copy.deepcopy(self.thermoDataA)
def testInPlaceExpected(self):
self.inPlace = True
self.createView = False
expSteps = [trajHelp.TrajStepBase(step=s) for s in [0, 2, 4, 6]]
expTraj = trajHelp.TrajectoryInMemory(expSteps)
self._runTestFunct()
actTraj = self.inpTrajA
self.assertEqual(expTraj, actTraj)
def testExpectedStepsWithUnitOverlap_overlapStratSimple(self):
self.stepsA.append(4)
self.createTestObjs()
expSteps = [1, 2, 3, 4, 5, 6, 7, 8, 9]
expTraj = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in expSteps])
actTraj = tCode.getMergedTrajInMemory(self.trajListA,
overlapStrat="simple")
self.assertEqual(expTraj, actTraj)
def testExpectedTrajReturnedA(self, mockGetFileList): #Set out mock mockGetFileList.side_effect = lambda *args,**kwargs: self.fileListA #Figure out expected trajectory cellA = uCellHelp.UnitCell.fromLattVects([[6.06,0,0],[-3, 5.2, 0], [0, 0, 9.8]]) cellB = uCellHelp.UnitCell.fromLattVects([[5,0,0], [0,6,0], [0,0,7]]) coordsA = [ [1,1,1,"Mg"], [3,3,3,"X"] ] coordsB = [ [2,3,4,"Mg"], [4,5,6,"X"] ] cellA.cartCoords, cellB.cartCoords = coordsA, coordsB stepA = trajHelp.TrajStepBase(unitCell=cellA) stepB = trajHelp.TrajStepBase(unitCell=cellB) expTraj = trajHelp.TrajectoryInMemory([stepA,stepB]) #Run + test actTraj = tCode.readTrajFromSimpleExtendedXyzFormat(self.inpPathA) mockGetFileList.assert_called_with(self.inpPathA) self.assertEqual(expTraj,actTraj)
def _loadExpectedObjsForFullStrA(self): lattVectsBoth = [ [9.63 , 0 , 0 ], [-4.81018, 8.33982, 0 ], [0 , 0 , 17.87895] ] cartCoordsA = [ [0.40125, 2.08496, 1.11743, "1"], [0.0226 , 3.0105 , 1.11743, "2"], [1.39212, 2.21981, 1.11743, "2"], [3.61125, 2.08496, 1.11743, "1"], [3.2326 , 3.0105 , 1.11743, "2"], [4.60212, 2.21981, 1.11743, "2"] ] cartCoordsB = [ [-0.426578, 1.73786, 0.96724 ,"1"], [0.148568 , 2.48075, 1.30372 ,"2"], [-1.43515 , 1.8717 , 1.23895 ,"2"], [4.47632 , 2.423 , 0.945189,"1"], [3.6439 , 2.54601, 1.57979 ,"2"], [4.44324 , 1.45043, 0.686697,"2"] ] if self.typeIdxToEle is not None: for idx,vals in enumerate(cartCoordsA): cartCoordsA[idx][-1] = self.typeIdxToEle[ cartCoordsA[idx][-1] ] for idx,vals in enumerate(cartCoordsB): cartCoordsB[idx][-1] = self.typeIdxToEle[ cartCoordsB[idx][-1] ] self.cellA = uCellHelp.UnitCell.fromLattVects(lattVectsBoth) self.cellB = uCellHelp.UnitCell.fromLattVects(lattVectsBoth) self.cellA.cartCoords = cartCoordsA self.cellB.cartCoords = cartCoordsB if self.timeStep is None: self.trajStepA = trajObjHelp.TrajStepBase(unitCell=self.cellA, step=0 , time=None) self.trajStepB = trajObjHelp.TrajStepBase(unitCell=self.cellB, step=50, time=None) else: self.trajStepA = trajObjHelp.TrajStepBase(unitCell=self.cellA, step=0 , time=0) self.trajStepB = trajObjHelp.TrajStepBase(unitCell=self.cellB, step=50, time=50*self.timeStep) self.expTrajObjA = trajObjHelp.TrajectoryInMemory([self.trajStepA, self.trajStepB])
def _loadTrajInMemoryA():
outStepVals = [0, 1, 2, 3]
outTimeVals = [2, 4, 6, 8]
outGeomVals = [mock.Mock() for x in outStepVals]
outIter = [[
a, b, c
] for a, b, c in it.zip_longest(outGeomVals, outStepVals, outTimeVals)]
outTrajSteps = [
tCode.TrajStepBase(unitCell=cell, step=step, time=time)
for cell, step, time in outIter
]
return tCode.TrajectoryInMemory(outTrajSteps)
def testExpectedStepsWithOverhang_trimStratSimple(self):
self.stepsA = [1, 2, 3, 4, 5]
self.stepsB = [
4, 6
] #Deleting step 5 makes it more likely we really are taking the step 4 from this set of trajs
self.stepsC = [7, 8, 9]
self.createTestObjs()
expSteps = [1, 2, 3, 4, 6, 7, 8, 9]
expTraj = tCode.TrajectoryInMemory(
[tCode.TrajStepBase(step=x) for x in expSteps])
actTraj = tCode.getMergedTrajInMemory(self.trajListA,
overlapStrat="simple",
trimStrat="simple")
self.assertEqual(expTraj, actTraj)
def createTestObjs(self):
self.thermoDataA = thermoHelp.ThermoDataStandard({"step": self.stepsA})
self.thermoDataB = thermoHelp.ThermoDataStandard({"step": self.stepsB})
self.trajA = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=x) for x in self.stepsA])
self.trajB = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=x) for x in self.stepsB])
self.retDictA = {
"trajectory": self.trajA,
"thermo_data": self.thermoDataA
}
self.retDictB = {
"trajectory": self.trajB,
"thermo_data": self.thermoDataB
}
self.expThermoData = thermoHelp.ThermoDataStandard(
{"step": self.stepsA + self.stepsB})
self.expTraj = trajHelp.TrajectoryInMemory(
[trajHelp.TrajStepBase(step=x) for x in self.stepsA + self.stepsB])
self.expDictA = {
"trajectory": self.expTraj,
"thermo_data": self.expThermoData
}
def createTestObjs(self): self.cellA = _getWaterDimerCellFromOxygenOxygenSep(self.oxyDistA) self.cellB = _getWaterDimerCellFromOxygenOxygenSep(self.oxyDistB) trajA = trajHelp.TrajStepBase(unitCell=self.cellA, step=0) trajB = trajHelp.TrajStepBase(unitCell=self.cellB, step=50) self.trajObj = trajHelp.TrajectoryInMemory([trajA,trajB])
def testExpValsA(self):
expSteps = [trajHelp.TrajStepBase(step=s) for s in [0, 2, 4, 6]]
expTraj = trajHelp.TrajectoryInMemory(expSteps)
actTraj = self._runTestFunct()
self.assertEqual(expTraj, actTraj)
def createTestObjs(self):
self.trajSteps = [
trajHelp.TrajStepBase(step=step) for step in self.steps
]
self.inpTrajA = trajHelp.TrajectoryInMemory(self.trajSteps)
def createTestObjs(self): self.cellA.cartCoords = self.coordsA self.cellB.cartCoords = self.coordsB self.trajStepA = trajHelp.TrajStepBase(unitCell=self.cellA, step=self.stepA, time=self.timeA) self.trajStepB = trajHelp.TrajStepBase(unitCell=self.cellB, step=self.stepB, time=self.timeB) self.testTrajA = trajHelp.TrajectoryInMemory([self.trajStepA, self.trajStepB])