def testUnequalObjsCompareUnequal_extraPropOnSecond(self):
objA = tCode.ThermoDataStandard({"keyA": [1, 2], "keyB": [3, 4]})
objB = tCode.ThermoDataStandard({
"keyA": [1, 2],
"keyB": [3, 4],
"keyC": [5, 6]
})
self.assertNotEqual(objA, objB)
def createTestObjs(self):
currKwargDict = {
"step": self.step,
"time": self.time,
"temp": self.temp
}
self.testObjA = tCode.ThermoDataStandard(currKwargDict)
def createTestObjs(self):
self.inpKwargDictA = {
"step": self.step,
"temp": self.temp,
"pressure": self.pressure
}
self.testObjA = tCode.ThermoDataStandard(self.inpKwargDictA)
def createTestObjs(self):
self.propDict = {
"step": self.steps,
"time": self.time,
"eTotal": self.eTotal
}
self.testObjA = tCode.ThermoDataStandard(self.propDict)
def createTestObjs(self):
thermoDataDict = {
"step": self.step,
"time": self.time,
"temp": self.temp
}
self.thermoDataObjA = thermoDataHelp.ThermoDataStandard(thermoDataDict)
def testExpectedFromMergingOrderedStructs(self):
expKwargDict = {
"step": self.stepsA + self.stepsB,
"temp": self.tempA + self.tempB
}
expObj = tCode.ThermoDataStandard(expKwargDict)
actObj = tCode.getMergedStandardThermoData(
self.dataList, overlapStrat=self.overlapStrat)
self.assertEqual(expObj, actObj)
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):
thermoDataDict = {
"step": self.step,
"time": self.time,
"temp": self.temp
}
self.thermoDataObjA = thermoDataHelp.ThermoDataStandard(thermoDataDict)
kwargDict = {
"startTime": self.startTime,
"endTime": self.endTime,
"startStep": self.startStep,
"endStep": self.endStep,
"props": self.props,
"timeTol": self.timeTol
}
self.testObjA = tCode.GetStatsForThermoProps(**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 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.tempA = [2 * x for x in self.stepsA]
self.tempB = [3 * x for x in self.stepsB]
self.createTestObjs()
expKwargDict = {
"step": self.stepsA[:3] + self.stepsB,
"temp": self.tempA[:3] + self.tempB
}
expObj = tCode.ThermoDataStandard(expKwargDict)
actObj = tCode.getMergedStandardThermoData(
self.dataList, overlapStrat=self.overlapStrat)
self.assertEqual(expObj, actObj)
def _mdStepsFinalStepFunct(parserInstance):
outThermoDict = parserInstance.outDict["thermo_arrays"]
parserInstance.outDict["thermo_data"] = thermoDataHelp.ThermoDataStandard(
outThermoDict)
trajSteps = list()
thermoInfo = parserInstance.outDict["thermo_arrays"]
assert len(thermoInfo["step"]) == len(parserInstance.outDict["traj_geoms"])
for idx, geom in enumerate(parserInstance.outDict["traj_geoms"]):
# currStep = trajHelp.TrajStepBase(unitCell=geom, step=thermoInfo["step"][idx], time=thermoInfo["time"][idx])
currStep = trajHelp.TrajStepFlexible(unitCell=geom,
step=thermoInfo["step"][idx],
time=thermoInfo["time"][idx])
trajSteps.append(currStep)
parserInstance.outDict["trajectory"] = trajHelp.TrajectoryInMemory(
trajSteps)
parserInstance.outDict.pop("thermo_arrays")
parserInstance.outDict.pop("traj_geoms")
def testFromSelectedStdKwargs(self):
objA = tCode.ThermoDataStandard({"step": [1, 2], "temp": [3, 4]})
objB = tCode.ThermoDataStandard.fromStdKwargs(temp=[3, 4], step=[1, 2])
self.assertEqual(objA, objB)
def testUnequalObjsCompareUnequal_diffPropList(self):
objA = tCode.ThermoDataStandard({"keyA": [1, 2], "keyB": [3, 4]})
objB = tCode.ThermoDataStandard({"keyA": [1, 2], "keyC": [3, 4]})
self.assertNotEqual(objA, objB)
def testExpectedCaseA(self):
kwargDict = {"step": [1, 3, 5], "temp": [10, 30, 50]}
expObj = tCode.ThermoDataStandard(kwargDict)
actObj = self._runTestFunct()
self.assertEqual(expObj, actObj)
def createTestObjs(self):
kwargDict = {"step": self.inpSteps, "temp": self.inpTemps}
self.inpObj = tCode.ThermoDataStandard(kwargDict)
def createTestObjs(self):
kwargDictA = {"step": self.stepsA, "temp": self.tempA}
kwargDictB = {"step": self.stepsB, "temp": self.tempB}
self.thermoObjA = tCode.ThermoDataStandard(kwargDictA)
self.thermoObjB = tCode.ThermoDataStandard(kwargDictB)
self.dataList = [self.thermoObjA, self.thermoObjB]
