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 parseMdInfoFromMultipleCpoutAndXyzPaths(cpoutPaths,
xyzPaths,
tempKindPaths=None,
velocityPaths=None,
forcePaths=None):
""" Parse an MD trajectory spread over multiple cp2k restarts
Args:
cpoutPaths: (iter of str) Paths to *.cpout files
xyzPaths: (iter of str) Paths to *.xyz files
tempKindPaths: (iter of str, Optional) Paths to files containing atomic temperatures
velocityPaths: (iter of str, Optional) Paths to files containing velocities as dumped by motion section (basically an xyz format)
forcePaths: (iter of str, Optional) Paths to files containing forces as dumped by motion section (basically an xyz format)
Returns
outDict: Contains trajectory/thermodynamic info
"""
outDict = dict()
tempKindPaths = [None for x in range(len(cpoutPaths))
] if tempKindPaths is None else tempKindPaths
velocityPaths = [None for x in range(len(cpoutPaths))
] if velocityPaths is None else velocityPaths
forcePaths = [None for x in range(len(cpoutPaths))
] if forcePaths is None else forcePaths
#1) Get all the dicts
parsedDicts = list()
for cpoutPath, xyzPath, tKindPath, vPath, fPath in it.zip_longest(
cpoutPaths, xyzPaths, tempKindPaths, velocityPaths, forcePaths):
currDict = parseFullMdInfoFromCpoutAndXyzFilePaths(
cpoutPath,
xyzPath,
tempKindPath=tKindPath,
velocityPath=vPath,
forcePath=fPath)
parsedDicts.append(currDict)
#2) Merge all the trajectories
allTraj = [currDict["trajectory"] for currDict in parsedDicts]
mergedTraj = trajHelp.getMergedTrajInMemory(allTraj)
outDict["trajectory"] = mergedTraj
#3) Merge the thermo data
allThermoData = [currDict["thermo_data"] for currDict in parsedDicts]
mergedThermo = thermoDataHelp.getMergedStandardThermoData(allThermoData)
outDict["thermo_data"] = mergedThermo
return outDict
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 testRaisesIfDataListsNotAllTheSame(self):
self.stepsB.append(20)
with self.assertRaises(AssertionError):
tCode.getMergedStandardThermoData(self.dataList,
overlapStrat=self.overlapStrat)
def testRaisesIfPropsNotTheSame(self):
self.dataList[1].dataDict["fake_prop"] = list()
with self.assertRaises(ValueError):
tCode.getMergedStandardThermoData(self.dataList,
overlapStrat=self.overlapStrat)