def createTestObjs(self):
#Geom/Trajectory
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
trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA,
step=0,
time=self.timeA)
trajStepB = trajCoreHelp.TrajStepFlexible(unitCell=self.cellB,
step=1,
time=self.timeB)
self.traj = trajCoreHelp.TrajectoryInMemory([trajStepA, trajStepB])
#Create the classification object options
currArgs = [[self.binResObjA], self.oxyIndices, self.hyIndices]
currKwargs = {"maxOHDist": self.maxOOHBond, "nNebs": self.nNebs}
hydroxylClassifier = classDistrOptObjs.WaterDerivativeBasedOnDistanceClassifierOptsObj(
*currArgs, **currKwargs)
#
currArgs = [
self.oxyIndices, self.hyIndices, hydroxylClassifier,
self.distrOptObjs, self.useGroups
]
currKwargs = {
"useNonHyIdx": self.useNonHyIdx,
"useIdxEach": self.useIdxEach
}
self.filteredOptObj = filteredOptObjHelp.WaterDerivativeFilteredOptsObj_simple(
*currArgs, **currKwargs)
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.coordsA
self.cellB.cartCoords = self.coordsB
extraAttrDictA = {
self.velKey: {
"value": self.velsA,
"cmpType": "numericalArray"
}
}
extraAttrDictB = {
self.velKey: {
"value": self.velsB,
"cmpType": "numericalArray"
}
}
self.trajStepA = trajHelp.TrajStepFlexible(
unitCell=self.cellA, extraAttrDict=extraAttrDictA)
self.trajStepB = trajHelp.TrajStepFlexible(
unitCell=self.cellB, extraAttrDict=extraAttrDictB)
self.inpTrajA = trajHelp.TrajectoryInMemory(
[self.trajStepA, self.trajStepB])
def createTestObjs(self):
#Geom/Trajectory
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
trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA,
step=0,
time=10)
trajStepB = trajCoreHelp.TrajStepFlexible(unitCell=self.cellB,
step=1,
time=20)
self.traj = trajCoreHelp.TrajectoryInMemory([trajStepA, trajStepB])
#Option object
currArgs = [
self.binResObjA, self.oxyIndices, self.hyIndices,
self.distFilterIndices,
[self.distRangeA, self.distRangeB, self.distRangeC]
]
self.optObj = classDistrOptObjs.WaterCountTypesMinDistAndHBondSimpleOpts(
*currArgs)
def createTestFunct(self):
self.stepA = trajHelp.TrajStepFlexible(step=self.steps[0],
time=self.times[0])
self.stepB = trajHelp.TrajStepFlexible(step=self.steps[1],
time=self.times[1])
self.stepC = trajHelp.TrajStepFlexible(step=self.steps[2],
time=self.times[2])
self.stepD = trajHelp.TrajStepFlexible(step=self.steps[3],
time=self.times[3])
self.allSteps = [self.stepA, self.stepB, self.stepC, self.stepD]
self.inpTraj = trajHelp.TrajectoryInMemory(self.allSteps)
def createTestObjs(self):
#Define some rotated water molecules
#setting up water with an angle of 90 degrees and sqrt(2) bondlengths makes this simpler
waterAzi90_pitch20 = [[0, 0, 0, "O"], [-1, 0.94, 0.34, "H"],
[1, 0.94, 0.34, "H"]] #bin [1][1]
waterAzi0_pitch20 = [[0, 0, 0, "O"], [0.94, 1.0, 0.34, "H"],
[0.94, -1, 0.34, "H"]] #bin [0][1]
waterAzi0_pitchm20 = [[0, 0, 0, "O"], [0.94, 1.0, -0.34, "H"],
[0.94, -1, -0.34, "H"]] #bin [0][0]
#Sort the trajectory; default is to use a one step trajectory
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = waterAzi90_pitch20 + waterAzi0_pitch20 + waterAzi0_pitchm20 + waterAzi0_pitchm20
self.stepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
self.trajA = trajCoreHelp.TrajectoryInMemory([self.stepA])
#Create the options objects
self.aziBins = binResHelp.BinnedResultsStandard.fromBinEdges(
self.aziEdges)
self.pitchBins = binResHelp.BinnedResultsStandard.fromBinEdges(
self.pitchEdges)
self.aziOpts = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.aziBins, self.waterIndicesAll, angleType="azimuth")
self.pitchOpts = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.pitchBins, self.waterIndicesAll, angleType="pitch")
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = self.cartCoords
self.trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
#Create the bin objs
self.binObjA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesA)
self.binObjB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesB)
#Create single binners
self.binnerA = tCode._WaterRotationAngleBinnerFixedIndices(
resBins=self.binObjA,
indices=self.indicesA,
angleIdx=self.angleIdxA)
self.binnerB = tCode._WaterRotationAngleBinnerFixedIndices(
resBins=self.binObjB,
indices=self.indicesB,
angleIdx=self.angleIdxB)
#Create the multi binner (the test obj)
self.testObj = tCode._WaterRotationAngleMultiBinnerFixedIndices(
[self.binnerA, self.binnerB])
def createTestObjs(self): #Create co-ordinates self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams, lattAngles=self.lattAngles) self.cellA.cartCoords = self.coords #Create a simple one-step trajectory self.stepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA) self.trajA = trajCoreHelp.TrajectoryInMemory([self.stepA]) #Create bins then options objects self.distBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(self.distBinEdgesA) self.planarBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(self.planarBinEdgesA) self.distBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(self.distBinEdgesB) self.planarBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(self.planarBinEdgesB) #binResObj, indicesA, indicesB, volume=None, minDistAToB=False): self.minDistsOptsA = calcDistribCoreHelp.CalcRdfOptions(self.distBinsA, self.indicesA_optsA, self.indicesB_optsA, minDistAToB=True) self.minDistsOptsB = calcDistribCoreHelp.CalcRdfOptions(self.distBinsB, self.indicesA_optsB, self.indicesB_optsB, minDistAToB=True) #binResObj, indices, planeEqn=None, volume=None): self.planarDistOptsA = calcRadImpl.CalcPlanarRdfOptions(self.planarBinsA, self.indicesA_optsA) self.planarDistOptsB = calcRadImpl.CalcPlanarRdfOptions(self.planarBinsB, self.indicesA_optsB) self.optsObjs = [ [self.minDistsOptsA, self.planarDistOptsA], [self.minDistsOptsB, self.planarDistOptsB] ]
def createTestObjs(self):
#Define some rotated water molecules
#setting up water with an angle of 90 degrees and sqrt(2) bondlengths makes this simpler
waterAzi90_pitch20 = [
[0, 0, 0 + 7, "O"], [-1, 0.94, 0.34 + 7, "H"],
[1, 0.94, 0.34 + 7, "H"]
] #Translated by +7 for planar dists stuff [means dist=3]
waterAzi0_pitch20 = [[0, 0, 0 + 1, "O"], [0.94, 1.0, 0.34 + 1, "H"],
[0.94, -1, 0.34 + 1, "H"]]
waterAzi0_pitchm20 = [[0, 0, 0, "O"], [0.94, 1.0, -0.34, "H"],
[0.94, -1, -0.34, "H"]]
#Sort the trajectory; default is to use a one step trajectory
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = waterAzi90_pitch20 + waterAzi0_pitch20 + waterAzi0_pitchm20 + waterAzi0_pitchm20
self.stepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
self.trajA = trajCoreHelp.TrajectoryInMemory([self.stepA])
#Create the options objects
self.aziBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.aziEdgesA)
self.pitchBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.pitchEdgesA)
self.planarBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.planarEdgesA)
self.oxyDistBinsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.oxyDistEdgesA)
self.aziBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.aziEdgesB)
self.pitchBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.pitchEdgesB)
self.planarBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.planarEdgesB)
self.oxyDistBinsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.oxyDistEdgesB)
#Create options objs
self.aziOptsA = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.aziBinsA, self.waterIndicesA, angleType="azimuth")
self.pitchOptsA = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.pitchBinsA, self.waterIndicesA, angleType="pitch")
self.planarOptsA = tCode.CalcWaterPlanarDistribOptions_fromOxy(
self.planarBinsA, self.waterIndicesA)
self.oxyDistOptsA = tCode.CalcWaterOxyMinimumDistOptions(
self.oxyDistBinsA, self.waterIndicesA, self.oxyDistIndices)
self.aziOptsB = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.aziBinsB, self.waterIndicesB, angleType="azimuth")
self.pitchOptsB = waterRotHelp.CalcStandardWaterOrientationDistribOptions(
self.pitchBinsB, self.waterIndicesB, angleType="pitch")
self.planarOptsB = tCode.CalcWaterPlanarDistribOptions_fromOxy(
self.planarBinsB, self.waterIndicesB)
self.oxyDistOptsB = tCode.CalcWaterOxyMinimumDistOptions(
self.oxyDistBinsB, self.waterIndicesB, self.oxyDistIndices)
self.optsObjs = [[self.aziOptsA, self.pitchOptsA],
[self.aziOptsB, self.pitchOptsB]]
def _getTrajFromStepIndices(self, stepIndices):
outSteps = list()
for idx in stepIndices:
currStepIdx, currTime = self.steps[idx], self.times[idx]
currTrajStep = trajHelp.TrajStepFlexible(step=currStepIdx,
time=currTime)
outSteps.append(currTrajStep)
return trajHelp.TrajectoryInMemory(outSteps)
def createTestObjs(self):
self.stepA = trajHelp.TrajStepFlexible(time=self.times[0],
extraAttrDict={
self.atomTempKey: {
"value": self.tempsA,
"cmpType":
"numericalArray"
}
})
self.stepB = trajHelp.TrajStepFlexible(time=self.times[1],
extraAttrDict={
self.atomTempKey: {
"value": self.tempsB,
"cmpType":
"numericalArray"
}
})
self.trajA = trajHelp.TrajectoryInMemory([self.stepA, self.stepB])
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParamsA,
lattAngles=self.lattAnglesA)
self.cellA.cartCoords = self.cartCoordsA
trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
self.trajA = trajCoreHelp.TrajectoryInMemory([trajStepA])
self.binResObjA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdges)
def parseFullMdInfoFromCpoutAndXyzFilePaths(cpoutPath,
xyzPath,
tempKindPath=None,
velocityPath=None,
forcePath=None):
""" Description of function
Args:
cpoutPath: (str) Path to *.cpout file
xyzPath: (str) Path to *.xyz file
tempKindPath: (str, optional) Path to a file containing atomic temperature for each kind of atom
"""
outDict = parseCpoutForMDJob(cpoutPath)
outSteps = parseCp2kMdXyzFile(xyzPath)
#If step 0 is in the xyz then we need to add the initial trajectory/thermal info to outDict
if outSteps[0]["step"] == 0:
# stepZero = trajHelp.TrajStepBase(unitCell=outDict["init_md_cell"], step=0, time=0)
stepZero = trajHelp.TrajStepFlexible(unitCell=outDict["init_md_cell"],
step=0,
time=0)
outDict["trajectory"].trajSteps.insert(0, stepZero)
for key in outDict["thermo_data"].dataDict:
outDict["thermo_data"].dataDict[key].insert(
0, outDict["init_thermo_dict"][key])
#Combine infor in cpout and xyz files to get full geometries
outDict["trajectory"] = _getMergedTrajectoryFromParsedCpoutAndXyz(
outDict, outSteps)
#Optionally add velocities and forces
if velocityPath is not None:
_parseVelocitiesAndAddToTrajSteps(velocityPath,
outDict["trajectory"].trajSteps)
if forcePath is not None:
_parseForcesXyzAndAddToTrajSteps(forcePath,
outDict["trajectory"].trajSteps)
#If tempKindPath is present, then parse it and add to the thermo data object
if tempKindPath is not None:
parsedTempKind = parseAtomTempFile(tempKindPath)
firstGeom = [x for unused, x in zip([0], iter(outDict["trajectory"]))
][0].unitCell
idxToLabelDict = _getKindIdxToSymbolDict(
[x[-1] for x in firstGeom.cartCoords])
_addAtomicTempsToThermoDataObj(parsedTempKind,
outDict["thermo_data"],
idxToLabelDict=idxToLabelDict)
assert outDict["thermo_data"].dataListLengthsAllEqual
outDict.pop("init_thermo_dict")
outDict.pop("init_md_cell")
return outDict
def createTestObjs(self):
self.extraAttrDict = copy.deepcopy(self.extraAttrA)
self.extraAttrDict.update(copy.deepcopy(self.extraAttrB))
currKwargs = {
"unitCell": self.unitCell,
"step": self.step,
"time": self.time,
"extraAttrDict": self.extraAttrDict
}
self.testObjA = tCode.TrajStepFlexible(**currKwargs)
def createTestObjs(self):
#Create the cells
cells = [
uCellHelp.UnitCell(lattParams=[x for x in self.lattParams],
lattAngles=[x for x in self.lattAngles])
for a in range(3)
]
for idx, coords in enumerate(
[self.coordsA, self.coordsB, self.coordsC]):
cells[idx].cartCoords = coords
#Create the trajectory
self.stepA = trajHelp.TrajStepFlexible(unitCell=cells[0],
step=0,
time=self.times[0])
self.stepB = trajHelp.TrajStepFlexible(unitCell=cells[1],
step=1,
time=self.times[1])
self.stepC = trajHelp.TrajStepFlexible(unitCell=cells[2],
step=2,
time=self.times[2])
self.inpTraj = trajHelp.TrajectoryInMemory(
[self.stepA, self.stepB, self.stepC])
def createTestObjs(self):
#Create the trajectory
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = self.cartCoords
self.trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
self.traj = trajCoreHelp.TrajectoryInMemory([self.trajStepA])
#Create two options objs
self.binsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesA)
self.binsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesB)
self.optsA = tCode.CalcStandardWaterOrientationDistribOptions(
self.binsA, self.indicesA, angleType=self.angleTypeA)
self.optsB = tCode.CalcStandardWaterOrientationDistribOptions(
self.binsB, self.indicesB, angleType=self.angleTypeB)
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParamsA,
lattAngles=self.lattAnglesA)
self.cellA.cartCoords = self.cartCoordsA
self.trajStepA = trajCoreHelp.TrajStepFlexible(unitCell=self.cellA)
#Sort the bins
self.binsA = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesA)
self.binsB = binResHelp.BinnedResultsStandard.fromBinEdges(
self.binEdgesB)
#Sort the single binners
self.binnerA = tCode._PlanarRdfBinnerFixedIndices(
resBins=self.binsA, indices=self.indicesA, planeEqn=self.planeEqnA)
self.binnerB = tCode._PlanarRdfBinnerFixedIndices(
resBins=self.binsB, indices=self.indicesB, planeEqn=self.planeEqnB)
#Create the test object
self.testObj = tCode._PlanarRdfMultiBinnerFixedIndices(
[self.binnerA, self.binnerB])
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 _loadStartTrajStepsArrayDataTwoStepsA():
stepA = trajHelp.TrajStepFlexible(step=1684, time=842.0)
stepB = trajHelp.TrajStepFlexible(step=1687, time=843.5)
return stepA, stepB