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 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 _createCells(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParamsA,
lattAngles=self.lattAnglesA)
self.cellB = uCellHelp.UnitCell(lattParams=self.lattParamsA,
lattAngles=self.lattAnglesA)
self.cellA.cartCoords = self.cartCoordsA
self.cellB.cartCoords = self.cartCoordsB
def createTestObjs(self): self.testCellMgTerminated = UCell.UnitCell(lattParams=self.lattParams, lattAngles=self.lattAngles) self.testCellMgTerminated.fractCoords = self.fractCoordsMgTerminated self.testCellMgTerminatedUpsideDown = UCell.UnitCell(lattParams=self.lattParams, lattAngles=self.lattAngles) self.testCellMgTerminatedUpsideDown.fractCoords = self.fractCoordsMgTerminatedUpsideDown self.testCellOHTerminated = UCell.UnitCell(lattParams=self.lattParams, lattAngles=self.lattAngles) self.testCellOHTerminated.fractCoords = self.fractCoordsOHTerminated
def setUp(self): self.cellA = uCellHelp.UnitCell(lattParams=[7,8,9],lattAngles=[90,90,90]) self.cellB = uCellHelp.UnitCell(lattParams=[4,5,6],lattAngles=[90,90,90]) self.coordsA = [ [1,2,3,"Mg"], [4,5,6,"Mg"] ] self.coordsB = [ [2,2,2,"Mg"], [3,3,3,"Mg"], [1,1,1,"Mg"] ] self.stepA, self.stepB = 4, 8 self.timeA, self.timeB = 12, 24 self.tempPath = "temp_file.exyz" self.createTestObjs()
def _createCells(self):
self.cellSurf = uCellHelp.UnitCell(lattParams=self.lattParamsSurf,
lattAngles=self.lattAnglesSurf)
self.cellAbove = uCellHelp.UnitCell(lattParams=self.lattParamsAbove,
lattAngles=self.lattAnglesAbove)
self.cellBelow = uCellHelp.UnitCell(lattParams=self.lattParamsBelow,
lattAngles=self.lattAnglesBelow)
self.cellSurf.cartCoords = self.cartCoordsSurf
self.cellAbove.cartCoords = self.cartCoordsAbove
self.cellBelow.cartCoords = self.cartCoordsBelow
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 setUp(self):
self.stepA, self.stepB = 0, 50
self.timeA, self.timeB = 0, 500
self.unitCellA = uCellHelp.UnitCell(lattParams=[10, 10, 10],
lattAngles=[90, 90, 90])
self.unitCellB = uCellHelp.UnitCell(lattParams=[1, 2, 3],
lattAngles=[90, 90, 90])
self.folderPathA = "/fake/path/to/folder"
self.fileNameA = "file_name_a"
self.folderKeyA = "md_traj_folder"
self.fileKeyA = "md_traj_file"
self.createTestObjs()
def createTestObjs(self):
currKwargs = {
"lattParams": self.primLattParamsA,
"lattAngles": self.primAnglesA
}
self.primCellA = uCellHelp.UnitCell(**currKwargs)
self.primCellA.fractCoords = self.primFractCoordsA
currKwargs = {
"lattParams": self.inpCellLattParamsA,
"lattAngles": self.inpCellLattAnglesA
}
self.inpCellA = uCellHelp.UnitCell(**currKwargs)
self.inpCellA.fractCoords = self.primFractCoordsA
self.testObjA = tCode.CellFillerStandard(self.primCellA)
def createTestObjs(self):
currKwargs = {
"lattParams": self.primLattParamsA,
"lattAngles": self.primAnglesA
}
self.primCellA = uCellHelp.UnitCell(**currKwargs)
self.primCellA.fractCoords = self.primFractCoordsA
currKwargs = {
"lattParams": self.inpCellLattParamsA,
"lattAngles": self.inpCellLattAnglesA
}
self.inpCellA = uCellHelp.UnitCell(**currKwargs)
self.inpCellA.fractCoords = self.primFractCoordsA
self.testObjA = tCode.MapPrimToInpCellToMinimiseAverageLatticeParamDeviation(
)
def createTestObjs(self): self.singleCellA = uCellHelp.UnitCell(lattParams=self.lattParamsA, lattAngles=self.lattAnglesA) self.singleCellA.cartCoords = self.cartCoordsA self.adsObjsA = [self.adsObjA] self.testObjA = tCode.GetWaterBoxForMDFromEmptyBoxStandard(self.singleCellA, self.adsObjsA,waterAdsGap=self.waterAdsGapA) self.emptyCellA = supCellHelp.superCellFromUCell(self.singleCellA,[2,1,1]) self.emptyCellA.cartCoords = list()
def createTestObjs(self):
#Geom
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = self.coords
#Get the test obj
currArgs = [
self.oxyIndices, self.hyIndices, self.distFilterIndices,
self.distFilterVals
]
currKwargs = {
"acceptor": self.acceptor,
"donor": self.donor,
"maxOO": self.maxOO
}
self.testObj = tCode._DiscHBondCounterBetweenGroupsWithOxyDistFilterPopulator(
*currArgs, **currKwargs)
self.testObj.nanMatrix = self.nanMatrix
#Get an outDict[covers one interface]
self.outDict = dict()
#Get a sparse matrix calculator
self.sparseMatrixCalculator = atomComboCoreHelp._SparseMatrixCalculatorStandard(
[self.testObj])
def _loadCellA():
lattParams, lattAngles = [10, 10, 10], [90, 90, 90]
cartCoords = [[2, 2, 3, "X"], [3, 3, 3, "X"], [5, 5, 5, "Y"],
[5, 5, 7, "Z"]]
outCell = uCell.UnitCell(lattParams=lattParams, lattAngles=lattAngles)
outCell.cartCoords = cartCoords
return outCell
def createTestObjs(self):
kwargDict = {
"lattParams": self.lattParamsA,
"lattAngles": self.lattAnglesA
}
self.testCellA = uCell.UnitCell(**kwargDict)
self.testCellA.cartCoords = self.cartCoordsA
def createTestObjs(self):
self.testMapperA = tCode.createMapGeomInfoToDataDictObjFromAtomStyle("full")
currArgs = [self.xRangeA, self.yRangeA, self.zRangeA]
self.testSimBoxA = tCode.LammpsSimulationBox(*currArgs,self.tiltFactorsA)
currKwargs = {"lattParams":self.lattParamsA, "lattAngles":self.lattAnglesA}
self.testCellA = uCellHelp.UnitCell(**currKwargs)
self.testCellA.cartCoords= self.cartCoordsA
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,lattAngles=self.lattAngles)
self.cellA.cartCoords = self.cartCoords
currArgs = [self.binResObj, self.oxyIndices, self.hyIndices]
currKwargs = {"planeEqn":self.planeEqn, "primaryIdxType":self.primaryIdxType}
self.testObj = tCode.WaterPlanarDistOptions(*currArgs, **currKwargs)
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):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = self.coordsA
self.inpIndices = [x for x in range(len(self.coordsA))]
self.filterFunctA = tCode.FilterToExcludeIndicesWithoutNebsAmongstRemaning(
self.maxDist, restrictToPairs=self.restrictToPairs)
def createTestObjs(self):
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParams,
lattAngles=self.lattAngles)
self.cellA.cartCoords = self.coordsA
self.inpIndices = [x for x in range(len(self.coordsA))]
self.filterFunctA = tCode.FilterToExcludeIndicesFurtherOutOfPlaneThanCutoff(
self.maxDist, self.planeEqn, self.inpPointsA)
def _loadTestCellA():
lattParams, lattAngles = [10, 10, 10], [90, 90, 90]
cartCoords = [[4, 4, 4, "X"], [6, 6, 4, "X"], [7, 6, 4, "X"],
[8, 8, 6, "Y"]]
outCell = uCellHelp.UnitCell(lattParams=lattParams, lattAngles=lattAngles)
outCell.cartCoords = cartCoords
return outCell
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):
#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 getNearestImageNebCoordsMatrixBasic(inpCell, indicesA=None, indicesB=None):
""" Gets a matrix where each element contains [coordA,coordB] where A,B are row/column indices. coordA is the same co-ordinate found in inpCell; coordB is the nearest neighbour for it
Args:
inpCell: (plato_pylib UnitCell object)
indicesA: (Optional, iter of ints) Indices of the atoms to include for the first dimension; Default is to include ALL atoms
indicesB: (Optional, iter of ints) Indices of the atoms to include for the second dimension; Default is indicesA
Returns
outMatrix: (NxM matrix) outMatrix[n][m] = [coordN, coordM] where N and M are lengths of indicesA and indicesB
"""
#Sort out default args
fractCoords = inpCell.fractCoords
fCoordsNoEles = np.array([x[:3] for x in fractCoords])
eleList = [x[-1] for x in fractCoords]
indicesA = [x for x in range(len(fractCoords))
] if indicesA is None else indicesA
indicesB = indicesA if indicesB is None else indicesB
#Figure out the value for each row; we need useCell to exploit some relevant function in the ucell_class thing
useCell = uCellHelp.UnitCell(lattParams=inpCell.getLattParamsList(),
lattAngles=inpCell.getLattAnglesList())
outMatrix = list()
for idxA in indicesA:
currRow = _getSingleRowOfNearestImageNebCoordsMatrix(
fCoordsNoEles, eleList, useCell, idxA, indicesB)
outMatrix.append(currRow)
return outMatrix
def createTestObjs(self):
#Sort the cell
self.cellA = uCellHelp.UnitCell(lattParams=[10, 10, 10],
lattAngles=[90, 90, 90])
self.cellA.cartCoords = self.cartCoords
#
self.binResObjs = [self.binResObjA, self.binResObjB]
currArgs = [
self.binResObjs, self.oxyIndices, self.hyIndices,
self.distFilterIndices, self.distFilterRanges
]
currKwargs = {
"nDonorFilterRanges":
self.nDonorFilterRanges,
"nAcceptorFilterRanges":
self.nAcceptorFilterRanges,
"nTotalFilterRanges":
self.nTotalFilterRanges,
"maxOOHBond":
self.maxOOHBond,
"maxAngleHBond":
self.maxAngleHBond,
"checkInputConsistent":
self.checkInputConsistent,
"adsSiteMinHozToOtherAdsSiteRanges":
self.adsSiteMinHozToOtherAdsSiteRanges
}
self.testObj = tCode.WaterAdsorbedClassifier_usingMinHozDistsBetweenAdsorptionSitesOptsObj(
*currArgs, **currKwargs)
def setUp(self):
self.unitCellA = uCellHelp.UnitCell(lattParams=[10, 10, 10],
lattAngles=[90, 90, 90])
self.timeA, self.timeB = 2, 3
self.stepA, self.stepB = 0, 50
self.fileNameA = "temp_file_a.traj"
self.createTestObjs()
def getSingleLayerRocksalt011FromPrimitiveCell(primCell):
"""
Args:
primCell: (plato_pylib UnitCell object) This must be a primitive rock salt cell. Meaning 2 atoms, with each lattice angle=60 degrees and a=b=c
Returns
outCell: (plato_pylib UnitCell object) Contains a 4-atom unit-cell which forms the basis for forming rock-salt 011 surfaces (it is one layer)
Raises:
AssertionError: If the input primitive cell is not a rock salt cell. Probably not garanteed to be raised if an incompatible cell is passed, but at least catches some errors.
"""
assert _uCellIsRockSaltPrimitive(
primCell, printError=True
), "UnitCell {} is not a primitive rock salt cell".format(primCell)
atomA, atomB = primCell.fractCoords[0][-1], primCell.fractCoords[1][-1]
conventLattParam = (2 * primCell.lattParams["a"]) / math.sqrt(2)
otherLattParams = primCell.lattParams["a"]
outputLattParams = [conventLattParam, otherLattParams, otherLattParams]
outputLattAngles = [90, 90, 90]
fractCoords = [[0.0, 0.0, 0.0, atomA], [0.0, 0.5, 0.5, atomB],
[0.5, 0.0, 0.0, atomB], [0.5, 0.5, 0.5, atomA]]
outCell = uCell.UnitCell(lattParams=outputLattParams,
lattAngles=outputLattAngles)
outCell.fractCoords = fractCoords
return outCell
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 testToDictAndFromDictConsistent(self):
self.unitCell = uCellHelp.UnitCell(lattParams=[1, 2, 3],
lattAngles=[90, 90, 90])
self.createTestObjs()
expObj = self.testObjA
outDict = self.testObjA.toDict()
actObj = tCode.TrajStepBase.fromDict(outDict)
self.assertEqual(expObj, actObj)
def _createCubicSurfaceGeom(self):
kwargs = {
"lattParams": [self.cellLengthA for x in range(3)],
"lattAngles": [90 for x in range(3)]
}
outCell = uCellHelp.UnitCell(**kwargs)
outCell.cartCoords = self.surfCartCoordsWithSymbols
return outCell
