def createTestObjs(self):
self.testSitesA = [self.siteA, self.siteB, self.siteC]
self.cellA = uCellHelp.UnitCell(lattParams=self.lattParamsA,
lattAngles=self.lattAnglesA,
fractCoords=[[0, 0, 0]],
elementList=["Mg"])
self.surfA = surfHelp.GenericSurface(self.cellA, 1, lenVac=2)
self.testFunctA = lambda inpSurf: self.testSitesA
def setUp(self): self.createCellParamsA() self.createCell() self.surfA = surfHelp.GenericSurface(self.cellA, self.nLayersA, lenAbsoluteVacuum=self.absVacLengthA) self.surfToSites = hcpSurfHelp.HcpSurfaceToHcpSites() self.adsorbateGeom = [[0.0,0.0,0.0,"O"]] self.fractCoverage = 1 self.distance = 2 # self.getAdsorbatesFunct = addAdsorbateHelp.SingleTypeGetAdsorbatesForSites self.createTestObjs()
def getStructWithNBilayersAdded_standard(inpCell,
nLayers,
topLayerWaterAdsDetector,
bilayerSpacing,
layerTol,
absVacLen=None,
topAdsTemplate=None):
""" Takes a water bilayer structure returns a structure with n-added bilayers
Args:
inpCell: (plato_pylib UnitCell object) The starting (water bilayer) structure
nLayers: (int) Number of layers to add (must be >=1)
topLayerWaterAdsDetector: (adsorption.detect_water_layer.DetectOuterAdsorbedWaterLayer object)
bilayerSpacing: (float) The closest O-O gap between two bilayers
layerTol: (float) Two O will be considered in the same "layer" if they are closer than this
absVacLen: (Optional, float) If None then output will have the same length as input cell. If absVacLen is set then this is the vacuum length in the cell
topAdsTemplate: (Optional, WaterAdsorbateStandard) If None then we use the "top" molecules of the current bilayer as a template for building the others. Idea is to set this to Hup or Hdown to build diff bilayers
Returns
outCell: (plato_pylib UnitCell object) With the additional bilayers added
"""
#0) Simple edge-case handling
if (nLayers < 1):
raise ValueError(
"nLayers must be 1 or greater; {} is not allowed".format(nLayers))
#4) Create the output cell;
estLayerHeight = bilayerSpacing + topLayerWaterAdsDetector.waterIdxDetector.maxHeightLayer
estNewLayersHeight = estLayerHeight * nLayers
outCell = surfHelp.GenericSurface(inpCell,
1,
lenVac=estNewLayersHeight * 2).unitCell
#1) Get the current top-adsorbed layer
startLayerAdsObjs = topLayerWaterAdsDetector.getAdsorbateObjsFromInpGeom(
outCell)
#2) Create the first extra layer (using topLayerTemplate)
args = [startLayerAdsObjs, bilayerSpacing]
kwargDict = {
"layerTolerance": layerTol,
"surfNormal": [0, 0, 1],
"topLayerTemplate": topAdsTemplate
}
extraLayers = [
waterAdsHelp.getAdsorbateObjsForNextWaterBilayerBasic(
*args, **kwargDict)
]
#3) Create any extra layers
kwargDict.pop("topLayerTemplate")
for idx in range(1, nLayers):
args[0] = extraLayers[-1]
currLayer = waterAdsHelp.getAdsorbateObjsForNextWaterBilayerBasic(
*args, **kwargDict)
extraLayers.append(currLayer)
# #5) Add co-ords to output cell AND set the absolute vacuum region
newCoords = list()
for adsObj in it.chain(*extraLayers):
newCoords.extend(adsObj.geom)
outCell.cartCoords += newCoords
if absVacLen is not None:
outCell = surfHelp.GenericSurface(outCell,
1,
lenAbsoluteVacuum=absVacLen).unitCell
else:
outCell = surfHelp.GenericSurface(outCell, 1, lenVac=0).unitCell
return outCell
def testInitWithLenAbsoluteVac(self): lenAbsVac = 10 outObj = tCode.GenericSurface(self.uCellA, self.nLayers, lenAbsoluteVacuum=lenAbsVac) self.assertAlmostEqual( lenAbsVac, outObj.lenAbsoluteVacuum )
def testRaisesIfBothLenVacAndLenAbsoluteVacuumAreSet(self): with self.assertRaises(AttributeError): outObj = tCode.GenericSurface(self.uCellA, self.nLayers, lenVac=4, lenAbsoluteVacuum=5)
def testRaisesIfInitWithoutSettingVacLength(self): with self.assertRaises(AttributeError): outObj = tCode.GenericSurface(self.uCellA, self.nLayers)
def createTestObjs(self): self.uCellA = UCell.UnitCell(lattParams=self.lattParams, lattAngles=self.lattAngles, fractCoords=self.fractCoords, elementList=self.eleList) self.surfA = tCode.GenericSurface(self.uCellA, self.nLayers, self.lenVac)
def createTestObjs(self): self._createUnitCells() self.surfA = surfHelp.GenericSurface(self.cellA, self.nLayersA, lenAbsoluteVacuum=self.absVacLengthA) self.surfToSiteObj = tCode.HcpSurfaceToWaterBilayerSites() self.atopCartCoordsA = [x[:3] for x in self.surfA.unitCell.cartCoords]
def createTestObjs(self): self._createUnitCells() self.surfA = surfHelp.GenericSurface(self.cellA, self.nLayersA, lenAbsoluteVacuum=self.absVacLengthA) self.surfToSiteObj = tCode.HcpSurfaceToHcpSites(top=self.top)
