def testOctaInExpectedPositionCoverAlessThanPerfect(self):
self.site = "octahedral"
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = self._getCoordForOctaInter()
expCartCoords.append(expNewCoord)
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele=self.ele,
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testCrowdionInExpectedPositionCoverALessThanPerfect(self):
self.site = "crowdion"
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = [0.5 * x for x in expCartCoords[1][:3]] + [self.ele]
expCartCoords.append(expNewCoord)
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele=self.ele,
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testBasalCrowdionInExpectedPositionCoverAlessThanPerfect(self):
self.site = "basal_crowdion"
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = [0.5 * self.lattParams[0], 0, 0] + [self.ele]
expCartCoords.append(expNewCoord)
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele=self.ele,
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testTetraBasalInExpectedPositionCoverALessThanPerfect(self):
self.site = "basal_tetrahedral"
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = expCartCoords[0][:2] + [
expCartCoords[0][2] + 0.5 * self.lattParams[-1]
] + ["X"]
expCartCoords.append(expNewCoord)
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele="X",
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testTetraInExpectedPositionA(self):
nearestNebOutOfPlaneDist = tCode._getNearestNebDistanceOutOfZPlane(
self.testCellA, 0)
nearestNebCartCoords = self.testCellA.cartCoords[1][:3]
angle = math.degrees(
math.acos(0.7924058156930613)) #Calculated "by hand"
expZDisplace = (0.5 * nearestNebOutOfPlaneDist) / math.cos(
math.radians(angle))
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = [
expCartCoords[0][0], expCartCoords[0][1],
expCartCoords[0][2] + expZDisplace
]
expCartCoords.append(expNewCoord + ["X"])
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele="X",
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testTetraInExpectedPositionWithCOverAGreaterThanPerfect(self):
self.lattParams[-1] = self.lattParams[0] * 2
self.createTestObjs()
#Largely C+P from above
nearestNebOutOfPlaneDist = tCode._getNearestNebDistanceOutOfZPlane(
self.testCellA, 0)
angle = 30
expZDisplace = (0.5 * nearestNebOutOfPlaneDist) / math.cos(
math.radians(angle))
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
expNewCoord = [
expCartCoords[0][0], expCartCoords[0][1],
expCartCoords[0][2] + expZDisplace
]
expCartCoords.append(expNewCoord + ["X"])
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele="X",
strat="utest")
self.assertEqual(expOutCell, self.testCellA)
def testBasalSplitInExpectedPositionCoverALessThanPerfect(self):
self.site = "basal_split"
#Need at least TWO atoms in-plane in the regular (non periodic) cell
self.fractPositions = [
[0.0, 0.0, 0.0],
[0.16666666666666677, 0.6666666666666664, 0.4999999999999999],
[0.5, 0.0, 0.0],
[0.6666666666666666, 0.6666666666666664, 0.4999999999999999]
]
self.createTestObjs()
expOutCell = copy.deepcopy(self.testCellA)
expCartCoords = expOutCell.cartCoords
displacement = (2 / 3) * 0.5 * 0.5 * self.lattParams[0]
newCoordPos = copy.deepcopy(expCartCoords[0])
newCoordPos[0] += displacement
expCartCoords[0][0] -= displacement
expCartCoords.append(newCoordPos)
expOutCell.cartCoords = expCartCoords
tCode.addSingleInterToHcpBulkGeom(self.testCellA,
self.site,
ele=self.ele,
strat="utest")
self.assertEqual(self.testCellA, expOutCell)
def testRaisesForIncorrectSite(self):
with self.assertRaises(ValueError):
tCode.addSingleInterToHcpBulkGeom(self.testCellA, "fake_site")
def testRaisesForIncorrectLatticeAngles(self):
self.lattAngles[2] = 50
self.createTestObjs()
with self.assertRaises(ValueError):
tCode.addSingleInterToHcpBulkGeom(self.testCellA, self.site)