def getXvsYStructsFromSkObj(parsedFileObj,
xProp="distance",
yProp="hVal".lower(),
tbintPath=None):
allBondTypes = ["sigma", "pi", "delta"]
#Need to figure out all shell combinations
shellIndA = parsedFileObj.getShellIndices(atomIdx=0)
shellIndB = parsedFileObj.getShellIndices(atomIdx=1)
#For looking at errors vs tbint we need the tbint output file
if tbintPath is not None:
tbintObjs = parseTbint.getIntegralsFromBdt(tbintPath)
else:
tbintObjs = None
#Put all the info in the required structure
outLists = list()
for shellAIdx in range(len(shellIndA)):
currListA = list()
for shellBIdx in range(len(shellIndB)):
currDict = dict()
for bondType in allBondTypes:
currDict[bondType] = getInvSKDataTwoShells(
parsedFileObj,
shellAIdx,
shellBIdx,
bondType,
xProp,
yProp,
tbintDataObjs=tbintObjs)
currListA.append(currDict)
outLists.append(currListA)
return outLists
def testParseKineticHoppingOverlap(self):
testedInts = ["kinetic", "overlap", "hopping", "hop3B2C"]
expectedInts = tData.loadExpIntsBdtFile_KineticHop3B2C_A()
actualInts = tCode.getIntegralsFromBdt(self.filePathDict["bdtFileA"],
inclPP=False)
for key in testedInts:
self.assertTrue(expectedInts[key] == actualInts[key])
def testParseWithOverallInterfaceFunct(self):
expectedVals = tData.loadTestBdtFileAExpectedVals()
expectedVals["nonLocPP"] = tData.loadTestBdtFileAExpectedVals_nlPPOnly(
)
actualVals = tCode.getIntegralsFromBdt("Mg_Mg.bdt")
#Note: Assumes order in each list (NOT DICT) is the same between expected/actual results
for key in expectedVals:
self.assertTrue(actualVals[key] == expectedVals[key])
def testVsKnownInput_HopPPpi(self):
testShellA = 1
testShellB = 1
testSubIdx = 2
allInitInts = tCode.getIntegralsFromBdt(self.filePathDict["bdtFileA"])
fakeInts = np.array(([0.0, 2.0], [6.0, 3.0], [12.0, 5.0]))
for intList in allInitInts.values():
if intList is not None:
for intSet in intList:
if intSet.intType == "hopping" and intSet.shellA == testShellA and intSet.shellB == testShellB and intSet.orbSubIdx == testSubIdx:
intSet.integrals = fakeInts
intSet.replaceIntsTbintFile(
self.filePathDict["bdtFileA"])
newInts = tCode.getIntegralsFromBdt(self.filePathDict["bdtFileA"])
for key in newInts.keys():
self.assertTrue(allInitInts[key] == newInts[key])
def testCorrectlyWritesPairPot_singleFile(self):
expPPCorr = self.integDicts[0]["pairpot"][0]
expPPCorr.integrals[:,
1] *= -1 #Total PP is zero, so the correction must exactly cancel the initial
self.testObj.writeTables() #Will always update before writing them
actualPPCorr = parseTbint.getIntegralsFromBdt(
self.outFileA)["PairPotCorrection0"][0]
self.assertEqual(expPPCorr, actualPPCorr)
def testVsKnownInput_PairPot(self):
''' Test bdt file correctly modified for pair pot '''
allInitInts = tData.loadTestBdtFileAExpectedVals()
fakePairPotInts = np.array(([0.0, 4.0], [1.0, 3.0], [2.0, 2.0]))
allInitInts["pairPot"][0].integrals = fakePairPotInts
allInitInts["pairPot"][0].intType = "pairPot"
allInitInts["pairPot"][0].replaceIntsTbintFile(
self.filePathDict["bdtFileA"])
newInts = tCode.getIntegralsFromBdt(self.filePathDict["bdtFileA"],
inclPP=False)
for key in allInitInts.keys():
self.assertTrue(allInitInts[key] == newInts[key])
def getAllIntInfoObjsFromIntegStrAndBdtPath(integStr: "str, e.g. hopping",
bdtPath):
integDict = parseTbint.getIntegralsFromBdt(bdtPath)
relevantInts = integDict[integStr]
modelFolder = os.path.split(bdtPath)[0]
outputObjs = list()
for x in relevantInts:
currObj = coeffTableConv.IntegralTableInfo(modelFolder, integStr,
x.atomAName, x.atomBName,
x.shellA, x.shellB,
x.orbSubIdx)
outputObjs.append(currObj)
#Need to filter out axAngMom = 1 (default in parseTbint) for atom-based integrals
for x in outputObjs:
if (x.shellA is None):
x.axAngMom = None
return outputObjs
def getTbintHoppingListStructFormat(tbintPath,
intType="hopping",
convToEv=False):
allInts = parseTbint.getIntegralsFromBdt(tbintPath)
adtPaths = parseTbint.getAdtFilePathsFromBdt(tbintPath)
shellsA, shellsB = parseTbint.parseAdtFile(
adtPaths[0])["numbShells"], parseTbint.parseAdtFile(
adtPaths[1])["numbShells"]
intTypesToConvToEv = [
"hopping",
"HopXcContrib",
]
if convToEv and (intType not in intTypesToConvToEv):
raise AttributeError(
"{} is an invalid integral type to convert to electron volts".
format(intType))
#Put all the info in the required structure (TODO: extract this method somehow w/strat patt.)
allBondTypes = ["sigma", "pi", "delta"]
outLists = list()
for shellAIdx in range(shellsA):
currListA = list()
for shellBIdx in range(shellsB):
currDict = dict()
for bondType in allBondTypes:
currDict[bondType] = getTbintIntegralTableFromObjDict(
allInts, shellAIdx, shellBIdx, bondType, intType=intType)
if (intType in intTypesToConvToEv) and (convToEv) and (
currDict[bondType] is not None):
currDict[bondType][:, 1] *= uConvs.RYD_TO_EV
currListA.append(currDict)
outLists.append(currListA)
return outLists
def testParseBdtForm4_usingInterfaceFunct(self):
expectedVals = tData.loadTestBdtFileAExpectedVals_format4()
actualVals = tCode.getIntegralsFromBdt(self.bdtFile)
for key in expectedVals:
self.assertTrue(actualVals[key] == expectedVals[key])
def testVsExpected(self):
expInts = self.loadExpectedBdtResults()
actualInts = tCode.getIntegralsFromBdt(self.bdt, inclPP=False)
for key in expInts:
self.assertTrue(actualInts[key] == expInts[key])
def _getAllIntegDictsFromBdtPaths(allPaths):
allIntegDicts = list()
for currPath in allPaths:
allIntegDicts.append(parseTbint.getIntegralsFromBdt(currPath))
return allIntegDicts
