def testModOptsCorrectInOutFile(self):
platoCode = "dft2"
expModdedOptDict = {
"blochstates": [1, 1, 1],
"e0method": 1,
"xtalxcmethod": -1,
"hopxcmethod": -1,
"xtalVnaMethod".lower(): 1,
"hopVnaMethod".lower(): -1,
"xtalVnlMethod".lower(): 1,
"hopVNLMethod".lower(): -1
}
expModdedOptStrDict = modInp.getStrDictFromOptDict(
expModdedOptDict, platoCode)
testWorkFlow = tCode.CreateEosWorkFlow(
self.structDict,
self.modOptDicts,
self.workFolder,
platoCode,
onlyCalcE0=True,
nonE0EnergyDict=self.testE1Vals)()
inpFilePaths = testWorkFlow._inpFilePaths
fullInpDict = modInp.tokenizePlatoInpFile(inpFilePaths[0])
for key in expModdedOptStrDict.keys():
self.assertEqual(expModdedOptStrDict[key], fullInpDict[key])
def _getOutputInvSkFileNames(inpFilePath):
tokenizedFile = {
k.lower(): v
for k, v in platoInp.tokenizePlatoInpFile(inpFilePath).items()
}
if int(tokenizedFile["format"]) != 0:
raise ValueError(
"Geometry format needs to be {}; but format={}".format(
0, tokenizedFile["format"]))
#Get the elements present
nAtoms = tokenizedFile["natom"]
atoms = tokenizedFile["atoms"].split("\n")
elementsPresent = list()
for x in atoms:
currElement = x.split()[-1]
if currElement not in (elementsPresent):
elementsPresent.append(currElement)
#Get the file names from them
outFileNames = [
"{}_{}_SK.csv".format(a, b)
for a, b in itertools.product(elementsPresent, elementsPresent)
]
return outFileNames
def createInputOptionsFromCmdLineArgs(cmdArgs):
outObj = InputOptions()
outObj.elementComboLists = optsToParams.getAllThreeBodyElementCombos(
cmdArgs.elementList)
baseStrDict = {
k.lower(): v
for k, v in platoInp.tokenizePlatoInpFile(
cmdArgs.templatePath).items()
}
outObj.geomRepStr = cmdArgs.geomRepr
outObj.nCores = int(cmdArgs.nCores)
dFolderPath = getDataFolderPathFromStrDict(baseStrDict)
cutoffDict = getCutoffValuesAllElements(cmdArgs.elementList, dFolderPath)
if cmdArgs.geomSteps is None:
cmdArgs.geomSteps = getDefaultStepValues(cmdArgs.geomRepr)
outObj.geomParams = getGeomParamsAllElementLists(
outObj.elementComboLists, [float(x) for x in cmdArgs.geomSteps],
cutoffDict, cmdArgs.geomRepr)
outObj.twoBodyStrDict = getStrDictTwoBodyCalc(baseStrDict)
outObj.threeBodyStrDict = getStrDictThreeBodyCalc(baseStrDict)
outObj.startFolder = os.path.abspath(cmdArgs.startFolder)
outObj.runJobs = cmdArgs.runCalcs
return outObj
def testModOptsCorrectInOutFile(self):
inpFilePaths = self.workFlowA._inpFilePaths
expModdedOpts = self.modOptDicts
expModdedOpts["hcp"]["addCorrectingPPFromBdt".lower()] = str(1)
fullInpDict = modInp.tokenizePlatoInpFile(inpFilePaths[0])
for key in expModdedOpts["hcp"]:
self.assertEqual(expModdedOpts["hcp"][key], fullInpDict[key])
def testMultiLineMod(self):
''' Test modPlatoInpOption works for replacing option that runs over multiple lines'''
testInpFile = self.filePathDict["testInpFragA"]
expectedVal = "2\n1\n2"
testOptVal = {'Pinned': expectedVal}
key = 'Pinned'.lower()
tCode.modPlatoInpOptions(testInpFile, testOptVal)
parsedOptions = tCode.tokenizePlatoInpFile(testInpFile)
self.assertEqual(expectedVal, parsedOptions[key])
def _grabAtomGridSpacingFromInpFile(filePath, mode, angIdx=0):
parsedFile = platoInp.tokenizePlatoInpFile(filePath)
gridPart = parsedFile["integralmesh"].split("\n")
if (mode == "angular"):
gridVal = int( gridPart[1].split()[angIdx+1] )
elif (mode == "radial"):
gridVal = int( gridPart[1].split()[0] )
else:
raise ValueError("{} is an invalid mode for _grabAtomGridSpacingFromInpFile".format(mode))
return gridVal
def testOneLineMod(self):
''' Test modPlatoInpOption works for a simple 1 line case (RFlag). NOTE: dependent '''
''' on tCode.tokenizePlatoInpFile '''
testInpFile = self.filePathDict["testInpFragA"]
testOptVal = {'RFlag': 5}
key = 'RFlag'.lower()
expectedVal = "5"
tCode.modPlatoInpOptions(testInpFile, testOptVal)
parsedOptions = tCode.tokenizePlatoInpFile(testInpFile)
self.assertEqual(expectedVal, parsedOptions[key])
def testMutliMods(self):
''' Test modPlatoInpOption works when replacing >1 option '''
testInpFile = self.filePathDict["testInpFragA"]
expectedVals = ["5", "2\n1\n2"]
keys = ["pinned", "rflag"]
testOptVals = {k: v for k, v in zip(keys, expectedVals)}
tCode.modPlatoInpOptions(testInpFile, testOptVals)
parsedOptions = tCode.tokenizePlatoInpFile(testInpFile)
[
self.assertEqual(expectedVals[x], parsedOptions[keys[x]])
for x in range(len(expectedVals))
]
def testTokenizeInpFragmentA(self):
testInpFile = self.filePathDict["testInpFragA"]
expectedVals = {
"rflag": "3",
"cellrelaxmode": "0",
"FTol".lower(): "0.0001",
"MaxDisplacement".lower(): "0.1",
"StressTol".lower(): "0.001",
"Pinned".lower(): "0\n1",
"Constrain".lower(): "0\n1 1.0 1.0 0.0",
"ReactionCoordinate".lower(): "0"
}
actualVals = tCode.tokenizePlatoInpFile(testInpFile)
self.assertEqual(expectedVals, actualVals)
def _modInvSkFlagToOn(inpFilePath):
tokenizedFile = platoInp.tokenizePlatoInpFile(inpFilePath)
outOptDict = {k.lower():v for k,v in tokenizedFile.items()}
outOptDict["inversesk"] = "1"
platoInp.writePlatoOutFileFromDict(inpFilePath,outOptDict)