def testAddInpVelocities(self):
testVelocities = [[1,2,3], [4,5,6]]
kwargDict = {"subsysInpVelocities": testVelocities}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputVelocitiesReadIn()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testSurfDipoleCorr(self):
kwargDict = {"useCorr":True,"surfDipoleDir":"x"}
testOptObj = miscObjs.SurfaceDipoleCorrectionCP2K(**kwargDict)
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, testOptObj.modPyCP2KDict)
expStr = _loadExpectedOutputSurfaceDipoleOptsA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testAgainstAtomicPosConstraintsA(self):
kwargDict = {"atPosConstraint_fixIdxPositions": [2,4,1] , #Note: This is one-indexed in cp2k
"atPosConstraint_fixComponents": ["XY","XY", "XYZ"] }
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputAtomicPosConstraintsA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testChangeDispNLCorr(self):
kwargDict = {"corrType":"DRSLL", "cutoff":100, "kernelFileName":"fake_file.dat",
"verboseOutput":True}
testOptObj = miscObjs.NonLocalDispersionsCorrOptsCP2K(**kwargDict)
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, testOptObj.modPyCP2KDict)
expStr = _loadExpectedOutputChangeNonLocalDispCorrObjA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testChangeGrimmeDispCorr(self):
kwargDict = {"corrType": "DFTD3", "excludeKindsD3":[1],
"paramFile":"fake_file", "refFunctional": "BLYP", "printDFTD":True}
grimmeObj = miscObjs.GrimmeDispersionCorrOptsCP2K(**kwargDict)
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, grimmeObj.modPyCP2KDict)
expStr = _loadExpectedOutputChangeGrimmeObjA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testNudgedBandOptionsSection(self):
kwargDict = {"nudgedband_numbReplicas": 12, "nudgedband_procsPerReplicaEnv": 2, "nudgedBand_springConstant": "5e-2",
"nudgedband_type": "IT-NEB", "nudgedband_rotateFrames":False, "nudgedband_alignFrames":False, "nudgedband_printInitConfigInfo":True,
"nudgedband_optEndPoints":True}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutNudgedBandFile_noReplicasSet()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testMDSection(self):
kwargDict = {"mdEnsemble":"NVT", "mdSteps":"100",
"mdTimeStep":"0.5", "mdTemperature":"300",
"mdThermostatType":"nose", "mdPrintKindTemps":True,
"mdStartTime":200, "mdStartStep":20}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputSimpleMDOptionsA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testNudgedBandReplicasSection(self, mockedUConvHelp):
mockedUConvHelp.BOHR_TO_ANG = 1
kwargDict = {"nudgedband_replica_coords": [ [[1,2,3],[4,5,6]],
[[7,8,9],[2,3,4]] ] }
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutNudgedBandReplicas()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def _createBaseCP2KObj(self, basisKeyDict):
basicObj = self._createBasicObject()
basisObjects = self._getBasisObjects(basisKeyDict)
pyCP2KHelp.modCp2kObjBasedOnDict(basicObj, {"kpts":self.kPts, "charge":self.charge} )
pyCP2KHelp.addGeomAndBasisInfoToSimpleCP2KObj(basicObj, self.geom, basisObjects)
baseCP2KObj = baseCalcObjCP2K.CP2KCalcObj( basicObj )
baseCP2KObj.maxScf = self.maxScf
return baseCP2KObj
def testChangeScfConvParams(self):
kwargDict = {"scfMixAlpha": "0.8", "scfMixMethod": "PULAY_MIXING", "scfMixingOn":False, "scfPrintRestart":True,
"scfPrintRestartHistoryOn":True, "scfPrintRestartHistory_eachMD":8, "scfPrintRestartHistory_eachSCF":12,
"scfPrintRestartHistory_backupCopies":5, "scfPrintRestart_eachMD":2, "scfPrintRestart_eachSCF":3,
"scfPrintRestart_backupCopies":7, "scfHistoryEps":1e-3,
"scfDiagOn":False, "scfOuterEps": 1e-5, "scfOuterMaxIters":20}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputScfMixA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testMetadynSection(self):
metaVar = colVarHelp.MetaVarStandard(index=2, scale=3)
kwargDict = {"metaVars":[metaVar], "metaDyn_doHills":True, "metaDyn_ntHills":5,
"metaDyn_hillHeight":7, "metaDyn_printColvarCommonIterLevels":3,
"metaDyn_printHills":True, "metaDyn_printHillsCommonIterLevels":3,
"metaDyn_spawnHillsHeight": [ 1,2,3 ] , "metaDyn_spawnHillsPos": [ [2,3],[4,5],[6,7] ],
"metaDyn_spawnHillsScale": [ [1,2], [3,4], [5,6] ],
"metaDyn_nHillsStartVal": 3}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputMetadynSectionA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testModBasedOnDictGivesExpectedObjTestA(self):
""" Modify multiple options on the CP2K object and check we get expected output file """
modKwargsDict = {"kpts" : [20,20,20],
"gridCutAbs" : 300,
"gridCutRel" : 50,
"maxscf" : 5,
"addedMOs": 10}
expStr = sorted(_loadExpectedOutputStrTestA())
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, modKwargsDict)
actStr = sorted( self.startCP2KObj.get_input_string() )
self.assertEqual(expStr, actStr)
def _getAllRequiredCP2KObjs(self, basisKeyDict, startFolder): allObjs = list() for gVals in self._gridValsToUse: currObj = self._createBaseCP2KObj(basisKeyDict) currObj.absGridCutoff = gVals.absCut currObj.relGridCutoff = gVals.relCut currObj.basePath = os.path.join(startFolder, gVals.toStr() ) currObj.addedMOs = self.addedMOs if self.extraKwargDictToModCP2KObj is not None: cp2kFileHelpers.modCp2kObjBasedOnDict(currObj.cp2kObj, self.extraKwargDictToModCP2KObj) allObjs.append(currObj) return allObjs
def testMiscOptsA(self):
kwargDict = {"scfPrintRestart":False, "qsExtrapolationMethod":"LINEAR_P", "nGrids":5,
"walltime":2500, "prefDiagLib":"sl",
"rsGrid_distrib":[-1,-1,48], "qsExtrapolationOrder":4, "scfDiagAlgorithm":"OT",
"scfOTMinimizer": "DIIS", "scfOTEnergies":True, "scfOTRotation":True, "scfGuess":"restart",
"scfOTPreconditioner": "FULL_SINGLE_INVERSE", "scfOTEnergyGap": "1e-2",
"scfOTSafeDIIS":False,
"extRestartName": "fake_restart_file.restart", "scfMaxIterAfterHistoryFull":1,
"scfOTStepsize" : 0.1, "dftInpWfnRestartFilename":"fake_restart_wfn.wfn",
"printForces":False, "printPdos":True, "ldosIndices":[[1,2],[3,4]],
"motion_cellopt_constraint":"XY",
"motionPrintForces":True, "motionPrintVelocities":True,
"dftPrintDensityCube":True}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputMiscOptsA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testSmearingFalseWorks(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"useSmearing":False})
expStr = _loadExpectedOutputNoSmearing()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testCellOpt(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"runType":"cell_opt", "geo_constrain_cell_angles":[True,True,True]})
expStr = _loadExpectedOutputCellOptA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testSetCharge(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"charge":2})
expStr = _loadExpectedOutputCharge2()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testPrintOrbitalMulliken(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"printAOMullikenPop":True})
expStr = _loadExpectedOutputStrPrintOrbitalMulliken()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testEpsRho(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"epsRho":3.7e-10})
expStr = _loadExpectedOutputEpsRho_3pt7_e10()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testEpsCoreCore(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"epsCoreCharge":4.5e-10})
expStr = _loadExpectedOutputEpsCoreCharge_4pt5_e10()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testAddThermoRegions(self):
thermoRegions = [mock.Mock(), mock.Mock()]
kwargDict = {"mdThermoRegions": thermoRegions}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
for region in thermoRegions:
region.addToPyCp2kObj.assert_called_with(self.startCP2KObj)
def testPrintHirshOptions(self):
kwargDict = {"hirshfeld_on":True, "hirshfeld_selfConsistent":True, "hirshfeld_shapeFunction":"density"}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputHirshfeldOpts()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testRunTypeBSSE(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"runtype":"bsse", "fragmentsBSSE":[[1,2],[3,4]]})
expStr = _loadExpectedOutputBSSE_a()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testChangeXCFunctional(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"xcFunctional":"blyp"})
expStr = _loadExpectedOutputChangeXcFunctional()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testAddThermostatOpts(self):
thermoOptObj = mock.Mock()
kwargDict = {"mdThermoStatOpts": thermoOptObj}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
thermoOptObj.addToPyCp2kObj.assert_called_with(self.startCP2KObj)
def testOptB88SpecialFunctional(self):
kwargDict = {"xcFunctional":"optb88_pw92"}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputOptB88Functional()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testReplaceEpsPPNL(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"epsPPNL":3.2e-10})
expStr = _loadExpectedOutputEpsPPNL_3pt2_e10()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
def testRestartPrintOptsA(self):
kwargDict = {"restartPrintEachMd":3}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
expStr = _loadExpectedOutputRestartOptsA()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr.replace(" ","")), sorted(actStr.replace(" ","")) )
def testAddColVars(self):
colVarA, colVarB = mock.Mock(), mock.Mock()
kwargDict = {"colVars": [colVarA, colVarB]}
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, kwargDict)
colVarA.addColVarToSubsys.assert_called_with(self.startCP2KObj)
colVarB.addColVarToSubsys.assert_called_with(self.startCP2KObj)
def testReplaceEpsGvgRspace(self):
tCode.modCp2kObjBasedOnDict(self.startCP2KObj, {"epsGvgRSpace":5.2e-10})
expStr = _loadExpectedOutputEpsGVG_5p2_e10()
actStr = self.startCP2KObj.get_input_string()
self.assertEqual( sorted(expStr), sorted(actStr) )
