def testParseOrbitals(self):
# Need to have a load of expected n/l/idx values (3 vals that uniquely define an orbital)
#Then for each need to attach the correct grid to a dict
OrbInfoStruct = namedtuple('OrbInfoStruct',['n', 'l', 'zetaIdx', 'occ', 'energy', 'cutoff', 'gridVals'])
gridVals = [ 1.741018362, 1.797138313, 1.855067232, 1.914863431, 1.9765871]
orbS1GridVals = [ (x,y) for x,y in zip(gridVals, [0.0989413852, 0.0986739085, 0.0981262476, 0.0972919597, 0.0961667723]) ]
orbP1GridVals = [ (x,y) for x,y in zip(gridVals, [0.0835960866, 0.0841920978, 0.0846214765, 0.0848668996, 0.0849112177]) ]
orbD1GridVals = [ (x,y) for x,y in zip(gridVals, [0.0682501546, 0.0693816424, 0.0704222457, 0.0713585989, 0.0721760637]) ]
orbS2GridVals = [ (x,y) for x,y in zip(gridVals, [-0.0325282329, -0.038983002, -0.0440527676, -0.0477287834, -0.0500195748]) ]
orbP2GridVals = [ (x,y) for x,y in zip(gridVals, [-0.1104856274, -0.1070121274, -0.102854406, -0.0979695372, -0.0923217034]) ]
orbD2GridVals = [ (x,y) for x,y in zip(gridVals, [-0.1083726475, -0.106048856, -0.1032277781, -0.0998785009, -0.0959702762]) ]
orbS1 = OrbInfoStruct(n=3, l=0, zetaIdx=1, occ=2, energy=-0.04327913674, cutoff=6, gridVals=orbS1GridVals)
orbP1 = OrbInfoStruct(n=3, l=1, zetaIdx=1, occ=0, energy=0.3498469233, cutoff=6, gridVals=orbP1GridVals)
orbD1 = OrbInfoStruct(n=3, l=2, zetaIdx=1, occ=0, energy=0.8783708167, cutoff=6, gridVals=orbD1GridVals)
orbS2 = OrbInfoStruct(n=3, l=0, zetaIdx=2, occ=0, energy=0.0, cutoff=6, gridVals=orbS2GridVals )
orbP2 = OrbInfoStruct(n=3, l=1, zetaIdx=2, occ=0, energy=0.0, cutoff=6, gridVals=orbP2GridVals )
orbD2 = OrbInfoStruct(n=3, l=2, zetaIdx=2, occ=0, energy=0.0, cutoff=6, gridVals=orbD2GridVals )
expectedInfo = [orbS1, orbP1, orbD1, orbS2, orbP2, orbD2]
actualInfo = tCode.parseBasFile(self.partBasAPath)["orbitals"]
for exp,act in itertools.zip_longest(expectedInfo,actualInfo):
self.assertEqual( exp.n, act.n )
self.assertEqual( exp.l, act.l )
self.assertEqual( exp.zetaIdx, act.zetaIdx )
self.assertAlmostEqual( exp.occ, act.occ )
self.assertAlmostEqual( exp.energy, act.energy )
self.assertAlmostEqual( exp.cutoff, act.cutoff )
gridValsExp, gridValsAct = exp.gridVals, act.gridVals
for rowExp, rowAct in itertools.zip_longest(gridValsExp, gridValsAct):
[self.assertAlmostEqual(x,y) for x,y in itertools.zip_longest(rowExp,rowAct)]
def testParsePPInfo(self):
expLVals, expSigns = [0,0,1], [1,1,1]
expDict = {"lVals":expLVals, "signVals":expSigns}
actVals = tCode.parseBasFile(self.partBasAPath)["nlPP"]
print("actVals = {}".format(actVals))
print("expVals = {}".format(expDict))
self.assertTrue( expDict["lVals"] == actVals["lVals"] )
self.assertTrue( expDict["signVals"] == actVals["signVals"] )
def testParseVNA(self): gridXVals = [ 1.741018362, 1.797138313, 1.855067232, 1.914863431, 1.9765871] expectedVNAVals = [-0.5938349748, -0.526176039, -0.4645687067, -0.4085946799, -0.3578461053] expectedParsedVNA = [(x,y) for x,y in zip(gridXVals, expectedVNAVals)] actualParsedVNA = tCode.parseBasFile(self.partBasAPath)["vna"].gridVals for exp,act in itertools.zip_longest(expectedParsedVNA, actualParsedVNA): self.assertAlmostEqual(exp[0],act[0]) self.assertAlmostEqual(exp[1],act[1])
def testParseDensity(self): gridXVals = [ 1.741018362, 1.797138313, 1.855067232, 1.914863431, 1.9765871] expectedDensityVals = [(x,y) for x,y in zip(gridXVals,[0.019578795395808, 0.019473080431912, 0.019257520949328, 0.018931450826999, 0.018496096177719])] actualDensities = tCode.parseBasFile(self.partBasAPath)["density"].gridVals for exp,act in zip(expectedDensityVals,actualDensities): self.assertAlmostEqual(exp[0],act[0]) self.assertAlmostEqual(exp[1],act[1])
def getFieldDataFromBasFile(basFile, field, fieldIdx=0):
parsedBas = parseBas.parseBasFile(basFile)
dataSection = parsedBas[field.lower()]
try:
fieldData = dataSection[fieldIdx]
except TypeError:
fieldData = dataSection
if field.lower() == "orbitals":
xyData = fieldData.getGridValsPlatoAOrep()
else:
xyData = fieldData.gridVals
return xyData
def testGenInfoParse(self):
expectedInfo = {"numbShells":6,
"ngridpoints":5,
"pcc":0,
"energy":-1.287901814,
"cutoff":6,
"zCore": 2,
"dNu": 0.03172536568,
"hubbard": 0.5,
"stoner": 0.05,
"xcfunctional":1}
actualInfo = tCode.parseBasFile(self.partBasAPath)
for key in expectedInfo.keys():
self.assertAlmostEqual(expectedInfo[key], actualInfo[key])
def testWrittenFileSameAsParsed(self): ''' get str-rep of partial file, parse it, write new file based on parsed file, get str-rep of newly written file and see if strings match ''' tempPath = "temp_file.bas" with open(self.partBasFile,"rt") as f: expectedStr = f.read() parsedFile = tCode.parseBasFile(self.partBasFile) tCode.writeBasFileFromParsedDict(tempPath,parsedFile) with open(tempPath,"rt") as f: actualStr = f.read() self.assertEqual(expectedStr,actualStr) os.remove(tempPath)
def testGetPlatoRadialRepr(self): gridXVals = [5.001975975, 5.162760327, 5.328712959, 5.5] orbSGridVals = [ (x,y) for x,y in zip(gridXVals, [0.0023404,0.001394,0.00063806,0.0]) ] orbPGridVals = [ (x,y) for x,y in zip(gridXVals, [0.0010947,0.0006362,0.00028348,0.0]) ] orbDGridVals = [ (x,y) for x,y in zip(gridXVals, [0.00038715,0.00021987,9.55E-05,0.0]) ] expectedInfo = [orbSGridVals, orbPGridVals, orbDGridVals] actualOrbs = tCode.parseBasFile(self.partBasBPath)["orbitals"] actualInfo = [x.getGridValsPlatoAOrep() for x in actualOrbs] for exp,act in itertools.zip_longest(expectedInfo,actualInfo): for expRow,actRow in zip(exp,act): self.assertAlmostEqual(expRow[0],actRow[0]) self.assertAlmostEqual(expRow[1],actRow[1])
def testParseVNlGrids(self): # Load expected results gridXVals = [ 1.741018362, 1.797138313, 1.855067232, 1.914863431, 1.9765871] expectedNlPPVals = [ [-0.2470763092, -0.1980057457, -0.1558129653, -0.1202483716, -0.0908952528], [0.0177225219, 0.0200599937, 0.0201398618, 0.0187164856, 0.0164123448], [0.316115369, 0.2675482131, 0.2235169044, 0.1841622352, 0.149512821] ] expectedParsedNlPP = list() for nlGrid in expectedNlPPVals: currList = [(x,y) for x,y in zip(gridXVals,nlGrid)] expectedParsedNlPP.append( currList ) #Run code parsedBas = tCode.parseBasFile(self.partBasAPath) actualParsedNlPP = [x.gridVals for x in parsedBas["nlPP"]["grids"]] for expList, actList in itertools.zip_longest(expectedParsedNlPP, actualParsedNlPP): for exp,act in itertools.zip_longest(expList, actList): [self.assertAlmostEqual(x,y) for x,y in itertools.zip_longest(exp,act)]
def setUp(self): basFile = createPartialBasFileA() newBasPath = os.path.join( os.getcwd(), "Mg.bas" ) os.rename( basFile, newBasPath) self.parsedFile = parseBas.parseBasFile(newBasPath) os.remove(newBasPath)