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How to use set_valueOf_ method in autotest
Best Python code snippet using autotest_python
csxwriter.py
Source:csxwriter.py 
...88 orbitalOccupancies=orbOccString)89 if hasOrbSym:90 wfn1.set_orbitalSymmetry(orbSymString)91 orbe1 = api.stringArrayType(unit='u:ElectronVolt')92 orbe1.set_valueOf_(orbEString)93 orbs1 = api.orbitalsType()94 for orbArray in data.mocoeffs:95 for iorb in range(orbNum):96 orbCaString = ' '.join(str(x) for x in orbArray[iorb])97 orb1 = api.stringArrayType(id=iorb+1)98 orb1.set_valueOf_(orbCaString)99 orbs1.add_orbital(orb1)100 wfn1.set_orbitals(orbs1)101 wfn1.set_orbitalEnergies(orbe1)102 else:103 orbNum = data.nmo104 orbCaEne = data.moenergies[0][:]105 orbCaEString = ' '.join(str(x) for x in orbCaEne)106 orbCbEne = data.moenergies[1][:]107 orbCbEString = ' '.join(str(x) for x in orbCbEne)108 orbCaOcc = []109 orbCbOcc = []110 for iorb in range (orbNum):111 elecCa = 1 if orbCaEne[iorb] < 0.0 else 0112 orbCaOcc.append(elecCa)113 elecCb = 1 if orbCbEne[iorb] < 0.0 else 0114 orbCbOcc.append(elecCb)115 orbCaOccString = ' '.join(str(x) for x in sorted(orbCaOcc,reverse=True))116 orbCbOccString = ' '.join(str(x) for x in sorted(orbCbOcc,reverse=True))117 orbCaSym = data.mosyms[0][:]118 orbCaSymString = ' '.join( x for x in orbCaSym)119 orbCbSym = data.mosyms[1][:]120 orbCbSymString = ' '.join( x for x in orbCbSym)121 wfn1 = api.waveFunctionType(orbitalCount=orbNum)122 orbe1 = api.stringArrayType(unit='u:ElectronVolt')123 orbe1.set_valueOf_(orbCaEString)124 orbs1 = api.orbitalsType()125 alphaOrb = data.mocoeffs[0][:]126 for iorb in range(orbNum):127 orbCaString = ' '.join(str(x) for x in alphaOrb[iorb])128 orb1 = api.stringArrayType(id=iorb+1)129 orb1.set_valueOf_(orbCaString)130 orbs1.add_orbital(orb1)131 wfn1.set_alphaOrbitals(orbs1)132 wfn1.set_alphaOrbitalEnergies(orbe1)133 wfn1.set_alphaOrbitalOccupancies(orbCaOccString)134 wfn1.set_alphaOrbitalSymmetry(orbCaSymString)135 orbe2 = api.stringArrayType(unit='u:ElectronVolt')136 orbe2.set_valueOf_(orbCbEString)137 orbs2 = api.orbitalsType()138 betaOrb = data.mocoeffs[1][:]139 for iorb in range(orbNum):140 orbCbString = ' '.join(str(x) for x in betaOrb[iorb])141 orb2 = api.stringArrayType(id=iorb+1)142 orb2.set_valueOf_(orbCbString)143 orbs2.add_orbital(orb2)144 wfn1.set_betaOrbitals(orbs2)145 wfn1.set_betaOrbitalEnergies(orbe2)146 wfn1.set_betaOrbitalOccupancies(orbCbOccString)147 wfn1.set_betaOrbitalSymmetry(orbCbSymString)148 #vibrational frequency149 if hasFreq:150 molFreqNum = len(data.vibfreqs)151 frqString = ' '.join(str(x) for x in data.vibfreqs)152 if hasattr(data, 'vibirs'):153 intString = ' '.join(str(x) for x in data.vibirs)154 else:155 intString = ' '.join(str(x) for x in [1.0]*molFreqNum)156 vib1 = api.vibAnalysisType(vibrationCount=molFreqNum)157 freq1 = api.stringArrayType(unit="gc:RecipricalCentimeter")158 freq1.set_valueOf_(frqString)159 vib1.set_frequencies(freq1)160 irint1 = api.stringArrayType()161 irint1.set_valueOf_(intString)162 vib1.set_irIntensities(irint1)163 norms1 = api.normalModesType()164 normMdString = []165 for ifrq in range(molFreqNum):166 normM = []167 for iatm in range(atomNum):168 for ixyz in range(3):169 normM.append(data.vibdisps[ifrq][iatm][ixyz])170 normMdString.append(' '.join(str(x) for x in normM))171 norm1 = api.normalModeType(id=ifrq+1)172 norm1.set_valueOf_(normMdString[ifrq])173 norms1.add_normalMode(norm1)174 vib1.set_normalModes(norms1)175 if hasProp or hasPolar:176 prop1 = api.propertiesType()177 #dipole moments information178 if hasProp:179 # au2db = 2.541766180 if len(data.moments) > 1:181 molDipoleX = data.moments[1][0]182 molDipoleY = data.moments[1][1]183 molDipoleZ = data.moments[1][2]184 molDipoleTot = math.sqrt(molDipoleX*molDipoleX+molDipoleY*molDipoleY+molDipoleZ*molDipoleZ)185 sprop1 = api.propertyType(name='dipoleMomentX',unit='u:Debye',moleculeId='m1')186 sprop1.set_valueOf_(molDipoleX)187 sprop2 = api.propertyType(name='dipoleMomentY',unit='u:Debye',moleculeId='m1')188 sprop2.set_valueOf_(molDipoleY)189 sprop3 = api.propertyType(name='dipoleMomentZ',unit='u:Debye',moleculeId='m1')190 sprop3.set_valueOf_(molDipoleZ)191 sprop4 = api.propertyType(name='dipoleMomentAverage',unit='u:Debye',moleculeId='m1')192 sprop4.set_valueOf_(molDipoleTot)193 prop1.add_systemProperty(sprop1)194 prop1.add_systemProperty(sprop2)195 prop1.add_systemProperty(sprop3)196 prop1.add_systemProperty(sprop4)197 #polarizability information198 if hasPolar:199 polarXX = data.polar[0][0]200 polarYY = data.polar[0][1]201 polarZZ = data.polar[0][2]202 polarAvg = (polarXX+polarYY+polarZZ)/3.0203 sprop5 = api.propertyType(name='polarizabilityXX',unit='u:Angstrom3',moleculeId='m1')204 sprop5.set_valueOf_(polarXX)205 sprop6 = api.propertyType(name='polarizabilityYY',unit='u:Angstrom3',moleculeId='m1')206 sprop6.set_valueOf_(polarYY)207 sprop7 = api.propertyType(name='polarizabilityZZ',unit='u:Angstrom3',moleculeId='m1')208 sprop7.set_valueOf_(polarZZ)209 sprop8 = api.propertyType(name='polarizabilityAverage',unit='u:Angstrom3')210 sprop8.set_valueOf_(polarAvg)211 prop1.add_systemProperty(sprop5)212 prop1.add_systemProperty(sprop6)213 prop1.add_systemProperty(sprop7)214 prop1.add_systemProperty(sprop8)215 #NMR chemical shielding information216 if hasNMR:217 prop2 = api.propertiesType()218 for iatm in range(atomNum):219 aprop1 = api.propertyType(atomId='a'+str(iatm+1), moleculeId='m1', \220 name='nmrShieldingIsotropic',unit='gc:PartsPerMillion')221 aprop1.set_valueOf_(data.nmriso[iatm])222 aprop2 = api.propertyType(atomId='a'+str(iatm+1), moleculeId='m1', \223 name='nmrShieldingAnisotropy',unit='gc:PartsPerMillion')224 aprop2.set_valueOf_(data.nmranis[iatm])225 prop2.add_atomProperty(aprop1)226 prop2.add_atomProperty(aprop2)227 #Electronic transition information228 if hasElec:229 transStr = ' '.join(str(x) for x in data.etenergies)230 oscilStr = ' '.join(str(x) for x in data.etoscs)231 elec1 = api.elecSpectraType(transitionCount=len(data.etenergies))232 trans1 = api.stringArrayType(unit="gc:RecipricalCentimeter")233 trans1.set_valueOf_(transStr)234 oscil1 = api.stringArrayType()235 oscil1.set_valueOf_(oscilStr)236 elec1.set_electronicTransitions(trans1)237 elec1.set_oscillatorStrength(oscil1)238 #Start to generate CSX elements239 cs1 = api.csType(version='2.0')240 #molecular publication section241 mp1 = api.mpubType(title='default title', \242 abstract='default abstract', \243 publisher='default publisher', \244 status='default status', \245 category=1, \246 visibility=0, \247 tag=data.package, \248 key=1 )249 source1 = api.sourcePackageType(name=data.package, version=data.version)250 mp1.set_sourcePackage(source1)251 ath1 = api.authorType(creator='Wang', \252 type_='gc:CorrespondingAuthor', \253 organization='default organization', \254 email='name@organization.com')255 mp1.add_author(ath1)256 cs1.set_molecularPublication(mp1)257 if hasCollection:258 mc1 = api.mcolType(type_='IRC', description='Internal Reaction Coordinates')259 ircpnt = int(data.ircpnt)260 if ( ircpnt != len(data.ircenergies) ):261 ircpnt = len(data.ircenergies)-1262 for ipnt in range(ircpnt):263 entry1 = api.entryType(id='pnt'+str(ipnt+1))264 param1 = api.propertyType(id='pnt'+str(ipnt+1)+'prm1', name='reaction coordinates')265 param1.set_valueOf_(data.irccoords[ipnt])266 entry1.add_parameter(param1)267 sys1 = api.itemType(ref='s'+str(ipnt+1))268 calc1 = api.itemType(ref='c'+str(ipnt+1))269 res1 = api.resType(id='pnt'+str(ipnt+1)+'r1', \270 name='total electronic energy for point '+str(ipnt+1))271 val1 = api.valType(ref='e'+str(ipnt+1)+'_'+'total_energy')272 res1.add_value(val1)273 entry1.add_result(res1)274 entry1.set_system(sys1)275 entry1.set_calculation(calc1)276 mc1.add_entry(entry1)277 cs1.add_molecularCollection(mc1)278 for ipnt in range(ircpnt+1):279 #molecular system section280 msys = api.msysType(systemCharge=molCharge, \281 systemMultiplicity=molMulti, id='s'+str(ipnt))282 temp1 = api.dataWithUnitsType(unit='u:Kelvin')283 temp1.set_valueOf_(0.0)284 msys.set_systemTemperature(temp1)285 if ipnt == 0:286 mol = api.moleculeType(id='m1',atomCount=atomNum)287 else:288 mol = api.moleculeType(ref='m1',atomCount=atomNum)289 if hasattr(data, "atomcharges"):290 atmCharge = data.atomcharges["mulliken"]291 else:292 atmCharge = [0]*atomNum293 for iatm in range(atomNum):294 # xCoord = float(data.atomcoords[iatm,0])295 xCoord = data.atomcoords[ipnt,iatm,0]296 yCoord = data.atomcoords[ipnt,iatm,1]297 zCoord = data.atomcoords[ipnt,iatm,2]298 xCoord1 = api.dataWithUnitsType(unit='u:Angstrom')299 xCoord1.set_valueOf_(xCoord)300 yCoord1 = api.dataWithUnitsType(unit='u:Angstrom')301 yCoord1.set_valueOf_(yCoord)302 zCoord1 = api.dataWithUnitsType(unit='u:Angstrom')303 zCoord1.set_valueOf_(zCoord)304 atomicNum = data.atomnos[iatm]305 if ipnt == 0:306 atm = api.atomType(id='a'+str(iatm+1), elementSymbol=chemElement.z2elm[atomicNum], \307 atomMass=chemElement.z2mass[atomicNum], \308 xCoord3D=xCoord1, \309 yCoord3D=yCoord1, \310 zCoord3D=zCoord1, \311 basisSet='bse:'+basisName, \312 calculatedAtomCharge=atmCharge[iatm], \313 formalAtomCharge=0)314 else:315 atm = api.atomType(ref='a'+str(iatm+1), elementSymbol=chemElement.z2elm[atomicNum], \316 atomMass=chemElement.z2mass[atomicNum], \317 xCoord3D=xCoord1, \318 yCoord3D=yCoord1, \319 zCoord3D=zCoord1, \320 basisSet='bse:'+basisName, \321 calculatedAtomCharge=atmCharge[iatm], \322 formalAtomCharge=0)323 mol.add_atom(atm)324 msys.add_molecule(mol)325 cs1.add_molecularSystem(msys)326 for ipnt in range(ircpnt):327 #molCalculation section328 sd_wfn_method = ['HF', 'DFT', 'MP2', 'MP3', 'MP4', 'AM1', 'PM3', 'PM6']329 md_wfn_method = ['CCD', 'CCSD', 'CCSD-T', 'CIS', 'CISD', 'FCI', 'QCISD', 'QCISD-T']330 mr_wfn_method = ['CASSCF', 'CASPT2', 'RASSCF', 'RASPT2', 'GVB', 'MCSCF', 'MRCC', 'MRCI']331 mc1 = api.mcalType(id='c'+str(ipnt+1), inputsystem='s'+str(ipnt), \332 outputsystem='s'+str(ipnt+1))333 qm1 = api.qmCalcType()334 if calcType in mr_wfn_method:335 mrs1 = api.mrsMethodType()336 mrsmd1 = api.mrsmdMethodType()337 if calcType == 'GVB':338 gvb1 = api.resultType(methodology='gc:normal', spinType='gc:'+molSpin, \339 basisSet='bse:'+basisName, pairCount='2')340 ene1 = api.energiesType(unit='u:ElectronVolt')341 ee_ene1 = api.energyType(type_='gc:totalPotential')342 ee_ene1.set_valueOf_(float(molEE))343 ene1.add_energy(ee_ene1)344 gvb1.set_energies(ene1)345 mrsmd1.set_gvb(gvb1)346 elif calcType == 'CASSCF':347 casscf1 = api.resultType(methodology='gc:normal', spinType='gc:'+molSpin, \348 basisSet='bse:'+basisName)349 ene1 = api.energiesType(unit='u:ElectronVolt')350 ee_ene1 = api.energyType(type_='gc:totalPotential')351 ee_ene1.set_valueOf_(float(molEE))352 ene1.add_energy(ee_ene1)353 casscf1.set_energies(ene1)354 mrsmd1.set_casscf(casscf1)355 mrs1.set_multipleDeterminant(mrsmd1)356 qm1.set_multipleReferenceState(mrs1)357 else:358 srs1 = api.srsMethodType()359 if calcType in sd_wfn_method:360 sdm1 = api.srssdMethodType()361 #SCF362 if (calcType == 'HF'):363 scf1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \364 basisSet='bse:'+basisName)365 ene1 = api.energiesType(unit='u:ElectronVolt')366 ee_ene1 = api.energyType(id='e'+str(ipnt+1)+'_'+'total_energy', \367 type_='gc:totalPotential')368 ee_ene1.set_valueOf_(data.ircenergies[ipnt])369 ene1.add_energy(ee_ene1)370 scf1.set_energies(ene1)371 sdm1.set_abinitioScf(scf1)372 #DFT373 elif (calcType == 'DFT'):374 if hasElec:375 dft1 = api.resultType(methodology='gc:tddft',spinType='gc:'+molSpin, \376 basisSet='bse:'+basisName, dftFunctional='gc:'+data.functional)377 else:378 dft1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \379 basisSet='bse:'+basisName, dftFunctional='gc:'+data.functional)380 ene1 = api.energiesType(unit='u:ElectronVolt')381 ee_ene1 = api.energyType(id='e'+str(ipnt+1)+'_'+'total_energy', \382 type_='gc:totalPotential')383 ee_ene1.set_valueOf_(data.ircenergies[ipnt])384 ene1.add_energy(ee_ene1)385 dft1.set_energies(ene1)386 sdm1.set_dft(dft1)387 #MP2388 elif (calcType == 'MP2'):389 mp21 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \390 basisSet='bse:'+basisName)391 ene1 = api.energiesType(unit='u:ElectronVolt')392 ee_ene1 = api.energyType(id='e'+str(ipnt+1)+'_'+'total_energy', \393 type_='gc:totalPotential')394 ee_ene1.set_valueOf_(data.ircenergies[ipnt])395 ene1.add_energy(ee_ene1)396 mp21.set_energies(ene1)397 sdm1.set_mp2(mp21)398 #Semiempirical methods399 elif (calcType == 'AM1' or calcType == 'PM3' or calcType == 'PM6'):400 sem1 = api.resultType(methodology=calcType,spinType='gc:'+molSpin)401 ene1 = api.energiesType(unit='u:ElectronVolt')402 ee_ene1 = api.energyType(type_='gc:totalPotential')403 ee_ene1.set_valueOf_(float(molEE))404 hof_ene1 = api.energyType(type_='gc:heatofformation')405 hof_ene1.set_valueOf_(float(data.hofenergies[-1]))406 ene1.add_energy(ee_ene1)407 ene1.add_energy(hof_ene1)408 sem1.set_energies(ene1)409 sdm1.set_semiEmpiricalScf(sem1)410 else:411 print ('The current CSX does not support this method')412 srs1.set_singleDeterminant(sdm1)413 if calcType in md_wfn_method:414 mdm1 = api.srsmdMethodType()415 if (calcType == 'CCSD'):416 ccsd1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \417 basisSet='bse:'+basisName)418 ene1 = api.energiesType(unit='u:ElectronVolt')419 ee_ene1 = api.energyType(type_='gc:totalPotential')420 ee_ene1.set_valueOf_(float(data.ccenergies[0]))421 ce_ene1 = api.energyType(type_='gc:correlation')422 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))423 ene1.add_energy(ee_ene1)424 ene1.add_energy(ce_ene1)425 ccsd1.set_energies(ene1)426 mdm1.set_ccsd(ccsd1)427 elif (calcType == 'CCSD-T'):428 ccsd_t1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \429 basisSet='bse:'+basisName)430 ene1 = api.energiesType(unit='u:ElectronVolt')431 ee_ene1 = api.energyType(type_='gc:totalPotential')432 ee_ene1.set_valueOf_(float(data.ccenergies[-1]))433 ce_ene1 = api.energyType(type_='gc:correlation')434 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))435 ene1.add_energy(ee_ene1)436 ene1.add_energy(ce_ene1)437 ccsd_t1.set_energies(ene1)438 mdm1.set_ccsd_t(ccsd_t1)439 else:440 print ('The current CSX does not support this method')441 srs1.set_multipleDeterminant(mdm1)442 qm1.set_singleReferenceState(srs1)443 mc1.set_quantumMechanics(qm1)444 cs1.add_molecularCalculation(mc1)445 else:446 #molecular system section447 ms1 = api.msysType(systemCharge=molCharge, \448 systemMultiplicity=molMulti, id='s1')449 temp1 = api.dataWithUnitsType(unit='u:Kelvin')450 temp1.set_valueOf_(0.0)451 ms1.set_systemTemperature(temp1)452 mol1 = api.moleculeType(id='m1',atomCount=atomNum)453 if hasattr(data, "atomcharges"):454 atmCharge = data.atomcharges["mulliken"]455 else:456 atmCharge = [0]*atomNum457 #obmol1 = openbabel.OBMol()458 for iatm in range(atomNum):459 # xCoord = float(data.atomcoords[iatm,0])460 xCoord = data.atomcoords[-1,iatm,0]461 yCoord = data.atomcoords[-1,iatm,1]462 zCoord = data.atomcoords[-1,iatm,2]463 xCoord1 = api.floatWithUnitType(unit='u:Angstrom')464 xCoord1.set_valueOf_(xCoord)465 yCoord1 = api.floatWithUnitType(unit='u:Angstrom')466 yCoord1.set_valueOf_(yCoord)467 zCoord1 = api.floatWithUnitType(unit='u:Angstrom')468 zCoord1.set_valueOf_(zCoord)469 atomicNum = data.atomnos[iatm]470 atm = api.atomType(id='a'+str(iatm+1), elementSymbol=chemElement.z2elm[atomicNum], \471 atomMass=chemElement.z2mass[atomicNum], \472 xCoord3D=xCoord1, \473 yCoord3D=yCoord1, \474 zCoord3D=zCoord1, \475 basisSet='bse:'+basisName, \476 calculatedAtomCharge=atmCharge[iatm], \477 formalAtomCharge=0)478 mol1.add_atom(atm)479 ms1.add_molecule(mol1)480 cs1.add_molecularSystem(ms1)481 #molCalculation section482 sd_wfn_method = ['HF', 'DFT', 'MP2', 'MP3', 'MP4', 'AM1', 'PM3', 'PM6']483 md_wfn_method = ['CCD', 'CCSD', 'CCSD-T', 'CIS', 'CISD', 'FCI', 'G2', 'QCISD', 'QCISD-T']484 mr_wfn_method = ['CASSCF', 'CASPT2', 'RASSCF', 'RASPT2', 'GVB', 'MCSCF', 'MRCC', 'MRCI']485 mc1 = api.mcalType(id='c1', inputsystem='s1')486 qm1 = api.qmCalcType()487 if calcType in mr_wfn_method:488 mrs1 = api.mrsMethodType()489 mrsmd1 = api.mrsmdMethodType()490 if calcType == 'GVB':491 gvb1 = api.resultType(methodology='gc:normal', spinType='gc:'+molSpin, \492 basisSet='bse:'+basisName, pairCount='2')493 ene1 = api.energiesType(unit='u:ElectronVolt')494 ee_ene1 = api.energyType(type_='gc:totalPotential')495 ee_ene1.set_valueOf_(float(molEE))496 ene1.add_energy(ee_ene1)497 gvb1.set_energies(ene1)498 mrsmd1.set_gvb(gvb1)499 elif calcType == 'CASSCF':500 casscf1 = api.resultType(methodology='gc:normal', spinType='gc:'+molSpin, \501 basisSet='bse:'+basisName)502 ene1 = api.energiesType(unit='u:ElectronVolt')503 ee_ene1 = api.energyType(type_='gc:totalPotential')504 ee_ene1.set_valueOf_(float(molEE))505 ene1.add_energy(ee_ene1)506 casscf1.set_energies(ene1)507 mrsmd1.set_casscf(casscf1)508 elif calcType == 'MCSCF':509 mcscf1 = api.resultType(methodology='gc:normal', spinType='gc:'+molSpin, \510 basisSet='bse:'+basisName)511 ene1 = api.energiesType(unit='u:ElectronVolt')512 ee_ene1 = api.energyType(type_='gc:totalPotential')513 ee_ene1.set_valueOf_(float(molEE))514 ene1.add_energy(ee_ene1)515 mcscf1.set_energies(ene1)516 mrsmd1.set_mcscf(mcscf1)517 mrs1.set_multipleDeterminant(mrsmd1)518 qm1.set_multipleReferenceState(mrs1)519 else:520 srs1 = api.srsMethodType()521 if calcType in sd_wfn_method:522 sdm1 = api.srssdMethodType()523 #SCF524 if (calcType == 'HF'):525 scf1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \526 basisSet='bse:'+basisName)527 ene1 = api.energiesType(unit='u:ElectronVolt')528 ee_ene1 = api.energyType(type_='gc:totalPotential')529 ee_ene1.set_valueOf_(float(molEE))530 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')531 nn_ene1.set_valueOf_(data.nnenergies[-1])532 ene1.add_energy(ee_ene1)533 ene1.add_energy(nn_ene1)534 scf1.set_energies(ene1)535 if hasOrb:536 scf1.set_waveFunction(wfn1)537 if hasProp or hasPolar:538 scf1.set_properties(prop1)539 if hasNMR:540 scf1.set_properties(prop2)541 if hasFreq:542 scf1.set_vibrationalAnalysis(vib1)543 if hasElec:544 scf1.set_electronicSpectra(elec1)545 sdm1.set_abinitioScf(scf1)546 #DFT547 elif (calcType == 'DFT'):548 if hasElec:549 dft1 = api.resultType(methodology='gc:tddft',spinType='gc:'+molSpin, \550 basisSet='bse:'+basisName, dftFunctional='gc:'+data.functional)551 else:552 if hasCfunctional:553 dft1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \554 basisSet='bse:'+basisName, \555 exchangeFunctional='gc:'+data.xfunctional, \556 correlationFunctional='gc:'+data.cfunctional)557 else:558 dft1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \559 basisSet='bse:'+basisName, dftFunctional='gc:'+data.functional)560 ene1 = api.energiesType(unit='u:ElectronVolt')561 ee_ene1 = api.energyType(type_='gc:totalPotential')562 ee_ene1.set_valueOf_(float(molEE))563 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')564 nn_ene1.set_valueOf_(data.nnenergies[-1])565 ene1.add_energy(ee_ene1)566 ene1.add_energy(nn_ene1)567 dft1.set_energies(ene1)568 if hasOrb:569 dft1.set_waveFunction(wfn1)570 if hasProp:571 dft1.set_properties(prop1)572 if hasNMR:573 dft1.set_properties(prop2)574 if hasFreq:575 dft1.set_vibrationalAnalysis(vib1)576 if hasElec:577 dft1.set_electronicSpectra(elec1)578 sdm1.set_dft(dft1)579 #MP2580 elif (calcType == 'MP2'):581 mp21 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \582 basisSet='bse:'+basisName)583 ene1 = api.energiesType(unit='u:ElectronVolt')584 ee_ene1 = api.energyType(type_='gc:totalPotential')585 ee_ene1.set_valueOf_(float(data.mpenergies[-1]))586 ce_ene1 = api.energyType(type_='gc:correlation')587 ce_ene1.set_valueOf_(float(data.mpenergies[-1])-float(molEE))588 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')589 nn_ene1.set_valueOf_(data.nnenergies[-1])590 ene1.add_energy(ee_ene1)591 ene1.add_energy(ce_ene1)592 ene1.add_energy(nn_ene1)593 mp21.set_energies(ene1)594 if hasOrb:595 mp21.set_waveFunction(wfn1)596 if hasProp:597 mp21.set_properties(prop1)598 if hasNMR:599 mp21.set_properties(prop2)600 if hasFreq:601 mp21.set_vibrationalAnalysis(vib1)602 sdm1.set_mp2(mp21)603 #Semiempirical methods604 elif (calcType == 'AM1' or calcType == 'PM3' or calcType == 'PM6'):605 sem1 = api.resultType(methodology=calcType,spinType='gc:'+molSpin)606 ene1 = api.energiesType(unit='u:ElectronVolt')607 ee_ene1 = api.energyType(type_='gc:totalPotential')608 ee_ene1.set_valueOf_(float(molEE))609 hof_ene1 = api.energyType(type_='gc:heatofformation')610 hof_ene1.set_valueOf_(float(data.hofenergies[-1]))611 ene1.add_energy(ee_ene1)612 ene1.add_energy(hof_ene1)613 sem1.set_energies(ene1)614 if hasOrb:615 sem1.set_waveFunction(wfn1)616 if hasProp:617 sem1.set_properties(prop1)618 if hasNMR:619 sem1.set_properties(prop2)620 if hasFreq:621 sem1.set_vibrationalAnalysis(vib1)622 sdm1.set_semiEmpiricalScf(sem1)623 else:624 print ('The current CSX does not support this method')625 srs1.set_singleDeterminant(sdm1)626 if calcType in md_wfn_method:627 mdm1 = api.srsmdMethodType()628 if (calcType == 'CCSD'):629 ccsd1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \630 basisSet='bse:'+basisName)631 ene1 = api.energiesType(unit='u:ElectronVolt')632 ee_ene1 = api.energyType(type_='gc:totalPotential')633 ee_ene1.set_valueOf_(float(data.ccenergies[0]))634 ce_ene1 = api.energyType(type_='gc:correlation')635 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))636 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')637 nn_ene1.set_valueOf_(data.nnenergies[-1])638 ene1.add_energy(ee_ene1)639 ene1.add_energy(ce_ene1)640 ene1.add_energy(nn_ene1)641 ccsd1.set_energies(ene1)642 if hasOrb:643 ccsd1.set_waveFunction(wfn1)644 if hasProp:645 ccsd1.set_properties(prop1)646 if hasNMR:647 ccsd1.set_properties(prop2)648 if hasFreq:649 ccsd1.set_vibrationalAnalysis(vib1)650 mdm1.set_ccsd(ccsd1)651 elif (calcType == 'CCD'):652 ccd1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \653 basisSet='bse:'+basisName)654 ene1 = api.energiesType(unit='u:ElectronVolt')655 ee_ene1 = api.energyType(type_='gc:totalPotential')656 ee_ene1.set_valueOf_(float(data.ccenergies[-1]))657 ce_ene1 = api.energyType(type_='gc:correlation')658 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))659 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')660 nn_ene1.set_valueOf_(data.nnenergies[-1])661 ene1.add_energy(ee_ene1)662 ene1.add_energy(ce_ene1)663 ene1.add_energy(nn_ene1)664 ccd1.set_energies(ene1)665 if hasOrb:666 ccd1.set_waveFunction(wfn1)667 if hasProp:668 ccd1.set_properties(prop1)669 if hasNMR:670 ccd1.set_properties(prop2)671 if hasFreq:672 ccd1.set_vibrationalAnalysis(vib1)673 mdm1.set_ccd(ccd1)674 elif (calcType == 'CCSD-T'):675 ccsd_t1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \676 basisSet='bse:'+basisName)677 ene1 = api.energiesType(unit='u:ElectronVolt')678 ee_ene1 = api.energyType(type_='gc:totalPotential')679 ee_ene1.set_valueOf_(float(data.ccenergies[-1]))680 ce_ene1 = api.energyType(type_='gc:correlation')681 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))682 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')683 nn_ene1.set_valueOf_(data.nnenergies[-1])684 ene1.add_energy(ee_ene1)685 ene1.add_energy(ce_ene1)686 ene1.add_energy(nn_ene1)687 ccsd_t1.set_energies(ene1)688 if hasOrb:689 ccsd_t1.set_waveFunction(wfn1)690 if hasProp:691 ccsd_t1.set_properties(prop1)692 if hasNMR:693 ccsd_t1.set_properties(prop2)694 if hasFreq:695 ccsd_t1.set_vibrationalAnalysis(vib1)696 mdm1.set_ccsd_t(ccsd_t1)697 elif (calcType == 'CID'):698 cid1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \699 basisSet='bse:'+basisName)700 ene1 = api.energiesType(unit='u:ElectronVolt')701 ee_ene1 = api.energyType(type_='gc:totalPotential')702 ee_ene1.set_valueOf_(float(data.cienergies[-1]))703 ce_ene1 = api.energyType(type_='gc:correlation')704 ce_ene1.set_valueOf_(float(data.cienergies[-1])-float(molEE))705 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')706 nn_ene1.set_valueOf_(data.nnenergies[-1])707 ene1.add_energy(ee_ene1)708 ene1.add_energy(ce_ene1)709 ene1.add_energy(nn_ene1)710 cid1.set_energies(ene1)711 if hasOrb:712 cid1.set_waveFunction(wfn1)713 if hasProp:714 cid1.set_properties(prop1)715 if hasNMR:716 cid1.set_properties(prop2)717 if hasFreq:718 cid1.set_vibrationalAnalysis(vib1)719 mdm1.set_cid(cid1)720 elif (calcType == 'CISD'):721 cisd1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \722 basisSet='bse:'+basisName)723 ene1 = api.energiesType(unit='u:ElectronVolt')724 ee_ene1 = api.energyType(type_='gc:totalPotential')725 ee_ene1.set_valueOf_(float(data.cienergies[-1]))726 ce_ene1 = api.energyType(type_='gc:correlation')727 ce_ene1.set_valueOf_(float(data.cienergies[-1])-float(molEE))728 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')729 nn_ene1.set_valueOf_(data.nnenergies[-1])730 ene1.add_energy(ee_ene1)731 ene1.add_energy(ce_ene1)732 ene1.add_energy(nn_ene1)733 cisd1.set_energies(ene1)734 if hasOrb:735 cisd1.set_waveFunction(wfn1)736 if hasProp:737 cisd1.set_properties(prop1)738 if hasNMR:739 cisd1.set_properties(prop2)740 if hasFreq:741 cisd1.set_vibrationalAnalysis(vib1)742 mdm1.set_cisd(cisd1)743 elif (calcType == 'QCISD'):744 qcisd1 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \745 basisSet='bse:'+basisName)746 ene1 = api.energiesType(unit='u:ElectronVolt')747 ee_ene1 = api.energyType(type_='gc:totalPotential')748 ee_ene1.set_valueOf_(float(data.ccenergies[-1]))749 ce_ene1 = api.energyType(type_='gc:correlation')750 ce_ene1.set_valueOf_(float(data.ccenergies[-1])-float(molEE))751 nn_ene1 = api.energyType(type_='gc:nuclearRepulsion')752 nn_ene1.set_valueOf_(data.nnenergies[-1])753 ene1.add_energy(ee_ene1)754 ene1.add_energy(ce_ene1)755 ene1.add_energy(nn_ene1)756 qcisd1.set_energies(ene1)757 if hasOrb:758 qcisd1.set_waveFunction(wfn1)759 if hasProp:760 qcisd1.set_properties(prop1)761 if hasNMR:762 qcisd1.set_properties(prop2)763 if hasFreq:764 qcisd1.set_vibrationalAnalysis(vib1)765 mdm1.set_qcisd(qcisd1)766 elif (calcType == 'G2'):767 g21 = api.resultType(methodology='gc:normal',spinType='gc:'+molSpin, \768 basisSet='bse:'+basisName)769 ene1 = api.energiesType(unit='u:Hartree')770 ee_ene1 = api.energyType(type_='gc:Ethalpy')771 ee_ene1.set_valueOf_(float(data.enthalpy))772 ce_ene1 = api.energyType(type_='gc:FreeEnergy')773 ce_ene1.set_valueOf_(float(data.freeenergy))774 ene1.add_energy(ee_ene1)775 ene1.add_energy(ce_ene1)776 g21.set_energies(ene1)777 if hasOrb:778 g21.set_waveFunction(wfn1)779 if hasProp:780 g21.set_properties(prop1)781 if hasNMR:782 g21.set_properties(prop2)783 if hasFreq:784 g21.set_vibrationalAnalysis(vib1)785 mdm1.set_g2(g21)786 else:787 print ('The current CSX does not support this method')...
qt_yaml.py
Source:qt_yaml.py
...156 label_wdget = UI.Widget(class__attr="QLabel", name="setting")157 label_property = UI.Property()158 label_property.set_name("text")159 text_label = UI.String()160 text_label.set_valueOf_(label)161 label_property.set_string(text_label)162 label_wdget.add_property(label_property)163 text_edit = UI.Widget(class__attr="QLineEdit", name="edit_setting_" + label)164 grid_layout.add_item(UI.LayoutItem(row=row, column=0, widget=label_wdget))165 grid_layout.add_item(UI.LayoutItem(row=row, column=1, widget=text_edit))166def __add_form_boolean_row(label: str, grid_layout: UI.Layout, row, checked: bool = False):167 """168 Adds a label and a QLineEdit on the same row of grid_layout169 :param label:170 :param grid_layout:171 :param row:172 :return:173 """174 label_wdget = UI.Widget(class__attr="QLabel", name="setting")175 label_property = UI.Property()176 label_property.set_name("text")177 text_label = UI.String()178 text_label.set_valueOf_(label)179 label_property.set_string(text_label)180 label_wdget.add_property(label_property)181 checkbox_text_label = UI.String()182 checkbox_text_label.set_valueOf_(label + "_check")183 checkbox_label_property = UI.Property()184 checkbox_label_property.set_name("text")185 checkbox_label_property.set_string(checkbox_text_label)186 check_box = UI.Widget(class__attr="QCheckBox", name="edit_setting_" + label)187 checked_property = UI.Property(bool=str(checked).lower(), name="checked")188 check_box.add_property(checked_property)189 check_box.add_property(checkbox_label_property)190 grid_layout.add_item(UI.LayoutItem(row=row, column=0, widget=label_wdget))191 grid_layout.add_item(UI.LayoutItem(row=row, column=1, widget=check_box))192# FIXME: Fiinish this function193def __add_form_dropdown_row(label: str, grid_layout: UI.Layout, row, checked: bool = False):194 """195 Adds a label and a QLineEdit on the same row of grid_layout196 :param label:197 :param grid_layout:198 :param row:199 :return:200 """201 label_wdget = UI.Widget(class__attr="QComboBox", name="setting")202 label_property = UI.Property()203 label_property.set_name("text")204 text_label = UI.String()205 text_label.set_valueOf_(label)206 label_property.set_string(text_label)207 label_wdget.add_property(label_property)208 dropdown_text_label = UI.String()209 dropdown_text_label.set_valueOf_(label + "_check")210 checkbox_label_property = UI.Property()211 checkbox_label_property.set_name("text")212 checkbox_label_property.set_string(dropdown_text_label)213 check_box = UI.Widget(class__attr="QCheckBox", name="edit_setting_" + label)214 checked_property = UI.Property(bool=str(checked).lower(), name="checked")215 check_box.add_property(checked_property)216 check_box.add_property(checkbox_label_property)217 grid_layout.add_item(UI.LayoutItem(row=row, column=0, widget=label_wdget))218 grid_layout.add_item(UI.LayoutItem(row=row, column=1, widget=check_box))219def from_schema_to_widget(schema: dict):220 widget_container = UI.Widget(class__attr="QWidget", name="YAMLForm")221 rect_property = UI.Property()222 rect_property.set_name("geometry")223 rect_property.set_rect(UI.Rect(width=400, height=400, x=0, y=0))...
mixins.py
Source:mixins.py
...45 value: Any) -> None:46 result_type = self.Results[attr_name]47 if hasattr(result_type, 'set_valueOf_'):48 wrapper_object = result_type()49 wrapper_object.set_valueOf_(value)50 value = wrapper_object51 result_dict[attr_name] = value52 def implements_scalar_result(self):53 "ÐейÑÑвие должно возвÑаÑаÑÑ ÐµÐ´Ð¸Ð½ÑÑвенное знаÑение"...
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