CDTK package

Subpackages

• CDTK.Dynamics package
  • Subpackages
    • CDTK.Dynamics.Models package
      • Submodules
      • Module contents
  • Submodules
    • CDTK.Dynamics.Constraints module
      • Constraints
    • CDTK.Dynamics.EhrenfestDyn module
      • EhrenfestDyn
    • CDTK.Dynamics.FieldCouplings module
      • FieldCouplings
    • CDTK.Dynamics.IniConSampler module
      • IniConSampler
      • bwd_fft()
      • get_omega()
      • rotation()
      • sampleRotation()
      • sampler_zero_point_energy()
      • sampler_zero_point_energy_rpmd()
    • CDTK.Dynamics.InputfileSH module
      • Inputfile_SurfaceHopping
    • CDTK.Dynamics.MCElectronDynamics module
      • ElectronicState
    • CDTK.Dynamics.MDIntegrators module
      • velocityVerlet()
    • CDTK.Dynamics.MINTF_DH module
      • Idx2Str()
      • flatten_list()
      • getAO_Coeff()
      • getAO_NOCC()
      • getCI_Cplmat()
      • getCI_Energy()
      • getCI_Gradient()
      • getCharge_onAtom()
      • runMolcasDHCplmat()
      • runMolcasDHEnergyGradient()
      • runMolcasDHGradient()
      • runMolcasHFKoopmansAOCoeff()
    • CDTK.Dynamics.MINTF_HFKEE module
      • getAO_Coeff()
      • getAO_NOCC()
      • getHFKoopmans_Cplmat()
      • getHFKoopmans_Energy()
      • getHFKoopmans_Gradient()
      • runMolcasHFKoopmansAOCoeff()
      • runMolcasHFKoopmansCplmat()
      • runMolcasHFKoopmansEnergy()
      • runMolcasHFKoopmansGradient()
    • CDTK.Dynamics.MINTF_ScfOrb module
      • getAO_Coeff()
      • getAO_NOCC()
      • getHFKoopmans_Cplmat()
      • getHFKoopmans_Energy()
      • getHFKoopmans_Gradient()
      • runMolcasHFKoopmansCplmat()
      • runMolcasHFKoopmansEnergy()
      • runMolcasHFKoopmansGradient()
    • CDTK.Dynamics.MolcasInterfaceSH module
      • getAOCoeff_mld()
      • getAO_Coeff()
      • getAO_NOCC()
      • getCASSCF_AnalyticalGrad()
      • getCASSCF_AnalyticalGradMultElecS()
      • getCASSCF_Cplmat()
      • getCASSCF_Energy()
      • getHFKoopmans_Cplmat()
      • getHFKoopmans_Energy()
      • getHFKoopmans_Gradient()
      • getKoopmans_Energy()
      • getTAS_DipEn()
      • load_input()
      • runMolcasAOCoeff()
      • runMolcasCplmat()
      • runMolcasEnergy()
      • runMolcasGradient()
      • runMolcasGradientMultElecS()
      • runMolcasHFKoopmansAOCoeff()
      • runMolcasHFKoopmansCplmat()
      • runMolcasHFKoopmansCplmatAlter()
      • runMolcasHFKoopmansEnergy()
      • runMolcasHFKoopmansGradient()
      • runMolcasKoopmansEnergy()
      • runMolcasTASpectra()
    • CDTK.Dynamics.ObservableCharge module
      • ObservableCharge
    • CDTK.Dynamics.ObservableEE module
      • ObservableEE
    • CDTK.Dynamics.ObservableEH module
      • ObservableEH
    • CDTK.Dynamics.ObservableTAS module
      • ObservableTAS
    • CDTK.Dynamics.QChemInterface module
      • flatten_float_list()
      • flatten_list()
      • getHF_Energy()
      • get_NMode()
      • load_input()
      • load_qchem()
      • runQchem()
      • runQchemNMode()
      • save_qchem()
    • CDTK.Dynamics.QChemInterface2 module
      • getHF_Energy()
      • getHartreeFockEnergy()
      • runQchem()
    • CDTK.Dynamics.SimulationBox module
      • SimulationBox
      • load()
    • CDTK.Dynamics.SimulationBox2 module
      • SimulationBox
      • load()
    • CDTK.Dynamics.SurfaceHoppingFS module
      • SurfaceHoppingFS
    • CDTK.Dynamics.SurfaceHoppingLZ module
      • SurfaceHoppingLZ
    • CDTK.Dynamics.SurfaceHoppingLZ2 module
      • SurfaceHoppingLZController
      • gap_parameters()
      • hopping_probability()
      • is_hopp()
      • is_hopp_energy()
      • velocity_correction()
    • CDTK.Dynamics.Thermostat module
      • Thermostat
    • CDTK.Dynamics.Tools module
      • calcCM()
      • energy_partition()
      • erot()
      • etrans()
      • evib()
      • flatten_list()
      • inertiaTensor()
      • internalcoords()
      • jtot()
      • principalAxes()
      • pvib()
      • velautocor()
      • veltoCM()
      • veltoprincipal()
    • CDTK.Dynamics.Trajectory module
      • Trajectory
    • CDTK.Dynamics.Trajectory_SH module
      • Trajectory_SH
      • W11_TA()
      • W11_TB()
      • W12_TA()
      • W12_TB()
      • W22_TA()
      • W22_TB()
      • W_TA()
      • W_TB()
      • dot()
      • dq_W11_TA()
      • dq_W11_TB()
      • dq_W12_TA()
      • dq_W12_TB()
      • dq_W22_TA()
      • dq_W22_TB()
      • return_TullyA_traj()
      • return_TullyB_traj()
      • run_TullyA()
      • run_TullyA_Fig4()
      • run_TullyB()
      • run_TullyB_Fig5()
    • CDTK.Dynamics.populationdynamic module
  • Module contents
• CDTK.Interfaces package
  • Submodules
    • CDTK.Interfaces.EmbeddingInterface module
      • embedding
    • CDTK.Interfaces.ForceField module
      • forcefield
      • furfuralFF
      • jointForceFields
      • ureaFF
      • waterFF_SPC
      • waterFF_SPCE
      • waterFF_TIP4P
      • waterFF_TIP4P2005
      • waterFF_TIP4P2005f
    • CDTK.Interfaces.GamessUSInterface module
      • gamess
      • parse_hessian()
    • CDTK.Interfaces.Interpolation_Interface module
      • interpolation
    • CDTK.Interfaces.MolcasInterface module
      • SmatrixFromOverlapMatrix()
      • molcas
      • readOverlapMatrix()
    • CDTK.Interfaces.WrapperInterface module
      • wrapperInterface
    • CDTK.Interfaces.XMoleculeInterface module
  • Module contents
• CDTK.Models package
  • Submodules
    • CDTK.Models.Coulomb module
      • Coulomb
    • CDTK.Models.DiabaticToAdiabatic2States module
      • DiabaticToAdiabatic2States
    • CDTK.Models.DoubleACM module
      • DoubleACM
    • CDTK.Models.HarmonicOsc module
      • HarmonicOsc
    • CDTK.Models.MDiabats module
      • MultDiabats
    • CDTK.Models.SimpleACM module
      • SimpleACM
    • CDTK.Models.TullyA module
      • W11_TA()
      • W12_TA()
      • W22_TA()
      • W_TA()
      • dq_W11_TA()
      • dq_W12_TA()
      • dq_W22_TA()
      • f_D()
      • f_EGrad()
      • f_NAC()
      • f_W()
  • Module contents
• CDTK.Tools package
  • Submodules
    • CDTK.Tools.Bath module
      • bathModeDensity()
      • listOfFrequenciesFromDistribution()
      • modeCouplings()
      • spectralDensityOhmic()
    • CDTK.Tools.Conversion module
      • factor()
      • numval()
      • stringToBool()
      • va2wcm2()
      • wcm22va()
    • CDTK.Tools.EField module
      • EField
      • gaussian_envelope()
    • CDTK.Tools.GaussianLog module
      • g03toVTF()
      • getAtomNumber()
      • getBOMD()
      • getCoordinates()
      • getMasses()
      • getNormalMode()
      • getNormalModeFreq()
      • getSCFEnergy()
      • getSymbols()
      • hasHighPrecisionModes()
      • tester()
    • CDTK.Tools.Geometry module
      • Coordinate
      • XYZGeometry
      • angularMomentumEckart()
      • centerOfMass()
      • eckartFrame()
      • inertiaTensor()
      • pbc_translation_matrix()
      • pbc_translation_vectors()
      • rotateGeometry()
    • CDTK.Tools.Inputfile module
      • Inputfile
    • CDTK.Tools.Iterators module
      • MultiCombination
      • MultiCounter
      • decreaseTuple()
      • excitations()
      • excitationsN()
      • mapTuple()
    • CDTK.Tools.Mathematics module
      • Convolution()
      • ENOInterpolation()
      • FourierTransform()
      • GaussianFunction()
      • WignerQuantumStep()
      • WignerStep()
      • WignerStep1D()
      • WignerWalkQuantumStep()
      • alignMatrix()
      • angle()
      • boltzmann_weights()
      • bssrSumOfStates()
      • calc_rdf()
      • classicalSumOfStates()
      • compute_density()
      • convolutionFilter()
      • corrspec()
      • cubicSplineInterpolation()
      • distributeMatrix()
      • distributeMatrixList()
      • distributionFromList()
      • dkron()
      • eulerMatrix()
      • gaussian_moments()
      • generateOrthonormalSpace()
      • gramSchmidt()
      • hprod_phi()
      • hprod_phi2()
      • ijk_shape()
      • invert_reg()
      • isPositiveDefinite()
      • krylov()
      • lag()
      • leviCivita()
      • linealInterpolation()
      • makeMesh()
      • matrix_tensor()
      • matrix_tensor2()
      • metropolisIntStep()
      • metropolisStep()
      • ndimIntGrid()
      • ndimIntPoint()
      • onedimInt()
      • overlap()
      • ovrMatrix()
      • ovrMatrix2()
      • pointsDistance()
      • pointsVector()
      • randomWalkIntStep()
      • randomWalkStep()
      • richardson()
      • rmsError()
      • rodriguesMatrix()
      • scattered2grid2D()
      • schroedinger_to_interaction()
      • sortEigValsVecs()
      • sphericalAngles()
      • toPositiveDefinite()
      • uniformPointsWithinSphere()
      • vector_tensor()
      • voigtConvolution()
      • wignerE()
      • wignerEFT()
      • wignerHarmonic1D()
      • wignerHarmonicFT1D()
      • wignerHarmonicFTND()
      • wignerHarmonicND()
    • CDTK.Tools.MolecularMechanics module
      • MolecularMechanics
    • CDTK.Tools.NormalCoordinates module
      • Coordinate
      • NormalMode
      • Projector
      • XYZGeometry
      • aunits2wavenumber()
      • centerOfMass()
      • closeListOfFiles()
      • inertiaTensor()
      • modesOrthonormalization()
      • openOutputFileList0()
      • openOutputFileList1()
      • openOutputFiles()
      • openOutputFilesProd()
      • outputEnerToFiles()
      • outputGradToFiles()
      • outputHessToFiles()
      • rangeOfModesFromGaussian()
      • rangeOfModesFromMatrix()
      • stringToFiles()
    • CDTK.Tools.NormalModeAnalysis module
      • normal_modes_from_HessianCart()
      • q_mw_to_x()
    • CDTK.Tools.NumericalDerivatives module
      • gradient()
      • hessian()
    • CDTK.Tools.OutputGrabber module
      • suppress_stdout()
      • suppress_stdoutstderr()
    • CDTK.Tools.TaylorAPES module
      • atomic_masses()
      • calc_coefficients()
      • calc_coeffs_cross()
      • calc_coeffs_cross_koopmans()
      • calc_coeffs_diag()
      • calc_coeffs_diag_koopmans()
      • cda_crossterm()
      • cda_curvature()
      • cda_gradient()
      • coeffs_x_to_q_mfw()
      • main()
      • nm_translate()
      • parse_gamess_options()
      • shift_energies_zero()
      • write_coefficients()
      • write_mctdh_op()
    • CDTK.Tools.Utils module
      • ReverseArray()
      • ShiftArray()
      • atomicCoordinatesFromRlog()
      • changeIsotopeSymbols()
      • fileLineParser()
      • getDataFromLog()
      • getDateString()
      • getDenTable()
      • getDirectoryList()
      • getNextTime()
      • getPopTable()
      • getTrajectoryTimeSteps()
      • getUniqueID()
      • listToFile()
      • loadDataStruct()
      • readAuto()
      • readColumnFile()
      • readFile()
      • readRlogRestricted()
      • readTableFile()
      • readTag()
      • readTagFromFile()
      • saveDataStruct()
      • traj2vtf()
      • traj2xyz()
    • CDTK.Tools.VibronicCouplingModel module
      • VibronicCouplingModel
      • coherence()
      • get_dm_t()
      • rdcheck_OK()
      • rdgpop_OK()
      • rho()
      • trace_squared()
    • CDTK.Tools.WaterModel module
      • angle_bending_potential()
      • coulomb_potential()
      • get_m_site_xyz()
      • lennard_jones_gradient()
      • lennard_jones_potential()
      • morse_potential()
      • water_to_point_charge()
    • CDTK.Tools.XPYDERCreator module
      • XPYDERCreator
      • el_string()
  • Module contents

Submodules

• CDTK.an_absorptionCS module
• CDTK.an_coord module
  • start()
• CDTK.an_coreEnergies module
• CDTK.an_getHessian module
  • start()
• CDTK.an_plt_rho1D module
  • start()
• CDTK.an_plt_rho2D module
  • start()
• CDTK.an_runall module
  • start()
• CDTK.an_traj2vtf module
  • start()
• CDTK.an_waterGeom module
  • start()
• CDTK.analyze module
  • angle()
  • bootstrap()
  • charge()
  • correlation_function()
  • doFourrier()
  • doParse()
  • getBins()
  • getParser()
  • kinetic()
  • observable()
  • operate()
  • outputBins()
  • outputData()
  • outputNtraj()
  • position()
  • red()
  • spec()
  • start()
  • state()
  • velocity()
• CDTK.cdtk2hdf5 module
  • parseCommandLine()
  • readAtomData()
  • readChargeLog()
  • readCoefLog()
  • readCoordLog()
  • readCurrentChargeLog()
  • readDir()
  • readEnergyLog()
  • readEventLog()
  • readLog()
  • readOccLog()
  • readPulseLog()
  • readStateLog()
  • readTrivCrossLog()
  • readVadLog()
  • start()
• CDTK.cdtk2xyz module
  • get_arg()
  • start()
• CDTK.gmx2cdtk module
  • atomName2Element()
  • atomName2atomMass()
  • atomName2atomNum()
  • get_coord_center()
  • get_parser()
  • makeResiduesWhole()
  • print_geom_files()
  • print_xpyder()
  • print_xsample()
  • readgmx()
  • readtrr()
  • shift_box()
  • sort_molec()
  • start()
  • writegmx()
  • writetrr()
• CDTK.gmxtopol2ffclass module
  • get_arg()
  • parse_top()
  • start()
• CDTK.xmodel module
  • start()
  • terminate()
• CDTK.xpyder module
  • start()
• CDTK.xsample module
  • start()

Module contents