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
    • EField.A()
    • EField.E()
    • EField.Envelope()
    • EField.init_from_input_options()
    • EField.plot()
    • EField.set_double_gaussian_pulse()
    • EField.set_gaussian_pulse()
    • EField.writeLog()
  • gaussian_envelope()
• CDTK.Tools.GaussianLog module
  • g03toVTF()
  • getAtomNumber()
  • getBOMD()
  • getCoordinates()
  • getMasses()
  • getNormalMode()
  • getNormalModeFreq()
  • getSCFEnergy()
  • getSymbols()
  • hasHighPrecisionModes()
  • tester()
• CDTK.Tools.Geometry module
  • Coordinate
    • Coordinate.coordinates
    • Coordinate.getCoordinates()
    • Coordinate.getLabels()
    • Coordinate.getMasses()
    • Coordinate.labels
    • Coordinate.masses
    • Coordinate.setCoordinates()
    • Coordinate.setLabels()
    • Coordinate.setMasses()
  • XYZGeometry
    • XYZGeometry.atomPositions
    • XYZGeometry.cartesianProjector()
    • XYZGeometry.cartesianRotationVector()
    • XYZGeometry.cartesianTranslationVector()
    • XYZGeometry.cartesianVectors()
    • XYZGeometry.centerGeometry()
    • XYZGeometry.centerOfMass()
    • XYZGeometry.getAtomPositions()
    • XYZGeometry.getLabels()
    • XYZGeometry.getMasses()
    • XYZGeometry.getPbcDims()
    • XYZGeometry.labels
    • XYZGeometry.masses
    • XYZGeometry.momentsOfInertia()
    • XYZGeometry.pbcDims
    • XYZGeometry.radiusGyration()
    • XYZGeometry.setAtomPositions()
    • XYZGeometry.setLabels()
    • XYZGeometry.setMasses()
    • XYZGeometry.setPbcDims()
    • XYZGeometry.translate()
  • angularMomentumEckart()
  • centerOfMass()
  • eckartFrame()
  • inertiaTensor()
  • pbc_translation_matrix()
  • pbc_translation_vectors()
  • rotateGeometry()
• CDTK.Tools.Inputfile module
  • Inputfile
• CDTK.Tools.Iterators module
  • MultiCombination
    • MultiCombination.next()
  • MultiCounter
    • MultiCounter.getLimits()
    • MultiCounter.getPointers()
    • MultiCounter.increase()
    • MultiCounter.next()
    • MultiCounter.reset()
    • MultiCounter.setLimits()
    • MultiCounter.setLimitsN()
    • MultiCounter.setMaxIter()
    • MultiCounter.setMaxIterN()
    • MultiCounter.setPointers()
    • MultiCounter.setPointersN()
  • 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
    • MolecularMechanics.mm_to_point_charge()
    • MolecularMechanics.update_grad_mm_mm()
    • MolecularMechanics.update_grad_mm_qm()
• CDTK.Tools.NormalCoordinates module
  • Coordinate
    • Coordinate.getCoordinates()
    • Coordinate.getMasses()
    • Coordinate.getSymbols()
    • Coordinate.massFromGaussian()
    • Coordinate.module()
    • Coordinate.setAngstrom()
    • Coordinate.setCoordinates()
    • Coordinate.setMassWeighted()
    • Coordinate.setMassWeightedAu()
    • Coordinate.setMasses()
    • Coordinate.setSymbols()
    • Coordinate.symbolsFromGaussian()
    • Coordinate.toAngstroms()
    • Coordinate.toAu()
    • Coordinate.toMassWeighted()
    • Coordinate.unweightCoordinates()
  • NormalMode
    • NormalMode.getModeNumber()
    • NormalMode.modeFromGaussian()
    • NormalMode.modeReducedMass()
    • NormalMode.normalize()
    • NormalMode.setModeNumber()
    • NormalMode.toMassWeighted()
    • NormalMode.unweightCoordinates()
  • Projector
    • Projector.conjugateSpace()
    • Projector.fromArray()
    • Projector.getMat()
    • Projector.setMat()
  • XYZGeometry
    • XYZGeometry.cartHessian()
    • XYZGeometry.cartMassWeightHessian()
    • XYZGeometry.centerMolecule()
    • XYZGeometry.centerOfMass()
    • XYZGeometry.coordinatesToFile()
    • XYZGeometry.energy()
    • XYZGeometry.frequencyFromMode()
    • XYZGeometry.geomFromGaussian()
    • XYZGeometry.gradient()
    • XYZGeometry.gradientElement()
    • XYZGeometry.hessian()
    • XYZGeometry.hessianElement()
    • XYZGeometry.momentsOfInertia()
    • XYZGeometry.projectionToModeS()
    • XYZGeometry.projectorRot()
    • XYZGeometry.projectorTrans()
    • XYZGeometry.projectorTransRot()
    • XYZGeometry.translate()
  • 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
    • VibronicCouplingModel.distance_min()
    • VibronicCouplingModel.print_parameters()
    • VibronicCouplingModel.run_mctdh()
    • VibronicCouplingModel.set_spf()
    • VibronicCouplingModel.set_xixfn()
    • VibronicCouplingModel.spatial_resolution()
    • VibronicCouplingModel.write_inp()
    • VibronicCouplingModel.write_op()
    • VibronicCouplingModel.write_results()
  • 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
    • XPYDERCreator.c_ix
    • XPYDERCreator.create_cluster_geometry()
    • XPYDERCreator.gbs
    • XPYDERCreator.get_xuvpes_targetpath()
    • XPYDERCreator.ic
    • XPYDERCreator.intensity
    • XPYDERCreator.md_type
    • XPYDERCreator.molCOMs
    • XPYDERCreator.n_QM
    • XPYDERCreator.n_tot
    • XPYDERCreator.pbc_dims
    • XPYDERCreator.r_xyz
    • XPYDERCreator.r_xyz_MM
    • XPYDERCreator.r_xyz_QM
    • XPYDERCreator.read_cp2k_trajectory()
    • XPYDERCreator.read_gromacs_trajectory()
    • XPYDERCreator.read_lammps_trajectory()
    • XPYDERCreator.sort_trajectory()
    • XPYDERCreator.t
    • XPYDERCreator.target_dir
    • XPYDERCreator.thz
    • XPYDERCreator.traj_path
    • XPYDERCreator.types
    • XPYDERCreator.types_MM
    • XPYDERCreator.types_QM
    • XPYDERCreator.v_xyz
    • XPYDERCreator.v_xyz_MM
    • XPYDERCreator.v_xyz_QM
    • XPYDERCreator.water_model
    • XPYDERCreator.write_xpyder_inputfile()
    • XPYDERCreator.write_xuvpes_inputfile()
    • XPYDERCreator.yes_embed
  • el_string()

Module contents

TOOLS: a module for utilities