Index

A

A() (CDTK.Tools.EField.EField method) add_ehrenfest_dynamics_cntrl() (CDTK.Dynamics.SimulationBox.SimulationBox method) add_field_coupling_cntrl() (CDTK.Dynamics.SimulationBox.SimulationBox method) add_observable_cntrl() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) add_population_dynamics_cntrl() (CDTK.Dynamics.SimulationBox.SimulationBox method) add_surface_hopping_cntrl() (CDTK.Dynamics.SimulationBox.SimulationBox method) alignMatrix() (in module CDTK.Tools.Mathematics) angle() (in module CDTK.analyze) (in module CDTK.Tools.Mathematics)

angle_bending_potential() (in module CDTK.Tools.WaterModel) angularMomentumEckart() (in module CDTK.Tools.Geometry) apply() (CDTK.Dynamics.Thermostat.Thermostat method) atomic_masses() (in module CDTK.Tools.TaylorAPES) atomicCoordinatesFromRlog() (in module CDTK.Tools.Utils) atomName2atomMass() (in module CDTK.gmx2cdtk) atomName2atomNum() (in module CDTK.gmx2cdtk) atomName2Element() (in module CDTK.gmx2cdtk) atomPositions (CDTK.Tools.Geometry.XYZGeometry property) aunits2wavenumber() (in module CDTK.Tools.NormalCoordinates)

B

bathModeDensity() (in module CDTK.Tools.Bath) boltzmann_weights() (in module CDTK.Tools.Mathematics) bootstrap() (in module CDTK.analyze)

bssrSumOfStates() (in module CDTK.Tools.Mathematics) burnin() (CDTK.Dynamics.IniConSampler.IniConSampler method) bwd_fft() (in module CDTK.Dynamics.IniConSampler)

C

c_ix (CDTK.Tools.XPYDERCreator.XPYDERCreator property) calc_coefficients() (in module CDTK.Tools.TaylorAPES) calc_coeffs_cross() (in module CDTK.Tools.TaylorAPES) calc_coeffs_cross_koopmans() (in module CDTK.Tools.TaylorAPES) calc_coeffs_diag() (in module CDTK.Tools.TaylorAPES) calc_coeffs_diag_koopmans() (in module CDTK.Tools.TaylorAPES) calc_rdf() (in module CDTK.Tools.Mathematics) calcCM() (in module CDTK.Dynamics.Tools) cartesianProjector() (CDTK.Tools.Geometry.XYZGeometry method) cartesianRotationVector() (CDTK.Tools.Geometry.XYZGeometry method) cartesianTranslationVector() (CDTK.Tools.Geometry.XYZGeometry method) cartesianVectors() (CDTK.Tools.Geometry.XYZGeometry method) cartHessian() (CDTK.Tools.NormalCoordinates.XYZGeometry method) cartMassWeightHessian() (CDTK.Tools.NormalCoordinates.XYZGeometry method) cda_crossterm() (in module CDTK.Tools.TaylorAPES) cda_curvature() (in module CDTK.Tools.TaylorAPES) cda_gradient() (in module CDTK.Tools.TaylorAPES) CDTK module CDTK.an_coord module CDTK.an_getHessian module CDTK.an_plt_rho1D module CDTK.an_plt_rho2D module CDTK.an_runall module CDTK.an_traj2vtf module CDTK.an_waterGeom module CDTK.analyze module CDTK.cdtk2hdf5 module CDTK.cdtk2xyz module CDTK.Dynamics module CDTK.Dynamics.Constraints module CDTK.Dynamics.EhrenfestDyn module CDTK.Dynamics.FieldCouplings module CDTK.Dynamics.IniConSampler module CDTK.Dynamics.InputfileSH module CDTK.Dynamics.MCElectronDynamics module CDTK.Dynamics.MDIntegrators module CDTK.Dynamics.MINTF_DH module CDTK.Dynamics.MINTF_HFKEE module CDTK.Dynamics.MINTF_ScfOrb module CDTK.Dynamics.Models module CDTK.Dynamics.Models.C2H2_3p module CDTK.Dynamics.Models.testModels module CDTK.Dynamics.MolcasInterfaceSH module CDTK.Dynamics.ObservableCharge module CDTK.Dynamics.ObservableEE module CDTK.Dynamics.ObservableEH module CDTK.Dynamics.ObservableTAS module CDTK.Dynamics.QChemInterface module CDTK.Dynamics.QChemInterface2 module CDTK.Dynamics.SimulationBox module CDTK.Dynamics.SimulationBox2 module CDTK.Dynamics.SurfaceHoppingFS module CDTK.Dynamics.SurfaceHoppingLZ module CDTK.Dynamics.SurfaceHoppingLZ2 module CDTK.Dynamics.Thermostat module CDTK.Dynamics.Tools module CDTK.Dynamics.Trajectory module CDTK.Dynamics.Trajectory_SH module CDTK.gmx2cdtk module CDTK.gmxtopol2ffclass module CDTK.Interfaces module

CDTK.Interfaces.EmbeddingInterface module CDTK.Interfaces.ForceField module CDTK.Interfaces.GamessUSInterface module CDTK.Interfaces.Interpolation_Interface module CDTK.Interfaces.MolcasInterface module CDTK.Interfaces.WrapperInterface module CDTK.Models module CDTK.Models.Coulomb module CDTK.Models.DiabaticToAdiabatic2States module CDTK.Models.DoubleACM module CDTK.Models.HarmonicOsc module CDTK.Models.MDiabats module CDTK.Models.SimpleACM module CDTK.Models.TullyA module CDTK.Tools module CDTK.Tools.Bath module CDTK.Tools.Conversion module CDTK.Tools.EField module CDTK.Tools.GaussianLog module CDTK.Tools.Geometry module CDTK.Tools.Inputfile module CDTK.Tools.Iterators module CDTK.Tools.Mathematics module CDTK.Tools.MolecularMechanics module CDTK.Tools.NormalCoordinates module CDTK.Tools.NormalModeAnalysis module CDTK.Tools.NumericalDerivatives module CDTK.Tools.OutputGrabber module CDTK.Tools.TaylorAPES module CDTK.Tools.Utils module CDTK.Tools.VibronicCouplingModel module CDTK.Tools.WaterModel module CDTK.Tools.XPYDERCreator module CDTK.xmodel module CDTK.xpyder module CDTK.xsample module centerGeometry() (CDTK.Tools.Geometry.XYZGeometry method) centerMolecule() (CDTK.Tools.NormalCoordinates.XYZGeometry method) centerOfMass() (CDTK.Tools.Geometry.XYZGeometry method) (CDTK.Tools.NormalCoordinates.XYZGeometry method) (in module CDTK.Tools.Geometry) (in module CDTK.Tools.NormalCoordinates) centerOfMassVelocity() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) changeIsotopeSymbols() (in module CDTK.Tools.Utils) charge() (in module CDTK.analyze) check_constraints() (CDTK.Dynamics.Constraints.Constraints method) check_input() (CDTK.Dynamics.InputfileSH.Inputfile_SurfaceHopping method) classicalSumOfStates() (in module CDTK.Tools.Mathematics) closeListOfFiles() (in module CDTK.Tools.NormalCoordinates) coeffs_x_to_q_mfw() (in module CDTK.Tools.TaylorAPES) coherence() (in module CDTK.Tools.VibronicCouplingModel) compute_density() (in module CDTK.Tools.Mathematics) conjugateSpace() (CDTK.Tools.NormalCoordinates.Projector method) Constraints (class in CDTK.Dynamics.Constraints) convert_waveform_unit() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) Convolution() (in module CDTK.Tools.Mathematics) convolutionFilter() (in module CDTK.Tools.Mathematics) Coordinate (class in CDTK.Tools.Geometry) (class in CDTK.Tools.NormalCoordinates) coordinates (CDTK.Tools.Geometry.Coordinate property) coordinatesToFile() (CDTK.Tools.NormalCoordinates.XYZGeometry method) correlation_function() (in module CDTK.analyze) corrspec() (in module CDTK.Tools.Mathematics) Coulomb (class in CDTK.Models.Coulomb) coulomb_egrad() (CDTK.Interfaces.ForceField.jointForceFields method) coulomb_potential() (in module CDTK.Tools.WaterModel) create_cluster_geometry() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) crossing2D() (in module CDTK.Dynamics.Models.testModels) cubicSplineInterpolation() (in module CDTK.Tools.Mathematics)

D

decay_of_mixing() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) decreaseTuple() (in module CDTK.Tools.Iterators) DiabaticToAdiabatic2States (class in CDTK.Models.DiabaticToAdiabatic2States) distance_min() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) distributeMatrix() (in module CDTK.Tools.Mathematics) distributeMatrixList() (in module CDTK.Tools.Mathematics) distributionFromList() (in module CDTK.Tools.Mathematics) dkron() (in module CDTK.Tools.Mathematics) doFourrier() (in module CDTK.analyze) doParse() (in module CDTK.analyze) dot() (in module CDTK.Dynamics.Trajectory_SH)

DoubleACM (class in CDTK.Models.DoubleACM) dq_W11_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) dq_W11_TB() (in module CDTK.Dynamics.Trajectory_SH) dq_W12_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) dq_W12_TB() (in module CDTK.Dynamics.Trajectory_SH) dq_W22_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) dq_W22_TB() (in module CDTK.Dynamics.Trajectory_SH) dt_efield() (CDTK.Interfaces.GamessUSInterface.gamess method) (CDTK.Interfaces.Interpolation_Interface.interpolation method)

E

E() (CDTK.Tools.EField.EField method) eAngles (CDTK.Interfaces.ForceField.forcefield attribute) eBonds (CDTK.Interfaces.ForceField.forcefield attribute) eckartFrame() (in module CDTK.Tools.Geometry) eCoul (CDTK.Interfaces.ForceField.forcefield attribute) eDihdedral (CDTK.Interfaces.ForceField.forcefield attribute) EField (class in CDTK.Tools.EField) efield() (CDTK.Interfaces.GamessUSInterface.gamess method) (CDTK.Interfaces.Interpolation_Interface.interpolation method) EhrenfestDyn (class in CDTK.Dynamics.EhrenfestDyn) el_string() (in module CDTK.Tools.XPYDERCreator) ElectronicState (class in CDTK.Dynamics.MCElectronDynamics) embedding (class in CDTK.Interfaces.EmbeddingInterface) energy() (CDTK.Tools.NormalCoordinates.XYZGeometry method) energy_CIS() (CDTK.Interfaces.GamessUSInterface.gamess method) energy_gradient() (CDTK.Interfaces.EmbeddingInterface.embedding method)

energy_gradient_HF() (CDTK.Interfaces.GamessUSInterface.gamess method) energy_HF() (CDTK.Interfaces.GamessUSInterface.gamess method) energy_HF_HOMO() (CDTK.Interfaces.GamessUSInterface.gamess method) energy_HF_KOOPMANS() (CDTK.Interfaces.GamessUSInterface.gamess method) energy_partition() (in module CDTK.Dynamics.Tools) enforceConstraints() (CDTK.Dynamics.Constraints.Constraints method) (CDTK.Interfaces.EmbeddingInterface.embedding method) (CDTK.Interfaces.ForceField.jointForceFields method) ENOInterpolation() (in module CDTK.Tools.Mathematics) eNonbonbded (CDTK.Interfaces.ForceField.forcefield attribute) Envelope() (CDTK.Tools.EField.EField method) erot() (in module CDTK.Dynamics.Tools) etrans() (in module CDTK.Dynamics.Tools) eulerMatrix() (in module CDTK.Tools.Mathematics) evib() (in module CDTK.Dynamics.Tools) excitations() (in module CDTK.Tools.Iterators) excitationsN() (in module CDTK.Tools.Iterators)

F

f_D() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) (in module CDTK.Models.TullyA) f_Dmu() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_E() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_E_Grd() (CDTK.Interfaces.Interpolation_Interface.interpolation method) f_EGrad() (in module CDTK.Models.TullyA) f_EGrad_ES() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_EGrad_GS() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_EGrad_NA() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_MOE() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) f_NAC() (CDTK.Interfaces.Interpolation_Interface.interpolation method) (CDTK.Interfaces.WrapperInterface.wrapperInterface method) (in module CDTK.Models.TullyA) f_overlap() (CDTK.Interfaces.EmbeddingInterface.embedding method) (CDTK.Interfaces.WrapperInterface.wrapperInterface method)

f_TD() (CDTK.Interfaces.Interpolation_Interface.interpolation method) f_W() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) (in module CDTK.Models.TullyA) factor() (in module CDTK.Tools.Conversion) FieldCouplings (class in CDTK.Dynamics.FieldCouplings) fileLineParser() (in module CDTK.Tools.Utils) flatten_float_list() (in module CDTK.Dynamics.QChemInterface) flatten_list() (in module CDTK.Dynamics.MINTF_DH) (in module CDTK.Dynamics.QChemInterface) (in module CDTK.Dynamics.Tools) forcefield (class in CDTK.Interfaces.ForceField) FourierTransform() (in module CDTK.Tools.Mathematics) frequencyFromMode() (CDTK.Tools.NormalCoordinates.XYZGeometry method) fromArray() (CDTK.Tools.NormalCoordinates.Projector method) furfuralFF (class in CDTK.Interfaces.ForceField)

G

g03toVTF() (in module CDTK.Tools.GaussianLog) gamess (class in CDTK.Interfaces.GamessUSInterface) gap_parameters() (in module CDTK.Dynamics.SurfaceHoppingLZ2) gaussian_envelope() (in module CDTK.Tools.EField) gaussian_moments() (in module CDTK.Tools.Mathematics) GaussianFunction() (in module CDTK.Tools.Mathematics) gbs (CDTK.Tools.XPYDERCreator.XPYDERCreator property) generateOrthonormalSpace() (in module CDTK.Tools.Mathematics) geomFromGaussian() (CDTK.Tools.NormalCoordinates.XYZGeometry method) geomWithVirtualSites() (CDTK.Interfaces.ForceField.jointForceFields method) get_arg() (in module CDTK.cdtk2xyz) (in module CDTK.gmxtopol2ffclass) get_coord_center() (in module CDTK.gmx2cdtk) get_correction_r() (CDTK.Dynamics.Constraints.Constraints method) get_correction_v() (CDTK.Dynamics.Constraints.Constraints method) get_dg0dg1_matrix() (CDTK.Dynamics.Constraints.Constraints method) get_dm_t() (in module CDTK.Tools.VibronicCouplingModel) get_funcDPL() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) get_funcE() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) (CDTK.Dynamics.SurfaceHoppingLZ.SurfaceHoppingLZ method) get_funcG() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) (CDTK.Dynamics.SurfaceHoppingLZ.SurfaceHoppingLZ method) get_funcVD() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) get_m_site_xyz() (in module CDTK.Tools.WaterModel) get_NMode() (in module CDTK.Dynamics.QChemInterface) get_occ() (CDTK.Interfaces.Interpolation_Interface.interpolation method) get_omega() (in module CDTK.Dynamics.IniConSampler) get_parser() (in module CDTK.gmx2cdtk) get_prob_FS() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) get_xuvpes_targetpath() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) getAdiabaticPopulation() (CDTK.Dynamics.SimulationBox.SimulationBox method) getAO_Coeff() (in module CDTK.Dynamics.MINTF_DH) (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) getAO_NOCC() (in module CDTK.Dynamics.MINTF_DH) (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) getAOCoeff_mld() (in module CDTK.Dynamics.MolcasInterfaceSH) getAtomNumber() (in module CDTK.Tools.GaussianLog) getAtomPositions() (CDTK.Tools.Geometry.XYZGeometry method) getBins() (in module CDTK.analyze) getBOMD() (in module CDTK.Tools.GaussianLog) getBonded() (CDTK.Interfaces.ForceField.forcefield method) getCASSCF_AnalyticalGrad() (in module CDTK.Dynamics.MolcasInterfaceSH) getCASSCF_AnalyticalGradMultElecS() (in module CDTK.Dynamics.MolcasInterfaceSH) getCASSCF_Cplmat() (in module CDTK.Dynamics.MolcasInterfaceSH) getCASSCF_Energy() (in module CDTK.Dynamics.MolcasInterfaceSH) getCharge() (CDTK.Dynamics.ObservableCharge.ObservableCharge method) getCharge_onAtom() (in module CDTK.Dynamics.MINTF_DH) getCharges() (CDTK.Interfaces.ForceField.forcefield method) getCI_Cplmat() (in module CDTK.Dynamics.MINTF_DH) getCI_Energy() (in module CDTK.Dynamics.MINTF_DH) getCI_Gradient() (in module CDTK.Dynamics.MINTF_DH) getCOM() (CDTK.Dynamics.Trajectory.Trajectory method) getConstraints() (CDTK.Interfaces.ForceField.forcefield method) getConstraintsCorrection() (CDTK.Interfaces.EmbeddingInterface.embedding method) getCoordinates() (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.NormalCoordinates.Coordinate method) (in module CDTK.Tools.GaussianLog) getCplMatrixElement() (CDTK.Models.DoubleACM.DoubleACM method) (CDTK.Models.HarmonicOsc.HarmonicOsc method) (CDTK.Models.MDiabats.MultDiabats method) (CDTK.Models.SimpleACM.SimpleACM method) getD() (CDTK.Interfaces.EmbeddingInterface.embedding method) getDataFromLog() (in module CDTK.Tools.Utils) getDateString() (in module CDTK.Tools.Utils) getDenTable() (in module CDTK.Tools.Utils) getDipoleEnergyTAS() (CDTK.Dynamics.ObservableTAS.ObservableTAS method) getDirectoryList() (in module CDTK.Tools.Utils) getDressedVd() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getDressedVd_dUdt() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getElecHolePosition() (CDTK.Dynamics.ObservableEE.ObservableEE method) (CDTK.Dynamics.ObservableEH.ObservableEH method) getElectricField() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getEnGrad() (CDTK.Interfaces.ForceField.jointForceFields method) getEpF_D_Umat() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getGamma() (CDTK.Interfaces.Interpolation_Interface.interpolation method) getGaussianPulse() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getHartreeFockEnergy() (in module CDTK.Dynamics.QChemInterface2) getHF_Energy() (in module CDTK.Dynamics.QChemInterface) (in module CDTK.Dynamics.QChemInterface2)

getHFKoopmans_Cplmat() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) getHFKoopmans_Energy() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) getHFKoopmans_Gradient() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) getKineticEnergy() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getKoopmans_Energy() (in module CDTK.Dynamics.MolcasInterfaceSH) getLabels() (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.Geometry.XYZGeometry method) getLimits() (CDTK.Tools.Iterators.MultiCounter method) getLJCombRule() (CDTK.Interfaces.ForceField.forcefield method) getLJeps() (CDTK.Interfaces.ForceField.forcefield method) getLJsigma() (CDTK.Interfaces.ForceField.forcefield method) getMapAO_Atom() (CDTK.Dynamics.ObservableEE.ObservableEE method) (CDTK.Dynamics.ObservableEH.ObservableEH method) getMasses() (CDTK.Interfaces.ForceField.forcefield method) (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.Geometry.XYZGeometry method) (CDTK.Tools.NormalCoordinates.Coordinate method) (in module CDTK.Tools.GaussianLog) getMat() (CDTK.Tools.NormalCoordinates.Projector method) getModeNumber() (CDTK.Tools.NormalCoordinates.NormalMode method) getMomentum() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getNextTime() (in module CDTK.Tools.Utils) getNonBondedInteractionPairs() (CDTK.Interfaces.ForceField.forcefield method) getNonBondedInteractionPairsFudgeLJ() (CDTK.Interfaces.ForceField.forcefield method) getNonBondedInteractionPairsFudgeQQ() (CDTK.Interfaces.ForceField.forcefield method) getNormalMode() (in module CDTK.Tools.GaussianLog) getNormalModeFreq() (in module CDTK.Tools.GaussianLog) getParser() (in module CDTK.analyze) getPartialCharges() (CDTK.Interfaces.EmbeddingInterface.embedding method) (CDTK.Interfaces.Interpolation_Interface.interpolation method) getPbcDims() (CDTK.Tools.Geometry.XYZGeometry method) getPointers() (CDTK.Tools.Iterators.MultiCounter method) getPopTable() (in module CDTK.Tools.Utils) getPotEnergy() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getPotentialFunction() (CDTK.Models.Coulomb.Coulomb method) (CDTK.Models.DoubleACM.DoubleACM method) (CDTK.Models.HarmonicOsc.HarmonicOsc method) (CDTK.Models.MDiabats.MultDiabats method) (CDTK.Models.SimpleACM.SimpleACM method) getProperty2D_F() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getPropertyTable() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getPropertyTableDir_E() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getPropertyTableDir_F() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getRattleCorrection() (CDTK.Interfaces.ForceField.jointForceFields method) getReducedMass() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getRotationalEnergy() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getSCFEnergy() (in module CDTK.Tools.GaussianLog) getSigmaNuc() (CDTK.Interfaces.ForceField.forcefield method) getSinusoidalPulse() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getSymbols() (CDTK.Tools.NormalCoordinates.Coordinate method) (in module CDTK.Tools.GaussianLog) getTAS_DipEn() (in module CDTK.Dynamics.MolcasInterfaceSH) getTrajectoryTimeSteps() (in module CDTK.Tools.Utils) getTranslationalEnergy() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getUniqueID() (in module CDTK.Tools.Utils) getUserDefinedPulse() (CDTK.Dynamics.FieldCouplings.FieldCouplings method) getVGeom() (CDTK.Interfaces.ForceField.forcefield method) (CDTK.Interfaces.ForceField.waterFF_TIP4P method) getVibrationalEnergy() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getVibrationalMomentum() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) getW() (CDTK.Interfaces.EmbeddingInterface.embedding method) gradient() (CDTK.Tools.NormalCoordinates.XYZGeometry method) (in module CDTK.Tools.NumericalDerivatives) gradient_ED() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) gradient_FS() (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) gradient_LZ() (CDTK.Dynamics.SurfaceHoppingLZ.SurfaceHoppingLZ method) gradient_simple() (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) gradient_virt2orig() (CDTK.Interfaces.ForceField.jointForceFields method) gradientElement() (CDTK.Tools.NormalCoordinates.XYZGeometry method) gramSchmidt() (in module CDTK.Tools.Mathematics) grd() (in module CDTK.Dynamics.Models.C2H2_3p)

H

HarmonicOsc (class in CDTK.Models.HarmonicOsc) hasConstraints() (CDTK.Interfaces.EmbeddingInterface.embedding method) (CDTK.Interfaces.ForceField.forcefield method) hasHighPrecisionModes() (in module CDTK.Tools.GaussianLog) hasVirtualSite() (CDTK.Interfaces.ForceField.forcefield method) (CDTK.Interfaces.ForceField.waterFF_TIP4P method)

hessian() (CDTK.Interfaces.GamessUSInterface.gamess method) (CDTK.Tools.NormalCoordinates.XYZGeometry method) (in module CDTK.Tools.NumericalDerivatives) hessianElement() (CDTK.Tools.NormalCoordinates.XYZGeometry method) hopping_probability() (in module CDTK.Dynamics.SurfaceHoppingLZ2) hprod_phi() (in module CDTK.Tools.Mathematics) hprod_phi2() (in module CDTK.Tools.Mathematics)

I

ic (CDTK.Tools.XPYDERCreator.XPYDERCreator property) Idx2Str() (in module CDTK.Dynamics.MINTF_DH) ijk_shape() (in module CDTK.Tools.Mathematics) increase() (CDTK.Tools.Iterators.MultiCounter method) inertiaTensor() (in module CDTK.Dynamics.Tools) (in module CDTK.Tools.Geometry) (in module CDTK.Tools.NormalCoordinates) IniConSampler (class in CDTK.Dynamics.IniConSampler) init_from_input_options() (CDTK.Tools.EField.EField method) init_input_options() (CDTK.Dynamics.Thermostat.Thermostat method) (CDTK.Interfaces.GamessUSInterface.gamess method) (CDTK.Interfaces.Interpolation_Interface.interpolation method) (CDTK.Interfaces.MolcasInterface.molcas method) init_log() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method) init_samplewigner() (CDTK.Dynamics.IniConSampler.IniConSampler method)

init_wigner() (CDTK.Dynamics.IniConSampler.IniConSampler method) initLogs() (CDTK.Dynamics.MCElectronDynamics.ElectronicState method) Inputfile (class in CDTK.Tools.Inputfile) Inputfile_SurfaceHopping (class in CDTK.Dynamics.InputfileSH) integrate() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method) intensity (CDTK.Tools.XPYDERCreator.XPYDERCreator property) internalcoords() (in module CDTK.Dynamics.Tools) interpolation (class in CDTK.Interfaces.Interpolation_Interface) invert_reg() (in module CDTK.Tools.Mathematics) is_gap_min_down() (CDTK.Dynamics.SurfaceHoppingLZ2.SurfaceHoppingLZController method) is_gap_min_up() (CDTK.Dynamics.SurfaceHoppingLZ2.SurfaceHoppingLZController method) is_hopp() (in module CDTK.Dynamics.SurfaceHoppingLZ2) is_hopp_energy() (in module CDTK.Dynamics.SurfaceHoppingLZ2) isPositiveDefinite() (in module CDTK.Tools.Mathematics)

J

jointForceFields (class in CDTK.Interfaces.ForceField)

jtot() (in module CDTK.Dynamics.Tools)

K

kinetic() (in module CDTK.analyze) kinetic_energy() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method)

krylov() (in module CDTK.Tools.Mathematics)

L

labels (CDTK.Tools.Geometry.Coordinate property) (CDTK.Tools.Geometry.XYZGeometry property) lag() (in module CDTK.Tools.Mathematics) lennard_jones_egrad() (CDTK.Interfaces.ForceField.jointForceFields method) lennard_jones_gradient() (in module CDTK.Tools.WaterModel) lennard_jones_potential() (in module CDTK.Tools.WaterModel) leviCivita() (in module CDTK.Tools.Mathematics) linealInterpolation() (in module CDTK.Tools.Mathematics) linear_interpolate() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) linear_interpolate_Vd() (CDTK.Dynamics.EhrenfestDyn.EhrenfestDyn method) (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) listOfFrequenciesFromDistribution() (in module CDTK.Tools.Bath) listToFile() (in module CDTK.Tools.Utils)

load() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) (in module CDTK.Dynamics.SimulationBox) (in module CDTK.Dynamics.SimulationBox2) load_input() (in module CDTK.Dynamics.MolcasInterfaceSH) (in module CDTK.Dynamics.QChemInterface) load_qchem() (in module CDTK.Dynamics.QChemInterface) loadDataStruct() (in module CDTK.Tools.Utils) loadDirectory() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) log() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method) log_to_file() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method)

M

main() (in module CDTK.Tools.TaylorAPES) makeMesh() (in module CDTK.Tools.Mathematics) makeResiduesWhole() (in module CDTK.gmx2cdtk) mapTuple() (in module CDTK.Tools.Iterators) masses (CDTK.Tools.Geometry.Coordinate property) (CDTK.Tools.Geometry.XYZGeometry property) massFromGaussian() (CDTK.Tools.NormalCoordinates.Coordinate method) matrix_tensor() (in module CDTK.Tools.Mathematics) matrix_tensor2() (in module CDTK.Tools.Mathematics) mcqdpt() (CDTK.Interfaces.GamessUSInterface.gamess method) mcscf() (CDTK.Interfaces.GamessUSInterface.gamess method) md_type (CDTK.Tools.XPYDERCreator.XPYDERCreator property) metropolisIntStep() (in module CDTK.Tools.Mathematics) metropolisStep() (in module CDTK.Tools.Mathematics) mm_region_to_input() (CDTK.Interfaces.WrapperInterface.wrapperInterface method) mm_to_point_charge() (CDTK.Tools.MolecularMechanics.MolecularMechanics method) modeCouplings() (in module CDTK.Tools.Bath) modeFromGaussian() (CDTK.Tools.NormalCoordinates.NormalMode method) modeReducedMass() (CDTK.Tools.NormalCoordinates.NormalMode method) modesOrthonormalization() (in module CDTK.Tools.NormalCoordinates) module CDTK CDTK.an_coord CDTK.an_getHessian CDTK.an_plt_rho1D CDTK.an_plt_rho2D CDTK.an_runall CDTK.an_traj2vtf CDTK.an_waterGeom CDTK.analyze CDTK.cdtk2hdf5 CDTK.cdtk2xyz CDTK.Dynamics CDTK.Dynamics.Constraints CDTK.Dynamics.EhrenfestDyn CDTK.Dynamics.FieldCouplings CDTK.Dynamics.IniConSampler CDTK.Dynamics.InputfileSH CDTK.Dynamics.MCElectronDynamics CDTK.Dynamics.MDIntegrators CDTK.Dynamics.MINTF_DH CDTK.Dynamics.MINTF_HFKEE CDTK.Dynamics.MINTF_ScfOrb CDTK.Dynamics.Models CDTK.Dynamics.Models.C2H2_3p CDTK.Dynamics.Models.testModels CDTK.Dynamics.MolcasInterfaceSH CDTK.Dynamics.ObservableCharge CDTK.Dynamics.ObservableEE CDTK.Dynamics.ObservableEH CDTK.Dynamics.ObservableTAS CDTK.Dynamics.QChemInterface CDTK.Dynamics.QChemInterface2 CDTK.Dynamics.SimulationBox CDTK.Dynamics.SimulationBox2 CDTK.Dynamics.SurfaceHoppingFS CDTK.Dynamics.SurfaceHoppingLZ CDTK.Dynamics.SurfaceHoppingLZ2 CDTK.Dynamics.Thermostat CDTK.Dynamics.Tools CDTK.Dynamics.Trajectory CDTK.Dynamics.Trajectory_SH CDTK.gmx2cdtk CDTK.gmxtopol2ffclass CDTK.Interfaces CDTK.Interfaces.EmbeddingInterface CDTK.Interfaces.ForceField CDTK.Interfaces.GamessUSInterface CDTK.Interfaces.Interpolation_Interface CDTK.Interfaces.MolcasInterface CDTK.Interfaces.WrapperInterface CDTK.Models CDTK.Models.Coulomb CDTK.Models.DiabaticToAdiabatic2States CDTK.Models.DoubleACM CDTK.Models.HarmonicOsc CDTK.Models.MDiabats CDTK.Models.SimpleACM CDTK.Models.TullyA CDTK.Tools CDTK.Tools.Bath CDTK.Tools.Conversion CDTK.Tools.EField CDTK.Tools.GaussianLog CDTK.Tools.Geometry CDTK.Tools.Inputfile CDTK.Tools.Iterators CDTK.Tools.Mathematics CDTK.Tools.MolecularMechanics CDTK.Tools.NormalCoordinates CDTK.Tools.NormalModeAnalysis CDTK.Tools.NumericalDerivatives CDTK.Tools.OutputGrabber CDTK.Tools.TaylorAPES CDTK.Tools.Utils CDTK.Tools.VibronicCouplingModel CDTK.Tools.WaterModel CDTK.Tools.XPYDERCreator CDTK.xmodel CDTK.xpyder CDTK.xsample

module() (CDTK.Tools.NormalCoordinates.Coordinate method) molcas (class in CDTK.Interfaces.MolcasInterface) molCOMs (CDTK.Tools.XPYDERCreator.XPYDERCreator property) MolecularMechanics (class in CDTK.Tools.MolecularMechanics) molecule2FF (CDTK.Interfaces.ForceField.jointForceFields attribute) momentsOfInertia() (CDTK.Tools.Geometry.XYZGeometry method) (CDTK.Tools.NormalCoordinates.XYZGeometry method) morse_potential() (in module CDTK.Tools.WaterModel) MultDiabats (class in CDTK.Models.MDiabats) MultiCombination (class in CDTK.Tools.Iterators) MultiCounter (class in CDTK.Tools.Iterators)

N

n_QM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) n_tot (CDTK.Tools.XPYDERCreator.XPYDERCreator property) nac() (CDTK.Interfaces.EmbeddingInterface.embedding method) nacme() (CDTK.Interfaces.GamessUSInterface.gamess method) name() (CDTK.Interfaces.ForceField.forcefield method) ndimIntGrid() (in module CDTK.Tools.Mathematics) ndimIntPoint() (in module CDTK.Tools.Mathematics) next() (CDTK.Tools.Iterators.MultiCombination method) (CDTK.Tools.Iterators.MultiCounter method)

nm2x_coord() (CDTK.Dynamics.IniConSampler.IniConSampler method) nm_translate() (in module CDTK.Tools.TaylorAPES) normal_modes_from_HessianCart() (in module CDTK.Tools.NormalModeAnalysis) normalize() (CDTK.Tools.NormalCoordinates.NormalMode method) NormalMode (class in CDTK.Tools.NormalCoordinates) numConstraints() (CDTK.Interfaces.ForceField.forcefield method) numval() (in module CDTK.Tools.Conversion)

O

observable() (in module CDTK.analyze) ObservableCharge (class in CDTK.Dynamics.ObservableCharge) ObservableEE (class in CDTK.Dynamics.ObservableEE) ObservableEH (class in CDTK.Dynamics.ObservableEH) ObservableTAS (class in CDTK.Dynamics.ObservableTAS) onedimInt() (in module CDTK.Tools.Mathematics) openOutputFileList0() (in module CDTK.Tools.NormalCoordinates) openOutputFileList1() (in module CDTK.Tools.NormalCoordinates) openOutputFiles() (in module CDTK.Tools.NormalCoordinates) openOutputFilesProd() (in module CDTK.Tools.NormalCoordinates)

operate() (in module CDTK.analyze) optimize() (CDTK.Interfaces.GamessUSInterface.gamess method) outputBins() (in module CDTK.analyze) outputData() (in module CDTK.analyze) outputEnerToFiles() (in module CDTK.Tools.NormalCoordinates) outputGradToFiles() (in module CDTK.Tools.NormalCoordinates) outputHessToFiles() (in module CDTK.Tools.NormalCoordinates) outputNtraj() (in module CDTK.analyze) overlap() (in module CDTK.Tools.Mathematics) ovrMatrix() (in module CDTK.Tools.Mathematics) ovrMatrix2() (in module CDTK.Tools.Mathematics)

P

parse_gamess_options() (in module CDTK.Tools.TaylorAPES) parse_hessian() (in module CDTK.Interfaces.GamessUSInterface) parse_top() (in module CDTK.gmxtopol2ffclass) parseCommandLine() (in module CDTK.cdtk2hdf5) pbc_dims (CDTK.Tools.XPYDERCreator.XPYDERCreator property) pbc_translation_matrix() (in module CDTK.Tools.Geometry) pbc_translation_vectors() (in module CDTK.Tools.Geometry) pbcDims (CDTK.Tools.Geometry.XYZGeometry property) pe() (CDTK.Interfaces.Interpolation_Interface.interpolation method) plot() (CDTK.Tools.EField.EField method) pointsDistance() (in module CDTK.Tools.Mathematics) pointsVector() (in module CDTK.Tools.Mathematics)

position() (in module CDTK.analyze) pot() (in module CDTK.Dynamics.Models.C2H2_3p) principalAxes() (in module CDTK.Dynamics.Tools) print_geom_files() (in module CDTK.gmx2cdtk) print_parameters() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) print_xpyder() (in module CDTK.gmx2cdtk) print_xsample() (in module CDTK.gmx2cdtk) projectionToModeS() (CDTK.Tools.NormalCoordinates.XYZGeometry method) Projector (class in CDTK.Tools.NormalCoordinates) projectorRot() (CDTK.Tools.NormalCoordinates.XYZGeometry method) projectorTrans() (CDTK.Tools.NormalCoordinates.XYZGeometry method) projectorTransRot() (CDTK.Tools.NormalCoordinates.XYZGeometry method) pvib() (in module CDTK.Dynamics.Tools)

Q

q_mw_to_x() (in module CDTK.Tools.NormalModeAnalysis)

qmmmRepEgrad() (CDTK.Interfaces.EmbeddingInterface.embedding method)

R

r_xyz (CDTK.Tools.XPYDERCreator.XPYDERCreator property) r_xyz_MM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) r_xyz_QM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) radiusGyration() (CDTK.Tools.Geometry.XYZGeometry method) randomWalkIntStep() (in module CDTK.Tools.Mathematics) randomWalkStep() (in module CDTK.Tools.Mathematics) rangeOfModesFromGaussian() (in module CDTK.Tools.NormalCoordinates) rangeOfModesFromMatrix() (in module CDTK.Tools.NormalCoordinates) rasci() (CDTK.Interfaces.MolcasInterface.molcas method) rasci_D() (CDTK.Interfaces.MolcasInterface.molcas method) rasci_D_num() (CDTK.Interfaces.MolcasInterface.molcas method) rate() (CDTK.Dynamics.MCElectronDynamics.ElectronicState method) rdcheck_OK() (in module CDTK.Tools.VibronicCouplingModel) rdgpop_OK() (in module CDTK.Tools.VibronicCouplingModel) read_cp2k_trajectory() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) read_gromacs_trajectory() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) read_input_template() (CDTK.Interfaces.GamessUSInterface.gamess method) read_lammps_trajectory() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) readAtomData() (in module CDTK.cdtk2hdf5) readAuto() (in module CDTK.Tools.Utils) readChargeLog() (in module CDTK.cdtk2hdf5) readCoefLog() (in module CDTK.cdtk2hdf5) readColumnFile() (in module CDTK.Tools.Utils) readCoordLog() (in module CDTK.cdtk2hdf5) readCurrentChargeLog() (in module CDTK.cdtk2hdf5) readDir() (in module CDTK.cdtk2hdf5) readEnergyLog() (in module CDTK.cdtk2hdf5) readEventLog() (in module CDTK.cdtk2hdf5) readFile() (in module CDTK.Tools.Utils) readgmx() (in module CDTK.gmx2cdtk) readLog() (in module CDTK.cdtk2hdf5) readOccLog() (in module CDTK.cdtk2hdf5) readOverlapMatrix() (in module CDTK.Interfaces.MolcasInterface) readPulseLog() (in module CDTK.cdtk2hdf5) readRlogRestricted() (in module CDTK.Tools.Utils) readStateLog() (in module CDTK.cdtk2hdf5) readTableFile() (in module CDTK.Tools.Utils) readTag() (in module CDTK.Tools.Utils) readTagFromFile() (in module CDTK.Tools.Utils) readTrivCrossLog() (in module CDTK.cdtk2hdf5) readtrr() (in module CDTK.gmx2cdtk) readVadLog() (in module CDTK.cdtk2hdf5) red() (in module CDTK.analyze) removeCenterMassMotion() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) reset() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Tools.Iterators.MultiCounter method)

restart() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method) ret_dqV1() (CDTK.Models.DiabaticToAdiabatic2States.DiabaticToAdiabatic2States method) ret_dqV2() (CDTK.Models.DiabaticToAdiabatic2States.DiabaticToAdiabatic2States method) ret_NAC() (CDTK.Models.DiabaticToAdiabatic2States.DiabaticToAdiabatic2States method) ret_V1() (CDTK.Models.DiabaticToAdiabatic2States.DiabaticToAdiabatic2States method) ret_V2() (CDTK.Models.DiabaticToAdiabatic2States.DiabaticToAdiabatic2States method) return_TullyA_traj() (in module CDTK.Dynamics.Trajectory_SH) return_TullyB_traj() (in module CDTK.Dynamics.Trajectory_SH) ReverseArray() (in module CDTK.Tools.Utils) rho() (in module CDTK.Tools.VibronicCouplingModel) richardson() (in module CDTK.Tools.Mathematics) rmsError() (in module CDTK.Tools.Mathematics) rodriguesMatrix() (in module CDTK.Tools.Mathematics) rotateGeometry() (in module CDTK.Tools.Geometry) rotation() (in module CDTK.Dynamics.IniConSampler) run() (CDTK.Interfaces.GamessUSInterface.gamess method) run_mctdh() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) run_TullyA() (in module CDTK.Dynamics.Trajectory_SH) run_TullyA_Fig4() (in module CDTK.Dynamics.Trajectory_SH) run_TullyB() (in module CDTK.Dynamics.Trajectory_SH) run_TullyB_Fig5() (in module CDTK.Dynamics.Trajectory_SH) runMolcasAOCoeff() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasCplmat() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasDHCplmat() (in module CDTK.Dynamics.MINTF_DH) runMolcasDHEnergyGradient() (in module CDTK.Dynamics.MINTF_DH) runMolcasDHGradient() (in module CDTK.Dynamics.MINTF_DH) runMolcasEnergy() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasGradient() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasGradientMultElecS() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasHFKoopmansAOCoeff() (in module CDTK.Dynamics.MINTF_DH) (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasHFKoopmansCplmat() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasHFKoopmansCplmatAlter() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasHFKoopmansEnergy() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasHFKoopmansGradient() (in module CDTK.Dynamics.MINTF_HFKEE) (in module CDTK.Dynamics.MINTF_ScfOrb) (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasKoopmansEnergy() (in module CDTK.Dynamics.MolcasInterfaceSH) runMolcasTASpectra() (in module CDTK.Dynamics.MolcasInterfaceSH) runQchem() (in module CDTK.Dynamics.QChemInterface) (in module CDTK.Dynamics.QChemInterface2) runQchemNMode() (in module CDTK.Dynamics.QChemInterface)

S

sample() (CDTK.Dynamics.IniConSampler.IniConSampler method) sampleR() (CDTK.Dynamics.IniConSampler.IniConSampler method) sampler_boltzmann() (CDTK.Dynamics.IniConSampler.IniConSampler method) sampler_zero_point_energy() (in module CDTK.Dynamics.IniConSampler) sampler_zero_point_energy_rpmd() (in module CDTK.Dynamics.IniConSampler) sampleRotation() (in module CDTK.Dynamics.IniConSampler) sampleW() (CDTK.Dynamics.IniConSampler.IniConSampler method) sampleWigner() (CDTK.Dynamics.IniConSampler.IniConSampler method) save() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) save_qchem() (in module CDTK.Dynamics.QChemInterface) saveDataStruct() (in module CDTK.Tools.Utils) scattered2grid2D() (in module CDTK.Tools.Mathematics) schroedinger_to_interaction() (in module CDTK.Tools.Mathematics) set_constraints() (CDTK.Dynamics.Trajectory.Trajectory method) (CDTK.Dynamics.Trajectory_SH.Trajectory_SH method) set_double_gaussian_pulse() (CDTK.Tools.EField.EField method) set_gaussian_pulse() (CDTK.Tools.EField.EField method) set_occ() (CDTK.Interfaces.Interpolation_Interface.interpolation method) set_spf() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) set_xixfn() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) setAngstrom() (CDTK.Tools.NormalCoordinates.Coordinate method) setAtomPositions() (CDTK.Tools.Geometry.XYZGeometry method) setCoordinates() (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.NormalCoordinates.Coordinate method) setLabels() (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.Geometry.XYZGeometry method) setLimits() (CDTK.Tools.Iterators.MultiCounter method) setLimitsN() (CDTK.Tools.Iterators.MultiCounter method) setMasses() (CDTK.Tools.Geometry.Coordinate method) (CDTK.Tools.Geometry.XYZGeometry method) (CDTK.Tools.NormalCoordinates.Coordinate method) setMassWeighted() (CDTK.Tools.NormalCoordinates.Coordinate method) setMassWeightedAu() (CDTK.Tools.NormalCoordinates.Coordinate method) setMat() (CDTK.Tools.NormalCoordinates.Projector method) setMaxIter() (CDTK.Tools.Iterators.MultiCounter method) setMaxIterN() (CDTK.Tools.Iterators.MultiCounter method) setModeNumber() (CDTK.Tools.NormalCoordinates.NormalMode method) setPbcDims() (CDTK.Tools.Geometry.XYZGeometry method) setPointers() (CDTK.Tools.Iterators.MultiCounter method) setPointersN() (CDTK.Tools.Iterators.MultiCounter method) setSymbols() (CDTK.Tools.NormalCoordinates.Coordinate method)

shift_box() (in module CDTK.gmx2cdtk) shift_energies_zero() (in module CDTK.Tools.TaylorAPES) ShiftArray() (in module CDTK.Tools.Utils) SimpleACM (class in CDTK.Models.SimpleACM) SimulationBox (class in CDTK.Dynamics.SimulationBox) (class in CDTK.Dynamics.SimulationBox2) SmatrixFromOverlapMatrix() (in module CDTK.Interfaces.MolcasInterface) sort_molec() (in module CDTK.gmx2cdtk) sort_trajectory() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) sortEigValsVecs() (in module CDTK.Tools.Mathematics) spatial_resolution() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) spec() (in module CDTK.analyze) spectralDensityOhmic() (in module CDTK.Tools.Bath) sphericalAngles() (in module CDTK.Tools.Mathematics) start() (in module CDTK.an_coord) (in module CDTK.an_getHessian) (in module CDTK.an_plt_rho1D) (in module CDTK.an_plt_rho2D) (in module CDTK.an_runall) (in module CDTK.an_traj2vtf) (in module CDTK.an_waterGeom) (in module CDTK.analyze) (in module CDTK.cdtk2hdf5) (in module CDTK.cdtk2xyz) (in module CDTK.gmx2cdtk) (in module CDTK.gmxtopol2ffclass) (in module CDTK.xmodel) (in module CDTK.xpyder) (in module CDTK.xsample) state() (in module CDTK.analyze) step() (CDTK.Dynamics.MCElectronDynamics.ElectronicState method) stop_protect() (CDTK.Dynamics.SimulationBox.SimulationBox method) stringToBool() (in module CDTK.Tools.Conversion) stringToFiles() (in module CDTK.Tools.NormalCoordinates) suppress_stdout() (in module CDTK.Tools.OutputGrabber) suppress_stdoutstderr() (in module CDTK.Tools.OutputGrabber) SurfaceHoppingFS (class in CDTK.Dynamics.SurfaceHoppingFS) SurfaceHoppingLZ (class in CDTK.Dynamics.SurfaceHoppingLZ) SurfaceHoppingLZController (class in CDTK.Dynamics.SurfaceHoppingLZ2) switch_condition() (CDTK.Dynamics.SurfaceHoppingFS.SurfaceHoppingFS method) (CDTK.Dynamics.SurfaceHoppingLZ.SurfaceHoppingLZ method) symbolsFromGaussian() (CDTK.Tools.NormalCoordinates.Coordinate method)

T

t (CDTK.Tools.XPYDERCreator.XPYDERCreator property) target_dir (CDTK.Tools.XPYDERCreator.XPYDERCreator property) terminate() (in module CDTK.xmodel) tester() (in module CDTK.Tools.GaussianLog) tetrahedron() (in module CDTK.Dynamics.Models.testModels) Thermostat (class in CDTK.Dynamics.Thermostat) thz (CDTK.Tools.XPYDERCreator.XPYDERCreator property) toAngstroms() (CDTK.Tools.NormalCoordinates.Coordinate method) toAu() (CDTK.Tools.NormalCoordinates.Coordinate method) toMassWeighted() (CDTK.Tools.NormalCoordinates.Coordinate method) (CDTK.Tools.NormalCoordinates.NormalMode method) toPositiveDefinite() (in module CDTK.Tools.Mathematics) trace_squared() (in module CDTK.Tools.VibronicCouplingModel)

traj2VTF() (CDTK.Dynamics.SimulationBox.SimulationBox method) (CDTK.Dynamics.SimulationBox2.SimulationBox method) traj2vtf() (in module CDTK.Tools.Utils) traj2xyz() (in module CDTK.Tools.Utils) traj_path (CDTK.Tools.XPYDERCreator.XPYDERCreator property) Trajectory (class in CDTK.Dynamics.Trajectory) Trajectory_SH (class in CDTK.Dynamics.Trajectory_SH) trajXeh2VTF() (CDTK.Dynamics.ObservableEE.ObservableEE method) (CDTK.Dynamics.ObservableEH.ObservableEH method) translate() (CDTK.Tools.Geometry.XYZGeometry method) (CDTK.Tools.NormalCoordinates.XYZGeometry method) types (CDTK.Tools.XPYDERCreator.XPYDERCreator property) types_MM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) types_QM (CDTK.Tools.XPYDERCreator.XPYDERCreator property)

U

uniformPointsWithinSphere() (in module CDTK.Tools.Mathematics) unweightCoordinates() (CDTK.Tools.NormalCoordinates.Coordinate method) (CDTK.Tools.NormalCoordinates.NormalMode method) update() (CDTK.Dynamics.SurfaceHoppingLZ2.SurfaceHoppingLZController method)

update_grad_mm_mm() (CDTK.Tools.MolecularMechanics.MolecularMechanics method) update_grad_mm_qm() (CDTK.Tools.MolecularMechanics.MolecularMechanics method) update_potentials() (CDTK.Dynamics.SurfaceHoppingLZ2.SurfaceHoppingLZController method) ureaFF (class in CDTK.Interfaces.ForceField)

V

v_xyz (CDTK.Tools.XPYDERCreator.XPYDERCreator property) v_xyz_MM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) v_xyz_QM (CDTK.Tools.XPYDERCreator.XPYDERCreator property) va2wcm2() (in module CDTK.Tools.Conversion) vector_tensor() (in module CDTK.Tools.Mathematics) velautocor() (in module CDTK.Dynamics.Tools) velocity() (in module CDTK.analyze)

velocity_correction() (in module CDTK.Dynamics.SurfaceHoppingLZ2) velocityVerlet() (in module CDTK.Dynamics.MDIntegrators) veltoCM() (in module CDTK.Dynamics.Tools) veltoprincipal() (in module CDTK.Dynamics.Tools) velWithVirtualSites() (CDTK.Interfaces.ForceField.jointForceFields method) VibronicCouplingModel (class in CDTK.Tools.VibronicCouplingModel) voigtConvolution() (in module CDTK.Tools.Mathematics)

W

W11_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) W11_TB() (in module CDTK.Dynamics.Trajectory_SH) W12_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) W12_TB() (in module CDTK.Dynamics.Trajectory_SH) W22_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) W22_TB() (in module CDTK.Dynamics.Trajectory_SH) W_TA() (in module CDTK.Dynamics.Trajectory_SH) (in module CDTK.Models.TullyA) W_TB() (in module CDTK.Dynamics.Trajectory_SH) water_model (CDTK.Tools.XPYDERCreator.XPYDERCreator property) water_to_point_charge() (in module CDTK.Tools.WaterModel) waterFF_SPC (class in CDTK.Interfaces.ForceField) waterFF_SPCE (class in CDTK.Interfaces.ForceField) waterFF_TIP4P (class in CDTK.Interfaces.ForceField) waterFF_TIP4P2005 (class in CDTK.Interfaces.ForceField) waterFF_TIP4P2005f (class in CDTK.Interfaces.ForceField) wcm22va() (in module CDTK.Tools.Conversion) wignerE() (in module CDTK.Tools.Mathematics)

wignerEFT() (in module CDTK.Tools.Mathematics) wignerHarmonic1D() (in module CDTK.Tools.Mathematics) wignerHarmonicFT1D() (in module CDTK.Tools.Mathematics) wignerHarmonicFTND() (in module CDTK.Tools.Mathematics) wignerHarmonicND() (in module CDTK.Tools.Mathematics) WignerQuantumStep() (in module CDTK.Tools.Mathematics) WignerStep() (in module CDTK.Tools.Mathematics) WignerStep1D() (in module CDTK.Tools.Mathematics) WignerWalkQuantumStep() (in module CDTK.Tools.Mathematics) wrapperInterface (class in CDTK.Interfaces.WrapperInterface) write_coefficients() (in module CDTK.Tools.TaylorAPES) write_inp() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) write_log() (CDTK.Dynamics.MCElectronDynamics.ElectronicState method) write_logs() (CDTK.Dynamics.MCElectronDynamics.ElectronicState method) write_mctdh_op() (in module CDTK.Tools.TaylorAPES) write_op() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) write_results() (CDTK.Tools.VibronicCouplingModel.VibronicCouplingModel method) write_xpyder_inputfile() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) write_xuvpes_inputfile() (CDTK.Tools.XPYDERCreator.XPYDERCreator method) writegmx() (in module CDTK.gmx2cdtk) writeLog() (CDTK.Tools.EField.EField method) writetrr() (in module CDTK.gmx2cdtk)

X

XPYDERCreator (class in CDTK.Tools.XPYDERCreator)

XYZGeometry (class in CDTK.Tools.Geometry) (class in CDTK.Tools.NormalCoordinates)

Y

yes_embed (CDTK.Tools.XPYDERCreator.XPYDERCreator property)