Index

_

__call__() (tamkin.nma.Transform method) (tamkin.nma.Treatment method) (tamkin.tunneling.Eckart method) (tamkin.tunneling.Miller method) (tamkin.tunneling.TunnelingCorrection method) (tamkin.tunneling.Wigner method)

A

ActivationKineticModel (class in tamkin.chemmod)

alter_freqs() (tamkin.chemmod.BaseModel method) AtomDivision (class in tamkin.nma)

B

backup_freqs() (tamkin.chemmod.BaseModel method) BareNucleus (class in tamkin.data)

BaseKineticModel (class in tamkin.chemmod) BaseModel (class in tamkin.chemmod) Blocks (class in tamkin.nma)

C

check_gradient() (tamkin.data.Molecule method) check_hessian() (tamkin.data.Molecule method) check_top_indexes() (tamkin.data.RotScan method) chemical_potential() (tamkin.partf.StatFys method) chemical_potential_terms() (tamkin.partf.StatFysTerms method) compute_cancel_frequency_mbh() (in module tamkin.rotor) compute_delta() (in module tamkin.nmatools) compute_hessian() (tamkin.nma.Constrain method) (tamkin.nma.ConstrainExt method) (tamkin.nma.Full method) (tamkin.nma.MBH method) (tamkin.nma.MBHConstrainExt method) (tamkin.nma.PHVA method) (tamkin.nma.PHVA_MBH method) (tamkin.nma.Treatment method) (tamkin.nma.VSA method) (tamkin.nma.VSANoMass method) compute_moments() (in module tamkin.rotor) compute_overlap() (in module tamkin.nmatools) compute_sensitivity_freq() (in module tamkin.nmatools)

compute_zeros() (tamkin.nma.Constrain method) (tamkin.nma.ConstrainExt method) (tamkin.nma.Full method) (tamkin.nma.MBH method) (tamkin.nma.MBHConstrainExt method) (tamkin.nma.PHVA method) (tamkin.nma.PHVA_MBH method) (tamkin.nma.Treatment method) (tamkin.nma.VSA method) (tamkin.nma.VSANoMass method) Constrain (class in tamkin.nma) constrain_ext() (tamkin.data.Molecule method) ConstrainExt (class in tamkin.nma) coordinates (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) cp (tamkin.partf.ExtTrans attribute) create_blocks_peptide_charmm() (in module tamkin.nmatools) create_enm_molecule() (in module tamkin.nmatools) create_subs_peptide_charmm() (in module tamkin.nmatools)

D

density (tamkin.partf.ExtTrans attribute) dihedral (tamkin.data.RotScan attribute) dump() (tamkin.chemmod.ActivationKineticModel method) (tamkin.chemmod.BaseModel method) (tamkin.chemmod.KineticModel method) (tamkin.chemmod.ThermodynamicModel method) (tamkin.partf.Electronic method) (tamkin.partf.ExtRot method) (tamkin.partf.ExtTrans method) (tamkin.partf.Info method) (tamkin.partf.PCMCorrection method) (tamkin.partf.PartFun method) (tamkin.partf.Vibrations method) (tamkin.pftools.ReactionAnalysis method) (tamkin.pftools.ThermoAnalysis method) (tamkin.pftools.ThermoTable method) (tamkin.rotor.Rotor method) (tamkin.timer.Timer method) (tamkin.tunneling.Eckart method) (tamkin.tunneling.Miller method) (tamkin.tunneling.TunnelingCorrection method) (tamkin.tunneling.Wigner method)

dump_chk() (in module tamkin.io.internal) dump_indices() (in module tamkin.io.internal) dump_modes_gaussian() (in module tamkin.io.trajectory) dump_modes_molden() (in module tamkin.io.trajectory) dump_modes_xyz() (in module tamkin.io.trajectory) dump_table() (tamkin.chemmod.BaseModel method) (tamkin.chemmod.KineticModel method) (tamkin.chemmod.ThermodynamicModel method) dump_values() (tamkin.partf.Info method)

E

Eckart (class in tamkin.tunneling) Electronic (class in tamkin.partf) energy (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) energy_difference() (tamkin.chemmod.BaseModel method) entropy() (tamkin.partf.StatFys method)

entropy_terms() (tamkin.partf.StatFysTerms method) equilibrium_constant() (tamkin.chemmod.BaseModel method) eval_deriv() (tamkin.rotor.HarmonicBasis method) eval_deriv2() (tamkin.rotor.HarmonicBasis method) eval_fn() (tamkin.rotor.HarmonicBasis method) external_basis (tamkin.data.Molecule attribute) ExtRot (class in tamkin.partf) ExtTrans (class in tamkin.partf)

F

fit_fn() (tamkin.rotor.HarmonicBasis method) fixed (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

free_energy() (tamkin.partf.StatFys method) free_energy_change() (tamkin.chemmod.BaseModel method) free_energy_terms() (tamkin.partf.StatFysTerms method) Full (class in tamkin.nma)

G

get_empty_op() (tamkin.rotor.HarmonicBasis method) get_external_basis_new() (tamkin.data.Molecule method) get_hamiltonian_op() (tamkin.rotor.HarmonicBasis method) get_submolecule() (tamkin.data.Molecule method) get_weighted() (tamkin.nma.Transform method) get_weighted_hessian() (tamkin.nma.MassMatrix method)

gradient (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) graph (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

H

HarmonicBasis (class in tamkin.rotor) heat_capacity() (tamkin.partf.StatFys method) heat_capacity_terms() (tamkin.partf.StatFysTerms method) helper() (tamkin.partf.Electronic method) (tamkin.partf.ExtRot method) (tamkin.partf.ExtTrans method) (tamkin.partf.PCMCorrection method) (tamkin.partf.PartFun method) (tamkin.partf.StatFys method) (tamkin.partf.StatFysTerms method) helper_levels() (in module tamkin.partf) helper_terms() (tamkin.partf.StatFysTerms method) (tamkin.partf.Vibrations method) (tamkin.rotor.Rotor method) helper_vibrations() (in module tamkin.partf) helpern() (tamkin.partf.ExtTrans method) (tamkin.partf.PartFun method) (tamkin.partf.StatFys method) (tamkin.partf.StatFysTerms method) helpern_terms() (tamkin.partf.StatFysTerms method) helpert() (tamkin.partf.Electronic method) (tamkin.partf.ExtRot method) (tamkin.partf.ExtTrans method) (tamkin.partf.PCMCorrection method) (tamkin.partf.PartFun method) (tamkin.partf.StatFys method) (tamkin.partf.StatFysTerms method)

helpert_levels() (in module tamkin.partf) helpert_terms() (tamkin.partf.StatFysTerms method) (tamkin.partf.Vibrations method) (tamkin.rotor.Rotor method) helpert_vibrations() (in module tamkin.partf) helpertt() (tamkin.partf.Electronic method) (tamkin.partf.ExtRot method) (tamkin.partf.ExtTrans method) (tamkin.partf.PCMCorrection method) (tamkin.partf.PartFun method) (tamkin.partf.StatFys method) (tamkin.partf.StatFysTerms method) helpertt_levels() (in module tamkin.partf) helpertt_terms() (tamkin.partf.StatFysTerms method) (tamkin.partf.Vibrations method) (tamkin.rotor.Rotor method) helpertt_vibrations() (in module tamkin.partf) helperv() (tamkin.partf.ExtTrans method) (tamkin.partf.PartFun method) (tamkin.partf.StatFys method) (tamkin.partf.StatFysTerms method) helperv_terms() (tamkin.partf.StatFysTerms method) hessian (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

I

Info (class in tamkin.partf) init_part_fun() (tamkin.partf.Electronic method) (tamkin.partf.ExtRot method) (tamkin.partf.ExtTrans method) (tamkin.partf.StatFys method) (tamkin.partf.Vibrations method) (tamkin.rotor.Rotor method)

internal_heat() (tamkin.partf.StatFys method) internal_heat_difference() (tamkin.chemmod.BaseModel method) internal_heat_terms() (tamkin.partf.StatFysTerms method)

K

KineticModel (class in tamkin.chemmod)

L

load_chk() (in module tamkin.io.internal) load_coordinates_charmm() (in module tamkin.io.charmm) load_fixed_cp2k() (in module tamkin.io.cp2k) load_fixed_g03com() (in module tamkin.io.gaussian) load_fixed_vasp() (in module tamkin.io.vasp) load_indices() (in module tamkin.io.internal) load_modes_charmm() (in module tamkin.io.charmm) load_molecule_charmm() (in module tamkin.io.charmm) load_molecule_cp2k() (in module tamkin.io.cp2k) load_molecule_cpmd() (in module tamkin.io.cpmd) load_molecule_g03fchk() (in module tamkin.io.gaussian) load_molecule_g98fchk() (in module tamkin.io.gaussian) load_molecule_qchem() (in module tamkin.io.qchem)

load_molecule_vasp() (in module tamkin.io.vasp) load_peptide_info_charmm() (in module tamkin.io.charmm) load_rotscan_g03log() (in module tamkin.io.gaussian) log() (tamkin.partf.StatFys method) log_terms() (tamkin.partf.StatFysTerms method) logn() (tamkin.partf.StatFys method) logn_terms() (tamkin.partf.StatFysTerms method) logt() (tamkin.partf.StatFys method) logt_terms() (tamkin.partf.StatFysTerms method) logtt() (tamkin.partf.StatFys method) logtt_terms() (tamkin.partf.StatFysTerms method) logv() (tamkin.partf.StatFys method) logv_terms() (tamkin.partf.StatFysTerms method)

M

make_weighted() (tamkin.nma.Transform method) masses (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) masses3 (tamkin.data.Molecule attribute) MassMatrix (class in tamkin.nma) MBH (class in tamkin.nma)

MBHConstrainExt (class in tamkin.nma) Miller (class in tamkin.tunneling) mobile (tamkin.partf.ExtTrans attribute) Molecule (class in tamkin.data) monte_carlo() (tamkin.pftools.ReactionAnalysis method) multiplicity (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

N

NMA (class in tamkin.nma) numbers (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

P

PartFun (class in tamkin.partf) PCMCorrection (class in tamkin.partf) periodic (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) PHVA (class in tamkin.nma) PHVA_MBH (class in tamkin.nma) plot_arrhenius() (tamkin.pftools.ReactionAnalysis method)

plot_levels() (tamkin.rotor.Rotor method) plot_parameters() (tamkin.pftools.ReactionAnalysis method) plot_spectrum_dos() (in module tamkin.nmatools) plot_spectrum_lines() (in module tamkin.nmatools) potential (tamkin.data.RotScan attribute) (tamkin.rotor.Rotor attribute) pressure (tamkin.partf.ExtTrans attribute) Proton (class in tamkin.data)

R

raise_ext() (tamkin.data.Molecule method) rank_linearity() (in module tamkin.geom) rate_constant() (tamkin.chemmod.ActivationKineticModel method) (tamkin.chemmod.BaseKineticModel method) (tamkin.chemmod.KineticModel method) ReactionAnalysis (class in tamkin.pftools)

read_from_file() (tamkin.data.Molecule class method) (tamkin.nma.NMA class method) restore_freqs() (tamkin.chemmod.BaseModel method) Rotor (class in tamkin.rotor) RotorError RotScan (class in tamkin.data)

S

sample() (tamkin.timer.Timer method) size (tamkin.rotor.HarmonicBasis attribute) solve() (tamkin.rotor.HarmonicBasis method) StatFys (class in tamkin.partf) StatFysTerms (class in tamkin.partf)

symbols (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) symmetry_number (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

T

tamkin.chemmod (module) tamkin.data (module) tamkin.geom (module) tamkin.io (module) tamkin.io.charmm (module) tamkin.io.cp2k (module) tamkin.io.cpmd (module) tamkin.io.gaussian (module) tamkin.io.internal (module) tamkin.io.qchem (module) tamkin.io.trajectory (module) tamkin.io.vasp (module) tamkin.nma (module) tamkin.nmatools (module) tamkin.partf (module) tamkin.pftools (module)

tamkin.rotor (module) tamkin.timer (module) tamkin.tunneling (module) ThermoAnalysis (class in tamkin.pftools) ThermodynamicModel (class in tamkin.chemmod) ThermoTable (class in tamkin.pftools) Timer (class in tamkin.timer) title (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute) top_indexes (tamkin.data.RotScan attribute) Transform (class in tamkin.nma) translate_pbc() (in module tamkin.data) transrot_basis() (in module tamkin.geom) Treatment (class in tamkin.nma) TunnelingCorrection (class in tamkin.tunneling)

U

unit_cell (tamkin.data.BareNucleus attribute) (tamkin.data.Molecule attribute) (tamkin.data.Proton attribute)

V

Vibrations (class in tamkin.partf)

VSA (class in tamkin.nma) VSANoMass (class in tamkin.nma)

W

weighted (tamkin.nma.Transform attribute) Wigner (class in tamkin.tunneling) write_overlap() (in module tamkin.nmatools) write_table() (tamkin.chemmod.BaseModel method) write_to_file() (tamkin.chemmod.BaseModel method) (tamkin.data.Molecule method) (tamkin.nma.NMA method) (tamkin.partf.PartFun method) (tamkin.pftools.ReactionAnalysis method) (tamkin.pftools.ThermoAnalysis method) (tamkin.timer.Timer method)

Z

zero_point_energy() (tamkin.partf.StatFys method)

zero_point_energy_difference() (tamkin.chemmod.BaseModel method) zero_point_energy_terms() (tamkin.partf.StatFysTerms method)