Index

_

_check_hierarchy_list() (HopsBasis method) _check_state_list() (HopsBasis method)

_determine_basis_from_list() (HopsBasis method) _determine_boundary_hier() (HopsBasis method) _determine_error_thresh() (HopsBasis static method)

A

AdaptiveTrajectoryStorage (class in mesohops.dynamics.hops_storage)

apply_filter() (HopsHierarchy method) AuxiliaryVector (class in mesohops.dynamics.hops_aux)

C

calc_delta_zmem() (in module mesohops.dynamics.eom_functions) calc_norm_corr() (in module mesohops.dynamics.eom_functions) calculate_ksuper() (in module mesohops.dynamics.eom_hops_ksuper)

check_long_edge() (in module mesohops.dynamics.hierarchy_functions) check_markovian() (in module mesohops.dynamics.hierarchy_functions) compress_zmem() (in module mesohops.dynamics.eom_functions)

D

define_basis() (HopsBasis method)

define_triangular_hierarchy() (HopsHierarchy static method) dot() (AuxiliaryVector method)

E

e_step() (AuxiliaryVector method) error_boundary_state() (HopsBasis method) error_deletion() (HopsBasis method) error_deriv() (HopsBasis method)

error_flux_down() (HopsBasis method) error_flux_up() (HopsBasis method) error_sflux_hier() (HopsBasis method) error_sflux_state() (HopsBasis method) error_stable_state() (HopsBasis method)

F

fft_filter_noise_diagonal() (FFTFilterNoise static method) FFTFilterNoise (class in mesohops.dynamics.noise_fft) filter_aux_list() (HopsHierarchy method)

filter_aux_longedge() (in module mesohops.dynamics.hierarchy_functions) filter_aux_triangular() (in module mesohops.dynamics.hierarchy_functions) filter_markovian() (in module mesohops.dynamics.hierarchy_functions)

G

get_noise() (HopsNoise method) (NumericNoiseTrajectory method) (ZeroNoise method)

get_values() (AuxiliaryVector method) get_values_nonzero() (AuxiliaryVector method)

H

hash_from_e_step() (AuxiliaryVector method) hier_stable_error() (HopsBasis method) HopsBasis (class in mesohops.dynamics.hops_basis) HopsEOM (class in mesohops.dynamics.hops_eom)

HopsHierarchy (class in mesohops.dynamics.hops_hierarchy) HopsNoise (class in mesohops.dynamics.hops_noise) HopsSystem (class in mesohops.dynamics.hops_system) HopsTrajectory (class in mesohops.dynamics.hops_trajectory)

I

inchworm_integrate() (HopsTrajectory method) index_analytic() (AuxiliaryVector method) initialize() (HopsBasis method) (HopsHierarchy method) (HopsSystem method) (HopsTrajectory method)

K

keys() (AuxiliaryVector method)

M

make_adaptive() (HopsTrajectory method) mesohops.dynamics.eom_functions (module) mesohops.dynamics.eom_hops_ksuper (module) mesohops.dynamics.hierarchy_functions (module) mesohops.dynamics.hops_aux (module) mesohops.dynamics.hops_basis (module) mesohops.dynamics.hops_eom (module) mesohops.dynamics.hops_hierarchy (module)

mesohops.dynamics.hops_noise (module) mesohops.dynamics.hops_storage (module) mesohops.dynamics.hops_system (module) mesohops.dynamics.hops_trajectory (module) mesohops.dynamics.noise_fft (module) mesohops.dynamics.noise_trajectories (module) mesohops.dynamics.noise_zero (module) mesohops.dynamics.prepare_functions (module)

N

NoiseTrajectory (class in mesohops.dynamics.noise_trajectories)

normalize() (HopsTrajectory method) NumericNoiseTrajectory (class in mesohops.dynamics.noise_trajectories)

O

operator_expectation() (in module mesohops.dynamics.eom_functions)

P

prepare_noise() (FFTFilterNoise method) (in module mesohops.dynamics.prepare_functions) (ZeroNoise method)

propagate() (HopsTrajectory method)

R

reduce_sparse_matrix() (HopsSystem static method)

S

sum() (AuxiliaryVector method)

T

toarray() (AuxiliaryVector method) todense() (AuxiliaryVector method)

TrajectoryStorage (class in mesohops.dynamics.hops_storage) tuple_from_e_step() (AuxiliaryVector method)

U

update_basis() (HopsBasis method)

update_ksuper() (in module mesohops.dynamics.eom_hops_ksuper)

V

values() (AuxiliaryVector method)

Z

ZeroNoise (class in mesohops.dynamics.noise_zero)