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B
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C
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D
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E
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F
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G
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H
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I
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K
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M
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N
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O
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P
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R
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S
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T
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U
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Z
_
_define_hierarchy_basis() (HopsBasis method)
_define_state_basis() (HopsBasis method)
_determine_basis_from_list() (HopsBasis static method)
_determine_boundary_hier() (HopsBasis method)
A
add_aux_connect() (AuxiliaryVector method)
add_connections() (HopsHierarchy method)
apply_filter() (HopsHierarchy method)
AuxiliaryVector (class in mesohops.dynamics.hops_aux)
B
binom_integer() (in module 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)
construct_noise_correlation_function() (HopsTrajectory method)
D
define_basis() (HopsBasis method)
define_markovian_and_LE_filtered_triangular_hierarchy() (HopsHierarchy static method)
define_markovian_filtered_triangular_hierarchy() (HopsHierarchy static method)
define_triangular_hierarchy() (HopsHierarchy static method)
difference_by_mode() (AuxiliaryVector method)
dot() (AuxiliaryVector method)
E
e_step() (AuxiliaryVector method)
F
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_list_identity_string_down() (AuxiliaryVector method)
get_list_identity_string_up() (AuxiliaryVector method)
get_noise() (HopsNoise method)
(NumericNoiseTrajectory method)
(ZeroNoise method)
get_values() (AuxiliaryVector method)
get_values_nonzero() (AuxiliaryVector method)
H
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)
HopsStorage (class in mesohops.dynamics.hops_storage)
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)
intsum() (in module mesohops.dynamics.hops_aux)
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)
remove_aux_connect() (AuxiliaryVector method)
remove_pointers() (AuxiliaryVector method)
S
state_stable_error() (HopsBasis method)
store_step() (HopsStorage method)
sum() (AuxiliaryVector method)
T
toarray() (AuxiliaryVector method)
todense() (AuxiliaryVector method)
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)
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