Index

A

aboveDiagFlat() (in module coniii.legacy.mean_field_ising) adj() (in module coniii.utils) adj_sym() (in module coniii.utils)

analyticEntropy() (in module coniii.legacy.mean_field_ising) avgE() (in module coniii.legacy.mean_field_ising) avgmHomogeneous() (in module coniii.legacy.mean_field_ising) avgxHomogeneous() (in module coniii.legacy.mean_field_ising)

B

base_repr() (in module coniii.utils) basic_setup() (coniii.solvers.Solver method) bin_states() (in module coniii.utils)

bracket1d() (coniii.solvers.RegularizedMeanField method) build_cluster() (coniii.samplers.WolffIsing method) burn_and_exchange() (coniii.samplers.ParallelTempering method) burn_in_replicas() (coniii.samplers.ParallelTempering method)

C

calc_de() (in module coniii.utils) calc_e() (in module coniii.experimental.samplers) calc_overlap() (in module coniii.utils) check_e_logp() (in module coniii.experimental.samplers) ClusterExpansion (class in coniii.solvers) clusterID() (coniii.solvers.ClusterExpansion method) coarse_grain() (in module coniii.ising.automaton) coarse_grain_with_func() (in module coniii.utils) conditionalHessian() (in module coniii.legacy.pseudo_inverse_ising) conditionalJacobian() (in module coniii.legacy.pseudo_inverse_ising) conditionalLogLikelihood() (in module coniii.legacy.pseudo_inverse_ising) coniii.enumerate module coniii.enumerate_potts module coniii.experimental.entropy module coniii.experimental.samplers module coniii.ising module coniii.ising.automaton module

coniii.legacy.mean_field_ising module coniii.legacy.pseudo_inverse_ising module coniii.models module coniii.samplers module coniii.solvers module coniii.utils module convert_corr() (in module coniii.utils) convert_params() (in module coniii.utils) coocCluster() (in module coniii.legacy.mean_field_ising) cooccurrence_matrix() (in module coniii.legacy.mean_field_ising) coocExpectations() (in module coniii.legacy.mean_field_ising) coocMatBayesianMean() (in module coniii.legacy.mean_field_ising) coocSampleCovariance() (in module coniii.legacy.mean_field_ising) coocStdevsFlat() (in module coniii.legacy.mean_field_ising) cross() (in module coniii.experimental.samplers) cross_() (in module coniii.experimental.samplers) cross_entropy() (in module coniii.experimental.entropy)

D

define_ising_helper_functions() (in module coniii.utils) define_ising_helper_functions_sym() (in module coniii.utils) define_potts_helper_functions() (in module coniii.utils) define_pseudo_ising_helper_functions() (in module coniii.utils) define_pseudo_potts_helper_functions() (in module coniii.utils)

define_ternary_helper_functions() (in module coniii.utils) define_triplet_helper_functions() (in module coniii.utils) deltaS() (coniii.solvers.ClusterExpansion method) dFdT() (in module coniii.legacy.mean_field_ising) diagFlatIndex() (in module coniii.legacy.mean_field_ising) dmdT() (in module coniii.legacy.mean_field_ising)

E

energy_terms_generator() (coniii.enumerate_potts.PythonFileWriterBase method) (coniii.enumerate_potts.SpecificFieldGenericCouplings method)

Enumerate (class in coniii.solvers) equilibrate_samples() (coniii.experimental.samplers.Heisenberg3DSampler method), [1] estimate_jac() (coniii.solvers.MCH method)

F

fast_logsumexp() (in module coniii.enumerate) FHomogeneous() (in module coniii.legacy.mean_field_ising) fightPossibilities() (in module coniii.legacy.mean_field_ising) fill_in() (coniii.solvers.Solver method)

find_neighbors() (coniii.samplers.WolffIsing method) findJmatrixAnalytic_CoocMat() (in module coniii.legacy.mean_field_ising) flip_metropolis() (coniii.ising.automaton.Ising2D static method) fourthOrderCoocMat() (in module coniii.legacy.mean_field_ising)

G

generate_cond_sample_boost() (coniii.samplers.Metropolis method) generate_cond_sample_py() (coniii.samplers.Metropolis method) generate_sample() (coniii.experimental.samplers.HamiltonianMC method) (coniii.experimental.samplers.Heisenberg3DSampler method), [1] (coniii.experimental.samplers.SWIsing method) (coniii.models.Model method) (coniii.samplers.ParallelTempering method) (coniii.samplers.Sampler method) (coniii.samplers.WolffIsing method) (coniii.solvers.MCHIncompleteData method) generate_sample_boost() (coniii.samplers.Metropolis method) generate_sample_parallel() (coniii.experimental.samplers.SWIsing method) (coniii.samplers.Sampler method) (coniii.samplers.WolffIsing method)

generate_sample_parallel_boost() (coniii.samplers.Metropolis method) (coniii.samplers.Potts3 method) generate_sample_parallel_py() (coniii.samplers.Metropolis method) generate_sample_py() (coniii.samplers.Metropolis method) get_3idx() (in module coniii.enumerate) get_clusters() (coniii.experimental.samplers.SWIsing method) get_nidx() (in module coniii.enumerate) get_terms() (in module coniii.enumerate) get_terms01() (in module coniii.enumerate) get_terms11() (in module coniii.enumerate) grad_E() (coniii.experimental.samplers.Heisenberg3DSampler method) grad_e() (in module coniii.experimental.samplers) grad_e_theta() (in module coniii.experimental.samplers)

H

HamiltonianMC (class in coniii.experimental.samplers)

Heisenberg3DSampler (class in coniii.experimental.samplers)

I

ind_to_sub() (in module coniii.utils) independentEntropyHomogeneous() (in module coniii.legacy.mean_field_ising) independentEntropyHomogeneous2() (in module coniii.legacy.mean_field_ising) initialize_beta() (coniii.samplers.ParallelTempering static method) insert_newlines() (in module coniii.enumerate_potts) Ising (class in coniii.models)

Ising2D (class in coniii.ising.automaton) ising_convert_params() (in module coniii.utils) isingDeltaCooc() (in module coniii.legacy.mean_field_ising) iter_cluster() (in module coniii.experimental.samplers) iterate() (coniii.ising.automaton.Ising2D method) iterate_beta() (coniii.samplers.ParallelTempering static method)

J

JfullFromCluster() (in module coniii.legacy.mean_field_ising) jit_sample() (in module coniii.experimental.samplers)

jit_sample_nearby_vector() (in module coniii.experimental.samplers) JmeanField() (in module coniii.legacy.mean_field_ising)

K

K() (coniii.solvers.MPF method)

k_corr() (in module coniii.utils)

L

learn_parameters_mch() (coniii.solvers.MCH method) (coniii.solvers.MCHIncompleteData method) (coniii.solvers.SparseMCH method) list_adjacent_states() (coniii.solvers.MPF method) logCosh() (in module coniii.legacy.mean_field_ising)

logK() (coniii.solvers.MPF method) logp() (coniii.solvers.Enumerate method) (coniii.solvers.Solver method) (coniii.solvers.SparseEnumerate method) logsumexp() (in module coniii.utils)

M

m() (in module coniii.legacy.mean_field_ising) mat2vec() (in module coniii.utils) MCH (class in coniii.solvers) MCHIncompleteData (class in coniii.solvers) meanFieldStability() (in module coniii.legacy.mean_field_ising) Metropolis (class in coniii.samplers) Model (class in coniii.models) module coniii.enumerate coniii.enumerate_potts coniii.experimental.entropy coniii.experimental.samplers coniii.ising coniii.ising.automaton coniii.legacy.mean_field_ising coniii.legacy.pseudo_inverse_ising coniii.models coniii.samplers coniii.solvers coniii.utils

mp_fast_logsumexp() (in module coniii.enumerate) MPF (class in coniii.solvers) multiInfoHomogeneous() (in module coniii.legacy.mean_field_ising)

O

one_step() (coniii.experimental.samplers.SWIsing method) (coniii.samplers.WolffIsing method)

optimize_beta() (coniii.samplers.ParallelTempering method)

P

pair_corr() (in module coniii.utils) pairCoocMat() (in module coniii.legacy.pseudo_inverse_ising) pairwise() (in module coniii.enumerate) pairwise_prod() (in module coniii.experimental.samplers) PairwiseMaxent (in module coniii.models) ParallelTempering (class in coniii.samplers)

Potts3 (class in coniii.models) (class in coniii.samplers) print_cluster_size() (coniii.experimental.samplers.SWIsing method) Pseudo (class in coniii.solvers) pseudoInverseIsing() (in module coniii.legacy.pseudo_inverse_ising) pseudoLogLikelihood() (in module coniii.legacy.pseudo_inverse_ising) PythonFileWriterBase (class in coniii.enumerate_potts)

R

random_sample() (coniii.samplers.Metropolis method) (coniii.samplers.Potts3 method) randomly_flip_clusters() (coniii.experimental.samplers.SWIsing method)

RegularizedMeanField (class in coniii.solvers) replace_diag() (in module coniii.utils) replaceDiag() (in module coniii.legacy.mean_field_ising)

S

S() (coniii.solvers.ClusterExpansion method) sample() (coniii.experimental.samplers.HamiltonianMC method) sample_bonds() (in module coniii.experimental.samplers) sample_energy_min() (coniii.experimental.samplers.Heisenberg3DSampler method), [1] sample_ising() (in module coniii.samplers) sample_metropolis() (coniii.experimental.samplers.Heisenberg3DSampler method), [1] (coniii.samplers.Metropolis method) (coniii.samplers.Potts3 method) (coniii.samplers.Sampler method) sample_nearby_sample() (coniii.experimental.samplers.Heisenberg3DSampler method) sample_nearby_vector() (coniii.experimental.samplers.Heisenberg3DSampler method) Sampler (class in coniii.samplers) seedGenerator() (in module coniii.legacy.mean_field_ising) set_insertion_ix() (coniii.solvers.Solver method) set_multipliers() (coniii.models.Ising method) (coniii.models.Potts3 method) (coniii.models.Triplet method) set_rng() (coniii.models.Model method) setup_replicas() (coniii.samplers.ParallelTempering method) setup_sampler() (coniii.models.Model method) SHomogeneous() (in module coniii.legacy.mean_field_ising) Sindependent() (coniii.solvers.ClusterExpansion method) SmeanField() (in module coniii.legacy.mean_field_ising)

solve() (coniii.solvers.ClusterExpansion method) (coniii.solvers.Enumerate method) (coniii.solvers.MCH method) (coniii.solvers.MCHIncompleteData method) (coniii.solvers.MPF method) (coniii.solvers.Pseudo method) (coniii.solvers.RegularizedMeanField method) (coniii.solvers.Solver method) (coniii.solvers.SparseEnumerate method) (coniii.solvers.SparseMCH method) Solver (class in coniii.solvers) SparseEnumerate (class in coniii.solvers) SparseMCH (class in coniii.solvers) spec_cluster() (in module coniii.experimental.samplers) SpecificFieldGenericCouplings (class in coniii.enumerate_potts) specificHeat() (in module coniii.legacy.mean_field_ising) split_concat_params() (in module coniii.utils) split_string() (in module coniii.enumerate_potts) state_probs() (in module coniii.utils) sub_to_ind() (in module coniii.utils) subsets() (coniii.solvers.ClusterExpansion method) susc() (in module coniii.legacy.mean_field_ising) SWIsing (class in coniii.experimental.samplers) symmetrizeUsingUpper() (in module coniii.legacy.mean_field_ising)

T

testDerivatives() (in module coniii.legacy.pseudo_inverse_ising) to_dict() (coniii.experimental.samplers.Heisenberg3DSampler class method)

Triplet (class in coniii.models) triplet() (in module coniii.enumerate)

U

unflatten() (in module coniii.legacy.mean_field_ising) unique_rows() (in module coniii.utils) unsummedLogZ() (in module coniii.legacy.mean_field_ising) unsummedZ() (in module coniii.legacy.mean_field_ising)

update_parameters() (coniii.samplers.Metropolis method) (coniii.samplers.Sampler method) (coniii.samplers.WolffIsing method) update_replica_parameters() (coniii.samplers.ParallelTempering method)

V

vec2mat() (in module coniii.utils)

W

WolffIsing (class in coniii.samplers) worker_objective_task() (coniii.solvers.MPF static method)

write() (coniii.enumerate_potts.PythonFileWriterBase method) write_eqns() (in module coniii.enumerate) write_py() (in module coniii.enumerate)

X

xbin_states() (in module coniii.utils)

xpotts_states() (in module coniii.utils)

Z

zero_diag() (in module coniii.utils)

zeroDiag() (in module coniii.legacy.mean_field_ising)