diff --git a/docs/_build/html/coniii_rst/coniii.samplers.html b/docs/_build/html/coniii_rst/coniii.samplers.html index 85c2829..d356925 100644 --- a/docs/_build/html/coniii_rst/coniii.samplers.html +++ b/docs/_build/html/coniii_rst/coniii.samplers.html @@ -85,7 +85,7 @@
-sample_energy_min(nFixed=0, rng=RandomState(MT19937) at 0x7F4DCC0E07C0, initialState=None, method='powell', **kwargs)
+sample_energy_min(nFixed=0, rng=RandomState(MT19937) at 0x7F8A7098F8D0, initialState=None, method='powell', **kwargs)

Find local energy minimum given state in angular form. Angular representation makes it easy to be explicit about constraints on the vectors.

@@ -275,7 +275,7 @@
sample_metropolis(sample0, E0, rng=None, flip_site=None, calc_e=None)
-

Metropolis sampling given an arbitrary sampling function.

+

Metropolis sampling given an arbitrary energy function.

sample0ndarray

Sample to start with. Passed by ref and changed.

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index a2280c4..6e4c52a 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({docnames:["coniii_rst/coniii","coniii_rst/coniii.enumerate","coniii_rst/coniii.enumerate_potts","coniii_rst/coniii.general_model_rmc","coniii_rst/coniii.ising","coniii_rst/coniii.ising.automaton","coniii_rst/coniii.ising.test_automaton","coniii_rst/coniii.mc_hist","coniii_rst/coniii.mean_field_ising","coniii_rst/coniii.pseudo_inverse_ising","coniii_rst/coniii.samplers","coniii_rst/coniii.solvers","coniii_rst/coniii.test_samplers","coniii_rst/coniii.test_solvers","coniii_rst/coniii.test_utils","coniii_rst/coniii.utils","coniii_rst/modules","index"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":2,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,sphinx:56},filenames:["coniii_rst/coniii.rst","coniii_rst/coniii.enumerate.rst","coniii_rst/coniii.enumerate_potts.rst","coniii_rst/coniii.general_model_rmc.rst","coniii_rst/coniii.ising.rst","coniii_rst/coniii.ising.automaton.rst","coniii_rst/coniii.ising.test_automaton.rst","coniii_rst/coniii.mc_hist.rst","coniii_rst/coniii.mean_field_ising.rst","coniii_rst/coniii.pseudo_inverse_ising.rst","coniii_rst/coniii.samplers.rst","coniii_rst/coniii.solvers.rst","coniii_rst/coniii.test_samplers.rst","coniii_rst/coniii.test_solvers.rst","coniii_rst/coniii.test_utils.rst","coniii_rst/coniii.utils.rst","coniii_rst/modules.rst","index.rst"],objects:{"":{coniii:[0,0,0,"-"]},"coniii.enumerate":{fast_logsumexp:[1,1,1,""],get_3idx:[1,1,1,""],get_nidx:[1,1,1,""],get_terms01:[1,1,1,""],get_terms11:[1,1,1,""],get_terms:[1,1,1,""],mp_fast_logsumexp:[1,1,1,""],pairwise:[1,1,1,""],triplet:[1,1,1,""],write_eqns:[1,1,1,""],write_py:[1,1,1,""]},"coniii.enumerate_potts":{PythonFileWriterBase:[2,2,1,""],SpecificFieldGenericCouplings:[2,2,1,""],insert_newlines:[2,1,1,""],split_string:[2,1,1,""]},"coniii.enumerate_potts.PythonFileWriterBase":{energy_terms_generator:[2,3,1,""],write:[2,3,1,""]},"coniii.enumerate_potts.SpecificFieldGenericCouplings":{energy_terms_generator:[2,3,1,""]},"coniii.ising":{automaton:[5,0,0,"-"]},"coniii.ising.automaton":{Ising2D:[5,2,1,""],coarse_grain:[5,1,1,""]},"coniii.ising.automaton.Ising2D":{flip_metropolis:[5,3,1,""],iterate:[5,3,1,""]},"coniii.mean_field_ising":{FHomogeneous:[8,1,1,""],JfullFromCluster:[8,1,1,""],JmeanField:[8,1,1,""],SHomogeneous:[8,1,1,""],SmeanField:[8,1,1,""],aboveDiagFlat:[8,1,1,""],analyticEntropy:[8,1,1,""],avgE:[8,1,1,""],avgmHomogeneous:[8,1,1,""],avgxHomogeneous:[8,1,1,""],coocCluster:[8,1,1,""],coocExpectations:[8,1,1,""],coocMatBayesianMean:[8,1,1,""],coocSampleCovariance:[8,1,1,""],coocStdevsFlat:[8,1,1,""],cooccurrence_matrix:[8,1,1,""],dFdT:[8,1,1,""],diagFlatIndex:[8,1,1,""],dmdT:[8,1,1,""],fightPossibilities:[8,1,1,""],findJmatrixAnalytic_CoocMat:[8,1,1,""],fourthOrderCoocMat:[8,1,1,""],independentEntropyHomogeneous2:[8,1,1,""],independentEntropyHomogeneous:[8,1,1,""],isingDeltaCooc:[8,1,1,""],logCosh:[8,1,1,""],m:[8,1,1,""],meanFieldStability:[8,1,1,""],multiInfoHomogeneous:[8,1,1,""],replaceDiag:[8,1,1,""],seedGenerator:[8,1,1,""],specificHeat:[8,1,1,""],susc:[8,1,1,""],symmetrizeUsingUpper:[8,1,1,""],unflatten:[8,1,1,""],unsummedLogZ:[8,1,1,""],unsummedZ:[8,1,1,""],zeroDiag:[8,1,1,""]},"coniii.pseudo_inverse_ising":{conditionalHessian:[9,1,1,""],conditionalJacobian:[9,1,1,""],conditionalLogLikelihood:[9,1,1,""],pairCoocMat:[9,1,1,""],pseudoInverseIsing:[9,1,1,""],pseudoLogLikelihood:[9,1,1,""],testDerivatives:[9,1,1,""]},"coniii.samplers":{HamiltonianMC:[10,2,1,""],Heisenberg3DSampler:[10,2,1,""],Metropolis:[10,2,1,""],ParallelTempering:[10,2,1,""],Potts3:[10,2,1,""],SWIsing:[10,2,1,""],Sampler:[10,2,1,""],WolffIsing:[10,2,1,""],calc_e:[10,1,1,""],check_e_logp:[10,1,1,""],cross:[10,1,1,""],cross_:[10,1,1,""],grad_e:[10,1,1,""],grad_e_theta:[10,1,1,""],iter_cluster:[10,1,1,""],iterate_neighbors:[10,1,1,""],jit_sample:[10,1,1,""],jit_sample_nearby_vector:[10,1,1,""],pairwise_prod:[10,1,1,""],sample_bonds:[10,1,1,""],sample_ising:[10,1,1,""],spec_cluster:[10,1,1,""]},"coniii.samplers.HamiltonianMC":{generate_samples:[10,3,1,""],sample:[10,3,1,""]},"coniii.samplers.Heisenberg3DSampler":{equilibrate_samples:[10,3,1,""],generate_samples:[10,3,1,""],grad_E:[10,3,1,""],sample_energy_min:[10,3,1,""],sample_metropolis:[10,3,1,""],sample_nearby_sample:[10,3,1,""],sample_nearby_vector:[10,3,1,""],to_dict:[10,3,1,""]},"coniii.samplers.Metropolis":{generate_cond_samples:[10,3,1,""],generate_samples_boost:[10,3,1,""],generate_samples_parallel_boost:[10,3,1,""],generate_samples_parallel_py:[10,3,1,""],generate_samples_py:[10,3,1,""],random_sample:[10,3,1,""],sample_metropolis:[10,3,1,""]},"coniii.samplers.ParallelTempering":{burn_and_exchange:[10,3,1,""],burn_in_replicas:[10,3,1,""],generate_samples:[10,3,1,""],initialize_beta:[10,3,1,""],iterate_beta:[10,3,1,""],optimize_beta:[10,3,1,""],setup_replicas:[10,3,1,""],update_replica_parameters:[10,3,1,""]},"coniii.samplers.Potts3":{generate_samples_parallel_boost:[10,3,1,""],random_sample:[10,3,1,""],sample_metropolis:[10,3,1,""]},"coniii.samplers.SWIsing":{generate_sample:[10,3,1,""],generate_sample_parallel:[10,3,1,""],get_clusters:[10,3,1,""],one_step:[10,3,1,""],print_cluster_size:[10,3,1,""],randomly_flip_clusters:[10,3,1,""]},"coniii.samplers.Sampler":{generate_samples:[10,3,1,""],generate_samples_parallel:[10,3,1,""],sample_metropolis:[10,3,1,""],update_parameters:[10,3,1,""]},"coniii.samplers.WolffIsing":{build_cluster:[10,3,1,""],find_neighbors:[10,3,1,""],generate_sample:[10,3,1,""],generate_sample_parallel:[10,3,1,""],one_step:[10,3,1,""],update_parameters:[10,3,1,""]},"coniii.solvers":{ClusterExpansion:[11,2,1,""],Enumerate:[11,2,1,""],MCH:[11,2,1,""],MCHIncompleteData:[11,2,1,""],MPF:[11,2,1,""],MonteCarloHistogram:[11,4,1,""],Pseudo:[11,2,1,""],RegularizedMeanField:[11,2,1,""],Solver:[11,2,1,""],unwrap_self_worker_obj:[11,1,1,""]},"coniii.solvers.ClusterExpansion":{S:[11,3,1,""],Sindependent:[11,3,1,""],clusterID:[11,3,1,""],deltaS:[11,3,1,""],solve:[11,3,1,""],subsets:[11,3,1,""]},"coniii.solvers.Enumerate":{solve:[11,3,1,""]},"coniii.solvers.MCH":{estimate_jac:[11,3,1,""],learn_parameters_mch:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.MCHIncompleteData":{generate_samples:[11,3,1,""],learn_parameters_mch:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.MPF":{K:[11,3,1,""],list_adjacent_states:[11,3,1,""],logK:[11,3,1,""],solve:[11,3,1,""],worker_objective_task:[11,3,1,""]},"coniii.solvers.Pseudo":{cond_hess:[11,3,1,""],cond_jac:[11,3,1,""],cond_log_likelihood:[11,3,1,""],pair_cooc_mat:[11,3,1,""],pseudo_log_likelihood:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.RegularizedMeanField":{bracket1d:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.Solver":{basic_setup:[11,3,1,""],solve:[11,3,1,""]},"coniii.test_samplers":{compare_samplers:[12,1,1,""],test_Metropolis:[12,1,1,""],test_ParallelTempering:[12,1,1,""],test_Potts3:[12,1,1,""],test_sample_ising:[12,1,1,""]},"coniii.test_solvers":{test_Enumerate:[13,1,1,""],test_MPF:[13,1,1,""],test_Pseudo:[13,1,1,""],test_init:[13,1,1,""],test_pickling:[13,1,1,""]},"coniii.test_utils":{test_adj:[14,1,1,""],test_base_repr:[14,1,1,""],test_calc_de:[14,1,1,""],test_convert_corr:[14,1,1,""],test_convert_params:[14,1,1,""],test_define_ising_helper_functions:[14,1,1,""],test_pair_corr:[14,1,1,""],test_state_gen_and_count:[14,1,1,""],test_sub_to_ind:[14,1,1,""],test_vec2mat:[14,1,1,""]},"coniii.utils":{adj:[15,1,1,""],adj_sym:[15,1,1,""],base_repr:[15,1,1,""],bin_states:[15,1,1,""],calc_de:[15,1,1,""],calc_overlap:[15,1,1,""],coarse_grain_with_func:[15,1,1,""],convert_corr:[15,1,1,""],convert_params:[15,1,1,""],define_ising_helper_functions:[15,1,1,""],define_ising_helper_functions_sym:[15,1,1,""],define_potts_helper_functions:[15,1,1,""],define_pseudo_ising_helper_functions:[15,1,1,""],define_pseudo_potts_helper_functions:[15,1,1,""],define_ternary_helper_functions:[15,1,1,""],define_triplet_helper_functions:[15,1,1,""],ind_to_sub:[15,1,1,""],ising_convert_params:[15,1,1,""],k_corr:[15,1,1,""],mat2vec:[15,1,1,""],multinomial:[15,1,1,""],pair_corr:[15,1,1,""],replace_diag:[15,1,1,""],split_concat_params:[15,1,1,""],state_probs:[15,1,1,""],sub_to_ind:[15,1,1,""],unique_rows:[15,1,1,""],unravel_index:[15,1,1,""],vec2mat:[15,1,1,""],xbin_states:[15,1,1,""],xpotts_states:[15,1,1,""],zero_diag:[15,1,1,""]},coniii:{enumerate:[1,0,0,"-"],enumerate_potts:[2,0,0,"-"],ising:[4,0,0,"-"],mean_field_ising:[8,0,0,"-"],pseudo_inverse_ising:[9,0,0,"-"],samplers:[10,0,0,"-"],solvers:[11,0,0,"-"],test_samplers:[12,0,0,"-"],test_solvers:[13,0,0,"-"],test_utils:[14,0,0,"-"],utils:[15,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","class","Python class"],"3":["py","method","Python method"],"4":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:function","2":"py:class","3":"py:method","4":"py:attribute"},terms:{"0x7f4dcc0e07c0":10,"10x":1,"break":[9,11],"case":[11,15],"class":[2,5,10,11,13,15],"default":[10,11],"float":[1,10,11,15],"function":[1,8,10,11,15],"import":[8,10,11],"int":[1,5,10,11,15],"long":[2,15],"new":[10,15],"return":[1,2,8,9,10,11,15],"static":[5,10,11],"switch":[11,15],"throw":15,"true":[1,5,8,10,11,15],"try":11,"while":10,For:[9,11,15],Ising:[1,5,10,11,15],Not:11,One:15,The:[1,2],There:[8,10,15],These:[1,10,11,15],Use:[8,10,11,15],Uses:11,Using:8,_sampl:10,about:[10,11],abov:8,abovediagflat:8,absolut:11,accept:10,acceptance_ratio:10,account:11,accuraci:11,adapt:11,add:1,adding:10,addit:11,adj:[10,11,15],adj_sym:15,adjac:11,adjacentst:11,adjust:11,after:[2,11],agre:2,algorithm:[10,11],alia:11,all:[1,2,8,10,11,13,15],all_connect:11,allow:[1,11,15],allstat:15,along:1,alreadi:10,alreadymark:10,also:[10,11],alternat:8,although:11,analog:15,analyt:11,analyticentropi:8,angl:10,angular:10,ani:[1,10,11,15],anoth:10,anyth:15,appear:[11,15],appli:10,appropri:15,approxim:11,arbitrari:[1,10,11],arctan2:10,arctan:10,arg:[10,11,15],argument:[8,10,11,15],around:[1,10,11],arrai:[1,10,15],arrang:10,arxiv:11,assum:[2,11,15],attribut:11,aurel:11,automat:11,automaton:[0,4],auxiliari:8,avail:11,averag:[2,10,15],avg:8,avgmhomogen:8,avgxhomogen:8,avoid:[10,11],azimuth:10,back:15,balanc:10,barton:11,base:[1,2,5,10,11,15],base_repr:15,basi:15,basic_setup:11,bayesianmean:8,becaus:[9,11,15],been:[10,15],befor:[2,10,11],behavior:11,behaviour:11,being:[9,11],belong:11,best:11,beta:10,better:[9,11],between:[10,11,15],bfg:11,bia:15,bialek:11,bias:[11,15],bin_stat:[1,14,15],binari:[1,9,11,14,15],binomi:15,binstat:1,block:[1,5],boltzmann:10,bond:10,bool:[1,5,8,10,11,15],boost:10,both:[10,15],bound:11,box:1,bracket1d:11,bracket:11,broderick:11,bryan:11,bug:10,build_clust:10,burn:[10,11],burn_and_exchang:10,burn_in:[10,11],burn_in_replica:10,calc_:[10,11,15],calc_d:[11,15],calc_observ:[11,15],calc_observables_r:[11,15],calc_overlap:15,calcul:[1,8,9,10,11,15],call:[10,15],can:[1,11,13,15],care:8,carlo:11,chang:[10,11],charact:2,check:[13,15],check_e_logp:10,choic:11,choos:[10,11],classmethod:10,cleanup:1,close:[10,11],close_pool:10,cluster:[8,10,11],clusterexpans:11,clusterid:11,coars:15,coarse_func:15,coarse_grain:5,coarse_grain_with_func:15,cocco:11,code:[1,10],coeff:1,col:15,column:15,combin:15,come:2,common:11,commun:11,compare_sampl:12,comparison:[1,10],complet:11,compon:8,comput:[1,11],concat:15,concaten:15,cond_hess:11,cond_jac:11,cond_log_likelihood:11,cond_sample_it:11,cond_sample_s:11,condit:[10,11],conditionalhessian:9,conditionaljacobian:9,conditionalloglikelihood:9,configur:[2,10,15],connect:11,consecut:[1,15],consid:2,consist:15,constrain:1,constraint:[10,11],contain:15,content:[16,17],contrainttermsix:1,control:[10,11],conveni:10,convent:2,converg:11,convers:15,convert:[11,15],convert_corr:15,convert_param:15,convert_to:15,cooc_cov:11,coocclust:8,cooccurr:11,cooccurrence_matrix:8,coocexpect:8,coocmat:[8,11],coocmatbayesianmean:8,coocmatdata:8,coocmatdesir:8,coocsamplecovari:[8,11],coocstdevsflat:8,coordin:15,correl:[1,2,8,11,15],correspond:[1,8,11,15],corrtermsix:1,could:[9,11,15],count:15,counter:11,coupl:[2,10,11,15],covari:11,cpu:10,creat:1,criterion:11,critic:11,cross:10,cross_:10,current:[9,10,11],custom:11,custom_convergence_f:11,cut:1,cycl:10,daniel:11,data:[10,11,15],david:11,debug:11,decim:15,declar:11,decreas:11,def:11,default_model_kwarg:11,defin:[11,15],define_ising_helper_funct:15,define_ising_helper_functions_sym:15,define_potts_helper_funct:15,define_pseudo_ising_helper_funct:15,define_pseudo_potts_helper_funct:15,define_ternary_helper_funct:15,define_triplet_helper_funct:15,delta:[10,11],deltacooc:8,deltajclust:11,deltajdict:11,deltamax:9,deltasclust:11,deltasdict:11,deltase:8,depend:[10,11],deprec:11,deriv:[10,13,15],descent:11,describ:11,detail:[10,11],determin:11,deviat:8,dfdt:8,diagflatindex:8,diagon:[8,15],dickstein:11,dict:[10,11],dictionari:10,differ:[9,10,11,15],dim:[5,10],dimens:[1,9,10,11,15],dimension:15,directli:11,discret:10,disord:5,disp:11,distinct:[2,15],distribut:[10,11,15],divid:8,dlamda:11,dmdt:8,doe:11,doesn:15,doi:11,doing:[8,9,11],don:15,down:[1,15],dudik:11,dupl:10,each:[1,5,10,11,15],easi:10,effici:[9,10,11],either:[11,15],ekeberg:11,element:[1,8,10,11,15],ell:[8,9],els:[8,11],emper:11,end:[1,10,11],energi:[1,2,8,10,11,15],energy_terms_gener:2,enough:15,ensur:11,entri:15,entropi:[8,11],enumer:[0,11,16,17],enumerate_pott:17,eps:11,equal:[8,9,11],equat:[1,2,8],equilibr:15,equilibrate_sampl:10,errflag:11,error:[11,15],estconstraint:11,estim:[10,11],estimate_jac:11,estimatedconstraint:11,eta:11,etc:2,evalu:[10,11],even:8,evenli:11,everi:[1,2,10],exact:[1,10],exactli:11,exampl:11,except:15,exchang:10,exclud:10,exclude_empti:15,exit:11,exp:10,expand:11,expans:11,expdj:10,expect:8,explicit:10,explicitli:[1,8],exponenti:1,express:2,expterm:1,extra:[1,10],extract:15,f_cond_sample_it:11,f_cond_sample_s:11,factor:[1,5,10,11],faith:11,fals:[1,8,10,11,12,15],fast:10,fast_logsumexp:1,faster:[8,11,15],fatol:11,ferromagnet:5,fewer:11,fhomogen:8,field:[2,5,8,10,11,15],fight:9,fightposs:8,file:[1,2],fill:8,find:[10,11],find_neighbor:10,findjmatrixanalytic_coocmat:8,finit:11,fire:1,first:[2,11,15],fit:11,fix:10,fixed_subset:10,flack:11,flag:11,flatlist:8,flatten:[8,15],flexibl:11,flip:[5,10,15],flip_metropoli:5,flip_sit:10,floor:10,fname:2,follow:[2,10],footnot:11,forc:11,force_gener:11,form:[8,10,15],format:[10,11],formul:[1,15],formula:11,found:[11,15],fourthordercoocmat:8,fraction:[11,15],free:8,freq:8,frequenc:[11,15],from:[9,10,11,15],front:1,ftol:11,full:8,full_output:11,fullfract:11,funclist:11,fvec:11,gaussian:10,gener:[2,10,11,14,15],general_model_rmc:[0,16],generate_cond_sampl:10,generate_kwarg:11,generate_sampl:[10,11],generate_sample_parallel:10,generate_samples_boost:10,generate_samples_kw:10,generate_samples_parallel:[10,11],generate_samples_parallel_boost:10,generate_samples_parallel_pi:10,generate_samples_pi:10,get:[1,10,11,15],get_3idx:1,get_clust:10,get_multipliers_r:[11,15],get_nidx:1,get_term:1,get_terms01:1,get_terms11:1,give:[11,15],given:[10,11,15],good:11,grad_:10,grad_e_theta:10,gradient:[10,11],grain:15,graph:10,grow:10,guess:11,h_i:15,hamiltonian:[10,15],hamiltonianmc:10,handl:11,hard:11,have:[8,10,15],haven:[9,11],heisenberg3dsampl:10,heisenberg:10,held:10,help:[10,11],helper:15,hext:8,hidden:11,high:[1,11],high_prec:1,higher:11,highest:15,histogram:11,histori:[10,11],homogen:8,how:10,hubbard:8,hukushima:10,i_1:15,i_2:15,i_k:15,idx:15,ignore_zero:15,ijk:[1,15],implement:[9,10,11,15],includ:[8,10,11],includeprior:8,incomplet:11,increas:[1,2,11,15],increasingli:10,increment:[2,10],ind_to_sub:15,independ:11,independententropyhomogen:8,independententropyhomogeneous2:8,independentref:11,index:[1,2,9,10,11,15,17],indic:[1,8,10,11,15],individu:[9,10,11,15],indterm:8,infin:8,initi:[10,11,13],initial_guess:11,initial_sampl:[10,11],initial_st:10,initialis:10,initialize_beta:10,initialsampl:10,initialsit:10,initialst:10,insert:2,insert_newlin:2,insid:1,inspir:11,instanc:10,instead:[10,11,15],integ:15,interact:[8,11,15],interpol:10,interv:11,invers:[8,10,11,15],invok:10,involv:10,iprint:[10,11],ising2d:5,ising:[0,16,17],ising_convert_param:15,isingdeltacooc:8,isingsampl:8,iter:[2,5,10,11,15],iter_clust:10,iterate_beta:10,iterate_neighbor:10,ith:15,its:10,ix0:1,j_ij:15,jac:11,jacobian:11,jcluster:8,jessica:11,jfull:11,jfullfromclust:8,jij:[10,15],jinit:8,jit_sampl:10,jit_sample_nearby_vector:10,jmeanfield:8,john:11,jri:[9,11],jrj:[9,11],just:[1,11,15],k_corr:15,keep:10,keep_diag:8,keepdiag:8,keyword:15,kijk:15,known:11,krakauer:11,krylov:11,kth:[1,15],kwarg:[1,8,10,11,15],l_r:[9,11],label:15,lambda:11,lamda:11,laplac:8,laplace_count:15,laplacian:10,larg:[9,11,15],larger:11,lattic:5,lead:10,leapfrogn:10,learn:11,learn_parameters_kwarg:11,learn_parameters_mch:11,learn_params_kwarg:11,learn_set:11,leav:15,left:11,length:15,less:15,like:[1,11,15],likelihood:11,line:1,linear:10,list:[1,2,8,10,11,15],list_adjacent_st:11,local:[5,10],locat:10,log:[1,11],logcosh:8,logk:11,logp:10,logsumexp:1,look:15,loop:10,loss:8,lot:10,lower:[1,11,15],lowest:[11,15],lst:8,made:[9,11],magnet:10,magnitud:[1,11],mai:[9,11],maintain:10,major:5,make:[9,10,11,15],mani:[10,15],margin:11,mat2vec:15,mat:[8,15],match:11,matrix:[1,8,9,10,11,15],matter:11,max:11,max_it:[10,11],max_param_valu:11,maxdlamda:11,maxdlamdanorm:11,maxent:[1,11],maxim:11,maximum:11,maxit:11,maxlearningstep:11,mc_hist:[0,16],mch:11,mch_approxim:[11,15],mchincompletedata:11,mcmc:[10,11],mean:[1,8,11,15],mean_field_is:[0,16],meanfieldpriorlmbda:[8,11],meanfieldref:11,meanfieldst:8,measur:15,mech:11,memori:[9,11],method:[8,10,11,15],metropoli:[5,10,11],might:10,min_covari:11,min_independ:11,min_siz:11,minim:11,minimize_scalar:11,minimum:[9,10,11,15],minsiz:[8,9],miss:11,mode:11,model:[1,5,10,11,15],model_kwarg:11,modifi:[10,11],modul:[16,17],monoton:11,mont:11,montecarlohistogram:11,more:[9,10,11],most:11,move:[1,10],mp_fast_logsumexp:1,mpf:[11,13,15],mpmath:1,mt19937:10,much:[9,11],multi:15,multiinfohomogen:8,multinomi:15,multipl:11,multipli:[10,11,15],multiprocess:10,must:[11,15],n_cpu:[10,11],n_dim:[11,15],n_dimens:15,n_featur:10,n_grid_point:11,n_iter:[5,10,11],n_random_neighbor:15,n_replica:10,n_sampl:[10,11,15],n_system:15,n_time:15,name:10,nat:8,natur:11,nburn:10,ncol:15,ncomms14301:11,ncpu:10,ndarrai:[1,5,8,10,11,15],ndata:11,ndim:[10,11],nearbi:10,necessari:11,need:[1,10,15],neg:15,neighbor:[10,15],new_paramet:10,newdiag:15,next:11,nfix:10,non:11,none:[1,5,8,9,10,11,15],noninteract:[8,11],nonzero:15,norm:11,normal:15,note:[8,9,10,11,15],nsampl:10,nspin:10,nth:15,number:[1,9,10,11,15],numer:[1,8,11,15],numfight:8,numpi:15,numsampl:[8,11],nx1:1,nxn:1,nxnxn:1,object:[2,5,10,11],observ:[11,15],occupi:15,offdiagmult:8,oldstat:10,one:[1,10,11,15],one_step:10,ones:[8,11],onli:[8,10,11,15],oparam:15,ophi:10,optim:[10,11],optimize_beta:10,option:[8,10,11,15],order:[1,2,10,15],origin:15,other:[11,15],otherwis:[10,15],otheta:10,out:1,output:11,over:[1,2,11],own:10,p03002:11,packag:[16,17],page:17,pair:15,pair_cooc_mat:11,pair_corr:15,paircooc:[9,11],paircoocmat:9,paircoocrhat:[9,11],pairwis:[1,8,10,11,15],pairwise_prod:10,parallel:10,paralleltemp:10,param:[11,15],paramet:[1,8,10,11,15],parameter_limit:11,particip:9,particular:10,partit:[1,8],pass:[9,10,11,15],pattern:1,per:9,perhap:8,period:5,perturb:10,phi:10,phi_0:10,phi_1:10,phi_n:10,plai:11,plane:1,plug:15,point:[11,15],polar:10,pool:10,possibl:[1,2,10,11,15],pott:[2,15],potts3:10,powel:10,precis:[1,8,11],predict:11,prefix:1,present:15,preset:11,print:1,print_cluster_s:10,prior:[8,11],priorlmbda:[8,11],prl:11,probabl:[9,10,11,15],problem:[11,15],problemat:15,product:[10,15],proport:11,propto:10,provid:[11,15],pseudo:[11,15],pseudo_inverse_is:[0,16],pseudo_log_likelihood:11,pseudoinverseis:9,pseudolikelihood:11,pseudologlikelihood:9,purpos:11,push:10,put:[1,11],python:1,pythonfilewriterbas:2,quantiti:[1,10,15],quench:5,question:10,rais:11,randnorm:10,random:[10,11,15],random_sampl:10,randomli:10,randomly_flip_clust:10,randomst:10,randunif:10,rang:10,rate:15,ratio:10,ravel:15,reach:[10,11],readi:[10,11],receiv:11,recogn:1,recommend:11,ref:10,refer:11,regular:[8,11],regularizedmeanfield:11,releas:11,remain:15,remc:11,rememb:10,renorm:5,renormalized_lattic:5,rep_ex_burnin:10,repeat:15,replac:15,replace_diag:15,replacediag:8,replica:[10,15],replica_burnin:10,replicaburnin:10,represent:10,reset:11,reset_rng:11,residu:[8,11],respect:15,result:10,return_invers:15,revers:10,right:8,rng:[5,10,11],root:11,routin:[10,11],row:[10,11,15],rseed:10,rule:5,run:10,run_cond_sampl:11,run_regular_sampl:11,run_tim:12,runtim:11,s_i:15,s_j:15,same:[10,15],sampl:[5,8,9,10,11,15],sample0:10,sample_bond:10,sample_energy_min:10,sample_is:10,sample_method:11,sample_metropoli:10,sample_nearby_sampl:10,sample_nearby_vector:10,sample_s:[10,11],sampler:[0,11,16,17],samples:10,satisfi:10,save:10,save_exchange_trajectori:10,save_histori:10,savehistori:10,scale:11,schapir:11,scipi:[1,11],scipy_solver_kwarg:11,score:8,search:17,second:[11,15],see:[8,10,11],seed:[10,11],seedgener:8,seedstart:8,self:[10,11],send:10,sens:[9,11],separ:[10,15],separate_field:15,sequenc:5,sequenti:1,set:[9,10,11,15],setup_replica:10,shape:[9,11],shomogen:8,should:[1,8,9,10,11,15],shouldn:15,si_a:15,si_b:15,sigma:10,sign:1,sim_func:15,similar:15,simona:11,simpl:[10,15],simplifi:[1,10],simul:[5,10],simultan:10,sind:11,sindepend:11,singl:[1,5,10,11,15],sisj:15,site:10,size:[1,10,11,15],slim:15,slow:[9,10,11],slower:[1,11],slowmethod:8,small:[8,11],smeanfield:8,social:11,sohl:11,solut:11,solv:11,solver:[0,13,15,16,17],solver_kwarg:11,some:[1,11,15],sort:[8,11],space:[10,11,15],spec_clust:10,specif:[1,11,15],specifi:[1,2,11,15],specificfieldgenericcoupl:2,specificheat:8,speed:[9,11],spin:[1,2,5,10,11,15],split:15,split_concat_param:15,split_str:2,squar:15,standard:8,start:[10,11,15],stat:11,state:[1,2,10,11,14,15],state_prob:15,step:[10,11],still:11,stop:10,str:[1,11,15],stratonovich:8,strength:11,string:[1,2,15],structur:1,sub_to_ind:15,subindex:15,subix:[1,15],submodul:[16,17],subpackag:16,subset:[10,11],subtract:15,subtract_mean:15,suffix:1,suitabl:10,sum:[1,11],summat:11,suppli:15,support:11,sure:[8,15],susc:8,swise:10,sym:[1,15],symmetr:[8,9,11,15],symmetrizeusingupp:8,system:[1,8,9,10,11,15],systemat:[5,10],systematic_it:10,take:[10,11,15],tbd:10,tell:10,temperatur:10,term:[1,8],terminolog:15,test:[11,14],test_adj:14,test_automaton:[0,4],test_base_repr:14,test_calc_d:14,test_convert_corr:14,test_convert_param:14,test_define_ising_helper_funct:14,test_enumer:13,test_init:13,test_metropoli:12,test_mpf:13,test_pair_corr:14,test_paralleltemp:12,test_pickl:13,test_potts3:12,test_pseudo:13,test_sampl:[0,16],test_sample_is:12,test_solv:[0,16],test_state_gen_and_count:14,test_sub_to_ind:14,test_util:[0,16],test_vec2mat:14,testderiv:9,tha:10,than:[10,11,15],thei:[2,15],them:[1,10],theta:10,theta_0:10,theta_1:10,theta_n:10,thi:[1,2,8,10,11,15],thing:11,think:[8,11],third:1,thisset:11,those:15,thought:[9,11],thread:10,three:11,threshold:11,through:[2,5,10,15],time:[10,11,15],tkacik:11,tkaschber06:11,to_dict:10,todo:[1,11],togeth:15,tol:[10,11],toler:11,tolnorm:11,too:[9,11],track:10,trajectori:10,treat:11,triangl:[1,8,15],triangular:15,triplet:1,truth:1,tupl:[11,15],turn:8,two:[10,15],twopl:15,type:10,typic:[11,15],uincompletest:11,uincompletestatescount:11,unflatten:8,uniqu:[11,15],unique_row:15,unless:15,unravel:15,unravel_index:15,unspecifi:11,unsummedlogz:8,unsummedz:8,until:11,unwrap_self_worker_obj:11,updat:[10,11],update_paramet:10,update_replica_paramet:10,upper:[1,8,15],use:[1,9,10,11],use_root:11,useanalyticresult:11,used:[8,9,10,11,15],useful:11,uselog:11,useregularizedeq:8,uses:[1,9,11],using:[1,5,8,10,11,14,15],util:[0,11,16,17],valu:[1,10,11],vari:11,variabl:15,vec1:10,vec2:10,vec2mat:[11,15],vector:[10,11,15],verbos:11,veri:15,versa:15,version:[1,2,15],veryverbos:11,vice:15,visibl:11,visit:10,wai:[8,9,10,11],want:11,warm:10,weight:[8,11,15],well:2,when:[1,2,8,11,15],where:[1,2,10,11,15],whether:[8,10,11],which:[1,10,11,15],whose:15,width:10,within:11,wolff:10,wolffis:10,won:15,word:15,work:11,worker_objective_task:11,would:[1,15],wrap:15,wrapper:[1,11],write:[1,2],write_eqn:1,write_pi:1,written:15,wrt:[10,11,15],xatol:11,xbin_stat:[14,15],xcount:11,xlist:11,xpotts_stat:15,xuniq:11,xyz:10,yet:[9,11],yield:2,you:[10,15],zero:[8,11,15],zero_diag:15,zerobelowdiag:8,zerodiag:8},titles:["coniii package","coniii.enumerate module","coniii.enumerate_potts module","coniii.general_model_rmc module","coniii.ising package","coniii.ising.automaton module","coniii.ising.test_automaton module","coniii.mc_hist module","coniii.mean_field_ising module","coniii.pseudo_inverse_ising module","coniii.samplers module","coniii.solvers module","coniii.test_samplers module","coniii.test_solvers module","coniii.test_utils module","coniii.utils module","coniii","Welcome to ConIII\u2019s documentation!"],titleterms:{automaton:5,coniii:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17],content:[0,4],document:17,enumer:1,enumerate_pott:2,general_model_rmc:3,indic:17,ising:[4,5,6],mc_hist:7,mean_field_is:8,modul:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15],packag:[0,4],pseudo_inverse_is:9,sampler:10,solver:11,submodul:[0,4],subpackag:0,tabl:17,test_automaton:6,test_sampl:12,test_solv:13,test_util:14,util:15,welcom:17}}) \ No newline at end of file +Search.setIndex({docnames:["coniii_rst/coniii","coniii_rst/coniii.enumerate","coniii_rst/coniii.enumerate_potts","coniii_rst/coniii.general_model_rmc","coniii_rst/coniii.ising","coniii_rst/coniii.ising.automaton","coniii_rst/coniii.ising.test_automaton","coniii_rst/coniii.mc_hist","coniii_rst/coniii.mean_field_ising","coniii_rst/coniii.pseudo_inverse_ising","coniii_rst/coniii.samplers","coniii_rst/coniii.solvers","coniii_rst/coniii.test_samplers","coniii_rst/coniii.test_solvers","coniii_rst/coniii.test_utils","coniii_rst/coniii.utils","coniii_rst/modules","index"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":2,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,sphinx:56},filenames:["coniii_rst/coniii.rst","coniii_rst/coniii.enumerate.rst","coniii_rst/coniii.enumerate_potts.rst","coniii_rst/coniii.general_model_rmc.rst","coniii_rst/coniii.ising.rst","coniii_rst/coniii.ising.automaton.rst","coniii_rst/coniii.ising.test_automaton.rst","coniii_rst/coniii.mc_hist.rst","coniii_rst/coniii.mean_field_ising.rst","coniii_rst/coniii.pseudo_inverse_ising.rst","coniii_rst/coniii.samplers.rst","coniii_rst/coniii.solvers.rst","coniii_rst/coniii.test_samplers.rst","coniii_rst/coniii.test_solvers.rst","coniii_rst/coniii.test_utils.rst","coniii_rst/coniii.utils.rst","coniii_rst/modules.rst","index.rst"],objects:{"":{coniii:[0,0,0,"-"]},"coniii.enumerate":{fast_logsumexp:[1,1,1,""],get_3idx:[1,1,1,""],get_nidx:[1,1,1,""],get_terms01:[1,1,1,""],get_terms11:[1,1,1,""],get_terms:[1,1,1,""],mp_fast_logsumexp:[1,1,1,""],pairwise:[1,1,1,""],triplet:[1,1,1,""],write_eqns:[1,1,1,""],write_py:[1,1,1,""]},"coniii.enumerate_potts":{PythonFileWriterBase:[2,2,1,""],SpecificFieldGenericCouplings:[2,2,1,""],insert_newlines:[2,1,1,""],split_string:[2,1,1,""]},"coniii.enumerate_potts.PythonFileWriterBase":{energy_terms_generator:[2,3,1,""],write:[2,3,1,""]},"coniii.enumerate_potts.SpecificFieldGenericCouplings":{energy_terms_generator:[2,3,1,""]},"coniii.ising":{automaton:[5,0,0,"-"]},"coniii.ising.automaton":{Ising2D:[5,2,1,""],coarse_grain:[5,1,1,""]},"coniii.ising.automaton.Ising2D":{flip_metropolis:[5,3,1,""],iterate:[5,3,1,""]},"coniii.mean_field_ising":{FHomogeneous:[8,1,1,""],JfullFromCluster:[8,1,1,""],JmeanField:[8,1,1,""],SHomogeneous:[8,1,1,""],SmeanField:[8,1,1,""],aboveDiagFlat:[8,1,1,""],analyticEntropy:[8,1,1,""],avgE:[8,1,1,""],avgmHomogeneous:[8,1,1,""],avgxHomogeneous:[8,1,1,""],coocCluster:[8,1,1,""],coocExpectations:[8,1,1,""],coocMatBayesianMean:[8,1,1,""],coocSampleCovariance:[8,1,1,""],coocStdevsFlat:[8,1,1,""],cooccurrence_matrix:[8,1,1,""],dFdT:[8,1,1,""],diagFlatIndex:[8,1,1,""],dmdT:[8,1,1,""],fightPossibilities:[8,1,1,""],findJmatrixAnalytic_CoocMat:[8,1,1,""],fourthOrderCoocMat:[8,1,1,""],independentEntropyHomogeneous2:[8,1,1,""],independentEntropyHomogeneous:[8,1,1,""],isingDeltaCooc:[8,1,1,""],logCosh:[8,1,1,""],m:[8,1,1,""],meanFieldStability:[8,1,1,""],multiInfoHomogeneous:[8,1,1,""],replaceDiag:[8,1,1,""],seedGenerator:[8,1,1,""],specificHeat:[8,1,1,""],susc:[8,1,1,""],symmetrizeUsingUpper:[8,1,1,""],unflatten:[8,1,1,""],unsummedLogZ:[8,1,1,""],unsummedZ:[8,1,1,""],zeroDiag:[8,1,1,""]},"coniii.pseudo_inverse_ising":{conditionalHessian:[9,1,1,""],conditionalJacobian:[9,1,1,""],conditionalLogLikelihood:[9,1,1,""],pairCoocMat:[9,1,1,""],pseudoInverseIsing:[9,1,1,""],pseudoLogLikelihood:[9,1,1,""],testDerivatives:[9,1,1,""]},"coniii.samplers":{HamiltonianMC:[10,2,1,""],Heisenberg3DSampler:[10,2,1,""],Metropolis:[10,2,1,""],ParallelTempering:[10,2,1,""],Potts3:[10,2,1,""],SWIsing:[10,2,1,""],Sampler:[10,2,1,""],WolffIsing:[10,2,1,""],calc_e:[10,1,1,""],check_e_logp:[10,1,1,""],cross:[10,1,1,""],cross_:[10,1,1,""],grad_e:[10,1,1,""],grad_e_theta:[10,1,1,""],iter_cluster:[10,1,1,""],iterate_neighbors:[10,1,1,""],jit_sample:[10,1,1,""],jit_sample_nearby_vector:[10,1,1,""],pairwise_prod:[10,1,1,""],sample_bonds:[10,1,1,""],sample_ising:[10,1,1,""],spec_cluster:[10,1,1,""]},"coniii.samplers.HamiltonianMC":{generate_samples:[10,3,1,""],sample:[10,3,1,""]},"coniii.samplers.Heisenberg3DSampler":{equilibrate_samples:[10,3,1,""],generate_samples:[10,3,1,""],grad_E:[10,3,1,""],sample_energy_min:[10,3,1,""],sample_metropolis:[10,3,1,""],sample_nearby_sample:[10,3,1,""],sample_nearby_vector:[10,3,1,""],to_dict:[10,3,1,""]},"coniii.samplers.Metropolis":{generate_cond_samples:[10,3,1,""],generate_samples_boost:[10,3,1,""],generate_samples_parallel_boost:[10,3,1,""],generate_samples_parallel_py:[10,3,1,""],generate_samples_py:[10,3,1,""],random_sample:[10,3,1,""],sample_metropolis:[10,3,1,""]},"coniii.samplers.ParallelTempering":{burn_and_exchange:[10,3,1,""],burn_in_replicas:[10,3,1,""],generate_samples:[10,3,1,""],initialize_beta:[10,3,1,""],iterate_beta:[10,3,1,""],optimize_beta:[10,3,1,""],setup_replicas:[10,3,1,""],update_replica_parameters:[10,3,1,""]},"coniii.samplers.Potts3":{generate_samples_parallel_boost:[10,3,1,""],random_sample:[10,3,1,""],sample_metropolis:[10,3,1,""]},"coniii.samplers.SWIsing":{generate_sample:[10,3,1,""],generate_sample_parallel:[10,3,1,""],get_clusters:[10,3,1,""],one_step:[10,3,1,""],print_cluster_size:[10,3,1,""],randomly_flip_clusters:[10,3,1,""]},"coniii.samplers.Sampler":{generate_samples:[10,3,1,""],generate_samples_parallel:[10,3,1,""],sample_metropolis:[10,3,1,""],update_parameters:[10,3,1,""]},"coniii.samplers.WolffIsing":{build_cluster:[10,3,1,""],find_neighbors:[10,3,1,""],generate_sample:[10,3,1,""],generate_sample_parallel:[10,3,1,""],one_step:[10,3,1,""],update_parameters:[10,3,1,""]},"coniii.solvers":{ClusterExpansion:[11,2,1,""],Enumerate:[11,2,1,""],MCH:[11,2,1,""],MCHIncompleteData:[11,2,1,""],MPF:[11,2,1,""],MonteCarloHistogram:[11,4,1,""],Pseudo:[11,2,1,""],RegularizedMeanField:[11,2,1,""],Solver:[11,2,1,""],unwrap_self_worker_obj:[11,1,1,""]},"coniii.solvers.ClusterExpansion":{S:[11,3,1,""],Sindependent:[11,3,1,""],clusterID:[11,3,1,""],deltaS:[11,3,1,""],solve:[11,3,1,""],subsets:[11,3,1,""]},"coniii.solvers.Enumerate":{solve:[11,3,1,""]},"coniii.solvers.MCH":{estimate_jac:[11,3,1,""],learn_parameters_mch:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.MCHIncompleteData":{generate_samples:[11,3,1,""],learn_parameters_mch:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.MPF":{K:[11,3,1,""],list_adjacent_states:[11,3,1,""],logK:[11,3,1,""],solve:[11,3,1,""],worker_objective_task:[11,3,1,""]},"coniii.solvers.Pseudo":{cond_hess:[11,3,1,""],cond_jac:[11,3,1,""],cond_log_likelihood:[11,3,1,""],pair_cooc_mat:[11,3,1,""],pseudo_log_likelihood:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.RegularizedMeanField":{bracket1d:[11,3,1,""],solve:[11,3,1,""]},"coniii.solvers.Solver":{basic_setup:[11,3,1,""],solve:[11,3,1,""]},"coniii.test_samplers":{compare_samplers:[12,1,1,""],test_Metropolis:[12,1,1,""],test_ParallelTempering:[12,1,1,""],test_Potts3:[12,1,1,""],test_sample_ising:[12,1,1,""]},"coniii.test_solvers":{test_Enumerate:[13,1,1,""],test_MPF:[13,1,1,""],test_Pseudo:[13,1,1,""],test_init:[13,1,1,""],test_pickling:[13,1,1,""]},"coniii.test_utils":{test_adj:[14,1,1,""],test_base_repr:[14,1,1,""],test_calc_de:[14,1,1,""],test_convert_corr:[14,1,1,""],test_convert_params:[14,1,1,""],test_define_ising_helper_functions:[14,1,1,""],test_pair_corr:[14,1,1,""],test_state_gen_and_count:[14,1,1,""],test_sub_to_ind:[14,1,1,""],test_vec2mat:[14,1,1,""]},"coniii.utils":{adj:[15,1,1,""],adj_sym:[15,1,1,""],base_repr:[15,1,1,""],bin_states:[15,1,1,""],calc_de:[15,1,1,""],calc_overlap:[15,1,1,""],coarse_grain_with_func:[15,1,1,""],convert_corr:[15,1,1,""],convert_params:[15,1,1,""],define_ising_helper_functions:[15,1,1,""],define_ising_helper_functions_sym:[15,1,1,""],define_potts_helper_functions:[15,1,1,""],define_pseudo_ising_helper_functions:[15,1,1,""],define_pseudo_potts_helper_functions:[15,1,1,""],define_ternary_helper_functions:[15,1,1,""],define_triplet_helper_functions:[15,1,1,""],ind_to_sub:[15,1,1,""],ising_convert_params:[15,1,1,""],k_corr:[15,1,1,""],mat2vec:[15,1,1,""],multinomial:[15,1,1,""],pair_corr:[15,1,1,""],replace_diag:[15,1,1,""],split_concat_params:[15,1,1,""],state_probs:[15,1,1,""],sub_to_ind:[15,1,1,""],unique_rows:[15,1,1,""],unravel_index:[15,1,1,""],vec2mat:[15,1,1,""],xbin_states:[15,1,1,""],xpotts_states:[15,1,1,""],zero_diag:[15,1,1,""]},coniii:{enumerate:[1,0,0,"-"],enumerate_potts:[2,0,0,"-"],ising:[4,0,0,"-"],mean_field_ising:[8,0,0,"-"],pseudo_inverse_ising:[9,0,0,"-"],samplers:[10,0,0,"-"],solvers:[11,0,0,"-"],test_samplers:[12,0,0,"-"],test_solvers:[13,0,0,"-"],test_utils:[14,0,0,"-"],utils:[15,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","class","Python class"],"3":["py","method","Python method"],"4":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:function","2":"py:class","3":"py:method","4":"py:attribute"},terms:{"0x7f4dcc0e07c0":[],"0x7f8a7098f8d0":10,"10x":1,"break":[9,11],"case":[11,15],"class":[2,5,10,11,13,15],"default":[10,11],"float":[1,10,11,15],"function":[1,8,10,11,15],"import":[8,10,11],"int":[1,5,10,11,15],"long":[2,15],"new":[10,15],"return":[1,2,8,9,10,11,15],"static":[5,10,11],"switch":[11,15],"throw":15,"true":[1,5,8,10,11,15],"try":11,"while":10,For:[9,11,15],Ising:[1,5,10,11,15],Not:11,One:15,The:[1,2],There:[8,10,15],These:[1,10,11,15],Use:[8,10,11,15],Uses:11,Using:8,_sampl:10,about:[10,11],abov:8,abovediagflat:8,absolut:11,accept:10,acceptance_ratio:10,account:11,accuraci:11,adapt:11,add:1,adding:10,addit:11,adj:[10,11,15],adj_sym:15,adjac:11,adjacentst:11,adjust:11,after:[2,11],agre:2,algorithm:[10,11],alia:11,all:[1,2,8,10,11,13,15],all_connect:11,allow:[1,11,15],allstat:15,along:1,alreadi:10,alreadymark:10,also:[10,11],alternat:8,although:11,analog:15,analyt:11,analyticentropi:8,angl:10,angular:10,ani:[1,10,11,15],anoth:10,anyth:15,appear:[11,15],appli:10,appropri:15,approxim:11,arbitrari:[1,10,11],arctan2:10,arctan:10,arg:[10,11,15],argument:[8,10,11,15],around:[1,10,11],arrai:[1,10,15],arrang:10,arxiv:11,assum:[2,11,15],attribut:11,aurel:11,automat:11,automaton:[0,4],auxiliari:8,avail:11,averag:[2,10,15],avg:8,avgmhomogen:8,avgxhomogen:8,avoid:[10,11],azimuth:10,back:15,balanc:10,barton:11,base:[1,2,5,10,11,15],base_repr:15,basi:15,basic_setup:11,bayesianmean:8,becaus:[9,11,15],been:[10,15],befor:[2,10,11],behavior:11,behaviour:11,being:[9,11],belong:11,best:11,beta:10,better:[9,11],between:[10,11,15],bfg:11,bia:15,bialek:11,bias:[11,15],bin_stat:[1,14,15],binari:[1,9,11,14,15],binomi:15,binstat:1,block:[1,5],boltzmann:10,bond:10,bool:[1,5,8,10,11,15],boost:10,both:[10,15],bound:11,box:1,bracket1d:11,bracket:11,broderick:11,bryan:11,bug:10,build_clust:10,burn:[10,11],burn_and_exchang:10,burn_in:[10,11],burn_in_replica:10,calc_:[10,11,15],calc_d:[11,15],calc_observ:[11,15],calc_observables_r:[11,15],calc_overlap:15,calcul:[1,8,9,10,11,15],call:[10,15],can:[1,11,13,15],care:8,carlo:11,chang:[10,11],charact:2,check:[13,15],check_e_logp:10,choic:11,choos:[10,11],classmethod:10,cleanup:1,close:[10,11],close_pool:10,cluster:[8,10,11],clusterexpans:11,clusterid:11,coars:15,coarse_func:15,coarse_grain:5,coarse_grain_with_func:15,cocco:11,code:[1,10],coeff:1,col:15,column:15,combin:15,come:2,common:11,commun:11,compare_sampl:12,comparison:[1,10],complet:11,compon:8,comput:[1,11],concat:15,concaten:15,cond_hess:11,cond_jac:11,cond_log_likelihood:11,cond_sample_it:11,cond_sample_s:11,condit:[10,11],conditionalhessian:9,conditionaljacobian:9,conditionalloglikelihood:9,configur:[2,10,15],connect:11,consecut:[1,15],consid:2,consist:15,constrain:1,constraint:[10,11],contain:15,content:[16,17],contrainttermsix:1,control:[10,11],conveni:10,convent:2,converg:11,convers:15,convert:[11,15],convert_corr:15,convert_param:15,convert_to:15,cooc_cov:11,coocclust:8,cooccurr:11,cooccurrence_matrix:8,coocexpect:8,coocmat:[8,11],coocmatbayesianmean:8,coocmatdata:8,coocmatdesir:8,coocsamplecovari:[8,11],coocstdevsflat:8,coordin:15,correl:[1,2,8,11,15],correspond:[1,8,11,15],corrtermsix:1,could:[9,11,15],count:15,counter:11,coupl:[2,10,11,15],covari:11,cpu:10,creat:1,criterion:11,critic:11,cross:10,cross_:10,current:[9,10,11],custom:11,custom_convergence_f:11,cut:1,cycl:10,daniel:11,data:[10,11,15],david:11,debug:11,decim:15,declar:11,decreas:11,def:11,default_model_kwarg:11,defin:[11,15],define_ising_helper_funct:15,define_ising_helper_functions_sym:15,define_potts_helper_funct:15,define_pseudo_ising_helper_funct:15,define_pseudo_potts_helper_funct:15,define_ternary_helper_funct:15,define_triplet_helper_funct:15,delta:[10,11],deltacooc:8,deltajclust:11,deltajdict:11,deltamax:9,deltasclust:11,deltasdict:11,deltase:8,depend:[10,11],deprec:11,deriv:[10,13,15],descent:11,describ:11,detail:[10,11],determin:11,deviat:8,dfdt:8,diagflatindex:8,diagon:[8,15],dickstein:11,dict:[10,11],dictionari:10,differ:[9,10,11,15],dim:[5,10],dimens:[1,9,10,11,15],dimension:15,directli:11,discret:10,disord:5,disp:11,distinct:[2,15],distribut:[10,11,15],divid:8,dlamda:11,dmdt:8,doe:11,doesn:15,doi:11,doing:[8,9,11],don:15,down:[1,15],dudik:11,dupl:10,each:[1,5,10,11,15],easi:10,effici:[9,10,11],either:[11,15],ekeberg:11,element:[1,8,10,11,15],ell:[8,9],els:[8,11],emper:11,end:[1,10,11],energi:[1,2,8,10,11,15],energy_terms_gener:2,enough:15,ensur:11,entri:15,entropi:[8,11],enumer:[0,11,16,17],enumerate_pott:17,eps:11,equal:[8,9,11],equat:[1,2,8],equilibr:15,equilibrate_sampl:10,errflag:11,error:[11,15],estconstraint:11,estim:[10,11],estimate_jac:11,estimatedconstraint:11,eta:11,etc:2,evalu:[10,11],even:8,evenli:11,everi:[1,2,10],exact:[1,10],exactli:11,exampl:11,except:15,exchang:10,exclud:10,exclude_empti:15,exit:11,exp:10,expand:11,expans:11,expdj:10,expect:8,explicit:10,explicitli:[1,8],exponenti:1,express:2,expterm:1,extra:[1,10],extract:15,f_cond_sample_it:11,f_cond_sample_s:11,factor:[1,5,10,11],faith:11,fals:[1,8,10,11,12,15],fast:10,fast_logsumexp:1,faster:[8,11,15],fatol:11,ferromagnet:5,fewer:11,fhomogen:8,field:[2,5,8,10,11,15],fight:9,fightposs:8,file:[1,2],fill:8,find:[10,11],find_neighbor:10,findjmatrixanalytic_coocmat:8,finit:11,fire:1,first:[2,11,15],fit:11,fix:10,fixed_subset:10,flack:11,flag:11,flatlist:8,flatten:[8,15],flexibl:11,flip:[5,10,15],flip_metropoli:5,flip_sit:10,floor:10,fname:2,follow:[2,10],footnot:11,forc:11,force_gener:11,form:[8,10,15],format:[10,11],formul:[1,15],formula:11,found:[11,15],fourthordercoocmat:8,fraction:[11,15],free:8,freq:8,frequenc:[11,15],from:[9,10,11,15],front:1,ftol:11,full:8,full_output:11,fullfract:11,funclist:11,fvec:11,gaussian:10,gener:[2,10,11,14,15],general_model_rmc:[0,16],generate_cond_sampl:10,generate_kwarg:11,generate_sampl:[10,11],generate_sample_parallel:10,generate_samples_boost:10,generate_samples_kw:10,generate_samples_parallel:[10,11],generate_samples_parallel_boost:10,generate_samples_parallel_pi:10,generate_samples_pi:10,get:[1,10,11,15],get_3idx:1,get_clust:10,get_multipliers_r:[11,15],get_nidx:1,get_term:1,get_terms01:1,get_terms11:1,give:[11,15],given:[10,11,15],good:11,grad_:10,grad_e_theta:10,gradient:[10,11],grain:15,graph:10,grow:10,guess:11,h_i:15,hamiltonian:[10,15],hamiltonianmc:10,handl:11,hard:11,have:[8,10,15],haven:[9,11],heisenberg3dsampl:10,heisenberg:10,held:10,help:[10,11],helper:15,hext:8,hidden:11,high:[1,11],high_prec:1,higher:11,highest:15,histogram:11,histori:[10,11],homogen:8,how:10,hubbard:8,hukushima:10,i_1:15,i_2:15,i_k:15,idx:15,ignore_zero:15,ijk:[1,15],implement:[9,10,11,15],includ:[8,10,11],includeprior:8,incomplet:11,increas:[1,2,11,15],increasingli:10,increment:[2,10],ind_to_sub:15,independ:11,independententropyhomogen:8,independententropyhomogeneous2:8,independentref:11,index:[1,2,9,10,11,15,17],indic:[1,8,10,11,15],individu:[9,10,11,15],indterm:8,infin:8,initi:[10,11,13],initial_guess:11,initial_sampl:[10,11],initial_st:10,initialis:10,initialize_beta:10,initialsampl:10,initialsit:10,initialst:10,insert:2,insert_newlin:2,insid:1,inspir:11,instanc:10,instead:[10,11,15],integ:15,interact:[8,11,15],interpol:10,interv:11,invers:[8,10,11,15],invok:10,involv:10,iprint:[10,11],ising2d:5,ising:[0,16,17],ising_convert_param:15,isingdeltacooc:8,isingsampl:8,iter:[2,5,10,11,15],iter_clust:10,iterate_beta:10,iterate_neighbor:10,ith:15,its:10,ix0:1,j_ij:15,jac:11,jacobian:11,jcluster:8,jessica:11,jfull:11,jfullfromclust:8,jij:[10,15],jinit:8,jit_sampl:10,jit_sample_nearby_vector:10,jmeanfield:8,john:11,jri:[9,11],jrj:[9,11],just:[1,11,15],k_corr:15,keep:10,keep_diag:8,keepdiag:8,keyword:15,kijk:15,known:11,krakauer:11,krylov:11,kth:[1,15],kwarg:[1,8,10,11,15],l_r:[9,11],label:15,lambda:11,lamda:11,laplac:8,laplace_count:15,laplacian:10,larg:[9,11,15],larger:11,lattic:5,lead:10,leapfrogn:10,learn:11,learn_parameters_kwarg:11,learn_parameters_mch:11,learn_params_kwarg:11,learn_set:11,leav:15,left:11,length:15,less:15,like:[1,11,15],likelihood:11,line:1,linear:10,list:[1,2,8,10,11,15],list_adjacent_st:11,local:[5,10],locat:10,log:[1,11],logcosh:8,logk:11,logp:10,logsumexp:1,look:15,loop:10,loss:8,lot:10,lower:[1,11,15],lowest:[11,15],lst:8,made:[9,11],magnet:10,magnitud:[1,11],mai:[9,11],maintain:10,major:5,make:[9,10,11,15],mani:[10,15],margin:11,mat2vec:15,mat:[8,15],match:11,matrix:[1,8,9,10,11,15],matter:11,max:11,max_it:[10,11],max_param_valu:11,maxdlamda:11,maxdlamdanorm:11,maxent:[1,11],maxim:11,maximum:11,maxit:11,maxlearningstep:11,mc_hist:[0,16],mch:11,mch_approxim:[11,15],mchincompletedata:11,mcmc:[10,11],mean:[1,8,11,15],mean_field_is:[0,16],meanfieldpriorlmbda:[8,11],meanfieldref:11,meanfieldst:8,measur:15,mech:11,memori:[9,11],method:[8,10,11,15],metropoli:[5,10,11],might:10,min_covari:11,min_independ:11,min_siz:11,minim:11,minimize_scalar:11,minimum:[9,10,11,15],minsiz:[8,9],miss:11,mode:11,model:[1,5,10,11,15],model_kwarg:11,modifi:[10,11],modul:[16,17],monoton:11,mont:11,montecarlohistogram:11,more:[9,10,11],most:11,move:[1,10],mp_fast_logsumexp:1,mpf:[11,13,15],mpmath:1,mt19937:10,much:[9,11],multi:15,multiinfohomogen:8,multinomi:15,multipl:11,multipli:[10,11,15],multiprocess:10,must:[11,15],n_cpu:[10,11],n_dim:[11,15],n_dimens:15,n_featur:10,n_grid_point:11,n_iter:[5,10,11],n_random_neighbor:15,n_replica:10,n_sampl:[10,11,15],n_system:15,n_time:15,name:10,nat:8,natur:11,nburn:10,ncol:15,ncomms14301:11,ncpu:10,ndarrai:[1,5,8,10,11,15],ndata:11,ndim:[10,11],nearbi:10,necessari:11,need:[1,10,15],neg:15,neighbor:[10,15],new_paramet:10,newdiag:15,next:11,nfix:10,non:11,none:[1,5,8,9,10,11,15],noninteract:[8,11],nonzero:15,norm:11,normal:15,note:[8,9,10,11,15],nsampl:10,nspin:10,nth:15,number:[1,9,10,11,15],numer:[1,8,11,15],numfight:8,numpi:15,numsampl:[8,11],nx1:1,nxn:1,nxnxn:1,object:[2,5,10,11],observ:[11,15],occupi:15,offdiagmult:8,oldstat:10,one:[1,10,11,15],one_step:10,ones:[8,11],onli:[8,10,11,15],oparam:15,ophi:10,optim:[10,11],optimize_beta:10,option:[8,10,11,15],order:[1,2,10,15],origin:15,other:[11,15],otherwis:[10,15],otheta:10,out:1,output:11,over:[1,2,11],own:10,p03002:11,packag:[16,17],page:17,pair:15,pair_cooc_mat:11,pair_corr:15,paircooc:[9,11],paircoocmat:9,paircoocrhat:[9,11],pairwis:[1,8,10,11,15],pairwise_prod:10,parallel:10,paralleltemp:10,param:[11,15],paramet:[1,8,10,11,15],parameter_limit:11,particip:9,particular:10,partit:[1,8],pass:[9,10,11,15],pattern:1,per:9,perhap:8,period:5,perturb:10,phi:10,phi_0:10,phi_1:10,phi_n:10,plai:11,plane:1,plug:15,point:[11,15],polar:10,pool:10,possibl:[1,2,10,11,15],pott:[2,15],potts3:10,powel:10,precis:[1,8,11],predict:11,prefix:1,present:15,preset:11,print:1,print_cluster_s:10,prior:[8,11],priorlmbda:[8,11],prl:11,probabl:[9,10,11,15],problem:[11,15],problemat:15,product:[10,15],proport:11,propto:10,provid:[11,15],pseudo:[11,15],pseudo_inverse_is:[0,16],pseudo_log_likelihood:11,pseudoinverseis:9,pseudolikelihood:11,pseudologlikelihood:9,purpos:11,push:10,put:[1,11],python:1,pythonfilewriterbas:2,quantiti:[1,10,15],quench:5,question:10,rais:11,randnorm:10,random:[10,11,15],random_sampl:10,randomli:10,randomly_flip_clust:10,randomst:10,randunif:10,rang:10,rate:15,ratio:10,ravel:15,reach:[10,11],readi:[10,11],receiv:11,recogn:1,recommend:11,ref:10,refer:11,regular:[8,11],regularizedmeanfield:11,releas:11,remain:15,remc:11,rememb:10,renorm:5,renormalized_lattic:5,rep_ex_burnin:10,repeat:15,replac:15,replace_diag:15,replacediag:8,replica:[10,15],replica_burnin:10,replicaburnin:10,represent:10,reset:11,reset_rng:11,residu:[8,11],respect:15,result:10,return_invers:15,revers:10,right:8,rng:[5,10,11],root:11,routin:[10,11],row:[10,11,15],rseed:10,rule:5,run:10,run_cond_sampl:11,run_regular_sampl:11,run_tim:12,runtim:11,s_i:15,s_j:15,same:[10,15],sampl:[5,8,9,10,11,15],sample0:10,sample_bond:10,sample_energy_min:10,sample_is:10,sample_method:11,sample_metropoli:10,sample_nearby_sampl:10,sample_nearby_vector:10,sample_s:[10,11],sampler:[0,11,16,17],samples:10,satisfi:10,save:10,save_exchange_trajectori:10,save_histori:10,savehistori:10,scale:11,schapir:11,scipi:[1,11],scipy_solver_kwarg:11,score:8,search:17,second:[11,15],see:[8,10,11],seed:[10,11],seedgener:8,seedstart:8,self:[10,11],send:10,sens:[9,11],separ:[10,15],separate_field:15,sequenc:5,sequenti:1,set:[9,10,11,15],setup_replica:10,shape:[9,11],shomogen:8,should:[1,8,9,10,11,15],shouldn:15,si_a:15,si_b:15,sigma:10,sign:1,sim_func:15,similar:15,simona:11,simpl:[10,15],simplifi:[1,10],simul:[5,10],simultan:10,sind:11,sindepend:11,singl:[1,5,10,11,15],sisj:15,site:10,size:[1,10,11,15],slim:15,slow:[9,10,11],slower:[1,11],slowmethod:8,small:[8,11],smeanfield:8,social:11,sohl:11,solut:11,solv:11,solver:[0,13,15,16,17],solver_kwarg:11,some:[1,11,15],sort:[8,11],space:[10,11,15],spec_clust:10,specif:[1,11,15],specifi:[1,2,11,15],specificfieldgenericcoupl:2,specificheat:8,speed:[9,11],spin:[1,2,5,10,11,15],split:15,split_concat_param:15,split_str:2,squar:15,standard:8,start:[10,11,15],stat:11,state:[1,2,10,11,14,15],state_prob:15,step:[10,11],still:11,stop:10,str:[1,11,15],stratonovich:8,strength:11,string:[1,2,15],structur:1,sub_to_ind:15,subindex:15,subix:[1,15],submodul:[16,17],subpackag:16,subset:[10,11],subtract:15,subtract_mean:15,suffix:1,suitabl:10,sum:[1,11],summat:11,suppli:15,support:11,sure:[8,15],susc:8,swise:10,sym:[1,15],symmetr:[8,9,11,15],symmetrizeusingupp:8,system:[1,8,9,10,11,15],systemat:[5,10],systematic_it:10,take:[10,11,15],tbd:10,tell:10,temperatur:10,term:[1,8],terminolog:15,test:[11,14],test_adj:14,test_automaton:[0,4],test_base_repr:14,test_calc_d:14,test_convert_corr:14,test_convert_param:14,test_define_ising_helper_funct:14,test_enumer:13,test_init:13,test_metropoli:12,test_mpf:13,test_pair_corr:14,test_paralleltemp:12,test_pickl:13,test_potts3:12,test_pseudo:13,test_sampl:[0,16],test_sample_is:12,test_solv:[0,16],test_state_gen_and_count:14,test_sub_to_ind:14,test_util:[0,16],test_vec2mat:14,testderiv:9,tha:10,than:[10,11,15],thei:[2,15],them:[1,10],theta:10,theta_0:10,theta_1:10,theta_n:10,thi:[1,2,8,10,11,15],thing:11,think:[8,11],third:1,thisset:11,those:15,thought:[9,11],thread:10,three:11,threshold:11,through:[2,5,10,15],time:[10,11,15],tkacik:11,tkaschber06:11,to_dict:10,todo:[1,11],togeth:15,tol:[10,11],toler:11,tolnorm:11,too:[9,11],track:10,trajectori:10,treat:11,triangl:[1,8,15],triangular:15,triplet:1,truth:1,tupl:[11,15],turn:8,two:[10,15],twopl:15,type:10,typic:[11,15],uincompletest:11,uincompletestatescount:11,unflatten:8,uniqu:[11,15],unique_row:15,unless:15,unravel:15,unravel_index:15,unspecifi:11,unsummedlogz:8,unsummedz:8,until:11,unwrap_self_worker_obj:11,updat:[10,11],update_paramet:10,update_replica_paramet:10,upper:[1,8,15],use:[1,9,10,11],use_root:11,useanalyticresult:11,used:[8,9,10,11,15],useful:11,uselog:11,useregularizedeq:8,uses:[1,9,11],using:[1,5,8,10,11,14,15],util:[0,11,16,17],valu:[1,10,11],vari:11,variabl:15,vec1:10,vec2:10,vec2mat:[11,15],vector:[10,11,15],verbos:11,veri:15,versa:15,version:[1,2,15],veryverbos:11,vice:15,visibl:11,visit:10,wai:[8,9,10,11],want:11,warm:10,weight:[8,11,15],well:2,when:[1,2,8,11,15],where:[1,2,10,11,15],whether:[8,10,11],which:[1,10,11,15],whose:15,width:10,within:11,wolff:10,wolffis:10,won:15,word:15,work:11,worker_objective_task:11,would:[1,15],wrap:15,wrapper:[1,11],write:[1,2],write_eqn:1,write_pi:1,written:15,wrt:[10,11,15],xatol:11,xbin_stat:[14,15],xcount:11,xlist:11,xpotts_stat:15,xuniq:11,xyz:10,yet:[9,11],yield:2,you:[10,15],zero:[8,11,15],zero_diag:15,zerobelowdiag:8,zerodiag:8},titles:["coniii package","coniii.enumerate module","coniii.enumerate_potts module","coniii.general_model_rmc module","coniii.ising package","coniii.ising.automaton module","coniii.ising.test_automaton module","coniii.mc_hist module","coniii.mean_field_ising module","coniii.pseudo_inverse_ising module","coniii.samplers module","coniii.solvers module","coniii.test_samplers module","coniii.test_solvers module","coniii.test_utils module","coniii.utils module","coniii","Welcome to ConIII\u2019s documentation!"],titleterms:{automaton:5,coniii:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17],content:[0,4],document:17,enumer:1,enumerate_pott:2,general_model_rmc:3,indic:17,ising:[4,5,6],mc_hist:7,mean_field_is:8,modul:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15],packag:[0,4],pseudo_inverse_is:9,sampler:10,solver:11,submodul:[0,4],subpackag:0,tabl:17,test_automaton:6,test_sampl:12,test_solv:13,test_util:14,util:15,welcom:17}}) \ No newline at end of file