diff --git a/searchindex.js b/searchindex.js
index 4032dd70..a24eb1b3 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["FOSI-forcing","api-driver","api-interface","api-internal","api-testcase","contributing","driver-example","generated/feisty.core.ecosystem.benthic_prey_type","generated/feisty.core.ecosystem.fish_type","generated/feisty.core.ecosystem.fishing","generated/feisty.core.ecosystem.food_web","generated/feisty.core.ecosystem.food_web_link","generated/feisty.core.ecosystem.reproduction_link","generated/feisty.core.ecosystem.reproduction_routing","generated/feisty.core.ecosystem.zooplankton_type","generated/feisty.core.process.compute_consumption","generated/feisty.core.process.compute_encounter","generated/feisty.core.process.compute_energy_avail","generated/feisty.core.process.compute_fish_catch","generated/feisty.core.process.compute_growth","generated/feisty.core.process.compute_ingestion","generated/feisty.core.process.compute_metabolism","generated/feisty.core.process.compute_natural_mortality","generated/feisty.core.process.compute_pred_encounter_consumption_max","generated/feisty.core.process.compute_predation","generated/feisty.core.process.compute_rate_T_mass_scaling","generated/feisty.core.process.compute_recruitment","generated/feisty.core.process.compute_reproduction","generated/feisty.core.process.compute_rescale_zoo_consumption","generated/feisty.core.process.compute_t_frac_pelagic","generated/feisty.core.process.compute_total_tendency","generated/feisty.core.process.t_weighted_mean_temp","generated/feisty.feisty_instance_type","generated/feisty.feisty_instance_type.compute_tendencies","generated/feisty.feisty_instance_type.get_prognostic","generated/feisty.testcase.domain_tanh_shelf","generated/feisty.testcase.forcing_cyclic","intro","matlab-comparison","references","scientific-background","settings","settings-show-defaults","testcase-datasets","usage"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["FOSI-forcing.ipynb","api-driver.rst","api-interface.rst","api-internal.rst","api-testcase.rst","contributing.rst","driver-example.ipynb","generated/feisty.core.ecosystem.benthic_prey_type.rst","generated/feisty.core.ecosystem.fish_type.rst","generated/feisty.core.ecosystem.fishing.rst","generated/feisty.core.ecosystem.food_web.rst","generated/feisty.core.ecosystem.food_web_link.rst","generated/feisty.core.ecosystem.reproduction_link.rst","generated/feisty.core.ecosystem.reproduction_routing.rst","generated/feisty.core.ecosystem.zooplankton_type.rst","generated/feisty.core.process.compute_consumption.rst","generated/feisty.core.process.compute_encounter.rst","generated/feisty.core.process.compute_energy_avail.rst","generated/feisty.core.process.compute_fish_catch.rst","generated/feisty.core.process.compute_growth.rst","generated/feisty.core.process.compute_ingestion.rst","generated/feisty.core.process.compute_metabolism.rst","generated/feisty.core.process.compute_natural_mortality.rst","generated/feisty.core.process.compute_pred_encounter_consumption_max.rst","generated/feisty.core.process.compute_predation.rst","generated/feisty.core.process.compute_rate_T_mass_scaling.rst","generated/feisty.core.process.compute_recruitment.rst","generated/feisty.core.process.compute_reproduction.rst","generated/feisty.core.process.compute_rescale_zoo_consumption.rst","generated/feisty.core.process.compute_t_frac_pelagic.rst","generated/feisty.core.process.compute_total_tendency.rst","generated/feisty.core.process.t_weighted_mean_temp.rst","generated/feisty.feisty_instance_type.rst","generated/feisty.feisty_instance_type.compute_tendencies.rst","generated/feisty.feisty_instance_type.get_prognostic.rst","generated/feisty.testcase.domain_tanh_shelf.rst","generated/feisty.testcase.forcing_cyclic.rst","intro.md","matlab-comparison.ipynb","references.md","scientific-background.md","settings.rst","settings-show-defaults.ipynb","testcase-datasets.ipynb","usage.rst"],objects:{"feisty.core.ecosystem":[[7,0,1,"","benthic_prey_type"],[8,0,1,"","fish_type"],[9,0,1,"","fishing"],[10,0,1,"","food_web"],[11,0,1,"","food_web_link"],[12,0,1,"","reproduction_link"],[13,0,1,"","reproduction_routing"],[14,0,1,"","zooplankton_type"]],"feisty.core.ecosystem.benthic_prey_type":[[7,1,1,"","__init__"]],"feisty.core.ecosystem.fish_type":[[8,1,1,"","__init__"]],"feisty.core.ecosystem.fishing":[[9,1,1,"","__init__"]],"feisty.core.ecosystem.food_web":[[10,1,1,"","__init__"]],"feisty.core.ecosystem.food_web_link":[[11,1,1,"","__init__"]],"feisty.core.ecosystem.reproduction_link":[[12,1,1,"","__init__"]],"feisty.core.ecosystem.reproduction_routing":[[13,1,1,"","__init__"]],"feisty.core.ecosystem.zooplankton_type":[[14,1,1,"","__init__"]],"feisty.core.process":[[15,2,1,"","compute_consumption"],[16,2,1,"","compute_encounter"],[17,2,1,"","compute_energy_avail"],[18,2,1,"","compute_fish_catch"],[19,2,1,"","compute_growth"],[20,2,1,"","compute_ingestion"],[21,2,1,"","compute_metabolism"],[22,2,1,"","compute_natural_mortality"],[23,2,1,"","compute_pred_encounter_consumption_max"],[24,2,1,"","compute_predation"],[25,2,1,"","compute_rate_T_mass_scaling"],[26,2,1,"","compute_recruitment"],[27,2,1,"","compute_reproduction"],[28,2,1,"","compute_rescale_zoo_consumption"],[29,2,1,"","compute_t_frac_pelagic"],[30,2,1,"","compute_total_tendency"],[31,2,1,"","t_weighted_mean_temp"]],"feisty.feisty_instance_type":[[32,1,1,"","__init__"],[33,1,1,"","compute_tendencies"],[34,1,1,"","get_prognostic"]],"feisty.testcase":[[35,2,1,"","domain_tanh_shelf"],[36,2,1,"","forcing_cyclic"]],feisty:[[32,0,1,"","feisty_instance_type"]]},objnames:{"0":["py","class","Python class"],"1":["py","method","Python method"],"2":["py","function","Python function"]},objtypes:{"0":"py:class","1":"py:method","2":"py:function"},terms:{"0":[0,6,8,25,32,36,38,41,42,43],"00":[0,38],"0000":0,"00000000e":0,"0000000e":0,"0000e":38,"0001":[0,6,38],"0002":[6,38],"001":[41,42],"00137":0,"001371":0,"001371long_nam":0,"001433":0,"001433long_nam":0,"002":32,"002346":36,"002347":36,"0039425":0,"003963":0,"003963long_nam":0,"003963xarrai":0,"004059long_nam":0,"004059xarrai":0,"00406":0,"0088":0,"009":0,"009start_tim":0,"00calendar":0,"00long_nam":0,"01":[0,6,38,42],"0100":38,"0111364e":0,"0117":0,"0144":0,"02":[0,38],"0206011e":0,"02381":[36,43],"0249":[0,38],"025":38,"0251":38,"0255419":0,"02775":36,"02785":36,"0285e":38,"0289702e":0,"03":[0,38],"0391":0,"04":[0,38],"0402":0,"04108171":43,"0435":0,"0464":0,"0464e":38,"05":[0,6,32,38],"0501752":0,"0534e":38,"0541e":38,"054e":0,"056e":0,"05855756e":0,"05984232e":0,"05long_nam":0,"05unit":0,"06":38,"06162255e":0,"063":[8,42],"07":0,"070855":0,"0739e":38,"075":[6,42],"08":38,"0855":[8,42],"09":38,"092e":0,"0936":0,"094e":0,"0986":0,"0content":0,"0long_nam":0,"0titl":0,"0x7f83f83fe190":43,"0x7f83f855ea10":43,"0x7f8400766d90":43,"1":[0,6,30,36,38,41,42,43],"10":[0,19,25,39,43],"100":[0,19,38],"100270080":0,"1005":43,"1015":43,"1016":39,"1021":43,"102124":39,"1024":43,"1026":43,"1028":43,"1029":43,"1029756":0,"1041":0,"105":0,"11":0,"110":0,"115263":0,"115294":0,"115324":0,"115644":0,"115674":0,"115705":0,"11677":38,"1171":0,"1177113":0,"1196":0,"12":[0,6,38],"120":0,"122880":0,"125000":[41,42],"12coordin":0,"13":38,"130":0,"131":43,"1318":0,"135":0,"13550705e":0,"1355070e":0,"1387":0,"14":0,"140":0,"1482":0,"15":[0,6,38],"150":0,"15208992":0,"15209":0,"1526":0,"153e":0,"15485412e":0,"1548541e":0,"1555511e":0,"1558":0,"1561459e":0,"15633":38,"157e":0,"16":[0,38],"160":0,"1649e":38,"166":0,"1664":0,"170":0,"175":42,"176":39,"17873201":43,"1794e":38,"18":[36,38],"180":[0,38],"18357879e":0,"1835788e":0,"1863":0,"19":[6,38,39],"191":0,"194":0,"195":38,"196":0,"1968":0,"19902725":43,"1arrai":0,"1e":[0,32,38],"1e4":0,"2":[0,6,36,38,42,43],"20":[0,38,42],"200":[37,42],"2012":0,"2015":0,"2019":[37,39],"202":38,"203":0,"2074":0,"21370613":43,"214":43,"215":0,"2184234e":0,"2193e":38,"22":[6,35,36,43],"220446049250313e":0,"22301965":43,"2263750":0,"2263750tavg_sum":0,"227":0,"229":0,"2298":0,"2331":0,"2354716":0,"2381":[36,43],"23z":0,"24":0,"2427e":38,"243":0,"248":0,"249":0,"25":42,"250":[41,42],"2529":0,"2553709e":0,"2561447e":0,"2564690e":0,"2574549":0,"2578e":38,"258":0,"2587210e":0,"259":0,"2603":0,"26384059e":0,"264":43,"26478225e":0,"26585299e":0,"2678400":0,"2755516":0,"276":0,"2768":0,"280":38,"2857":[36,43],"28726324e":0,"288":0,"2883":0,"29384024e":0,"294":0,"29419917e":0,"2961":0,"2962":0,"2986151":0,"2arrai":0,"2long_nam":0,"3":[0,36,38,42],"30":[0,38,43],"300":[0,38],"30074963":0,"300gb":38,"301":0,"3010":0,"30191126":0,"302":0,"308":0,"30994225":0,"31":[6,38,43],"3111long_nam":0,"3113521":0,"3122":0,"3147912":0,"315":0,"319":0,"32":6,"320":0,"320time":0,"321":[0,36],"3217907e":0,"322":0,"3256":0,"3273806e":0,"329":36,"338":0,"3466e":38,"34734988":43,"349":0,"35":38,"3503":0,"36":[38,43],"361":36,"362":36,"36295935e":0,"3629593e":0,"363":[0,36],"364":36,"365":[0,6,36,43],"36555832e":0,"3655583e":0,"3682":0,"3689165e":0,"36907406e":0,"3690741e":0,"3692071e":0,"3699600e":0,"37":0,"3706082e":0,"3729831e":0,"37300191":43,"3746414e":0,"375":[6,42],"3751":0,"3809236e":0,"384":0,"384nlon":0,"3882658e":0,"39":6,"392":0,"398":0,"399731":0,"4":[0,6,36,38,42,43],"40":[0,6],"4001":0,"4009069":0,"4021814":0,"4040368":0,"404898":0,"4067074":0,"41939":0,"42098685":43,"4237":0,"424":0,"4250":0,"4277e":38,"4326100e":0,"4331030e":0,"4334931e":0,"43508524":43,"437":43,"43821886":0,"43825188":0,"43828985":0,"4393732e":0,"4487":0,"45":[0,6,42],"4500":0,"46067247":0,"4607256":0,"46078444":0,"461":0,"4683":0,"46831194":0,"46832138":0,"46832347":0,"4683long_nam":0,"469914":0,"4748":0,"4748102":0,"47482634":0,"4748649":0,"4748long_nam":0,"4750":0,"476":[36,43],"48250174e":0,"4825017e":0,"48400059e":0,"4840006e":0,"48503680e":0,"4850368e":0,"48569869":43,"4993":0,"4e":6,"5":[0,6,36,38,41,42,43],"50":[0,6],"5000":0,"5022994":0,"5025004":0,"50253665":0,"503":0,"51505888e":0,"5150589e":0,"5244":0,"5249030e":0,"5250":0,"52743149":43,"53462509":43,"5367837e":0,"5469234e":0,"5499":0,"55000":38,"551":0,"5526e":38,"55383604":43,"5547771e":0,"55885696e":0,"5588570e":0,"56":38,"562509":0,"56255509e":0,"5650e":38,"57984342e":0,"58":[0,6],"5804":0,"5845":0,"58585157e":0,"58739719":43,"5915e":38,"5922561e":0,"5long_nam":0,"6":[0,6,38],"60":0,"6012949e":0,"60281624e":0,"6028162e":0,"60381520e":0,"6038152e":0,"606":0,"6069":0,"6086453":0,"609":43,"61":43,"6100825":0,"6102467":0,"6105724e":0,"6109915e":0,"6115820e":0,"6124141":0,"6131761":0,"6132909":0,"6186378":0,"6188763":0,"6191071":0,"62053943e":0,"6205394e":0,"6269054e":0,"6302508e":0,"6302e":38,"6337e":38,"64590645":0,"64590846e":0,"6459085e":0,"64599246":0,"64608306":0,"64647889e":0,"6464789e":0,"6465223":0,"646928":0,"6469871":0,"64724785":0,"64728695":0,"6472e":38,"6474208":0,"6490371e":0,"6491e":38,"6563296e":0,"659942":0,"6610518e":0,"6614746e":0,"6619680e":0,"6649286e":0,"670":0,"6709":0,"675":0,"6750705":0,"6755391":0,"676":0,"6762853":0,"677646":0,"6781813":0,"6782286":0,"67901599e":0,"6790160e":0,"679559":0,"67955939":0,"68":[0,38],"6802498e":0,"687509":0,"68long_nam":0,"6908929":0,"6940153":0,"6973624":0,"7":[0,42,43],"70":[0,42],"701605":0,"702":0,"7068":0,"7094808e":0,"7137914e":0,"714111":0,"7159530e":0,"7167169":0,"7193749":0,"7207031":0,"7222056":0,"7234391":0,"725169":0,"725241":0,"7254934":0,"7270881":0,"7276651":0,"7282004":0,"7286":0,"729":0,"7291213":0,"730":[6,38],"7308325":0,"7312745":0,"7320296":0,"733":0,"733403":0,"7343705":0,"7369074":0,"7369847":0,"737":0,"738":[0,36,43],"738227":0,"7382345":0,"7382551":0,"7391715":0,"74":0,"7401036e":0,"744":0,"7457155e":0,"7465262":0,"74763227e":0,"7476323e":0,"749":43,"7491":0,"75":[6,42],"7508115":0,"752547":0,"7526e":38,"7527065":0,"7529848":0,"7530627":0,"7537823":0,"754208":0,"754467":0,"7545877":0,"7565235":0,"7570819":0,"7580512":0,"7581507e":0,"7583826":0,"7587181":0,"7588273":0,"7596801e":0,"7601882e":0,"7604":0,"7613":0,"761343":0,"7630517e":0,"7642565":0,"7655563":0,"76570279":43,"7665":0,"7679":0,"76989":38,"7722":36,"7748":0,"7756":36,"77653456":0,"776535":0,"78":0,"7815877":0,"786091":0,"7932765e":0,"7971e":38,"7982550e":0,"7986882e":0,"7histori":0,"8":[0,5,6,38],"80":[0,42],"8008100e":0,"8025139e":0,"8032774":43,"8034658":0,"8037182":0,"8039566":0,"804067":0,"8040985e":0,"8042675":0,"8044078":0,"806642":0,"807":0,"8092e":38,"8099785":0,"8108238":0,"810999":0,"8111901":0,"8118666":0,"8121454":0,"812509":0,"8147":0,"816":0,"8161112":0,"8163347":0,"8167795":0,"816coordin":0,"816long_nam":0,"817":0,"8172491":0,"8174808":0,"8177130e":0,"8179355":0,"817long_nam":0,"818":0,"8212":0,"829":0,"8295599":0,"8316668":0,"8321355":43,"8330e":38,"8334056":0,"8361694":0,"8377023":0,"8391787":0,"8403429":0,"8413076":0,"8422267":0,"8425745":0,"8448023":0,"8457245":0,"845775":0,"846":0,"8460748":0,"8488038":0,"849":0,"8493931":0,"849752":0,"85":0,"85055796":43,"851":43,"8511611":0,"852575":0,"8536096":0,"854":0,"8542347":0,"854long_nam":0,"85502453":43,"8554877":0,"85813":[0,38],"85813time":0,"858323":0,"858912":0,"85long_nam":0,"862084":0,"8674443":0,"868257":0,"87":0,"87359974":0,"8736":0,"874":0,"8747":0,"88":0,"8828746e":0,"8921":0,"9":[0,6,38,42],"90":0,"90032256":0,"9008":0,"902904":0,"9040008":0,"9041":0,"90535":0,"905367":0,"90565":0,"90594":0,"90625":0,"90655":0,"90686":0,"90716":0,"90747":0,"90778":0,"90808":0,"90839":0,"90869":0,"90900":0,"90916":0,"90930":0,"90944":0,"90959":0,"90975":0,"90990":0,"91020":0,"91051":0,"91081":0,"91112":0,"91143":0,"91173":0,"91204":0,"91234":0,"91716307":43,"919":43,"9234":0,"9276e":38,"928":0,"9296982e":0,"9298e":38,"9355e":38,"94160815":43,"9498423":0,"9608721e":0,"9613757e":0,"962":43,"9621306e":0,"9625051e":0,"9632749e":0,"9808744e":0,"98388666":0,"9845928":0,"98466176":0,"98605941":43,"9888":0,"989":43,"9897":0,"9905e":38,"9907996":0,"9921":0,"9966":0,"9989e":38,"9997e":38,"9arrai":0,"boolean":[29,41],"case":[36,38],"class":[7,8,9,10,11,12,13,14,32,37,38,41],"dani\u00ebl":39,"default":[6,36,38],"do":[38,41],"final":[5,38],"float":[0,8,16],"function":[0,8,35,36,41,43],"import":[0,6,32,38,42,43,44],"int":0,"long":0,"new":[0,5,6],"return":[0,29,32,34,36,43],"true":[0,29,38,42],"var":[0,38],A:39,For:[0,36,38],If:[29,36],In:32,It:5,Or:43,The:[5,8,21,22,36,37,41,43],Then:32,There:38,To:44,__init__:[7,8,9,10,11,12,13,14,32],_build:5,_fillvalu:0,_flux:30,_rate:30,_solv:[6,38],_toc:5,a_consumpt:42,a_encount:42,a_metabol:42,ab:38,abil:38,about:0,abov:[38,41],absent:0,absolut:38,access:32,action:5,activ:[5,38],actual:30,ad:38,adult:19,after:38,afterward:5,again:5,against:5,al:37,all:[0,5],all_group:13,allow:[0,38],also:38,amet:8,among:41,amp_fract:[36,43],an:[0,1,2,3,4,11,32,37,38,41,43],analyt:[35,38],andersen:39,annual:43,answer:38,anyth:0,apart:38,api:[2,4],append:0,appli:[5,38,41],appreci:5,approach:5,ar:[0,5,30,32,36,38,41,42],area:[0,16],arrai:[0,24,29,33,34,43],array_lik:[16,20,21,22,24,29,30,32,33],arrow:37,aspect:41,assign_coord:[0,38],assim_effici:42,assum:38,astyp:0,attr:0,attribut:[0,6,8,36,43],auto:[1,2,3,4],autoc:0,automat:5,autoreload:[6,38,43],av:0,avail:[5,17,19,27,41],averag:0,ax:[38,43],axi:0,b:[5,25,43],b_consumpt:42,b_encount:42,b_metabol:42,back:5,base:5,baselin:0,baseline_compar:38,baselines_from_nc:38,baselines_tmp:38,bathymetri:[32,35],bathymetry_data:32,bbox_to_anchor:[6,38],becaus:5,befor:[0,38],below:41,benthic:[7,32,33,38,41],benthic_effici:[6,42],benthic_pelagic_depth_cutoff:[41,42],benthic_prei:[6,38,41,42],benthic_prey_biomass:33,benthic_prey_ic_data:32,best:5,better:0,between:0,biomass:[6,16,24,26,28,29,30,32,33,34,36,37,38,41,43],biomass_convers:0,biomass_init_fil:32,biomass_prei:16,biomass_slic:32,book:5,both:[0,38],bottom:[0,31,39],bound:41,bpow:8,branch:5,browser:5,bug:5,bugfix:5,build:[5,41],built:5,c:0,calendar:[0,38],call:0,can:[5,32,38],cap:[33,41],carrai:0,carrying_capac:[6,42],casper:38,categori:37,ccsm:0,cd:5,cell:[0,38],cell_method:0,cellcell_method:0,centimet:0,cesm2_0:0,cesm:38,cesm_output:0,cesmdata:0,cf:0,cftime:0,cgd:0,chang:[5,38],charl:39,checkout:5,ci:5,client:38,clone:5,close:38,cm:0,cmlong_nam:0,code:[5,38],coeff:8,collect:43,colleen:39,column:[0,38],com:5,come:[0,40],comm:38,command:5,commit:5,common:0,compar:5,compare_forc:38,compare_nc:38,comparison:[0,38],compon:[0,34,41],componentcell_method:0,comput:[16,17,18,19,20,21,22,23,24,26,27,29,30,31,32,33,35,38,41],compute_tend:32,concaten:0,conda:5,condit:[32,38],config:38,config_and_run_from_netcdf:38,config_and_run_testcas:[6,38],configur:41,connect:38,consid:5,consist:5,constant:42,constitu:41,consumpt:[15,23,28],consumption_rate_link:[6,15,20,24,28,30],consumption_rate_max_pr:[6,15,23],consumption_zoo_frac_mort:28,consumption_zoo_raw:28,consumption_zoo_sc:28,contain:[7,9,14,32,36],content:0,context:32,contributor:5,conveni:5,convent:0,coordin:[0,36,43],copi:[0,5],core:38,could:38,coupl:41,cov:5,cover:5,cpu:[0,38],creat:[0,5],critic:5,cseg:0,curr:0,current:0,cut:0,cutoff:41,cycl:[38,43],cyclic:[6,36,38,43],d:[0,19,30,43],da1:38,da2:38,da:[0,16],dai:[0,18,36,38],daili:38,dash:37,dashboard:38,dask_jobqueu:38,data:[0,5,6,7,9,10,12,13,14,33,36],dataarrai:[16,20,21,22,24,29,43],dataset:[0,6,32,36,38,43],datasetdimens:0,date:38,datetimenoleap:0,decode_tim:0,deepest:0,def:0,default_config:38,default_flow_styl:42,defin:[10,41],degc:[0,43],degre:0,degrees_eastlong_nam:0,degrees_north:0,degrees_northaxi:0,degrees_northlong_nam:0,demers:[8,39,41,42],demersal_functional_typ:29,demersal_functional_type_kei:[41,42],denderen:39,denot:37,densiti:16,dep:[0,8],depend:5,depth:[0,37,38,43],depthstandard_nam:0,depthunit:0,describ:[5,11],descript:41,detail:5,devel:5,diagnost:0,diagnostic_nam:[6,38],diatc:0,diatc_150m:0,diatom:0,diazc:0,diazc_150m:0,dict:[0,6,32,33,36],dictionari:[32,36,41],differ:38,dim:0,dimens:[0,6,36,38,43],directli:[0,5],directori:5,disp:0,distribut:38,doc:5,doe:41,doi:39,domain:[32,36,43],domain_dict:[32,36,43],domain_param:[8,9,29],domain_tanh_shelf:43,done:38,dot:37,driver:[38,39],driver_config:38,ds:0,ds_forc:0,ds_forcing_spinup:0,ds_in:0,ds_out:[6,38],ds_read_forc:0,ds_t:32,dtype:0,due:38,dump:42,dxdt:32,e11_len:0,e:[8,26,36],each:38,eaton:0,ecosys_param:[16,29],ecosystem:[21,22,29,30],edit:5,edu:0,effici:[12,42],els:[0,38],enabl:[5,41],encod:0,encount:[16,23],encounter_rate_link:[6,15,16],encounter_rate_pr:[16,23],encounter_rate_tot:[6,15,16],end_dat:[6,38],energi:[17,19,27,41],energy_avail_r:[6,17,19,27,30],energy_frac_somatic_growth:[8,41,42],engag:41,ensur:[5,38],entri:41,env:5,environ:5,ep:0,equilibri:38,err:38,error:38,esm:37,et:37,evenli:38,evolv:38,exact:38,exactli:0,exampl:[32,36,41,43],experienc:[16,21,22],express:5,extrapol:38,f90:0,f:[0,5,18,38],faithfulli:0,fals:[0,29,38,41,42],featur:38,feed:[10,11,37],feeding_link:6,feeding_set:10,feel:5,feisti:[0,3,6,38,42,44],feisty_input_from_fosi_monthli:0,feisty_input_from_fosi_monthly_1year:0,feisty_inst:32,few:38,field:[38,41,43],fiesti:0,fig:[38,43],fig_suptitl:38,figsiz:38,figur:43,file:[5,38],filenam:0,fill:16,fine:5,finish:[6,38],first:[0,38],first_fish_id:30,fish:[0,6,8,18,19,21,22,29,30,32,33,37,39,41,42],fish_biomass:33,fish_catch_r:[6,18,19,30],fish_ic_data:32,fish_list:[13,17,18,19,21,22,23,27,29],fisheri:18,fishing_r:18,fishing_rate_per_year:[9,41,42],fix:5,float320:0,float329:0,float32:0,float6415:0,float64320:0,float64829:0,float649:0,float64:[0,6,36,43],floor:38,flux:[0,30,36,43],flux_convers:0,fn:8,follow:[5,8,32],food:[20,24,29,41],food_web:[6,11,15,16,20,24,28,29,30,41,42],forag:[8,39,41,42],forc:[33,36,38,41],force_nonneg:38,forcing_cycl:43,forcing_file_nam:0,forcing_tim:43,fork:5,format:[0,5],forward:32,fosi:38,fosi_cesm:38,fosi_cesm_daili:38,fosi_cesm_spinup:38,fosi_spinup:38,frac:0,fracl:0,fraction:[0,16,29,31,41],framework:5,frate:19,free:5,from:[26,27,32,37,38,42],full:38,functional_typ:[8,41,42],functional_type_kei:[41,42],g:[0,8,30,43],gamma:[19,27],gb:38,gca:43,gcm:33,gcm_state_update_kwarg:33,gecoiaf:0,gener:[1,2,3,4,5,6,36,38,43],geometr:8,get_default:42,get_model_domain:32,git:5,github:5,given:0,glade:0,global:[6,39,43],good:38,gram:41,grid:[0,38],group:[6,8,38,41],group_ind:[7,8,14],growth:[17,19,26,27,41],growth_rat:[6,19,26,27,30,38],gt:0,guidelin:5,gx1v7:38,gx1v7_vert_grid:0,h:39,habitat:37,hand:43,happi:5,harmon:[36,43],harmonic_parm:43,harvest:[19,41],harvest_select:[8,41,42],has_year_zero:0,have:0,head:5,helper:0,here:[5,41,42,43],highli:5,histori:0,hook:5,how:[38,41],html:5,htmsourc:0,http:[0,5],i:[0,8,11,26,36,43],i_fish:12,i_fish_from:12,ic:0,id:0,ideal:[35,36,38],ignore_year_in_forc:38,illustr:43,improv:5,includ:[37,41,43],index:[0,5],individu:[8,11],info:[6,43],inform:[11,12,13,32,33],ingest:[20,41],ingestion_r:[6,17,20],inhabit:41,initi:[32,38],input:[30,37],input_fil:0,input_templ:0,instal:5,instead:[0,38],instruct:5,integ:36,integr:[6,38],interact:37,interfac:[5,32,37],intermedi:0,interpol:38,interv:0,introduc:37,invert_yaxi:43,io:0,ipynb:0,is_larv:[12,42],isel:[0,6,38,43],isel_dict:38,isfil:0,issu:5,item:16,its:[5,37,38],j:39,jame:39,join:0,junit:5,junitxml:5,jupyt:5,just:0,juvenil:19,k:[0,25],k_consumpt:42,k_encount:42,k_metabol:42,ken:39,kept:38,keyword:33,kmt:0,kristen:0,kristenk:0,kt:8,kwarg:[7,8,14],label:43,languag:5,larg:[0,38,41,42],larger:38,larval:26,last:38,lat:0,latest:5,latitud:0,latitudestandard_nam:0,latitudeunit:0,layer:0,layout:5,ld:[6,38,42],legend:[6,38,43],len:[32,38],level:38,like:43,limit:28,line2d:43,line:[0,37,43],linewidth:6,link:[11,12,38],list:[12,21,22,29,30,36,41],live:5,load_ext:[6,38,43],loc:38,local:5,locat:38,lofflin:[41,42],log:[6,38],long_nam:[0,43],longitud:0,look:[38,43],loss:[0,19],lp:[6,38,42],lt:0,lzoo_loss_150m:0,lzooc_150m:0,m:[0,5,37,39,43],main:5,maintain:5,make_err_plot:38,make_plot:38,manag:5,markdown:5,marker:43,mask:0,mass:[8,25,30],master:5,match:38,matlab:0,matlab_baselin:38,matlab_script:38,matlab_script_loc:38,matplotlib:[0,6,38,43],matter:0,max_output_time_dim:38,maxi:0,maximum:23,md:[6,38,42],mean:[0,8,21,22,31],meanunit:0,mechanist:37,medium:[38,41,42],mem:38,member:[6,42],member_obj_list:[10,30],memori:38,meso:0,mesozooplankton:0,mesozooplanktonunit:0,messag:5,met:8,metab:8,metabol:[8,21],metabolism_r:[6,17,21],metadata:0,meter:41,method:[7,8,9,10,11,12,13,14,32],mf:[6,38,42],minimum:[0,38],mlevi:0,mmol:0,mod_param:[7,8,10,14],mode:41,model:[32,33,36,41,43],model_set:[41,42],modifi:38,modul:43,month:0,monthli:[0,38],mortal:[0,19,22,28,33,38,41,43],mortality_coeff_per_yr:42,mortality_r:[6,19,22,30],mortality_typ:[22,42],mp:[6,38,42],ms:[0,38],mu:[36,43],multi:5,multipl:37,must:41,my_reshap:0,myst:5,name:[0,5,6,7,8,14,41,42],natur:[19,22],nc:[0,38],ncar:5,ncore:38,ncpu:38,ndx_from:12,necessari:5,neg:38,netcdf:[0,38],new_tim:0,next:38,nlat:0,nlon:0,nmolc:0,nmort:19,noleap:0,noleapaxi:0,noleapbound:0,non:0,none:[0,32,36,38],noneconvent:0,note:[0,36,38,43],notebook:[0,5,38],noth:5,now:[0,5],np:[0,38,43],nrow:43,nsteps_tot:0,nt:36,nu:[17,27],num_chunk:38,number:36,numer:[21,22,31,32],numpi:[0,38,43],nx:[32,35,43],o:43,object0001:0,object:[0,6,20,21,22,24,29,30,32,43],occur:37,ocean:[0,38],oceanographi:39,off:[0,5,38],offlin:[0,38,41],offline_driv:1,old_set:38,onc:5,one:[0,8],onli:37,open:0,open_dataset:[0,38],option:[29,32,38],organ:0,orig:8,os:0,other:37,output:38,over:[0,38],own:5,p:[0,39],packag:37,page:[1,2,3,4,41],pair:33,paramet:[0,7,8,9,14,16,20,21,22,24,29,30,31,32,33,36,41],parameter:[37,41],paramter:8,particul:0,pass:5,path:[0,5],pattern:39,pbscluster:38,pelag:[0,16,29,31,39,41],pelagic_demersal_coupl:[8,41,42],pelagic_demersal_coupling_apply_pref_type_kei:[41,42],pelagic_demersal_coupling_type_kei:[41,42],pelagic_functional_typ:29,pelagic_functional_type_kei:[41,42],pep:5,per:18,pertain:12,petrik:[37,39],phase:[36,43],phyto:0,pi_be_cutoff:29,pip:5,piscivor:[8,42],pleas:5,plot:[6,38,43],plot_set:38,plt:[0,6,38,43],poc:[0,36,43],poc_flux:30,poc_flux_bottom:[0,36,38,43],poc_flux_in_bottom:0,pocean:39,point:43,pop2:0,pop:[0,38],port:38,post:0,potenti:0,power:8,pre:5,predat:[6,19,23,24,41,42],predation_flux:[6,24,30],predation_r:[6,19],predation_zoo_flux:24,prefer:[6,41,42],prei:[6,7,16,32,33,37,41,42],previou:0,primari:32,print:[0,38,42],prior:38,probabl:0,process:[0,38],product:26,prognost:[0,34,41],progress:39,project:44,properti:32,proport:41,provid:[1,2,3,4,37,38,41,43],proxi:38,psa:39,pull:[5,38],purpos:38,push:5,pyplot:[0,6,38,43],pytest:5,python:[5,37,38],quadmesh:43,quadrat:43,question:5,queue:38,quick:38,r:39,rais:38,ran:38,rang:[38,43],rate:[15,16,18,19,21,23,30,41],rather:38,re:5,read:[0,38],realli:[0,41],recruit:26,recruitment_flux:[6,26,30],reduc:38,regard:5,region:37,rel:38,relationship:[10,41],releas:0,remov:0,replac:0,repo:5,report:5,repositori:5,repres:43,reproduc:[0,38],reproduct:[12,13,26,27,38,41],reproduction_r:[6,26,27,30],reproduction_rout:[26,41,42],reset:29,resource_spec:38,respect:38,restructuredtext:5,result:[0,20,21,22,24,29,38],revis:0,robust:5,round:38,rout:[12,13,41],routing_set:13,run:[5,41],s:[0,5,38],sandbox:5,scale:[0,38],scipi:0,script:38,sd:[6,38,42],seafloor:0,seafloorunit:0,season:36,section:[5,41],sel:[6,38],selec:[18,19],select:[18,19,38],sep:0,seri:0,set:[5,32,36],set_titl:38,set_ylabel:38,set_ylim:38,set_yscal:38,set_yticklabel:38,settings_dict:32,settings_in:[6,38],setup:[6,38],sever:0,sf:[6,38,41,42],shape:43,shelf:37,should:[0,5],show:37,similarli:38,simpl:[5,38],simul:[38,41],sinc:0,singl:43,size:41,size_class:[8,41,42],size_class_bound:[41,42],slice:0,small:[0,5,38,41,42],smaller:0,so:38,solut:38,somat:[19,27],some:[0,5,43],soon:40,sort_kei:42,sourc:0,sp:[6,38,42],space:38,spc:0,spc_150m:0,specif:[12,30],specifi:[36,41],spent:[16,29,31],spinup_forcing_file_nam:0,split:0,standard_nam:0,start:[6,38],start_dat:[6,38],start_tim:0,state:33,statu:38,step:[5,6,32,38],still:0,stock:39,stone:5,store:[13,20,21,22,24,29],string:8,strip:0,structur:[7,9,10,12,13,14,37,41],style:5,subject:41,submit:5,subpackag:43,subplot:[38,43],suffix:30,suggest:5,sum:41,summari:[1,2,3,4],suppos:0,suptitl:38,surround:37,sy:[0,38],t0:25,t62_g16:0,t:[0,5,8,25,38],t_bottom:[0,31,36,43],t_frac_pelag:[16,29,31],t_frac_pelagic_stat:[8,29,41,42],t_frac_prei:16,t_habitat:[6,15,16,21,22,23],t_pelag:[0,31,36,43],take:0,taken:37,tanh:35,tanh_shelf:[6,38],tarea:0,tarrai:0,task:0,tavg:0,tavg_sum:0,tavg_sum_qflux:0,tcp:38,temp_150m:0,temp_bottom:0,temperatur:[0,16,21,22,31,36,43],temperaturecell_method:0,temperatureunit:0,templat:[6,38],tendenc:[30,32,33],tendency_data:32,term:[28,41],test:[5,36,38],test_cas:38,test_d:6,test_locs3:38,testcas:[38,43],text:43,than:[0,38],them:0,thi:[0,1,2,3,4,5,8,32,37,38,41,43],thick:0,thre:[0,38],three:[37,38],threshold:0,through:[5,38],time0:0,time1:0,time:[0,6,16,29,30,31,32,33,36,38],time_boundarrai:0,timeaxi:0,timecalendar:0,timegrid_loc:0,timeout:38,timestep:6,timeunit:0,tini:0,titl:[0,38,43],tlat:0,tlong:0,to_netcdf:0,tool:5,total:[0,30,38],total_tend:30,totc:0,tracker:5,treat:0,two:37,type:[8,36,41],typic:38,u12:6,u15:6,u2:6,u3:[36,43],u:5,ucar:0,under:5,underflow:0,underli:37,unit:43,unknown:38,up:39,updat:5,us:[0,5,35,36,37,38,41,43,44],usabl:5,user:[0,5,38],util:[5,38],utilit:43,utilti:43,valu:[0,33,36,38],valueerror:38,van:39,vari:36,variabl:[0,6,36,43],variablesrevis:0,varieti:38,verbos:5,verifi:38,version:5,vert_grid_fil:0,via:[5,32],view:5,wa:[0,38],wall:[0,38],walltim:38,watson:39,we:[38,43],web:[5,20,24,29,41],websit:5,weight:[21,22,31,41],welcom:5,well:[0,38],were:38,when:[0,5,41],whenev:5,where:[0,38],within:38,without:[0,5],work:[0,5],workflow:5,write:0,write_netcdf:0,ww:0,www:0,x:[0,6,36,38,43],xarrai:[0,6,16,24,29,32,36,37,38,43],xml:5,xr:[0,38,43],y:0,yaml:[38,42],yarrai:0,year:[0,38],ylim:[6,38],yml:5,you:5,your:5,your_github_usernam:5,yscale:6,z:0,z_t:0,zarrai:0,zero:[0,38],zone:41,zoo1:36,zoo2:36,zoo:[0,6,36,41,42,43],zoo_loss_150m:0,zoo_mort:[0,28,36,38,43],zoo_mortality_data:33,zoo_nam:36,zoo_spec:36,zooc:[0,36,38,43],zooc_150m:0,zooplankton:[14,28,33,36,37,38,41,42,43],zooplankton_biomass:33,zooplankton_functional_type_kei:[41,42]},titles:["Generate forcing (does not contain biomass) from CESM output","FEISTY Driver","FEISTY Interface","Internal API","FEISTY testcase","Contributing to the FEISTY model","Running the model","feisty.core.ecosystem.benthic_prey_type","feisty.core.ecosystem.fish_type","feisty.core.ecosystem.fishing","feisty.core.ecosystem.food_web","feisty.core.ecosystem.food_web_link","feisty.core.ecosystem.reproduction_link","feisty.core.ecosystem.reproduction_routing","feisty.core.ecosystem.zooplankton_type","feisty.core.process.compute_consumption","feisty.core.process.compute_encounter","feisty.core.process.compute_energy_avail","feisty.core.process.compute_fish_catch","feisty.core.process.compute_growth","feisty.core.process.compute_ingestion","feisty.core.process.compute_metabolism","feisty.core.process.compute_natural_mortality","feisty.core.process.compute_pred_encounter_consumption_max","feisty.core.process.compute_predation","feisty.core.process.compute_rate_T_mass_scaling","feisty.core.process.compute_recruitment","feisty.core.process.compute_reproduction","feisty.core.process.compute_rescale_zoo_consumption","feisty.core.process.compute_t_frac_pelagic","feisty.core.process.compute_total_tendency","feisty.core.process.t_weighted_mean_temp","feisty.feisty_instance_type","feisty.feisty_instance_type.compute_tendencies","feisty.feisty_instance_type.get_prognostic","feisty.testcase.domain_tanh_shelf","feisty.testcase.forcing_cyclic","Fisheries Size and Functional Type Model (FEISTY)","Comparing with matlab Baselines","References","Scientific Background","FEISTY Settings","Default settings","FEISTY test cases","Usage"],titleterms:{"case":43,"default":42,"do":0,"function":37,addit:38,also:0,api:[1,3],background:40,baselin:38,bathymetri:43,benthic_prey_typ:7,biomass:0,cesm:0,chunk:38,cluster:38,compar:38,compon:3,compute_consumpt:15,compute_encount:16,compute_energy_avail:17,compute_fish_catch:18,compute_growth:19,compute_ingest:20,compute_metabol:21,compute_natural_mort:22,compute_pred:24,compute_pred_encounter_consumption_max:23,compute_rate_t_mass_sc:25,compute_recruit:26,compute_reproduct:27,compute_rescale_zoo_consumpt:28,compute_t_frac_pelag:29,compute_tend:33,compute_total_tend:30,condit:0,configur:[6,38],contain:0,contribut:5,convers:0,core:[7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31],dask:38,data:[38,43],develop:5,document:5,doe:0,domain_tanh_shelf:35,driver:1,drop:0,ecosystem:[7,8,9,10,11,12,13,14],featur:5,feedback:5,feisti:[1,2,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,41,43],feisty_instance_typ:[32,33,34],file:0,fish:9,fish_typ:8,fisheri:37,food_web:10,food_web_link:11,forc:[0,43],forcing_cycl:36,from:0,gener:0,get:0,get_prognost:34,ideal:43,improv:38,initi:0,interfac:2,intern:3,land:0,mat:0,matlab:38,model:[3,5,6,37,38],object:2,out:0,output:[0,6],primari:2,process:[3,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31],refer:39,reproduction_link:12,reproduction_rout:13,request:5,reshap:0,run:[6,38],scientif:40,set:[38,41,42],size:37,spinup:0,t_weighted_mean_temp:31,test:43,testcas:[4,6,35,36],type:37,unit:0,up:38,usag:44,util:4,visual:43,write:5,zooplankton_typ:14}})
\ No newline at end of file
+Search.setIndex({docnames:["FOSI-forcing","api-driver","api-interface","api-internal","api-testcase","contributing","driver-example","generated/feisty.core.ecosystem.benthic_prey_type","generated/feisty.core.ecosystem.fish_type","generated/feisty.core.ecosystem.fishing","generated/feisty.core.ecosystem.food_web","generated/feisty.core.ecosystem.food_web_link","generated/feisty.core.ecosystem.reproduction_link","generated/feisty.core.ecosystem.reproduction_routing","generated/feisty.core.ecosystem.zooplankton_type","generated/feisty.core.process.compute_consumption","generated/feisty.core.process.compute_encounter","generated/feisty.core.process.compute_energy_avail","generated/feisty.core.process.compute_fish_catch","generated/feisty.core.process.compute_growth","generated/feisty.core.process.compute_ingestion","generated/feisty.core.process.compute_metabolism","generated/feisty.core.process.compute_natural_mortality","generated/feisty.core.process.compute_pred_encounter_consumption_max","generated/feisty.core.process.compute_predation","generated/feisty.core.process.compute_rate_T_mass_scaling","generated/feisty.core.process.compute_recruitment","generated/feisty.core.process.compute_reproduction","generated/feisty.core.process.compute_rescale_zoo_consumption","generated/feisty.core.process.compute_t_frac_pelagic","generated/feisty.core.process.compute_total_tendency","generated/feisty.core.process.t_weighted_mean_temp","generated/feisty.feisty_instance_type","generated/feisty.feisty_instance_type.compute_tendencies","generated/feisty.feisty_instance_type.get_prognostic","generated/feisty.testcase.domain_tanh_shelf","generated/feisty.testcase.forcing_cyclic","intro","matlab-comparison","references","scientific-background","settings","settings-show-defaults","testcase-datasets","usage"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["FOSI-forcing.ipynb","api-driver.rst","api-interface.rst","api-internal.rst","api-testcase.rst","contributing.rst","driver-example.ipynb","generated/feisty.core.ecosystem.benthic_prey_type.rst","generated/feisty.core.ecosystem.fish_type.rst","generated/feisty.core.ecosystem.fishing.rst","generated/feisty.core.ecosystem.food_web.rst","generated/feisty.core.ecosystem.food_web_link.rst","generated/feisty.core.ecosystem.reproduction_link.rst","generated/feisty.core.ecosystem.reproduction_routing.rst","generated/feisty.core.ecosystem.zooplankton_type.rst","generated/feisty.core.process.compute_consumption.rst","generated/feisty.core.process.compute_encounter.rst","generated/feisty.core.process.compute_energy_avail.rst","generated/feisty.core.process.compute_fish_catch.rst","generated/feisty.core.process.compute_growth.rst","generated/feisty.core.process.compute_ingestion.rst","generated/feisty.core.process.compute_metabolism.rst","generated/feisty.core.process.compute_natural_mortality.rst","generated/feisty.core.process.compute_pred_encounter_consumption_max.rst","generated/feisty.core.process.compute_predation.rst","generated/feisty.core.process.compute_rate_T_mass_scaling.rst","generated/feisty.core.process.compute_recruitment.rst","generated/feisty.core.process.compute_reproduction.rst","generated/feisty.core.process.compute_rescale_zoo_consumption.rst","generated/feisty.core.process.compute_t_frac_pelagic.rst","generated/feisty.core.process.compute_total_tendency.rst","generated/feisty.core.process.t_weighted_mean_temp.rst","generated/feisty.feisty_instance_type.rst","generated/feisty.feisty_instance_type.compute_tendencies.rst","generated/feisty.feisty_instance_type.get_prognostic.rst","generated/feisty.testcase.domain_tanh_shelf.rst","generated/feisty.testcase.forcing_cyclic.rst","intro.md","matlab-comparison.ipynb","references.md","scientific-background.md","settings.rst","settings-show-defaults.ipynb","testcase-datasets.ipynb","usage.rst"],objects:{"feisty.core.ecosystem":[[7,0,1,"","benthic_prey_type"],[8,0,1,"","fish_type"],[9,0,1,"","fishing"],[10,0,1,"","food_web"],[11,0,1,"","food_web_link"],[12,0,1,"","reproduction_link"],[13,0,1,"","reproduction_routing"],[14,0,1,"","zooplankton_type"]],"feisty.core.ecosystem.benthic_prey_type":[[7,1,1,"","__init__"]],"feisty.core.ecosystem.fish_type":[[8,1,1,"","__init__"]],"feisty.core.ecosystem.fishing":[[9,1,1,"","__init__"]],"feisty.core.ecosystem.food_web":[[10,1,1,"","__init__"]],"feisty.core.ecosystem.food_web_link":[[11,1,1,"","__init__"]],"feisty.core.ecosystem.reproduction_link":[[12,1,1,"","__init__"]],"feisty.core.ecosystem.reproduction_routing":[[13,1,1,"","__init__"]],"feisty.core.ecosystem.zooplankton_type":[[14,1,1,"","__init__"]],"feisty.core.process":[[15,2,1,"","compute_consumption"],[16,2,1,"","compute_encounter"],[17,2,1,"","compute_energy_avail"],[18,2,1,"","compute_fish_catch"],[19,2,1,"","compute_growth"],[20,2,1,"","compute_ingestion"],[21,2,1,"","compute_metabolism"],[22,2,1,"","compute_natural_mortality"],[23,2,1,"","compute_pred_encounter_consumption_max"],[24,2,1,"","compute_predation"],[25,2,1,"","compute_rate_T_mass_scaling"],[26,2,1,"","compute_recruitment"],[27,2,1,"","compute_reproduction"],[28,2,1,"","compute_rescale_zoo_consumption"],[29,2,1,"","compute_t_frac_pelagic"],[30,2,1,"","compute_total_tendency"],[31,2,1,"","t_weighted_mean_temp"]],"feisty.feisty_instance_type":[[32,1,1,"","__init__"],[33,1,1,"","compute_tendencies"],[34,1,1,"","get_prognostic"]],"feisty.testcase":[[35,2,1,"","domain_tanh_shelf"],[36,2,1,"","forcing_cyclic"]],feisty:[[32,0,1,"","feisty_instance_type"]]},objnames:{"0":["py","class","Python class"],"1":["py","method","Python method"],"2":["py","function","Python function"]},objtypes:{"0":"py:class","1":"py:method","2":"py:function"},terms:{"0":[0,6,8,25,32,36,38,41,42,43],"00":[0,38],"0000":0,"00000000e":0,"0000000e":0,"0000e":38,"0001":[0,6,38],"0002":[6,38],"001":[41,42],"00137":0,"001371":0,"001371long_nam":0,"001433":0,"001433long_nam":0,"002":32,"002346":36,"002347":36,"0039425":0,"003963":0,"003963long_nam":0,"003963xarrai":0,"004059long_nam":0,"004059xarrai":0,"00406":0,"0088":0,"009":0,"009start_tim":0,"00calendar":0,"00long_nam":0,"01":[0,6,38,42],"0100":38,"0111364e":0,"0117":0,"0144":0,"02":[0,38],"0206011e":0,"02381":[36,43],"0249":[0,38],"025":38,"0251":38,"0255419":0,"02775":36,"02785":36,"0285e":38,"0289702e":0,"03":[0,38],"0391":0,"04":[0,38],"0402":0,"04108171":43,"0435":0,"0464":0,"0464e":38,"05":[0,6,32,38],"0501752":0,"0534e":38,"0541e":38,"054e":0,"056e":0,"05855756e":0,"05984232e":0,"05long_nam":0,"05unit":0,"06":38,"06162255e":0,"063":[8,42],"07":0,"070855":0,"0739e":38,"075":[6,42],"08":38,"0855":[8,42],"09":38,"092e":0,"0936":0,"094e":0,"0986":0,"0content":0,"0long_nam":0,"0titl":0,"0x7ff149df9310":43,"0x7ff152225d50":43,"0x7ff17860b150":43,"1":[0,6,30,36,38,41,42,43],"10":[0,19,25,39,43],"100":[0,19,38],"100270080":0,"1005":43,"1015":43,"1016":39,"1021":43,"102124":39,"1024":43,"1026":43,"1028":43,"1029":43,"1029756":0,"1041":0,"105":0,"11":0,"110":0,"115263":0,"115294":0,"115324":0,"115644":0,"115674":0,"115705":0,"11677":38,"1171":0,"1177113":0,"1196":0,"12":[0,6,38],"120":0,"122880":0,"125000":[41,42],"12coordin":0,"13":38,"130":0,"131":43,"1318":0,"135":0,"13550705e":0,"1355070e":0,"1387":0,"14":0,"140":0,"1482":0,"15":[0,6,38],"150":0,"15208992":0,"15209":0,"1526":0,"153e":0,"15485412e":0,"1548541e":0,"1555511e":0,"1558":0,"1561459e":0,"15633":38,"157e":0,"16":[0,38],"160":0,"1649e":38,"166":0,"1664":0,"170":0,"175":42,"176":39,"17873201":43,"1794e":38,"18":[36,38],"180":[0,38],"18357879e":0,"1835788e":0,"1863":0,"19":[6,38,39],"191":0,"194":0,"195":38,"196":0,"1968":0,"19902725":43,"1arrai":0,"1e":[0,32,38],"1e4":0,"2":[0,6,36,38,42,43],"20":[0,38,42],"200":[37,42],"2012":0,"2015":0,"2019":[37,39],"202":38,"203":0,"2074":0,"21370613":43,"214":43,"215":0,"2184234e":0,"2193e":38,"22":[6,35,36,43],"220446049250313e":0,"22301965":43,"2263750":0,"2263750tavg_sum":0,"227":0,"229":0,"2298":0,"2331":0,"2354716":0,"2381":[36,43],"23z":0,"24":0,"2427e":38,"243":0,"248":0,"249":0,"25":42,"250":[41,42],"2529":0,"2553709e":0,"2561447e":0,"2564690e":0,"2574549":0,"2578e":38,"258":0,"2587210e":0,"259":0,"2603":0,"26384059e":0,"264":43,"26478225e":0,"26585299e":0,"2678400":0,"2755516":0,"276":0,"2768":0,"280":38,"2857":[36,43],"28726324e":0,"288":0,"2883":0,"29384024e":0,"294":0,"29419917e":0,"2961":0,"2962":0,"2986151":0,"2arrai":0,"2long_nam":0,"3":[0,36,38,42],"30":[0,38,43],"300":[0,38],"30074963":0,"300gb":38,"301":0,"3010":0,"30191126":0,"302":0,"308":0,"30994225":0,"31":[6,38,43],"3111long_nam":0,"3113521":0,"3122":0,"3147912":0,"315":0,"319":0,"32":6,"320":0,"320time":0,"321":[0,36],"3217907e":0,"322":0,"3256":0,"3273806e":0,"329":36,"338":0,"3466e":38,"34734988":43,"349":0,"35":38,"3503":0,"36":[38,43],"361":36,"362":36,"36295935e":0,"3629593e":0,"363":[0,36],"364":36,"365":[0,6,36,43],"36555832e":0,"3655583e":0,"3682":0,"3689165e":0,"36907406e":0,"3690741e":0,"3692071e":0,"3699600e":0,"37":0,"3706082e":0,"3729831e":0,"37300191":43,"3746414e":0,"375":[6,42],"3751":0,"3809236e":0,"384":0,"384nlon":0,"3882658e":0,"39":6,"392":0,"398":0,"399731":0,"4":[0,6,36,38,42,43],"40":[0,6],"4001":0,"4009069":0,"4021814":0,"4040368":0,"404898":0,"4067074":0,"41939":0,"42098685":43,"4237":0,"424":0,"4250":0,"4277e":38,"4326100e":0,"4331030e":0,"4334931e":0,"43508524":43,"437":43,"43821886":0,"43825188":0,"43828985":0,"4393732e":0,"4487":0,"45":[0,6,42],"4500":0,"46067247":0,"4607256":0,"46078444":0,"461":0,"4683":0,"46831194":0,"46832138":0,"46832347":0,"4683long_nam":0,"469914":0,"4748":0,"4748102":0,"47482634":0,"4748649":0,"4748long_nam":0,"4750":0,"476":[36,43],"48250174e":0,"4825017e":0,"48400059e":0,"4840006e":0,"48503680e":0,"4850368e":0,"48569869":43,"4993":0,"4e":6,"5":[0,6,36,38,41,42,43],"50":[0,6],"5000":0,"5022994":0,"5025004":0,"50253665":0,"503":0,"51505888e":0,"5150589e":0,"5244":0,"5249030e":0,"5250":0,"52743149":43,"53462509":43,"5367837e":0,"5469234e":0,"5499":0,"55000":38,"551":0,"5526e":38,"55383604":43,"5547771e":0,"55885696e":0,"5588570e":0,"56":38,"562509":0,"56255509e":0,"5650e":38,"57984342e":0,"58":[0,6],"5804":0,"5845":0,"58585157e":0,"58739719":43,"5915e":38,"5922561e":0,"5long_nam":0,"6":[0,6,38],"60":0,"6012949e":0,"60281624e":0,"6028162e":0,"60381520e":0,"6038152e":0,"606":0,"6069":0,"6086453":0,"609":43,"61":43,"6100825":0,"6102467":0,"6105724e":0,"6109915e":0,"6115820e":0,"6124141":0,"6131761":0,"6132909":0,"6186378":0,"6188763":0,"6191071":0,"62053943e":0,"6205394e":0,"6269054e":0,"6302508e":0,"6302e":38,"6337e":38,"64590645":0,"64590846e":0,"6459085e":0,"64599246":0,"64608306":0,"64647889e":0,"6464789e":0,"6465223":0,"646928":0,"6469871":0,"64724785":0,"64728695":0,"6472e":38,"6474208":0,"6490371e":0,"6491e":38,"6563296e":0,"659942":0,"6610518e":0,"6614746e":0,"6619680e":0,"6649286e":0,"670":0,"6709":0,"675":0,"6750705":0,"6755391":0,"676":0,"6762853":0,"677646":0,"6781813":0,"6782286":0,"67901599e":0,"6790160e":0,"679559":0,"67955939":0,"68":[0,38],"6802498e":0,"687509":0,"68long_nam":0,"6908929":0,"6940153":0,"6973624":0,"7":[0,42,43],"70":[0,42],"701605":0,"702":0,"7068":0,"7094808e":0,"7137914e":0,"714111":0,"7159530e":0,"7167169":0,"7193749":0,"7207031":0,"7222056":0,"7234391":0,"725169":0,"725241":0,"7254934":0,"7270881":0,"7276651":0,"7282004":0,"7286":0,"729":0,"7291213":0,"730":[6,38],"7308325":0,"7312745":0,"7320296":0,"733":0,"733403":0,"7343705":0,"7369074":0,"7369847":0,"737":0,"738":[0,36,43],"738227":0,"7382345":0,"7382551":0,"7391715":0,"74":0,"7401036e":0,"744":0,"7457155e":0,"7465262":0,"74763227e":0,"7476323e":0,"749":43,"7491":0,"75":[6,42],"7508115":0,"752547":0,"7526e":38,"7527065":0,"7529848":0,"7530627":0,"7537823":0,"754208":0,"754467":0,"7545877":0,"7565235":0,"7570819":0,"7580512":0,"7581507e":0,"7583826":0,"7587181":0,"7588273":0,"7596801e":0,"7601882e":0,"7604":0,"7613":0,"761343":0,"7630517e":0,"7642565":0,"7655563":0,"76570279":43,"7665":0,"7679":0,"76989":38,"7722":36,"7748":0,"7756":36,"77653456":0,"776535":0,"78":0,"7815877":0,"786091":0,"7932765e":0,"7971e":38,"7982550e":0,"7986882e":0,"7histori":0,"8":[0,5,6,38],"80":[0,42],"8008100e":0,"8025139e":0,"8032774":43,"8034658":0,"8037182":0,"8039566":0,"804067":0,"8040985e":0,"8042675":0,"8044078":0,"806642":0,"807":0,"8092e":38,"8099785":0,"8108238":0,"810999":0,"8111901":0,"8118666":0,"8121454":0,"812509":0,"8147":0,"816":0,"8161112":0,"8163347":0,"8167795":0,"816coordin":0,"816long_nam":0,"817":0,"8172491":0,"8174808":0,"8177130e":0,"8179355":0,"817long_nam":0,"818":0,"8212":0,"829":0,"8295599":0,"8316668":0,"8321355":43,"8330e":38,"8334056":0,"8361694":0,"8377023":0,"8391787":0,"8403429":0,"8413076":0,"8422267":0,"8425745":0,"8448023":0,"8457245":0,"845775":0,"846":0,"8460748":0,"8488038":0,"849":0,"8493931":0,"849752":0,"85":0,"85055796":43,"851":43,"8511611":0,"852575":0,"8536096":0,"854":0,"8542347":0,"854long_nam":0,"85502453":43,"8554877":0,"85813":[0,38],"85813time":0,"858323":0,"858912":0,"85long_nam":0,"862084":0,"8674443":0,"868257":0,"87":0,"87359974":0,"8736":0,"874":0,"8747":0,"88":0,"8828746e":0,"8921":0,"9":[0,6,38,42],"90":0,"90032256":0,"9008":0,"902904":0,"9040008":0,"9041":0,"90535":0,"905367":0,"90565":0,"90594":0,"90625":0,"90655":0,"90686":0,"90716":0,"90747":0,"90778":0,"90808":0,"90839":0,"90869":0,"90900":0,"90916":0,"90930":0,"90944":0,"90959":0,"90975":0,"90990":0,"91020":0,"91051":0,"91081":0,"91112":0,"91143":0,"91173":0,"91204":0,"91234":0,"91716307":43,"919":43,"9234":0,"9276e":38,"928":0,"9296982e":0,"9298e":38,"9355e":38,"94160815":43,"9498423":0,"9608721e":0,"9613757e":0,"962":43,"9621306e":0,"9625051e":0,"9632749e":0,"9808744e":0,"98388666":0,"9845928":0,"98466176":0,"98605941":43,"9888":0,"989":43,"9897":0,"9905e":38,"9907996":0,"9921":0,"9966":0,"9989e":38,"9997e":38,"9arrai":0,"boolean":[29,41],"case":[36,38],"class":[7,8,9,10,11,12,13,14,32,37,38,41],"dani\u00ebl":39,"default":[6,36,38],"do":[38,41],"final":[5,38],"float":[0,8,16],"function":[0,8,35,36,41,43],"import":[0,6,32,38,42,43,44],"int":0,"long":0,"new":[0,5,6],"return":[0,29,32,34,36,43],"true":[0,29,38,42],"var":[0,38],A:39,For:[0,36,38],If:[29,36],In:32,It:5,Or:43,The:[5,8,21,22,36,37,41,43],Then:32,There:38,To:44,__init__:[7,8,9,10,11,12,13,14,32],_build:5,_fillvalu:0,_flux:30,_rate:30,_solv:[6,38],_toc:5,a_consumpt:42,a_encount:42,a_metabol:42,ab:38,abil:38,about:0,abov:[38,41],absent:0,absolut:38,access:32,action:5,activ:[5,38],actual:30,ad:38,adult:19,after:38,afterward:5,again:5,against:5,al:37,all:[0,5],all_group:13,allow:[0,38],also:38,amet:8,among:41,amp_fract:[36,43],an:[0,1,2,3,4,11,32,37,38,41,43],analyt:[35,38],andersen:39,annual:43,answer:38,anyth:0,apart:38,api:[2,4],append:0,appli:[5,38,41],appreci:5,approach:5,ar:[0,5,30,32,36,38,41,42],area:[0,16],arrai:[0,24,29,33,34,43],array_lik:[16,20,21,22,24,29,30,32,33],arrow:37,aspect:41,assign_coord:[0,38],assim_effici:42,assum:38,astyp:0,attr:0,attribut:[0,6,8,36,43],auto:[1,2,3,4],autoc:0,automat:5,autoreload:[6,38,43],av:0,avail:[5,17,19,27,41],averag:0,ax:[38,43],axi:0,b:[5,25,43],b_consumpt:42,b_encount:42,b_metabol:42,back:5,base:5,baselin:0,baseline_compar:38,baselines_from_nc:38,baselines_tmp:38,bathymetri:[32,35],bathymetry_data:32,bbox_to_anchor:[6,38],becaus:5,befor:[0,38],below:41,benthic:[7,32,33,38,41],benthic_effici:[6,42],benthic_pelagic_depth_cutoff:[41,42],benthic_prei:[6,38,41,42],benthic_prey_biomass:33,benthic_prey_ic_data:32,best:5,better:0,between:0,biomass:[6,16,24,26,28,29,30,32,33,34,36,37,38,41,43],biomass_convers:0,biomass_init_fil:32,biomass_prei:16,biomass_slic:32,book:5,both:[0,38],bottom:[0,31,39],bound:41,bpow:8,branch:5,browser:5,bug:5,bugfix:5,build:[5,41],built:5,c:0,calendar:[0,38],call:0,can:[5,32,38],cap:[33,41],carrai:0,carrying_capac:[6,42],casper:38,categori:37,ccsm:0,cd:5,cell:[0,38],cell_method:0,cellcell_method:0,centimet:0,cesm2_0:0,cesm:38,cesm_output:0,cesmdata:0,cf:0,cftime:0,cgd:0,chang:[5,38],charl:39,checkout:5,ci:5,client:38,clone:5,close:38,cm:0,cmlong_nam:0,code:[5,38],coeff:8,collect:43,colleen:39,column:[0,38],com:5,come:[0,40],comm:38,command:5,commit:5,common:0,compar:5,compare_forc:38,compare_nc:38,comparison:[0,38],compon:[0,34,41],componentcell_method:0,comput:[16,17,18,19,20,21,22,23,24,26,27,29,30,31,32,33,35,38,41],compute_tend:32,concaten:0,conda:5,condit:[32,38],config:38,config_and_run_from_netcdf:38,config_and_run_testcas:[6,38],configur:41,connect:38,consid:5,consist:5,constant:42,constitu:41,consumpt:[15,23,28],consumption_rate_link:[6,15,20,24,28,30],consumption_rate_max_pr:[6,15,23],consumption_zoo_frac_mort:28,consumption_zoo_raw:28,consumption_zoo_sc:28,contain:[7,9,14,32,36],content:0,context:32,contributor:5,conveni:5,convent:0,coordin:[0,36,43],copi:[0,5],core:38,could:38,coupl:41,cov:5,cover:5,cpu:[0,38],creat:[0,5],critic:5,cseg:0,curr:0,current:0,cut:0,cutoff:41,cycl:[38,43],cyclic:[6,36,38,43],d:[0,19,30,43],da1:38,da2:38,da:[0,16],dai:[0,18,36,38],daili:38,dash:37,dashboard:38,dask_jobqueu:38,data:[0,5,6,7,9,10,12,13,14,33,36],dataarrai:[16,20,21,22,24,29,43],dataset:[0,6,32,36,38,43],datasetdimens:0,date:38,datetimenoleap:0,decode_tim:0,deepest:0,def:0,default_config:38,default_flow_styl:42,defin:[10,41],degc:[0,43],degre:0,degrees_eastlong_nam:0,degrees_north:0,degrees_northaxi:0,degrees_northlong_nam:0,demers:[8,39,41,42],demersal_functional_typ:29,demersal_functional_type_kei:[41,42],denderen:39,denot:37,densiti:16,dep:[0,8],depend:5,depth:[0,37,38,43],depthstandard_nam:0,depthunit:0,describ:[5,11],descript:41,detail:5,devel:5,diagnost:0,diagnostic_nam:[6,38],diatc:0,diatc_150m:0,diatom:0,diazc:0,diazc_150m:0,dict:[0,6,32,33,36],dictionari:[32,36,41],differ:38,dim:0,dimens:[0,6,36,38,43],directli:[0,5],directori:5,disp:0,distribut:38,doc:5,doe:41,doi:39,domain:[32,36,43],domain_dict:[32,36,43],domain_param:[8,9,29],domain_tanh_shelf:43,done:38,dot:37,driver:[38,39],driver_config:38,ds:0,ds_forc:0,ds_forcing_spinup:0,ds_in:0,ds_out:[6,38],ds_read_forc:0,ds_t:32,dtype:0,due:38,dump:42,dxdt:32,e11_len:0,e:[8,26,36],each:38,eaton:0,ecosys_param:[16,29],ecosystem:[21,22,29,30],edit:5,edu:0,effici:[12,42],els:[0,38],enabl:[5,41],encod:0,encount:[16,23],encounter_rate_link:[6,15,16],encounter_rate_pr:[16,23],encounter_rate_tot:[6,15,16],end_dat:[6,38],energi:[17,19,27,41],energy_avail_r:[6,17,19,27,30],energy_frac_somatic_growth:[8,41,42],engag:41,ensur:[5,38],entri:41,env:5,environ:5,ep:0,equilibri:38,err:38,error:38,esm:37,et:37,evenli:38,evolv:38,exact:38,exactli:0,exampl:[32,36,41,43],experienc:[16,21,22],express:5,extrapol:38,f90:0,f:[0,5,18,38],faithfulli:0,fals:[0,29,38,41,42],featur:38,feed:[10,11,37],feeding_link:6,feeding_set:10,feel:5,feisti:[0,3,6,38,42,44],feisty_input_from_fosi_monthli:0,feisty_input_from_fosi_monthly_1year:0,feisty_inst:32,few:38,field:[38,41,43],fiesti:0,fig:[38,43],fig_suptitl:38,figsiz:38,figur:43,file:[5,38],filenam:0,fill:16,fine:5,finish:[6,38],first:[0,38],first_fish_id:30,fish:[0,6,8,18,19,21,22,29,30,32,33,37,39,41,42],fish_biomass:33,fish_catch_r:[6,18,19,30],fish_ic_data:32,fish_list:[13,17,18,19,21,22,23,27,29],fisheri:18,fishing_r:18,fishing_rate_per_year:[9,41,42],fix:5,float320:0,float329:0,float32:0,float6415:0,float64320:0,float64829:0,float649:0,float64:[0,6,36,43],floor:38,flux:[0,30,36,43],flux_convers:0,fn:8,follow:[5,8,32],food:[20,24,29,41],food_web:[6,11,15,16,20,24,28,29,30,41,42],forag:[8,39,41,42],forc:[33,36,38,41],force_nonneg:38,forcing_cycl:43,forcing_file_nam:0,forcing_tim:43,fork:5,format:[0,5],forward:32,fosi:38,fosi_cesm:38,fosi_cesm_daili:38,fosi_cesm_spinup:38,fosi_spinup:38,frac:0,fracl:0,fraction:[0,16,29,31,41],framework:5,frate:19,free:5,from:[26,27,32,37,38,42],full:38,functional_typ:[8,41,42],functional_type_kei:[41,42],g:[0,8,30,43],gamma:[19,27],gb:38,gca:43,gcm:33,gcm_state_update_kwarg:33,gecoiaf:0,gener:[1,2,3,4,5,6,36,38,43],geometr:8,get_default:42,get_model_domain:32,git:5,github:5,given:0,glade:0,global:[6,39,43],good:38,gram:41,grid:[0,38],group:[6,8,38,41],group_ind:[7,8,14],growth:[17,19,26,27,41],growth_rat:[6,19,26,27,30,38],gt:0,guidelin:5,gx1v7:38,gx1v7_vert_grid:0,h:39,habitat:37,hand:43,happi:5,harmon:[36,43],harmonic_parm:43,harvest:[19,41],harvest_select:[8,41,42],has_year_zero:0,have:0,head:5,helper:0,here:[5,41,42,43],highli:5,histori:0,hook:5,how:[38,41],html:5,htmsourc:0,http:[0,5],i:[0,8,11,26,36,43],i_fish:12,i_fish_from:12,ic:0,id:0,ideal:[35,36,38],ignore_year_in_forc:38,illustr:43,improv:5,includ:[37,41,43],index:[0,5],individu:[8,11],info:[6,43],inform:[11,12,13,32,33],ingest:[20,41],ingestion_r:[6,17,20],inhabit:41,initi:[32,38],input:[30,37],input_fil:0,input_templ:0,instal:5,instead:[0,38],instruct:5,integ:36,integr:[6,38],interact:37,interfac:[5,32,37],intermedi:0,interpol:38,interv:0,introduc:37,invert_yaxi:43,io:0,ipynb:0,is_larv:[12,42],isel:[0,6,38,43],isel_dict:38,isfil:0,issu:5,item:16,its:[5,37,38],j:39,jame:39,join:0,junit:5,junitxml:5,jupyt:5,just:0,juvenil:19,k:[0,25],k_consumpt:42,k_encount:42,k_metabol:42,ken:39,kept:38,keyword:33,kmt:0,kristen:0,kristenk:0,kt:8,kwarg:[7,8,14],label:43,languag:5,larg:[0,38,41,42],larger:38,larval:26,last:38,lat:0,latest:5,latitud:0,latitudestandard_nam:0,latitudeunit:0,layer:0,layout:5,ld:[6,38,42],legend:[6,38,43],len:[32,38],level:38,like:43,limit:28,line2d:43,line:[0,37,43],linewidth:6,link:[11,12,38],list:[12,21,22,29,30,36,41],live:5,load_ext:[6,38,43],loc:38,local:5,locat:38,lofflin:[41,42],log:[6,38],long_nam:[0,43],longitud:0,look:[38,43],loss:[0,19],lp:[6,38,42],lt:0,lzoo_loss_150m:0,lzooc_150m:0,m:[0,5,37,39,43],main:5,maintain:5,make_err_plot:38,make_plot:38,manag:5,markdown:5,marker:43,mask:0,mass:[8,25,30],master:5,match:38,matlab:0,matlab_baselin:38,matlab_script:38,matlab_script_loc:38,matplotlib:[0,6,38,43],matter:0,max_output_time_dim:38,maxi:0,maximum:23,md:[6,38,42],mean:[0,8,21,22,31],meanunit:0,mechanist:37,medium:[38,41,42],mem:38,member:[6,42],member_obj_list:[10,30],memori:38,meso:0,mesozooplankton:0,mesozooplanktonunit:0,messag:5,met:8,metab:8,metabol:[8,21],metabolism_r:[6,17,21],metadata:0,meter:41,method:[7,8,9,10,11,12,13,14,32],mf:[6,38,42],minimum:[0,38],mlevi:0,mmol:0,mod_param:[7,8,10,14],mode:41,model:[32,33,36,41,43],model_set:[41,42],modifi:38,modul:43,month:0,monthli:[0,38],mortal:[0,19,22,28,33,38,41,43],mortality_coeff_per_yr:42,mortality_r:[6,19,22,30],mortality_typ:[22,42],mp:[6,38,42],ms:[0,38],mu:[36,43],multi:5,multipl:37,must:41,my_reshap:0,myst:5,name:[0,5,6,7,8,14,41,42],natur:[19,22],nc:[0,38],ncar:5,ncore:38,ncpu:38,ndx_from:12,necessari:5,neg:38,netcdf:[0,38],new_tim:0,next:38,nlat:0,nlon:0,nmolc:0,nmort:19,noleap:0,noleapaxi:0,noleapbound:0,non:0,none:[0,32,36,38],noneconvent:0,note:[0,36,38,43],notebook:[0,5,38],noth:5,now:[0,5],np:[0,38,43],nrow:43,nsteps_tot:0,nt:36,nu:[17,27],num_chunk:38,number:36,numer:[21,22,31,32],numpi:[0,38,43],nx:[32,35,43],o:43,object0001:0,object:[0,6,20,21,22,24,29,30,32,43],occur:37,ocean:[0,38],oceanographi:39,off:[0,5,38],offlin:[0,38,41],offline_driv:1,old_set:38,onc:5,one:[0,8],onli:37,open:0,open_dataset:[0,38],option:[29,32,38],organ:0,orig:8,os:0,other:37,output:38,over:[0,38],own:5,p:[0,39],packag:37,page:[1,2,3,4,41],pair:33,paramet:[0,7,8,9,14,16,20,21,22,24,29,30,31,32,33,36,41],parameter:[37,41],paramter:8,particul:0,pass:5,path:[0,5],pattern:39,pbscluster:38,pelag:[0,16,29,31,39,41],pelagic_demersal_coupl:[8,41,42],pelagic_demersal_coupling_apply_pref_type_kei:[41,42],pelagic_demersal_coupling_type_kei:[41,42],pelagic_functional_typ:29,pelagic_functional_type_kei:[41,42],pep:5,per:18,pertain:12,petrik:[37,39],phase:[36,43],phyto:0,pi_be_cutoff:29,pip:5,piscivor:[8,42],pleas:5,plot:[6,38,43],plot_set:38,plt:[0,6,38,43],poc:[0,36,43],poc_flux:30,poc_flux_bottom:[0,36,38,43],poc_flux_in_bottom:0,pocean:39,point:43,pop2:0,pop:[0,38],port:38,post:0,potenti:0,power:8,pre:5,predat:[6,19,23,24,41,42],predation_flux:[6,24,30],predation_r:[6,19],predation_zoo_flux:24,prefer:[6,41,42],prei:[6,7,16,32,33,37,41,42],previou:0,primari:32,print:[0,38,42],prior:38,probabl:0,process:[0,38],product:26,prognost:[0,34,41],progress:39,project:44,properti:32,proport:41,provid:[1,2,3,4,37,38,41,43],proxi:38,psa:39,pull:[5,38],purpos:38,push:5,pyplot:[0,6,38,43],pytest:5,python:[5,37,38],quadmesh:43,quadrat:43,question:5,queue:38,quick:38,r:39,rais:38,ran:38,rang:[38,43],rate:[15,16,18,19,21,23,30,41],rather:38,re:5,read:[0,38],realli:[0,41],recruit:26,recruitment_flux:[6,26,30],reduc:38,regard:5,region:37,rel:38,relationship:[10,41],releas:0,remov:0,replac:0,repo:5,report:5,repositori:5,repres:43,reproduc:[0,38],reproduct:[12,13,26,27,38,41],reproduction_r:[6,26,27,30],reproduction_rout:[26,41,42],reset:29,resource_spec:38,respect:38,restructuredtext:5,result:[0,20,21,22,24,29,38],revis:0,robust:5,round:38,rout:[12,13,41],routing_set:13,run:[5,41],s:[0,5,38],sandbox:5,scale:[0,38],scipi:0,script:38,sd:[6,38,42],seafloor:0,seafloorunit:0,season:36,section:[5,41],sel:[6,38],selec:[18,19],select:[18,19,38],sep:0,seri:0,set:[5,32,36],set_titl:38,set_ylabel:38,set_ylim:38,set_yscal:38,set_yticklabel:38,settings_dict:32,settings_in:[6,38],setup:[6,38],sever:0,sf:[6,38,41,42],shape:43,shelf:37,should:[0,5],show:37,similarli:38,simpl:[5,38],simul:[38,41],sinc:0,singl:43,size:41,size_class:[8,41,42],size_class_bound:[41,42],slice:0,small:[0,5,38,41,42],smaller:0,so:38,solut:38,somat:[19,27],some:[0,5,43],soon:40,sort_kei:42,sourc:0,sp:[6,38,42],space:38,spc:0,spc_150m:0,specif:[12,30],specifi:[36,41],spent:[16,29,31],spinup_forcing_file_nam:0,split:0,standard_nam:0,start:[6,38],start_dat:[6,38],start_tim:0,state:33,statu:38,step:[5,6,32,38],still:0,stock:39,stone:5,store:[13,20,21,22,24,29],string:8,strip:0,structur:[7,9,10,12,13,14,37,41],style:5,subject:41,submit:5,subpackag:43,subplot:[38,43],suffix:30,suggest:5,sum:41,summari:[1,2,3,4],suppos:0,suptitl:38,surround:37,sy:[0,38],t0:25,t62_g16:0,t:[0,5,8,25,38],t_bottom:[0,31,36,43],t_frac_pelag:[16,29,31],t_frac_pelagic_stat:[8,29,41,42],t_frac_prei:16,t_habitat:[6,15,16,21,22,23],t_pelag:[0,31,36,43],take:0,taken:37,tanh:35,tanh_shelf:[6,38],tarea:0,tarrai:0,task:0,tavg:0,tavg_sum:0,tavg_sum_qflux:0,tcp:38,temp_150m:0,temp_bottom:0,temperatur:[0,16,21,22,31,36,43],temperaturecell_method:0,temperatureunit:0,templat:[6,38],tendenc:[30,32,33],tendency_data:32,term:[28,41],test:[5,36,38],test_cas:38,test_d:6,test_locs3:38,testcas:[38,43],text:43,than:[0,38],them:0,thi:[0,1,2,3,4,5,8,32,37,38,41,43],thick:0,thre:[0,38],three:[37,38],threshold:0,through:[5,38],time0:0,time1:0,time:[0,6,16,29,30,31,32,33,36,38],time_boundarrai:0,timeaxi:0,timecalendar:0,timegrid_loc:0,timeout:38,timestep:6,timeunit:0,tini:0,titl:[0,38,43],tlat:0,tlong:0,to_netcdf:0,tool:5,total:[0,30,38],total_tend:30,totc:0,tracker:5,treat:0,two:37,type:[8,36,41],typic:38,u12:6,u15:6,u2:6,u3:[36,43],u:5,ucar:0,under:5,underflow:0,underli:37,unit:43,unknown:38,up:39,updat:5,us:[0,5,35,36,37,38,41,43,44],usabl:5,user:[0,5,38],util:[5,38],utilit:43,utilti:43,valu:[0,33,36,38],valueerror:38,van:39,vari:36,variabl:[0,6,36,43],variablesrevis:0,varieti:38,verbos:5,verifi:38,version:5,vert_grid_fil:0,via:[5,32],view:5,wa:[0,38],wall:[0,38],walltim:38,watson:39,we:[38,43],web:[5,20,24,29,41],websit:5,weight:[21,22,31,41],welcom:5,well:[0,38],were:38,when:[0,5,41],whenev:5,where:[0,38],within:38,without:[0,5],work:[0,5],workflow:5,write:0,write_netcdf:0,ww:0,www:0,x:[0,6,36,38,43],xarrai:[0,6,16,24,29,32,36,37,38,43],xml:5,xr:[0,38,43],y:0,yaml:[38,42],yarrai:0,year:[0,38],ylim:[6,38],yml:5,you:5,your:5,your_github_usernam:5,yscale:6,z:0,z_t:0,zarrai:0,zero:[0,38],zone:41,zoo1:36,zoo2:36,zoo:[0,6,36,41,42,43],zoo_loss_150m:0,zoo_mort:[0,28,36,38,43],zoo_mortality_data:33,zoo_nam:36,zoo_spec:36,zooc:[0,36,38,43],zooc_150m:0,zooplankton:[14,28,33,36,37,38,41,42,43],zooplankton_biomass:33,zooplankton_functional_type_kei:[41,42]},titles:["Generate forcing (does not contain biomass) from CESM output","FEISTY Driver","FEISTY Interface","Internal API","FEISTY testcase","Contributing to the FEISTY model","Running the model","feisty.core.ecosystem.benthic_prey_type","feisty.core.ecosystem.fish_type","feisty.core.ecosystem.fishing","feisty.core.ecosystem.food_web","feisty.core.ecosystem.food_web_link","feisty.core.ecosystem.reproduction_link","feisty.core.ecosystem.reproduction_routing","feisty.core.ecosystem.zooplankton_type","feisty.core.process.compute_consumption","feisty.core.process.compute_encounter","feisty.core.process.compute_energy_avail","feisty.core.process.compute_fish_catch","feisty.core.process.compute_growth","feisty.core.process.compute_ingestion","feisty.core.process.compute_metabolism","feisty.core.process.compute_natural_mortality","feisty.core.process.compute_pred_encounter_consumption_max","feisty.core.process.compute_predation","feisty.core.process.compute_rate_T_mass_scaling","feisty.core.process.compute_recruitment","feisty.core.process.compute_reproduction","feisty.core.process.compute_rescale_zoo_consumption","feisty.core.process.compute_t_frac_pelagic","feisty.core.process.compute_total_tendency","feisty.core.process.t_weighted_mean_temp","feisty.feisty_instance_type","feisty.feisty_instance_type.compute_tendencies","feisty.feisty_instance_type.get_prognostic","feisty.testcase.domain_tanh_shelf","feisty.testcase.forcing_cyclic","Fisheries Size and Functional Type Model (FEISTY)","Comparing with matlab Baselines","References","Scientific Background","FEISTY Settings","Default settings","FEISTY test cases","Usage"],titleterms:{"case":43,"default":42,"do":0,"function":37,addit:38,also:0,api:[1,3],background:40,baselin:38,bathymetri:43,benthic_prey_typ:7,biomass:0,cesm:0,chunk:38,cluster:38,compar:38,compon:3,compute_consumpt:15,compute_encount:16,compute_energy_avail:17,compute_fish_catch:18,compute_growth:19,compute_ingest:20,compute_metabol:21,compute_natural_mort:22,compute_pred:24,compute_pred_encounter_consumption_max:23,compute_rate_t_mass_sc:25,compute_recruit:26,compute_reproduct:27,compute_rescale_zoo_consumpt:28,compute_t_frac_pelag:29,compute_tend:33,compute_total_tend:30,condit:0,configur:[6,38],contain:0,contribut:5,convers:0,core:[7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31],dask:38,data:[38,43],develop:5,document:5,doe:0,domain_tanh_shelf:35,driver:1,drop:0,ecosystem:[7,8,9,10,11,12,13,14],featur:5,feedback:5,feisti:[1,2,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,41,43],feisty_instance_typ:[32,33,34],file:0,fish:9,fish_typ:8,fisheri:37,food_web:10,food_web_link:11,forc:[0,43],forcing_cycl:36,from:0,gener:0,get:0,get_prognost:34,ideal:43,improv:38,initi:0,interfac:2,intern:3,land:0,mat:0,matlab:38,model:[3,5,6,37,38],object:2,out:0,output:[0,6],primari:2,process:[3,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31],refer:39,reproduction_link:12,reproduction_rout:13,request:5,reshap:0,run:[6,38],scientif:40,set:[38,41,42],size:37,spinup:0,t_weighted_mean_temp:31,test:43,testcas:[4,6,35,36],type:37,unit:0,up:38,usag:44,util:4,visual:43,write:5,zooplankton_typ:14}})
\ No newline at end of file
diff --git a/testcase-datasets.html b/testcase-datasets.html
index 5bb2d0c0..1bc90d6b 100644
--- a/testcase-datasets.html
+++ b/testcase-datasets.html
@@ -547,7 +547,7 @@ Visualizing forcing data
@@ -563,7 +563,7 @@ 
@@ -605,7 +605,7 @@ 