text: Search.setIndex({docnames:["_themes/README","change_log","index","modules","pymatgen_diffusion","pymatgen_diffusion.aimd","pymatgen_diffusion.neb"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"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.ext.viewcode":1,sphinx:56},filenames:["_themes/README.rst","change_log.rst","index.rst","modules.rst","pymatgen_diffusion.rst","pymatgen_diffusion.aimd.rst","pymatgen_diffusion.neb.rst"],objects:{"":{pymatgen_diffusion:[4,0,0,"-"]},"pymatgen_diffusion.aimd":{clustering:[5,0,0,"-"],pathway:[5,0,0,"-"]},"pymatgen_diffusion.aimd.clustering":{Kmeans:[5,1,1,""],KmeansPBC:[5,1,1,""],get_random_centroid:[5,3,1,""],get_random_centroids:[5,3,1,""]},"pymatgen_diffusion.aimd.clustering.Kmeans":{cluster:[5,2,1,""],get_centroids:[5,2,1,""],get_labels:[5,2,1,""],should_stop:[5,2,1,""]},"pymatgen_diffusion.aimd.clustering.KmeansPBC":{get_centroids:[5,2,1,""],get_labels:[5,2,1,""],should_stop:[5,2,1,""]},"pymatgen_diffusion.aimd.pathway":{ProbabilityDensityAnalysis:[5,1,1,""],SiteOccupancyAnalyzer:[5,1,1,""]},"pymatgen_diffusion.aimd.pathway.ProbabilityDensityAnalysis":{from_diffusion_analyzer:[5,2,1,""],generate_stable_sites:[5,2,1,""],get_full_structure:[5,2,1,""],to_chgcar:[5,2,1,""]},"pymatgen_diffusion.aimd.pathway.SiteOccupancyAnalyzer":{coords_ref:[5,4,1,""],from_diffusion_analyzer:[5,2,1,""],get_average_site_occupancy:[5,2,1,""],nsites:[5,4,1,""],site_occ:[5,4,1,""],structure:[5,4,1,""]},"pymatgen_diffusion.neb":{full_path_mapper:[6,0,0,"-"],io:[6,0,0,"-"],pathfinder:[6,0,0,"-"]},"pymatgen_diffusion.neb.full_path_mapper":{ComputedEntryPath:[6,1,1,""],FullPathMapper:[6,1,1,""],generic_groupby:[6,3,1,""],get_all_sym_sites:[6,3,1,""]},"pymatgen_diffusion.neb.full_path_mapper.ComputedEntryPath":{get_full_sites:[6,2,1,""],match_ent_to_base:[6,2,1,""],populate_edges_with_chg_density_info:[6,2,1,""]},"pymatgen_diffusion.neb.full_path_mapper.FullPathMapper":{add_data_to_similar_edges:[6,2,1,""],get_only_sites:[6,2,1,""],get_unique_hops_dict:[6,2,1,""],group_and_label_hops:[6,2,1,""],populate_edges_with_migration_paths:[6,2,1,""]},"pymatgen_diffusion.neb.io":{MVLCINEBEndPointSet:[6,1,1,""],MVLCINEBSet:[6,1,1,""],get_endpoint_dist:[6,3,1,""],get_endpoints_from_index:[6,3,1,""]},"pymatgen_diffusion.neb.pathfinder":{DistinctPathFinder:[6,1,1,""],IDPPSolver:[6,1,1,""],MigrationPath:[6,1,1,""]},"pymatgen_diffusion.neb.pathfinder.DistinctPathFinder":{get_paths:[6,2,1,""],write_all_paths:[6,2,1,""]},"pymatgen_diffusion.neb.pathfinder.IDPPSolver":{from_endpoints:[6,2,1,""],get_unit_vector:[6,2,1,""],run:[6,2,1,""]},"pymatgen_diffusion.neb.pathfinder.MigrationPath":{get_structures:[6,2,1,""],length:[6,2,1,""],write_path:[6,2,1,""]},pymatgen_diffusion:{aimd:[5,0,0,"-"],neb:[6,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","function","Python function"],"4":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:function","4":"py:attribute"},terms:{"001":6,"0910":2,"1000":[5,6],"113":6,"140":6,"1436976":2,"2000":6,"2014":6,"2015":[2,5],"2019":6,"214106":6,"3rp":5,"534":2,"5815":2,"8318":5,"8325":5,"858":2,"92093":2,"9500":2,"9901":6,"case":6,"class":[2,5,6],"default":6,"final":[5,6],"float":[5,6],"function":[5,6],"int":[5,6],"new":5,"public":2,"return":[5,6],"static":6,"true":6,"while":6,AND:2,ARE:2,BUT:2,FOR:2,For:[2,6],HAS:2,ITS:2,NOT:2,N_s:5,Pls:2,SUCH:2,THE:2,The:[0,2,5,6],USE:2,__eq__:6,_theme:0,about:6,abov:[2,5],absolut:6,abspath:0,accompani:2,add:[0,2],add_data_to_similar_edg:6,addit:6,addon:0,advis:2,aeccar0:6,aeccar2:6,agreement:2,aimd:[2,3,4],algo:6,all:[2,5,6],allow:6,also:0,altern:0,alwai:[2,6],analys:2,analysi:[2,5,6],analyz:[5,6],andvac:6,angle_tol:6,angstrom:[5,6],ani:2,appear:2,append:0,appli:6,approach:6,april:6,arg:6,aris:2,arrai:5,associ:[5,6],assum:6,atol:6,atom:6,attribut:5,averag:5,back:[2,6],barrier:6,base:[5,6],base_aeccar:6,base_struct_entri:6,basi:2,becaus:6,been:2,better:6,between:[5,6],binari:2,bool:6,both:6,boundari:[2,6],built:6,busi:2,calcul:6,california:2,call:6,can:[0,5,6],cation:6,caus:2,centroid:5,chang:[5,6],check:[0,2,6],chem:[5,6],chgcar:[5,6],chosen:6,chu:5,cite:5,classmethod:[5,6],cleanup:1,closer:5,cluster:[2,3,4],code:2,combin:6,commerci:2,comp:6,compar:6,compat:1,complet:6,compon:[5,6],compris:6,comput:[5,6],computedentrypath:6,computedstructureentri:6,condit:[2,6],conduct:5,conductor:5,conf:0,consecut:6,consequenti:2,consid:[2,5],constant:6,construct:6,contact:2,contain:[0,6],content:[0,2,3],contract:2,contributor:2,conveni:6,converg:5,coordin:5,coords_ref:5,copi:[2,6],correl:6,creat:[5,6],crystal:[5,6],cubic:5,cutoff:[5,6],d_cutoff:5,damag:2,data:[2,5,6],deng:5,densiti:[2,5],depend:6,deriv:2,design:2,detail:[2,6],determin:[5,6],develop:2,dict:6,dictionari:6,dictset:6,differ:6,diffus:[2,6],diffusion_analyz:5,diffusionanalyz:[2,5],direct:2,disclaim:2,displac:6,dist:6,distanc:[5,6],distinct:6,distinctpathfind:6,distinguish:6,distribut:[2,5],dmref:2,doc:[0,2],document:0,doe:[2,6],dopant:5,driv:0,drive:2,dure:6,each:[2,5,6],easi:6,easier:6,edg:6,edu:[2,6],educ:2,either:6,element:6,elment:6,empti:6,encut:6,end:[2,5,6],endors:2,endpoint:6,energi:[5,6],engin:2,enhanc:[2,5],enregi:6,ent:6,entir:6,entri:6,ep_0:6,ep_1:6,equival:6,equlivaelnt:6,error:2,esit:6,even:2,event:2,exclud:6,exclus:2,exemplari:2,exist:[0,6],express:2,extract:2,extrem:6,fals:6,fast:5,featur:5,fee:2,file:[2,6],filenam:[5,6],find:[2,6],first:6,fit:2,flask:0,fname:6,folder:0,follow:[0,2,5],forc:6,fork:2,form:[2,6],format:5,formula:6,foundat:2,fraction:5,free:2,from:[2,5,6],from_diffusion_analyz:5,from_endpoint:6,full:6,full_path_mapp:[2,3,4],full_sites_struct:6,fullpathmapp:6,funciton:6,fund:2,funtion:6,further:5,futur:2,gener:[5,6],generate_stable_sit:5,generic_groupbi:6,get:[5,6],get_all_sym_sit:6,get_average_site_occup:5,get_centroid:5,get_endpoint_dist:6,get_endpoints_from_index:6,get_full_sit:6,get_full_structur:5,get_label:5,get_only_sit:6,get_path:6,get_random_centroid:5,get_structur:6,get_unique_hops_dict:6,get_unit_vector:6,gilman:2,git:0,given:[5,6],good:2,grant:2,grid:5,group:6,group_and_label_hop:6,gtol:6,guess:[5,6],guid:0,has:5,have:5,heavili:2,henkelman:6,here:6,herebi:2,hereund:2,hierach:5,higher:5,his:0,holder:2,hop:6,host:6,hove:2,howev:2,html_theme:0,html_theme_path:0,http:6,hydrogen:6,idpp:[1,2,6],idpp_kwarg:6,idppsolv:6,imag:6,implement:1,impli:2,improv:6,incar:6,incident:2,includ:[1,2,5,6],increas:6,index:[2,5],indic:[5,6],indirect:2,individu:6,inequival:6,info:6,initi:[5,6],initial_centroid:5,input:6,insert:6,instead:6,int_:5,intend:0,intercol:6,interest:5,interpol:6,interrupt:2,interstiti:[5,6],interv:5,invent:2,ion:6,ionic:5,isit:6,iter:[5,6],its:2,jolla:2,json:6,just:6,kenneth:0,kmean:5,kmeanspbc:5,known:6,kr_small:0,kwarg:6,lab:2,label:[5,6],landscap:5,larg:0,lattic:[5,6],length:6,li3fe4p4o16:6,li4fe4p4o16:6,liabil:2,liabl:2,librari:0,life4p4o16:6,like:[2,6],limit:[2,6],linear:6,list:[2,5,6],list_in:6,loss:2,lost:2,low:5,ltol:6,mai:[2,5],mail:2,mainli:6,mainten:2,make:[2,6],manipul:2,manner:6,map:6,match:6,match_ent_to_bas:6,mater:5,materi:[2,6],matrix:6,mavrl:6,max_disp:6,max_iter:5,max_path_length:6,maximum:6,maxit:6,mean:[2,5,6],mechan:6,merchant:2,met:2,method:[5,6],metric:5,migrat:[2,6],migrating_speci:6,migration_speci:6,migrationpath:6,min:6,minim:6,minimum:6,mit:2,mitnebset:6,mitrelaxset:6,mitsuhiko:0,modif:[2,6],modifi:[2,6],modul:[2,3],monti:6,more:[2,5,6],most:0,move:6,msonabl:6,must:2,mvlcinebendpointset:6,mvlcinebset:6,mxn:5,na3ps4:5,name:[2,6],nation:2,ndarrai:5,nearest:5,neb:[1,2,3,4],nebpath:6,need:6,neglig:2,neither:2,nest:5,network:6,nimag:6,nion:5,node:6,none:[5,6],nor:2,note:[2,5,6],notic:2,nsite:5,ntimestep:5,number:[5,6],numpi:5,nx3:5,object:[5,6],oblig:2,obtain:[2,5,6],occup:5,offic:2,old_centroid:5,omega:5,one:[0,6],ong:5,onli:6,oper:[2,6],other:[2,6],otherwis:2,out:[0,2],over:5,p_ratio:5,packag:[2,3],page:[0,2],pair:6,paper:5,paragraph:2,param:[5,6],paramet:[5,6],parti:2,particular:2,pass:6,passthrough:6,path:[0,2,6],pathfind:[2,3,4],pathwai:[2,3,4],pbc:5,per:6,perc_mod:6,percol:6,perfect:6,perform:6,period:[2,6],permiss:2,permit:2,phy:6,placehold:6,pleas:[2,5,6],pmg_structur:[5,6],point:[5,6],popul:6,populate_edges_with_chg_density_info:6,populate_edges_with_migration_path:6,posit:6,possibl:[2,6],potenti:6,precis:6,preliminari:2,prior:2,probabilitydensityanalysi:5,probabl:[2,5],process:6,procur:2,product:2,profit:2,program:2,progress:2,project:0,promot:2,properti:6,provid:[2,5,6],pull:2,purpos:2,put:0,py3k:1,pymatgen:[1,2,5,6],pymatgen_diffus:2,random:5,rdf:[2,3,4],read:6,reason:2,redistribut:2,refer:[2,5,6],regent:2,regular:6,reitz:0,relat:0,relax:6,releas:2,relev:2,reli:2,remov:6,repons:6,repositori:[0,2],repres:6,reproduc:2,request:2,requir:6,research:2,reserv:2,retain:2,revolution:2,right:2,role:5,rtype:6,run:6,same:[5,6],save:5,scheme:5,scienc:2,scientif:2,search:2,second:6,see:6,select:5,send:2,sequenc:5,servic:2,set:[5,6],shall:2,shallow:5,shortest:5,should:5,should_stop:5,simul:5,singl:6,single_cat_entri:6,site:[5,6],site_indic:6,site_occ:5,siteoccupancyanalyz:5,size:6,slow:5,slowli:5,small:0,smallest:6,smidstrup:6,softwar:[2,6],solver:[1,6],some:6,sort_tol:6,sourc:[2,5,6],speci:[5,6],special:2,specif:2,specifi:6,spring:6,spring_const:6,squar:5,stabl:5,stable_sit:5,standard:[0,6],start:6,step:[5,6],step_siz:6,stol:6,store:[5,6],str:[5,6],strict:2,string:6,structur:[2,5,6],structuregraph:6,structurematch:6,submodul:[0,2,3,4],subpackag:[2,3],subsequ:6,subset:5,substitut:2,sum:5,superion:5,suppli:[2,5],support:[2,6],symbol:6,symm_structur:6,symmetr:6,symmetri:6,symmetrizedstructur:6,symprec:6,sys:0,taget_label:6,technolog:2,term:[2,5],test:6,than:5,them:6,theme:0,theori:[2,6],thi:[0,2,5,6],those:6,three:2,threshold:5,through:6,time:5,to_chgcar:5,togeth:6,tol:6,toler:6,tool:1,tort:2,total:6,trajectori:[2,5],transfer:2,transform:6,tube_radiu:6,two:[5,6],type:[5,6],ucsd:2,under:2,understand:2,uniform:5,uninterrupt:2,uniqu:6,unit:6,univers:2,unset:6,unset_encut:6,unsort:6,until:6,updat:2,use:[0,2,5],used:[0,2,5,6],useful:6,user:2,user_incar_set:6,uses:0,using:[2,5,6],usual:6,utexa:6,vac_mod:6,vacanc:6,valu:6,van:2,van_hov:[2,3,4],vasp:[5,6],vec:6,veri:0,version:5,vesta:[5,6],via:6,view:6,virtual:[2,6],visual:[5,6],vtst:6,vtsttool:6,wai:2,want:6,warrant:2,warranti:2,welcom:2,well:5,were:6,where:5,whether:[2,6],which:[5,6],without:[2,6],work:[2,5,6],would:6,write:6,write_all_path:6,write_path:6,written:2,yield:6,you:[0,2,5,6],your:0,zhu:5},titles:["krTheme Sphinx Style","Change Log","Introduction","pymatgen_diffusion","pymatgen_diffusion package","pymatgen_diffusion.aimd package","pymatgen_diffusion.neb package"],titleterms:{acknowledg:2,aimd:5,api:2,chang:[1,2],cite:2,cluster:5,content:[4,5,6],contribut:2,copyright:2,document:2,exhaust:2,featur:2,full_path_mapp:6,indic:2,introduct:2,krtheme:0,licens:2,log:[1,2],modul:[4,5,6],neb:6,non:2,our:2,packag:[4,5,6],pathfind:6,pathwai:5,polici:2,pymatgen_diffus:[3,4,5,6],rdf:5,sphinx:0,style:0,submodul:[5,6],subpackag:[4,5,6],tabl:2,v2018:1,v2019:1,van_hov:5}})