-
Notifications
You must be signed in to change notification settings - Fork 0
/
searchindex.js
1 lines (1 loc) · 5.57 KB
/
searchindex.js
1
Search.setIndex({docnames:["commandlines","index","mdparams","post_processing","start_simulation","topology"],envversion:52,filenames:["commandlines.rst","index.rst","mdparams.rst","post_processing.rst","start_simulation.rst","topology.rst"],objects:{},objnames:{},objtypes:{},terms:{"default":[3,4,5],"final":3,"function":5,"new":3,"static":5,"true":4,And:5,The:[2,3,4,5],Use:4,abc:3,accord:2,add:[2,3],after:[3,4],algorithm:2,all:[2,4],allow:3,along:2,alpha:3,anchor_typ:3,angl:4,ani:2,appropri:5,arithmet:5,arrheniu:4,atom:[4,5],atomist:4,atrpactiv:3,attach:3,avail:[3,5],barostat:4,barostat_gammap:4,barostat_mass:4,barostat_tau:4,base:[4,5],becom:3,befor:4,below:[3,5],benchmark_data:4,berendsen:4,boltzmann:[2,4],bond:2,bonds_to_remov:3,both:3,box:3,build:4,cach:3,cache_fil:3,calcul:5,can:2,cap:5,certain:3,cfg:3,cg_cutoff:4,chang:4,changeneighboursproperti:3,changeparticletyp:3,charg:[3,4],check_topolog:4,chemic:[2,3,4,5],chemlab:[2,5],choic:4,classic:4,coars:4,collect:[2,4],comma:[3,4],command:[1,2],complet:[2,3],comput:[2,4],condit:4,conf:[2,4],configur:4,constant:[3,4,5],constraint:3,construct:5,content:1,coordin:[2,4],correspond:[3,5],coulomb:4,coulomb_cutoff:4,coulomb_epsilon1:4,coulomb_epsilon2:4,coulomb_kappa:4,count:[4,5],count_fix_dist:4,count_tupl:4,count_typ:4,count_types_st:4,coupl:4,creat:4,cuoff:4,current:[2,5],custom:2,cut:4,cutoff:4,data:4,debug:4,declar:3,defin:[3,5],definit:3,deg:5,describ:2,differ:5,dihedr:4,direct:2,directli:3,disabl:2,disk:4,distanc:[3,4],distribut:2,divid:5,do_not_exclude_bond:4,dummi:3,dure:3,dynam:1,edg:3,effect:5,either:2,element:4,empti:4,enabl:2,energi:[2,4],energy_collect:[2,4],entri:2,epsilon:5,epsilon_1:4,epsilon_2:4,eq1:5,eq2:5,eq3:5,eq4:5,eq5:5,eq7:5,eq_length:3,eq_step:4,eqfen:5,eqfenelj:5,equat:4,everi:[2,3,4,5],exampl:3,exclud:[2,4],exclus:4,exclusion_list:[2,4],expect:5,ext_:3,ext_remove_bond:3,ext_typ:3,extens:3,extern:4,factor:5,fade:3,fals:4,field:5,file:[1,2,3,4],filenam:5,final_typ:3,first:5,fix:4,flush:4,follow:5,footnot:5,forc:[2,4,5],format:[1,2,4],found:2,freezeregion:3,from:[2,3,4,5],func:5,gammap:4,gen_veloc:[2,4],given:[3,5],grain:4,grid:2,gro:[2,4],gro_trj_collect:4,gromac:[2,5],group:[3,4],group_abc:3,harmon:3,harmonicnco:5,have:3,hdf5:2,here:[2,3],host:3,host_typ:3,how:3,howev:5,includ:[],increment:5,index:[1,5],init_r:3,initi:3,input:[2,4,5],int_step:4,integr:4,interact:[2,4],intern:5,invis:3,invok:3,invoke_on:3,is_default:5,iso:4,join_molecul:3,joinmolecul:3,kappa:4,keep:4,keep_simul:4,lambda:[4,5],langevin:4,larger:2,least:3,like:[2,3,5],line:[1,2,5],link:3,list:[2,3,4,5],lj_cutoff:4,load:2,log:4,make:3,mani:3,mass:[3,4],mass_factor:4,max:4,max_forc:[2,4,5],maximum:2,maximum_convers:4,maxwel:2,measur:[3,4],mechan:4,messag:4,modul:1,mol:4,molecular:1,multi:5,multipl:5,name:[3,4,5],new_typ:3,newli:4,node:2,node_grid:[2,4],node_i:2,node_x:2,node_z:2,non:[2,3,4,5],number:[2,3,4,5],off:4,old_typ:3,one:3,onli:[2,3,4],opt1:3,opt2:3,option:3,option_nam:2,order:5,other:[2,3],output:[2,4],output_fil:4,output_prefix:[2,4],overrid:3,p_max:5,p_min:5,page:1,pair:[2,5],param:[2,5],paramet:[1,3,5],paramt:4,particl:[2,4,5],particular:3,pass:2,phi0:5,place:[2,3],plai:3,posit:4,possibl:[3,4],post:1,potenti:[2,3,4],potential_opt:3,precis:4,prefix:[2,4],preserv:2,pressur:4,principl:5,print:4,process:1,provid:2,python:2,radiu:5,random:2,rate:[3,4],rate_arrheniu:4,reach:[3,4],react:3,reactant:3,reaction:[2,4],read:4,relat:3,release_count:3,release_molecul:3,release_on:3,releasemolecul:3,remove_bond:3,removeneighboursbond:3,replic:3,requir:3,res_id:4,rescal:4,resolut:3,rng:4,rng_seed:[2,4],role:3,root:3,run:4,save:4,save_before_react:4,scale:5,script:2,search:1,second:5,section:3,see:2,seed:[2,4],select:[4,5],separ:[3,4],set:[2,3,4,5],should:[3,4,5],show:[3,4,5],sigma:5,sim:4,simul:2,singl:[3,4],size:4,skin:[2,4],some:5,sphinx:4,src:2,start:4,start_ar:[2,4],start_simul:[0,2],state:[3,4],step:[2,4],stochast:4,stop:4,stop_ar:[2,4],store:[2,4],store_angdih:4,store_charg:4,store_forc:4,store_lambda:4,store_mass:4,store_posit:4,store_pressur:4,store_res_id:4,store_single_precis:4,store_speci:4,store_st:4,store_veloc:4,support:2,symbol:4,syntax:3,system:[2,4],system_monitor_filt:4,systemmonitor:4,t_hybrid_angl:4,t_hybrid_bond:4,t_hybrid_dihedr:4,tab1:5,tab2:5,tab:5,tabl:5,table1:5,table2:5,table_group:4,table_t1_t2:5,tabul:4,taken:5,target_typ:3,tau:4,temperatur:[2,4],term:3,than:2,thermal:4,thermal_group:4,thermostat:4,thermostat_gamma:4,theta0:5,thi:[2,3],those:3,three:3,time:4,top:4,topol:2,topol_collect:[2,4],topolog:[1,2,3,4],topologymanag:4,total:[4,5],total_numb:5,trajectori:[2,4],trj_collect:[2,4],trj_flush:4,trjout:4,ts_:5,tupl:4,turn:4,two:[3,5],type1:3,type2:3,type:[4,5],type_1:3,type_2:3,type_transf:3,unit:4,until:4,usag:4,use:[2,4],used:[2,3],uses:5,valu:[2,4,5],variabl:3,vector:2,veloc:[2,4],verlet:[2,4],when:[2,4],whenev:3,where:[3,5],which:[2,3,4],write:4,xvg:5},titles:["Command lines","Welcome to ChemLab\u2019s documentation!","Molecular dynamics parameters","Post-processing modules","start_simulation.py","Topology file format"],titleterms:{"class":3,angl:5,angletyp:5,atrp:3,belleman:5,bond:[3,4,5],bondtyp:5,chang:3,chemlab:1,command:0,convers:[4,5],cosin:5,counter:4,dihedr:5,dihedraltyp:5,document:1,dynam:2,fene:5,file:5,format:5,freez:3,gener:[2,4],h5md:4,harmon:5,hybrid:4,includ:5,indic:1,inform:2,interact:5,join:3,jone:5,lennard:5,line:0,maximum:4,mix:5,modul:3,molecul:3,molecular:2,neighbour:3,nonbond:5,nonbond_param:5,option:[2,4],paramet:[2,4],particl:3,post:3,potenti:5,process:3,properti:3,randomli:3,reaction:3,region:3,releas:3,remov:3,run:2,ryckaert:5,simul:[3,4],start_simul:4,storag:4,tabl:1,tabul:5,term:4,topolog:5,type:3,welcom:1}})