lammps/doc/html/searchindex.js

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133],brows:0,browser:57,bryantsev:121,btype:[106,123,127,131,154],buc:100,buck:[2,4,32,99],buckingham:[99,100,101,108,134],buckplusattr:148,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,73,74,76,77,79,80,81,84,85,86,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],bulatov:[136,137],bulk:[2,29,67,72,107,135,138,148],bundl:[57,163],button:163,bypass:2,c11:135,c_0:[81,95,152,153],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:81,c_flux:35,c_gauss:117,c_hb:121,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:98,c_prop:2,c_sigma:98,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:77,calcforc:67,calclat:35,calcluat:[37,39,42,106],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:73,call:[1,2,3,4,73,95,104,161,163],callabl:3,callback:3,caltech:[2,114],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,74,81,82,83,92,93,100,101,103,112,118,120,123,127,129,131,144,146,147,154],canon:[68,71,73,80,138],cao1:73,cao2:73,cao:73,capabl:[3,4,95,103],capac:[64,81,151],capolungo:[40,43],captur:[2,95,101,114,119,127,135],carbid:106,carbon:[57,90,95,105,135],card:[4,32,121],care:[2,44,55,67,68,97],carefulli:[3,28],carlo:[2,60],caro:112,carri:[4,81,119],carrillo:4,cartesian:[2,94],cascad:81,cat:[4,57],cate:67,categori:[0,95],cation:[115,148],caus:[1,2,4,44,61,68,72,76,77,82,83,92,93,121,123,129,132,133],caution:1,cautious:95,caveat:95,cbecker:[94,112],cc1:[2,34],ccc:[113,155,156,158,159],ccflag:4,ccflags:4,ccm6:112,ccsi:[113,155,156,158,159],ccu:98,cd2:43,cdeam:112,cdll:3,cdof:2,cdte:98,cdte_bop:98,cdtese:98,cdzn:98,cdznte:98,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,74,81,114,138],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,78,80,82,83,84,97,113,114,118,119,132,133,135,136,137,155,156,157,158,159],centr:63,central:[29,36,38,41,72,77,78,87,138,143,159],centro:2,centroid:73,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:147,ch2:77,ch2lmp:[0,2],ch3:77,chain:[0,2,13,28,60,68,69,71,73,77,80,90,109,110,154],challeng:2,champaign:132,chan:138,chandler:[94,112],chandrasekhar:[2,123],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,74,75,76,77,79,80,81,83,92,93,110,114,119,132,133,135,138,148,154,163],change_box:2,chapter:73,charact:[2,19,57,59,65,76,114,116,122,141,142,145,148],character:[2,29,38,41,149],characterist:79,charg:[1,2,3,32,40,43,44,99,100,105,106,108,109,112,114,115,123,127,131,144,148,158,159,161,162],charl:62,charmm:0,cheaper:[118,146],check:[2,3,19,35,59,75,77,80,92,93,122],checkout:163,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,73,74,79,80,82,84,90,91,93,95,99,102,103,105,106,107,109,110,111,114,117,118,120,121,123,127,128,131,135,139,141,142,144,148,154],chemic:[31,40,43,58,116,142],chemistri:[74,95,98,114],chen:81,cheng:105,chi:[72,115,118],chiral:90,chmod:3,cho:135,choic:[2,4,19,28,29,32,42,55,59,60,67,68,73,93,131],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[156,158],chosen:[2,41,44,50,57,61,62,66,67,68,69,73,111,114,119,122,125,147,156],chunk:0,chunkid:34,ciccotti:77,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:148,cl1:43,clarendon:[13,109],clarifi:[156,158],clark:144,classic:[0,2,4,73,74,81,91,114],classifi:159,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,93,163],climb:93,clockwis:45,clone:163,close:[2,3,19,42,60,61,67,68,70,77,83,93,95,98,106,107,135,141,142,158,163],closer:[19,59,61,79,93],closest:[72,118,146,154],cloud:148,cluster:[2,4,42,63,77],cmax:135,cmd:[3,73],cmdarg:3,cmin:135,cmm:[18,147],cna:29,co2:[43,76,77,116],coars:[13,18,28,50,65,76,116,120,142,147],coarsest:41,code:[0,1],coeff:[6,45,46,55,84,122,150],coeffici:0,coefficienct:110,coefficient0:112,coefficient1:112,coeffieci:[2,96],coeffincientn:112,coexist:114,cohes:[2,115,135],coincid:[83,102,132,133],cold:2,coleman:[40,43],collect:[2,34,44,104],colliex:43,collis:[67,119,162],colloid:2,color:[19,57,59,66,74],column:[2,29,34,36,38,41,42,43,74,81,95,117,121],colvar:0,com:[2,37,63,97,163],comand:60,combiant:107,combin:[2,3,18,32,55,57,58,63,68,70,71,73,83,84,104,106,107,111,114,115,116,130,131,149,155,156,158,159,161],come:[0,2,13,61,62,68,79,80,155,156,158,159,163],comit:163,comm:[0,3,30,93,110],comm_modifi:[2,98,104,110,114,119],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,76,81,93,94,112,113,115,116,122,135,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,61,73,83,84,119,121,155,156,158],commonli:[2,9,37,38,57,91,120,125,149,156,158],commun:[1,2,3,4,19,57,59,61,67,68,81,111],comp:[70,71,77,93,114,146,153,157],compar:[1,2,4,40,43,56,92,93,135,148],comparison:0,compass:[6,20,46,56,84,103],compat:[3,19,49,59,62,63,82,138],compens:[2,114],compil:[4,57,138],complain:3,complement:135,complementari:[106,123],complet:[2,3,19,59,73,93,115],complex:[2,3,9,36,38,41,44,67,70,83,93,114,138],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,73,77,83,92,93,110,114,119,132,133,148,149],componenet:2,composit:[2,67,112],compound:[105,114,115,159],compress:[2,57,69,74],compris:[83,116,146],compton:[40,43],comput:[0,1],computation:[2,81,98],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:83,concentr:[65,76,112,116,142],concept:2,conceptu:[2,61,93,106,135],concern:[2,30,32,66],concis:3,concurr:4,conden:[81,156,158],condens:[2,81,95,108,112,123,159],condit:[2,39,40,42,43,57,58,67,69,72,74,77,78,81,111,114,120],conducit:2,conduct:0,confer:[4,138],configur:[1,2,4,57,61,73,92,93,95,98,113,135,138,155,156,158,159,163],conflict:163,conform:[2,60,61,75,90,93,114],confus:159,conjuct:110,conjug:114,conjunct:[2,32,44,67,93,99,100,106,110,114,121,123,144,147],connect:[2,32,60,77,93,107,119,154,158],conner:95,connor:95,consecut:[3,44,106,123,127],consequ:[1,2,81,122],conserv:[13,60,66,67,68,70,76,77,93,109,110,111,119,129,148],consid:[2,29,32,59,60,81,114,146,148,154],consider:2,consist:[2,3,39,44,50,62,66,68,69,74,75,76,93,95,98,104,106,114,118,132,133,135,138,141,142,146,148],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,82,83,104,146],constrain:[2,63,66,70,71,77,78,92,114],constraint:[19,39,42,59,63,70,77,78,82,92,133],construct:[2,28,29,30,36,38,40,41,43,61,68,75,76,83,109,138,154,155],constructor:3,consult:4,consum:1,contact:[0,107,113,115,118,119,146],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,72,74,76,81,83,93,94,95,98,105,106,109,112,113,114,116,135,138,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,74,79,80,81,83,98,110,125,128,146,157],continuum:[2,58,81],contour_integr:58,contract:[61,68],contrain:77,contrast:[1,2,161],contrib:81,contribut:[2,29,32,33,34,35,39,41,42,61,67,77,92,93,110,112,114,132,133,138,148,163],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,149,163],convent:[13,49,54,56,75,112,114],converg:[2,19,57,59,60,61,69,70,71,74,75,77,92,93,105,106,123,148],convers:[41,57,106,107,108,114,123,127,131,144],convert:[2,5,6,8,12,16,17,18,35,44,46,57,84,85,89,90,93,94,112,138,156,158,162],convex:83,cool:63,coord:[2,3,36,38,72,82,93],coordb:148,coordbb:148,coordiat:92,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,72,77,78,80,81,92,93,94,95,97,113,148],coords:148,copi:[0,3,57,81,93,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,100,106,108],cornel:[2,45],corner:[2,57,83,163],corpor:4,corr:105,correct:[2,3,32,45,57,63,68,74,82,83,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:58,correctli:[3,68,77,83,93,108,133,138,163],correl:[2,35,36,41,66,73],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,72,73,76,77,82,83,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[132,133],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,76,81,106,123,127,138,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,45,92],could:[2,3,19,32,34,35,39,57,59,62,74,81,82,83,92,95,117,121],coulomb:[2,42,92,99,100,101,102,103,105,106,107,108,109,114,119,120,123,127,131,134,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,45,59,61,68,77,83,92,93,117,121],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,75,82,132,150],cov:148,coval:[2,13,114,135,148],cover:[2,58,67,114],cpp:[1,2,3,32,77],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,72,73,75,81,93,95,98,105,112,113,131,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,154],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,92],criterion:[19,44,59,60,92,93,105,114,119,148],critic:[2,24,25,81,92],cross:[4,33,57,93,102,110,112,120,121,123,125,127,145,147,156,158,162],crossov:1,crozier:0,crucial:74,crystal:[2,4,29,30,38,72,80],crystallin:[2,157],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,149],cscl:135,csequ:2,csh:[3,4],cshrc:3,csic:[113,155,156,158,159],csinfo:2,csisi:[113,155,156,158,159],cst:112,cstherm:2,csvr:2,ctcm:[94,112],ctype:3,cu1:43,cu2:43,cu3au:135,cube:[2,83],cubes:[19,59],cubic:[38,67,72,112],cuda:1,cuh:98,cummul:[2,60,121],cumul:[2,68,69,93],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,70,71,75,76,77,78,81,82,92,93,98,105,109,112,114,115,119,122,132,133,135,136,137,145,150,156,158,163],curv:[2,44,70,71],curvatur:[118,146,162],custom:[0,2,3,33,34,35,42,57,60,61,68,69,74,92,95,117,121],cut:[1,2,4,19],cuthi:72,cutinn:[132,133],cutlo:72,cutmax:145,cutoff1:[103,109,123,127,131,134,144,147],cutoff2:[99,100,101,103,108,109,123,127,131,134,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,72,74,82,83,92,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:113,cutoffc:113,cuu3:112,cval:43,cvar:62,cvff:4,cwiggl:82,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,71,83],cylindr:2,cyrot:98,d3q15:67,d3q19:67,d_e:81,daan:80,damp:[2,68,69,71,74,92,93,99,100,102,106,109,114,119,123,131,144,147],dampflag:119,danger:110,darden:109,darken:57,dash:119,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:134,davi:82,david:[156,158],daw:[112,145],dcd:[2,57,73],deactiv:131,debug:[2,3,40,43,44,73],decai:[36,106,162],decid:[2,4,163],decod:57,decompos:[32,149],decomposit:[58,73],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,138],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,72,73,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,99,100,101,102,103,104,106,107,109,110,111,113,114,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,41,62,64,69,82,98,104,111,114,145,149],deform:[2,42,61,68,132,133],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,73,75,77,80,84,85,89,90,91,92,109,112,121],delai:2,delet:[28,60,68,154,163],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:76,dellago:[2,63],deloc:[114,148],delr:135,delta_1:98,delta_3:98,delta_7:98,delta_ij:[135,145],delta_pi:98,delta_r:145,delta_sigma:98,deltah_f:65,demo:3,demonstr:[74,135],dendrim:121,denniston:67,denot:[40,63,106,120],dens:[60,76,114],densiti:[2,19,41,44,58,59,67,81,82,94,95,98,112,135,136,137,141,142,145,146,148,151,152,153],depart:0,departur:74,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,72,76,77,79,81,82,83,84,85,86,88,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,77],depth:[26,57,81,116,118,146],der:[32,104,105,131,161],deriv:[2,32,41,61,62,63,68,69,72,79,80,81,82,83,95,98,104,109,114,115,120,125,129,130,135,138,161],derjagin:161,derlet:72,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,72,73,74,76,79,80,82,92,93,95,97,99,100,102,103,104,105,106,109,112,114,115,116,118,119,120,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,72,81,96,97,102,106,108,114,131,132,133,136,137,145],desir:[2,3,4,35,39,42,44,61,62,66,68,77,92,93,110,112,121,132,133,155,156,158],desktop:[2,57],destabil:98,destre:90,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,74,77,80,81,92,94,95,97,98,101,102,103,104,105,106,109,110,114,115,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,139,141,142,146,148,149,150,160,161,163],detect:[36,93,105,121,122],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,72,73,74,75,76,82,83,95,101,105,109,112,116,117,119,127,135,138,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,62,69,74,95,98,114,137,138,148,159],deviat:[69,72,117],devic:1,devin:105,devis:137,dfactor:57,dft:138,dhug:74,dhugoniot:74,dia:135,diag:76,diagnost:[4,60,76],diagon:[2,41,42,61,68],diagonalstyl:149,diagram:[19,40,43,56,59,73],diallo:121,diam:57,diamet:[2,44,57,104,118,119,125,146,161],diamond:[114,135],dick:2,dicken:62,did:[92,110,112,119,156,158],dielectr:[102,106,107,108,123,127,131,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,72,73,74,77,78,79,80,81,82,83,84,93,94,95,98,101,102,104,105,110,111,112,114,116,118,119,120,123,124,126,127,134,135,136,137,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,76,106,145,157],difficult:[61,62,73,121],difficulti:[36,38,77],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:138,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,75,85,86,87,89,92,95,98,102],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:114,dij:77,dilat:[61,68,69],dim:[44,135],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,74,82,93],dimension:[36,39,40,41,43,81,93,145],dimensionless:[37,41,62,81,149,161],dimer:[2,135],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:109,dir:[1,3,72,74,145],dirac:41,direc:145,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,72,74,79,80,81,82,83,92,93,110,111,119,133],directli:[2,3,32,41,44,57,62,67,76,83,94,95,99,100,101,106,109,112,114,123,127,144,147,154],directori:[0,1,2,3,4,62,79,80,93,94,95,98,105,106,112,113,115,131,135,136,137,138,143,145,148,149,155,156,157,158,159],disabl:[4,81,122],disadvantag:[2,59],disallow:68,discard:[19,59,83],discontinu:[92,129],discourag:135,discret:[2,57,62,67,71],discuss:[0,1],disk:[2,36],disloc:[29,138],disord:[29,138],disp:0,dispar:146,disperion:[109,127],dispers:[2,101,109,127,132,159],displac:[2,37,61,68,72,119],displai:[3,56,57],disregard:138,dissip:[2,31,64,66,79,80,110,111,119,132,133],dist:[2,35,73,75,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,72,74,75,77,78,80,81,82,83,84],distinct:[2,146],distinguish:[2,41,114],distort:94,distrbut:94,distribut:[0,2,3,19,32,41,56,59,66,67,68,94,98,106,112,113,115,135,136,137,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[80,95],divid:[2,4,19,35,39,42,56,59,72,92,93,115,148,159],divis:[2,55,67,98,131],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[104,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,83,92,93,94,95,97,105,106,112,113,115,121,135,136,137,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,71,81,82,83,85,86,87,89,90,93,94,95,96,97,98,101,102,103,104,105,106,107,109,110,112,113,114,116,117,118,119,120,122,125,126,128,129,130,132,133,135,136,137,138,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[44,95,105,113,155,156,157,158,159],dof:39,doi:[2,72],domain:[2,19,40,43,57,59,61,67,68,73,81,82,93],domin:[1,114],don:[0,4,83,135,148,163],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,73,77,79,80,92,93,95,101,112,127,133,134,135,141,142,154,163],donor:121,dot:42,doti:[98,145],doubl:[1,2,3,4,32,45,61,83,98,115,120,138],dover:58,down:[2,3,61,114,148],download:3,downsid:2,dpd:2,dpdtheta:[31,111],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,78],dragforc:67,drai:[57,74],drain:92,dramat:[60,61,68,148],drautz:98,draw:57,drawn:[57,66],drayleigh:74,dreid:2,dreiding:0,drfourth:37,drho:[94,112,141,142],drift:[2,37,63,66],drive:[3,61,68,72,93],driven:[2,50],driver:2,drop:110,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:74,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,72,75,79,80,81,82,83,92,93,107,110,111,112,117,118,132,133,145,146,147,154,156,158,161,162],duffi:81,dullweb:68,dummi:[13,157],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,102],duplic:[19,59,72],durat:[56,81,119],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,92,93,110,131,138,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,70,73,74,75,79,80,81,92,93,110,111,114,132,133,153],dynamo:[94,112,135],dyre:128,e28637:13,e_1:98,e_2:98,e_a:76,e_b:115,e_ee:114,e_hbond:121,e_i:[2,98,115],e_j:[2,98],e_k:98,e_ke:114,e_kl:2,e_lj:[95,109],e_n:[62,98],e_ne:114,e_nn:114,e_pr:114,e_rebo:95,e_torsion:95,e_tot:138,e_vol:138,eaa:84,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,72,73,76,77,78,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,59],eam:[0,94,106],earli:[19,59],earlier:[93,119,135],earth:114,easi:[2,3,32,42,82],easier:[4,57],easili:[3,57,93],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:135,ec_ij:135,ec_jj:135,echo:[3,40,43],ecp:114,edg:[2,19,40,43,57,82,83],edge:82,edit:[4,163],edition:4,edu:[3,112,132],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,72,73,74,75,77,80,81,82,83,84,85,86,88,89,90,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,109,110,112,113,114,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,138,140,141,142,143,144,146,147,148,150,155,156,157,158,159,160,161,162],effici:[0,1,2,4,39,55,57,61,68,73,77,98,104,106,123,127,138,141,142,146],efficienc:4,efield:[77,92],eggebrecht:[106,148],ehex:2,eigenvalu:73,einstein:[2,80],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,72,76,77,83,92,98,104,112,116,119,132,133,135,138,142,145,154,156,158],ejtehadi:[104,118,146],elaps:[82,150],elast:[2,21,22,93,119,157],elastic:0,elba:13,electr:[2,58,115,162],electric:4,electrolyt:161,electron:[2,40,58,81,94,105,109,112,114,115,135,138,145,148,158,159,162],electron_integr:58,electron_temperatur:58,electron_unit:114,electroneg:[2,105,115,148],electroneg_compon:148,electrostat:[2,4,104,109,114,123,131,133,148,161],elem1:[115,135,149],elem2:[115,135,149],elem:148,element1:[94,112,148],element2:[94,112,148],element:[2,33,37,39,41,42,57,58,94,95,98,105,112,113,114,115,135,136,137,138,143,145,148,149,155,156,157,158,159],elementn:[94,112],elementset:58,elif:41,elig:121,elimin:[2,66,77,79,80],elj:109,ellips:2,ellipsoid:[2,44,70,92,118,133,146],els:[57,62,68,81],elsewher:135,elt:135,emac:0,email:[0,3,115],emb:83,emb_lin_neg:135,embed:[3,13,81,94,112,115,131,135,136,137,145],embt:46,emin:61,emphas:119,empir:[58,114],empiric:95,emploi:[63,157],empti:122,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,79,80,81,82,83,84,85,86,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],enclos:[2,135,148],encod:57,encompass:2,encount:38,encourag:[76,78],end:[1,2,3,4,19,46,57,60,61,63,66,68,71,75,76,81,93,110,112,118,134,138,146,149,150],endbondtors:46,energet:[60,95],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110],energy_compon:148,enforc:[2,57,60,68,77,123],enforce2d:[2,92],eng:[3,105,137],engineer:[58,79,112],enginer:136,enhanc:[58,63],enlarg:57,enough:[44,59,74,82,83,106],enpub:112,ensembl:[2,32,35,68,71,73,74,110,148],ensight:2,ensur:[2,41,61,66,68,98,131,155,159],enter:[115,138,159],enthalpi:[76,112],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,72,73,76,78,81,109,127],entiti:2,entri:[40,65,74,98,113,135,141,142,143,149,155,156,157,158,159],entry1:[141,142],enumuer:2,environ:[1,2,3,4,57,72,94,98,105,113,114,145,156],eos:65,epair:[95,117,121],epp:109,epq:109,eps0:161,eps14:131,epsilon0:158,epsilon:[2,18,21,22,27,28,32,45,82,83,92,97,102,103,104,106,107,108,109,116,118,120,121,122,123,124,125,126,127,128,129,130,131,134,139,144,146,147,155,160,161],epsilon_0:162,epsilon_14:102,epsilon_:146,epsilon_d:107,epsilon_i:[118,146],epsilon_i_:146,epsilon_i_a:[118,146],epsilon_i_b:[118,146],epsilon_i_c:[118,146],epsilon_j:[118,146],epsilon_j_:146,epsilon_j_a:[118,146],epsilon_j_b:[118,146],epsilon_j_c:[118,146],epsilon_lj:146,eqp:109,eqq:109,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,72,73,74,75,76,79,80,81,82,92,93,95,105,110,111,117,118,121,132,138,139,145,146,148,149,150,159,162],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,72,73,74,76,77,81,82,104,109,110,111,114,115,116,119,132,133,135,142,146,151,152,153,162],equation:[72,90],equilibr:[2,35,44,60,61,68,74,79,80,105,106],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,74,75,77,80,84,85,89,90,105,135,143,148],equilibrium_start:58,equival:[2,13,61,68,75,95,110,114,148,156,158],equlibrium:2,er3:43,eradiu:114,eras:79,erat:133,erc:106,erfc:[106,123],erhart:[112,156,158],eros:135,erose_form:135,erot:2,errata:[156,158],erratum:82,error:[0,1,2,3,11,47,57,61,62,63,65,68,70,76,81,82,83,92,106,123,146,154,156,158],erta:119,especi:[4,44,59,74,75],essenti:[3,11,47,95,106,123,158],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,76],esub:135,eta:[2,67,68,74,113,115,118,145,157,159],eta_dot:68,eta_ij:145,eta_ji:115,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,81,83,92,93,112,113,131,133,138,155,156,158,159],etol:[92,93],etot0:74,etot:[2,42,74],eu2:43,eu3:43,euler:[76,92,93],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,76,82,92,138,141,142,145,148],evanseck:[2,5,45,102],evaul:92,even:[2,4,19,29,55,59,61,63,68,81,82,83,92,93,97,114,115,119,146,159],evenli:[19,42,59,67],event:[2,68,81],eventu:2,ever:28,everaer:[104,118,146],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,71,72,74,76,77,81,93,110,131,148,163],everyth:163,everywher:125,eviri:114,evolut:[63,67,73],evolv:[67,73],ewald:[2,40,42,92,99,100,101,106,109,114,123,127,144,147],ewald_disp:109,exact:[19,59,60,66,81],exactli:[2,19,35,44,59,66,74,110,112,119,132,141,142],examin:[2,60,76],exampl:[0,1],exce:[2,4,19,59,61,68,92],exceed:[19,59,68],excel:114,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,73,77,81,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,108,109,110,112,113,114,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:114,exchang:[2,58,63,81,114],excit:114,excite:114,exclud:[2,4,39,41,92,119,132,133,154],exclus:[1,4,32,45,105,138],excurs:68,execut:[1,2,3,57],exempl:148,exemplari:66,exemplifi:114,exert:[2,70,83],exhaust:58,exhibit:[36,63,68,114],exist:[2,3,29,44,56,57,61,84,85,86,87,89,111,154,163],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,72,74,135,138],expens:[2,72,81],experi:[2,75,93,110],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,72,93,97,112,148,150,163],explan:[2,41,72],explic:139,explicit:[2,3,32,76,95,98,102,112,114,122,132,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,74,77,81,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,136,138,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:73,explor:[40,43],expon:[76,112,116,118,121,131,139,147],exponenti:[32,76,116,145,155,159,162],expos:3,exposit:[58,110],express:[2,41,44,61,72,76,81,98,112,114,125,135,148,149],expressiont:98,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,72,75,79,80,81,82,83,118,135,138,146,149],extent:[1,19,21,59,95],exterior:[2,83],extern:[32,57,61,66,67,68,69,71,81,92,136,137],extra:[2,3,4,19,22,39,40,42,43,44,59,68,74,92,109,119,135],extract:[2,3,18,32,93,106,115,135,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,80,114,157],extrema:131,extreme:114,extrins:58,f_1:[2,61],f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:74,f_harm:80,f_i:[13,145],f_id:[2,62],f_ij:145,f_int:79,f_j:13,f_jj:35,f_k:145,f_langevin:81,f_max:74,f_r:[156,157,158],f_sigma:98,f_solid:80,f_ss:2,face:[2,82,83,118,135,146],facil:0,facilit:2,fact:[2,4,80,119,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,73,75,76,77,82,83,89,95,98,99,100,102,106,107,108,110,111,114,119,122,123,135,138,141,142,143,144,147,150,155],fail:[3,61,92,93,108],fairli:[3,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,59,61,68,72,75,82,85,89,93],farrel:[156,158],fashion:[2,19,44,59,62,68,69,74,80,81,82,93,132],fast:[2,4,62,74,76,132,133,138],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,77,79,81,84,85,86,88,89,90,91,94,95,96,98,99,100,101,102,103,104,105,106,109,110,112,113,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,81],fault:29,fava:118,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,76],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,73,83,92,163],fecr:112,feedback:62,feel:[72,83,93],fehlberg:76,felling:137,felt:83,fene:[2,4],fennel:[106,123],fep:0,ferguson:[2,45],fermi:[1,158],fermion:114,fernando:134,few:[1,2,3,63,68,77,92,93,95,148],fewer:[1,3,4],feynman:73,ffield:[105,115,148],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:154,fictiti:[2,73,75,106,123,127,154],field:0,fifth:[2,116,143],figshar:72,figur:[1,4,74,163],fij:109,file0:72,file1:[3,65,72],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,72,76,81,93,94,95,98,106,112,113,115,116,135,136,137,141,142,143,145,148,149,155,156,157,158,159],fill:[44,57,81,98,138,163],filter:58,finchham:[2,108],find:[0,2,3,4,30,32,60,61,62,65,72,75,92,93,106,123,127,135,141,142,148,163],fine:[4,80,163],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:112,fire:[92,93],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,72,73,74,77,78,79,80,81,84,92,93,94,95,97,98,99,100,102,105,106,112,114,115,116,119,120,122,123,127,132,133,135,137,138,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,45,102],fit:[2,75,95,98,135,141,142,157,163],five:[30,74,98,136],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,74],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:77,fix_shak:77,fixedpoint:[61,68],fixid:[57,58],fji:109,flag:[3,4,33,34,40,43,57,60,95,121,122,135,138,154,163],flag_buck:101,flag_coul:[101,109,127],flag_lj:[109,127],flagfld:[132,133],flaghi:[132,133],flaglog:[132,133],flagvf:[132,133],flat:[2,4,81,82],fld:[82,132,133],flexibl:[2,57,114,157],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,72,80,81,90,111],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,77,98,138],fmass:73,fmax:92,fmsec:68,fno:4,fnorm:92,fnve:63,focu:77,foil:[41,72,149],fold:[4,78],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,73,74,75,76,77,79,80,81,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,57,76],foo_species:76,foot:2,forc:[0,1],forcefield:[75,121],forcegroup:67,ford:109,forgiv:68,fork:163,form:[2,28,32,33,34,36,41,42,62,66,75,76,81,82,83,84,87,90,93,95,98,111,112,114,117,121,122,134,135,137,138,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,73,148],format:[2,19,57,59,65,76,81,93,94,95,98,112,115,116,122,135,137,141,142,147,149,159],formation:65,former:[2,19,59,81,98],formul:[1,2,42,68,75,77,95,98,112,114,118,135],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,72,78,82,84,86,95,97,98,102,103,104,109,110,112,113,118,119,120,121,122,123,125,126,127,129,130,132,133,135,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,112,135],forward:[32,93],foster:[98,145],found:[2,30,60,63,67,106,109],four:[2,3,28,41,62,81,90,93,138],fourier:2,fourth:[2,4,37,75,102,116,143,148],fox:[2,40,45,153],fqq:109,fraction:[1,2,4,19,42,57,60,61,74,76,93,98,116,119,132,133],frame:[41,58,74,118],framer:57,framework:[94,149],frattl:63,free:[2,13,29,32,72,79,80,81,93,114,131,138,140,145,161],freedom:[2,39,60,68,69,73,77,80,92,109],freeli:[0,2,57],freez:2,frenkel:[2,63,80],frequenc:[2,4,73,74,76,110,114,148],frequent:[29,30,36,38,41,63],fri:74,friction:[2,74,81,119],from:[0,1],front:74,frontend:57,frozen:[2,39,66,117],fs2:[2,35],ftol:[92,93],fuction:106,fudg:77,fulfil:2,full:[1,2,4,35,57,63,67,72,76,98,112,114,115,118],fuller:92,fulli:[2,72,92,93,106,145,163],fulton:112,fumi:99,funcfl:112,fund:0,funrol:138,further:[2,37,57,67,73,81,92,93,94,97,105,138,148],furthermor:[11,47,63,76,111,114],futur:[0,2,59,66,93,136,137],g_jik:145,g_p:81,ga3:43,gaa:98,gai:118,gain:[4,62],galindo:139,gamma0:13,gamma:[2,13,67,74,110,111,113,118,135,139,151,152,153,155,156,158,159],gamma_:81,gamma_ijk:156,gamma_n:119,gamma_p:81,gamma_t:119,gammaa:139,gammafactor:67,gammar:139,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,45,102],gap:[132,133,149],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:107,gaussian:[2,35,37,66,73,75,110,114,117],gavhan:4,gaybern:[2,4,92],gd3:43,gdot:133,ge4:43,gec:[156,158],gen:68,gener:0,gentler:82,gentli:113,geom:2,geometr:[2,44,59,68,83,93,97,103,104,106,109,114,116,118,120,123,124,125,126,127,128,129,130,131,132,133,134,139,142,146,150,160,161],geometri:[2,9,19,44,59,61],gerber:131,germann:[69,125],germano:118,get:[0,1,2,3,4,19,35,41,44,57,59,61,83,93,106,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[106,123],ghost:[2,4,30,61,68,110,111,114,119,122],gif:57,gifsicl:57,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,44,61,68,72,92,95,98,114,121,135,138,146,156,157,158],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,72,73,74,75,76,77,78,81,82,83,94,95,98,99,100,101,103,104,105,106,107,110,111,112,114,115,116,118,119,121,123,124,125,127,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:138,glotzer:110,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,91,114,121],goe:[28,41,44,63,92,109,113,120,125,128,150,162],gold:29,goldman:74,good:[1,2,4,19,30,40,43,59,62,68,77,93,94,104,112,138,159,163],gordan:41,gordon:2,got:163,gould:[2,45],gov:[0,94,112,115],govern:67,gpa:95,gpl:0,gpt:138,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,77,84,85,86,88,89,90,91,94,95],grab:2,grad:2,gradient:[2,61,63,81,93,133,141,142],graft:60,grain:[2,13,18,28,44,50,65,72,76,116,120,138,142,147],gram:112,gran:[2,82,83],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[74,163],greater:[1,61,66,68,72,97,99,100,101],greatli:[40,63],green:[2,35,57,73,98,163],green_kubo:2,grest:[21,22,60,101,119,127],grid:[19,40,43,59,67,81],grigera:2,gromac:92,gromacs:[2,92,120],groot:110,ground:[2,31,64,114],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,93,148,159],group_id:3,grow:[2,68,72,76,119],growth:2,gsmooth_factor:135,guarante:44,guess:163,gui:[3,163],guid:[1,151,152,153],gui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[67,115],zfactor:57,zhang:119,zhi:[2,82],zhi_bound:2,zhou:[98,115,145,156,158],zhu:153,ziegler:[135,158,162],zimmerman2004:58,zimmerman2010:58,zimmerman:[29,58,98],zlim:148,zlo:[2,82],zlo_bound:2,zmax:67,zmin:67,zn2:43,zone:40,zoom:57,zr4:43,zwall:82,zwall_veloc:67},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix nve/manifold/rattle command","fix nvt/manifold/rattle command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,40,41,43,44,56,57,58,61,66,67,68,69,73,74,79,80,82,98,114,132,133,138,154],"long":[99,100,101,102,103,106,108,109,123,127,131,144,147],acceler:1,adiabat:2,adp:94,airebo:95,alloi:112,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:58,atom:[2,29,30,36,38,41,42],aug:0,balanc:[19,59],barostat:2,bcc:72,beck:96,between:2,bodi:[2,97],bond:60,bond_styl:[20,21,22,23,24,25,26,27,28],bop:98,born:[99,108],box:[2,61],buck:[100,101,108,134],build:3,calcul:2,centro:29,charmm:[2,5,45,102,131],chunk:[2,34],class2:[6,20,46,84,103],cna:30,code:2,coeffici:2,colloid:[82,104,161],comb3:105,comb:105,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,control:62,core:2,cosin:[7,8,9,10,11,12,47],cossq:85,coul:[99,100,101,102,103,106,107,108,120,123,127,131,144,147],coupl:2,create_atom:44,cubic:125,cut:[25,100,103,106,109,114,117,123,124,131,139,144],cvff:86,data:2,deby:[106,123],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],diel:107,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,109],discuss:2,disp:2,distanc:87,document:0,dpd:[31,110,111],dreid:121,dreiding:2,drude:2,dsf:[106,123],dump:[2,57],eam:112,edip:113,eff:114,ehex:63,eim:115,elastic:2,energi:111,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],exp6:116,exp:[11,47],expand:[22,126],extend:3,fcc:72,fdt:111,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83],fix_modifi:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],flow:2,fluid:67,flux:35,forc:2,fourier:[14,15,48,88],from:[2,3],gauss:117,gaybern:118,gener:[1,2],github:163,gld:66,global:2,gpu:[96,99,100,102,103,104,106,109,110,112,117,118,120,123,124,125,126,139,140,146,147,150,155,156,157,158,160,161,162],gran:119,granular:2,gromac:120,gyrat:[33,34],harmon:[16,23,24,25,49,51,82,89,143],hbond:121,heat:35,helix:50,hertz:119,hexord:36,histori:119,hook:119,how:2,idealga:151,imag:57,implicit:102,improper_styl:[84,85,86,87,88,89,90,91],indice:0,induc:2,info:[0,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,68,86,89,100,102,118,123,155,156],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,163],lennard:134,librari:[2,3],linear:[130,140],list:122,lj1043:82,lj126:82,lj93:82,lj96:124,local:2,lubric:132,lubricateu:133,luci:[141,142],manifold:[70,71],mdf:134,meam:[135,136,137],measur:1,mgpt:138,mie:139,minim:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83,92],mod:[81,157],model:2,morri:153,mors:[26,95,121,140],movi:57,mpi:3,msd:37,msm:[99,100,102,106,123],multi:[2,51,141,142],multipl:2,nb3b:143,neb:93,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:68,nphug:69,npt:68,nve:70,nvt:[68,71],omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,68,69,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,137,140,143,144,146,147,150,155,156,157,158,159,160,161,162],opl:53,opt:[102,112,123,127,140],optim:1,option:2,orient:72,orientord:38,orthogon:2,other:2,output:[2,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],overview:3,packag:[1,4],pair:2,pair_styl:[94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,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