1 line
149 KiB
JavaScript
1 line
149 KiB
JavaScript
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:147,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,29,67,70,106,134,137,147],bundl:[57,162],button:162,bypass:2,c11:134,c_0:[79,94,151,152],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_gauss:116,c_hb:120,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:97,c_prop:2,c_sigma:97,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,105],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,94,103,160,162],callabl:3,callback:3,caltech:[2,113],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],canon:[68,71,78,137],cao1:71,cao2:71,cao:71,capabl:[3,4,94,102],capac:[64,79,150],capolungo:[40,43],captur:[2,94,100,113,118,126,134],carbid:105,carbon:[57,89,94,104,134],card:[4,32,120],care:[2,44,55,67,68,96],carefulli:[3,28],carlo:[2,60],caro:111,carri:[4,79,118],carrillo:4,cartesian:[2,93],cascad:79,cat:[4,57],cate:67,categori:[0,94],cation:[114,147],caus:[1,2,4,44,61,68,70,74,75,80,81,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,34],ccc:[112,154,155,157,158],ccflag:4,ccflags:4,ccm6:111,ccsi:[112,154,155,157,158],ccu:97,cd2:43,cdeam:111,cdll:3,cdof:2,cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,72,79,113,137],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:63,central:[29,36,38,41,70,75,76,86,137,142,158],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:146,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,91,92,109,113,118,131,132,134,137,147,153,162],change_box:2,chapter:71,charact:[2,19,57,59,65,74,113,115,121,140,141,144,147],character:[2,29,38,41,148],characterist:77,charg:[1,2,3,32,40,43,44,98,99,104,105,107,108,111,113,114,122,126,130,143,147,157,158,160,161],charl:62,charmm:0,cheaper:[117,145],check:[2,3,19,35,59,73,75,78,91,92,121],checkout:162,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,83,89,90,92,94,98,101,102,104,105,106,108,109,110,113,116,117,119,120,122,126,127,130,134,138,140,141,143,147,153],chemic:[31,40,43,58,115,141],chemistri:[72,94,97,113],chen:79,cheng:104,chi:[70,114,117],chiral:89,chmod:3,cho:134,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,92,130],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[155,157],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,110,113,118,121,124,146,155],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:147,cl1:43,clarendon:[13,108],clarifi:[155,157],clark:143,classic:[0,2,4,71,72,79,90,113],classifi:158,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,92,162],climb:92,clockwis:45,clone:162,close:[2,3,19,42,60,61,67,68,75,81,92,94,97,105,106,134,140,141,157,162],closer:[19,59,61,77,92],closest:[70,117,145,153],cloud:147,cluster:[2,4,42,63,75],cmax:134,cmd:[3,71],cmdarg:3,cmin:134,cmm:[18,146],cna:29,co2:[43,74,75,115],coars:[13,18,28,50,65,74,115,119,141,146],coarsest:41,code:[0,1],coeff:[6,45,46,55,83,121,149],coeffici:0,coefficienct:109,coefficient0:111,coefficient1:111,coeffieci:[2,95],coeffincientn:111,coexist:113,cohes:[2,114,134],coincid:[81,101,131,132],cold:2,coleman:[40,43],collect:[2,34,44,103],colliex:43,collis:[67,118,161],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,94,116,120],colvar:0,com:[2,37,63,96,162],comand:60,combiant:106,combin:[2,3,18,32,55,57,58,63,68,71,81,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,13,61,62,68,77,78,154,155,157,158,162],comit:162,comm:[0,3,30,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,74,79,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:2,common:[0,1,2,3,4,30,61,71,81,83,118,120,154,155,157],commonli:[2,9,37,38,57,90,119,124,148,155,157],commun:[1,2,3,4,19,57,59,61,67,68,79,110],comp:[75,92,113,145,152,156],compar:[1,2,4,40,43,56,91,92,134,147],comparison:0,compass:[6,20,46,56,83,102],compat:[3,19,49,59,62,63,80,137],compens:[2,113],compil:[4,57,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,59,71,92,114],complex:[2,3,9,36,38,41,44,67,81,92,113,137],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,91,92,109,113,118,131,132,147,148],componenet:2,composit:[2,67,111],compound:[104,113,114,158],compress:[2,57,69,72],compris:[81,115,145],compton:[40,43],comput:[0,1],computation:[2,79,97],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,111,115,141],concept:2,conceptu:[2,61,92,105,134],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,155,157],condens:[2,79,94,107,111,122,158],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,57,61,71,91,92,94,97,112,134,137,154,155,157,158,162],conflict:162,conform:[2,60,61,73,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,32,44,67,92,98,99,105,109,113,120,122,143,146],connect:[2,32,60,75,92,106,118,153,157],conner:94,connor:94,consecut:[3,44,105,122,126],consequ:[1,2,79,121],conserv:[13,60,66,67,68,74,75,92,108,109,110,118,128,147],consid:[2,29,32,59,60,79,113,145,147,153],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,82,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,103,145],constrain:[2,63,66,75,76,91,113],constraint:[19,39,42,59,63,75,76,80,91,132],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,108,137,153,154],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,145],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],context:[2,4,160],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,97,109,124,127,145,156],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,160],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,91,92,109,111,113,131,132,137,147,162],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,148,162],convent:[13,49,54,56,73,111,113],converg:[2,19,57,59,60,61,69,72,73,75,91,92,104,105,122,147],convers:[41,57,105,106,107,113,122,126,130,143],convert:[2,5,6,8,12,16,17,18,35,44,46,57,83,84,88,89,92,93,111,137,155,157,161],convex:81,cool:63,coord:[2,3,36,38,70,80,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,91,92,93,94,96,112,147],coords:147,copi:[0,3,57,79,92,162],copper:161,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,45],corner:[2,57,81,162],corpor:4,corr:104,correct:[2,3,32,45,57,63,68,72,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:58,correctli:[3,68,75,81,92,107,132,137,162],correl:[2,35,36,41,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,4],coul:[2,4,18,21,22,32,45,91],could:[2,3,19,32,34,35,39,57,59,62,72,79,80,81,91,94,116,120],coulomb:[2,42,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:2,count:[1,2,3,19,35,45,59,61,68,75,81,91,92,116,120],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,131,149],cov:147,coval:[2,13,113,134,147],cover:[2,58,67,113],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,82,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,153],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,91],criterion:[19,44,59,60,91,92,104,113,118,147],critic:[2,24,25,79,91],cross:[4,33,57,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,156],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,148],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,154,155,157,158],csinfo:2,csisi:[112,154,155,157,158],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:43,cu2:43,cu3au:134,cube:[2,81],cubes:[19,59],cubic:[38,67,70,111],cuda:1,cuh:97,cummul:[2,60,120],cumul:[2,68,69,92],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[2,44],curvatur:[117,145,161],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,91,94,116,120],cut:[1,2,4,19],cuthi:70,cutinn:[131,132],cutlo:70,cutmax:144,cutoff1:[102,108,122,126,130,133,143,146],cutoff2:[98,99,100,102,107,108,122,126,130,133,143,146],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:43,cvar:62,cvff:4,cwiggl:80,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:97,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:109,darden:108,darken:57,dash:118,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:80,david:[155,157],daw:[111,144],dcd:[2,57,71],deactiv:130,debug:[2,3,40,43,44,71],decai:[36,105,161],decid:[2,4,162],decod:57,decompos:[32,148],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,41,62,64,69,80,97,103,110,113,144,148],deform:[2,42,61,68,131,132],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,83,84,88,89,90,91,108,111,120],delai:2,delet:[28,60,68,153,162],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:74,dellago:[2,63],deloc:[113,147],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,144],delta_pi:97,delta_r:144,delta_sigma:97,deltah_f:65,demo:3,demonstr:[72,134],dendrim:120,denniston:67,denot:[40,63,105,119],dens:[60,74,113],densiti:[2,19,41,44,58,59,67,79,80,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:2,deposit:[68,75],depth:[26,57,79,115,117,145],der:[32,103,104,130,160],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,35,39,42,44,61,62,66,68,75,91,92,109,111,120,131,132,154,155,157],desktop:[2,57],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,62,69,72,94,97,113,136,137,147,158],deviat:[69,70,116],devic:1,devin:104,devis:136,dfactor:57,dft:137,dhug:72,dhugoniot:72,dia:134,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:148,diagram:[19,40,43,56,59,71],diallo:120,diam:57,diamet:[2,44,57,103,117,118,124,145,160],diamond:[113,134],dick:2,dicken:62,did:[91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,2,13,74,105,144,156],difficult:[61,62,71,120],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,84,85,86,88,91,94,97,101],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:113,dij:75,dilat:[61,68,69],dim:[44,134],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,72,80,92],dimension:[36,39,40,41,43,79,92,144],dimensionless:[37,41,62,79,148,160],dimer:[2,134],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,70,72,144],dirac:41,direc:144,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,70,72,77,78,79,80,81,91,92,109,110,118,132],directli:[2,3,32,41,44,57,62,67,74,81,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,62,77,78,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,79,121],disadvantag:[2,59],disallow:68,discard:[19,59,81],discontinu:[91,128],discourag:134,discret:[2,57,62,67],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:145,disperion:[108,126],dispers:[2,100,108,126,131,158],displac:[2,37,61,68,70,118],displai:[3,56,57],disregard:137,dissip:[2,31,64,66,77,78,109,110,118,131,132],dist:[2,35,71,73,153],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,70,72,73,75,76,78,79,80,81,83],distinct:[2,145],distinguish:[2,41,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,41,56,59,66,67,68,93,97,105,111,112,114,134,135,136,142,144,145,154,155,156,157,158],distro:144,ditto:161,div:4,diverg:[78,94],divid:[2,4,19,35,39,42,56,59,70,91,92,114,147,158],divis:[2,55,67,97,130],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:[103,160],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,81,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,79,80,81,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[44,94,104,112,154,155,156,157,158],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,67,68,71,79,80,92],domin:[1,113],don:[0,4,81,134,147,162],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,71,75,77,78,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:42,doti:[97,144],doubl:[1,2,3,4,32,45,61,81,97,114,119,137],dover:58,down:[2,3,61,113,147],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,76],dragforc:67,drai:[57,72],drain:91,dramat:[60,61,68,147],drautz:97,draw:57,drawn:[57,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[93,111,140,141],drift:[2,37,63,66],drive:[3,61,68,70,92],driven:[2,50],driver:2,drop:109,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,70,73,77,78,79,80,81,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:79,dullweb:68,dummi:[13,156],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,101],duplic:[19,59,70],durat:[56,79,118],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,71,72,73,77,78,79,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:13,e_1:97,e_2:97,e_a:74,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:[62,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161],eacn:[19,59],eam:[0,93,105],earli:[19,59],earlier:[92,118,134],earth:113,easi:[2,3,32,42,80],easier:[4,57],easili:[3,57,92],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,40,43],ecp:113,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,162],edition:4,edu:[3,111,131],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161],effici:[0,1,2,4,39,55,57,61,68,71,75,97,103,105,122,126,137,140,141,145],efficienc:4,efield:[75,91],eggebrecht:[105,147],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaps:[80,149],elast:[2,21,22,92,118,156],elastic:0,elba:13,electr:[2,58,114,161],electric:4,electrolyt:160,electron:[2,40,58,79,93,104,108,111,113,114,134,137,144,147,157,158,161],electron_integr:58,electron_temperatur:58,electron_unit:113,electroneg:[2,104,114,147],electroneg_compon:147,electrostat:[2,4,103,108,113,122,130,132,147,160],elem1:[114,134,148],elem2:[114,134,148],elem:147,element1:[93,111,147],element2:[93,111,147],element:[2,33,37,39,41,42,57,58,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158],elementn:[93,111],elementset:58,elif:41,elig:120,elimin:[2,66,75,77,78],elj:108,ellips:2,ellipsoid:[2,44,91,117,132,145],els:[57,62,68,79],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:81,emb_lin_neg:134,embed:[3,13,79,93,111,114,130,134,135,136,144],embt:46,emin:61,emphas:118,empir:[58,113],empiric:94,emploi:[63,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,134,147],encod:57,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,46,57,60,61,63,66,68,73,74,79,92,109,111,117,133,137,145,148,149],endbondtors:46,energet:[60,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:147,enforc:[2,57,60,68,75,122],enforce2d:[2,91],eng:[3,104,136],engineer:[58,77,111],enginer:135,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,105],enpub:111,ensembl:[2,32,35,68,71,72,82,109,147],ensight:2,ensur:[2,41,61,66,68,97,130,154,158],enter:[114,137,158],enthalpi:[74,111],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,108,126],entiti:2,entri:[40,65,72,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,57,70,93,97,104,112,113,144,155],eos:65,epair:[94,116,120],epp:108,epq:108,eps0:160,eps14:130,epsilon0:157,epsilon:[2,18,21,22,27,28,32,45,80,81,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,143,145,146,154,159,160],epsilon_0:161,epsilon_14:101,epsilon_:145,epsilon_d:106,epsilon_i:[117,145],epsilon_i_:145,epsilon_i_a:[117,145],epsilon_i_b:[117,145],epsilon_i_c:[117,145],epsilon_j:[117,145],epsilon_j_:145,epsilon_j_a:[117,145],epsilon_j_b:[117,145],epsilon_j_c:[117,145],epsilon_lj:145,eqp:108,eqq:108,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[70,89],equilibr:[2,35,44,60,61,68,72,77,78,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,83,84,88,89,104,134,142,147],equilibrium_start:58,equival:[2,13,61,68,73,94,109,113,147,155,157],equlibrium:2,er3:43,eradiu:113,eras:77,erat:132,erc:105,erfc:[105,122],erhart:[111,155,157],eros:134,erose_form:134,erot:2,errata:[155,157],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,91,105,122,145,153,155,157],erta:118,especi:[4,44,59,72,73],essenti:[3,11,47,94,105,122,157],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:134,eta:[2,67,68,72,112,114,117,144,156,158],eta_dot:68,eta_ij:144,eta_ji:114,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,91,92],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,91,137,140,141,144,147],evanseck:[2,5,45,101],evaul:91,even:[2,4,19,29,55,59,61,63,68,79,80,81,91,92,96,113,114,118,145,158],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[103,117,145],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[19,59,60,66,79],exactli:[2,19,35,44,59,66,72,109,111,118,131,140,141],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,91],exceed:[19,59,68],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,58,63,79,113],excit:113,excite:113,exclud:[2,4,39,41,91,118,131,132,153],exclus:[1,4,32,45,104,137],excurs:68,execut:[1,2,3,57],exempl:147,exemplari:66,exemplifi:113,exert:[2,81],exhaust:58,exhibit:[36,63,68,113],exist:[2,3,29,44,56,57,61,83,84,85,86,88,110,153,162],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,70,72,134,137],expens:[2,70,79],experi:[2,73,92,109],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,92,96,111,147,149,162],explan:[2,41,70],explic:138,explicit:[2,3,32,74,94,97,101,111,113,121,131,162],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,72,75,79,82,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:4,exploit:71,explor:[40,43],expon:[74,111,115,117,120,130,138,146],exponenti:[32,74,115,144,154,158,161],expos:3,exposit:[58,109],express:[2,41,44,61,70,74,79,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,117,134,137,145,148],extent:[1,19,21,59,94],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,91,135,136],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,91,108,118,134],extract:[2,3,18,32,92,105,114,134,148],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,113,156],extrema:130,extreme:113,extrins:58,f_1:[2,61],f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:72,f_harm:78,f_i:[13,144],f_id:[2,62],f_ij:144,f_int:77,f_j:13,f_jj:35,f_k:144,f_langevin:79,f_max:72,f_r:[155,156,157],f_sigma:97,f_solid:78,f_ss:2,face:[2,80,81,117,134,145],facil:0,facilit:2,fact:[2,4,78,118,147],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[3,61,91,92,107],fairli:[3,162],faken:30,fall:2,fals:147,famili:158,familiar:[0,3,162],fan:144,far:[2,59,61,68,70,73,80,84,88,92],farrel:[155,157],fashion:[2,19,44,59,62,68,69,72,78,79,80,92,131],fast:[2,4,62,72,74,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,79],fault:29,fava:117,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,91,162],fecr:111,feedback:62,feel:[70,81,92],fehlberg:74,felling:136,felt:81,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,45],fermi:[1,157],fermion:113,fernando:133,few:[1,2,3,63,68,75,91,92,94,147],fewer:[1,3,4],feynman:71,ffield:[104,114,147],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:153,fictiti:[2,71,73,105,122,126,153],field:0,fifth:[2,115,142],figshar:70,figur:[1,4,72,162],fij:108,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,92,93,94,97,105,111,112,114,115,134,135,136,140,141,142,144,147,148,154,155,156,157,158],fill:[44,57,79,97,137,162],filter:58,finchham:[2,107],find:[0,2,3,4,30,32,60,61,62,65,70,73,91,92,105,122,126,134,140,141,147,162],fine:[4,78,162],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,83,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,140,141,142,144,147,148,153,154,155,156,157,158,161,162],fischer:[2,5,45,101],fit:[2,73,94,97,134,140,141,156,162],five:[30,72,97,135],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:162,fix_modifi:2,fix_nv:162,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:108,flag:[3,4,33,34,40,43,57,60,94,120,121,134,137,153,162],flag_buck:100,flag_coul:[100,108,126],flag_lj:[108,126],flagfld:[131,132],flaghi:[131,132],flaglog:[131,132],flagvf:[131,132],flat:[2,4,79,80],fld:[80,131,132],flexibl:[2,57,113,156],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,70,78,79,89,110],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,97,137],fmass:71,fmax:91,fmsec:68,fno:4,fnorm:91,fnve:63,focu:75,foil:[41,70,148],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],foo:[3,57,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,120],forcegroup:67,ford:108,forgiv:68,fork:162,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,83,86,89,92,94,97,110,111,113,116,120,121,133,134,136,137,140,141,142,143,144,145,147,148,149,155,156,157,160],formal:[2,35,66,68,71,147],format:[2,19,57,59,65,74,79,92,93,94,97,111,114,115,121,134,136,140,141,146,148,158],formation:65,former:[2,19,59,79,97],formul:[1,2,42,68,73,75,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,70,76,80,83,85,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,145,146,149,154,155,156,157,158,159,160],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,144],found:[2,30,60,63,67,105,108],four:[2,3,28,41,62,79,89,92,137],fourier:2,fourth:[2,4,37,73,101,115,142,147],fox:[2,40,45,152],fqq:108,fraction:[1,2,4,19,42,57,60,61,72,74,92,97,115,118,131,132],frame:[41,58,72,117],framer:57,framework:[93,148],frattl:63,free:[2,13,29,32,70,77,78,79,92,113,130,137,139,144,160],freedom:[2,39,60,68,69,71,75,78,91,108],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,109,113,147],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,118],from:[0,1],front:72,frontend:57,frozen:[2,39,66,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,97,111,113,114,117],fuller:91,fulli:[2,70,91,92,105,144,162],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,57,67,71,79,91,92,93,96,104,137,147],furthermor:[11,47,63,74,110,113],futur:[0,2,59,66,92,135,136],g_jik:144,g_p:79,ga3:43,gaa:97,gai:117,gain:[4,62],galindo:138,gamma0:13,gamma:[2,13,67,72,109,110,112,117,134,138,150,151,152,154,155,157,158],gamma_:79,gamma_ijk:155,gamma_n:118,gamma_p:79,gamma_t:118,gammaa:138,gammafactor:67,gammar:138,gan:[144,154,155,157,158],gan_sw:144,gan_tersoff:144,gao:[2,5,45,101],gap:[131,132,148],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:106,gaussian:[2,35,37,66,71,73,109,113,116],gavhan:4,gaybern:[2,4,91],gd3:43,gdot:132,ge4:43,gec:[155,157],gen:68,gener:0,gentler:80,gentli:112,geom:2,geometr:[2,44,59,68,81,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,141,145,149,159,160],geometri:[2,9,19,44,59,61],gerber:130,germann:[69,124],germano:117,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,92,105,158,162],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,61,68,109,110,113,118,121],gif:57,gifsicl:57,gillan:148,gingold:[150,151],git:162,give:[0,1,2,3,4,28,36,38,44,61,68,70,91,94,97,113,120,134,137,145,155,156,157],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,161],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,90,113,120],goe:[28,41,44,63,91,108,112,119,124,127,149,161],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,92,93,103,111,137,158,162],gordan:41,gordon:2,got:162,gould:[2,45],gov:[0,93,111,114],govern:67,gpa:94,gpl:0,gpt:137,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,85,87,88,89,90,93,94],grab:2,grad:2,gradient:[2,61,63,79,92,132,140,141],graft:60,grain:[2,13,18,28,44,50,65,70,74,115,119,137,141,146],gram:111,gran:[2,80,81],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[72,162],greater:[1,61,66,68,70,96,98,99,100],greatli:[40,63],green:[2,35,57,71,97,162],green_kubo:2,grest:[21,22,60,100,118,126],grid:[19,40,43,59,67,79],grigera:2,gromac:91,gromacs:[2,91,119],groot:109,ground:[2,31,64,113],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,92,147,158],group_id:3,grow:[2,68,70,74,118],growth:2,gsmooth_factor:134,guarante:44,guess:162,gui:[3,162],guid:[1,150,151,152],guidelin:1,gullet:134,gulp:2,gunnel:137,gunsteren:130,guo:[2,5,45,50,101],gyrat:2,gzip:[57,92],h12:117,h2o:[115,141],had:[2,3,60,61,66,68,69,79,109,118,153],hafskjold:[2,63],half:[1,2,4,19,57,59,68,79,80,81,97,103,113,137],halfwai:[19,57,162],halperin:36,ha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ameter_fil:58,parameterizaion:105,parametr:[2,18,112,146],paramt:[37,145],paramter:104,paratem:130,parenthes:[65,74,115,118,140,141],parenthesi:4,parinello:2,pariticl:59,park:[58,136],parmin:137,parrinello1981:61,parrinello:[61,68,72],pars:0,part:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,31,36,37,39,40,41,42,43,45,46,47,48,49,50,51,52,53,54,56,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],partial:[1,2,61,67,69,71,134],partic:2,particip:[55,96],particl:0,particular:[1,2,29,41,44,57,59,60,66,67,68,70,73,75,83,96,97,98,99,101,102,103,107,110,112,113,117,119,122,126,130,133,139,142,143,145,146,154,155,156,157,158,162],particularli:[2,9,57,61,113],partit:[2,19,59,71,92,100,101,113,122,123,126,133,138,144],partner:60,pass:[2,3,33,34,37,57,61,68,80,153],password:162,past:[0,62,72,109],patch:0,patel:137,path:[2,3,71,79,92,93,94,97,111,112,114,134,135,136,142,144,147,148,154,155,157,158],pathtolammp:147,patrick:156,pattern:30,paul:0,pauli:[113,147],paves:71,payn:[41,148],pb2:43,pb4:43,pbc:80,pchain:[68,69],pcie:1,pd2:43,pd4:43,pdamp:[68,69],pdb:2,pdf:[0,150,151,152],pe_eta:68,pe_etap:68,pe_omega:68,pe_strain:68,peak:116,pearlman:32,pencil:2,peng:43,per:[0,1],peratom:42,perceiv:57,percent:[4,61,154],percentag:[1,61,68],perfect:[2,19,29,30,36,59,70,92],perfectli:[19,59],perfom:[2,92],perform:0,performac:1,pergamon:[134,157,161],peri:[2,44],peridynam:2,perimitt:106,period:2,perioid:80,perl:2,perman:[28,73,120],permit:[2,67,137],permitt:[106,157,160,161],permut:[112,154,155,157,158],perpendicular:[2,57,70,80],perram:117,persepct:57,person:162,persp:57,perspect:57,perturb:[29,32,80],peskin:67,pettifor:97,pettifor_1:97,pettifor_2:97,pettifor_3:97,pfactor:57,phase:[4,68,97,122,156],phenomena:113,phi0:[54,73],phi1:46,phi2:[46,112,154],phi3:[46,112,154],phi:[1,4,36,38,41,55,56,57,73,85,93,97,111,114,134,135,136],phi_ij:[97,114,144],phillip:109,phillpot:[104,105,147],philosoph:111,philosophi:2,phonon:[0,58,79],phophor:148,phosphid:148,phy:[2,5,6,9,20,21,22,29,30,32,36,38,39,41,42,45,46,53,61,63,66,67,68,69,71,72,75,77,78,79,80,83,89,90,92,94,97,98,101,102,103,104,105,106,107,108,109,110,111,112,113,116,117,118,119,120,122,124,126,127,130,131,132,133,134,136,138,140,141,143,144,145,147,148,153,154,155,156,157,158],physic:[2,4,27,55,58,63,67,79,92,94,95,100,103,111,120,137,150,151,152],physica:[131,132],pick:62,picosend:113,pid:62,piec:[3,41,68],pimd:2,pin:4,pipe:[2,57],pipelin:[2,4],pisarev:79,pishevar:109,pitera:2,pixel:57,pizza:[2,3,19,57,59],pka:79,place:[2,3,19,32,44,57,60,63,66,68,79,80,120],placehold:[93,94,104,111,114,134,135,136,142,144,148,153,154,155,156,157,158],placement:122,plai:[2,57],plain:130,plan:[2,4],planar:[2,70,89,90],planck:71,plane:[2,19,36,57,58,59,70,79,83,84,85,86,87,88,90,132],planeforc:91,plasma:[79,113],plateau:62,platform:[1,4,57],plath:[2,35],player:57,pleas:[0,3,4,58,62,67,112,114,147],plimpton:[0,4,29,39,42,60,70,118],ploop:[68,69],plos:13,plot:[3,4,72,128,130],plu:[3,61,69,113],pm3:43,png:57,pni:57,poariz:2,poem:2,poems:2,point:[1,2,3,4,13,19,29,40,41,43,44,49,57,59,61,65,67,68,71,72,79,81,91,92,96,104,106,108,110,113,117,124,137,140,141,144,145,147,153,156,160],pointer:3,poisson:118,poisson_solv:58,polar:[2,38,41,43,58,104,105,122],polar_off:104,polar_on:104,polariz:0,politano:147,polydispers:[103,118,131,132,160],polyethylen:94,polygon:2,polym:[0,2,21,22,28,60,71,75,76,109,153],polynomi:[111,128,147],poor:[19,59,75,128],poorli:91,popular:112,porou:67,portion:[1,3,19,28,35,42,59,61,63,67,68,98,99,100,101,102,105,106,108,109,113,115,116,117,119,120,122,126,130,133,143,145,146,157,162],poschel:118,posit:[2,11,19,22,29,33,34,40,41,42,43,44,47,49,55,57,59,60,61,62,63,66,67,68,70,71,72,74,75,77,78,79,80,81,82,83,92,94,96,109,110,113,116,125,140,141,147,153],possibl:[1,2,3,19,29,32,41,42,58,59,60,64,70,74,79,87,91,120,134,147,158],post:[0,2,35,58,72],pot:118,potentail:114,potenti:0,potentiel:130,potin:137,pour:[2,75],power:[3,4,37,41,97],pparam:32,ppm:57,ppn:4,pppm:[0,1],pproni:66,pr3:43,pr4:43,practic:[61,68,158,162],prb:[155,157],prd:[2,92],pre:[2,73,80,97,118,140,141,147,149],prec:[4,147],preced:[2,45,74,92,97,120],preceed:[3,80],precis:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,63,68,69,75,82,83,84,85,87,88,89,90,91,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,142,143,145,146,147,149,154,155,156,157,158,159,160,161],predefin:[54,113],predict:[1,2],prefactor:[8,9,12,16,17,18,56,80,84,88,89,91,103,116,142,145,146,149,160],prefer:[73,94,162],prefix:[3,57,62,74],preliminari:[65,140,141],prematur:91,preprint:[41,14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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 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","fix nve 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":[29,32,36,37,38,40,41,43,44,56,57,58,61,66,67,68,69,71,72,77,78,80,97,113,131,132,137,153],"long":[98,99,100,101,102,105,107,108,122,126,130,143,146],acceler:1,adiabat:2,adp:93,airebo:94,alloi:111,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:70,beck:95,between:2,bodi:[2,96],bond:60,bond_styl:[20,21,22,23,24,25,26,27,28],bop:97,born:[98,107],box:[2,61],buck:[99,100,107,133],build:3,calcul:2,centro:29,charmm:[2,5,45,101,130],chunk:[2,34],class2:[6,20,46,83,102],cna:30,code:2,coeffici:2,colloid:[80,103,160],comb3:104,comb:104,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],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:84,coul:[98,99,100,101,102,105,106,107,119,122,126,130,143,146],coupl:2,create_atom:44,cubic:124,cut:[25,99,102,105,108,113,116,122,123,130,138,143],cvff:85,data:2,deby:[105,122],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],diel:106,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,108],discuss:2,disp:2,distanc:86,document:0,dpd:[31,109,110],dreid:120,dreiding:2,drude:2,dsf:[105,122],dump:[2,57],eam:111,edip:112,eff:113,ehex:63,eim:114,elastic:2,energi:110,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],exp6:115,exp:[11,47],expand:[22,125],extend:3,fcc:70,fdt:110,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],fix_modifi:[58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],flow:2,fluid:67,flux:35,forc:2,fourier:[14,15,48,87],from:[2,3],gauss:116,gaybern:117,gener:[1,2],github:162,gld:66,global:2,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,139,145,146,149,154,155,156,157,159,160,161],gran:118,granular:2,gromac:119,gyrat:[33,34],harmon:[16,23,24,25,49,51,80,88,142],hbond:120,heat:35,helix:50,hertz:118,hexord:36,histori:118,hook:118,how:2,idealga:150,imag:57,implicit:101,improper_styl:[83,84,85,86,87,88,89,90],indice:0,induc:2,info:[0,58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,68,82,85,88,99,101,117,122,154,155],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,162],lennard:133,librari:[2,3],linear:[129,139],list:121,lj1043:80,lj126:80,lj93:80,lj96:123,local:2,lubric:131,lubricateu:132,luci:[140,141],mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82,91],mod:[79,156],model:2,morri:152,mors:[26,94,120,139],movi:57,mpi:3,msd:37,msm:[98,99,101,105,122],multi:[2,51,140,141],multipl:2,nb3b:142,neb:92,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:68,nphug:69,npt:68,nve:82,nvt:68,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,68,69,82,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,139,142,143,145,146,149,154,155,156,157,158,159,160,161],opl:53,opt:[101,111,122,126,139],optim:1,option:2,orient:70,orientord:38,orthogon:2,other:2,output:[2,58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],overview:3,packag:[1,4],pair:2,pair_styl:[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],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:71,polariz:2,poli:[131,132],polymorph:144,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:72,quadrat:54,quantiti:2,quartic:[17,28],rattl:75,rebo:94,region:81,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,74,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],relax:61,replica:2,resquar:145,restart:[2,58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],restrain:73,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rigid:2,ring:89,run:[2,3,58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],scalar:2,script:[2,3],sdk:[18,146],serial:3,set:2,shake:75,share:3,shell:2,shift:[10,11,24,25,47],simpl:15,simul:2,size:2,smooth:[128,129,139],smtbq:147,sna:41,snad:41,snap:148,snapshot:2,snav:41,soft:[130,139,149],spc:2,sph:[150,151,152],spheric:[2,55],spline:[135,136],spring:[76,78],squar:12,srp:153,start:[58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],stop:[58,59,61,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:42,style:[1,2],summari:2,swap:60,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],system:2,tabl:[0,2,65,155],taitwat:[151,152],temperatur:2,tersoff:[155,156,157],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,105,122,126,130],triclin:2,tstat:109,ttm:79,tutori:162,umbrella:90,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:158,vector:2,version:0,viscos:2,visual:2,wall:[2,80,81],water:2,wolf:[98,105],wrapper:3,write:2,xrd:43,yukawa:[159,160],zbl:[157,161]}}) 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