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,153,155],commun:[1,2,3,4,19,57,59,61,66,67,78,108],comp:[74,90,111,143,150,154],compar:[1,2,4,40,43,56,89,90,132,145],comparison:0,compass:[6,20,46,56,81,100],compat:[3,19,49,59,62,79,135],compens:[2,111],compil:[4,57,135],complain:3,complement:132,complementari:[103,120],complet:[2,3,19,59,70,90,112],complex:[2,3,9,36,38,41,44,66,80,90,111,135],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,66,67,68,70,74,80,89,90,107,111,116,129,130,145,146],componenet:2,composit:[2,66,109],compound:[102,111,112,156],compress:[2,57,68,71],compris:[80,113,143],compton:[40,43],comput:[0,1],computation:[2,78,95],compute_modifi:[60,61,67,68],compute_sa:40,compute_xrd:43,concav:80,concentr:[64,73,109,113,139],concept:2,conceptu:[2,61,90,103,132],concern:[2,30,32,65],concis:3,concurr:4,conden:[78,153,155],condens:[2,78,92,105,109,120,156],condit:[2,39,40,42,43,57,58,66,68,69,71,74,75,78,108,111,117],conducit:2,conduct:0,confer:[4,135],configur:[1,2,4,57,61,70,89,90,92,95,110,132,135,152,153,155,156,160],conflict:160,conform:[2,60,61,72,87,90,111],confus:156,conjuct:107,conjug:111,conjunct:[2,32,44,66,90,96,97,103,107,111,118,120,141,144],connect:[2,32,60,74,90,104,116,151,155],conner:92,connor:92,consecut:[3,44,103,120,124],consequ:[1,2,78,119],conserv:[13,60,65,66,67,73,74,90,106,107,108,116,126,145],consid:[2,29,32,59,60,78,111,143,145,151],consider:2,consist:[2,3,39,44,50,65,67,68,71,72,73,90,92,95,101,103,111,115,129,130,132,135,138,139,143,145],consistent_fe_initi:58,constant:0,constantli:62,constitu:[2,79,80,101,143],constrain:[2,62,65,74,75,89,111],constraint:[19,39,42,59,62,74,75,79,89,130],construct:[2,28,29,30,36,38,40,41,43,61,67,72,73,80,106,135,151,152],constructor:3,consult:4,consum:1,contact:[0,104,110,112,115,116,143],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,64,66,69,71,73,78,80,90,91,92,95,102,103,106,109,110,111,113,132,135,138,139,140,142,146,152,153,154,155,156,160],context:[2,4,158],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,65,67,68,71,76,77,78,80,95,107,122,125,143,154],continuum:[2,58,78],contour_integr:58,contract:[61,67],contrain:74,contrast:[1,2,158],contrib:78,contribut:[2,29,32,33,34,35,39,41,42,61,66,74,89,90,107,109,111,129,130,135,145,160],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61,67,68,73,78,111,115,135,152,155],control_typ:58,convect:35,conveni:[2,13,146,160],convent:[13,49,54,56,72,109,111],converg:[2,19,57,59,60,61,68,71,72,74,89,90,102,103,120,145],convers:[41,57,103,104,105,111,120,124,128,141],convert:[2,5,6,8,12,16,17,18,35,44,46,57,81,82,86,87,90,91,109,135,153,155,159],convex:80,cool:62,coord:[2,3,36,38,69,79,90],coordb:145,coordbb:145,coordiat:89,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,62,67,69,74,75,77,78,89,90,91,92,94,110,145],coords:145,copi:[0,3,57,78,90,160],copper:159,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,97,103,105],cornel:[2,45],corner:[2,57,80,160],corpor:4,corr:102,correct:[2,3,32,45,57,62,67,71,79,80,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],correction_max_iter:58,correctli:[3,67,74,80,90,105,130,135,160],correl:[2,35,36,41,65,70],correpond:64,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,64,66,67,68,69,70,73,74,79,80,81,82,83,85,86,87,88,90,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,132,133,135,137,139,140,141,142,143,144,145,146,147,152,153,154,155,156,157,158,159],correspondingli:[129,130],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,67,73,78,103,120,124,135,152],costheta0:[152,153,155,156],costheta:142,costli:[3,4],coul:[2,4,18,21,22,32,45,89],could:[2,3,19,32,34,39,57,59,71,78,79,80,89,92,114,118],coulomb:[2,42,89,96,97,98,99,100,102,103,104,105,106,111,116,117,120,124,128,131,141,144,145,155,156,158],coulommb:2,count:[1,2,3,19,35,45,59,67,74,80,89,90,114,118],counterbal:62,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,65,72,79,129,147],cov:145,coval:[2,13,111,132,145],cover:[2,58,66,111],cpp:[1,2,3,32,74],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,64,67,68,69,70,72,78,90,92,95,102,109,110,128,137,138,139,142,145,152,153,154,155,156,160],create_atom:[2,19,35],create_box:[2,19,35,44,61,67,151],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,89],criterion:[19,44,59,60,89,90,102,111,116,145],critic:[2,24,25,78,89],cross:[4,33,57,90,99,107,109,117,118,120,122,124,142,144,153,155,159],crossov:1,crozier:0,crucial:71,crystal:[2,4,29,30,38,69,77],crystallin:[2,154],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,146],cscl:132,csequ:2,csh:[3,4],cshrc:3,csic:[110,152,153,155,156],csinfo:2,csisi:[110,152,153,155,156],cst:109,cstherm:2,csvr:2,ctcm:[91,109],ctype:3,cu1:43,cu2:43,cu3au:132,cube:[2,80],cubes:[19,59],cubic:[38,66,69,109],cuda:1,cuh:95,cummul:[2,60,118],cumul:[2,67,68,90],current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,67,72,73,74,75,78,79,89,90,95,102,106,109,111,112,116,119,129,130,132,133,134,142,147,153,155,160],curv:[2,44],curvatur:[115,143,159],custom:[0,2,3,33,34,35,42,57,60,61,67,68,71,89,92,114,118],cut:[1,2,4,19],cuthi:69,cutinn:[129,130],cutlo:69,cutmax:142,cutoff1:[100,106,120,124,128,131,141,144],cutoff2:[96,97,98,100,105,106,120,124,128,131,141,144],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,64,69,71,79,80,89,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],cutoffa:110,cutoffc:110,cuu3:109,cval:43,cvff:4,cwiggl:79,cyan:57,cycl:[67,68],cyclic:45,cylind:[57,80],cylindr:2,cyrot:95,d3q15:66,d3q19:66,d_e:78,daan:77,damp:[2,67,68,71,89,90,96,97,99,103,106,111,116,120,128,141,144],dampflag:116,danger:107,darden:106,darken:57,dash:116,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:131,davi:79,david:[153,155],daw:[109,142],dcd:[2,57,70],deactiv:128,debug:[2,3,40,43,44,70],decai:[36,103,159],decid:[2,4,160],decod:57,decompos:[32,146],decomposit:[58,70],decoupl:2,decreas:[4,60,62],dedic:4,defect:[2,29,135],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,63,64,66,67,68,69,70,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,92,93,94,96,97,98,99,100,101,103,104,106,107,108,110,111,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,135,136,137,138,139,140,141,142,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159],definit:[2,41,63,68,79,95,101,108,111,142,146],deform:[2,42,61,67,129,130],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,67,68,70,72,74,77,81,82,86,87,88,89,106,109,118],delai:2,delet:[28,60,67,151,160],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:73,dellago:[2,62],deloc:[111,145],delr:132,delta_1:95,delta_3:95,delta_7:95,delta_ij:[132,142],delta_pi:95,delta_r:142,delta_sigma:95,deltah_f:64,demo:3,demonstr:[71,132],dendrim:118,denniston:66,denot:[40,62,103,117],dens:[60,73,111],densiti:[2,19,41,44,58,59,66,78,79,91,92,95,109,132,133,134,138,139,142,143,145,148,149,150],depart:0,departur:71,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,64,66,67,68,69,73,74,76,78,79,80,81,82,83,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,132,133,135,136,137,138,139,140,141,142,143,144,145,146,147,152,153,154,155,156,157,158,159],dependend:2,deposit:[67,74],depth:[26,57,78,113,115,143],der:[32,101,102,128,158],deriv:[2,32,41,61,62,67,68,69,76,77,78,79,80,92,95,101,106,111,112,117,122,126,127,132,135,158],derjagin:158,derlet:69,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,64,65,66,67,68,69,70,71,73,76,77,79,89,90,92,94,96,97,99,100,101,102,103,106,109,111,112,113,115,116,117,120,121,122,123,124,125,126,127,128,129,130,131,132,135,136,138,139,142,143,144,145,146,147,151,152,153,154,155,156,157,158,159,160],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,67,69,78,93,94,99,103,105,111,128,129,130,133,134,142],desir:[2,3,4,35,39,42,44,61,65,67,74,89,90,107,109,118,129,130,152,153,155],desktop:[2,57],destabil:95,destre:87,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,65,66,67,68,71,74,77,78,89,91,92,94,95,98,99,100,101,102,103,106,107,111,112,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,136,138,139,143,145,146,147,157,158,160],detect:[36,90,102,118,119],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,64,67,69,70,71,72,73,79,80,92,98,102,106,109,113,114,116,124,132,135,139,143,145,151,158],devan:144,devanathan:155,develop:[0,2,3,4,68,71,92,95,111,134,135,145,156],deviat:[68,69,114],devic:1,devin:102,devis:134,dfactor:57,dft:135,dhug:71,dhugoniot:71,dia:132,diag:73,diagnost:[4,60,73],diagon:[2,41,42,61,67],diagonalstyl:146,diagram:[19,40,43,56,59,70],diallo:118,diam:57,diamet:[2,44,57,101,115,116,122,143,158],diamond:[111,132],dick:2,did:[89,107,109,116,153,155],dielectr:[99,103,104,105,120,124,128,141],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,65,66,67,69,70,71,74,75,76,77,78,79,80,81,90,91,92,95,98,99,101,102,107,108,109,111,113,115,116,117,120,121,123,124,131,132,133,134,136,137,138,139,140,142,143,144,145,146,147,152,153,155,156,158],differenti:[1,2,13,73,103,142,154],difficult:[61,70,118],difficulti:[36,38,74],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:135,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,72,82,83,84,86,89,92,95,99],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:111,dij:74,dilat:[61,67,68],dim:[44,132],dimens:[1,2,19,35,42,44,57,59,61,66,67,68,71,79,90],dimension:[36,39,40,41,43,78,90,142],dimensionless:[37,41,78,146,158],dimer:[2,132],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:106,dir:[1,3,69,71,142],dirac:41,direc:142,direct:[2,4,13,29,38,40,41,43,44,45,57,66,68,69,71,76,77,78,79,80,89,90,107,108,116,130],directli:[2,3,32,41,57,66,73,80,91,92,96,97,98,103,106,109,111,120,124,141,144,151],directori:[0,1,2,3,4,76,77,90,91,92,95,102,103,109,110,112,128,132,133,134,135,140,142,145,146,152,153,154,155,156],disabl:[4,78,119],disadvantag:[2,59],disallow:67,discard:[19,59,80],discontinu:[89,126],discourag:132,discret:[2,57,66],discuss:[0,1],disk:[2,36],disloc:[29,135],disord:[29,135],disp:0,dispar:143,disperion:[106,124],dispers:[2,98,106,124,129,156],displac:[2,37,61,67,69,116],displai:[3,56,57],disregard:135,dissip:[2,31,63,65,76,77,107,108,116,129,130],dist:[2,35,70,72,151],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,62,66,67,68,69,71,72,74,75,77,78,79,80,81],distinct:[2,143],distinguish:[2,41,111],distort:91,distrbut:91,distribut:[0,2,3,19,32,41,56,59,65,66,67,91,95,103,109,110,112,132,133,134,140,142,143,152,153,154,155,156],distro:142,ditto:159,div:4,diverg:[77,92],divid:[2,4,19,35,39,42,56,59,69,89,90,112,145,156],divis:[2,55,66,95,128],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:67,dlmp_intel_offload:4,dlopen:2,dlvo:[101,158],dm_lb:66,doc:[0,1,2,3,32,34,37,39,42,44,56,57,67,80,89,90,91,92,94,102,103,109,110,112,118,132,133,134,140,142,146,152,153,155,156,160],docuement:143,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,64,65,66,67,78,79,80,82,83,84,86,87,90,91,92,93,94,95,98,99,100,101,102,103,104,106,107,109,110,111,113,114,115,116,117,119,122,123,125,126,127,129,130,132,133,134,135,138,139,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],doesn:[44,92,102,110,152,153,154,155,156],dof:39,doi:[2,69],domain:[2,19,40,43,57,59,61,66,67,70,78,79,90],domin:[1,111],don:[0,4,80,132,145,160],done:[1,2,19,44,55,57,58,59,60,61,64,67,70,74,76,77,89,90,92,98,109,124,130,131,132,138,139,151,160],donor:118,dot:42,doti:[95,142],doubl:[1,2,3,4,32,45,80,95,112,117,135],dover:58,down:[2,3,61,111,145],download:3,downsid:2,dpd:2,dpdtheta:[31,108],dpdtheta_i:[63,64],dr_ewald:40,drag:[2,35,67,68,75],dragforc:66,drai:[57,71],drain:89,dramat:[60,61,67,145],drautz:95,draw:57,drawn:[57,65],drayleigh:71,dreid:2,dreiding:0,drfourth:37,drho:[91,109,138,139],drift:[2,37,62,65],drive:[3,61,67,69,90],driven:[2,50],driver:2,drop:107,drsquar:37,drude:0,dt_collis:66,dt_lb:66,dt_md:66,dtqm:71,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,65,66,67,68,69,72,76,77,78,79,80,89,90,104,107,108,109,114,115,129,130,142,143,144,151,153,155,158,159],duffi:78,dullweb:67,dummi:[13,154],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,99],duplic:[19,59,69],durat:[56,78,116],dure:[2,4,19,32,45,58,59,60,61,62,64,65,66,67,68,69,70,71,72,74,75,76,77,78,79,80,89,90,107,128,135,137,138,139],dvlo:158,dvx:2,dx_lb:66,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,63,65,67,68,70,71,72,76,77,78,89,90,107,108,111,129,130,150],dynamo:[91,109,132],dyre:125,e28637:13,e_1:95,e_2:95,e_a:73,e_b:112,e_ee:111,e_hbond:118,e_i:[2,95,112],e_j:[2,95],e_k:95,e_ke:111,e_kl:2,e_lj:[92,106],e_n:95,e_ne:111,e_nn:111,e_pr:111,e_rebo:92,e_torsion:92,e_tot:135,e_vol:135,eaa:81,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,64,65,66,67,68,69,70,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,155,156,157,158,159],eacn:[19,59],eam:[0,91,103],earli:[19,59],earlier:[90,116,132],earth:111,easi:[2,3,32,42,79],easier:[4,57],easili:[3,57,90],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:132,ec_ij:132,ec_jj:132,echo:[3,40,43],ecp:111,edg:[2,19,40,43,57,79,80],edge:79,edit:[4,160],edition:4,edu:[3,109,129],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,62,65,67,68,69,70,71,72,74,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,95,96,97,98,99,100,101,102,103,106,107,109,110,111,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,135,137,138,139,140,141,143,144,145,147,152,153,154,155,156,157,158,159],effici:[0,1,2,4,39,55,57,61,67,70,74,95,101,103,120,124,135,138,139,143],efficienc:4,efield:[74,89],eggebrecht:[103,145],ehex:2,eigenvalu:70,einstein:[2,77],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,66,67,68,69,73,74,80,89,95,101,109,113,116,129,130,132,135,139,142,151,153,155],ejtehadi:[101,115,143],elaps:[79,147],elast:[2,21,22,90,116,154],elastic:0,elba:13,electr:[2,58,112,159],electric:4,electrolyt:158,electron:[2,40,58,78,91,102,106,109,111,112,132,135,142,145,155,156,159],electron_integr:58,electron_temperatur:58,electron_unit:111,electroneg:[2,102,112,145],electroneg_compon:145,electrostat:[2,4,101,106,111,120,128,130,145,158],elem1:[112,132,146],elem2:[112,132,146],elem:145,element1:[91,109,145],element2:[91,109,145],element:[2,33,37,39,41,42,57,58,91,92,95,102,109,110,111,112,132,133,134,135,140,142,145,146,152,153,154,155,156],elementn:[91,109],elementset:58,elif:41,elig:118,elimin:[2,65,74,76,77],elj:106,ellips:2,ellipsoid:[2,44,89,115,130,143],els:[57,67,78],elsewher:132,elt:132,emac:0,email:[0,3,112],emb:80,emb_lin_neg:132,embed:[3,13,78,91,109,112,128,132,133,134,142],embt:46,emphas:116,empir:[58,111],empiric:92,emploi:[62,154],empti:119,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],enclos:[2,132,145],encod:57,encompass:2,encount:38,encourag:[73,75],end:[1,2,3,4,19,46,57,60,62,65,67,72,73,78,90,107,109,115,131,135,143,146,147],endbondtors:46,energet:[60,92],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107],energy_compon:145,enforc:[2,57,60,67,74,120],enforce2d:[2,89],eng:[3,102,134],engineer:[58,76,109],enginer:133,enhanc:[58,62],enlarg:57,enough:[44,59,71,79,80,103],enpub:109,ensembl:[2,32,35,67,70,71,107,145],ensight:2,ensur:[2,41,61,65,67,95,128,152,156],enter:[112,135,156],enthalpi:[73,109],entir:[0,2,3,19,31,39,40,42,43,44,59,60,62,65,67,68,69,70,73,75,78,106,124],entiti:2,entri:[40,64,71,95,110,132,138,139,140,146,152,153,154,155,156],entry1:[138,139],enumuer:2,environ:[1,2,3,4,57,69,91,95,102,110,111,142,153],eos:64,epair:[92,114,118],epp:106,epq:106,eps0:158,eps14:128,epsilon0:155,epsilon:[2,18,21,22,27,28,32,45,79,80,89,94,99,100,101,103,104,105,106,113,115,117,118,119,120,121,122,123,124,125,126,127,128,131,136,141,143,144,152,157,158],epsilon_0:159,epsilon_14:99,epsilon_:143,epsilon_d:104,epsilon_i:[115,143],epsilon_i_:143,epsilon_i_a:[115,143],epsilon_i_b:[115,143],epsilon_i_c:[115,143],epsilon_j:[115,143],epsilon_j_:143,epsilon_j_a:[115,143],epsilon_j_b:[115,143],epsilon_j_c:[115,143],epsilon_lj:143,eqp:106,eqq:106,equal:[2,3,19,28,32,35,42,44,57,59,61,65,66,68,69,70,71,72,73,76,77,78,79,89,90,92,102,107,108,114,115,118,129,135,136,142,143,145,146,147,156,159],equat:[2,35,38,39,40,43,56,61,62,63,64,66,67,68,69,70,71,73,74,78,79,101,106,107,108,111,112,113,116,129,130,132,139,143,148,149,150,159],equation:[69,87],equilibr:[2,35,44,60,61,67,71,76,77,102,103],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,65,66,67,68,71,72,74,77,81,82,86,87,102,132,140,145],equilibrium_start:58,equival:[2,13,61,67,72,92,107,111,145,153,155],equlibrium:2,er3:43,eradiu:111,eras:76,erat:130,erc:103,erfc:[103,120],erhart:[109,153,155],eros:132,erose_form:132,erot:2,errata:[153,155],erratum:79,error:[0,1,2,3,11,47,57,61,62,64,67,73,78,79,80,89,103,120,143,151,153,155],erta:116,especi:[4,44,59,71,72],essenti:[3,11,47,92,103,120,155],essential:68,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,73],esub:132,eta:[2,66,67,71,110,112,115,142,154,156],eta_dot:67,eta_ij:142,eta_ji:112,etap:67,etap_dot:67,etc:[1,2,3,4,28,33,34,35,42,44,57,58,65,67,78,80,89,90,109,110,128,130,135,152,153,155,156],etol:[89,90],etot0:71,etot:[2,42,71],eu2:43,eu3:43,euler:[73,89,90],eulerian:58,europhi:66,evalu:[3,32,35,41,44,45,57,58,65,73,79,89,135,138,139,142,145],evanseck:[2,5,45,99],evaul:89,even:[2,4,19,29,55,59,61,62,67,78,79,80,89,90,94,111,112,116,143,156],evenli:[19,42,59,66],event:[2,67,78],eventu:2,ever:28,everaer:[101,115,143],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,66,67,68,69,71,73,74,78,90,107,128,145,160],everyth:160,everywher:122,eviri:111,evolut:[62,66,70],evolv:[66,70],ewald:[2,40,42,89,96,97,98,103,106,111,120,124,141,144],ewald_disp:106,exact:[19,59,60,65,78],exactli:[2,19,35,44,59,65,71,107,109,116,129,138,139],examin:[2,60,73],exampl:[0,1],exce:[2,4,19,59,61,67,89],exceed:[19,59,67],excel:111,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,67,68,70,74,78,81,82,83,85,86,87,88,90,91,92,93,96,97,98,99,100,101,102,103,105,106,107,109,110,111,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,133,137,140,141,143,144,147,152,153,154,155,156,157,158,159],excess:111,exchang:[2,58,62,78,111],excit:111,excite:111,exclud:[2,4,39,41,89,116,129,130,151],exclus:[1,4,32,45,102,135],excurs:67,execut:[1,2,3,57],exempl:145,exemplari:65,exemplifi:111,exert:[2,80],exhaust:58,exhibit:[36,62,67,111],exist:[2,3,29,44,56,57,61,81,82,83,84,86,108,151,160],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,69,71,132,135],expens:[2,69,78],experi:[2,72,90,107],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,67,69,90,94,109,145,147,160],explan:[2,41,69],explic:136,explicit:[2,3,32,73,92,95,99,109,111,119,129,160],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,65,67,68,71,74,78,81,82,83,85,86,87,88,91,92,93,96,97,98,99,100,101,102,103,104,106,107,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,133,135,137,138,139,140,141,143,144,147,148,149,150,152,153,154,155,156,157,158,159,160],explictli:4,exploit:70,explor:[40,43],expon:[73,109,113,115,118,128,136,144],exponenti:[32,73,113,142,152,156,159],expos:3,exposit:[58,107],express:[2,41,44,61,69,73,78,95,109,111,122,132,145,146],expressiont:95,extend:[0,2],extens:[2,4,21,22,27,32,35,62,67,68,69,72,76,77,78,79,80,115,132,135,143,146],extent:[1,19,21,59,92],exterior:[2,80],extern:[32,57,61,65,66,67,68,78,89,133,134],extra:[2,3,4,19,22,39,40,42,43,44,59,67,71,89,106,116,132],extract:[2,3,18,32,90,103,112,132,146],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,67,77,111,154],extrema:128,extreme:111,extrins:58,f_1:2,f_a:[153,154,155],f_c:154,f_f:155,f_fix_id:71,f_harm:77,f_i:[13,142],f_id:2,f_ij:142,f_int:76,f_j:13,f_jj:35,f_k:142,f_langevin:78,f_max:71,f_r:[153,154,155],f_sigma:95,f_solid:77,f_ss:2,face:[2,79,80,115,132,143],facil:0,facilit:2,fact:[2,4,77,116,145],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,62,66,67,68,70,72,73,74,79,80,86,92,95,96,97,99,103,104,105,107,108,111,116,119,120,132,135,138,139,140,141,144,147,152],fail:[3,61,89,90,105],fairli:[3,160],faken:30,fall:2,fals:145,famili:156,familiar:[0,3,160],fan:142,far:[2,59,61,67,69,72,79,82,86,90],farrel:[153,155],fashion:[2,19,44,59,67,68,71,77,78,79,90,129],fast:[2,4,71,73,129,130,135],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,67,68,74,76,78,81,82,83,85,86,87,88,91,92,93,95,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,137,140,141,143,144,147,152,153,154,155,156,157,158,159],fastest:[1,2,78],fault:29,fava:115,favor:60,fcc:[2,29,30,35,38],fcold:62,fdt:[63,64,73],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,65,70,80,89],fecr:109,feel:[69,80,90],fehlberg:73,felling:134,felt:80,fene:[2,4],fennel:[103,120],fep:0,ferguson:[2,45],fermi:[1,155],fermion:111,fernando:131,few:[1,2,3,62,67,74,89,90,92,145],fewer:[1,3,4],feynman:70,ffield:[102,112,145],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:62,ficiti:151,fictiti:[2,70,72,103,120,124,151],field:0,fifth:[2,113,140],figshar:69,figur:[1,4,71,160],fij:106,file0:69,file1:[3,64,69],file2:[3,64],file:[0,1],filenam:[4,19,57,58,59,64,69,73,78,90,91,92,95,103,109,110,112,113,132,133,134,138,139,140,142,145,146,152,153,154,155,156],fill:[44,57,78,95,135,160],filter:58,finchham:[2,105],find:[0,2,3,4,30,32,60,61,64,69,72,89,90,103,120,124,132,138,139,145,160],fine:[4,77,160],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:109,fire:[89,90],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,64,65,66,67,69,70,71,74,75,76,77,78,81,89,90,91,92,94,95,96,97,99,102,103,109,111,112,113,116,117,119,120,124,129,130,132,134,135,138,139,140,142,145,146,151,152,153,154,155,156,159,160],fischer:[2,5,45,99],fit:[2,72,92,95,132,138,139,154,160],five:[30,71,95,133],fix:[0,1],fix_flux:58,fix_heat:62,fix_id:[61,67,68,71],fix_manifoldforc:160,fix_modifi:2,fix_nv:160,fix_rattl:74,fix_shak:74,fixedpoint:[61,67],fixid:[57,58],fji:106,flag:[3,4,33,34,40,43,57,60,92,118,119,132,135,151,160],flag_buck:98,flag_coul:[98,106,124],flag_lj:[106,124],flagfld:[129,130],flaghi:[129,130],flaglog:[129,130],flagvf:[129,130],flat:[2,4,78,79],fld:[79,129,130],flexibl:[2,57,111,154],flip:[2,67],fluctuat:[2,32,61,65,66,67,68,69,77,78,87,108],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,74,95,135],fmass:70,fmax:89,fmsec:67,fno:4,fnorm:89,fnve:62,focu:74,foil:[41,69,146],fold:[4,75],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,63,64,65,66,67,68,70,71,72,73,74,76,77,78,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],foo:[3,57,73],foo_species:73,foot:2,forc:[0,1],forcefield:[72,118],forcegroup:66,ford:106,forgiv:67,form:[2,28,32,33,34,36,41,42,65,72,73,78,79,80,81,84,87,90,92,95,108,109,111,114,118,119,131,132,134,135,138,139,140,141,142,143,145,146,147,153,154,155,158],formal:[2,35,65,67,70,145],format:[2,19,57,59,64,73,78,90,91,92,95,109,112,113,119,132,134,138,139,144,146,156],formation:64,former:[2,19,59,78,95],formul:[1,2,42,67,72,74,92,95,109,111,115,132],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,44,46,56,69,75,79,81,83,92,94,95,99,100,101,106,107,109,110,115,116,117,118,119,120,122,123,124,126,127,129,130,132,136,137,143,144,147,152,153,154,155,156,157,158],forth:[1,2,3],fortran:[2,3,109,132],forward:[32,90],foster:[95,142],found:[2,30,60,62,66,103,106],four:[2,3,28,41,78,87,90,135],fourier:2,fourth:[2,4,37,72,99,113,140,145],fox:[2,40,45,150],fqq:106,fraction:[1,2,4,19,42,57,60,61,71,73,90,95,113,116,129,130],frame:[41,58,71,115],framer:57,framework:[91,146],frattl:62,free:[2,13,29,32,69,76,77,78,90,111,128,135,137,142,158],freedom:[2,39,60,67,68,70,74,77,89,106],freeli:[0,2,57],freez:2,frenkel:[2,62,77],frequenc:[2,4,70,71,73,107,111,145],frequent:[29,30,36,38,41,62],fri:71,friction:[2,71,78,116],from:[0,1],front:71,frontend:57,frozen:[2,39,65,114],fs2:[2,35],ftol:[89,90],fuction:103,fudg:74,fulfil:2,full:[1,2,4,35,57,62,66,69,73,95,109,111,112,115],fuller:89,fulli:[2,69,89,90,103,142,160],fulton:109,fumi:96,funcfl:109,fund:0,funrol:135,further:[2,37,57,66,70,78,89,90,91,94,102,135,145],furthermor:[11,47,62,73,108,111],futur:[0,2,59,65,90,133,134],g_jik:142,g_p:78,ga3:43,gaa:95,gai:115,gain:4,galindo:136,gamma0:13,gamma:[2,13,66,71,107,108,110,115,132,136,148,149,150,152,153,155,156],gamma_:78,gamma_ijk:153,gamma_n:116,gamma_p:78,gamma_t:116,gammaa:136,gammafactor:66,gammar:136,gan:[142,152,153,155,156],gan_sw:142,gan_tersoff:142,gao:[2,5,45,99],gap:[129,130,146],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:104,gaussian:[2,35,37,65,70,72,107,111,114],gavhan:4,gaybern:[2,4,89],gd3:43,gdot:130,ge4:43,gec:[153,155],gen:67,gener:0,gentler:79,gentli:110,geom:2,geometr:[2,44,59,67,80,90,94,100,101,103,106,111,113,115,117,120,121,122,123,124,125,126,127,128,129,130,131,136,139,143,147,157,158],geometri:[2,9,19,44,59,61],gerber:128,germann:[68,122],germano:115,get:[0,1,2,3,4,19,35,41,44,57,59,61,80,90,103,156,160],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[103,120],ghost:[2,4,30,61,67,107,108,111,116,119],gif:57,gifsicl:57,gillan:146,gingold:[148,149],git:160,give:[0,1,2,3,4,28,36,38,44,61,67,69,89,92,95,111,118,132,135,143,153,154,155],given:[2,3,4,11,38,41,42,47,56,61,62,65,66,67,68,69,70,71,72,73,74,75,78,79,80,91,92,95,96,97,98,100,101,102,103,104,107,108,109,111,112,113,115,116,118,120,121,122,124,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,159],glosli:135,glotzer:107,glue:3,gnu:0,gnuplot:3,goddard:[2,9,88,111,118],goe:[28,41,44,62,89,106,110,117,122,125,147,159],gold:29,goldman:71,good:[1,2,4,19,30,40,43,59,67,74,90,91,101,109,135,156,160],gordan:41,gordon:2,got:160,gould:[2,45],gov:[0,91,109,112],govern:66,gpa:92,gpl:0,gpt:135,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,74,81,82,83,85,86,87,88,91,92],grab:2,grad:2,gradient:[2,61,62,78,90,130,138,139],graft:60,grain:[2,13,18,28,44,50,64,69,73,113,117,135,139,144],gram:109,gran:[2,79,80],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[71,160],greater:[1,61,65,67,69,94,96,97,98],greatli:[40,62],green:[2,35,57,70,95,160],green_kubo:2,grest:[21,22,60,98,116,124],grid:[19,40,43,59,66,78],grigera:2,gromac:89,gromacs:[2,89,117],groot:107,ground:[2,31,63,111],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,90,145,156],group_id:3,grow:[2,67,69,73,116],growth:2,gsmooth_factor:132,guarante:44,guess:160,gui:[3,160],guid:[1,148,149,150],guidelin:1,gullet:132,gulp:2,gunnel:135,gunsteren:128,guo:[2,5,45,50,99],gyrat:2,gzip:[57,90],h12:115,h2o:[113,139],had:[2,3,60,61,65,67,68,78,107,116,151],hafskjold:[2,62],half:[1,2,4,19,57,59,67,78,79,80,95,101,111,135],halfwai:[19,57,160],halperin:36,halsei:116,halt:[19,59,62],halv:57,hamak:[79,80,101,143],hamilton:29,hamiltonian:[67,111],han:109,hand:[2,28,29,44,54,57,66,73,103,111],handl:[4,57,111,129,156],happen:2,hara:154,hard:[1,72,145],harden:147,harder:[79,80],hardi:58,hardwar:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,74,81,82,83,85,86,87,88,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,137,140,141,143,144,147,152,153,154,155,156,157,158,159],harmon:[2,4],harmonic_fix_wal:130,harrison:92,hartre:[109,111,135],hassl:72,hat:2,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9,72,74,75,76,79,80,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,106,107,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],infrequ:[2,67,107],infti:[104,129,130],ingtegr:95,inher:89,inherit:2,inhomogen:78,inidividu:89,init:145,init_fil:78,initi:[2,3,19,32,57,58,59,60,61,64,65,66,67,68,70,71,72,73,76,77,78,79,89,90,92,106,107,135,138,139,145],initial:2,initialt:78,inlclud:3,inner2:[99,117],inner:[4,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,109,110,111,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],inner_distance_cutoff:118,innner:126,inorgan:[2,156],inp:[146,156],input:[0,1],insert:[44,146,151],insid:[2,3,44,62,66,79,80],inside:[66,122],insight:2,instabl:[66,106],instal:[1,2,3,4,57,90,98,99,120,124,128,135,160],install:0,instanc:[2,3,114,142],instantan:[2,60,61,65,67,68,71],instanti:[2,3,58],instead:[1,2,3,4,19,29,34,45,59,61,66,97,98,109,119,121,128,132,135,137],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,57,67,68,74,81,82,83,85,86,87,88,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,137,140,141,143,144,147,152,153,154,155,156,157,158,159],instruction:3,insuffici:2,insult:67,insur:[2,3,30,44,57,78,79,80,101,115,143],integ:[2,3,29,38,41,44,45,48,49,52,55,57,60,65,66,71,73,78,85,107,108,132,146],integral:[70,138,139],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,65],intens:[1,2,33,34,35,37,39,40,43,59,60,67,68,78],inter:[60,90,95],interact:[1,2,3,13,28,32,36,38,39,41,42,45,50,55,56,60,69,70,72,73,78,79,80,82,83,84,86,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,141,142,143,144,145,146,147,151,152,153,154,155,156,157,158,159],interatom:[44,76,77,91,95,109,111,132,135,145,154],intercept:40,interchang:2,interconvert:111,interesect:80,interest:[1,3,43,70,77,110,130],interf:160,interfac:0,interfer:[67,92],interg:2,interi:130,interior:[2,19,80],interlac:132,interleav:[2,44],intermedi:[2,57,69,87,90],intermolecular:92,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,42,46,57,58,63,64,67,68,73,81,82,86,87,89,108,113,138,139,148],internal:57,internal_element_set:58,internal_quadratur:58,internat:[4,40,43,58],interpenetr:132,interpentr:[148,149],interpol:[2,57,58,64,66,69,90,95,138,139,153],interpret:[2,3,55,57,116,147],interrupt:71,intersect:[2,40,80],intersert:80,interspers:89,interstiti:135,interv:[2,35,67,71,145],intestieti:40,intial:[2,92],intiial:19,intramolecular:13,introduc:[2,36,38,57,62,67,71,87,91,103,111,120,124,128,152],introduct:0,inv:[40,43],invalid:[33,90,129,130],invari:[38,41],invent:74,invers:[2,26,40,43,71,87,88,96,103,120,157,158],invert:[1,2],invis:80,invoc:60,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,65,66,67,68,69,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,133,137,140,141,143,144,146,147,152,153,154,155,156,157,158,159],involv:[2,66,89,90,94,115,152,153,155],ion:[2,78,95,104,112,114,132,135,145,155,159],ionic:[2,96,97,104,111,112,141,145],ioniz:[102,111],ipp:0,ir3:43,ir4:43,irregular:[2,19,59,61,67],irrelev:140,irrespect:[129,130],irrevers:73,isbn:158,isenthalp:67,ismail:[98,124],isn:[3,62],iso:[61,67,68],isobar:[67,108],isodem:111,isoenerget:108,isoenthalp:108,isol:116,isomorph:70,isotherm:[67,108],isotrop:[2,36,115,129,130],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,45,46,47,48,49,50,51,52,53,54,57,60,61,62,67,68,70,74,77,81,82,83,85,86,87,88,90,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,137,140,141,143,144,147,151,152,153,154,155,156,157,158,159],issue:58,item:[2,19,59],iter:[2,19,59,61,74,89,90,145],iterat:89,itself:[2,3,35,57,78,90,103,112,115,138,139],ityp:44,izumi:154,j0jt:35,j_m:41,jackson:136,jacs:[2,45],janssen:69,januari:132,jaramillo:111,jcp:79,jeffer:4,jello:67,jeremi:134,jik:95,jmm:41,job:74,jochim:67,join:[2,29,116],joint:118,jon:29,jone:[1,2,21,22,32,45,58,62,79,80,89,92,94,97,98,99,100,101,106,115,117,118,119,120,121,122,124,125,127,128,131,136,142,143,144],jonsson:[30,90,145],jorgensen:[2,53,103,120,124],journal:[50,58,109,135,148,149],jpeg:57,jpg:57,judici:2,jump:[2,18,68],jun:4,just:[2,3,13,35,42,57,78,90,92,94,142,160],justo:110,jusufi:[104,114],jut:80,k11:35,k22:35,k33:35,k_2:84,k_4:84,k_sigma:95,k_ub:5,kalia:156,kapfer:38,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refactor:2,refer:[2,3,4,13,32,44,58,60,61,62,67,68,69,70,71,74,81,88,91,115,132,134,135,143,149,150,153,155],referenc:[2,103,118,140,143],reflect:[2,40,41,43,56,57,79,95],refresh:58,regard:[2,74],regardless:[44,67],regim:[2,104],region:[0,2,19,35,43,44,50,57,58,59,62,67,78,79],region_styl:80,regoin:2,regspher:44,regul:2,regular:[1,19,57,59,78,104],reinder:4,reinhardt:[76,77],reject:[44,60],rel:[1,2,11,18,19,36,41,44,47,59,62,69,73,78,89,111,115,116,129,130,132,143,158],relat:[1,2],relationship:[2,145,158],relax:2,releas:0,relev:[2,19,44,58,59,62,65,66,74,75,78,79,89,93,101,103,104,106,107,111,114,115,116,117,118,119,121,122,123,125,126,127,129,130,137,138,139,143,147,151,157,158,159],reli:[111,159],reltol:73,remain:[19,32,55,56,61,67,78,95,111,128,135,160],remaina:95,remaind:[44,155],remap:[2,44],remedi:2,rememb:160,remot:160,remov:[2,28,36,38,41,44,67,73,74,90,106,130,135,160],remove_molecul:58,remove_sourc:58,remove_speci:58,ren:43,renam:160,render:57,rendon:67,reneighbor:[59,107],repeat:[2,57,60,61,73,95,153,155],replac:[2,3,19,33,34,57,59,60,68,92,103,116,122,138,139],replica:0,report:[0,1,4,40,43,71,72,73,78,90,106,111,132],reprens:78,repres:[1,2,19,29,34,50,57,61,64,65,66,67,70,73,78,80,90,91,95,115,128,129,130,132,133,134,141,142],represent:[2,65,70,78,95,111,115,135,143],reproduc:[4,67,103,109,116],repul:132,repuls:[2,18,21,22,79,80,92,95,101,103,107,111,113,116,118,128,132,136,145,151,155,156,158,159],request:[2,19,66,160],requir:[1,2,3,4,18,19,28,31,32,40,42,43,44,45,55,57,58,59,60,63,64,65,66,67,73,74,78,79,81,89,90,91,92,94,95,99,101,102,103,107,108,109,110,111,112,115,116,118,126,128,129,130,132,133,134,135,137,138,139,140,142,143,144,145,146,151,152,153,154,155,156,158,159],rerun:[36,38,41,57],rescal:[2,62,67,68,76,77],research:[31,63,66,135],resembl:160,resepct:2,reservoir:[35,62,78],reset:[2,3,33,34,61,67,68,74,78,89,130],reset_atomic_reference_posit:58,reset_tim:58,reset_timestep:[2,35],resist:2,resolut:145,resolv:[61,70,130,160],resourc:[91,109],respa:[4,67,69,72,75,79,80,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,109,110,111,114,115,116,117,118,119,120,121,122,123,124,125,126,127,129,130,131,132,133,134,135,136,137,138,139,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],respecifi:135,respect:[1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,33,39,40,43,45,46,47,48,49,50,51,52,53,54,57,60,61,62,66,67,68,74,78,79,81,82,83,85,86,87,88,89,91,92,93,95,96,97,98,99,100,101,102,103,106,107,109,110,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,132,133,135,137,140,141,143,144,145,146,147,152,153,154,155,156,157,158,159],respond:[2,111],respons:2,resquar:[2,115],rest:[2,72,95,130,132],restart1:70,restart2:70,restart2data:0,restart:[0,1],restor:44,restrain:13,restraint:[72,119],restratin:72,restrict:[1,2],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,34,35,39,40,42,43,44,45,46,47,48,49,50,51,52,53,54,57,59,60,61,62,65,66,67,68,70,73,74,76,77,78,79,81,82,83,85,86,87,88,90,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,111,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,132,133,135,137,138,139,140,141,143,144,147,152,153,154,155,156,157,158,159],retain:[92,95,135],retriev:[2,133,134],rev:[2,29,36,38,41,42,67,68,76,77,95,101,102,103,106,109,110,111,115,116,122,129,130,131,132,134,138,139,142,143,146,152,153,154,155,156],revers:[2,32,49,60,67,69,76,90,128],review:[41,135,146,160],rfac0:[41,146],rg0:75,rh3:43,rh4:43,rheolog:2,rhi:[138,139],rho0:[132,149,150],rho0_meam:132,rho:[66,91,96,97,98,109,131,132,133,134,138,139,143,148],rho_0:[149,150],rho_alpha_beta:109,rho_bkgd:132,rho_colloid:79,rho_e:78,rho_i:[133,134],rho_ref_meam:132,rho_wal:79,rhodopsin:[1,4],rhosum:[148,149,150],rhot:62,rhs:73,rick:[102,145],right:[2,3,19,29,44,54,56,59,60,66,69,73,103,160],rightmost:[19,59],rii:[33,34],rij:[36,38,69,107,108,138,139,151],rin:[118,125,126],ring:[2,45,70],rino:[30,156],rirj:116,risi:[41,146],risk:72,rix:[33,34],rk4:73,rkf45:73,rlo:[138,139],rmin0:[41,146],rmin:122,rms:73,rnemd:2,robust:89,rock:132,rockett:142,role:2,ronchetti:38,root:[3,32,33,34,109],rose:132,ross:132,rosski:70,rot:[2,35,70,72],rotat:[2,41,44,80,89,106,115,143],rotation:38,rough:[2,44,57],roughli:[19,57,67,90],round:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,74,81,82,83,85,86,87,88,91,92,93,96,97,98,99,100,101,102,103,106,107,109,110,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,137,138,139,140,141,143,144,147,152,153,154,155,156,157,158,159],rous:65,rout:[32,118,128],routin:[2,3,4,66,135],roux:2,row:[2,34,43,78,111],rozero:132,rrespa:[1,4,67,91,92,93,94,96,97,98,99,100,101,102,103,104,106,107,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,129,130,131,132,133,134,136,137,138,139,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],rsq:[138,139],rsurfac:78,ru3:43,ru4:43,rub:5,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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 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","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":[29,32,36,37,38,40,41,43,44,56,57,58,61,65,66,67,68,70,71,76,77,79,95,111,129,130,135,151],"long":[96,97,98,99,100,103,105,106,120,124,128,141,144],acceler:1,account:160,adding:160,addition:160,adiabat:2,adp:91,after:160,airebo:92,alloi:109,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],axel:160,balanc:[19,59],barostat:2,bcc:69,beck:93,between:2,bodi:[2,94],bond:60,bond_styl:[20,21,22,23,24,25,26,27,28],bop:95,born:[96,105],box:[2,61],branch:160,buck:[97,98,105,131],build:3,calcul:2,centro:29,chang:160,charmm:[2,5,45,99,128],chunk:[2,34],class2:[6,20,46,81,100],cna:30,code:2,coeffici:2,colloid:[79,101,158],comb3:102,comb:102,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],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,core:2,cosin:[7,8,9,10,11,12,47],cossq:82,coul:[96,97,98,99,100,103,104,105,117,120,124,128,141,144],coupl:2,create_atom:44,cubic:122,cut:[25,97,100,103,106,111,114,120,121,128,136,141],cvff:83,data:2,deby:[103,120],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],diel:104,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,106],discuss:2,disp:2,distanc:84,document:0,dpd:[31,107,108],dreid:118,dreiding:2,drude:2,dsf:[103,120],dump:[2,57],eam:109,edip:110,eff:111,ehex:62,eim:112,elastic:2,energi:108,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159],exp6:113,exp:[11,47],expand:[22,123],extend:3,fcc:69,fdt:108,featur:160,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],fix_modifi:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],flow:2,fluid:66,flux:35,forc:2,fork:160,fourier:[14,15,48,85],from:[2,3],gauss:114,gaybern:115,gener:[1,2],github:160,gld:65,global:2,gpu:[93,96,97,99,100,101,103,106,107,109,114,115,117,120,121,122,123,136,137,143,144,147,152,153,154,155,157,158,159],gran:116,granular:2,gromac:117,gyrat:[33,34],harmon:[16,23,24,25,49,51,79,86,140],hbond:118,heat:35,helix:50,hertz:116,hexord:36,histori:116,hook:116,how:2,idealga:148,imag:57,implicit:99,improper_styl:[81,82,83,84,85,86,87,88],indice:0,induc:2,info:[0,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,67,83,86,97,99,115,120,152,153],interfac:[2,3],jul:0,kspace_styl:2,lammps:[0,1,2,3,160],lennard:131,librari:[2,3],linear:[127,137],list:119,lj1043:79,lj126:79,lj93:79,lj96:121,local:2,lubric:129,lubricateu:130,luci:[138,139],make:160,mdf:131,meam:[132,133,134],measur:1,merg:160,mgpt:135,mie:136,minim:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80,89],mod:[78,154],model:2,morri:150,mors:[26,92,118,137],movi:57,mpi:3,msd:37,msm:[96,97,99,103,120],multi:[2,51,138,139],multipl:2,nb3b:140,neb:90,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:67,nphug:68,npt:67,nvt:67,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,67,68,81,82,83,85,86,87,88,91,92,93,96,97,98,99,100,101,102,103,104,106,107,109,112,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,133,134,137,140,141,143,144,147,152,153,154,155,156,157,158,159],opl:53,opt:[99,109,120,124,137],optim:1,option:2,orient:69,orientord:38,orthogon:2,other:2,output:[2,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],overview:3,own:160,packag:[1,4],pair:2,pair_styl:[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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