lammps/doc/html/searchindex.js

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,40,63,96,163],comand:61,combiant:106,combin:[2,3,18,32,56,58,59,63,68,71,81,82,103,105,106,110,113,114,115,129,130,149,155,156,158,159,161],come:[0,2,13,62,68,77,78,139,155,156,158,159,163],comit:163,comm:[0,3,30,92,109,139],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,60],comm_world:3,command:[0,1],comment:[3,46,65,74,79,92,93,111,112,114,115,121,134,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,62,71,81,82,118,120,155,156,158],commonli:[2,9,37,38,58,89,119,124,149,156,158],commun:[1,2,3,4,19,58,60,62,67,68,79,110],comp:[75,92,113,139,146,153,157],compar:[1,2,4,41,44,57,91,92,134,148],comparison:0,compart:90,compass:[6,20,47,57,82,102],compat:[3,19,50,60,63,80,137,139],compens:[2,113],compil:[4,58,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,60,71,92,114],complex:[2,3,9,36,38,42,45,67,81,92,113,137],complic:[2,40],compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,61,62,63,67,68,69,71,75,81,91,92,109,113,118,131,132,148,149],componenet:2,componennt:40,composit:[2,67,111],compound:[104,113,114,159],compress:[2,58,69,72],compris:[81,115,146],compton:[41,44],comput:[0,1],computation:[2,79,97],compute_modifi:[61,62,68,69],compute_sa:41,compute_xrd:44,concav:81,concentr:[65,74,111,115,142],concept:2,conceptu:[2,62,92,105,134],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,156,158],condens:[2,79,94,107,111,122,159],condit:[2,39,41,43,44,58,59,67,69,70,72,75,76,79,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,58,62,71,91,92,94,97,112,134,137,155,156,158,159,163],conflict:[139,163],conform:[2,61,62,73,88,92,113],confus:159,conjuct:109,conjug:113,conjunct:[2,32,45,67,92,98,99,105,109,113,120,122,139,144,147],connect:[2,32,61,75,90,92,106,118,154,158],conner:94,connor:94,consecut:[3,45,105,122,126],consequ:[1,2,79,121],conserv:[13,61,66,67,68,74,75,92,108,109,110,118,128,148],consid:[2,29,32,40,60,61,79,113,146,148,154],consider:2,consist:[2,3,39,40,45,51,66,68,69,72,73,74,90,92,94,97,103,105,113,117,131,132,134,137,139,141,142,146,148],consistent_fe_initi:59,constant:0,constantli:63,constitu:[2,80,81,103,146],constrain:[2,63,66,75,76,91,113],constraint:[19,39,43,60,63,75,76,80,91,132],construct:[2,28,29,30,36,38,41,42,44,62,68,73,74,81,108,137,139,154,155],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,146],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,65,67,70,72,74,79,81,92,93,94,97,104,105,108,111,112,113,115,134,137,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,60,61,62,63,66,68,69,72,77,78,79,81,97,109,124,127,146,157],continuum:[2,59,79],contour_integr:59,contract:[62,68],contrain:75,contrast:[1,2,161],contrib:79,contribut:[2,29,32,33,34,35,39,42,43,62,67,75,91,92,109,111,113,131,132,137,139,148,163],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,62,68,69,74,79,113,117,137,155,158],control_typ:59,convect:35,conveni:[2,13,149,163],convent:[13,50,55,57,73,111,113],converg:[2,19,58,60,61,62,69,72,73,75,91,92,104,105,122,148],convers:[42,58,105,106,107,113,122,126,130,144],convert:[2,5,6,8,12,16,17,18,35,45,47,58,82,83,87,88,92,93,111,137,156,158,162],convex:81,cool:63,coord:[2,3,36,38,40,70,80,92],coordb:148,coordbb:148,coordiat:91,coordin:[1,2,3,19,32,33,34,40,42,45,58,60,61,62,63,68,70,75,76,78,79,91,92,93,94,96,112,148],coords:148,copi:[0,3,58,79,92,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,46],corner:[2,58,81,163],corpor:4,corr:104,correct:[2,3,32,46,58,63,68,72,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:59,correctli:[3,68,75,81,92,107,132,137,163],correl:[2,35,36,42,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,58,60,68,74,79,105,122,126,137,139,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,46,91],could:[2,3,19,32,34,39,58,60,72,79,80,81,91,94,116,120],coulomb:[2,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,139,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,46,60,68,75,81,91,92,116,120,139],counterbal:63,counterbalanc:13,counterclockwis:46,coupl:0,couple:[2,3],cours:[4,66,73,80,131,150],cov:148,coval:[2,13,113,134,148],cover:[2,59,67,113],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:44,cr3:44,creat:[0,1,2,3,19,35,39,41,45,58,59,60,61,62,65,68,69,70,71,73,79,92,94,97,104,111,112,130,139,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,45,62,68,154],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:45,criteria:[58,61,91],criterion:[19,45,60,61,91,92,104,113,118,148],critic:[2,24,25,79,91],cross:[4,33,40,58,92,101,109,111,119,120,122,124,126,145,147,156,158,162],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,157],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,149],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,155,156,158,159],csinfo:2,csisi:[112,155,156,158,159],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:44,cu2:44,cu3au:134,cube:[2,81],cubes:[19,60],cubic:[38,67,70,111],cuda:1,cuh:97,cummul:[2,61,120],cumul:[2,68,69,92],current:[0,1,2,3,4,19,30,32,43,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,139,145,150,156,158,163],curv:[2,45],curvatur:[117,146,162],custom:[0,2,3,33,34,35,43,58,61,62,68,69,72,91,94,116,120],cut:[1,2,4,19],cuthi:70,cutinn:[131,132],cutlo:70,cutmax:145,cutoff1:[102,108,122,126,130,133,144,147],cutoff2:[98,99,100,102,107,108,122,126,130,133,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,42,61,65,70,72,80,81,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvff:4,cwiggl:80,cyan:58,cycl:[68,69],cyclic:46,cylind:[58,81,90],cylinder_d:90,cylindr:2,cyrot:97,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,91,92,98,99,101,105,108,113,118,122,130,144,147],dampflag:118,danger:109,darden:108,darken:58,dash:118,dat:[2,35,59],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:80,david:[156,158],daw:[111,145],dcd:[2,58,71],deactiv:130,debug:[2,3,41,44,45,71,139],decai:[36,105,162],decid:[2,4,163],decod:58,decompos:[32,149],decomposit:[59,71],decoupl:2,decreas:[4,61,63],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,42,64,69,80,97,103,110,113,145,149],deform:[2,43,62,68,131,132],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,38,39,44,45,46,47,49,50,55,56,58,61,68,69,71,73,75,78,82,83,87,88,89,91,108,111,120],delai:2,delet:[28,61,68,139,154,163],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:59,delimit:74,dellago:[2,63],deloc:[113,148],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,145],delta_pi:97,delta_r:145,delta_sigma:97,deltah_f:65,demo:3,demonstr:[72,134],dendrim:120,dendtrit:90,denniston:67,denot:[41,63,105,119],dens:[61,74,113],densiti:[2,19,42,45,59,60,67,79,80,93,94,97,111,134,135,136,141,142,145,146,148,151,152,153],dent:90,depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,75],depth:[26,58,79,115,117,146],der:[32,103,104,130,161],deriv:[2,32,42,62,63,68,69,70,77,78,79,80,81,94,97,103,108,113,114,119,124,128,129,134,137,161],derjagin:161,derlet:70,descib:58,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:42,design:[0,2,3,41,44,59,61,68,70,79,95,96,101,105,107,113,130,131,132,135,136,145],desir:[2,3,4,35,39,43,45,62,66,68,75,91,92,109,111,120,131,132,155,156,158],desktop:[2,58],destabil:97,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,40,42,43,45,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,139,141,142,146,148,149,150,160,161,163],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,41,43,44,45,58,60,62,65,68,70,71,72,73,74,80,81,94,100,104,108,111,115,116,118,126,134,137,139,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,69,72,94,97,113,136,137,148,159],deviat:[69,70,116],devic:1,devin:104,devis:136,dfactor:58,dft:137,dhug:72,dhugoniot:72,dia:134,diag:74,diagnost:[4,61,74],diagon:[2,40,42,43,62,68],diagonalstyl:149,diagram:[19,41,44,57,60,71],diallo:120,diam:58,diamet:[2,45,58,103,117,118,124,146,161],diamond:[113,134],dick:2,did:[91,109,111,118,139,156,158],dielectr:[101,105,106,107,122,126,130,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,74,105,145,157],difficult:[62,71,120],difficulti:[36,38,75],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,73,83,84,85,87,91,94,97,101],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:113,dij:75,dilat:[62,68,69],dim:[45,134],dimens:[1,2,19,35,40,43,45,58,60,62,67,68,69,72,80,92,139],dimension:[36,39,41,42,44,79,92,145],dimensionless:[37,42,79,149,161],dimer:[2,134],dimstr:[19,60],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,70,72,145],dirac:42,direc:145,direct:[2,4,13,29,38,41,42,44,45,46,58,67,69,70,72,77,78,79,80,81,91,92,109,110,118,132],directli:[2,3,32,40,42,58,67,74,81,93,94,98,99,100,105,108,111,113,122,126,139,144,147,154],directori:[0,1,2,3,4,77,78,92,93,94,97,104,105,111,112,114,130,134,135,136,137,143,145,148,149,155,156,157,158,159],disabl:[4,79,121],disadvantag:[2,60],disallow:68,discard:[19,60,81],discontinu:[91,128],discourag:134,discret:[2,58,67],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:146,disperion:[108,126],dispers:[2,100,108,126,131,139,159],displac:[2,37,62,68,70,118],displai:[3,57,58],disregard:137,dissip:[2,31,64,66,77,78,109,110,118,131,132],dist:[2,35,71,73,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,42,45,47,58,61,62,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,146],distinguish:[2,42,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,42,57,60,66,67,68,93,97,105,111,112,114,134,135,136,139,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[78,94],divid:[2,4,19,35,39,43,57,60,70,91,92,114,148,159],divis:[2,56,67,97,130],dl_poly:2,dlammps_ffmpeg:58,dlammps_gzip:58,dlammps_jpeg:58,dlammps_memalign:4,dlammps_png:58,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[103,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,40,43,45,57,58,68,81,90,91,92,93,94,96,104,105,111,112,114,120,134,135,136,139,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,41,44,45,46,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,139,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[45,94,104,112,155,156,157,158,159],dof:39,doi:[2,70],domain:[2,19,41,44,58,60,62,67,68,71,79,80,92,139],domin:[1,113],don:[0,4,81,134,148,163],done:[1,2,19,45,56,58,59,60,61,62,65,68,71,75,77,78,91,92,94,100,111,126,132,133,134,139,141,142,154,163],donor:120,dot:43,doti:[97,145],doubl:[1,2,3,4,32,46,81,97,114,119,137],dover:59,down:[2,3,62,113,139,148],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[64,65],dr_ewald:41,drag:[2,35,68,69,76],dragforc:67,drai:[58,72],drain:91,dramat:[61,62,68,139,148],drautz:97,draw:58,drawn:[58,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[93,111,141,142],drift:[2,37,63,66],drive:[3,62,68,70,92],driven:[2,51],driver:2,drop:109,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:44,due:[1,2,4,28,29,33,34,37,41,42,43,44,45,58,61,62,66,67,68,69,70,73,77,78,79,80,81,91,92,106,109,110,111,116,117,131,132,139,145,146,147,154,156,158,161,162],duffi:79,dullweb:68,dumbbel:90,dummi:[13,157],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,5,46,101],duplic:[19,60,70],durat:[57,79,118],dure:[2,4,19,32,40,46,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,91,92,109,130,137,139,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,61,64,66,68,69,71,72,73,77,78,79,91,92,109,110,113,131,132,139,153],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:97,e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:82,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,60],eam:[0,93,105],earli:[19,60],earlier:[92,118,134,139],earth:113,easi:[2,3,32,43,80],easier:[4,58],easili:[3,58,92],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebt:47,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,41,44],ecp:113,edg:[2,19,41,44,58,80,81],edge:80,edit:[4,163],edition:4,edu:[3,111,131],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,148,150,155,156,157,158,159,160,161,162],effici:[0,1,2,4,39,56,58,62,68,71,75,97,103,105,122,126,137,141,142,146],efficienc:4,efield:[75,91],eggebrecht:[105,148],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,41,42,43,44,45,58,60,61,62,63,67,68,69,70,74,75,81,91,97,103,111,115,118,131,132,134,137,139,142,145,154,156,158],ejtehadi:[103,117,146],elaps:[80,150],elast:[2,21,22,92,118,157],elastic:0,elba:13,electr:[2,59,114,162],electric:4,electrolyt:161,electron:[2,41,59,79,93,104,108,111,113,114,134,137,145,148,158,159,162],electron_integr:59,electron_temperatur:59,electron_unit:113,electroneg:[2,104,114,148],electroneg_compon:148,electrostat:[2,4,103,108,113,122,130,132,148,161],elem1:[114,134,149],elem2:[114,134,149],elem:148,element1:[93,111,148],element2:[93,111,148],element:[2,33,37,39,42,43,58,59,93,94,97,104,111,112,113,114,134,135,136,137,143,145,148,149,155,156,157,158,159],elementn:[93,111],elementset:59,elif:42,elig:120,elimin:[2,66,75,77,78],elj:108,ellips:2,ellipsoid:[2,45,90,91,117,132,146],els:[58,68,79],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:81,emb_lin_neg:134,embed:[3,13,79,93,111,114,130,134,135,136,145],embt:47,emphas:118,empir:[59,113],empiric:94,emploi:[63,157],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],enclos:[2,134,148],encod:58,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,47,58,61,63,66,68,73,74,79,92,109,111,117,133,137,146,149,150],endbondtors:47,energet:[61,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:148,enforc:[2,58,61,68,75,122],enforce2d:[2,91],eng:[3,104,136],engineer:[59,77,111],enginer:135,enhanc:[59,63],enlarg:58,enough:[45,60,72,80,81,105],enpub:111,ensembl:[2,32,35,68,71,72,109,148],ensight:2,ensur:[2,42,62,66,68,97,130,155,159],enter:[114,137,159],enthalpi:[74,111],entir:[0,2,3,19,31,39,40,41,43,44,45,60,61,63,66,68,69,70,71,74,76,79,108,126,139],entiti:2,entri:[40,41,65,72,97,112,134,141,142,143,149,155,156,157,158,159],entry1:[141,142],enumuer:2,environ:[1,2,3,4,58,70,93,97,104,112,113,145,156],eos:65,epair:[94,116,120],epp:108,epq:108,eps0:161,eps14:130,epsilon0:158,epsilon:[2,18,21,22,27,28,32,46,80,81,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,144,146,147,155,160,161],epsilon_0:162,epsilon_14:101,epsilon_:146,epsilon_d:106,epsilon_i:[117,139,146],epsilon_i_:146,epsilon_i_a:[117,146],epsilon_i_b:[117,146],epsilon_i_c:[117,146],epsilon_ij:139,epsilon_j:[117,139,146],epsilon_j_:146,epsilon_j_a:[117,146],epsilon_j_b:[117,146],epsilon_j_c:[117,146],epsilon_lj:146,eqp:108,eqq:108,equal:[2,3,19,28,32,35,43,45,58,60,62,66,67,69,70,71,72,73,74,77,78,79,80,91,92,94,104,109,110,116,117,120,131,137,138,145,146,148,149,150,159,162],equat:[2,35,38,39,41,44,57,62,63,64,65,67,68,69,70,71,72,74,75,79,80,90,103,108,109,110,113,114,115,118,131,132,134,139,142,146,151,152,153,162],equation:[70,88],equilibr:[2,35,45,61,62,68,72,77,78,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,62,66,67,68,69,72,73,75,78,82,83,87,88,104,134,143,148],equilibrium_start:59,equival:[2,13,62,68,73,94,109,113,148,156,158],equlibrium:2,er3:44,eradiu:113,eras:77,erat:132,erc:105,erfc:[105,122,139],erhart:[111,156,158],eros:134,erose_form:134,erot:2,errata:[156,158],erratum:80,error:[0,1,2,3,11,48,58,62,63,65,68,74,79,80,81,91,105,122,139,146,154,156,158],erta:118,especi:[4,45,60,72,73],essenti:[3,11,48,94,105,122,158],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,43,59,60,74,139],esub:134,eta:[2,67,68,72,112,114,117,145,157,159],eta_dot:68,eta_ij:145,eta_ji:114,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,40,43,45,58,59,66,68,79,81,91,92,111,112,130,132,137,155,156,158,159],etol:[91,92],etot0:72,etot:[2,43,72],eu2:44,eu3:44,euler:[74,91,92],eulerian:59,europhi:67,evalu:[3,32,35,42,45,46,58,59,66,74,80,91,137,139,141,142,145,148],evanseck:[2,5,46,101],evaul:91,even:[2,4,19,29,56,60,62,63,68,79,80,81,91,92,96,113,114,118,139,146,159],evenli:[19,43,60,67],event:[2,68,79],eventu:2,ever:28,everaer:[103,117,146],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,67,68,69,70,72,74,75,79,92,109,130,148,163],everyth:163,everywher:124,eviri:113,evolut:[63,67,71],evolv:[67,71],ewald:[2,41,43,91,98,99,100,105,108,113,122,126,144,147],ewald_disp:108,exact:[19,60,61,66,79],exactli:[2,19,35,45,60,66,72,109,111,118,131,139,141,142],examin:[2,61,74],exampl:[0,1],exce:[2,4,19,60,62,68,91],exceed:[19,60,68],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,68,69,71,75,79,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:113,exchang:[2,59,63,79,113],excit:113,excite:113,exclud:[2,4,39,40,42,91,118,131,132,139,154],exclus:[1,4,32,46,104,137,139],excurs:68,execut:[1,2,3,58],exempl:148,exemplari:66,exemplifi:113,exert:[2,81],exhaust:59,exhibit:[36,63,68,113],exist:[2,3,29,45,57,58,62,82,83,84,85,87,110,154,163],exit:[3,19,60],expans:[42,56],expect:[1,4,19,60,70,72,134,137,139],expens:[2,70,79],experi:[2,73,92,109,139],experienc:[2,4],explain:[1,2,3,19,30,40,58,60,62,68,70,92,96,111,148,150,163],explan:[2,40,42,70],explic:138,explicit:[2,3,32,74,94,97,101,111,113,121,131,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,66,68,69,72,75,79,82,83,84,86,87,88,89,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:71,explor:[41,44],expon:[74,111,115,117,120,130,138,147],exponenti:[32,74,115,145,155,159,162],expos:3,exposit:[59,109],express:[2,42,45,62,70,74,79,97,111,113,124,134,148,149],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,63,68,69,70,73,77,78,79,80,81,117,134,137,146,149],extent:[1,19,21,60,94],exterior:[2,81],extern:[32,58,62,66,67,68,69,79,91,135,136],extra:[2,3,4,19,22,39,41,43,44,45,60,68,72,91,108,118,134,139],extract:[2,3,18,32,92,105,114,134,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,58,62,68,78,113,157],extrema:130,extreme:113,extrins:59,f_1:2,f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:72,f_harm:78,f_i:[13,145],f_id:2,f_ij:145,f_int:77,f_j:13,f_jj:35,f_k:145,f_langevin:79,f_max:72,f_r:[156,157,158],f_sigma:97,f_solid:78,f_ss:2,face:[2,80,81,117,134,146],facil:0,facilit:2,fact:[2,4,78,118,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,60,62,63,67,68,69,71,73,74,75,80,81,87,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,139,141,142,143,144,147,150,155],fail:[3,62,91,92,107],fairli:[3,139,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,60,62,68,70,73,80,83,87,92],farrel:[156,158],fashion:[2,19,45,60,68,69,72,78,79,80,92,131],fast:[2,4,72,74,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,46,47,48,49,50,51,52,53,54,55,60,68,69,75,77,79,82,83,84,86,87,88,89,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,79],fault:29,fava:117,favor:61,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,42,58,61,66,71,81,91,163],fecr:111,feel:[70,81,92,139],fehlberg:74,felling:136,felt:81,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,46],fermi:[1,158],fermion:113,fernando:133,few:[1,2,3,63,68,75,91,92,94,148],fewer:[1,3,4],feynman:71,ffield:[104,114,148],fflag1:58,fflag2:58,ffmpeg:58,ffplai:58,fft:[1,3,43],fhot:63,ficiti:154,fictiti:[2,71,73,105,122,126,154],field:0,fifth:[2,115,143],figshar:70,figur:[1,4,72,163],fij:108,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,58,59,60,65,70,74,79,92,93,94,97,105,111,112,114,115,134,135,136,141,142,143,145,148,149,155,156,157,158,159],fill:[45,58,79,97,137,163],filter:59,finchham:[2,107],find:[0,2,3,4,30,32,61,62,65,70,73,91,92,105,122,126,134,141,142,148,163],fine:[4,78,163],finer:[42,45],finger:45,finish:[2,3,19,60],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,43,44,47,58,60,61,65,66,67,68,70,71,72,75,76,77,78,79,82,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,139,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,46,101],fit:[2,73,94,97,134,139,141,142,157,163],five:[30,72,97,135],fix:[0,1],fix_flux:59,fix_heat:63,fix_id:[62,68,69,72],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:75,fix_shak:75,fixedpoint:[62,68],fixid:[58,59],fji:108,flag:[3,4,33,34,40,41,44,58,61,94,120,121,134,137,154,163],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:[2,58,113,157],flip:[2,68],fluctuat:[2,32,62,66,67,68,69,70,78,79,88,110],fluid:[2,62],flux:2,flv:58,fly:[19,58,59,75,97,137],fmass:71,fmax:91,fmsec:68,fno:4,fnorm:91,fnve:63,focu:75,foil:[42,70,149],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,58,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,120],forcegroup:67,ford:108,forgiv:68,fork:163,form:[2,28,32,33,34,36,42,43,66,73,74,79,80,81,82,85,88,92,94,97,110,111,113,116,120,121,133,134,136,137,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,71,148],format:[2,19,58,60,65,74,79,92,93,94,97,111,114,115,121,134,136,141,142,147,149,159],formation:65,former:[2,19,60,79,97],formul:[1,2,43,68,73,75,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,41,43,44,45,47,57,70,76,80,82,84,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,145],found:[2,30,61,63,67,105,108],four:[2,3,28,42,79,88,92,137],fourier:2,fourth:[2,4,37,73,101,115,143,148],fox:[2,41,46,153],fqq:108,fraction:[1,2,4,19,43,58,61,62,72,74,92,97,115,118,131,132],frame:[42,59,72,117],framer:58,framework:[93,149],frattl:63,free:[2,13,29,32,70,77,78,79,92,113,130,137,140,145,161],freedom:[2,39,61,68,69,71,75,78,91,108],freeli:[0,2,58],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,109,113,148],frequent:[29,30,36,38,42,63,139],fri:72,friction:[2,72,79,118],from:[0,1],front:72,frontend:58,frozen:[2,39,66,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:75,fulfil:2,full:[1,2,4,35,58,63,67,70,74,97,111,113,114,117],fuller:91,fulli:[2,70,91,92,105,145,163],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,58,67,71,79,91,92,93,96,104,137,148],furthermor:[11,48,63,74,110,113],futur:[0,2,60,66,92,135,136],g_jik:145,g_p:79,ga3:44,gaa:97,gai:117,gain:4,galindo:138,gamma0:13,gamma:[2,13,67,72,109,110,112,117,134,138,151,152,153,155,156,158,159],gamma_:79,gamma_ijk:156,gamma_n:118,gamma_p:79,gamma_t:118,gammaa:138,gammafactor:67,gammar:138,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,46,101],gap:[131,132,149],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:106,gaussian:[2,35,37,66,71,73,109,113,116],gave:139,gavhan:4,gaybern:[2,4,91],gcmc:139,gd3:44,gdot:132,ge4:44,gec:[156,158],gen:68,gener:0,gentler:80,gentli:112,geom:2,geometr:[2,40,45,60,68,81,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,139,142,146,150,160,161],geometri:[2,9,19,45,60,62,139],gerber:130,germann:[69,124],germano:117,get:[0,1,2,3,4,19,35,40,42,45,58,60,62,81,92,105,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,62,68,109,110,113,118,121],gif:58,gifsicl:58,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,45,62,68,70,91,94,97,113,120,134,137,139,146,156,157,158],given:[2,3,4,11,38,42,43,48,57,62,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goddard:[2,9,89,113,120],goe:[28,42,45,63,91,108,112,119,124,127,150,162],gold:29,goldman:72,good:[1,2,4,19,30,41,44,60,68,75,92,93,103,111,137,139,159,163],gordan:42,gordon:2,got:163,gould:[2,46],gov:[0,93,111,114],govern:67,gpa:94,gpl:0,gpt:137,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,68,69,75,82,83,84,86,87,88,89,93,94],grab:2,grad:2,gradient:[2,62,63,79,92,132,141,142],graft:61,grain:[2,13,18,28,45,51,65,70,74,115,119,137,142,147],gram:111,gran:[2,80,81],grana:90,granular:0,graph:3,graphic:3,graviti:2,grdient:59,great:[72,163],greater:[1,62,66,68,70,96,98,99,100,139],greatli:[41,63],green:[2,35,58,71,97,163],green_kubo:2,grest:[21,22,61,100,118,126],grid:[19,41,44,60,67,79],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,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:2,section_howto:[2,3,29,30,32,33,34,36,38,42,43,96,107],section_modifi:[2,58],section_python:2,section_start:[2,3,92],section_tool:2,see:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],seed:[45,58,61,66,67,71,72,79,109,110],seek:[19,60],seem:[2,62,134],seen:[4,67,81],segment:[2,58,109,154],select:[2,41,44,45,58,80,92,120,121,134,148],self:[2,72,73,74,76,78,91,104,105,137,145,148],semi:59,semimet:113,semin:4,send:[0,3],sens:[1,2,19,57,60,61,66,72,79,92,105,122,126,156,157,158],sensit:[2,30,62],sep:[2,3],separ:[2,4,19,42,45,56,58,59,60,61,62,68,71,75,98,99,105,106,108,110,122,131,132,134,141,142,143,149,155,158,161],seper:106,sequenc:[19,58,60,92,145],sequenti:145,seri:[2,4,42,58,66,94,117,134,137,139,141,142,146,150],serial:1,serv:[2,154],server:1,set:[0,1],set_vari:[2,3],setarea:67,sete:61,setenv:3,setfl:[93,111],setforc:[2,91,92],setgamma:67,settl:62,setup:[2,3,4,32,35,57,59,61],seven:136,sever:[1,2,3,4,32,57,59,62,67,68,91,97,100,111,126,130,134,139,145,148],sexton:137,sfactor:58,shade:58,shake:[2,13,39,43,63],shan:104,shape:[2,19,45,58,60,62,68,72,81,96,117,146],shardlow:[64,74,110],share:[0,1,2],sharp:[81,134,158],shear:[2,62,67,68,118,131,132],shell:0,shenderova:94,shift:[1,2],shiga:[2,68],shini:58,shinoda:[2,68,147],shiny:58,shlib:3,shm:4,shock:[69,72,124],shockvel:72,shortcut:[62,68],shorter:[70,139],shortest:58,should:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,32,35,39,40,43,45,46,47,48,49,50,51,52,53,54,55,58,60,61,62,66,67,68,69,70,71,72,73,74,75,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,134,135,137,139,140,141,142,143,144,146,147,148,150,154,155,156,157,158,159,160,161,162,163],show:[2,3,92,120,134,137],shown:[1,4,19,41,42,44,57,60,61,63,68,70,71,113,114,117,118,130,137,146,148],shrink:[2,19,58,60,67,70,91,105,122,126,139],shrunk:74,shut:[2,3],si4:44,sic:[105,134,143,155,156,158,159],sic_tersoff:145,sicc:[112,155,156,158,159],sicg:[156,158],sicsi:[112,155,156,158,159],side:[19,45,60,61,67,70,74,80,81,92,105,117,118,146],sige:[156,158],sigma0:97,sigma14:130,sigma1:97,sigma2:97,sigma:[2,21,22,28,32,40,46,67,70,80,81,94,96,97,98,101,102,103,108,109,110,112,113,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,139,146,147,155],sigma_14:101,sigma_:106,sigma_c:103,sigma_cc:[94,103],sigma_h:116,sigma_i:[114,139],sigma_ij:139,sigma_j:139,sigma_ss:103,sign:[2,50,57,137,163],signifi:[34,115,142],signific:[66,74,113,117,134,137,139],significantli:[1,2,43,67,68,73,113,155],silbert:118,silicon:[112,134,155],sim:147,similar:[2,3,4,19,22,32,39,40,43,45,60,66,72,73,80,94,96,97,109,111,113,118,130,131,139,140,145],similarli:[2,39,58,68,75,81,82,92,94,100,118,126,155],simluat:[2,131],simlul:79,simpl:[1,2,3,4],simpler:3,simplest:34,simpli:[1,2,3,34,40,62,68,71,92,100,108,126,134,139],simplif:113,simplifi:[73,137],simplist:3,simul:[0,1],simulatan:4,simulationub:148,simultan:[2,4],sin:[56,80,90,145],sinc:[0,1,2,3,6,19,28,29,30,33,34,40,41,46,58,60,61,62,67,68,69,70,71,74,79,80,81,82,91,92,93,94,97,99,100,101,102,103,104,108,109,111,112,117,118,119,121,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,141,142,144,145,146,147,148,149,150,155,156,157,158,159,162,163],sinclair:[70,111],sine:145,singapor:42,singh:93,singl:[1,2,3,4,19,32,34,40,45,56,58,60,61,62,67,68,69,71,73,75,79,80,92,93,94,97,101,104,111,112,113,114,118,119,120,134,135,136,137,143,144,145,146,148,149,150,155,156,157,158,159],singleel:97,singular:[56,130,131,132,140],sinnott:[94,104],sinusoid:[45,80,90],sio2:159,sio:104,sirk:[43,154],sisic:[112,155,156,158,159],sisisi:[112,155,156,157,158,159],site:[0,1,2,3,29,32,63,67,75,93,97,105,111,115,116,122,126,130,140,142,144],situat:[62,67,68,71,97],sival:44,six:[2,42,143,145],sixth:143,sixthpow:[102,139],size:[0,1],sjplimp:[0,3],skew:[2,58,68],skin:[30,79],skip:[4,40,46,121],slab:[2,139],slater:[105,148],sleight:28,slepoi:134,slice:[2,41,71],slider:3,slight:[63,79],slightli:[1,2,4,58,68,94,105,122,126,156,158,159],sligthli:108,sliozberg:154,sllod:[2,4],slope:[2,78,106],slot:1,slow:[2,66,68,92,139,148],slower:[1,97],slowest:79,slowli:[60,91,137,150],sm3:44,small:[2,19,29,32,40,41,43,44,60,61,63,66,68,70,72,74,75,88,90,91,92,94,103,105,106,107,122,131,132,134,146,149,155,158,163],smaller:[1,2,4,58,67,74,78,139],smallest:29,smd:76,smith:144,smooth:[2,81,97,101,105,119,124,127],smoother:45,smoothli:[28,42,101,119,128,130,133,158,162],smt:4,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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 rigid/local 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","Manifolds (surfacse)","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_modify 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":[29,32,36,37,38,41,42,44,45,57,58,59,62,66,67,68,69,71,72,77,78,80,97,113,131,132,137,139,154],"long":[98,99,100,101,102,105,107,108,122,126,130,144,147],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:59,atom:[2,29,30,36,38,42,43],balanc:[19,60],barostat:2,bcc:70,beck:95,between:2,bodi:[2,96],bond:61,bond_styl:[20,21,22,23,24,25,26,27,28],bop:97,born:[98,107],box:[2,62],buck:[99,100,107,133],build:3,calcul:2,centro:29,charmm:[2,5,46,101,130],chunk:[2,34],class2:[6,20,47,82,102],cna:30,code:2,coeffici:2,colloid:[80,103,161],comb3:104,comb:104,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,core:2,cosin:[7,8,9,10,11,12,48],cossq:83,coul:[98,99,100,101,102,105,106,107,119,122,126,130,144,147],coupl:2,create_atom:45,cubic:124,cut:[25,99,102,105,108,113,116,122,123,130,138,144],cvff:84,data:2,deby:[105,122],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],diel:106,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,13,108],discuss:2,disp:2,distanc:85,document:0,dpd:[31,109,110],dreid:120,dreiding:2,drude:2,dsf:[105,122],dump:[2,58],eam:111,edip:112,eff:113,ehex:63,eim:114,elastic:2,energi:110,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],exp6:115,exp:[11,48],expand:[22,125],extend:3,fcc:70,fdt:110,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81],fix_modifi:[59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],flow:2,fluid:67,flux:35,forc:2,fourier:[14,15,49,86],from:[2,3],gauss:116,gaybern:117,gener:[1,2],github:163,gld:66,global:2,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,140,146,147,150,155,156,157,158,160,161,162],gran:118,granular:2,gromac:119,gyrat:[33,34],harmon:[16,23,24,25,50,52,80,87,143],hbond:120,heat:35,helix:51,hertz:118,hexord:36,histori:118,hook:118,how:2,idealga:151,imag:58,implicit:101,improper_styl:[82,83,84,85,86,87,88,89],indice:0,induc:2,info:[0,59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],input:2,install:3,integr:2,intel:[4,5,16,21,23,46,50,54,68,84,87,99,101,117,122,155,156],interfac:[2,3],jul:0,kspace_styl:2,lammps:[0,1,2,3,163],lennard:133,librari:[2,3],linear:[129,140],list:121,lj1043:80,lj126:80,lj93:80,lj96:123,local:[2,40],lubric:131,lubricateu:132,luci:[141,142],manifold:90,mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81,91],mod:[79,157],model:2,morri:153,mors:[26,94,120,140],movi:58,mpi:3,msd:37,msm:[98,99,101,105,122],multi:[2,52,141,142],multipl:2,nb3b:143,neb:92,nemd:2,nharmon:53,non:2,nongauss:37,nonlinear:27,nph:68,nphug:69,npt:68,nvt:68,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,46,47,48,49,50,51,52,53,54,55,68,69,82,83,84,86,87,88,89,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],opl:54,opt:[101,111,122,126,140],optim:1,option:2,orient:70,orientord:38,orthogon:2,other:2,output:[2,59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],overview:3,packag:[1,4],pair:2,pair_modifi:139,pair_styl:[93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:71,polariz:2,poli:[131,132],polymorph:145,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:72,quadrat:55,quantiti:2,quartic:[17,28],rattl:75,rebo:94,region:81,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,74,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],relax:62,replica:2,resquar:146,restart:[2,59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],restrain:73,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],rigid:[2,40],ring:88,run:[2,3,59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],scalar:2,script:[2,3],sdk:[18,147],serial:3,set:2,shake:75,share:3,shell:2,shift:[10,11,24,25,48],simpl:15,simul:2,size:2,smooth:[128,129,140],smtbq:148,sna:42,snad:42,snap:149,snapshot:2,snav:42,soft:[130,140,150],spc:2,sph:[151,152,153],spheric:[2,56],spline:[135,136],spring:[76,78],squar:12,srp:154,start:[59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],stop:[59,60,62,63,67,68,69,70,72,73,75,76,77,78,79,80,81],strategi:1,streitz:105,stress:43,style:[1,2],summari:2,surfacs:90,swap:61,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],system:2,tabl:[0,2,65,156],taitwat:[152,153],temperatur:2,tersoff:[156,157,158],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:163,umbrella:89,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:159,vector:2,version:0,viscos:2,visual:2,wall:[2,80,81],water:2,wolf:[98,105],wrapper:3,write:2,xrd:44,yukawa:[160,161],zbl:[158,162]}})