diff --git a/doc/html/_sources/fix_ave_histo.txt b/doc/html/_sources/fix_ave_histo.txt
index 8e56ec77ce..9adf1610ef 100644
--- a/doc/html/_sources/fix_ave_histo.txt
+++ b/doc/html/_sources/fix_ave_histo.txt
@@ -116,8 +116,7 @@ is used.
 
 If *mode* = vector, then the input values must be vectors, or arrays
 with a bracketed term appended, indicating the Ith column of the array
-is used.  All vectors must be the same length, which is the length of
-the vector or number of rows in the array.
+is used.
 
 Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html
index 4935a91c00..cd54bcef35 100644
--- a/doc/html/fix_ave_histo.html
+++ b/doc/html/fix_ave_histo.html
@@ -229,8 +229,7 @@ with a bracketed term appended, indicating the Ith value of the vector
 is used.</p>
 <p>If <em>mode</em> = vector, then the input values must be vectors, or arrays
 with a bracketed term appended, indicating the Ith column of the array
-is used.  All vectors must be the same length, which is the length of
-the vector or number of rows in the array.</p>
+is used.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
 specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index a7c7d62d9e..3187b1bc59 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],bulatov:[134,135],bulk:[2,29,67,70,105,133,136,146],bundl:[57,161],button:161,bypass:2,c11:133,c_0:[79,93,150,151],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_gauss:115,c_hb:119,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:96,c_prop:2,c_sigma:96,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,104],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,93,102,159,161],callabl:3,callback:3,caltech:[2,112],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,90,91,98,99,101,110,116,118,121,125,127,129,142,144,145,152],canon:[68,71,78,136],cao1:71,cao2:71,cao:71,capabl:[3,4,93,101],capac:[64,79,149],capolungo:[40,43],captur:[2,93,99,112,117,125,133],carbid:104,carbon:[57,88,93,103,133],card:[4,32,119],care:[2,44,55,67,68,95],carefulli:[3,28],carlo:[2,60],caro:110,carri:[4,79,117],carrillo:4,cartesian:[2,92],cascad:79,cat:[4,57],cate:67,categori:[0,93],cation:[113,146],caus:[1,2,4,44,61,68,70,74,75,80,81,90,91,119,121,127,130,131],caution:1,cautious:93,caveat:93,cbecker:[92,110],cc1:[2,34],ccc:[111,153,154,156,157],ccflag:4,ccflags:4,ccm6:110,ccsi:[111,153,154,156,157],ccu:96,cd2:43,cdeam:110,cdll:3,cdof:2,cdte:96,cdte_bop:96,cdtese:96,cdzn:96,cdznte:96,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,72,79,112,136],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,82,95,111,112,116,117,130,131,133,134,135,153,154,155,156,157],centr:63,central:[29,36,38,41,70,75,76,85,136,141,157],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:145,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,88,107,108,152],challeng:2,champaign:130,chan:136,chandler:[92,110],chandrasekhar:[2,121],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,90,91,108,112,117,130,131,133,136,146,152,161],change_box:2,chapter:71,charact:[2,19,57,59,65,74,112,114,120,139,140,143,146],character:[2,29,38,41,147],characterist:77,charg:[1,2,3,32,40,43,44,97,98,103,104,106,107,110,112,113,121,125,129,142,146,156,157,159,160],charl:62,charmm:0,cheaper:[116,144],check:[2,3,19,35,59,73,75,78,90,91,120],checkout:161,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,82,88,89,91,93,97,100,101,103,104,105,107,108,109,112,115,116,118,119,121,125,126,129,133,137,139,140,142,146,152],chemic:[31,40,43,58,114,140],chemistri:[72,93,96,112],chen:79,cheng:103,chi:[70,113,116],chiral:88,chmod:3,cho:133,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,91,129],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[154,156],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,109,112,117,120,123,145,154],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:146,cl1:43,clarendon:[13,107],clarifi:[154,156],clark:142,classic:[0,2,4,71,72,79,89,112],classifi:157,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,91,161],climb:91,clockwis:45,clone:161,close:[2,3,19,42,60,61,67,68,75,81,91,93,96,104,105,133,139,140,156,161],closer:[19,59,61,77,91],closest:[70,116,144,152],cloud:146,cluster:[2,4,42,63,75],cmax:133,cmd:[3,71],cmdarg:3,cmin:133,cmm:[18,145],cna:29,co2:[43,74,75,114],coars:[13,18,28,50,65,74,114,118,140,145],coarsest:41,code:[0,1],coeff:[6,45,46,55,82,120,148],coeffici:0,coefficienct:108,coefficient0:110,coefficient1:110,coeffieci:[2,94],coeffincientn:110,coexist:112,cohes:[2,113,133],coincid:[81,100,130,131],cold:2,coleman:[40,43],collect:[2,34,44,102],colliex:43,collis:[67,117,160],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,93,115,119],colvar:0,com:[2,37,63,95,161],comand:60,combiant:105,combin:[2,3,18,32,55,57,58,63,68,71,81,82,102,104,105,109,112,113,114,128,129,147,153,154,156,157,159],come:[0,2,13,61,62,68,77,78,153,154,156,157,161],comit:161,comm:[0,3,30,91,108],comm_modifi:[2,96,102,108,112,117],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,74,79,91,92,110,111,113,114,120,133,139,140,141,146,147,153,154,155,156,157,161],commit:161,commmand:2,common:[0,1,2,3,4,30,61,71,81,82,117,119,153,154,156],commonli:[2,9,37,38,57,89,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,67,68,79,109],comp:[75,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,82,101],compat:[3,19,49,59,62,63,80,136],compens:[2,112],compil:[4,57,136],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,71,91,113],complex:[2,3,9,36,38,41,44,67,81,91,112,136],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,90,91,108,112,117,130,131,146,147],componenet:2,composit:[2,67,110],compound:[103,112,113,157],compress:[2,57,69,72],compris:[81,114,144],compton:[40,43],comput:[0,1],computation:[2,79,96],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,154,156],condens:[2,79,93,106,110,121,157],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,71,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,73,88,91,112],confus:157,conjuct:108,conjug:112,conjunct:[2,32,44,67,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,75,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,79,120],conserv:[13,60,66,67,68,74,75,91,107,108,109,117,127,146],consid:[2,29,32,59,60,79,112,144,146,152],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,102,144],constrain:[2,63,66,75,76,90,112],constraint:[19,39,42,59,63,75,76,80,90,131],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,107,136,152,153],constructor:3,consult:4,consum:1,contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161],context:[2,4,159],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,96,108,123,126,144,155],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,159],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,147,161],convent:[13,49,54,56,73,110,112],converg:[2,19,57,59,60,61,69,72,73,75,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,82,83,87,88,91,92,110,136,154,156,160],convex:81,cool:63,coord:[2,3,36,38,70,80,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,90,91,92,93,95,111,146],coords:146,copi:[0,3,57,79,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,81,161],corpor:4,corr:103,correct:[2,3,32,45,57,63,68,72,80,81,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,68,75,81,91,106,131,136,161],correl:[2,35,36,41,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,35,39,57,59,62,72,79,80,81,90,93,115,119],coulomb:[2,42,90,97,98,99,100,101,103,104,105,106,107,112,117,118,121,125,129,132,142,145,146,156,157,159],coulommb:2,count:[1,2,3,19,35,45,59,61,68,75,81,90,91,115,119],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,130,148],cov:146,coval:[2,13,112,133,146],cover:[2,58,67,112],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,79,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,81],cubes:[19,59],cubic:[38,67,70,110],cuda:1,cuh:96,cummul:[2,60,119],cumul:[2,68,69,91],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,90,93,115,119],cut:[1,2,4,19],cuthi:70,cutinn:[130,131],cutlo:70,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvar:62,cvff:4,cwiggl:80,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:96,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:132,davi:80,david:[154,156],daw:[110,143],dcd:[2,57,71],deactiv:129,debug:[2,3,40,43,44,71],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],definit:[2,41,62,64,69,80,96,102,109,112,143,147],deform:[2,42,61,68,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,82,83,87,88,89,90,107,110,119],delai:2,delet:[28,60,68,152,161],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:74,dellago:[2,63],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:65,demo:3,demonstr:[72,133],dendrim:119,denniston:67,denot:[40,63,104,118],dens:[60,74,112],densiti:[2,19,41,44,58,59,67,79,80,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],dependend:2,deposit:[68,75],depth:[26,57,79,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,62,66,68,75,90,91,108,110,119,130,131,153,154,156],desktop:[2,57],destabil:96,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161],detect:[36,91,103,119,120],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159],devan:145,devanathan:156,develop:[0,2,3,4,62,69,72,93,96,112,135,136,146,157],deviat:[69,70,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:72,dhugoniot:72,dia:133,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:147,diagram:[19,40,43,56,59,71],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,dicken:62,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,91,92,93,96,99,100,102,103,108,109,110,112,114,116,117,118,121,122,124,125,132,133,134,135,137,138,139,140,141,143,144,145,146,147,148,153,154,156,157,159],differenti:[1,2,13,74,104,143,155],difficult:[61,62,71,119],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:136,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,83,84,85,87,90,93,96,100],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:112,dij:75,dilat:[61,68,69],dim:[44,133],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,72,80,91],dimension:[36,39,40,41,43,79,91,143],dimensionless:[37,41,62,79,147,159],dimer:[2,133],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:107,dir:[1,3,70,72,143],dirac:41,direc:143,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,70,72,77,78,79,80,81,90,91,108,109,117,131],directli:[2,3,32,41,44,57,62,67,74,81,92,93,97,98,99,104,107,110,112,121,125,142,145,152],directori:[0,1,2,3,4,62,77,78,91,92,93,96,103,104,110,111,113,129,133,134,135,136,141,143,146,147,153,154,155,156,157],disabl:[4,79,120],disadvantag:[2,59],disallow:68,discard:[19,59,81],discontinu:[90,127],discourag:133,discret:[2,57,62,67],discuss:[0,1],disk:[2,36],disloc:[29,136],disord:[29,136],disp:0,dispar:144,disperion:[107,125],dispers:[2,99,107,125,130,157],displac:[2,37,61,68,70,117],displai:[3,56,57],disregard:136,dissip:[2,31,64,66,77,78,108,109,117,130,131],dist:[2,35,71,73,152],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,144],distinguish:[2,41,112],distort:92,distrbut:92,distribut:[0,2,3,19,32,41,56,59,66,67,68,92,96,104,110,111,113,133,134,135,141,143,144,153,154,155,156,157],distro:143,ditto:160,div:4,diverg:[78,93],divid:[2,4,19,35,39,42,56,59,70,90,91,113,146,157],divis:[2,55,67,96,129],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[102,159],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,81,90,91,92,93,95,103,104,110,111,113,119,133,134,135,141,143,147,153,154,156,157,161],docuement:144,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,91,92,93,94,95,96,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,120,123,124,126,127,128,130,131,133,134,135,136,139,140,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],doesn:[44,93,103,111,153,154,155,156,157],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,67,68,71,79,80,91],domin:[1,112],don:[0,4,81,133,146,161],donald:62,done:[1,2,19,44,55,57,58,59,60,61,62,65,68,71,75,77,78,90,91,93,99,110,125,131,132,133,139,140,152,161],donor:119,dot:42,doti:[96,143],doubl:[1,2,3,4,32,45,61,81,96,113,118,136],dover:58,down:[2,3,61,112,146],download:3,downsid:2,dpd:2,dpdtheta:[31,109],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,76],dragforc:67,drai:[57,72],drain:90,dramat:[60,61,68,146],drautz:96,draw:57,drawn:[57,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[92,110,139,140],drift:[2,37,63,66],drive:[3,61,68,70,91],driven:[2,50],driver:2,drop:108,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,70,73,77,78,79,80,81,90,91,105,108,109,110,115,116,130,131,143,144,145,152,154,156,159,160],duffi:79,dullweb:68,dummi:[13,155],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,100],duplic:[19,59,70],durat:[56,79,117],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,90,91,108,129,136,138,139,140],dvlo:159,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,71,72,73,77,78,79,90,91,108,109,112,130,131,151],dynamo:[92,110,133],dyre:126,e28637:13,e_1:96,e_2:96,e_a:74,e_b:113,e_ee:112,e_hbond:119,e_i:[2,96,113],e_j:[2,96],e_k:96,e_ke:112,e_kl:2,e_lj:[93,107],e_n:[62,96],e_ne:112,e_nn:112,e_pr:112,e_rebo:93,e_torsion:93,e_tot:136,e_vol:136,eaa:82,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160],eacn:[19,59],eam:[0,92,104],earli:[19,59],earlier:[91,117,133],earth:112,easi:[2,3,32,42,80],easier:[4,57],easili:[3,57,91],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:133,ec_ij:133,ec_jj:133,echo:[3,40,43],ecp:112,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,161],edition:4,edu:[3,110,130],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160],effici:[0,1,2,4,39,55,57,61,68,71,75,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[75,90],eggebrecht:[104,146],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156],ejtehadi:[102,116,144],elaps:[80,148],elast:[2,21,22,91,117,155],elastic:0,elba:13,electr:[2,58,113,160],electric:4,electrolyt:159,electron:[2,40,58,79,92,103,107,110,112,113,133,136,143,146,156,157,160],electron_integr:58,electron_temperatur:58,electron_unit:112,electroneg:[2,103,113,146],electroneg_compon:146,electrostat:[2,4,102,107,112,121,129,131,146,159],elem1:[113,133,147],elem2:[113,133,147],elem:146,element1:[92,110,146],element2:[92,110,146],element:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,66,75,77,78],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,62,68,79],elsewher:133,elt:133,emac:0,email:[0,3,113],emb:81,emb_lin_neg:133,embed:[3,13,79,92,110,113,129,133,134,135,143],embt:46,emin:61,emphas:117,empir:[58,112],empiric:93,emploi:[63,155],empti:120,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],enclos:[2,133,146],encod:57,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,46,57,60,61,63,66,68,73,74,79,91,108,110,116,132,136,144,147,148],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,68,75,121],enforce2d:[2,90],eng:[3,103,135],engineer:[58,77,110],enginer:134,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,104],enpub:110,ensembl:[2,32,35,68,71,72,108,146],ensight:2,ensur:[2,41,61,66,68,96,129,153,157],enter:[113,136,157],enthalpi:[74,110],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,107,125],entiti:2,entri:[40,65,72,96,111,133,139,140,141,147,153,154,155,156,157],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,70,92,96,103,111,112,143,154],eos:65,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,80,81,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[70,88],equilibr:[2,35,44,60,61,68,72,77,78,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,82,83,87,88,103,133,141,146],equilibrium_start:58,equival:[2,13,61,68,73,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:77,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,90,104,121,144,152,154,156],erta:117,especi:[4,44,59,72,73],essenti:[3,11,47,93,104,121,156],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:133,eta:[2,67,68,72,111,113,116,143,155,157],eta_dot:68,eta_ij:143,eta_ji:113,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,90,91,110,111,129,131,136,153,154,156,157],etol:[90,91],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,90,91],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,90,136,139,140,143,146],evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,63,68,79,80,81,90,91,95,112,113,117,144,157],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,91,108,129,146,161],everyth:161,everywher:123,eviri:112,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,66,79],exactli:[2,19,35,44,59,66,72,108,110,117,130,139,140],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,90],exceed:[19,59,68],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],excess:112,exchang:[2,58,63,79,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:68,execut:[1,2,3,57],exempl:146,exemplari:66,exemplifi:112,exert:[2,81],exhaust:58,exhibit:[36,63,68,112],exist:[2,3,29,44,56,57,61,82,83,84,85,87,109,152,161],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,70,72,133,136],expens:[2,70,79],experi:[2,73,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,91,95,110,146,148,161],explan:[2,41,70],explic:137,explicit:[2,3,32,74,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,72,75,79,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:71,explor:[40,43],expon:[74,110,114,116,119,129,137,145],exponenti:[32,74,114,143,153,157,160],expos:3,exposit:[58,108],express:[2,41,44,61,70,74,79,96,110,112,123,133,146,147],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,90,107,117,133],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,112,155],extrema:129,extreme:112,extrins:58,f_1:[2,61],f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:72,f_harm:78,f_i:[13,143],f_id:[2,62],f_ij:143,f_int:77,f_j:13,f_jj:35,f_k:143,f_langevin:79,f_max:72,f_r:[154,155,156],f_sigma:96,f_solid:78,f_ss:2,face:[2,80,81,116,133,144],facil:0,facilit:2,fact:[2,4,78,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,87,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153],fail:[3,61,90,91,106],fairli:[3,161],faken:30,fall:2,fals:146,famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,68,70,73,80,83,87,91],farrel:[154,156],fashion:[2,19,44,59,62,68,69,72,78,79,80,91,130],fast:[2,4,62,72,74,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,86,87,88,89,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,79],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,90,161],fecr:110,feedback:62,feel:[70,81,91],fehlberg:74,felling:135,felt:81,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,63,68,75,90,91,93,146],fewer:[1,3,4],feynman:71,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:152,fictiti:[2,71,73,104,121,125,152],field:0,fifth:[2,114,141],figshar:70,figur:[1,4,72,161],fij:107,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157],fill:[44,57,79,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,62,65,70,73,90,91,104,121,125,133,139,140,146,161],fine:[4,78,161],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:110,fire:[90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,82,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161],fischer:[2,5,45,100],fit:[2,73,93,96,133,139,140,155,161],five:[30,72,96,134],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,79,80],fld:[80,130,131],flexibl:[2,57,112,155],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,70,78,79,88,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,96,136],fmass:71,fmax:90,fmsec:68,fno:4,fnorm:90,fnve:63,focu:75,foil:[41,70,147],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],foo:[3,57,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,119],forcegroup:67,ford:107,forgiv:68,fork:161,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,82,85,88,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159],formal:[2,35,66,68,71,146],format:[2,19,57,59,65,74,79,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157],formation:65,former:[2,19,59,79,96],formul:[1,2,42,68,73,75,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,70,76,80,82,84,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,63,67,104,107],four:[2,3,28,41,62,79,88,91,136],fourier:2,fourth:[2,4,37,73,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,72,74,91,96,114,117,130,131],frame:[41,58,72,116],framer:57,framework:[92,147],frattl:63,free:[2,13,29,32,70,77,78,79,91,112,129,136,138,143,159],freedom:[2,39,60,68,69,71,75,78,90,107],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,108,112,146],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,117],from:[0,1],front:72,frontend:57,frozen:[2,39,66,115],fs2:[2,35],ftol:[90,91],fuction:104,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,96,110,112,113,116],fuller:90,fulli:[2,70,90,91,104,143,161],fulton:110,fumi:97,funcfl:110,fund:0,funrol:136,further:[2,37,57,67,71,79,90,91,92,95,103,136,146],furthermor:[11,47,63,74,109,112],futur:[0,2,59,66,91,134,135],g_jik:143,g_p:79,ga3:43,gaa:96,gai:116,gain:[4,62],galindo:137,gamma0:13,gamma:[2,13,67,72,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:79,gamma_ijk:154,gamma_n:117,gamma_p:79,gamma_t:117,gammaa:137,gammafactor:67,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,66,71,73,108,112,115],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:68,gener:0,gentler:80,gentli:111,geom:2,geometr:[2,44,59,68,81,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159],geometri:[2,9,19,44,59,61],gerber:129,germann:[69,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,91,104,157,161],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,68,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,68,70,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,89,112,119],goe:[28,41,44,63,90,107,111,118,123,126,148,160],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],govern:67,gpa:93,gpl:0,gpt:136,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,86,87,88,89,92,93],grab:2,grad:2,gradient:[2,61,63,79,91,131,139,140],graft:60,grain:[2,13,18,28,44,50,65,70,74,114,118,136,140,145],gram:110,gran:[2,80,81],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[72,161],greater:[1,61,66,68,70,95,97,98,99],greatli:[40,63],green:[2,35,57,71,96,161],green_kubo:2,grest:[21,22,60,99,117,125],grid:[19,40,43,59,67,79],grigera:2,gromac:90,gromacs:[2,90,118],groot:108,ground:[2,31,64,112],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,91,146,157],group_id:3,grow:[2,68,70,74,117],growth:2,gsmooth_factor:133,guarante:44,guess:161,gui:[3,161],guid:[1,149,150,151],guidelin:1,gullet:133,gulp:2,gunnel:136,gunsteren:129,guo:[2,5,45,50,100],gyrat:2,gzip:[57,91],h12:116,h2o:[114,140],had:[2,3,60,61,66,68,69,79,108,117,152],hafskjold:[2,63],half:[1,2,4,19,57,59,68,79,80,81,96,102,112,136],halfwai:[19,57,161],halperin:36,halsei:117,halt:[19,59,63],halv:57,hamak:[80,81,102,144],hamilton:29,hamiltonian:[68,112],han:110,hand:[2,28,29,44,54,57,67,7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59,60,61,66,67,68,78,79,117,136],index:[0,2,3,65,71,79,139,140],indic:[2,3,4,6,28,31,33,35,37,39,42,46,57,61,62,68,79,82,88,103,113,133,136,141,146,154,156,161],indirectli:[2,62],indium:147,individu:[0,1,2,3,4,32,39,42,44,56,57,61,62,63,67,68,75,90,97,98,100,101,104,110,112,118,120,121,125,142,145],induc:0,ineffici:[2,29,30,36,38,41,57,68],inerti:131,inertia:[2,131],infer:[59,113],infin:90,infininti:57,infinit:[67,79,112],infinitesim:2,inflect:[105,123],influenc:[19,154,155,156],inform:[0,1,2,3,4,19,40,43,44,45,57,58,59,60,61,62,63,67,70,73,75,76,77,80,81,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],infrequ:[2,68,108],infti:[105,130,131],ingtegr:96,inher:90,inherit:2,inhomogen:79,inidividu:90,init:146,init_fil:79,initi:[2,3,19,32,44,57,58,59,60,61,62,65,66,67,68,69,71,72,73,74,77,78,79,80,90,91,93,107,108,136,139,140,146],initial:2,initialt:79,inlclud:3,inner2:[100,118],inner:[4,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],inner_distance_cutoff:119,innner:127,inorgan:[2,157],inp:[147,157],input:[0,1],insert:[44,62,147,152],insid:[2,3,44,63,67,80,81],inside:[67,123],insight:2,instabl:[67,107],instal:[1,2,3,4,57,91,99,100,121,125,129,136,161],install:0,instanc:[2,3,115,143],instantan:[2,60,61,62,66,68,69,72],instanti:[2,3,58],instead:[1,2,3,4,19,29,34,45,59,61,67,98,99,110,120,122,129,133,136,138],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,57,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],instruction:3,insuffici:2,insult:68,insur:[2,3,30,44,57,79,80,81,102,116,144],integ:[2,3,29,38,41,44,45,48,49,52,55,57,60,62,66,67,72,74,79,86,108,109,133,147],integral:[71,139,140],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,66],intens:[1,2,33,34,35,37,39,40,43,59,60,68,69,79],inter:[60,91,96],interact:[1,2,3,13,28,32,36,38,39,41,42,45,50,55,56,60,70,71,73,74,79,80,81,83,84,85,87,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,142,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160],interatom:[44,77,78,92,96,110,112,133,136,146,155],intercept:40,interchang:[2,62],interconvert:112,interesect:81,interest:[1,3,43,71,78,111,131],interf:161,interfac:0,interfer:[68,93],interg:2,interi:131,interior:[2,19,81],interlac:133,interleav:[2,44],intermedi:[2,57,70,88,91],intermolecular:93,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,42,44,46,57,58,62,64,65,68,69,74,82,83,87,88,90,109,114,139,140,149],internal:57,internal_element_set:58,internal_quadratur:58,internat:[4,40,43,58],interpenetr:133,interpentr:[149,150],interpol:[2,57,58,65,67,70,91,96,139,140,154],interpret:[2,3,55,57,117,148],interrupt:72,intersect:[2,40,81],intersert:81,interspers:90,interstiti:136,interv:[2,35,62,68,72,146],intestieti:40,intial:[2,93],intiial:19,intramolecular:13,introduc:[2,36,38,57,63,68,72,88,92,104,112,121,125,129,153],introduct:0,inv:[40,43],invalid:[33,91,130,131],invari:[38,41,62],invent:75,invers:[2,26,40,43,72,88,89,97,104,121,158,159],invert:[1,2],invis:81,invoc:60,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,63,66,67,68,69,70,75,76,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,147,148,153,154,155,156,157,158,159,160],involv:[2,67,90,91,95,116,153,154,156],ion:[2,79,96,105,113,115,133,136,146,156,160],ionic:[2,97,98,105,112,113,142,146],ioniz:[103,112],ipp:0,ir3:43,ir4:43,irregular:[2,19,59,61,68],irrelev:141,irrespect:[130,131],irrevers:74,isbn:159,isenthalp:68,ismail:[99,125],isn:[3,63],iso:[61,68,69],isobar:[68,109],isodem:112,isoenerget:109,isoenthalp:109,isol:117,isomorph:71,isotherm:[68,109],isotrop:[2,36,116,130,131],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,45,46,47,48,49,50,51,52,53,54,57,60,61,63,68,69,71,75,78,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,152,153,154,155,156,157,158,159,160],issue:58,item:[2,19,59],iter:[2,19,59,61,75,90,91,146],iterat:90,ith:62,itself:[2,3,35,57,79,91,104,113,116,139,140],ityp:44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112,115,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,137,138,142,144,145,148,152,158,159],readabl:57,readi:3,readme:[1,2,3,4,136],real:[2,3,11,14,15,35,36,38,41,44,47,71,72,80,86,104,136,156],realli:[1,39,42,161],reamin:[80,81],rearrang:91,reason:[2,3,44,55,77,78,91,105,112,113,115,131],reax:[0,72],rebal:[19,59],rebalanc:[19,59],rebuild:[3,4,108],rebuilt:57,recalcul:32,receiv:70,recent:[3,4,59,62,133],reciproc:[2,40,43,97,98,99,104,107,112,121,125,142,145],recogn:[30,68,74,110,133],recomend:2,recommed:74,recommend:[4,57,63,72,78,112,130,131,136,144,146,161],recompil:[1,75],reconstruct:146,recov:[61,63,68],rectangl:[19,59],rectangular:[19,59],rectilinear:[40,43],rector:27,recurs:[19,59,96],recust:19,red:[57,60,71],reduc:[1,2,11,19,39,40,42,43,57,59,60,70,73,74,90,112,116,143,144,153,154,156],reduct:[40,43,72],redund:113,reed:72,ref:[77,78],refactor:2,refer:[2,3,4,13,32,44,58,60,61,62,63,68,69,70,71,72,75,82,89,92,116,133,135,136,144,150,151,154,156],referenc:[2,62,104,119,141,144],reflect:[2,40,41,43,56,57,62,80,96],refresh:58,regard:[2,75],regardless:[44,68],regim:[2,105],region:[0,2,19,35,43,44,50,57,58,59,63,68,79,80],region_styl:81,regoin:2,regspher:44,regul:2,regular:[1,19,57,59,79,105],reinder:4,reinhardt:[77,78],reject:[44,60],rel:[1,2,11,18,19,36,41,44,47,59,63,70,74,79,90,112,116,117,130,131,133,144,159],relat:[1,2],relationship:[2,146,159],relax:2,releas:0,relev:[2,19,44,58,59,62,63,66,67,75,76,79,80,90,94,102,104,105,107,108,112,115,116,117,118,119,120,122,123,124,126,127,128,130,131,138,139,140,144,148,152,158,159,160],reli:[112,160],reltol:74,remain:[19,32,55,56,61,68,79,96,112,129,136,161],remaina:96,remaind:[44,156],remap:[2,44],remedi:2,rememb:161,remot:161,remov:[2,28,36,38,41,44,68,74,75,91,107,131,136,161],remove_molecul:58,remove_sourc:58,remove_speci:58,ren:43,renam:161,render:57,rendon:68,reneighbor:[59,108],repeat:[2,57,60,61,74,96,154,156],replac:[2,3,19,33,34,57,59,60,69,93,104,117,123,139,140],replica:0,repons:62,report:[0,1,4,40,43,61,72,73,74,79,91,107,112,133],repositori:161,reprens:79,repres:[1,2,19,29,34,50,57,61,62,65,66,67,68,71,74,79,81,91,92,96,116,129,130,131,133,134,135,142,143],represent:[2,66,71,79,96,112,116,136,144],reproduc:[4,68,104,110,117],repul:133,repuls:[2,18,21,22,80,81,93,96,102,104,108,112,114,117,119,129,133,137,146,152,156,157,159,160],request:[2,19,67,161],requir:[1,2,3,4,18,19,28,31,32,40,42,43,44,45,55,57,58,59,60,64,65,66,67,68,74,75,79,80,82,90,91,92,93,95,96,100,102,103,104,108,109,110,111,112,113,116,117,119,127,129,130,131,133,134,135,136,138,139,140,141,143,144,145,146,147,152,153,154,155,156,157,159,160],rerun:[36,38,41,57],rescal:[2,63,68,69,77,78],research:[31,64,67,136],resembl:161,resepct:2,reservoir:[35,63,79],reset:[2,3,33,34,44,61,68,69,75,79,90,131],reset_atomic_reference_posit:58,reset_tim:58,reset_timestep:[2,35],resist:2,resolut:146,resolv:[61,71,131,161],resourc:[92,110],respa:[4,68,70,73,76,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],respecifi:136,respect:[1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,33,39,40,43,45,46,47,48,49,50,51,52,53,54,57,60,61,63,67,68,69,75,79,80,82,83,84,86,87,88,89,90,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,141,142,144,145,146,147,148,153,154,155,156,157,158,159,160],respond:[2,62,112],respons:[2,62],resquar:[2,116],rest:[2,73,96,131,133],restart1:71,restart2:71,restart2data:0,restart:[0,1],restrain:13,restraint:[73,120],restratin:73,restrict:[1,2],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,34,35,39,40,42,43,44,45,46,47,48,49,50,51,52,53,54,57,59,60,61,62,63,66,67,68,69,71,74,75,77,78,79,80,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,133,134,136,138,139,140,141,142,144,145,148,153,154,155,156,157,158,159,160],retain:[93,96,136],retriev:[2,134,135],rev:[2,29,36,38,41,42,68,69,77,78,96,102,103,104,107,110,111,112,116,117,123,130,131,132,133,135,139,140,143,144,147,153,154,155,156,157],revers:[2,32,49,60,68,70,77,91,129],review:[41,136,147,161],rfac0:[41,147],rg0:76,rh3:43,rh4:43,rheolog:2,rhi:[139,140],rho0:[133,150,151],rho0_meam:133,rho:[67,92,97,98,99,110,132,133,134,135,139,140,144,149],rho_0:[150,151],rho_alpha_beta:110,rho_bkgd:133,rho_colloid:80,rho_e:79,rho_i:[134,135],rho_ref_meam:133,rho_wal:80,rhodopsin:[1,4],rhosum:[149,150,151],rhot:63,rhs:74,rick:[103,146],right:[2,3,19,29,44,54,56,59,60,67,70,74,104,161],rightmost:[19,59],rii:[33,34],rij:[36,38,70,108,109,139,140,152],rin:[119,126,127],ring:[2,45,71],rino:[30,157],rirj:117,risi:[41,147],risk:73,rix:[33,34],rk4:74,rkf45:74,rlo:[139,140],rmin0:[41,147],rmin:123,rms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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. 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v:120,btype:[105,122,126,130,153],buc:99,buck:[2,4,32,98],buckingham:[98,99,100,107,133],buckplusattr:147,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,61,64,65,66,67,68,69,70,71,72,73,75,76,78,79,80,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,29,68,71,106,134,137,147],bundl:[57,162],button:162,bypass:2,c11:134,c_0:[80,94,151,152],c_1:[40,43,67],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:80,c_flux:35,c_gauss:116,c_hb:120,c_i:66,c_id:[2,32,59,63],c_ij:2,c_ijkl:2,c_k:67,c_mychunk:[2,34],c_mycom:59,c_mytemp:59,c_n_k:67,c_p:42,c_peratom:42,c_pi:97,c_prop:2,c_sigma:97,c_size:2,c_thermo_press:59,c_thermo_temp:63,c_xrd:59,ca2:43,cach:4,cacul:76,calcforc:68,calclat:35,calcluat:[37,39,42,105],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:72,call:[1,2,3,4,72,94,103,160,162],callabl:3,callback:3,caltech:[2,113],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,19,28,57,59,60,61,62,67,69,73,80,81,82,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],canon:[69,72,79,137],cao1:72,cao2:72,cao:72,capabl:[3,4,94,102],capac:[65,80,150],capolungo:[40,43],captur:[2,94,100,113,118,126,134],carbid:105,carbon:[57,89,94,104,134],card:[4,32,120],care:[2,44,55,68,69,96],carefulli:[3,28],carlo:[2,61],caro:111,carri:[4,80,118],carrillo:4,cartesian:[2,93],cascad:80,cat:[4,57],cate:68,categori:[0,94],cation:[114,147],caus:[1,2,4,44,62,69,71,75,76,81,82,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,34],ccc:[112,154,155,157,158],ccflag:4,ccflags:4,ccm6:111,ccsi:[112,154,155,157,158],ccu:97,cd2:43,cdeam:111,cdll:3,cdof:2,cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:43,ce4:43,cell:[2,40,43,44,62,69,70,73,80,113,137],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,59,62,67,69,77,79,81,82,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:64,central:[29,36,38,41,71,76,77,86,137,142,158],centro:2,centroid:72,centrosymmetri:29,certain:[1,2,57,59,61,63],cfg:[2,57],cg_type:146,ch2:76,ch2lmp:[0,2],ch3:76,chain:[0,2,13,28,61,69,70,72,76,79,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,19,22,32,44,57,58,60,61,62,63,68,69,70,71,73,74,75,76,78,79,80,82,91,92,109,113,118,131,132,134,137,147,153,162],change_box:2,chapter:72,charact:[2,19,57,60,66,75,113,115,121,140,141,144,147],character:[2,29,38,41,148],characterist:78,charg:[1,2,3,32,40,43,44,98,99,104,105,107,108,111,113,114,122,126,130,143,147,157,158,160,161],charl:63,charmm:0,cheaper:[117,145],check:[2,3,19,35,60,74,76,79,91,92,121],checkout:162,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,64,67,68,69,72,73,78,79,81,83,89,90,92,94,98,101,102,104,105,106,108,109,110,113,116,117,119,120,122,126,127,130,134,138,140,141,143,147,153],chemic:[31,40,43,58,115,141],chemistri:[73,94,97,113],chen:80,cheng:104,chi:[71,114,117],chiral:89,chmod:3,cho:134,choic:[2,4,19,28,29,32,42,55,60,61,68,69,72,92,130],choos:[1,2,13,28,32,57,61,62,63,68,69,70],chose:[155,157],chosen:[2,41,44,50,57,62,63,67,68,69,70,72,110,113,118,121,124,146,155],chunk:0,chunkid:34,ciccotti:76,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,68],cite:147,cl1:43,clarendon:[13,108],clarifi:[155,157],clark:143,classic:[0,2,4,72,73,80,90,113],classifi:158,clean:2,clear:[2,3,63],clebsch:41,click:[3,44,56,57,92,162],climb:92,clockwis:45,clone:162,close:[2,3,19,42,61,62,68,69,76,82,92,94,97,105,106,134,140,141,157,162],closer:[19,60,62,78,92],closest:[71,117,145,153],cloud:147,cluster:[2,4,42,64,76],cmax:134,cmd:[3,72],cmdarg:3,cmin:134,cmm:[18,146],cna:29,co2:[43,75,76,115],coars:[13,18,28,50,66,75,115,119,141,146],coarsest:41,code:[0,1],coeff:[6,45,46,55,83,121,149],coeffici:0,coefficienct:109,coefficient0:111,coefficient1:111,coeffieci:[2,95],coeffincientn:111,coexist:113,cohes:[2,114,134],coincid:[82,101,131,132],cold:2,coleman:[40,43],collect:[2,34,44,103],colliex:43,collis:[68,118,161],colloid:2,color:[19,57,60,67,73],column:[2,29,34,36,38,41,42,43,59,73,80,94,116,120],colvar:0,com:[2,37,59,64,96,162],comand:61,combiant:106,combin:[2,3,18,32,55,57,58,59,64,69,72,82,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,13,62,63,69,78,79,154,155,157,158,162],comit:162,comm:[0,3,30,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,60],comm_world:3,command:[0,1],comment:[3,45,66,75,80,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:2,common:[0,1,2,3,4,30,62,72,82,83,118,120,154,155,157],commonli:[2,9,37,38,57,90,119,124,148,155,157],commun:[1,2,3,4,19,57,60,62,68,69,80,110],comp:[76,92,113,145,152,156],compar:[1,2,4,40,43,56,91,92,134,147],comparison:0,compass:[6,20,46,56,83,102],compat:[3,19,49,59,60,63,64,81,137],compens:[2,113],compil:[4,57,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,60,72,92,114],complex:[2,3,9,36,38,41,44,68,82,92,113,137],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,59,61,62,63,64,68,69,70,72,76,82,91,92,109,113,118,131,132,147,148],componenet:2,composit:[2,68,111],compound:[104,113,114,158],compress:[2,57,70,73],compris:[82,115,145],compton:[40,43],comput:[0,1],computation:[2,80,97],compute_modifi:[61,62,69,70],compute_sa:40,compute_xrd:43,concav:82,concentr:[66,75,111,115,141],concept:2,conceptu:[2,62,92,105,134],concern:[2,30,32,67],concis:3,concurr:4,conden:[80,155,157],condens:[2,80,94,107,111,122,158],condit:[2,39,40,42,43,57,58,68,70,71,73,76,77,80,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,57,62,72,91,92,94,97,112,134,137,154,155,157,158,162],conflict:162,conform:[2,61,62,74,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,32,44,68,92,98,99,105,109,113,120,122,143,146],connect:[2,32,61,76,92,106,118,153,157],conner:94,connor:94,consecut:[3,44,105,122,126],consequ:[1,2,80,121],conserv:[13,61,67,68,69,75,76,92,108,109,110,118,128,147],consid:[2,29,32,60,61,80,113,145,147,153],consider:2,consist:[2,3,39,44,50,63,67,69,70,73,74,75,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:58,constant:0,constantli:64,constitu:[2,81,82,103,145],constrain:[2,64,67,76,77,91,113],constraint:[19,39,42,60,64,76,77,81,91,132],construct:[2,28,29,30,36,38,40,41,43,62,69,74,75,82,108,137,153,154],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,145],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,60,63,66,68,71,73,75,80,82,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],context:[2,4,160],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,64,67,69,70,73,78,79,80,82,97,109,124,127,145,156],continuum:[2,58,80],contour_integr:58,contract:[62,69],contrain:76,contrast:[1,2,160],contrib:80,contribut:[2,29,32,33,34,35,39,41,42,59,62,68,76,91,92,109,111,113,131,132,137,147,162],control:[2,3,4,11,13,19,32,35,41,47,57,58,60,62],control_typ:58,convect:35,conveni:[2,13,148,162],convent:[13,49,54,56,74,111,113],converg:[2,19,57,60,61,62,70,73,74,76,91,92,104,105,122,147],convers:[41,57,105,106,107,113,122,126,130,143],convert:[2,5,6,8,12,16,17,18,35,44,46,57,83,84,88,89,92,93,111,137,155,157,161],convex:82,cool:64,coord:[2,3,36,38,59,71,81,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,62,64,69,71,76,77,79,80,91,92,93,94,96,112,147],coords:147,copi:[0,3,57,80,92,162],copper:161,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,45],corner:[2,57,82,162],corpor:4,corr:104,correct:[2,3,32,45,57,64,69,73,81,82,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:58,correctli:[3,69,76,82,92,107,132,137,162],correl:[2,35,36,41,59,67,72],correpond:66,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,59,62,63,64,66,68,69,70,71,72,75,76,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,60,69,75,80,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,4],coul:[2,4,18,21,22,32,45,91],could:[2,3,19,32,34,35,39,57,60,63,73,80,81,82,91,94,116,120],coulomb:[2,42,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:2,count:[1,2,3,19,35,45,59,60,62,69,76,82,91,92,116,120],counteract:63,counterbal:64,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,67,74,81,131,149],cov:147,coval:[2,13,113,134,147],cover:[2,58,68,113],cpp:[1,2,3,32,76],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,62,66,69,70,71,72,74,80,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,19,35],create_box:[2,19,35,44,62,69,153],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,61,91],criterion:[19,44,60,61,91,92,104,113,118,147],critic:[2,24,25,80,91],cross:[4,33,57,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:73,crystal:[2,4,29,30,38,71,79],crystallin:[2,156],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,148],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,154,155,157,158],csinfo:2,csisi:[112,154,155,157,158],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:43,cu2:43,cu3au:134,cube:[2,82],cubes:[19,60],cubic:[38,68,71,111],cuda:1,cuh:97,cummul:[2,61,120],cumul:[2,59,69,70,92],currenlti:63,current:[0,1,2,3,4,19,30,32,42,57,58,60,61,62,63,64,69,74,75,76,77,80,81,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[2,44],curvatur:[117,145,161],custom:[0,2,3,33,34,35,42,57,61,62,69,70,73,91,94,116,120],cut:[1,2,4,19],cuthi:71,cutinn:[131,132],cutlo:71,cutmax:144,cutoff1:[102,108,122,126,130,133,143,146],cutoff2:[98,99,100,102,107,108,122,126,130,133,143,146],cutoff:[2,4,21,22,28,29,30,32,36,38,41,61,66,71,73,81,82,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:43,cvar:63,cvff:4,cwiggl:81,cyan:57,cycl:[69,70],cyclic:45,cylind:[57,82],cylindr:2,cyrot:97,d3q15:68,d3q19:68,d_e:80,daan:79,damp:[2,69,70,73,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:109,darden:108,darken:57,dash:118,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:81,david:[155,157],daw:[111,144],dcd:[2,57,72],deactiv:130,debug:[2,3,40,43,44,72],decai:[36,105,161],decid:[2,4,162],decod:57,decompos:[32,148],decomposit:[58,72],decoupl:2,decreas:[4,61,64],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,41,59,63,65,70,81,97,103,110,113,144,148],deform:[2,42,62,69,131,132],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,61,69,70,72,74,76,79,83,84,88,89,90,91,108,111,120],delai:2,delet:[28,59,61,69,153,162],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:75,dellago:[2,64],deloc:[113,147],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,144],delta_pi:97,delta_r:144,delta_sigma:97,deltah_f:66,demo:3,demonstr:[73,134],dendrim:120,denniston:68,denot:[40,64,105,119],dens:[61,75,113],densiti:[2,19,41,44,58,60,68,80,81,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:73,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,60,62,66,68,69,70,71,75,76,78,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:2,deposit:[69,76],depth:[26,57,80,115,117,145],der:[32,103,104,130,160],deriv:[2,32,41,62,63,64,69,70,71,78,79,80,81,82,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:71,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,63,66,67,68,69,70,71,72,73,75,78,79,81,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,61,69,71,80,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,35,39,42,44,62,63,67,69,76,91,92,109,111,120,131,132,154,155,157],desktop:[2,57],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,64,67,68,69,70,73,76,79,80,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,42,43,44,57,59,60,62,66,69,71,72,73,74,75,81,82,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,63,70,73,94,97,113,136,137,147,158],deviat:[70,71,116],devic:1,devin:104,devis:136,dfactor:57,dft:137,dhug:73,dhugoniot:73,dia:134,diag:75,diagnost:[4,61,75],diagon:[2,41,42,62,69],diagonalstyl:148,diagram:[19,40,43,56,60,72],diallo:120,diam:57,diamet:[2,44,57,103,117,118,124,145,160],diamond:[113,134],dick:2,dicken:63,did:[91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,64,67,68,69,71,72,73,76,77,78,79,80,81,82,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,2,13,75,105,144,156],difficult:[62,63,72,120],difficulti:[36,38,76],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,61,74,84,85,86,88,91,94,97,101],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:113,dij:76,dilat:[62,69,70],dim:[44,134],dimens:[1,2,19,35,42,44,57,60,62,68,69,70,73,81,92],dimension:[36,39,40,41,43,80,92,144],dimensionless:[37,41,63,80,148,160],dimer:[2,134],dimstr:[19,60],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,71,73,144],dirac:41,direc:144,direct:[2,4,13,29,38,40,41,43,44,45,57,68,70,71,73,78,79,80,81,82,91,92,109,110,118,132],directli:[2,3,32,41,44,57,63,68,75,82,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,63,78,79,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,80,121],disadvantag:[2,60],disallow:69,discard:[19,60,82],discontinu:[91,128],discourag:134,discret:[2,57,63,68],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:145,disperion:[108,126],dispers:[2,100,108,126,131,158],displac:[2,37,62,69,71,118],displai:[3,56,57],disregard:137,dissip:[2,31,65,67,78,79,109,110,118,131,132],dist:[2,35,72,74,153],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,61,62,64,68,69,70,71,73,74,76,77,79,80,81,82,83],distinct:[2,145],distinguish:[2,41,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,41,56,60,67,68,69,93,97,105,111,112,114,134,135,136,142,144,145,154,155,156,157,158],distro:144,ditto:161,div:4,diverg:[79,94],divid:[2,4,19,35,39,42,56,59,60,71,91,92,114,147,158],divis:[2,55,68,97,130],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:69,dlmp_intel_offload:4,dlopen:2,dlvo:[103,160],dm_lb:68,doc:[0,1,2,3,32,34,37,39,42,44,56,57,59,63,69,82,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,60,61,62,63,64,66,67,68,69,80,81,82,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[44,94,104,112,154,155,156,157,158],dof:39,doi:[2,71],domain:[2,19,40,43,57,60,62,68,69,72,80,81,92],domin:[1,113],don:[0,4,82,134,147,162],donald:63,done:[1,2,19,44,55,57,58,59,60,61,62,63,66,69,72,76,78,79,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:42,doti:[97,144],doubl:[1,2,3,4,32,45,62,82,97,114,119,137],dover:58,down:[2,3,62,113,147],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[65,66],dr_ewald:40,drag:[2,35,69,70,77],dragforc:68,drai:[57,73],drain:91,dramat:[61,62,69,147],drautz:97,draw:57,drawn:[57,67],drayleigh:73,dreid:2,dreiding:0,drfourth:37,drho:[93,111,140,141],drift:[2,37,64,67],drive:[3,62,69,71,92],driven:[2,50],driver:2,drop:109,drsquar:37,drude:0,dt_collis:68,dt_lb:68,dt_md:68,dtqm:73,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,59,61,62,67,68,69,70,71,74,78,79,80,81,82,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:80,dullweb:69,dummi:[13,156],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,101],duplic:[19,60,71],durat:[56,80,118],dure:[2,4,19,32,45,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:2,dx_lb:68,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,60,61,63,65,67,69,70,72,73,74,78,79,80,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:13,e_1:97,e_2:97,e_a:75,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:[63,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,72,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161],eacn:[19,60],eam:[0,93,105],earli:[19,59,60],earlier:[92,118,134],earth:113,easi:[2,3,32,42,81],easier:[4,57],easili:[3,57,92],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,40,43],ecp:113,edg:[2,19,40,43,57,81,82],edge:81,edit:[4,162],edition:4,edu:[3,111,131],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,59,61,62,64,67,69,70,71,72,73,74,76,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161],effici:[0,1,2,4,39,55,57,62,69,72,76,97,103,105,122,126,137,140,141,145],efficienc:4,efield:[76,91],eggebrecht:[105,147],ehex:2,eigenvalu:72,einstein:[2,79],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,64,68,69,70,71,75,76,82,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaps:[81,149],elast:[2,21,22,92,118,156],elastic:0,elba:13,electr:[2,58,114,161],electric:4,electrolyt:160,electron:[2,40,58,80,93,104,108,111,113,114,134,137,144,147,157,158,161],electron_integr:58,electron_temperatur:58,electron_unit:113,electroneg:[2,104,114,147],electroneg_compon:147,electrostat:[2,4,103,108,113,122,130,132,147,160],elem1:[114,134,148],elem2:[114,134,148],elem:147,element1:[93,111,147],element2:[93,111,147],element:[2,33,37,39,41,42,57,58,59,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158],elementn:[93,111],elementset:58,elif:41,elig:120,elimin:[2,67,76,78,79],elj:108,ellips:2,ellipsoid:[2,44,91,117,132,145],els:[57,59,63,69,80],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:82,emb_lin_neg:134,embed:[3,13,80,93,111,114,130,134,135,136,144],embt:46,emin:62,emphas:118,empir:[58,113],empiric:94,emploi:[64,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,134,147],encod:57,encompass:2,encount:[38,59],encourag:[75,77],end:[1,2,3,4,19,46,57,59,61,62,64,67,69,74,75,80,92,109,111,117,133,137,145,148,149],endbondtors:46,energet:[61,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:147,enforc:[2,57,61,69,76,122],enforce2d:[2,91],eng:[3,104,136],engineer:[58,78,111],enginer:135,enhanc:[58,64],enlarg:57,enough:[44,60,73,81,82,105],enpub:111,ensembl:[2,32,35,69,72,73,109,147],ensight:2,ensur:[2,41,62,67,69,97,130,154,158],enter:[114,137,158],enthalpi:[75,111],entir:[0,2,3,19,31,39,40,42,43,44,60,61,64,67,69,70,71,72,75,77,80,108,126],entiti:2,entri:[40,59,66,73,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,57,71,93,97,104,112,113,144,155],eos:66,epair:[94,116,120],epp:108,epq:108,eps0:160,eps14:130,epsilon0:157,epsilon:[2,18,21,22,27,28,32,45,81,82,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,143,145,146,154,159,160],epsilon_0:161,epsilon_14:101,epsilon_:145,epsilon_d:106,epsilon_i:[117,145],epsilon_i_:145,epsilon_i_a:[117,145],epsilon_i_b:[117,145],epsilon_i_c:[117,145],epsilon_j:[117,145],epsilon_j_:145,epsilon_j_a:[117,145],epsilon_j_b:[117,145],epsilon_j_c:[117,145],epsilon_lj:145,eqp:108,eqq:108,equal:[2,3,19,28,32,35,42,44,57,59,60,62,63,67,68,70,71,72,73,74,75,78,79,80,81,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161],equat:[2,35,38,39,40,43,56,62,63,64,65,66,68,69,70,71,72,73,75,76,80,81,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[71,89],equilibr:[2,35,44,61,62,69,73,78,79,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,62,67,68,69,70,73,74,76,79,83,84,88,89,104,134,142,147],equilibrium_start:58,equival:[2,13,59,62,69,74,94,109,113,147,155,157],equlibrium:2,er3:43,eradiu:113,eras:78,erat:132,erc:105,erfc:[105,122],erhart:[111,155,157],eros:134,erose_form:134,erot:2,errata:[155,157],erratum:81,error:[0,1,2,3,11,47,57,59,62,63,64,66,69,75,80,81,82,91,105,122,145,153,155,157],erta:118,especi:[4,44,60,73,74],essenti:[3,11,47,94,105,122,157],essential:70,essex:13,establish:32,estim:[1,2,19,29,35,42,58,60,75],esub:134,eta:[2,68,69,73,112,114,117,144,156,158],eta_dot:69,eta_ij:144,eta_ji:114,etap:69,etap_dot:69,etc:[1,2,3,4,28,33,34,35,42,44,57,58,59,67,69,80,82,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:73,etot:[2,42,73],eu2:43,eu3:43,euler:[75,91,92],eulerian:58,europhi:68,evalu:[3,32,35,41,44,45,57,58,59,63,67,75,81,91,137,140,141,144,147],evanseck:[2,5,45,101],evaul:91,even:[2,4,19,29,55,59,60,62,64,69,80,81,82,91,92,96,113,114,118,145,158],evenli:[19,42,60,68],event:[2,69,80],eventu:2,ever:28,everaer:[103,117,145],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,64,68,69,70,71,73,75,76,80,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[64,68,72],evolv:[68,72],ewald:[2,40,42,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[19,60,61,67,80],exactli:[2,19,35,44,59,60,67,73,109,111,118,131,140,141],examin:[2,61,75],exampl:[0,1],exce:[2,4,19,59,60,62,69,91],exceed:[19,60,69],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,60,62,69,70,72,76,80,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,58,64,80,113],excit:113,excite:113,exclud:[2,4,39,41,91,118,131,132,153],exclus:[1,4,32,45,104,137],excurs:69,execut:[1,2,3,57],exempl:147,exemplari:67,exemplifi:113,exert:[2,82],exhaust:58,exhibit:[36,64,69,113],exist:[2,3,29,44,56,57,62,83,84,85,86,88,110,153,162],exit:[3,19,60],expans:[41,55],expect:[1,4,19,60,71,73,134,137],expens:[2,71,80],experi:[2,74,92,109],experienc:[2,4],explain:[1,2,3,19,30,57,60,62,69,71,92,96,111,147,149,162],explan:[2,41,71],explanatori:59,explic:138,explicit:[2,3,32,75,94,97,101,111,113,121,131,162],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,62,67,69,70,73,76,80,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:4,exploit:72,explor:[40,43],expon:[75,111,115,117,120,130,138,146],exponenti:[32,75,115,144,154,158,161],expos:3,exposit:[58,109],express:[2,41,44,62,71,75,80,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,63,64,69,70,71,74,78,79,80,81,82,117,134,137,145,148],extent:[1,19,21,60,94],exterior:[2,82],extern:[32,57,62,67,68,69,70,80,91,135,136],extra:[2,3,4,19,22,39,40,42,43,44,59,60,69,73,91,108,118,134],extract:[2,3,18,32,92,105,114,134,148],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,62,69,79,113,156],extrema:130,extreme:113,extrins:58,f_1:[2,62],f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:73,f_harm:79,f_i:[13,144],f_id:[2,59,63],f_ij:144,f_int:78,f_j:13,f_jj:35,f_k:144,f_langevin:80,f_max:73,f_r:[155,156,157],f_sigma:97,f_solid:79,f_ss:2,face:[2,81,82,117,134,145],facil:0,facilit:2,fact:[2,4,79,118,147],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,60,62,64,68,69,70,72,74,75,76,81,82,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[3,62,91,92,107],fairli:[3,162],faken:30,fall:[2,59],fals:147,famili:158,familiar:[0,3,162],fan:144,far:[2,60,62,69,71,74,81,84,88,92],farrel:[155,157],fashion:[2,19,44,60,63,69,70,73,79,80,81,92,131],fast:[2,4,63,73,75,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,60,69,70,76,78,80,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,80],fault:29,fava:117,favor:61,fcc:[2,29,30,35,38],fcold:64,fdt:[65,66,75],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,61,67,72,82,91,162],fecr:111,feedback:63,feel:[71,82,92],fehlberg:75,felling:136,felt:82,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,45],fermi:[1,157],fermion:113,fernando:133,few:[1,2,3,59,64,69,76,91,92,94,147],fewer:[1,3,4],feynman:72,ffield:[104,114,147],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:64,ficiti:153,fictiti:[2,72,74,105,122,126,153],field:0,fifth:[2,115,142],figshar:71,figur:[1,4,73,162],fij:108,file0:71,file1:[3,66,71],file2:[3,66],file:[0,1],filenam:[4,19,57,58,59,60,66,71,75,80,92,93,94,97,105,111,112,114,115,134,135,136,140,141,142,144,147,148,154,155,156,157,158],fill:[44,57,80,97,137,162],filter:58,finchham:[2,107],find:[0,2,3,4,30,32,61,62,63,66,71,74,91,92,105,122,126,134,140,141,147,162],fine:[4,79,162],finer:[41,44],finger:44,finish:[2,3,19,60],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,61,63,66,67,68,69,71,72,73,76,77,78,79,80,83,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,140,141,142,144,147,148,153,154,155,156,157,158,161,162],fischer:[2,5,45,101],fit:[2,74,94,97,134,140,141,156,162],five:[30,73,97,135],fix:[0,1]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retriev:[2,135,136],rev:[2,29,36,38,41,42,69,70,78,79,97,103,104,105,108,111,112,113,117,118,124,131,132,133,134,136,140,141,144,145,148,154,155,156,157,158],revers:[2,32,49,61,69,71,78,92,130],review:[41,137,148,162],rfac0:[41,148],rg0:77,rh3:43,rh4:43,rheolog:2,rhi:[140,141],rho0:[134,151,152],rho0_meam:134,rho:[68,93,98,99,100,111,133,134,135,136,140,141,145,150],rho_0:[151,152],rho_alpha_beta:111,rho_bkgd:134,rho_colloid:81,rho_e:80,rho_i:[135,136],rho_ref_meam:134,rho_wal:81,rhodopsin:[1,4],rhosum:[150,151,152],rhot:64,rhs:75,rick:[104,147],right:[2,3,19,29,44,54,56,60,61,68,71,75,105,162],rightmost:[19,60],rii:[33,34],rij:[36,38,71,109,110,140,141,153],rin:[120,127,128],ring:[2,45,72],rino:[30,158],rirj:118,risi:[41,148],risk:74,rix:[33,34],rk4:75,rkf45:75,rlo:[140,141],rmin0:[41,148],rmin:124,rms:75,rnemd:2,robust:91,rock:134,rockett:144,role:2,ronchetti:38,root:[3,32,33,34,111],rose:134,ross:134,rosski:72,rot:[2,35,72,74],rotat:[2,41,44,82,91,108,117,145],rotation:38,rough:[2,44,57],roughli:[19,57,69,92],round:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,69,70,76,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,140,141,142,143,145,146,149,154,155,156,157,158,159,160,161],rous:67,rout:[32,120,130],routin:[2,3,4,68,137],roux:2,row:[2,34,43,59,80,113],rozero:134,rrespa:[1,4,69,93,94,95,96,98,99,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rsq:[140,141],rsurfac:80,ru3:43,ru4:43,rub:5,rubia:[135,136],rule:[0,2,13,29,44,61,69,82,93,95,96,102,103,108,120,125,134,138,149,153,154,155,157,161],run1:2,run2:2,run3:2,run4:2,run5:2,run6:2,run7:2,run8:2,run:[0,1],run_styl:[4,69,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rung:75,runtim:57,rutherford:80,rutuparna:[155,157],rxn:75,ryckaert:[76,89],rydberg:137,s0st:2,s2050:1,s2629:111,s319:58,s_i:[2,113],s_ij:2,saddl:92,sadigh:[111,135,136],saed_vtk:40,safe:[57,162],safran:160,sagui:108,sai:[1,162],said:91,sakai:156,sall:147,salt:[106,116,134],salter:147,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,35,36,37,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,63,64,67,68,69,70,71,72,73,74,76,78,79,80,82,83,84,85,87,88,89,90,92,93,94,95,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,138,139,142,143,144,145,146,147,149,153,154,155,156,157,158,159,160,161,162],sampl:[1,2,3,35,57,69,72,77,79,97],sample_frequ:58,sandia:[0,29,114,134],saniti:74,satellit:2,satisfi:[30,40,41,43,62,64,68,70,76,91,118],satur:106,save:[2,57,61,67,75,80,97],sb3:43,sb5:43,sc3:43,scalabl:[0,1,4],scale:[0,1,2,4,35,41,45,57,58,62,68,69,70,72,73,78,79,80,93,94,106,113,115,118,131,132,134,137],scalegamma:68,scalexi:[62,69,70],scalexz:[62,69,70],scaleyz:[62,69,70],scatter:[3,40,43],scatter_atom:3,scatter_coord:3,scenario:[2,61,82],schaik:130,schell:156,schemat:61,scheme:[2,63,67,69,72,76,80],schmid:109,schroding:113,schroeder:38,sci:[30,104,136,144,147],scienc:[58,61,71,78,111,135,147,156],scientif:[41,111],scm:3,scratch:[19,60],screen:[0,1,2,3,4,40,43,57,68,76,92,101,105,122,134,154,157,158,159,160,161],screenshot:3,scripe:3,script:[0,1],sea:3,search:[0,36,38,91,92,118],secant:66,second:[1,2,3,4,28,29,35,37,38,39,42,43,55,59,61,63,64,66,67,72,74,76,77,78,79,80,91,92,96,97,98,99,100,104,105,111,113,114,115,118,119,121,124,134,142,147,154,156,157,158,161],second_mo:147,secondari:50,section:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,31,32,33,34,35,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,64,65,66,67,68,69,70,71,72,73,75,76,78,79,80,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],section_acceler:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,69,70,76,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],section_accerl:111,section_command:[0,1],section_exampl:2,section_howto:[2,3,29,30,32,33,34,36,38,41,42,96,107],section_modifi:[2,57],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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om:1,uncompress:57,uncorrel:67,uncoupl:72,under:[0,2,4,6,41,46,57,62,63,69,73,83,110,113,130,148],underflow:57,undergo:[2,32,67,69],undergon:61,underli:[2,29,57,69,80],underpredict:2,underscor:[61,62,69,70],understand:[1,2,137],understood:97,undesir:[62,69],undisturb:[131,132],undump:57,unfix:[2,35,58,59,74,78],unfix_flux:58,unfold:77,uniaxi:70,uniform:[4,19,58,60,68,117,145],uniformli:[68,80,140,141,144],uninterrupt:[69,70,73,79,80],union:[2,82],uniqu:[2,67,70,92,111,113],unit:[2,5,6,16,17,18,29,30,31,32,33,34,35,36,37,39,40,41,42,43,44,46,57,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,79,80,81,82,83,84,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],uniti:112,unitless:[29,63,69,73,75,91,118,139,143,154,155,156,157,158],univers:[2,32,92,131,136,157],unknown:30,unless:[3,4,40,43,44,62,69,91,103],unlik:[33,44,93,97,111,114,134,135,136,148],unlike:[69,70,111,120,121,135,136],unlimit:144,unnecessari:4,unoccupi:80,unoptim:57,unpack:[0,3],unperturb:32,unphys:[2,69],unpublish:137,unrel:[45,162],unrestrain:74,unset:113,unshift:108,unsmooth:128,unsolv:101,unstabl:68,unstag:162,until:[2,19,57,60,62,63,66,78,97,118,140,141],unus:97,unwant:44,unwrap:[33,34,42,61],up_intern:57,updat:[0,2,4,63,67,68,69,73,80,97,108,137],upenn:3,upon:[2,75,97],upper:[19,37,60,62,68,69,73,81,91,118,147],uppercas:0,upsid:2,upsilon:117,upstream:162,urbana:131,urey_bradlei:5,url:162,usabl:111,usag:[2,71,130],use:[2,57,59,80,117,134,145,147,162],useful:137,user:[0,1,2,3],user_manifold:162,user_misc:[14,15,17,48,52,54,55,87],usernam:162,using:[0,1],usr:3,usual:[2,8,12,16,17,18,23,32,53,55,57,61,62,70,73,74,80,81,82,88,92,101,103,106,108,117,121,130,131,132,142,148,153,154],util:117,v11:2,v22:2,v33:2,v_0:80,v_2:137,v_3:137,v_4:137,v_avp:63,v_delta:32,v_dhug:73,v_drai:73,v_e_hbond:120,v_ij:144,v_jx:35,v_jy:35,v_jz:35,v_k11:35,v_k22:35,v_k33:35,v_lgr_po:73,v_lgr_vel:73,v_linear:81,v_lj:94,v_mu:131,v_n:[68,137],v_name:[2,32,57,59,63,81],v_occ:116,v_prefactor:149,v_press:42,v_pxxwall:63,v_pxy:2,v_pxz:2,v_pyz:2,v_ramp:81,v_rebo:94,v_t_qm:73,v_torsion:94,v_v11:2,v_v22:2,v_v33:2,v_valu:57,v_wiggl:81,v_x:[44,81],v_xave:2,v_xmax:2,v_xx:44,v_y:44,v_yi:44,vacanc:[78,137],vacf:2,vacuum:[80,106,157,161],valanc:97,valenc:[97,113],valent:97,valid:[2,3,40,43,62,71,111,113,117,137,144],valon:134,value1:[59,70],value2:[59,70],van:[27,32,103,104,130,134,160],vanadium:137,vanilla:2,vanish:76,vapor:[19,60],vare:80,vari:[1,19,32,40,43,58,60,62,69,74,80,81,101,109,110,119,128,131,149],variabl:0,varianc:109,variant:[1,2,62,69,70,118,135,136,139,155,157],variat:[19,60],varieti:[1,2,57,134,158],variou:0,varshalovich:41,vashishta1990:158,vashishta2007:158,vbia:2,vcm:2,vdisplac:81,vdw:104,vec:71,vector:1,vel:[2,109,110,113,118],veld:[100,126],veloc:[2,35,39,42,44,57,59,62,64,68,69,70,71,72,73,74,76,79,80,81,91,92,109,113,118,131,132],velocit:[109,110,113,118],velocity_bottom:68,velocity_top:68,verbos:147,veri:[1,2,19,32,57,59,60,62,63,69,72,76,92,113,118,131,132,140,141,148,149,162],verifi:162,verlet:[1,4,58,64,69,72,76,80],versa:[2,61],versu:[2,19,60,63,76,100,108,118,126],vertic:[4,19,57,60],via:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,68,69,70,72,74,76,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],vibrat:[2,71,73,89,113],vice:[2,61],video:57,view:[2,57,97,113,114,147],viewer:57,viewpoint:57,vij:109,vim:0,virial:[35,39,41,42,62,69,70,76,109,110,113],virtual:[2,154],viscoelast:118,viscos:0,viscosity:2,viscou:[2,67,68,91,92],vision:147,visual:0,viz:3,viz_tool:3,vizplotgui_tool:3,vmax:62,vmd:[2,3],voigt:[2,41],vol:[2,35,42,134,157],volpress:137,volum:[2,19,32,35,39,40,42,43,44,60,62,65,68,69,70,73,80,81,82,131,132,137,151,152,161],voronoi:42,voter:[135,136],voth:72,vri:119,vstream:2,vtk:[2,40],w_1:41,w_2:41,w_i:41,w_ik:144,waal:[32,103,104,130,160],wadlei:97,wagner:[58,68,134],wai:[1,2,3,29,32,34,35,36,38,41,42,44,57,59,61,62,63,67,68,69,70,72,80,81,84,85,86,88,89,91,92,93,94,105,106,109,111,112,114,117,120,122,134,135,136,142,144,145,147,148,149,153,154,155,157,158,162],wait:[1,4],walk:[67,69],wall:0,wallhi:81,wang:[134,144],want:[0,1,2,3,31,34,39,42,44,57,60,61,71,74,79,81,82,92,93,94,97,103,104,109,111,114,134,140,141,142,144,147,149,154,155,157,158,162],ward:97,warm:[4,113],warmup:4,warn:[0,21,22,30,57,69,70,75,131,132,134,140,141,162],warner:93,warning:134,warp:134,warren:[109,140,141],watanab:[78,79],watch:92,water:0,watkin:53,wave:113,wavefunct:113,wavelength:[40,43],wavepacket:113,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69,70,72,73,75,76,79,80,81,87,91,92,97,98,99,100,101,103,105,108,109,110,113,117,119,120,122,124,126,127,130,132,133,134,137,139,145,146,147,153,158,161],zeta:[68,114],zfactor:57,zhang:118,zhi:[2,81],zhi_bound:2,zhou:[97,114,144,155,157],zhu:152,ziegler:[134,157,161],zimmerman2004:58,zimmerman2010:58,zimmerman:[29,58,97],zlim:147,zlo:[2,81],zlo_bound:2,zmax:68,zmin:68,zn2:43,zone:40,zoom:57,zr4:43,zwall:81,zwall_veloc:68},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix ave/histo command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","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":[29,32,36,37,38,40,41,43,44,56,57,58,62,67,68,69,70,72,73,78,79,81,97,113,131,132,137,153],"long":[98,99,100,101,102,105,107,108,122,126,130,143,146],acceler:1,adiabat:2,adp:93,airebo:94,alloi:111,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:58,atom:[2,29,30,36,38,41,42],aug:0,balanc:[19,60],barostat:2,bcc:71,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:[2,5,45,101,130],chunk:[2,34],class2:[6,20,46,83,102],cna:30,code:2,coeffici:2,colloid:[81,103,160],comb3:104,comb:104,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,control:63,core:2,cosin:[7,8,9,10,11,12,47],cossq:84,coul:[98,99,100,101,102,105,106,107,119,122,126,130,143,146],coupl:2,create_atom:44,cubic:124,cut:[25,99,102,105,108,113,116,122,123,130,138,143],cvff:85,data:2,deby:[105,122],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],diel:106,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,108],discuss:2,disp:2,distanc:86,document:0,dpd:[31,109,110],dreid:120,dreiding:2,drude:2,dsf:[105,122],dump:[2,57],eam:111,edip:112,eff:113,ehex:64,eim:114,elastic:2,energi:110,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],exp6:115,exp:[11,47],expand:[22,125],extend:3,fcc:71,fdt:110,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82],fix_modifi:[58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],flow:2,fluid:68,flux:35,forc:2,fourier:[14,15,48,87],from:[2,3],gauss:116,gaybern:117,gener:[1,2],github:162,gld:67,global:2,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,139,145,146,149,154,155,156,157,159,160,161],gran:118,granular:2,gromac:119,gyrat:[33,34],harmon:[16,23,24,25,49,51,81,88,142],hbond:120,heat:35,helix:50,hertz:118,hexord:36,histo:59,histori:118,hook:118,how:2,idealga:150,imag:57,implicit:101,improper_styl:[83,84,85,86,87,88,89,90],indice:0,induc:2,info:[0,58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,69,85,88,99,101,117,122,154,155],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,162],lennard:133,librari:[2,3],linear:[129,139],list:121,lj1043:81,lj126:81,lj93:81,lj96:123,local:2,lubric:131,lubricateu:132,luci:[140,141],mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82,91],mod:[80,156],model:2,morri:152,mors:[26,94,120,139],movi:57,mpi:3,msd:37,msm:[98,99,101,105,122],multi:[2,51,140,141],multipl:2,nb3b:142,neb:92,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:69,nphug:70,npt:69,nvt:69,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,69,70,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,139,142,143,145,146,149,154,155,156,157,158,159,160,161],opl:53,opt:[101,111,122,126,139],optim:1,option:2,orient:71,orientord:38,orthogon:2,other:2,output:[2,58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],overview:3,packag:[1,4],pair:2,pair_styl:[93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:72,polariz:2,poli:[131,132],polymorph:144,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:73,quadrat:54,quantiti:2,quartic:[17,28],rattl:76,rebo:94,region:82,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],relax:62,replica:2,resquar:145,restart:[2,58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],restrain:74,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rigid:2,ring:89,run:[2,3,58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],scalar:2,script:[2,3],sdk:[18,146],serial:3,set:2,shake:76,share:3,shell:2,shift:[10,11,24,25,47],simpl:15,simul:2,size:2,smooth:[128,129,139],smtbq:147,sna:41,snad:41,snap:148,snapshot:2,snav:41,soft:[130,139,149],spc:2,sph:[150,151,152],spheric:[2,55],spline:[135,136],spring:[77,79],squar:12,srp:153,start:[58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],stop:[58,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:42,style:[1,2],summari:2,swap:61,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],system:2,tabl:[0,2,66,155],taitwat:[151,152],temperatur:2,tersoff:[155,156,157],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,105,122,126,130],triclin:2,tstat:109,ttm:80,tutori:162,umbrella:90,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:158,vector:2,version:0,viscos:2,visual:2,wall:[2,81,82],water:2,weight:59,wolf:[98,105],wrapper:3,write:2,xrd:43,yukawa:[159,160],zbl:[157,161]}})
\ No newline at end of file
diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt
index 0c8a2f31c7..6f6cdc4a04 100644
--- a/doc/src/fix_ave_histo.txt
+++ b/doc/src/fix_ave_histo.txt
@@ -108,8 +108,7 @@ is used.
 
 If {mode} = vector, then the input values must be vectors, or arrays
 with a bracketed term appended, indicating the Ith column of the array
-is used.  All vectors must be the same length, which is the length of
-the vector or number of rows in the array.
+is used.
 
 Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively