From 1cdd1fd4f809b5771a562123e2ac383245894f0f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 1 Aug 2016 22:43:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15420 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/fix_ave_chunk.txt | 8 ++++---- doc/html/fix_ave_chunk.html | 8 ++++---- doc/html/searchindex.js | 2 +- doc/src/fix_ave_chunk.txt | 8 ++++---- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/doc/html/_sources/fix_ave_chunk.txt b/doc/html/_sources/fix_ave_chunk.txt index 6c63d7d2d2..12b1dcca13 100644 --- a/doc/html/_sources/fix_ave_chunk.txt +++ b/doc/html/_sources/fix_ave_chunk.txt @@ -141,14 +141,14 @@ asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). -Using a wildcard is the same as if the individual elements of the -vector or columns of the array had been listed one by one. E.g. these -2 fix ave/chunk commands are equivalent, since the :doc:`compute property/atom ` command creates, in this +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 fix ave/chunk commands are +equivalent, since the :doc:`compute property/atom ` command creates, in this case, a per-atom array with 3 columns: .. parsed-literal:: - compute myAng all property/atom 50 angmomx angmomy angmomz + compute myAng all property/atom angmomx angmomy angmomz fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index 69b4b9a5e0..e7bfd31839 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -249,11 +249,11 @@ with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive).

-

Using a wildcard is the same as if the individual elements of the -vector or columns of the array had been listed one by one. E.g. these -2 fix ave/chunk commands are equivalent, since the compute property/atom command creates, in this +

Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 fix ave/chunk commands are +equivalent, since the compute property/atom command creates, in this case, a per-atom array with 3 columns:

-
compute myAng all property/atom 50 angmomx angmomy angmomz
+
compute myAng all property/atom angmomx angmomy angmomz
 fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
 fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
 

diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 6e3c503661..00ca6184ae 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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:25,bond_interact:60,bond_styl:[0,2],bondangl:6,bondbond13:47,bondbond:6,bonet:115,book:[165,168],bookmark:0,boost:1,border:[4,85],boresch:32,boreschkarplu:32,born:[2,32],boron:118,botero:118,both:[1,2,3,4,11,28,32,45,48,57,58,59,62,63,64,65,67,68,69,73,74,78,81,83,84,85,86,87,88,96,97,99,102,103,104,105,106,107,108,113,114,116,117,118,122,123,125,127,129,131,132,133,135,136,137,142,143,144,148,150,151,159,160,161,162,163,167],bottleneck:1,bottom:73,bound:[2,10,11,19,48,58,64,66,74,86,87,96,118],boundari:[2,33,34,35,37,39,41,43,44,45,58,59,60,61,64,68,73,74,76,78,82,85,86,87,124,136,137,142,167],boundary_dynam:60,boundary_faceset:60,boundary_integr:60,bounds:[2,19,58,66],bount:3,box:[0,1],boxcolor:59,boxxlo:3,bptype:158,br1:44,bracket:[2,19,40,58,61,62,63,64,65,66,167],bragg:[41,44],branch:[3,168],branicio2009:163,branicio:[30,163],breakdown:[1,99],brennan:[31,70,115,145,146,158],brenner:99,brick:[19,66],brief:[1,2,74,99,102],briefli:[2,77,109,152,168],brilliantov:123,broadwel:4,broken:[28,29,74,102],brook:2,brown:[4,41,43],brownian:[2,37,136,137],brows:0,browser:59,bryantsev:125,btype:[58,110,127,131,135,158],buc:104,buck:[2,4,32,103],buckingham:[103,104,105,112,138],buckplusattr:152,buffer:59,bufi:59,bug:0,bui:59,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,58,67,69,70,71,72,73,74,75,76,77,78,80,81,83,84,85,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],bulatov:[140,141],bulk:[2,29,73,76,111,139,142,152],bundl:[59,168],button:168,bypass:2,c11:[63,139],c12:63,c13:63,c1n:63,c21:63,c22:63,c23:63,c2n:63,c31:63,c32:63,c33:63,c34:63,c3n:63,c41:63,c42:63,c43:63,c44:63,c_0:[85,99,156,157],c_1:[40,41,44,58,72],c_2:[40,41,44,58],c_3:40,c_cluster:2,c_cstherm:2,c_dist:40,c_doubl:3,c_e:85,c_flux:35,c_forc:40,c_gauss:121,c_hb:125,c_i:71,c_id:[2,32,40,58,61,62,63,64,65,167],c_ij:2,c_ijkl:2,c_index:40,c_k:72,c_my_stress:61,c_myang:62,c_mycentro:62,c_mychunk:[2,34],c_mycom:64,c_mycomput:62,c_myf:58,c_mypress:63,c_myrdf:65,c_mytemp:[63,64,65,167],c_n_k:72,c_p:43,c_peratom:43,c_pi:102,c_press:40,c_prop:2,c_sigma:102,c_size:2,c_stress:58,c_thermo_press:[63,64,65],c_thermo_temp:65,c_xrd:64,ca2:44,cach:4,cacul:81,calcforc:73,calclat:35,calcluat:[37,39,43,110],calcualt:[35,62],calcul:[0,1],caldwel:[2,46],calhoun:77,call:[1,2,3,4,58,77,99,108,165,168],callabl:3,callback:3,caltech:[2,118],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],cannot:[1,2,3,4,19,28,40,58,59,61,62,63,64,65,66,67,68,72,74,78,85,86,87,96,97,104,105,107,116,122,124,127,131,133,135,148,150,151,158],canon:[74,77,84,142],cao1:77,cao2:77,cao:77,capabl:[3,4,99,107],capac:[70,85,155],capolungo:[41,44],captur:[2,99,105,118,123,131,139],carbid:110,carbon:[59,94,99,109,139],card:[4,32,125],care:[2,45,56,62,73,74,101],carefulli:[3,28],carlo:[2,67],caro:116,carri:[4,85,123],carrillo:4,cartesian:[2,98],cascad:85,cat:[4,59],cate:73,categori:[0,99],cation:[119,152],caus:[1,2,4,45,58,68,74,76,80,81,86,87,96,97,125,127,133,136,137],caution:1,cautious:99,caveat:99,cbecker:[98,116],cc1:[2,34,62],ccc:[117,159,160,162,163],ccflag:4,ccflags:[4,58],ccm6:116,ccsi:[117,159,160,162,163],ccu:102,cd2:44,cdeam:116,cdll:3,cdof:[2,62],cdte:102,cdte_bop:102,cdtese:102,cdzn:102,cdznte:102,ce3:44,ce4:44,cell:[2,41,44,45,58,68,74,75,78,85,118,142,167],cella:[2,167],cellalpha:[2,167],cellb:[2,167],cellbeta:[2,167],cellc:[2,167],cellgamma:[2,167],center:[2,9,33,34,37,41,45,59,62,64,68,72,74,82,84,86,87,88,101,117,118,122,123,136,137,139,140,141,159,160,161,162,163],centr:69,central:[29,36,38,42,76,81,82,91,142,147,163],centro:2,centroid:77,centrosymmetri:29,certain:[1,2,40,58,59,61,62,63,64,65,67],cfg:[2,58,59],cg_type:151,ch2:81,ch2lmp:[0,2],ch3:81,chain:[0,2,13,28,67,74,75,77,81,84,94,113,114,158],challeng:2,champaign:136,chan:142,chandler:[98,116],chandrasekhar:[2,127],chang:[1,2,3,4,19,22,32,45,58,59,60,66,67,68,73,74,75,76,78,79,80,81,83,84,85,87,96,97,114,118,123,136,137,139,142,152,158,167,168],change_box:2,changeabl:58,chapter:77,charact:[2,19,58,59,66,71,80,118,120,126,145,146,149,152],character:[2,29,38,42,153],characterist:83,charg:[1,2,3,32,41,44,45,58,103,104,109,110,112,113,116,118,119,127,131,135,148,152,162,163,165,166],charmm:0,cheaper:[122,150],check:[2,3,19,35,66,79,81,84,96,97,126,167],checkout:168,chem:[2,5,6,9,20,21,22,32,38,39,43,46,47,54,69,72,73,74,77,78,83,84,86,88,94,95,97,99,103,106,107,109,110,111,113,114,115,118,121,122,124,125,127,131,132,135,139,143,145,146,148,152,158],chemic:[31,41,44,58,60,120,146],chemistri:[78,99,102,118],chen:85,cheng:109,chi:[76,119,122],chiral:94,chmod:3,cho:139,choic:[2,4,19,28,29,32,43,56,62,66,67,73,74,77,97,135],choos:[1,2,13,28,32,40,59,67,68,73,74,75],chose:[160,162],chosen:[2,42,45,51,59,68,72,73,74,75,77,115,118,123,126,129,151,160],chunk:0,chunkid:[34,62],ciccotti:81,cieplak:[2,46],cii:63,cij:63,circular:2,circumv:[36,38],citat:[0,73],cite:152,cl1:44,clarendon:[13,113],clarifi:[160,162],clark:148,classic:[0,2,4,77,78,85,95,118],classifi:163,clean:2,cleanli:167,clear:[2,3],clebsch:42,click:[3,45,57,59,97,168],climb:97,clockwis:46,clone:168,close:[2,3,19,43,58,67,68,73,74,81,87,97,99,102,110,111,139,145,146,162,168],closer:[19,58,66,68,83,97],closest:[76,122,150,158],cloud:152,cluster:[2,4,43,58,69,81],cmax:139,cmd:[3,77],cmdarg:3,cmin:139,cmm:[18,151],cn1:63,cn2:63,cna:29,cnn:63,co2:[44,80,81,120],coars:[13,18,28,51,71,80,120,124,146,151],coarsest:42,code:[0,1],coeff:[6,46,47,56,88,126,154],coeffici:0,coefficienct:114,coefficient0:116,coefficient1:116,coeffieci:[2,100],coeffincientn:116,coexist:118,cohes:[2,119,139],coincid:[87,106,136,137],cold:2,coleman:[41,44],collect:[2,34,45,58,62,108],colliex:44,collis:[73,123,166],colloid:2,color:[19,58,59,66,72,78],column:[2,29,34,36,38,40,42,43,44,58,61,62,63,64,65,78,85,99,121,125,167],colvar:0,com:[2,37,64,69,101,168],comand:67,combiant:111,combin:[2,3,18,32,56,58,59,60,64,69,74,77,87,88,108,110,111,115,118,119,120,134,135,153,159,160,162,163,165],come:[0,2,13,68,74,83,84,159,160,162,163,167,168],comit:168,comm:[0,3,30,97,114],comm_modifi:[2,102,108,114,118,123],comm_styl:[19,66],comm_world:3,command:[0,1],comment:[3,46,58,71,80,85,97,98,116,117,119,120,126,139,145,146,147,152,153,159,160,161,162,163,168],commit:168,commmand:2,common:[0,1,2,3,4,30,68,77,87,88,123,125,159,160,162],commonli:[2,9,37,38,58,59,95,124,129,153,160,162],commun:[1,2,3,4,19,59,66,68,73,74,85,115],comp:[81,97,118,150,157,161],compar:[1,2,4,41,44,57,96,97,139,152],comparison:0,compass:[6,20,47,57,88,107],compat:[3,19,40,50,58,61,62,63,64,65,66,69,86,142],compens:[2,118],compil:[4,58,59,142],complain:3,complement:139,complementari:[110,127],complet:[2,3,19,66,77,97,119],complex:[2,3,9,36,38,42,45,73,87,97,118,142],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,59,61,62,63,64,65,67,68,69,73,74,75,77,81,87,96,97,114,118,123,136,137,152,153,167],componenet:2,composit:[2,73,116],compound:[109,118,119,163],compres:62,compress:[2,58,59,62,75,78],compris:[87,120,150],compton:[41,44],comput:[0,1],computation:[2,85,102],compute_modifi:[67,68,74,75,167],compute_sa:41,compute_xrd:44,concav:87,concentr:[71,80,116,120,146],concept:[2,62],conceptu:[2,68,97,110,139],concern:[2,30,32,72],concis:3,concurr:4,conden:[85,160,162],condens:[2,85,99,112,116,127,163],condit:[2,39,41,43,44,58,59,60,73,75,76,78,81,82,85,115,118,124],conducit:2,conduct:0,confer:[4,142],config:58,configur:[1,2,4,58,59,68,77,96,97,99,102,117,139,142,159,160,162,163,167,168],conflict:168,conform:[2,67,68,79,94,97,118],confus:163,conjuct:114,conjug:118,conjunct:[2,32,45,73,97,103,104,110,114,118,125,127,148,151],connect:[2,32,67,81,97,111,123,158,162],conner:99,connor:99,consecut:[3,45,110,127,131],consequ:[1,2,85,126],conserv:[13,67,72,73,74,80,81,97,113,114,115,123,133,152],consid:[2,29,32,58,61,63,66,67,85,118,150,152,158,167],consider:2,consist:[2,3,39,45,51,62,72,74,75,78,79,80,97,99,102,108,110,118,122,136,137,139,142,145,146,150,152],consistent_fe_initi:60,constant:0,constantli:69,constitu:[2,86,87,108,150],constrain:[2,62,69,72,81,82,96,118],constraint:[19,39,43,62,66,69,81,82,86,96,137],construct:[2,28,29,30,36,38,41,42,44,68,74,79,80,87,113,142,158,159],constructor:3,consult:4,consum:1,contact:[0,111,117,119,122,123,150],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,61,62,63,64,65,66,71,73,76,78,80,85,87,97,98,99,102,109,110,113,116,117,118,120,139,142,145,146,147,149,153,159,160,161,162,163,167,168],content:167,context:[2,4,40,165],contibut:29,contin:4,continu:[0,2,19,62,63,64,65,66,67,68,69,72,74,75,78,83,84,85,87,102,114,129,132,150,161,167],continuum:[2,60,85],contour_integr:60,contract:[68,74],contrain:81,contrast:[1,2,165],contrib:85,contribut:[2,29,32,33,34,35,39,40,42,43,61,62,63,64,65,68,73,81,96,97,114,116,118,136,137,142,152,167,168],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,66,68,74,75,80,85,118,122,142,159,162],control_typ:60,convect:35,conveni:[2,13,58,65,153,168],convent:[13,50,55,57,79,116,118],converg:[2,19,58,59,66,67,68,75,78,79,81,96,97,109,110,127,152],convers:[42,59,63,110,111,112,118,127,131,135,148],convert:[2,5,6,8,12,16,17,18,35,45,47,58,59,63,65,88,89,93,94,97,98,116,142,160,162,166],convex:87,cool:69,cooordin:58,coord1:62,coord2:62,coord3:62,coord:[2,3,36,38,58,64,76,86,97],coordb:152,coordbb:152,coordiat:96,coordin:[1,2,3,19,32,33,34,42,45,58,59,61,62,64,66,67,68,69,74,76,81,82,84,85,96,97,98,99,101,117,152],coordn:62,coords:152,copi:[0,3,59,85,97,168],copper:166,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,104,110,112],cornel:[2,46],corner:[2,59,87,168],corpor:4,corr:109,correct:[2,3,32,46,59,69,74,78,86,87,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],correction_max_iter:60,correctli:[3,58,74,81,87,97,112,137,142,168],correl:[2,35,36,42,62],correpond:71,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,59,62,64,68,69,71,73,74,75,76,77,80,81,86,87,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,139,140,142,144,146,147,148,149,150,151,152,153,154,159,160,161,162,163,164,165,166,167],correspondingli:[136,137],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,59,62,66,74,80,85,110,127,131,142,159],costheta0:[159,160,162,163],costheta:149,costli:[3,4],coul:[2,4,18,21,22,32,46,96],could:[2,3,19,32,34,39,58,59,62,63,66,78,85,86,87,96,99,121,125],coulomb:[2,43,96,103,104,105,106,107,109,110,111,112,113,118,123,124,127,131,135,138,148,151,152,162,163,165,167],coulommb:2,count:[1,2,3,19,35,40,46,62,64,66,74,81,87,96,97,121,125,167],counterbal:69,counterbalanc:13,counterclockwis:46,counterpart:58,coupl:0,couple:[2,3],cours:[4,58,72,79,86,136,154],cov:152,coval:[2,13,118,139,152],cover:[2,60,73,118],cpp:[1,2,3,32,58,81],cpu:[1,4,167],cpuinfo:4,cpuremain:167,cr2:44,cr3:44,crai:58,creat:[0,1,2,3,19,35,39,40,41,45,58,59,60,61,62,63,64,65,66,67,68,71,74,75,76,77,79,85,97,99,102,109,116,117,135,144,145,146,149,152,159,160,161,162,163,167,168],create_atom:[2,19,35],create_box:[2,19,35,45,68,74,158,167],create_elementset:60,create_faceset:60,create_nodeset:60,createatom:0,creation:45,criteria:[59,67,96],criterion:[19,45,66,67,96,97,109,118,123,152],critic:[2,24,25,85,96],cross:[4,33,58,59,61,97,106,114,116,124,125,127,129,131,149,151,160,162,166],crossov:1,crozier:0,crucial:78,crystal:[2,4,29,30,38,76,84,167],crystallin:[2,161],crystallogr:[41,44],crystallograph:167,crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,153],cscl:139,csequ:2,csh:[3,4],cshrc:3,csic:[117,159,160,162,163],csinfo:2,csisi:[117,159,160,162,163],cst:116,cstherm:2,csvr:2,ctcm:[98,116],ctype:3,cu1:44,cu2:44,cu3au:139,cube:[2,87],cubes:[19,66],cubic:[38,73,76,116],cuda:1,cuh:102,cummul:[2,65,67,125,167],cumul:[2,62,64,74,75,97],current:[0,1,2,3,4,19,30,32,40,43,58,59,60,62,65,66,67,68,69,74,79,80,81,82,85,86,96,97,102,109,113,116,118,119,123,126,136,137,139,140,141,149,154,160,162,167,168],curv:[2,45],curvatur:[122,150,166],custom:[0,2,3,33,34,35,40,43],cut:[1,2,4,19],cuthi:76,cutinn:[136,137],cutlo:76,cutmax:149,cutoff1:[107,113,127,131,135,138,148,151],cutoff2:[103,104,105,107,112,113,127,131,135,138,148,151],cutoff:[2,4,21,22,28,29,30,32,36,38,42,67,71,76,78,86,87,96,98,99,100,101,102,103,104,105,106,107,108,110,111,112,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],cutoffa:117,cutoffc:117,cuu3:116,cval:44,cvff:4,cwiggl:86,cyan:59,cycl:[74,75],cyclic:46,cylind:[59,62,87],cylindr:2,cyrot:102,d3q15:73,d3q19:73,d_e:85,d_name:58,daan:84,damp:[2,74,75,78,96,97,103,104,106,110,113,118,123,127,135,148,151],dampflag:123,danger:[114,167],darden:113,darken:59,dash:123,dat:[2,35,60],data2xmovi:0,data:1,databas:0,date:[0,2],datum:[2,58,63],davenport:138,davi:86,david:[160,162],daw:[116,149],dcd:[2,58,59,77],deactiv:135,debug:[2,3,41,44,45,77],decai:[36,110,166],decid:[2,4,168],decod:59,decompos:[32,153],decomposit:[60,77],decoupl:2,decreas:[4,58,67,69],dedic:4,defect:[2,29,142],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,99,100,101,103,104,105,106,107,108,110,111,113,114,115,117,118,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,142,143,144,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],definit:[2,42,62,63,64,65,70,75,86,102,108,115,118,149,153],defint:167,deform:[2,43,68,74,136,137],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,38,39,44,45,46,47,49,50,55,56,59,62,67,74,75,77,79,81,84,88,89,93,94,95,96,113,116,125,167],degress:62,delai:[2,167],delet:[28,62,63,64,65,67,74,158,168],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:60,delimit:80,dellago:[2,69],deloc:[118,152],delr:139,delta_1:102,delta_3:102,delta_7:102,delta_ij:[139,149],delta_pi:102,delta_r:149,delta_sigma:102,deltah_f:71,demo:3,demonstr:[78,139],dendrim:125,denniston:73,denot:[41,69,110,124],dens:[67,80,118],densiti:[2,19,42,45,60,62,66,73,85,86,98,99,102,116,139,140,141,145,146,149,150,152,155,156,157,167],depart:0,departur:78,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,42,45,46,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,68,71,73,74,75,76,80,81,83,85,86,87,88,89,90,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,119,120,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,159,160,161,162,163,164,165,166,167],dependend:2,deposit:[74,81],deprect:62,depth:[26,59,85,120,122,150],der:[32,108,109,135,165],deriv:[2,32,42,63,68,69,74,75,76,83,84,85,86,87,99,102,108,113,118,119,124,129,133,134,139,142,165],derjagin:165,derlet:76,descib:59,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,58,62,63,64,65,66,67,68,71,72,73,74,75,76,77,78,80,83,84,86,96,97,99,101,103,104,106,107,108,109,110,113,116,118,119,120,122,123,124,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,145,146,149,150,151,152,153,154,158,159,160,161,162,163,164,165,166,168],descript:[2,3],descriptor:[42,58],design:[0,2,3,41,44,60,67,74,76,85,100,101,106,110,112,118,135,136,137,140,141,149],desir:[2,3,4,35,39,40,43,45,62,65,68,72,74,81,96,97,114,116,125,136,137,159,160,162,167],desktop:[2,59],destabil:102,destre:94,destroi:3,detail:[1,2,3,4,19,34,35,39,40,42,43,45,57,58,59,60,62,63,64,65,66,67,68,69,72,73,74,75,78,81,84,85,96,98,99,101,102,105,106,107,108,109,110,113,114,118,119,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,143,145,146,150,152,153,154,164,165,167,168],detect:[36,97,109,125,126],determin:[1,2,4,26,32,39,41,43,44,45,58,59,61,62,63,64,65,66,68,71,74,76,77,78,79,80,86,87,99,105,109,113,116,120,121,123,131,139,142,146,150,152,158,165],devan:151,devanathan:162,develop:[0,2,3,4,75,78,99,102,118,141,142,152,163],deviat:[75,76,121],devic:1,devin:109,devis:141,dfactor:59,dft:142,dhug:78,dhugoniot:78,dia:139,diag:80,diagnost:[4,67,80],diagon:[2,42,43,68,74],diagonalstyl:153,diagram:[19,41,44,57,66,77],diallo:125,diam:59,diamet:[2,45,58,59,108,122,123,129,150,165],diamond:[118,139],dick:2,did:[96,114,116,123,160,162],dielectr:[106,110,111,112,127,131,135,148],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,59,62,64,66,67,68,69,72,73,74,76,77,78,81,82,83,84,85,86,87,88,97,98,99,102,105,106,108,109,114,115,116,118,120,122,123,124,127,128,130,131,138,139,140,141,143,144,145,146,147,149,150,151,152,153,154,159,160,162,163,165,167],differenti:[1,2,13,80,110,149,161],difficult:[68,77,125],difficulti:[36,38,81],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:142,dihedr:[0,4,28,36,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,67,79,89,90,91,93,96,99,102,106,167],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:118,dij:81,dilat:[68,74,75],dim:[45,139],dimens:[1,2,19,35,43,45,58,59,62,66,68,73,74,75,78,86,97,167],dimension:[36,39,41,42,44,62,85,97,149],dimensionless:[37,42,85,153,165],dimer:[2,139],dimstr:[19,66],dintel_offload_noaffinity:4,dipol:0,dipolar:[13,58],dipole:113,dir:[1,3,76,78,149],dirac:42,direc:149,direct:[2,4,13,29,38,41,42,44,45,46,58,59,73,75,76,78,83,84,85,86,87,96,97,114,115,123,137],directli:[2,3,32,42,58,59,73,80,87,98,99,103,104,105,110,113,116,118,127,131,148,151,158,167],directori:[0,1,2,3,4,83,84,97,98,99,102,109,110,116,117,119,135,139,140,141,142,147,149,152,153,159,160,161,162,163],disabl:[4,85,126],disadvantag:[2,66],disallow:[58,74],discard:[19,66,87],discontinu:[96,133],discourag:139,discret:[2,59,73],discuss:[0,1],disk:[2,36],disloc:[29,142],disord:[29,142],disp:0,dispar:150,disperion:[113,131],dispers:[2,105,113,131,136,163],displac:[2,37,68,74,76,123],displai:[3,57,58,59],disregard:142,dissip:[2,31,70,72,83,84,114,115,123,136,137],dist:[2,35,40,58,77,79,158],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,42,45,47,58,59,62,67,68,69,73,74,75,76,78,79,81,82,84,85,86,87,88],distinct:[2,150],distinguish:[2,42,118],distort:98,distrbut:98,distribut:[0,2,3,19,32,42,57,66,72,73,74,98,102,110,116,117,119,139,140,141,147,149,150,159,160,161,162,163],distro:149,ditto:166,div:4,divd:40,diverg:[84,99],divid:[2,4,19,35,39,40,43,57,62,63,64,66,76,96,97,119,152,163],divis:[2,56,73,102,135,167],dl_poly:2,dlammps_ffmpeg:59,dlammps_gzip:[58,59],dlammps_jpeg:59,dlammps_memalign:4,dlammps_png:59,dlammps_xdr:58,dlm:74,dlmp_intel_offload:4,dlopen:2,dlvo:[108,165],dm_lb:73,doc:[0,1,2,3,32,34,37,39,40,43,45,57,58,59,61,62,63,64,65,74,87,96,97,98,99,101,109,110,116,117,119,125,139,140,141,147,149,153,159,160,162,163,167,168],docuement:150,doe:[0,1,2,3,19,28,29,32,35,40,41,44,45,46,57,58,59,60,62,66,67,68,69,71,72,73,74,85,86,87,89,90,91,93,94,97,98,99,100,101,102,105,106,107,108,109,110,111,113,114,116,117,118,120,121,122,123,124,126,129,130,132,133,134,136,137,139,140,141,142,145,146,149,150,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168],doesn:[45,58,99,109,117,159,160,161,162,163],dof:[39,62],dof_per_atom:62,dof_per_chunk:62,doi:[2,76],domain:[2,19,41,44,59,66,68,73,74,77,85,86,97],domin:[1,118],don:[0,4,87,139,152,168],done:[1,2,19,45,56,58,59,60,62,64,65,66,67,68,71,74,77,81,83,84,96,97,99,105,116,131,137,138,139,145,146,158,167,168],donor:125,dot:43,doti:[102,149],doubl:[1,2,3,4,32,46,87,102,119,124,142],dover:60,down:[2,3,68,118,152],download:3,downsid:2,dpd:2,dpdtheta:[31,115],dpdtheta_i:[70,71],dr_ewald:41,drag:[2,35,74,75,82],dragforc:73,drai:[59,78],drain:96,dramat:[67,68,74,152],drautz:102,draw:59,drawn:[58,59,72],drayleigh:78,dreid:2,dreiding:0,drfourth:37,drho:[98,116,145,146],drift:[2,37,69,72],drive:[3,68,74,76,97],driven:[2,51],driver:2,drop:114,drsquar:37,drude:0,dt_collis:73,dt_lb:73,dt_md:73,dtqm:78,dudarev:44,due:[1,2,4,28,29,33,34,37,41,42,43,44,45,58,59,64,67,68,72,73,74,75,76,79,83,84,85,86,87,96,97,111,114,115,116,121,122,136,137,149,150,151,158,160,162,165,166,167],duffi:85,dullweb:74,dummi:[13,161],dump:[0,1],dump_modifi:[2,58,59],dunbrack:[2,5,46,106],duplic:[19,66,76],durat:[57,62,85,123],dure:[2,4,19,32,46,58,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,81,82,83,84,85,86,87,96,97,114,135,142,144,145,146,167],dvlo:165,dvx:2,dx_lb:73,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,66,67,70,72,74,75,77,78,79,83,84,85,96,97,114,115,118,136,137,157],dynamo:[98,116,139],dyre:132,e28637:13,e_1:102,e_2:102,e_a:80,e_b:119,e_ee:118,e_hbond:125,e_i:[2,102,119],e_j:[2,102],e_k:102,e_ke:118,e_kl:2,e_lj:[99,113],e_n:102,e_ne:118,e_nn:118,e_pr:118,e_rebo:99,e_torsion:99,e_tot:142,e_vol:142,eaa:88,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,71,72,73,74,75,76,77,80,81,82,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,162,163,164,165,166,167],eacn:[19,66],eam:[0,98,110],eangl:167,earli:[19,62,64,65,66],earlier:[97,123,139],earth:118,easi:[2,3,32,43,58,86],easier:[4,58,59],easili:[3,59,97],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebond:167,ebt:47,ec_ii:139,ec_ij:139,ec_jj:139,echo:[3,41,44],ecoul:167,ecp:118,edg:[2,19,41,44,58,59,86,87],edge:86,edih:167,edit:[4,168],edition:4,edu:[3,116,136],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,40,43,46,47,48,49,50,51,52,53,54,55,57,58,59,60,61,62,63,64,65,67,68,69,72,74,75,76,77,78,79,81,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,102,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,142,144,145,146,147,148,150,151,152,154,159,160,161,162,163,164,165,166,167],effici:[0,1,2,4,39,56,58,59,63,68,74,77,81,102,108,110,127,131,142,145,146,150],efficienc:4,efield:[81,96],eggebrecht:[110,152],ehex:2,eigenvalu:77,eimp:167,einstein:[2,84],either:[1,2,3,4,19,29,41,42,43,44,45,58,59,61,63,64,65,66,67,68,69,73,74,75,76,80,81,87,96,102,108,116,120,123,136,137,139,142,146,149,158,160,162],ejtehadi:[108,122,150],elaplong:167,elaps:[86,154,167],elast:[2,21,22,97,123,161],elastic:0,elba:13,electr:[2,60,119,166],electric:4,electrolyt:165,electron:[2,41,60,85,98,109,113,116,118,119,139,142,149,152,162,163,166],electron_integr:60,electron_temperatur:60,electron_unit:118,electroneg:[2,109,119,152],electroneg_compon:152,electrostat:[2,4,108,113,118,127,135,137,152,165],elem1:[119,139,153],elem2:[119,139,153],elem:152,element1:[98,116,152],element2:[98,116,152],element:[2,33,37,39,40,42,43,58,59,60,62,63,64,65,98,99,102,109,116,117,118,119,139,140,141,142,147,149,152,153,159,160,161,162,163,167],elementn:[98,116],elementset:60,elif:42,elig:125,elimin:[2,72,81,83,84],elj:113,ellips:2,ellipsoid:[2,45,58,96,122,137,150],elong:167,els:[40,59,61,62,63,64,65,74,85],elsewher:[139,167],elt:139,emac:0,email:[0,3,119],emb:87,emb_lin_neg:139,embed:[3,13,85,98,116,119,135,139,140,141,149],embt:47,emol:167,emphas:123,empir:[60,118],empiric:99,emploi:[69,161],empti:126,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,57,58,67,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],enclos:[2,58,139,152],encod:[58,59],encompass:2,encount:[38,64],encourag:[80,82],end:[1,2,3,4,19,47,58,59,63,64,65,67,69,72,74,79,80,85,97,114,116,122,138,142,150,153,154,167],endbondtors:47,energet:[67,99],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,43,45,46,47,48,49,50,51,52,53,54,55,56,57,58,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114],energy_compon:152,enforc:[2,58,59,67,74,81,127],enforce2d:[2,96],eng:[3,58,109,141],engineer:[60,83,116],enginer:140,enhanc:[60,69],enlarg:59,enough:[45,66,78,86,87,110],enpub:116,ensembl:[2,32,35,74,77,78,114,152],ensight:2,ensur:[2,42,58,68,72,74,102,135,159,163],enter:[119,142,163],enthalpi:[80,116,167],entir:[0,2,3,19,31,39,41,43,44,45,62,66,67,69,72,74,75,76,77,80,82,85,113,131],entiti:[2,58],entri:[41,64,71,78,102,117,139,145,146,147,153,159,160,161,162,163],entry1:[145,146],enumer:58,enumuer:2,environ:[1,2,3,4,59,76,98,102,109,117,118,149,160],eos:71,epair:[99,121,125,167],epp:113,epq:113,eps0:165,eps14:135,epsilon0:162,epsilon:[2,18,21,22,27,28,32,46,86,87,96,101,106,107,108,110,111,112,113,120,122,124,125,126,127,128,129,130,131,132,133,134,135,138,143,148,150,151,159,164,165],epsilon_0:166,epsilon_14:106,epsilon_:150,epsilon_d:111,epsilon_i:[122,150],epsilon_i_:150,epsilon_i_a:[122,150],epsilon_i_b:[122,150],epsilon_i_c:[122,150],epsilon_j:[122,150],epsilon_j_:150,epsilon_j_a:[122,150],epsilon_j_b:[122,150],epsilon_j_c:[122,150],epsilon_lj:150,eqp:113,eqq:113,equal:[2,3,19,28,32,35,40,43,45,59,63,64,65,66,68,72,73,75,76,77,78,79,80,83,84,85,86,96,97,99,109,114,115,121,122,125,136,142,143,149,150,152,153,154,163,166,167],equat:[2,35,38,39,41,44,57,68,69,70,71,73,74,75,76,77,78,80,81,85,86,108,113,114,115,118,119,120,123,136,137,139,146,150,155,156,157,166],equation:[76,94],equilibr:[2,35,45,63,67,68,74,78,83,84,109,110],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,68,72,73,74,75,78,79,81,84,88,89,93,94,109,139,147,152],equilibrium_start:60,equival:[2,13,40,58,61,62,63,64,65,68,74,79,99,114,118,152,160,162,167],equlibrium:2,er3:44,eradiu:118,eras:83,erat:137,erc:110,erfc:[110,127],erhart:[116,160,162],eros:139,erose_form:139,erot:2,errata:[160,162],erratum:86,error:[0,1,2,3,11,40,48,58,59,61,62,63,64,65,68,69,71,74,80,85,86,87,96,110,127,150,158,160,162],erta:123,especi:[4,45,66,78,79],essenti:[3,11,48,63,99,110,127,162,167],essential:75,essex:13,establish:32,estim:[1,2,19,29,35,43,60,66,80,167],esub:139,eta:[2,73,74,78,117,119,122,149,161,163],eta_dot:74,eta_ij:149,eta_ji:119,etail:167,etap:74,etap_dot:74,etc:[1,2,3,4,28,33,34,35,43,45,58,59,60,61,62,64,65,72,74,85,87,96,97,116,117,135,137,142,159,160,162,163,167],etol:[96,97],etot0:78,etot:[2,43,78,167],eu2:44,eu3:44,euler:[80,96,97],eulerian:60,europhi:73,evalu:[3,32,35,40,42,45,46,58,59,60,61,62,63,64,65,72,80,86,96,142,145,146,149,152,167],evanseck:[2,5,46,106],evaul:96,evdwl:167,even:[2,4,19,29,56,58,61,62,64,65,66,68,69,74,85,86,87,96,97,101,118,119,123,150,163,167],evenli:[19,43,66,73],event:[2,74,85],eventu:2,ever:28,everaer:[108,122,150],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,64,65,66,67,68,69,73,74,75,76,78,80,81,85,97,114,135,152,167,168],everyth:168,everywher:129,eviri:118,evolut:[69,73,77],evolv:[73,77],ewald:[2,41,43,96,103,104,105,110,113,118,127,131,148,151],ewald_disp:113,exact:[19,66,67,72,85],exactli:[2,19,35,45,64,66,72,78,114,116,123,136,145,146],examin:[2,67,80],exampl:[0,1],exce:[2,4,19,61,62,64,65,66,68,74,96],exceed:[19,66,74],excel:118,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,40,43,45,46,47,48,49,50,51,52,53,54,55,57,58,62,63,64,66,68,74,75,77,81,85,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166,167],excess:118,exchang:[2,60,69,85,118],excit:118,excite:118,exclud:[2,4,39,42,58,62,96,123,136,137,158],exclus:[1,4,32,46,109,142],excurs:74,execut:[1,2,3,59],exempl:152,exemplari:72,exemplifi:118,exert:[2,87],exhaust:60,exhibit:[36,69,74,118],exist:[2,3,29,45,57,59,68,88,89,90,91,93,115,158,168],exit:[3,19,58,66,167],expans:[42,56,58],expect:[1,4,19,66,76,78,139,142],expens:[2,76,85],experi:[2,79,97,114],experienc:[2,4],expir:167,explain:[1,2,3,19,30,58,59,62,63,65,66,68,74,76,97,101,116,152,154,168],explan:[2,42,58,62,76],explanatori:[40,58,61,62,64],explic:143,explicit:[2,3,32,80,99,102,106,116,118,126,136,168],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,58,72,74,75,78,81,85,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,111,113,114,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,140,142,144,145,146,147,148,150,151,154,155,156,157,159,160,161,162,163,164,165,166,168],explictli:4,exploit:77,explor:[41,44],expon:[80,116,120,122,125,135,143,151],exponenti:[32,80,120,149,159,163,166],expos:3,exposit:[60,114],express:[2,42,45,68,76,80,85,102,116,118,129,139,152,153],expressiont:102,extend:[0,2],extens:[2,4,21,22,27,32,35,40,65,69,74,75,76,79,83,84,85,86,87,122,139,142,150,153,167],extensiv:167,extent:[1,19,21,58,66,99],exterior:[2,87],extern:[32,59,68,72,73,74,75,85,96,140,141],extra:[2,3,4,19,22,39,41,43,44,45,64,66,74,78,96,113,123,139],extract:[2,3,18,32,40,97,110,119,139,153],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,59,68,74,84,118,161],extrema:135,extreme:118,extrins:60,f_1:2,f_a:[160,161,162],f_ave:40,f_c:161,f_f:162,f_fix_id:78,f_harm:84,f_i:[13,149],f_id:[2,40,58,61,62,63,64,65,167],f_ij:149,f_indent:65,f_int:83,f_j:13,f_jj:35,f_k:149,f_langevin:85,f_max:78,f_r:[160,161,162],f_sigma:102,f_solid:84,f_ss:2,face:[2,86,87,122,139,150],facil:0,facilit:2,fact:[2,4,84,123,152],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,59,63,66,68,69,73,74,75,77,79,80,81,86,87,93,99,102,103,104,106,110,111,112,114,115,118,123,126,127,139,142,145,146,147,148,151,154,159,167],fail:[3,68,96,97,112],fairli:[3,168],faken:30,fall:[2,64],fals:152,famili:163,familiar:[0,3,168],fan:149,far:[2,58,66,68,74,76,79,86,89,93,97,167],farrel:[160,162],farther:58,fashion:[2,19,45,66,74,75,78,84,85,86,97,136],fast:[2,4,58,78,80,136,137,142,167],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,46,47,48,49,50,51,52,53,54,55,58,66,74,75,81,83,85,88,89,90,92,93,94,95,98,99,100,102,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],fastest:[1,2,85],fault:29,fava:122,favor:67,fcc:[2,29,30,35,38],fcold:69,fdt:[70,71,80],fdti:32,fe2:44,fe3:44,fe_md_boundari:60,featur:[0,2,3,42,59,67,72,77,87,96,168],fecr:116,feel:[76,87,97],fehlberg:80,felling:141,felt:87,fene:[2,4],fennel:[110,127],fep:0,ferguson:[2,46],fermi:[1,162],fermion:118,fernando:138,few:[1,2,3,61,62,63,64,65,69,74,81,96,97,99,152],fewer:[1,3,4],feynman:77,ffield:[109,119,152],fflag1:59,fflag2:59,ffmpeg:59,ffplai:59,fft:[1,3,43],fhot:69,ficiti:158,fictiti:[2,77,79,110,127,131,158],field:0,fifth:[2,120,147],figshar:76,figur:[1,4,78,168],fij:113,file0:76,file1:[3,71,76],file2:[3,71],file:[0,1],filenam:[4,19,58,59,60,62,63,64,65,66,71,76,80,85,97,98,99,102,110,116,117,119,120,139,140,141,145,146,147,149,152,153,159,160,161,162,163,167],filep:58,fill:[45,59,85,102,142,168],filter:60,finchham:[2,112],find:[0,2,3,4,30,32,40,67,68,71,76,79,96,97,110,127,131,139,145,146,152,168],fine:[4,84,168],finer:[42,45],finger:45,finish:[2,3,19,66],finit:0,finni:116,fire:[96,97],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,40,43,44,47,58,59,62,63,64,65,66,67,71,72,73,74,76,77,78,81,82,83,84,85,88,96,97,98,99,101,102,103,104,106,109,110,116,118,119,120,123,124,126,127,131,136,137,139,141,142,145,146,147,149,152,153,158,159,160,161,162,163,166,167,168],fischer:[2,5,46,106],fit:[2,79,99,102,139,145,146,161,168],five:[30,78,102,140],fix:[0,1],fix_flux:60,fix_heat:69,fix_id:[68,74,75,78],fix_manifoldforc:168,fix_modifi:2,fix_nv:168,fix_rattl:81,fix_shak:81,fixedpoint:[68,74],fixid:[59,60],fji:113,flag:[3,4,33,34,41,44,58,59,65,67,99,125,126,139,142,158,168],flag_buck:105,flag_coul:[105,113,131],flag_lj:[113,131],flagfld:[136,137],flaghi:[136,137],flaglog:[136,137],flagvf:[136,137],flat:[2,4,85,86],fld:[86,136,137],flexibl:[2,59,62,118,161,167],flip:[2,74],fluctuat:[2,32,68,72,73,74,75,76,84,85,94,115],fluid:[2,40,68],flux:2,flv:59,fly:[19,59,60,81,102,142,167],fmass:77,fmax:[96,167],fmsec:74,fno:4,fnorm:[96,167],fnve:69,focu:81,foil:[42,76,153],fold:[4,82],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,40,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,70,71,72,73,74,75,77,78,79,80,81,83,84,85,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168],foo:[3,58,59,80],foo_species:80,foot:2,forc:[0,1],forcefield:[79,125],forcegroup:73,ford:113,forgiv:74,fork:[58,168],form:[2,28,32,33,34,36,40,42,43,58,61,62,63,64,65,72,79,80,85,86,87,88,91,94,97,99,102,115,116,118,121,125,126,138,139,141,142,145,146,147,148,149,150,152,153,154,160,161,162,165,167],formal:[2,35,72,74,77,152],format:[2,19,58,59,62,64,65,66,71,80,85,97,98,99,102,116,119,120,126,139,141,145,146,151,153,163,167],formation:71,former:[2,19,66,85,102],formul:[1,2,43,74,79,81,99,102,116,118,122,139],formula:[2,6,28,29,30,32,33,34,35,39,41,43,44,45,47,57,58,62,63,64,65,76,82,86,88,90,99,101,102,106,107,108,113,114,116,117,122,123,124,125,126,127,129,130,131,133,134,136,137,139,143,144,150,151,154,159,160,161,162,163,164,165,167],forth:[1,2,3],fortran:[2,3,116,139],forward:[32,97],foster:[102,149],found:[2,30,58,67,69,73,110,113],four:[2,3,28,42,85,94,97,142],fourier:2,fourth:[2,4,37,79,106,120,147,152],fox:[2,41,46,157],fqq:113,fraction:[1,2,4,19,43,59,67,68,78,80,97,102,120,123,136,137],frame:[42,60,78,122],framer:59,framework:[98,153],frattl:69,free:[2,13,29,32,76,83,84,85,97,118,135,142,144,149,165],freedom:[2,39,62,67,74,75,77,81,84,96,113,167],freeli:[0,2,59],freez:2,frenkel:[2,69,84],frequenc:[2,4,77,78,80,114,118,152],frequent:[29,30,36,38,42,69],fri:78,friction:[2,78,85,123],from:[0,1],front:78,frontend:59,frozen:[2,39,72,121],fs2:[2,35],ftol:[96,97],fuction:110,fudg:81,fulfil:2,full:[1,2,4,35,59,63,69,73,76,80,102,116,118,119,122],fuller:96,fulli:[2,76,96,97,110,149,168],fulton:116,fumi:103,funcfl:116,fund:0,funrol:142,further:[2,37,59,62,64,65,73,77,85,96,97,98,101,109,142,152],furthermor:[11,48,69,80,115,118],futur:[0,2,66,72,97,140,141],g_jik:149,g_p:85,ga3:44,gaa:102,gai:122,gain:4,galindo:143,gamma0:13,gamma:[2,13,73,78,114,115,117,122,139,143,155,156,157,159,160,162,163,167],gamma_:85,gamma_ijk:160,gamma_n:123,gamma_p:85,gamma_t:123,gammaa:143,gammafactor:73,gammar:143,gan:[149,159,160,162,163],gan_sw:149,gan_tersoff:149,gao:[2,5,46,106],gap:[136,137,153],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:111,gaussian:[2,35,37,72,77,79,114,118,121],gavhan:4,gaybern:[2,4,96],gd3:44,gdot:137,ge4:44,gec:[160,162],gen:74,gener:0,gentler:86,gentli:117,geom:2,geometr:[2,45,58,66,74,87,97,101,107,108,110,113,118,120,122,124,127,128,129,130,131,132,133,134,135,136,137,138,143,146,150,154,164,165,167],geometri:[2,9,19,45,66,68],gerber:135,germann:[75,129],germano:122,get:[0,1,2,3,4,19,35,42,45,58,59,61,66,68,87,97,110,163,168],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[110,127],ghost:[2,4,30,68,74,114,115,118,123,126],gif:59,gifsicl:59,gillan:153,gingold:[155,156],git:168,give:[0,1,2,3,4,28,36,38,45,58,62,63,64,65,68,74,76,96,99,102,118,125,139,142,150,160,161,162],given:[2,3,4,11,38,42,43,48,57,58,62,68,69,72,73,74,75,76,77,78,79,80,81,82,85,86,87,98,99,102,103,104,105,107,108,109,110,111,114,115,116,118,119,120,122,123,125,127,128,129,131,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,166],glosli:142,glotzer:114,glue:3,gnu:0,gnuplot:3,goddard:[2,9,95,118,125],goe:[28,42,45,69,96,113,117,124,129,132,154,166],gold:29,goldman:78,good:[1,2,4,19,30,41,44,66,74,81,97,98,108,116,142,163,167,168],gordan:42,gordon:2,got:168,gould:[2,46],gov:[0,98,116,119],govern:73,gpa:99,gpl:0,gpt:142,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99],grab:2,grad:2,gradient:[2,68,69,85,97,137,145,146],graft:67,grain:[2,13,18,28,45,51,71,76,80,120,124,142,146,151],gram:[62,116],gran:[2,86,87],granular:0,graph:3,graphic:3,graviti:2,grdient:60,great:[78,168],greater:[1,68,72,74,76,101,103,104,105],greatli:[41,69],green:[2,35,59,77,102,168],green_kubo:2,grest:[21,22,67,105,123,131],grid:[19,41,44,66,73,85],grigera:2,gromac:96,gromacs:[2,58,96,124],groot:114,ground:[2,31,70,118],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,97,152,163,167],group_id:3,grow:[2,74,76,80,123],growth:2,gsmooth_factor:139,guarante:[45,58],guess:[58,168],gui:[3,168],guid:[1,155,156,157],guidelin:1,gullet:139,gulp:2,gunnel:142,gunsteren:135,guo:[2,5,46,51,106],gyrat:2,gzip:[58,59,97],h12:122,h2o:[120,146],had:[2,3,40,58,61,62,63,64,65,67,68,72,74,75,85,114,123,158,167],hafskjold:[2,69],half:[1,2,4,19,59,61,66,74,85,86,87,102,108,118,142],halfwai:[19,59,168],halperin:36,halsei:123,halt:[19,66,69],halv:59,hamak:[86,87,108,150],hamilton:29,hamiltonian:[74,118],han:116,hand:[2,28,29,45,55,59,73,80,110,118],handl:[4,59,118,136,163],happen:[2,63],hara:161,hard:[1,79,152],harden:154,harder:[86,87],hardi:60,hardwar:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],harmon:[2,4],harmonic_fix_wal:137,harrison:99,hartre:[116,118,142],hassl:79,hat:2,have:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,34,35,36,37,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,65,66,67,68,72,73,74,75,76,77,78,81,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,102,103,104,105,106,107,108,109,110,113,114,115,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,144,145,146,147,148,149,150,151,152,154,159,160,161,162,163,164,165,166,167,168],hbond:2,hcn:80,hcp:[29,30,139],he1:44,head:[2,6,47,88,99,121,125,168],header:[2,58,59,62,63,64,65,78,85,98,102,116,158],heat:2,heavili:[19,66],heavisid:85,hebenstreit:4,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159,160,161,162,163,164,165,166],infrequ:[2,74,114],infti:[111,136,137],ingtegr:102,inher:96,inherit:2,inhomogen:85,inidividu:96,init:152,init_fil:85,initi:[2,3,19,32,58,59,60,63,66,67,68,71,72,73,74,75,77,78,79,80,83,84,85,86,96,97,99,113,114,142,145,146,152,167],initial:2,initialt:85,inlclud:3,inner2:[106,124],inner:[4,58,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],inner_distance_cutoff:125,innner:133,inorgan:[2,163],inp:[153,163],input1:40,input2:40,input:[0,1],insert:[45,153,158],insid:[2,3,45,58,61,69,73,86,87],inside:[73,129],insight:2,instabl:[73,113],instal:[1,2,3,4,58,59,97,105,106,127,131,135,142,168],install:0,instanc:[2,3,121,149],instantan:[2,67,68,72,74,75,78,167],instanti:[2,3,60],instead:[1,2,3,4,19,29,34,40,46,58,62,64,65,66,68,73,104,105,116,126,128,135,139,142,144],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,59,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,159,160,161,162,163,164,165,166],instruction:3,insuffici:2,insult:74,insur:[2,3,30,45,58,59,85,86,87,108,122,150,167],integ:[2,3,29,38,40,42,45,46,49,50,53,56,58,59,62,67,72,73,78,80,85,92,114,115,139,153],integral:[77,145,146],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,72],intens:[1,2,33,34,35,37,39,40,41,44,62,63,64,65,66,67,74,75,85,167],intensiv:167,inter:[58,67,97,102],interact:[1,2,3,13,28,32,36,38,39,42,43,46,51,56,57,58,67,76,77,79,80,85,86,87,89,90,91,93,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,148,149,150,151,152,153,154,158,159,160,161,162,163,164,165,166,167],interatom:[45,58,83,84,98,102,116,118,139,142,152,161],intercept:41,interchang:2,interconvert:118,interesect:87,interest:[1,3,44,77,84,117,137],interf:168,interfac:0,interfer:[74,99],interg:2,interi:137,interior:[2,19,87],interlac:139,interleav:[2,45],intermedi:[2,59,76,94,97],intermolecular:99,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,43,47,59,60,70,71,74,75,80,88,89,93,94,96,115,120,145,146,155,167],internal:59,internal_element_set:60,internal_quadratur:60,internat:[4,41,44,60],interpenetr:139,interpentr:[155,156],interpol:[2,59,60,71,73,76,97,102,145,146,160],interpret:[2,3,56,59,64,123,154],interrupt:78,intersect:[2,41,87],intersert:87,interspers:96,interstiti:142,interv:[2,35,63,74,78,152],intestieti:41,intial:[2,99],intiial:19,intramolecular:13,introduc:[2,36,38,59,69,74,78,94,98,110,118,127,131,135,159],introduct:0,inv:[41,44],invalid:[33,97,136,137],invari:[38,42],invent:81,invers:[2,26,41,44,78,94,95,103,110,127,164,165],invert:[1,2],invis:87,invoc:67,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,40,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,65,66,67,68,69,72,73,74,75,76,81,82,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,140,144,147,148,150,151,153,154,159,160,161,162,163,164,165,166,167],involv:[2,40,73,96,97,101,122,159,160,162],ion:[2,85,102,111,119,121,139,142,152,162,166],ionic:[2,103,104,111,118,119,148,152],ioniz:[109,118],ipp:0,ir3:44,ir4:44,irregular:[2,19,66,68,74],irrelev:147,irrespect:[136,137],irrevers:80,isbn:165,isenthalp:74,ismail:[105,131],isn:[3,69],iso:[68,74,75],isobar:[74,115],isodem:118,isoenerget:115,isoenthalp:115,isol:123,isomorph:77,isotherm:[74,115],isotrop:[2,36,122,136,137],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,46,47,48,49,50,51,52,53,54,55,59,67,68,69,74,75,77,81,84,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,150,151,154,158,159,160,161,162,163,164,165,166,167],issue:60,item:[2,19,58,66],iter:[2,19,66,68,81,96,97,152,167],iterat:96,ith:[40,58,61,62,63,64,65,167],itself:[2,3,35,58,59,63,85,97,110,119,122,145,146],ityp:45,izumi:161,j0jt:35,j20:63,j_m:42,jackson:143,jacs:[2,46],janssen:76,januari:139,jaramillo:118,jcp:86,jeffer:4,jello:74,jeremi:141,jik:102,jmm:42,job:81,jochim:74,join:[2,29,123],joint:125,jon:29,jone:[1,2,21,22,32,46,60,69,86,87,96,99,101,104,105,106,107,108,113,122,124,125,126,127,128,129,131,132,134,135,138,143,149,150,151],jonsson:[30,97,152],jorgensen:[2,54,110,127,131],journal:[51,60,116,142,155,156],jpeg:59,jpg:[58,59],judici:2,jump:[2,18,75],jun:4,just:[2,3,13,35,43,58,59,62,85,97,99,101,149,168],justo:117,jusufi:[111,121],jut:87,k11:35,k22:35,k33:35,k_2:91,k_4:91,k_s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2,42,43,58,60,66,67,70,76,80,85,92,96,125,139,152,163,167],post:[0,2,35,58,60,78],pot:123,potentail:119,potenti:0,potentiel:135,potin:142,pour:[2,81],power:[3,4,37,42,102],pparam:32,ppm:[58,59],ppn:4,pppm:[0,1],pproni:72,pr3:44,pr4:44,practic:[68,74,163,168],prb:[160,162],prd:[2,97],pre:[2,79,86,102,123,145,146,152,154],prec:[4,152],preced:[2,46,61,62,63,64,65,80,97,102,125,167],preceed:[3,63,86],precis:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,58,62,65,68,69,74,75,81,88,89,90,92,93,94,95,96,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,142,144,147,148,150,151,152,154,159,160,161,162,163,164,165,166,167],predefin:[55,118],predict:[1,2],prefactor:[8,9,12,16,17,18,57,63,86,89,93,94,96,108,121,147,150,151,154,165],prefer:[79,99,168],prefix:[3,59,80],preliminari:[71,145,146],prematur:96,preprint:[42,153],prescrib:[2,60,62],presenc:[58,73,136,137,142,165],present:[1,4,59,72,73,87,109,118,126,135,142,150,152],preserv:[68,74,81],press:[2,4,13,32,43,68,74,75,113,139,162,165,167],pressur:[1,2],pressure_with_eviri:118,presum:[30,97],prevent:[2,56,94,96,97,114,155,156,158],previou:[0,2,3,62,64,65,66,96,102,123,125,139,145,146,167],previous:[3,40,45,58,61,62,63,64,65,81,85,86,123,167],price:[2,113],primari:[0,2,85],prime:[124,142,160,162],primit:[2,87],princip:152,principl:[2,3,118,142,159,168],print:[0,1,2,3,4,19,35,40,42,58,59,62,63,64,65,67,68,73,74,75,76,78,80,81,96,97,99,114,121,125,152,167],printfluid:73,prism:2,privileg:3,probab:154,probabl:[56,66,67,74,86,96,145,146],problem:[0,1,2,3,19,35,60,66,68,79,84,87,96,97,110,113,125,168],proc:[1,3,4,58],proce:[19,28,66,97,142,167],procedur:[2,19,66,74,75,83,84,96,97,99],proceed:142,procesor:19,process:1,processor:[1,2,3,4,19,45,58,59,60,62,66,67,68,72,73,74,77,81,85,97,114,152],processsor:[19,66],procp1:58,produc:[1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,39,40,43,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,64,65,66,67,72,74,75,78,80,81,85,86,88,89,90,92,93,94,95,96,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,147,148,149,150,151,154,159,160,161,162,163,164,165,166,167],product:[2,4,42,80,118,120,146],profil:[2,62,65,69,97],program:[2,3,4,58,59,73,116],progress:[1,19,66,78,96,97,167],project:[2,168],promot:102,prompt:3,proni:72,prop:2,propag:[74,78,118],propens:2,proper:[67,76,139,168],properli:[97,115],properti:0,proport:[2,19,32,66,78,80,123],propos:[2,42,68,74,127,141,161],protein:[4,45,82],proton:[162,166],prouduc:65,prove:[31,70,73],provid:[1,2,3,4,13,29,41,44,45,59,61,62,65,67,68,73,74,78,83,84,97,99,102,109,110,114,117,118,123,125,126,135,136,139,141,142,149,152,153,158,159,160,161,162,163,167,168],pscrozi:0,psec:74,pseudo:118,pseudopotenti:142,psf:2,psi:[119,165],psi_ij:119,pstart:[74,75],pstop:[74,75],pstyle:32,psxevar:4,pt2:44,pt4:44,ptarget:68,pthread:4,ptr:[2,3],pu3:44,pu4:44,pu6:44,publish:[73,110,139,142,160,162],pull:168,puls:85,pump:[136,137],purchas:59,pure:[3,140,141,160,162],purport:3,purpos:[2,41,44,45,58,65,67,68,76,77,79,105,131,142],push:[76,96,123,154,168],put:[2,3,45,58],pxx:[68,74,167],pxy:[2,167],pxz:[2,167],pydir:3,pyi:[68,74,167],pymol:3,pymol_aspher:0,pympi:3,pypar:3,python:[0,2],pythonpath:3,pyz:[2,167],pzz:[68,74,78,167],q_1:152,q_2:152,q_3:152,q_i:[119,135],q_j:135,qdist:[110,127,131,135],qeq:[2,109,110,152],qeqall:152,qeqallparallel:152,qfile:110,qinitmod:152,qoffload:4,qopenmp:4,qoverrid:4,qtb:78,quadrant:4,quadratur:[32,60],quadrupl:98,quadruplet:[57,88,89,90,91,93,94],qualiti:[59,99],quantic:152,quantit:[37,123],quantiti:1,quantum:[2,42,77,78,99,102,118,142,152],quantum_temperatur:78,quartic_spher:60,quartz:78,quasi:77,quaternion:[2,45,122],queri:[3,28],quest:2,question:[76,168],quick:[0,4],quickli:[36,66,96,97,99],quickmin:[96,97],quicktim:59,quit:[73,153,167],quot:139,quotat:152,r10:102,r12:122,r_1:42,r_2:42,r_c:[111,113,121,162],r_cut:[102,138],r_e:119,r_fu:[136,137],r_i:[13,42],r_ii:42,r_ij:[13,102,118,149,166],r_ik:149,r_j:13,r_jik:149,r_m:138,r_me:111,r_mh:121,r_min:112,r_ub:5,ra2:44,rad2theta:44,radial:[42,62,96,118,125,145,146],radian:[5,6,8,12,16,17,18,44,47,55,79,88,89,93,94],radiat:[41,44,85],radii:[42,67,108,116,122,123,136,137,142,165],radit:118,radiu:[2,33,34,41,42,58,59,73,82,86,87,102,108,118,119,123,127,135,136,137,138,139,152,153,162,165],rahman:[2,68,74,78],rai:44,ram:162,raman:4,ramp:[2,72,74,78,86,106,114,124,135,136,138,154,166],ran:[2,3],random:[2,45,59,67,72,73,74,77,78,85,114,115],randomli:45,rang:[1,2,4,38,39,40,42,43,44,51,58,59,60,96,99,100,102,103,104,105,106,107,108,110,111,112,113,114,116,118,120,122,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,142,143,144,148,149,150,151,152,158,162,164,165,166,167],rank:[2,3],rankin:75,rapid:[2,3],rapidli:[67,74,110,114],rare:2,rasmol:2,rasmussen:122,raster3d:2,rate:[2,4,60,78,80,83,84,120,136,13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135,136,139,140,142,144,147,148,150,151,152,153,154,159,160,161,162,163,164,165,166],respond:[2,118],respons:2,resquar:[2,122],rest:[2,79,102,137,139,167],restart1:77,restart2:77,restart2data:0,restart:[0,1],restor:[45,167],restrain:13,restraint:[79,126],restratin:79,restrict:[1,2],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,34,35,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,61,62,63,64,65,66,67,68,69,72,73,74,75,77,80,81,83,84,85,86,88,89,90,92,93,94,95,97,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,118,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,139,140,142,144,145,146,147,148,150,151,154,159,160,161,162,163,164,165,166],retain:[99,102,142],retriev:[2,140,141],rev:[2,29,36,38,42,43,74,75,83,84,102,108,109,110,113,116,117,118,122,123,129,136,137,138,139,141,145,146,149,150,153,159,160,161,162,163],revers:[2,32,50,67,74,76,83,97,135],review:[42,142,153,168],rewrap:58,rfac0:[42,153],rg0:82,rh3:44,rh4:44,rheolog:2,rhi:[145,146],rho0:[139,156,157],rho0_meam:139,rho:[73,98,103,104,105,116,138,139,140,141,145,146,150,155],rho_0:[156,157],rho_alpha_beta:116,rho_bkgd:139,rho_colloid:86,rho_e:85,rho_i:[140,141],rho_ref_meam:139,rho_wal:86,rhodopsin:[1,4],rhosum:[155,156,157],rhot:69,rhs:80,rick:[109,152],right:[2,3,19,29,45,55,57,66,67,73,76,80,110,168],rightmost:[19,66],rii:[33,34],rij:[36,38,76,114,115,145,146,158],rin:[125,132,133],ring:[2,46,77],rino:[30,163],rirj:123,risi:[42,153],risk:79,rix:[33,34],rk4:80,rkf45:80,rlo:[145,146],rmin0:[42,153],rmin:129,rms:80,rnemd:2,robust:96,rock:139,rockett:149,role:2,ronchetti:38,root:[3,32,33,34,116],rose:139,ross:139,rosski:77,rot:[2,35,77,79],rotat:[2,42,45,58,62,87,96,113,122,150,167],rotation:38,rough:[2,45,59],roughli:[19,59,74,97],round:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,74,75,81,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,113,114,116,117,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,144,145,146,147,148,150,151,154,159,160,161,162,163,164,165,166],rous:72,rout:[32,125,135],routin:[2,3,4,73,142],roux:2,row:[2,34,44,62,63,64,65,85,118],rozero:139,rrespa:[1,4,74,98,99,100,101,103,104,105,106,107,108,109,110,111,113,114,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],rsq:[145,146],rsurfac:85,ru3:44,ru4:44,rub:5,rubia:[140,141],rule:[0,2,13,29,45,63,67,74,87,98,100,101,107,108,113,125,130,139,143,154,158,159,160,162,166],run1:2,run2:2,run3:2,run4:2,run5:2,run6:2,run7:2,run8:2,run:[0,1],run_styl:[4,74,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,142,143,144,145,146,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166],rung:80,runtim:59,rutherford:85,rutuparna:[160,162],rxn:80,ryckaert:[81,94],rydberg:142,s0st:2,s2050:1,s2629:116,s319:60,s_i:[2,118],s_ij:2,saddl:97,sadigh:[116,140,141],saed_vtk:41,safe:[59,168],safran:165,sagui:113,sai:[1,168],said:96,sakai:161,sall:152,salt:[111,121,139],salter:152,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,35,36,37,38,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,65,66,67,68,69,72,73,74,75,76,77,78,79,81,83,84,85,87,88,89,90,92,93,94,95,97,98,99,100,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,143,144,147,148,149,150,151,152,154,158,159,160,161,162,163,164,165,166,167,168],sampl:[1,2,3,35,59,62,63,74,77,82,84,102],sample_frequ:60,sandia:[0,29,119,139],saniti:79,satellit:2,satisfi:[30,41,42,44,68,69,73,75,81,96,123],satur:111,save:[2,59,67,72,80,85,102],sb3:44,sb5:44,sc3:44,scalabl:[0,1,4],scale:[0,1,2,4,35,40,42,46,58,59,60,63,68,73,74,75,77,78,83,84,85,98,99,111,118,120,123,136,137,139,142,167],scalegamma:73,scalexi:[68,74,75],scalexz:[68,74,75],scaleyz:[68,74,75],scatter:[3,41,44],scatter_atom:3,scatter_coord:3,scenario:[2,67,87],schaik:135,schell:161,schemat:67,scheme:[2,72,74,77,81,85],schmid:114,schroding:118,schroeder:38,sci:[30,109,141,149,152],scienc:[60,67,76,83,116,140,152,161],scientif:[42,116],scm:3,scratch:[19,66],screen:[0,1,2,3,4,41,44,59,73,81,97,106,110,127,139,159,162,163,164,165,166,167],screenshot:3,scripe:3,script:[0,1],sea:3,search:[0,36,38,96,97,123],secant:71,second:[1,2,3,4,28,29,35,37,38,39,43,44,56,58,62,63,64,65,67,69,71,72,77,79,81,82,83,84,85,96,97,101,102,103,104,105,109,110,116,118,119,120,123,124,126,129,139,147,152,159,161,162,163,166,167],second_mo:152,secondari:51,section:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,31,32,33,34,35,37,39,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,62,63,64,65,66,67,69,70,71,72,73,74,75,76,77,78,80,81,83,84,85,88,89,90,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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute reduce 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 command","dump image command","fix atc command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/time command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","thermo_style command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,41,42,44,45,57,58,59,60,62,65,68,72,73,74,75,77,78,83,84,86,102,118,136,137,142,158,167],"long":[103,104,105,106,107,110,112,113,127,131,135,148,151],acceler:1,adiabat:2,adp:98,airebo:99,alloi:116,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:60,atom:[2,29,30,36,38,42,43,61],balanc:[19,66],barostat:2,bcc:76,beck:100,between:2,bodi:[2,101],bond:67,bond_styl:[20,21,22,23,24,25,26,27,28],bop:102,born:[103,112],box:[2,68],buck:[104,105,112,138],build:3,calcul:2,centro:29,charmm:[2,5,46,106,135],chunk:[2,34,62],class2:[6,20,47,88,107],cna:30,code:2,coeffici:2,colloid:[86,108,165],comb3:109,comb:109,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,core:2,correl:63,cosin:[7,8,9,10,11,12,48],cossq:89,coul:[103,104,105,106,107,110,111,112,124,127,131,135,148,151],coupl:2,create_atom:45,cubic:129,custom:58,cut:[25,104,107,110,113,118,121,127,128,135,143,148],cvff:90,data:2,deby:[110,127],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],diel:111,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,13,113],discuss:2,disp:2,distanc:91,document:0,dpd:[31,114,115],dreid:125,dreiding:2,drude:2,dsf:[110,127],dump:[2,58,59],eam:116,edip:117,eff:118,ehex:69,eim:119,elastic:2,energi:115,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167],exp6:120,exp:[11,48],expand:[22,130],extend:3,fcc:76,fdt:115,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87],fix_modifi:[60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],flow:2,fluid:73,flux:35,forc:2,fourier:[14,15,49,92],from:[2,3],gauss:121,gaybern:122,gener:[1,2],github:168,gld:72,global:2,gpu:[100,103,104,106,107,108,110,113,114,116,121,122,124,127,128,129,130,143,144,150,151,154,159,160,161,162,164,165,166],gran:123,granular:2,gromac:124,gyrat:[33,34],h5md:58,harmon:[16,23,24,25,50,52,86,93,147],hbond:125,heat:35,helix:51,hertz:123,hexord:36,histo:64,histori:123,hook:123,how:2,idealga:155,imag:[58,59],implicit:106,improper_styl:[88,89,90,91,92,93,94,95],indice:0,induc:2,info:[0,60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],input:2,install:3,integr:2,intel:[4,5,16,21,23,46,50,54,74,90,93,104,106,122,127,159,160],interfac:[2,3],jul:0,kspace_styl:2,lammps:[0,1,2,3,168],lennard:138,librari:[2,3],linear:[134,144],list:126,lj1043:86,lj126:86,lj93:86,lj96:128,local:2,lubric:136,lubricateu:137,luci:[145,146],mdf:138,meam:[139,140,141],measur:1,mgpt:142,mie:143,minim:[60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87,96],mod:[85,161],model:2,molfil:58,morri:157,mors:[26,99,125,144],movi:[58,59],mpi:3,msd:37,msm:[103,104,106,110,127],multi:[2,52,145,146],multipl:2,nb3b:147,neb:97,nemd:2,nharmon:53,non:2,nongauss:37,nonlinear:27,nph:74,nphug:75,npt:74,nvt:74,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,46,47,48,49,50,51,52,53,54,55,74,75,88,89,90,92,93,94,95,98,99,100,103,104,105,106,107,108,109,110,111,113,114,116,119,121,122,123,124,125,127,128,129,130,131,132,133,134,135,136,140,141,144,147,148,150,151,154,159,160,161,162,163,164,165,166],opl:54,opt:[106,116,127,131,144],optim:1,option:2,orient:76,orientord:38,orthogon:2,other:2,output:[2,60,61,62,63,64,65,66,68,69,73,74,75,76,78,79,81,82,83,84,85,86,87],overview:3,packag:[1,4],pair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\ No newline at end of file
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1,94],brennan:[31,65,110,140,141,153],brenner:94,brick:[19,61],brief:[1,2,69,94,97],briefli:[2,72,104,147,163],brilliantov:118,broadwel:4,broken:[28,29,69,97],brook:2,brown:[4,40,42],brownian:[2,37,131,132],brows:0,browser:57,bryantsev: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:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,62,64,65,66,67,68,69,70,71,72,73,75,76,78,79,80,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,29,68,71,106,134,137,147],bundl:[57,163],button:163,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:[2,32,59,60,162],c_ij:2,c_ijkl:2,c_k:67,c_my_stress:59,c_myang:60,c_mycentro:60,c_mychunk:[2,34],c_mycomput:60,c_mytemp:162,c_n_k:67,c_p:42,c_peratom:42,c_pi:97,c_prop:2,c_sigma:97,c_size:2,ca2:43,cach:4,cacul:76,calcforc:68,calclat:35,calcluat:[37,39,42,105],calcualt:[35,60],calcul:[0,1],caldwel:[2,45],calhoun:72,call:[1,2,3,4,72,94,103,160,163],callabl:3,callback:3,caltech:[2,113],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cannot:[1,2,3,4,19,28,57,59,60,61,62,63,67,69,73,80,81,82,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],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:[2,44,55,60,68,69,96],carefulli:[3,28],carlo:[2,62],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:[1,2,4,44,63,69,71,75,76,81,82,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,34,60],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:[2,60],cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:43,ce4:43,cell:[2,40,43,44,63,69,70,73,80,113,137,162],cella:[2,162],cellalpha:[2,162],cellb:[2,162],cellbeta:[2,162],cellc:[2,162],cellgamma:[2,162],center:[2,9,33,34,37,40,44,57,60,63,67,69,77,79,81,82,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:64,central:[29,36,38,41,71,76,77,86,137,142,158],centro:2,centroid:72,centrosymmetri:29,certain:[1,2,57,59,60,62],cfg:[2,57],cg_type:146,ch2:76,ch2lmp:[0,2],ch3:76,chain:[0,2,13,28,62,69,70,72,76,79,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,19,22,32,44,57,58,61,62,63,68,69,70,71,73,74,75,76,78,79,80,82,91,92,109,113,118,131,132,134,137,147,153,162,163],change_box:2,chapter:72,charact:[2,19,57,61,66,75,113,115,121,140,141,144,147],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],charmm:0,cheaper:[117,145],check:[2,3,19,35,61,74,76,79,91,92,121,162],checkout:163,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:[2,4,19,28,29,32,42,55,60,61,62,68,69,72,92,130],choos:[1,2,13,28,32,57,62,63,68,69,70],chose:[155,157],chosen:[2,41,44,50,57,63,67,68,69,70,72,110,113,118,121,124,146,155],chunk:0,chunkid:[34,60],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,cleanli:162,clear:[2,3],clebsch:41,click:[3,44,56,57,92,163],climb:92,clockwis:45,clone:163,close:[2,3,19,42,62,63,68,69,76,82,92,94,97,105,106,134,140,141,157,163],closer:[19,61,63,78,92],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:[2,34,44,60,103],colliex:43,collis:[68,118,161],colloid:2,color:[19,57,61,67,73],column:[2,29,34,36,38,41,42,43,59,60,73,80,94,116,120,162],colvar:0,com:[2,37,64,96,163],comand:62,combiant:106,combin:[2,3,18,32,55,57,58,64,69,72,82,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,13,63,69,78,79,154,155,157,158,162,163],comit:163,comm:[0,3,30,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,61],comm_world:3,command:[0,1],comment:[3,45,66,75,80,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,163],commit:163,commmand:2,common:[0,1,2,3,4,30,63,72,82,83,118,120,154,155,157],commonli:[2,9,37,38,57,90,119,124,148,155,157],commun:[1,2,3,4,19,57,61,63,68,69,80,110],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:[3,19,49,59,60,61,64,81,137],compens:[2,113],compil:[4,57,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,61,72,92,114],complex:[2,3,9,36,38,41,44,68,82,92,113,137],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,59,60,62,63,64,68,69,70,72,76,82,91,92,109,113,118,131,132,147,148,162],componenet:2,composit:[2,68,111],compound:[104,113,114,158],compres:60,compress:[2,57,60,70,73],compris:[82,115,145],compton:[40,43],comput:[0,1],computation:[2,80,97],compute_modifi:[62,63,69,70,162],compute_sa:40,compute_xrd:43,concav:82,concentr:[66,75,111,115,141],concept:[2,60],conceptu:[2,63,92,105,134],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:[1,2,4,57,63,72,91,92,94,97,112,134,137,154,155,157,158,162,163],conflict:163,conform:[2,62,63,74,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,32,44,68,92,98,99,105,109,113,120,122,143,146],connect:[2,32,62,76,92,106,118,153,157],conner:94,connor:94,consecut:[3,44,105,122,126],consequ:[1,2,80,121],conserv:[13,62,67,68,69,75,76,92,108,109,110,118,128,147],consid:[2,29,32,59,61,62,80,113,145,147,153,162],consider:2,consist:[2,3,39,44,50,60,67,69,70,73,74,75,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:58,constant:0,constantli:64,constitu:[2,81,82,103,145],constrain:[2,60,64,67,76,77,91,113],constraint:[19,39,42,60,61,64,76,77,81,91,132],construct:[2,28,29,30,36,38,40,41,43,63,69,74,75,82,108,137,153,154],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,145],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,60,61,66,68,71,73,75,80,82,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162,163],content:162,context:[2,4,160],contibut:29,contin:4,continu:[0,2,19,60,61,62,63,64,67,69,70,73,78,79,80,82,97,109,124,127,145,156,162],continuum:[2,58,80],contour_integr:58,contract:[63,69],contrain:76,contrast:[1,2,160],contrib:80,contribut:[2,29,32,33,34,35,39,41,42,59,60,63,68,76,91,92,109,111,113,131,132,137,147,162,163],control:[2,3,4,11,13,19,32,35,41,47,57,58,61,63,69,70,75,80,113,117,137,154,157],control_typ:58,convect:35,conveni:[2,13,148,163],convent:[13,49,54,56,74,111,113],converg:[2,19,57,61,62,63,70,73,74,76,91,92,104,105,122,147],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,coord1:60,coord2:60,coord3:60,coord:[2,3,36,38,71,81,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,62,63,64,69,71,76,77,79,80,91,92,93,94,96,112,147],coordn:60,coords:147,copi:[0,3,57,80,92,163],copper:161,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,45],corner:[2,57,82,163],corpor:4,corr:104,correct:[2,3,32,45,57,64,69,73,81,82,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:58,correctli:[3,69,76,82,92,107,132,137,163],correl:[2,35,36,41,60,67,72],correpond:66,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,60,63,64,66,68,69,70,71,72,75,76,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161,162],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,60,61,69,75,80,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,4],coul:[2,4,18,21,22,32,45,91],could:[2,3,19,32,34,39,57,60,61,73,80,81,82,91,94,116,120],coulomb:[2,42,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160,162],coulommb:2,count:[1,2,3,19,35,45,60,61,69,76,82,91,92,116,120,162],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:[1,4,162],cpuinfo:4,cpuremain:162,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,62,63,66,69,70,71,72,74,80,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162,163],create_atom:[2,19,35],create_box:[2,19,35,44,63,69,153,162],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,62,91],criterion:[19,44,61,62,91,92,104,113,118,147],critic:[2,24,25,80,91],cross:[4,33,57,59,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:73,crystal:[2,4,29,30,38,71,79,162],crystallin:[2,156],crystallogr:[40,43],crystallograph:162,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:[19,61],cubic:[38,68,71,111],cuda:1,cuh:97,cummul:[2,62,120,162],cumul:[2,60,69,70,92],current:[0,1,2,3,4,19,30,32,42,57,58,60,61,62,63,64,69,74,75,76,77,80,81,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162,163],curv:[2,44],curvatur:[117,145,161],custom:[0,2,3,33,34,35,42,57,59,60,62,63,69,70,73,91,94,116,120,162],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:[2,4,21,22,28,29,30,32,36,38,41,62,66,71,73,81,82,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:43,cvff:4,cwiggl:81,cyan:57,cycl:[69,70],cyclic:45,cylind:[57,60,82],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:[109,162],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:[2,4,163],decod:57,decompos:[32,148],decomposit:[58,72],decoupl:2,decreas:[4,62,64],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,41,60,65,70,81,97,103,110,113,144,148],defint:162,deform:[2,42,63,69,131,132],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,62,69,70,72,74,76,79,83,84,88,89,90,91,108,111,120,162],degress:60,delai:[2,162],delet:[28,60,62,69,153,163],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:[62,75,113],densiti:[2,19,41,44,58,60,61,68,80,81,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152,162],depart:0,departur:73,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,60,61,63,66,68,69,70,71,75,76,78,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161,162],dependend:2,deposit:[69,76],deprect:60,depth:[26,57,80,115,117,145],der:[32,103,104,130,160],deriv:[2,32,41,63,64,69,70,71,78,79,80,81,82,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:71,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,60,61,62,63,66,67,68,69,70,71,72,73,75,78,79,81,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,163],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,62,69,71,80,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,35,39,42,44,60,63,67,69,76,91,92,109,111,120,131,132,154,155,157,162],desktop:[2,57],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,60,61,62,63,64,67,68,69,70,73,76,79,80,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162,163],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,42,43,44,57,59,60,61,63,66,69,71,72,73,74,75,81,82,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,70,73,94,97,113,136,137,147,158],deviat:[70,71,116],devic:1,devin:104,devis:136,dfactor:57,dft:137,dhug:73,dhugoniot:73,dia:134,diag:75,diagnost:[4,62,75],diagon:[2,41,42,63,69],diagonalstyl:148,diagram:[19,40,43,56,61,72],diallo:120,diam:57,diamet:[2,44,57,103,117,118,124,145,160],diamond:[113,134],dick:2,did:[91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,60,61,62,63,64,67,68,69,71,72,73,76,77,78,79,80,81,82,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160,162],differenti:[1,2,13,75,105,144,156],difficult:[63,72,120],difficulti:[36,38,76],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,62,74,84,85,86,88,91,94,97,101,162],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:[63,69,70],dim:[44,134],dimens:[1,2,19,35,42,44,57,60,61,63,68,69,70,73,81,92,162],dimension:[36,39,40,41,43,60,80,92,144],dimensionless:[37,41,80,148,160],dimer:[2,134],dimstr:[19,61],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:[2,3,32,41,57,68,75,82,93,94,98,99,100,105,108,111,113,122,126,143,146,153,162],directori:[0,1,2,3,4,78,79,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,80,121],disadvantag:[2,61],disallow:69,discard:[19,61,82],discontinu:[91,128],discourag:134,discret:[2,57,68],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:[2,37,63,69,71,118],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:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,62,63,64,68,69,70,71,73,74,76,77,79,80,81,82,83],distinct:[2,145],distinguish:[2,41,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,41,56,61,67,68,69,93,97,105,111,112,114,134,135,136,142,144,145,154,155,156,157,158],distro:144,ditto:161,div:4,diverg:[79,94],divid:[2,4,19,35,39,42,56,60,61,71,91,92,114,147,158],divis:[2,55,68,97,130,162],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:[0,1,2,3,32,34,37,39,42,44,56,57,59,60,69,82,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162,163],docuement:145,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,60,61,62,63,64,66,67,68,69,80,81,82,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[44,94,104,112,154,155,156,157,158],dof:[39,60],dof_per_atom:60,dof_per_chunk:60,doi:[2,71],domain:[2,19,40,43,57,61,63,68,69,72,80,81,92],domin:[1,113],don:[0,4,82,134,147,163],done:[1,2,19,44,55,57,58,60,61,62,63,66,69,72,76,78,79,91,92,94,100,111,126,132,133,134,140,141,153,162,163],donor:120,dot:42,doti:[97,144],doubl:[1,2,3,4,32,45,82,97,114,119,137],dover:58,down:[2,3,63,113,147],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:[62,63,69,147],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:[3,63,69,71,92],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:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,62,63,67,68,69,70,71,74,78,79,80,81,82,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161,162],duffi:80,dullweb:69,dummi:[13,156],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,101],duplic:[19,61,71],durat:[56,60,80,118],dure:[2,4,19,32,45,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141,162],dvlo:160,dvx:2,dx_lb:68,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,61,62,65,67,69,70,72,73,74,78,79,80,91,92,109,110,113,131,132,152],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: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:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,72,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161,162],eacn:[19,61],eam:[0,93,105],eangl:162,earli:[19,60,61],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,ebond:162,ebt:46,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,40,43],ecoul:162,ecp:113,edg:[2,19,40,43,57,81,82],edge:81,edih:162,edit:[4,163],edition:4,edu:[3,111,131],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,59,60,62,63,64,67,69,70,71,72,73,74,76,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161,162],effici:[0,1,2,4,39,55,57,63,69,72,76,97,103,105,122,126,137,140,141,145],efficienc:4,efield:[76,91],eggebrecht:[105,147],ehex:2,eigenvalu:72,eimp:162,einstein:[2,79],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,61,62,63,64,68,69,70,71,75,76,82,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaplong:162,elaps:[81,149,162],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:[2,33,37,39,41,42,57,58,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158,162],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],elong:162,els:[57,59,60,69,80],elsewher:[134,162],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,emol:162,emphas:118,empir:[58,113],empiric:94,emploi:[64,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,62,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,134,147],encod:57,encompass:2,encount:38,encourag:[75,77],end:[1,2,3,4,19,46,57,62,64,67,69,74,75,80,92,109,111,117,133,137,145,148,149,162],endbondtors:46,energet:[62,94],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:[2,57,62,69,76,122],enforce2d:[2,91],eng:[3,104,136],engineer:[58,78,111],enginer:135,enhanc:[58,64],enlarg:57,enough:[44,61,73,81,82,105],enpub:111,ensembl:[2,32,35,69,72,73,109,147],ensight:2,ensur:[2,41,63,67,69,97,130,154,158],enter:[114,137,158],enthalpi:[75,111,162],entir:[0,2,3,19,31,39,40,42,43,44,60,61,62,64,67,69,70,71,72,75,77,80,108,126],entiti:2,entri:[40,66,73,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,57,71,93,97,104,112,113,144,155],eos:66,epair:[94,116,120,162],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:[2,3,19,28,32,35,42,44,57,61,63,67,68,70,71,72,73,74,75,78,79,80,81,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161,162],equat:[2,35,38,39,40,43,56,63,64,65,66,68,69,70,71,72,73,75,76,80,81,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[71,89],equilibr:[2,35,44,62,63,69,73,78,79,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,63,67,68,69,70,73,74,76,79,83,84,88,89,104,134,142,147],equilibrium_start:58,equival:[2,13,59,60,63,69,74,94,109,113,147,155,157,162],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:[0,1,2,3,11,47,57,59,60,63,64,66,69,75,80,81,82,91,105,122,145,153,155,157],erta:118,especi:[4,44,61,73,74],essenti:[3,11,47,94,105,122,157,162],essential:70,essex:13,establish:32,estim:[1,2,19,29,35,42,58,61,75,162],esub:134,eta:[2,68,69,73,112,114,117,144,156,158],eta_dot:69,eta_ij:144,eta_ji:114,etail:162,etap:69,etap_dot:69,etc:[1,2,3,4,28,33,34,35,42,44,57,58,59,60,67,69,80,82,91,92,111,112,130,132,137,154,155,157,158,162],etol:[91,92],etot0:73,etot:[2,42,73,162],eu2:43,eu3:43,euler:[75,91,92],eulerian:58,europhi:68,evalu:[3,32,35,41,44,45,57,58,59,60,67,75,81,91,137,140,141,144,147,162],evanseck:[2,5,45,101],evaul:91,evdwl:162,even:[2,4,19,29,55,59,60,61,63,64,69,80,81,82,91,92,96,113,114,118,145,158,162],evenli:[19,42,61,68],event:[2,69,80],eventu:2,ever:28,everaer:[103,117,145],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,64,68,69,70,71,73,75,76,80,92,109,130,147,162,163],everyth:163,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:[19,61,62,67,80],exactli:[2,19,35,44,61,67,73,109,111,118,131,140,141],examin:[2,62,75],exampl:[0,1],exce:[2,4,19,59,60,61,63,69,91],exceed:[19,61,69],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,60,61,63,69,70,72,76,80,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161,162],excess:113,exchang:[2,58,64,80,113],excit:113,excite:113,exclud:[2,4,39,41,60,91,118,131,132,153],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:[2,3,29,44,56,57,63,83,84,85,86,88,110,153,163],exit:[3,19,61,162],expans:[41,55],expect:[1,4,19,61,71,73,134,137],expens:[2,71,80],experi:[2,74,92,109],experienc:[2,4],expir:162,explain:[1,2,3,19,30,57,60,61,63,69,71,92,96,111,147,149,163],explan:[2,41,60,71],explanatori:[59,60],explic:138,explicit:[2,3,32,75,94,97,101,111,113,121,131,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,67,69,70,73,76,80,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,163],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:[2,41,44,63,71,75,80,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,64,69,70,71,74,78,79,80,81,82,117,134,137,145,148,162],extensiv:162,extent:[1,19,21,61,94],exterior:[2,82],extern:[32,57,63,67,68,69,70,80,91,135,136],extra:[2,3,4,19,22,39,40,42,43,44,61,69,73,91,108,118,134],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:[1,2,57,63,69,79,113,156],extrema:130,extreme:113,extrins:58,f_1:2,f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:73,f_harm:79,f_i:[13,144],f_id:[2,59,60,162],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:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,61,63,64,68,69,70,72,74,75,76,81,82,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154,162],fail:[3,63,91,92,107],fairli:[3,163],faken:30,fall:2,fals:147,famili:158,familiar:[0,3,163],fan:144,far:[2,61,63,69,71,74,81,84,88,92,162],farrel:[155,157],fashion:[2,19,44,61,69,70,73,79,80,81,92,131],fast:[2,4,73,75,131,132,137,162],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,61,69,70,76,78,80,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,80],fault:29,fava:117,favor:62,fcc:[2,29,30,35,38],fcold:64,fdt:[65,66,75],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,62,67,72,82,91,163],fecr:111,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:[1,2,3,59,60,64,69,76,91,92,94,147],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:[1,4,73,163],fij:108,file0:71,file1:[3,66,71],file2:[3,66],file:[0,1],filenam:[4,19,57,58,60,61,66,71,75,80,92,93,94,97,105,111,112,114,115,134,135,136,140,141,142,144,147,148,154,155,156,157,158,162],fill:[44,57,80,97,137,163],filter:58,finchham:[2,107],find:[0,2,3,4,30,32,62,63,66,71,74,91,92,105,122,126,134,140,141,147,163],fine:[4,79,163],finer:[41,44],finger:44,finish:[2,3,19,61],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,60,61,62,66,67,68,69,71,72,73,76,77,78,79,80,83,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,140,141,142,144,147,148,153,154,155,156,157,158,161,162,163],fischer:[2,5,45,101],fit:[2,74,94,97,134,140,141,156,163],five:[30,73,97,135],fix:[0,1],fix_flux:58,fix_heat:64,fix_id:[63,69,70,73],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:76,fix_shak:76,fixedpoint:[63,69],fixid:[57,58],fji:108,flag:[3,4,33,34,40,43,57,62,94,120,121,134,137,153,163],flag_buck:100,flag_coul:[100,108,126],flag_lj:[108,126],flagfld:[131,132],flaghi:[131,132],flaglog:[131,132],flagvf:[131,132],flat:[2,4,80,81],fld:[81,131,132],flexibl:[2,57,60,113,156,162],flip:[2,69],fluctuat:[2,32,63,67,68,69,70,71,79,80,89,110],fluid:[2,63],flux:2,flv:57,fly:[19,57,58,76,97,137,162],fmass:72,fmax:[91,162],fmsec:69,fno:4,fnorm:[91,162],fnve:64,focu:76,foil:[41,71,148],fold:[4,77],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,60,61,65,66,67,68,69,70,72,73,74,75,76,78,79,80,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163],foo:[3,57,75],foo_species:75,foot:2,forc:[0,1],forcefield:[74,120],forcegroup:68,ford:108,forgiv:69,fork:163,form:[2,28,32,33,34,36,41,42,59,60,67,74,75,80,81,82,83,86,89,92,94,97,110,111,113,116,120,121,133,134,136,137,140,141,142,143,144,145,147,148,149,155,156,157,160,162],formal:[2,35,67,69,72,147],format:[2,19,57,60,61,66,75,80,92,93,94,97,111,114,115,121,134,136,140,141,146,148,158,162],formation:66,former:[2,19,61,80,97],formul:[1,2,42,69,74,76,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,44,46,56,60,71,77,81,83,85,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,145,146,149,154,155,156,157,158,159,160,162],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,144],found:[2,30,62,64,68,105,108],four:[2,3,28,41,80,89,92,137],fourier:2,fourth:[2,4,37,74,101,115,142,147],fox:[2,40,45,152],fqq:108,fraction:[1,2,4,19,42,57,62,63,73,75,92,97,115,118,131,132],frame:[41,58,73,117],framer:57,framework:[93,148],frattl:64,free:[2,13,29,32,71,78,79,80,92,113,130,137,139,144,160],freedom:[2,39,60,62,69,70,72,76,79,91,108,162],freeli:[0,2,57],freez:2,frenkel:[2,64,79],frequenc:[2,4,72,73,75,109,113,147],frequent:[29,30,36,38,41,64],fri:73,friction:[2,73,80,118],from:[0,1],front:73,frontend:57,frozen:[2,39,67,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:76,fulfil:2,full:[1,2,4,35,57,64,68,71,75,97,111,113,114,117],fuller:91,fulli:[2,71,91,92,105,144,163],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,57,60,68,72,80,91,92,93,96,104,137,147],furthermor:[11,47,64,75,110,113],futur:[0,2,61,67,92,135,136],g_jik:144,g_p:80,ga3:43,gaa:97,gai:117,gain:4,galindo:138,gamma0:13,gamma:[2,13,68,73,109,110,112,117,134,138,150,151,152,154,155,157,158,162],gamma_:80,gamma_ijk:155,gamma_n:118,gamma_p:80,gamma_t:118,gammaa:138,gammafactor:68,gammar:138,gan:[144,154,155,157,158],gan_sw:144,gan_tersoff:144,gao:[2,5,45,101],gap:[131,132,148],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:106,gaussian:[2,35,37,67,72,74,109,113,116],gavhan:4,gaybern:[2,4,91],gd3:43,gdot:132,ge4:43,gec:[155,157],gen:69,gener:0,gentler:81,gentli:112,geom:2,geometr:[2,44,61,69,82,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,141,145,149,159,160,162],geometri:[2,9,19,44,61,63],gerber:130,germann:[70,124],germano:117,get:[0,1,2,3,4,19,35,41,44,57,59,61,63,82,92,105,158,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,63,69,109,110,113,118,121],gif:57,gifsicl:57,gillan:148,gingold:[150,151],git:163,give:[0,1,2,3,4,28,36,38,44,60,63,69,71,91,94,97,113,120,134,137,145,155,156,157],given:[2,3,4,11,38,41,42,47,56,60,63,64,67,68,69,70,71,72,73,74,75,76,77,80,81,82,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,161],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goddard:[2,9,90,113,120],goe:[28,41,44,64,91,108,112,119,124,127,149,161],gold:29,goldman:73,good:[1,2,4,19,30,40,43,61,69,76,92,93,103,111,137,158,162,163],gordan:41,gordon:2,got:163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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix ave/atom command","fix ave/chunk command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","thermo_style command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,40,41,43,44,56,57,58,60,63,67,68,69,70,72,73,78,79,81,97,113,131,132,137,153,162],"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:[2,29,30,36,38,41,42,59],balanc:[19,61],barostat:2,bcc:71,beck:95,between:2,bodi:[2,96],bond:62,bond_styl:[20,21,22,23,24,25,26,27,28],bop:97,born:[98,107],box:[2,63],buck:[99,100,107,133],build:3,calcul:2,centro:29,charmm:[2,5,45,101,130],chunk:[2,34,60],class2:[6,20,46,83,102],cna:30,code:2,coeffici:2,colloid:[81,103,160],comb3:104,comb:104,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,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:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],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:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],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:[58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],flow:2,fluid:68,flux:35,forc:2,fourier:[14,15,48,87],from:[2,3],gauss:116,gaybern:117,gener:[1,2],github:163,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,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:[0,58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],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],jul:0,kspace_styl:2,lammps:[0,1,2,3,163],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:[58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82,91],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:[2,58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],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:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],relax:63,replica:2,resquar:145,restart:[2,58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],restrain:74,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],rigid:2,ring:89,run:[2,3,58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],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:[58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],stop:[58,59,60,61,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:42,style:[1,2],summari:2,swap:62,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],system:2,tabl:[0,2,66,155],taitwat:[151,152],temperatur:2,tersoff:[155,156,157],test:3,thermal:2,thermo:2,thermo_styl:162,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,105,122,126,130],triclin:2,tstat:109,ttm:80,tutori:163,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,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_chunk.txt b/doc/src/fix_ave_chunk.txt
index 65cd27c2f2..796cf5e331 100644
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@@ -138,13 +138,13 @@ asterisk means all indices from 1 to n (inclusive).  A trailing
 asterisk means all indices from n to N (inclusive).  A middle asterisk
 means all indices from m to n (inclusive).
 
-Using a wildcard is the same as if the individual elements of the
-vector or columns of the array had been listed one by one.  E.g. these
-2 fix ave/chunk commands are equivalent, since the "compute
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 fix ave/chunk commands are
+equivalent, since the "compute
 property/atom"_compute_property/atom.html command creates, in this
 case, a per-atom array with 3 columns:
 
-compute myAng all property/atom 50 angmomx angmomy angmomz
+compute myAng all property/atom angmomx angmomy angmomz
 fix 1 all ave/chunk 100 1 100 cc1 c_myAng\[*\] file tmp.angmom
 fix 2 all ave/chunk 100 1 100 cc1 c_myAng\[1\] c_myAng\[2\] c_myAng\[3\] file tmp.angmom :pre