diff --git a/doc/html/_sources/min_style.txt b/doc/html/_sources/min_style.txt
index 310646f5b8..1a625a0f24 100644
--- a/doc/html/_sources/min_style.txt
+++ b/doc/html/_sources/min_style.txt
@@ -76,8 +76,8 @@ nudged elastic band (NEB) calculations via the :doc:`neb <neb>` command.
 
 .. note::
 
-   The *quickmin* and *fire* styles do not yet support the use of
-   the :doc:`fix box/relax <fix_box_relax>` command or minimizations
+   The *quickmin*\ , *fire*\ , and *hftn* styles do not yet support the
+   use of the :doc:`fix box/relax <fix_box_relax>` command or minimizations
    involving the electron radius in :doc:`eFF <pair_eff>` models.
 
 Restrictions
diff --git a/doc/html/min_style.html b/doc/html/min_style.html
index 1415ebe811..158cf94d45 100644
--- a/doc/html/min_style.html
+++ b/doc/html/min_style.html
@@ -190,8 +190,8 @@ would normally use for dynamics simulations.</p>
 </div>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">The <em>quickmin</em> and <em>fire</em> styles do not yet support the use of
-the <a class="reference internal" href="fix_box_relax.html"><span class="doc">fix box/relax</span></a> command or minimizations
+<p class="last">The <em>quickmin</em>, <em>fire</em>, and <em>hftn</em> styles do not yet support the
+use of the <a class="reference internal" href="fix_box_relax.html"><span class="doc">fix box/relax</span></a> command or minimizations
 involving the electron radius in <a class="reference internal" href="pair_eff.html"><span class="doc">eFF</span></a> models.</p>
 </div>
 </div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 8439732d0c..35037f48a1 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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1],commit:161,commmand:2,common:[0,1,2,3,4,30,61,71,81,82,117,119,153,154,156],commonli:[2,9,37,38,57,89,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,66,67,79,109],comp:[75,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,82,101],compat:[3,19,49,59,62,80,136],compens:[2,112],compil:[4,57,136],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,71,91,113],complex:[2,3,9,36,38,41,44,66,81,91,112,136],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,66,67,68,71,75,81,90,91,108,112,117,130,131,146,147],componenet:2,composit:[2,66,110],compound:[103,112,113,157],compress:[2,57,68,72],compris:[81,114,144],compton:[40,43],comput:[0,1],computation:[2,79,96],compute_modifi:[60,61,67,68],compute_sa:40,compute_xrd:43,concav:81,concentr:[64,74,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,65],concis:3,concurr:4,conden:[79,154,156],condens:[2,79,93,106,110,121,157],condit:[2,39,40,42,43,57,58,66,68,70,72,75,76,79,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,71,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,73,88,91,112],confus:157,conjuct:108,conjug:112,conjunct:[2,32,44,66,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,75,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,79,120],conserv:[13,60,65,66,67,69,74,75,91,107,108,109,117,127,146],consid:[2,29,32,59,60,79,112,144,146,152],consider:2,consist:[2,3,39,44,50,65,67,68,69,72,73,74,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146],consistent_fe_initi:58,constant:0,constantli:62,constitu:[2,80,81,102,144],constrain:[2,62,65,75,76,90,112],constraint:[19,39,42,59,62,75,76,80,90,131],construct:[2,28,29,30,36,38,40,41,43,61,67,73,74,81,107,136,152,153],constructor:3,consult:4,consum:1,contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,64,66,70,72,74,79,81,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161],context:[2,4,159],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,65,67,68,72,77,78,79,81,96,108,123,126,144,155],continuum:[2,58,79],contour_integr:58,contract:[61,67],contrain:75,contrast:[1,2,159],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,66,75,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61,67,68,74,79,112,116,136,153,156],control_typ:58,convect:35,conveni:[2,13,147,161],convent:[13,49,54,56,73,110,112],converg:[2,19,57,59,60,61,68,72,73,75,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,82,83,87,88,91,92,110,136,154,156,160],convex:81,cool:62,coord:[2,3,36,38,70,80,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,62,67,70,75,76,78,79,90,91,92,93,95,111,146],coords:146,copi:[0,3,57,79,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,81,161],corpor:4,corr:103,correct:[2,3,32,45,57,62,67,72,80,81,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,67,75,81,91,106,131,136,161],correl:[2,35,36,41,65,71],correpond:64,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,64,66,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,67,69,74,79,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,39,57,59,72,79,80,81,90,93,115,119],coulomb:[2,42,90,97,98,99,100,101,103,104,105,106,107,112,117,118,121,125,129,132,142,145,146,156,157,159],coulommb:2,count:[1,2,3,19,35,45,59,67,75,81,90,91,115,119],counterbal:62,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,65,73,80,130,148],cov:146,coval:[2,13,112,133,146],cover:[2,58,66,112],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,64,67,68,69,70,71,73,79,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161],create_atom:[2,19,35],create_box:[2,19,35,44,61,67,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,79,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,81],cubes:[19,59],cubic:[38,66,70,110],cuda:1,cuh:96,cummul:[2,60,119],cumul:[2,67,68,91],current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,67,73,74,75,76,79,80,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,67,68,72,90,93,115,119],cut:[1,2,4,19],cuthi:70,cutinn:[130,131],cutlo:70,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,64,70,72,80,81,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvff:4,cwiggl:80,cyan:57,cycl:[67,68],cyclic:45,cylind:[57,81],cylindr:2,cyrot:96,d3q15:66,d3q19:66,d_e:79,daan:78,damp:[2,67,68,72,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:132,davi:80,david:[154,156],daw:[110,143],dcd:[2,57,71],deactiv:129,debug:[2,3,40,43,44,71],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,71],decoupl:2,decreas:[4,60,62],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,63,64,66,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],definit:[2,41,63,68,80,96,102,109,112,143,147],deform:[2,42,61,67,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,67,68,71,73,75,78,82,83,87,88,89,90,107,110,119],delai:2,delet:[28,60,67,152,161],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:74,dellago:[2,62],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:64,demo:3,demonstr:[72,133],dendrim:119,denniston:66,denot:[40,62,104,118],dens:[60,74,112],densiti:[2,19,41,44,58,59,66,79,80,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,64,66,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],dependend:2,deposit:[67,75],depth:[26,57,79,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,67,68,70,77,78,79,80,81,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,64,65,66,67,68,70,71,72,74,77,78,80,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,67,70,79,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,65,67,75,90,91,108,110,119,130,131,153,154,156],desktop:[2,57],destabil:96,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,65,66,67,68,72,75,78,79,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161],detect:[36,91,103,119,120],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,64,67,70,71,72,73,74,80,81,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159],devan:145,devanathan:156,develop:[0,2,3,4,68,72,93,96,112,135,136,146,157],deviat:[68,70,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:72,dhugoniot:72,dia:133,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,67],diagonalstyl:147,diagram:[19,40,43,56,59,71],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,65,66,67,69,70,71,72,75,76,77,78,79,80,81,82,91,92,93,96,99,100,102,103,108,109,110,112,114,116,117,118,121,122,124,125,132,133,134,135,137,138,139,140,141,143,144,145,146,147,148,153,154,156,157,159],differenti:[1,2,13,74,104,143,155],difficult:[61,71,119],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:136,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,83,84,85,87,90,93,96,100],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:112,dij:75,dilat:[61,67,68],dim:[44,133],dimens:[1,2,19,35,42,44,57,59,61,66,67,68,72,80,91],dimension:[36,39,40,41,43,79,91,143],dimensionless:[37,41,79,147,159],dimer:[2,133],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:107,dir:[1,3,70,72,143],dirac:41,direc:143,direct:[2,4,13,29,38,40,41,43,44,45,57,66,68,70,72,77,78,79,80,81,90,91,108,109,117,131],directli:[2,3,32,41,57,66,74,81,92,93,97,98,99,104,107,110,112,121,125,142,145,152],directori:[0,1,2,3,4,77,78,91,92,93,96,103,104,110,111,113,129,133,134,135,136,141,143,146,147,153,154,155,156,157],disabl:[4,79,120],disadvantag:[2,59],disallow:67,discard:[19,59,81],discontinu:[90,127],discourag:133,discret:[2,57,66],discuss:[0,1],disk:[2,36],disloc:[29,136],disord:[29,136],disp:0,dispar:144,disperion:[107,125],dispers:[2,99,107,125,130,157],displac:[2,37,61,67,70,117],displai:[3,56,57],disregard:136,dissip:[2,31,63,65,77,78,108,109,117,130,131],dist:[2,35,71,73,152],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,62,66,67,68,70,72,73,75,76,78,79,80,81,82],distinct:[2,144],distinguish:[2,41,112],distort:92,distrbut:92,distribut:[0,2,3,19,32,41,56,59,65,66,67,92,96,104,110,111,113,133,134,135,141,143,144,153,154,155,156,157],distro:143,ditto:160,div:4,diverg:[78,93],divid:[2,4,19,35,39,42,56,59,70,90,91,113,146,157],divis:[2,55,66,96,129],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:[67,69],dlmp_intel_offload:4,dlopen:2,dlvo:[102,159],dm_lb:66,doc:[0,1,2,3,32,34,37,39,42,44,56,57,67,81,90,91,92,93,95,103,104,110,111,113,119,133,134,135,141,143,147,153,154,156,157,161],docuement:144,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,64,65,66,67,79,80,81,83,84,85,87,88,91,92,93,94,95,96,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,120,123,124,126,127,128,130,131,133,134,135,136,139,140,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],doesn:[44,93,103,111,153,154,155,156,157],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,66,67,71,79,80,91],domin:[1,112],don:[0,4,81,133,146,161],done:[1,2,19,44,55,57,58,59,60,61,64,67,71,75,77,78,90,91,93,99,110,125,131,132,133,139,140,152,161],donor:119,dot:42,doti:[96,143],doubl:[1,2,3,4,32,45,81,96,113,118,136],dover:58,down:[2,3,61,112,146],download:3,downsid:2,dpd:2,dpdtheta:[31,109],dpdtheta_i:[63,64],dr_ewald:40,drag:[2,35,67,68,76],dragforc:66,drai:[57,72],drain:90,dramat:[60,61,67,146],drautz:96,draw:57,drawn:[57,65],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[92,110,139,140],drift:[2,37,62,65],drive:[3,61,67,70,91],driven:[2,50],driver:2,drop:108,drsquar:37,drude:0,dt_collis:66,dt_lb:66,dt_md:66,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,65,66,67,68,70,73,77,78,79,80,81,90,91,105,108,109,110,115,116,130,131,143,144,145,152,154,156,159,160],duffi:79,dullweb:[67,69],dummi:[13,155],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,100],duplic:[19,59,70],durat:[56,79,117],dure:[2,4,19,32,45,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,90,91,108,129,136,138,139,140],dvlo:159,dvx:2,dx_lb:66,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,63,65,67,68,71,72,73,77,78,79,90,91,108,109,112,130,131,151],dynamo:[92,110,133],dyre:126,e28637:13,e_1:96,e_2:96,e_a:74,e_b:113,e_ee:112,e_hbond:119,e_i:[2,96,113],e_j:[2,96],e_k:96,e_ke:112,e_kl:2,e_lj:[93,107],e_n:96,e_ne:112,e_nn:112,e_pr:112,e_rebo:93,e_torsion:93,e_tot:136,e_vol:136,eaa:82,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,64,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160],eacn:[19,59],eam:[0,92,104],earli:[19,59],earlier:[91,117,133],earth:112,easi:[2,3,32,42,80],easier:[4,57],easili:[3,57,91],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:133,ec_ij:133,ec_jj:133,echo:[3,40,43],ecp:112,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,161],edition:4,edu:[3,110,130],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,62,65,67,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160],effici:[0,1,2,4,39,55,57,61,67,71,75,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[75,90],eggebrecht:[104,146],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,66,67,68,70,74,75,81,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156],ejtehadi:[102,116,144],elaps:[80,148],elast:[2,21,22,91,117,155],elastic:0,elba:13,electr:[2,58,113,160],electric:4,electrolyt:159,electron:[2,40,58,79,92,103,107,110,112,113,133,136,143,146,156,157,160],electron_integr:58,electron_temperatur:58,electron_unit:112,electroneg:[2,103,113,146],electroneg_compon:146,electrostat:[2,4,102,107,112,121,129,131,146,159],elem1:[113,133,147],elem2:[113,133,147],elem:146,element1:[92,110,146],element2:[92,110,146],element:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,65,75,77,78],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,67,79],elsewher:133,elt:133,emac:0,email:[0,3,113],emb:81,emb_lin_neg:133,embed:[3,13,79,92,110,113,129,133,134,135,143],embt:46,emphas:117,empir:[58,112],empiric:93,emploi:[62,155],empti:120,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],enclos:[2,133,146],encod:57,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,46,57,60,62,65,67,73,74,79,91,108,110,116,132,136,144,147,148],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,67,75,121],enforce2d:[2,90],eng:[3,103,135],engineer:[58,77,110],enginer:134,enhanc:[58,62],enlarg:57,enough:[44,59,72,80,81,104],enpub:110,ensembl:[2,32,35,67,69,71,72,108,146],ensight:2,ensur:[2,41,61,65,67,96,129,153,157],enter:[113,136,157],enthalpi:[74,110],entir:[0,2,3,19,31,39,40,42,43,44,59,60,62,65,67,68,70,71,74,76,79,107,125],entiti:2,entri:[40,64,72,96,111,133,139,140,141,147,153,154,155,156,157],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,70,92,96,103,111,112,143,154],eos:64,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,80,81,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,65,66,68,70,71,72,73,74,77,78,79,80,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160],equat:[2,35,38,39,40,43,56,61,62,63,64,66,67,68,70,71,72,74,75,79,80,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[70,88],equilibr:[2,35,44,60,61,67,72,77,78,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,65,66,67,68,72,73,75,78,82,83,87,88,103,133,141,146],equilibrium_start:58,equival:[2,13,61,67,73,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:77,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:80,error:[0,1,2,3,11,47,57,61,62,64,67,74,79,80,81,90,104,121,144,152,154,156],erta:117,especi:[4,44,59,72,73],essenti:[3,11,47,93,104,121,156],essential:68,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:133,eta:[2,66,67,72,111,113,116,143,155,157],eta_dot:67,eta_ij:143,eta_ji:113,etap:67,etap_dot:67,etc:[1,2,3,4,28,33,34,35,42,44,57,58,65,67,79,81,90,91,110,111,129,131,136,153,154,156,157],etol:[90,91],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,90,91],eulerian:58,europhi:66,evalu:[3,32,35,41,44,45,57,58,65,74,80,90,136,139,140,143,146],evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,62,67,79,80,81,90,91,95,112,113,117,144,157],evenli:[19,42,59,66],event:[2,67,79],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,66,67,68,70,72,74,75,79,91,108,129,146,161],everyth:161,everywher:123,eviri:112,evolut:[62,66,71],evolv:[66,71],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,65,79],exactli:[2,19,35,44,59,65,72,108,110,117,130,139,140],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,67,90],exceed:[19,59,67],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,67,68,69,71,75,79,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],excess:112,exchang:[2,58,62,79,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:67,execut:[1,2,3,57],exempl:146,exemplari:65,exemplifi:112,exert:[2,81],exhaust:58,exhibit:[36,62,67,112],exist:[2,3,29,44,56,57,61,82,83,84,85,87,109,152,161],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,70,72,133,136],expens:[2,70,79],experi:[2,73,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,67,70,91,95,110,146,148,161],explan:[2,41,70],explic:137,explicit:[2,3,32,74,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,65,67,68,69,72,75,79,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:71,explor:[40,43],expon:[74,110,114,116,119,129,137,145],exponenti:[32,74,114,143,153,157,160],expos:3,exposit:[58,108],express:[2,41,44,61,70,74,79,96,110,112,123,133,146,147],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,67,68,70,73,77,78,79,80,81,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,81],extern:[32,57,61,65,66,67,68,79,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,67,72,90,107,117,133],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,67,78,112,155],extrema:129,extreme:112,extrins:58,f_1:2,f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:72,f_harm:78,f_i:[13,143],f_id:2,f_ij:143,f_int:77,f_j:13,f_jj:35,f_k:143,f_langevin:79,f_max:72,f_r:[154,155,156],f_sigma:96,f_solid:78,f_ss:2,face:[2,80,81,116,133,144],facil:0,facilit:2,fact:[2,4,78,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,62,66,67,68,71,73,74,75,80,81,87,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153],fail:[3,61,90,91,106],fairli:[3,161],faken:30,fall:2,fals:146,famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,67,70,73,80,83,87,91],farrel:[154,156],fashion:[2,19,44,59,67,68,72,78,79,80,91,130],fast:[2,4,72,74,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,67,68,69,75,77,79,82,83,84,86,87,88,89,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,79],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcold:62,fdt:[63,64,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,65,71,81,90],fecr:110,feel:[70,81,91],fehlberg:74,felling:135,felt:81,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,62,67,75,90,91,93,146],fewer:[1,3,4],feynman:71,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:62,ficiti:152,fictiti:[2,71,73,104,121,125,152],field:0,fifth:[2,114,141],figshar:70,figur:[1,4,72,161],fij:107,file0:70,file1:[3,64,70],file2:[3,64],file:[0,1],filenam:[4,19,57,58,59,64,70,74,79,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157],fill:[44,57,79,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,64,70,73,90,91,104,121,125,133,139,140,146,161],fine:[4,78,161],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:110,fire:[90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,64,65,66,67,70,71,72,75,76,77,78,79,82,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161],fischer:[2,5,45,100],fit:[2,73,93,96,133,139,140,155,161],five:[30,72,96,134],fix:[0,1],fix_flux:58,fix_heat:62,fix_id:[61,67,68,72],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:75,fix_shak:75,fixedpoint:[61,67],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,79,80],fld:[80,130,131],flexibl:[2,57,112,155],flip:[2,67],fluctuat:[2,32,61,65,66,67,68,70,78,79,88,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,96,136],fmass:71,fmax:90,fmsec:67,fno:4,fnorm:90,fnve:62,focu:75,foil:[41,70,147],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,63,64,65,66,67,68,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],foo:[3,57,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,119],forcegroup:66,ford:107,forgiv:67,form:[2,28,32,33,34,36,41,42,65,73,74,79,80,81,82,85,88,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159],formal:[2,35,65,67,71,146],format:[2,19,57,59,64,74,79,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157],formation:64,former:[2,19,59,79,96],formul:[1,2,42,67,73,75,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,44,46,56,70,76,80,82,84,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,62,66,104,107],four:[2,3,28,41,79,88,91,136],fourier:2,fourth:[2,4,37,73,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,72,74,91,96,114,117,130,131],frame:[41,58,72,116],framer:57,framework:[92,147],frattl:62,free:[2,13,29,32,70,77,78,79,91,112,129,136,138,143,159],freedom:[2,39,60,67,68,71,75,78,90,107],freeli:[0,2,57],freez:2,frenkel:[2,62,78],frequenc:[2,4,71,72,74,108,112,146],frequent:[29,30,36,38,41,62],fri:72,friction:[2,72,79,117],from:[0,1],front:72,frontend:57,frozen:[2,39,65,115],fs2:[2,35],ftol:[90,91],fuction:104,fudg:75,fulfil:2,full:[1,2,4,35,57,62,66,70,74,96,110,112,113,116],fuller:90,fulli:[2,70,90,91,104,143,161],fulton:110,fumi:97,funcfl:110,fund:0,funrol:136,further:[2,37,57,66,71,79,90,91,92,95,103,136,146],furthermor:[11,47,62,74,109,112],futur:[0,2,59,65,91,134,135],g_jik:143,g_p:79,ga3:43,gaa:96,gai:116,gain:4,galindo:137,gamma0:13,gamma:[2,13,66,72,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:79,gamma_ijk:154,gamma_n:117,gamma_p:79,gamma_t:117,gammaa:137,gammafactor:66,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,65,71,73,108,112,115],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:67,gener:0,gentler:80,gentli:111,geom:2,geometr:[2,44,59,67,81,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159],geometri:[2,9,19,44,59,61],gerber:129,germann:[68,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,91,104,157,161],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,67,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,67,69,70,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,62,65,66,67,68,70,71,72,73,74,75,76,79,80,81,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gnu:0,gnuplot:3,goddard:[2,9,89,112,119],goe:[28,41,44,62,90,107,111,118,123,126,148,160],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,67,75,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],govern:66,gpa:93,gpl:0,gpt:136,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,69,75,82,83,84,86,87,88,89,92,93],grab:2,grad:2,gradient:[2,61,62,79,91,131,139,140],graft:60,grain:[2,13,18,28,44,50,64,70,74,114,118,136,140,145],gram:110,gran:[2,80,81],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[72,161],greater:[1,61,65,67,70,95,97,98,99],greatli:[40,62],green:[2,35,57,71,96,161],green_kubo:2,grest:[21,22,60,99,117,125],grid:[19,40,43,59,66,79],grigera:2,gromac:90,gromacs:[2,90,118],groot:108,ground:[2,31,63,112],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,91,146,157],group_id:3,grow:[2,67,70,74,117],growth:2,gsmooth_factor:133,guarante:44,guess:161,gui:[3,161],guid:[1,149,150,151],guidelin:1,gullet:133,gulp:2,gunnel:136,gunsteren:129,guo:[2,5,45,50,100],gyrat:2,gzip:[57,91],h12:116,h2o:[114,140],had:[2,3,60,61,65,67,68,79,108,117,152],hafskjold:[2,62],half:[1,2,4,19,57,59,67,79,80,81,96,102,112,136],halfwai:[19,57,161],halperin:36,halsei:117,halt:[19,59,62],halv:57,hamak:[80,81,102,144],hamilton:29,hamiltonian:[67,112],han:110,hand:[2,28,29,44,54,57,66,74,104,112],handl:[4,57,112,130,157],happen:2,hara:155,hard:[1,73,146],harden:148,harder:[80,81],hardi:58,hardwar:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,10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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 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27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,62,63,64,65,66,67,68,69,70,71,73,74,76,77,78,81,82,83,84,85,86,87,88,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],bulatov:[134,135],bulk:[2,29,66,69,105,133,136,146],bundl:[57,161],button:161,bypass:2,c11:133,c_0:[78,93,150,151],c_1:[40,43,65],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:78,c_flux:35,c_gauss:115,c_hb:119,c_i:64,c_id:[2,32],c_ij:2,c_ijkl:2,c_k:65,c_mychunk:[2,34],c_n_k:65,c_p:42,c_peratom:42,c_pi:96,c_prop:2,c_sigma:96,c_size:2,ca2:43,cach:4,cacul:74,calcforc:66,calclat:35,calcluat:[37,39,42,104],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:70,call:[1,2,3,4,70,93,102,159,161],callabl:3,callback:3,caltech:[2,112],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cannot:[1,2,3,4,19,28,57,59,60,61,65,67,71,78,79,80,90,91,98,99,101,110,116,118,121,125,127,129,142,144,145,152],canon:[67,70,77,136],cao1:70,cao2:70,cao:70,capabl:[3,4,93,101],capac:[63,78,149],capolungo:[40,43],captur:[2,93,99,112,117,125,133],carbid:104,carbon:[57,87,93,103,133],card:[4,32,119],care:[2,44,55,66,67,95],carefulli:[3,28],carlo:[2,60],caro:110,carri:[4,78,117],carrillo:4,cartesian:[2,92],cascad:78,cat:[4,57],cate:66,categori:[0,93],cation:[113,146],caus:[1,2,4,44,61,67,69,73,74,79,80,90,91,119,121,127,130,131],caution:1,cautious:93,caveat:93,cbecker:[92,110],cc1:[2,34],ccc:[111,153,154,156,157],ccflag:4,ccflags:4,ccm6:110,ccsi:[111,153,154,156,157],ccu:96,cd2:43,cdeam:110,cdll:3,cdof:2,cdte:96,cdte_bop:96,cdtese:96,cdzn:96,cdznte:96,ce3:43,ce4:43,ceas:89,cell:[2,40,43,44,61,67,68,71,78,112,136],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,65,67,75,77,79,80,81,95,111,112,116,117,130,131,133,134,135,153,154,155,156,157],centr:62,central:[29,36,38,41,69,74,75,84,136,141,157],centro:2,centroid:70,centrosymmetri:29,certain:[1,2,57,60],cfg:[2,57],cg_type:145,ch2:74,ch2lmp:[0,2],ch3:74,chain:[0,2,13,28,60,67,68,70,74,77,87,107,108,152],challeng:2,champaign:130,chan:136,chandler:[92,110],chandrasekhar:[2,121],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,66,67,68,69,71,72,73,74,76,77,78,80,90,91,108,112,117,130,131,133,136,146,152],change_box:2,chapter:70,charact:[2,19,57,59,64,73,112,114,120,139,140,143,146],character:[2,29,38,41,147],characterist:76,charg:[1,2,3,32,40,43,44,97,98,103,104,106,107,110,112,113,121,125,129,142,146,156,157,159,160],charmm:0,cheaper:[116,144],check:[2,3,19,35,59,72,74,77,90,91,120],checkout:161,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,62,65,66,67,70,71,76,77,79,81,87,88,89,91,93,97,100,101,103,104,105,107,108,109,112,115,116,118,119,121,125,126,129,133,137,139,140,142,146,152],chemic:[31,40,43,58,114,140],chemistri:[71,93,96,112],chen:78,cheng:103,chi:[69,113,116],chiral:87,chmod:3,cho:133,choic:[2,4,19,28,29,32,42,55,59,60,66,67,70,89,91,129],choos:[1,2,13,28,32,57,60,61,66,67,68,89],chose:[154,156],chosen:[2,41,44,50,57,61,65,66,67,68,70,89,109,112,117,120,123,145,154],chunk:0,chunkid:34,ciccotti:74,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,66],cite:146,cl1:43,clarendon:[13,107],clarifi:[154,156],clark:142,classic:[0,2,4,70,71,78,88,112],classifi:157,clean:2,clear:[2,3],clebsch:41,click:[3,44,56,57,91,161],climb:91,clockwis:45,clone:161,close:[2,3,19,42,60,61,66,67,74,80,89,91,93,96,104,105,133,139,140,156,161],closer:[19,59,61,76,91],closest:[69,116,144,152],cloud:146,cluster:[2,4,42,62,74],cmax:133,cmd:[3,70],cmdarg:3,cmin:133,cmm:[18,145],cna:29,co2:[43,73,74,114],coars:[13,18,28,50,64,73,114,118,140,145],coarsest:41,code:[0,1],coeff:[6,45,46,55,81,120,148],coeffici:0,coefficienct:108,coefficient0:110,coefficient1:110,coeffieci:[2,94],coeffincientn:110,coexist:112,cohes:[2,113,133],coincid:[80,100,130,131],cold:2,coleman:[40,43],collect:[2,34,44,102],colliex:43,collis:[66,117,160],colloid:2,color:[19,57,59,65,71],column:[2,29,34,36,38,41,42,43,71,78,93,115,119],colvar:0,com:[2,37,62,95,161],comand:60,combiant:105,combin:[2,3,18,32,55,57,58,62,67,70,80,81,89,102,104,105,109,112,113,114,128,129,147,153,154,156,157,159],come:[0,2,13,61,67,76,77,153,154,156,157,161],comit:161,comm:[0,3,30,91,108],comm_modifi:[2,96,102,108,112,117],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,64,73,78,91,92,110,111,113,114,120,133,139,140,141,146,147,153,154,155,156,157,161],commit:161,commmand:2,common:[0,1,2,3,4,30,61,70,80,81,117,119,153,154,156],commonli:[2,9,37,38,57,88,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,66,67,78,109],comp:[74,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,81,101],compat:[3,19,49,59,62,79,136],compens:[2,112],compil:[4,57,136],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,70,91,113],complex:[2,3,9,36,38,41,44,66,80,91,112,136],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,66,67,68,70,74,80,89,90,91,108,112,117,130,131,146,147],componenet:2,composit:[2,66,110],compound:[103,112,113,157],compress:[2,57,68,71],compris:[80,114,144],compton:[40,43],comput:[0,1],computation:[2,78,96],compute_modifi:[60,61,67,68],compute_sa:40,compute_xrd:43,concav:80,concentr:[64,73,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,65],concis:3,concurr:4,conden:[78,154,156],condens:[2,78,93,106,110,121,157],condit:[2,39,40,42,43,57,58,66,68,69,71,74,75,78,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,70,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,72,87,91,112],confus:157,conjuct:108,conjug:[89,112],conjunct:[2,32,44,66,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,74,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,78,120],conserv:[13,60,65,66,67,73,74,91,107,108,109,117,127,146],consid:[2,29,32,59,60,78,112,144,146,152],consider:2,consist:[2,3,39,44,50,65,67,68,71,72,73,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146],consistent_fe_initi:58,constant:0,constantli:62,constitu:[2,79,80,102,144],constrain:[2,62,65,74,75,90,112],constraint:[19,39,42,59,62,74,75,79,90,131],construct:[2,28,29,30,36,38,40,41,43,61,67,72,73,80,107,136,152,153],constructor:3,consult:4,consum:1,contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,64,66,69,71,73,78,80,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161],context:[2,4,89,159],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,65,67,68,71,76,77,78,80,96,108,123,126,144,155],continuum:[2,58,78],contour_integr:58,contract:[61,67],contrain:74,contrast:[1,2,159],contrib:78,contribut:[2,29,32,33,34,35,39,41,42,61,66,74,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61,67,68,73,78,112,116,136,153,156],control_typ:58,convect:35,conveni:[2,13,147,161],convent:[13,49,54,56,72,110,112],converg:[2,19,57,59,60,61,68,71,72,74,89,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,81,82,86,87,91,92,110,136,154,156,160],convex:80,cool:62,coord:[2,3,36,38,69,79,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,62,67,69,74,75,77,78,90,91,92,93,95,111,146],coords:146,copi:[0,3,57,78,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,80,161],corpor:4,corr:103,correct:[2,3,32,45,57,62,67,71,79,80,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,67,74,80,91,106,131,136,161],correl:[2,35,36,41,65,70],correpond:64,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,64,66,67,68,69,70,73,74,79,80,81,82,83,85,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,67,73,78,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,39,57,59,71,78,79,80,90,93,115,119],coulomb:[2,42,90,97,98,99,100,101,103,104,105,106,107,112,117,118,121,125,129,132,142,145,146,156,157,159],coulommb:2,count:[1,2,3,19,35,45,59,67,74,80,90,91,115,119],counterbal:62,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,65,72,79,130,148],cov:146,coval:[2,13,112,133,146],cover:[2,58,66,112],cpp:[1,2,3,32,74],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,64,67,68,69,70,72,78,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161],create_atom:[2,19,35],create_box:[2,19,35,44,61,67,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,78,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:71,crystal:[2,4,29,30,38,69,77],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,80],cubes:[19,59],cubic:[38,66,69,110],cuda:1,cuh:96,cummul:[2,60,119],cumul:[2,67,68,91],current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,67,72,73,74,75,78,79,89,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,67,68,71,90,93,115,119],cut:[1,2,4,19],cuthi:69,cutinn:[130,131],cutlo:69,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,64,69,71,79,80,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvff:4,cwiggl:79,cyan:57,cycl:[67,68],cyclic:45,cylind:[57,80],cylindr:2,cyrot:96,d3q15:66,d3q19:66,d_e:78,daan:77,damp:[2,67,68,71,89,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:132,davi:79,david:[154,156],daw:[110,143],dcd:[2,57,70],deactiv:129,debug:[2,3,40,43,44,70],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,70],decoupl:2,decreas:[4,60,62],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,63,64,66,67,68,69,70,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],definit:[2,41,63,68,79,96,102,109,112,143,147],deform:[2,42,61,67,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,67,68,70,72,74,77,81,82,86,87,88,90,107,110,119],delai:2,delet:[28,60,67,152,161],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:73,dellago:[2,62],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:64,demo:3,demonstr:[71,133],dendrim:119,denniston:66,denot:[40,62,104,118],dens:[60,73,112],densiti:[2,19,41,44,58,59,66,78,79,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:71,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,64,66,67,68,69,73,74,76,78,79,80,81,82,83,85,86,87,88,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],dependend:2,deposit:[67,74],depth:[26,57,78,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,67,68,69,76,77,78,79,80,89,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:69,descent:89,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,64,65,66,67,68,69,70,71,73,76,77,79,89,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,67,69,78,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,65,67,74,90,91,108,110,119,130,131,153,154,156],desktop:[2,57],destabil:96,destre:87,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,65,66,67,68,71,74,77,78,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161],detect:[36,91,103,119,120],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,64,67,69,70,71,72,73,79,80,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159],devan:145,devanathan:156,develop:[0,2,3,4,68,71,93,96,112,135,136,146,157],deviat:[68,69,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:71,dhugoniot:71,dia:133,diag:73,diagnost:[4,60,73],diagon:[2,41,42,61,67],diagonalstyl:147,diagram:[19,40,43,56,59,70],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,65,66,67,69,70,71,74,75,76,77,78,79,80,81,89,91,92,93,96,99,100,102,103,108,109,110,112,114,116,117,118,121,122,124,125,132,133,134,135,137,138,139,140,141,143,144,145,146,147,148,153,154,156,157,159],differenti:[1,2,13,73,104,143,155],difficult:[61,70,119],difficulti:[36,38,74],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:136,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,72,82,83,84,86,90,93,96,100],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:112,dij:74,dilat:[61,67,68],dim:[44,133],dimens:[1,2,19,35,42,44,57,59,61,66,67,68,71,79,91],dimension:[36,39,40,41,43,78,91,143],dimensionless:[37,41,78,147,159],dimer:[2,133],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:107,dir:[1,3,69,71,143],dirac:41,direc:143,direct:[2,4,13,29,38,40,41,43,44,45,57,66,68,69,71,76,77,78,79,80,89,90,91,108,109,117,131],directli:[2,3,32,41,57,66,73,80,89,92,93,97,98,99,104,107,110,112,121,125,142,145,152],directori:[0,1,2,3,4,76,77,91,92,93,96,103,104,110,111,113,129,133,134,135,136,141,143,146,147,153,154,155,156,157],disabl:[4,78,120],disadvantag:[2,59],disallow:67,discard:[19,59,80],discontinu:[90,127],discourag:133,discret:[2,57,66],discuss:[0,1],disk:[2,36],disloc:[29,136],disord:[29,136],disp:0,dispar:144,disperion:[107,125],dispers:[2,99,107,125,130,157],displac:[2,37,61,67,69,117],displai:[3,56,57],disregard:136,dissip:[2,31,63,65,76,77,108,109,117,130,131],dist:[2,35,70,72,152],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,62,66,67,68,69,71,72,74,75,77,78,79,80,81],distinct:[2,144],distinguish:[2,41,112],distort:92,distrbut:92,distribut:[0,2,3,19,32,41,56,59,65,66,67,92,96,104,110,111,113,133,134,135,141,143,144,153,154,155,156,157],distro:143,ditto:160,div:4,diverg:[77,93],divid:[2,4,19,35,39,42,56,59,69,90,91,113,146,157],divis:[2,55,66,96,129],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:67,dlmp_intel_offload:4,dlopen:2,dlvo:[102,159],dm_lb:66,doc:[0,1,2,3,32,34,37,39,42,44,56,57,67,80,90,91,92,93,95,103,104,110,111,113,119,133,134,135,141,143,147,153,154,156,157,161],docuement:144,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,64,65,66,67,78,79,80,82,83,84,86,87,91,92,93,94,95,96,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,120,123,124,126,127,128,130,131,133,134,135,136,139,140,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],doesn:[44,93,103,111,153,154,155,156,157],dof:39,doi:[2,69],domain:[2,19,40,43,57,59,61,66,67,70,78,79,91],domin:[1,112],don:[0,4,80,133,146,161],done:[1,2,19,44,55,57,58,59,60,61,64,67,70,74,76,77,90,91,93,99,110,125,131,132,133,139,140,152,161],donor:119,dot:42,doti:[96,143],doubl:[1,2,3,4,32,45,80,96,113,118,136],dover:58,down:[2,3,61,112,146],downhil:89,download:3,downsid:2,dpd:2,dpdtheta:[31,109],dpdtheta_i:[63,64],dr_ewald:40,drag:[2,35,67,68,75],dragforc:66,drai:[57,71],drain:90,dramat:[60,61,67,146],drautz:96,draw:57,drawn:[57,65],drayleigh:71,dreid:2,dreiding:0,drfourth:37,drho:[92,110,139,140],drift:[2,37,62,65],drive:[3,61,67,69,91],driven:[2,50],driver:2,drop:108,drsquar:37,drude:0,dt_collis:66,dt_lb:66,dt_md:66,dtqm:71,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,65,66,67,68,69,72,76,77,78,79,80,90,91,105,108,109,110,115,116,130,131,143,144,145,152,154,156,159,160],duffi:78,dullweb:67,dummi:[13,155],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,100],duplic:[19,59,69],durat:[56,78,117],dure:[2,4,19,32,45,58,59,60,61,62,64,65,66,67,68,69,70,71,72,74,75,76,77,78,79,80,90,91,108,129,136,138,139,140],dvlo:159,dvx:2,dx_lb:66,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,63,65,67,68,70,71,72,76,77,78,89,90,91,108,109,112,130,131,151],dynamo:[92,110,133],dyre:126,e28637:13,e_1:96,e_2:96,e_a:73,e_b:113,e_ee:112,e_hbond:119,e_i:[2,96,113],e_j:[2,96],e_k:96,e_ke:112,e_kl:2,e_lj:[93,107],e_n:96,e_ne:112,e_nn:112,e_pr:112,e_rebo:93,e_torsion:93,e_tot:136,e_vol:136,eaa:81,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,64,65,66,67,68,69,70,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160],eacn:[19,59],eam:[0,92,104],earli:[19,59],earlier:[91,117,133],earth:112,easi:[2,3,32,42,79],easier:[4,57],easili:[3,57,91],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:133,ec_ij:133,ec_jj:133,echo:[3,40,43],ecp:112,edg:[2,19,40,43,57,79,80],edge:79,edit:[4,161],edition:4,edu:[3,110,130],eebt:46,eff:[0,89],effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,62,65,67,68,69,70,71,72,74,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160],effici:[0,1,2,4,39,55,57,61,67,70,74,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[74,90],eggebrecht:[104,146],ehex:2,eigenvalu:70,einstein:[2,77],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,66,67,68,69,73,74,80,89,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156],ejtehadi:[102,116,144],elaps:[79,148],elast:[2,21,22,89,91,117,155],elastic:0,elba:13,electr:[2,58,113,160],electric:4,electrolyt:159,electron:[2,40,58,78,89,92,103,107,110,112,113,133,136,143,146,156,157,160],electron_integr:58,electron_temperatur:58,electron_unit:112,electroneg:[2,103,113,146],electroneg_compon:146,electrostat:[2,4,102,107,112,121,129,131,146,159],elem1:[113,133,147],elem2:[113,133,147],elem:146,element1:[92,110,146],element2:[92,110,146],element:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,65,74,76,77],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,67,78],elsewher:133,elt:133,emac:0,email:[0,3,113],emb:80,emb_lin_neg:133,embed:[3,13,78,92,110,113,129,133,134,135,143],embt:46,emphas:117,empir:[58,112],empiric:93,emploi:[62,155],empti:120,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,83,85,86,87,88,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],enclos:[2,133,146],encod:57,encompass:2,encount:38,encourag:[73,75],end:[1,2,3,4,19,46,57,60,62,65,67,72,73,78,91,108,110,116,132,136,144,147,148],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,67,74,121],enforce2d:[2,90],eng:[3,103,135],engineer:[58,76,110],enginer:134,enhanc:[58,62],enlarg:57,enough:[44,59,71,79,80,104],enpub:110,ensembl:[2,32,35,67,70,71,108,146],ensight:2,ensur:[2,41,61,65,67,96,129,153,157],enter:[113,136,157],enthalpi:[73,110],entir:[0,2,3,19,31,39,40,42,43,44,59,60,62,65,67,68,69,70,73,75,78,107,125],entiti:2,entri:[40,64,71,96,111,133,139,140,141,147,153,154,155,156,157],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,69,92,96,103,111,112,143,154],eos:64,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,79,80,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,65,66,68,69,70,71,72,73,76,77,78,79,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160],equat:[2,35,38,39,40,43,56,61,62,63,64,66,67,68,69,70,71,73,74,78,79,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[69,87],equilibr:[2,35,44,60,61,67,71,76,77,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,65,66,67,68,71,72,74,77,81,82,86,87,103,133,141,146],equilibrium_start:58,equival:[2,13,61,67,72,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:76,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:79,error:[0,1,2,3,11,47,57,61,62,64,67,73,78,79,80,90,104,121,144,152,154,156],erta:117,especi:[4,44,59,71,72],essenti:[3,11,47,93,104,121,156],essential:68,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,73],esub:133,eta:[2,66,67,71,111,113,116,143,155,157],eta_dot:67,eta_ij:143,eta_ji:113,etap:67,etap_dot:67,etc:[1,2,3,4,28,33,34,35,42,44,57,58,65,67,78,80,90,91,110,111,129,131,136,153,154,156,157],etol:[90,91],etot0:71,etot:[2,42,71],eu2:43,eu3:43,euler:[73,90,91],eulerian:58,europhi:66,evalu:[3,32,35,41,44,45,57,58,65,73,79,90,136,139,140,143,146],evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,62,67,78,79,80,90,91,95,112,113,117,144,157],evenli:[19,42,59,66],event:[2,67,78],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,66,67,68,69,71,73,74,78,91,108,129,146,161],everyth:161,everywher:123,eviri:112,evolut:[62,66,70],evolv:[66,70],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,65,78],exactli:[2,19,35,44,59,65,71,108,110,117,130,139,140],examin:[2,60,73],exampl:[0,1],exce:[2,4,19,59,61,67,90],exceed:[19,59,67],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,67,68,70,74,78,81,82,83,85,86,87,88,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],excess:112,exchang:[2,58,62,78,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:67,execut:[1,2,3,57],exempl:146,exemplari:65,exemplifi:112,exert:[2,80],exhaust:58,exhibit:[36,62,67,89,112],exist:[2,3,29,44,56,57,61,81,82,83,84,86,109,152,161],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,69,71,133,136],expens:[2,69,78],experi:[2,72,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,67,69,91,95,110,146,148,161],explan:[2,41,69],explic:137,explicit:[2,3,32,73,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,65,67,68,71,74,78,81,82,83,85,86,87,88,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:70,explor:[40,43],expon:[73,110,114,116,119,129,137,145],exponenti:[32,73,114,143,153,157,160],expos:3,exposit:[58,108],express:[2,41,44,61,69,73,78,96,110,112,123,133,146,147],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,67,68,69,72,76,77,78,79,80,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,80],extern:[32,57,61,65,66,67,68,78,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,67,71,90,107,117,133],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,67,77,112,155],extrema:129,extreme:112,extrins:58,f_1:2,f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:71,f_harm:77,f_i:[13,143],f_id:2,f_ij:143,f_int:76,f_j:13,f_jj:35,f_k:143,f_langevin:78,f_max:71,f_r:[154,155,156],f_sigma:96,f_solid:77,f_ss:2,face:[2,79,80,116,133,144],facil:0,facilit:2,fact:[2,4,77,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,62,66,67,68,70,72,73,74,79,80,86,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153],fail:[3,61,90,91,106],fairli:[3,161],faken:30,fall:2,fals:146,famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,67,69,72,79,82,86,91],farrel:[154,156],fashion:[2,19,44,59,67,68,71,77,78,79,91,130],fast:[2,4,71,73,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,67,68,74,76,78,81,82,83,85,86,87,88,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,78],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcold:62,fdt:[63,64,73],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,65,70,80,90],fecr:110,feel:[69,80,91],fehlberg:73,felling:135,felt:80,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,62,67,74,90,91,93,146],fewer:[1,3,4],feynman:70,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:62,ficiti:152,fictiti:[2,70,72,104,121,125,152],field:0,fifth:[2,114,141],figshar:69,figur:[1,4,71,161],fij:107,file0:69,file1:[3,64,69],file2:[3,64],file:[0,1],filenam:[4,19,57,58,59,64,69,73,78,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157],fill:[44,57,78,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,64,69,72,90,91,104,121,125,133,139,140,146,161],fine:[4,77,161],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:110,fire:[89,90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,64,65,66,67,69,70,71,74,75,76,77,78,81,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161],fischer:[2,5,45,100],fit:[2,72,93,96,133,139,140,155,161],five:[30,71,96,134],fix:[0,1],fix_flux:58,fix_heat:62,fix_id:[61,67,68,71],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:74,fix_shak:74,fixedpoint:[61,67],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,78,79],fld:[79,130,131],flexibl:[2,57,112,155],flip:[2,67],fluctuat:[2,32,61,65,66,67,68,69,77,78,87,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,74,96,136],fmass:70,fmax:90,fmsec:67,fno:4,fnorm:90,fnve:62,focu:74,foil:[41,69,147],fold:[4,75],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,63,64,65,66,67,68,70,71,72,73,74,76,77,78,82,83,84,85,86,87,88,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],foo:[3,57,73],foo_species:73,foot:2,forc:[0,1],forcefield:[72,119],forcegroup:66,ford:107,forgiv:67,form:[2,28,32,33,34,36,41,42,65,72,73,78,79,80,81,84,87,89,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159],formal:[2,35,65,67,70,146],format:[2,19,57,59,64,73,78,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157],formation:64,former:[2,19,59,78,96],formul:[1,2,42,67,72,74,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,44,46,56,69,75,79,81,83,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,62,66,104,107],four:[2,3,28,41,78,87,91,136],fourier:2,fourth:[2,4,37,72,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,71,73,91,96,114,117,130,131],frame:[41,58,71,116],framer:57,framework:[92,147],frattl:62,free:[2,13,29,32,69,76,77,78,89,91,112,129,136,138,143,159],freedom:[2,39,60,67,68,70,74,77,90,107],freeli:[0,2,57],freez:2,frenkel:[2,62,77],frequenc:[2,4,70,71,73,108,112,146],frequent:[29,30,36,38,41,62],fri:71,friction:[2,71,78,117],from:[0,1],front:71,frontend:57,frozen:[2,39,65,115],fs2:[2,35],ftol:[90,91],fuction:104,fudg:74,fulfil:2,full:[1,2,4,35,57,62,66,69,73,96,110,112,113,116],fuller:90,fulli:[2,69,90,91,104,143,161],fulton:110,fumi:97,funcfl:110,fund:0,funrol:136,further:[2,37,57,66,70,78,90,91,92,95,103,136,146],furthermor:[11,47,62,73,109,112],futur:[0,2,59,65,91,134,135],g_jik:143,g_p:78,ga3:43,gaa:96,gahler:89,gai:116,gain:4,galindo:137,gamma0:13,gamma:[2,13,66,71,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:78,gamma_ijk:154,gamma_n:117,gamma_p:78,gamma_t:117,gammaa:137,gammafactor:66,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,65,70,72,108,112,115],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:67,gener:0,gentler:79,gentli:111,geom:2,geometr:[2,44,59,67,80,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159],geometri:[2,9,19,44,59,61],gerber:129,germann:[68,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,80,91,104,157,161],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,67,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,67,69,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,62,65,66,67,68,69,70,71,72,73,74,75,78,79,80,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gnu:0,gnuplot:3,goddard:[2,9,88,112,119],goe:[28,41,44,62,90,107,111,118,123,126,148,160],gold:29,goldman:71,good:[1,2,4,19,30,40,43,59,67,74,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],govern:66,gpa:93,gpl:0,gpt:136,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,68,74,81,82,83,85,86,87,88,92,93],grab:2,grad:2,gradient:[2,61,62,78,89,91,131,139,140],graft:60,grain:[2,13,18,28,44,50,64,69,73,114,118,136,140,145],gram:110,gran:[2,79,80],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[71,161],greater:[1,61,65,67,69,95,97,98,99],greatli:[40,62],green:[2,35,57,70,96,161],green_kubo:2,grest:[21,22,60,99,117,125],grid:[19,40,43,59,66,78],grigera:2,gromac:90,gromacs:[2,90,118],groot:108,ground:[2,31,63,112],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,91,146,157],group_id:3,grow:[2,67,69,73,117],growth:2,gsmooth_factor:133,guarante:44,guess:161,gui:[3,161],guid:[1,149,150,151],guidelin:1,gullet:133,gulp:2,gumbsch:89,gunnel:136,gunsteren:129,guo:[2,5,45,50,100],gyrat:2,gzip:[57,91],h12:116,h2o:[114,140],had:[2,3,60,61,65,67,68,78,108,117,152],hafskjold:[2,62],half:[1,2,4,19,57,59,67,78,79,80,96,102,112,136],halfwai:[19,57,161],halperin:36,halsei:117,halt:[19,59,62],halv:57,hamak:[79,80,102,144],hamilton:29,hamiltonian:[67,112],han:110,hand:[2,28,29,44,54,57,66,73,104,112],handl:[4,57,112,130,157],happen:2,hara:155,hard:[1,72,146],harden:148,harder:[79,80],hardi:58,hardwar:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,67,6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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","min_style command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,40,41,43,44,56,57,58,61,65,66,67,68,70,71,76,77,79,89,96,112,130,131,136,152],"long":[97,98,99,100,101,104,106,107,121,125,129,142,145],acceler:1,account:161,adding:161,addition:161,adiabat:2,adp:92,after:161,airebo:93,alloi:110,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:58,atom:[2,29,30,36,38,41,42],axel:161,balanc:[19,59],barostat:2,bcc:69,beck:94,between:2,bodi:[2,95],bond:60,bond_styl:[20,21,22,23,24,25,26,27,28],bop:96,born:[97,106],box:[2,61],branch:161,buck:[98,99,106,132],build:3,calcul:2,centro:29,chang:161,charmm:[2,5,45,100,129],chunk:[2,34],class2:[6,20,46,81,101],cna:30,code:2,coeffici:2,colloid:[79,102,159],comb3:103,comb:103,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],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,core:2,cosin:[7,8,9,10,11,12,47],cossq:82,coul:[97,98,99,100,101,104,105,106,118,121,125,129,142,145],coupl:2,create_atom:44,cubic:123,cut:[25,98,101,104,107,112,115,121,122,129,137,142],cvff:83,data:2,deby:[104,121],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],diel:105,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,107],discuss:2,disp:2,distanc:84,document:0,dpd:[31,108,109],dreid:119,dreiding:2,drude:2,dsf:[104,121],dump:[2,57],eam:110,edip:111,eff:112,ehex:62,eim:113,elastic:2,energi:109,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],exp6:114,exp:[11,47],expand:[22,124],extend:3,fcc:69,fdt:109,featur:161,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80],fix_modifi:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],flow:2,fluid:66,flux:35,forc:2,fork:161,fourier:[14,15,48,85],from:[2,3],gauss:115,gaybern:116,gener:[1,2],github:161,gld:65,global:2,gpu:[94,97,98,100,101,102,104,107,108,110,115,116,118,121,122,123,124,137,138,144,145,148,153,154,155,156,158,159,160],gran:117,granular:2,gromac:118,gyrat:[33,34],harmon:[16,23,24,25,49,51,79,86,141],hbond:119,heat:35,helix:50,hertz:117,hexord:36,histori:117,hook:117,how:2,idealga:149,imag:57,implicit:100,improper_styl:[81,82,83,84,85,86,87,88],indice:0,induc:2,info:[0,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,67,83,86,98,100,116,121,153,154],interfac:[2,3],jul:0,kspace_styl:2,lammps:[0,1,2,3,161],lennard:132,librari:[2,3],linear:[128,138],list:120,lj1043:79,lj126:79,lj93:79,lj96:122,local:2,lubric:130,lubricateu:131,luci:[139,140],make:161,mdf:132,meam:[133,134,135],measur:1,merg:161,mgpt:136,mie:137,min_styl:89,minim:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80,90],mod:[78,155],model:2,morri:151,mors:[26,93,119,138],movi:57,mpi:3,msd:37,msm:[97,98,100,104,121],multi:[2,51,139,140],multipl:2,nb3b:141,neb:91,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:67,nphug:68,npt:67,nvt:67,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,67,68,81,82,83,85,86,87,88,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,135,138,141,142,144,145,148,153,154,155,156,157,158,159,160],opl:53,opt:[100,110,121,125,138],optim:1,option:2,orient:69,orientord:38,orthogon:2,other:2,output:[2,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],overview:3,own:161,packag:[1,4],pair:2,pair_styl:[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],paquai:161,parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:70,polariz:2,poli:[130,131],polymorph:143,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:71,quadrat:54,quantiti:2,quartic:[17,28],rattl:74,rebo:93,region:80,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,71,73,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],relax:61,replica:2,repositori:161,resquar:144,restart:[2,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],restrain:72,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],rigid:2,ring:87,run:[2,3,58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],scalar:2,script:[2,3],sdk:[18,145],serial:3,set:2,shake:74,share:3,shell:2,shift:[10,11,24,25,47],simpl:15,simul:2,size:2,smooth:[127,128,138],smtbq:146,sna:41,snad:41,snap:147,snapshot:2,snav:41,soft:[129,138,148],spc:2,sph:[149,150,151],spheric:[2,55],spline:[134,135],spring:[75,77],squar:12,srp:152,start:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],stefan:161,stop:[58,59,61,62,66,67,68,69,71,72,74,75,76,77,78,79,80],strategi:1,streitz:104,stress:42,style:[1,2],summari:2,swap:60,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],system:2,tabl:[0,2,64,154],taitwat:[150,151],temperatur:2,tersoff:[154,155,156],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,104,121,125,129],triclin:2,tstat:108,ttm:78,tutori:161,umbrella:88,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:157,vector:2,version:0,viscos:2,visual:2,wall:[2,79,80],water:2,wisdom:161,wolf:[97,104],wrapper:3,write:2,written:161,xrd:43,your:161,yukawa:[158,159],zbl:[156,160]}})
\ No newline at end of file
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
index 15a666742b..245ac5864c 100755
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
@@ -69,8 +69,8 @@ defined via the "timestep"_timestep.html command.  Often they will
 converge more quickly if you use a timestep about 10x larger than you
 would normally use for dynamics simulations.
 
-NOTE: The {quickmin} and {fire} styles do not yet support the use of
-the "fix box/relax"_fix_box_relax.html command or minimizations
+NOTE: The {quickmin}, {fire}, and {hftn} styles do not yet support the
+use of the "fix box/relax"_fix_box_relax.html command or minimizations
 involving the electron radius in "eFF"_pair_eff.html models.
 
 [Restrictions:] none