From 159d722cc2e74a212f83b9396264f1b417980d30 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 1 Sep 2016 01:55:31 +0000
Subject: [PATCH] removing searchindex.js
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15533 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Makefile | 4 +-
doc/html/searchindex.js | 1 -
.../_themes/lammps_theme/search.html | 54 +++++--------------
python/lammps.py | 45 ++++++++++++++++
4 files changed, 60 insertions(+), 44 deletions(-)
delete mode 100644 doc/html/searchindex.js
diff --git a/doc/Makefile b/doc/Makefile
index 8ee8379c58..52ed2d0d73 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -42,7 +42,9 @@ html: $(OBJECTS)
cp -r src/* $(RSTDIR)/ ;\
sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
deactivate ;\
- )
+ )
+ -rm html/searchindex.js
+ -rm -rf html/_sources
@echo "Build finished. The HTML pages are in doc/html."
pdf: utils/txt2html/txt2html.exe
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
deleted file mode 100644
index 4c867b7219..0000000000
--- a/doc/html/searchindex.js
+++ /dev/null
@@ -1 +0,0 @@
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anch:[3,162],branicio2009:158,branicio:[31,158],breakdown:[1,4,94],brennan:[32,65,110,140,141,153],brenner:94,brick:[20,60],brief:[1,2,4,69,94,97],briefli:[2,72,104,147,162],brilliantov:118,broadwel:5,broken:[29,30,69,97],brook:2,brown:[5,41,43],brownian:[2,38,131,132],brows:0,browser:58,bryantsev:120,bsd:4,btype:[105,122,126,130,153],buc:99,buck:[2,5,33,98],buckingham:[98,99,100,107,133],buckplusattr:147,buffer:58,bufi:58,bug:[0,4],bui:58,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,32,33,38,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,61,64,65,66,67,68,69,70,71,72,73,75,76,78,79,80,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,30,68,71,106,134,137,147],bundl:[58,162],button:162,bypass:2,c11:134,c_0:[80,94,151,152],c_1:[41,44,67],c_2:[41,44],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:80,c_flux:36,c_gauss:116,c_hb:120,c_i:66,c_id:[2,33,63],c_ij:2,c_ijkl:2,c_k:67,c_mychunk:[2,35],c_n_k:67,c_p:43,c_peratom:43,c_pi:97,c_prop:2,c_sigma:97,c_size:2,c_thermo_temp:63,ca2:44,cach:5,cacul:76,calcforc:68,calclat:36,calcluat:[38,40,43,105],calcualt:36,calcul:[0,1],caldwel:[2,46],calhoun:72,call:[1,2,3],callabl:3,callback:3,caller:4,caltech:[2,113],calucl:2,calul:[3,4,30],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,5,20,29,58,60,61,62,67,69,73,80,81,82,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],canon:[69,72,79,137],cao1:72,cao2:72,cao:72,capabl:[3,5,94,102],capac:[65,80,150],capolungo:[41,44],captur:[2,94,100,113,118,126,134],carbid:105,carbon:[58,89,94,104,134],card:[4,5,33,120],care:[2,45,56,68,69,96],carefulli:[3,4,29],carlo:[2,61],caro:111,carri:[5,80,118],carrillo:5,cartesian:[2,93],cascad:80,cat:[5,58],cate:68,categori:[0,4,94],cation:[114,147],caus:[1,2,4,5,45,62,69,71,75,76,81,82,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,35],ccc:[112,154,155,157,158],ccflag:5,ccflags:5,ccm6:111,ccsi:[112,154,155,157,158],ccu:97,cd2:44,cdeam:111,cdll:3,cdof:2,cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:44,ce4:44,cell:[2,41,44,45,62,69,70,73,80,113,137],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,10,34,35,38,41,45,58,62,67,69,77,79,81,82,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:64,central:[30,37,39,42,71,76,77,86,137,142,158],centro:2,centroid:72,centrosymmetri:30,certain:[1,2,4,58,61,63],cfg:[2,58],cg_type:146,ch2:76,ch2lmp:[0,2],ch3:76,chain:[0,2,14,29,61,69,70,72,76,79,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,5,20,23,33,45,58,59,60,61,62,63,68,69,70,71,73,74,75,76,78,79,80,82,91,92,109,113,118,131,132,134,137,147,153,162],change_box:2,chapter:72,charact:[2,4,20,58,60,66,75,113,115,121,140,141,144,147],character:[2,30,39,42,148],characterist:78,charg:[1,2,3,33,41,44,45,98,99,104,105,107,108,111,113,114,122,126,130,143,147,157,158,160,161],charl:63,charmm:0,cheaper:[117,145],check:[2,3,4,20,36,60,74,76,79,91,92,121],checkout:162,chem:[2,6,7,10,21,22,23,33,39,40,43,46,47,54,64,67,68,69,72,73,78,79,81,83,89,90,92,94,98,101,102,104,105,106,108,109,110,113,116,117,119,120,122,126,127,130,134,138,140,141,143,147,153],chemic:[32,41,44,59,115,141],chemistri:[73,94,97,113],chen:80,cheng:104,chi:[71,114,117],chiral:89,chmod:[3,4],cho:134,choic:[2,4,5,20,29,30,33,43,56,60,61,68,69,72,92,130],choos:[1,2,4,14,29,33,58,61,62,63,68,69,70],chose:[155,157],chosen:[2,4,42,45,51,58,62,63,67,68,69,70,72,110,113,118,121,124,146,155],chunk:0,chunkid:35,ciccotti:76,cieplak:[2,46],circular:2,circumv:[37,39],citat:[0,4,68],cite:[4,147],cl1:44,clarendon:[14,108],clarifi:[155,157],clark:143,classic:[0,2,5,72,73,80,90,113],classifi:158,clean:[2,4],clear:[2,3,63],clebsch:42,click:[3,45,57,58,92,162],climb:92,clock:4,clockwis:46,clone:162,close:[2,3,4,20,43,61,62,68,69,76,82,92,94,97,105,106,134,140,141,157,162],closer:[20,60,62,78,92],closest:[71,117,145,153],cloud:147,cluster:[2,4,5,43,64,76],cmax:134,cmd:[3,4,72],cmdarg:3,cmin:134,cmm:[19,146],cna:30,co2:[44,75,76,115],coars:[14,19,29,51,66,75,115,119,141,146],coarsest:42,code:[0,1],coeff:[4,7,46,47,56,83,121,149],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:[41,44],collect:[2,35,45,103],colliex:44,collis:[68,118,161],colloid:[2,4],color:[20,58,60,67,73],column:[2,4,30,35,37,39,42,43,44,73,80,94,116,120],colvar:[0,4],colvarmodul:4,com:[2,38,64,96,162],comand:61,combiant:106,combin:[2,3,19,33,56,58,59,64,69,72,82,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,14,62,63,69,78,79,154,155,157,158,162],comfort:4,comit:162,comm:[0,3,4,31,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[20,60],comm_world:3,command:[0,1],comment:[3,4,46,66,75,80,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:[2,4],common:[0,1,2,3,4,5,31,62,72,82,83,118,120,154,155,157],commonli:[2,4,10,38,39,58,90,119,124,148,155,157],commun:[1,2,3,4,5,20,58,60,62,68,69,80,110],comp:[76,92,113,145,152,156],compar:[1,2,4,5,41,44,57,91,92,134,147],comparison:0,compass:[7,21,47,57,83,102],compat:[3,4,20,50,60,63,64,81,137],compens:[2,113],compil:[4,5,58,137],complain:[3,4],complement:134,complementari:[105,122],complet:[2,3,4,20,60,72,92,114],complex:[2,3,4,10,37,39,42,45,68,82,92,113,137],complic:[2,4],complier:4,compon:[2,4,30,31,34,35,36,37,38,39,40,42,43,58,61,62,63,64,68,69,70,72,76,82,91,92,109,113,118,131,132,147,148],componenet:2,composit:[2,68,111],compound:[104,113,114,158],compress:[2,4,58,70,73],compris:[82,115,145],compton:[41,44],comput:[0,1],computation:[2,80,97],compute_modifi:[61,62,69,70],compute_sa:41,compute_xrd:44,concav:82,concentr:[66,75,111,115,141],concept:2,conceptu:[2,62,92,105,134],concern:[2,31,33,67],concis:3,conclud:4,concurr:5,conden:[80,155,157],condens:[2,80,94,107,111,122,158],condit:[2,40,41,43,44,58,59,68,70,71,73,76,77,80,110,113,119],conducit:2,conduct:0,confer:[5,137],config:4,configur:[1,2,4,5,58,62,72,91,92,94,97,112,134,137,154,155,157,158,162],conflict:[4,162],conform:[2,61,62,74,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,33,45,68,92,98,99,105,109,113,120,122,143,146],connect:[2,33,61,76,92,106,118,153,157],conner:94,connor:94,consecut:[3,4,45,105,122,126],consequ:[1,2,80,121],conserv:[14,61,67,68,69,75,76,92,108,109,110,118,128,147],consid:[2,30,33,60,61,80,113,145,147,153],consider:2,consist:[2,3,4,40,45,51,63,67,69,70,73,74,75,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:59,constant:0,constantli:64,constitu:[2,81,82,103,145],constrain:[2,64,67,76,77,91,113],constraint:[20,40,43,60,64,76,77,81,91,132],construct:[2,4,29,30,31,37,39,41,42,44,62,69,74,75,82,108,137,153,154],constructor:3,consult:5,consum:1,contact:[0,4,106,112,114,117,118,145],contain:[0,1,2,3,4,20,33,36,41,42,44,45,46,57,58,59,60,63,66,68,71,73,75,80,82,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],content:4,context:[2,4,5,160],contibut:30,contin:5,continu:[0,2,4,20,60,61,62,63,64,67,69,70,73,78,79,80,82,97,109,124,127,145,156],continuum:[2,59,80],contour_integr:59,contract:[62,69],contrain:76,contrast:[1,2,160],contrib:80,contribut:[2,4,30,33,34,35,36,40,42,43,62,68,76,91,92,109,111,113,131,132,137,147,162],contributor:4,control:[2,3,4,5,12,14,20,33,36,42,48,58,59,60,62],control_typ:59,convect:36,conveni:[2,4,14,148,162],convent:[14,50,55,57,74,111,113],converg:[2,20,58,60,61,62,70,73,74,76,91,92,104,105,122,147],convers:[42,58,105,106,107,113,122,126,130,143],convert:[2,4,6,7,9,13,17,18,19,36,45,47,58,83,84,88,89,92,93,111,137,155,157,161],convex:82,convinc:4,cool:64,coord:[2,3,37,39,71,81,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,20,33,34,35,42,45,58,60,61,62,64,69,71,76,77,79,80,91,92,93,94,96,112,147],coords:147,copi:[0,3,4,58,80,92,162],copper:161,coprocessor:[1,5],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,46],corner:[2,58,82,162],corpor:5,corr:104,correct:[2,3,4,33,46,58,64,69,73,81,82,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:59,correctli:[3,69,76,82,92,107,132,137,162],correl:[2,36,37,42,67,72],correpond:66,correspond:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,33,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,64,66,68,69,70,71,72,75,76,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:2,cosineshift:12,cost:[1,2,3,4,20,41,43,44,58,60,69,75,80,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,5],coul:[2,5,19,22,23,33,46,91],could:[2,3,4,20,33,35,36,40,58,60,63,73,80,81,82,91,94,116,120],coulomb:[2,4,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:2,count:[1,2,3,4,20,36,46,60,62,69,76,82,91,92,116,120],counteract:63,counterbal:64,counterbalanc:14,counterclockwis:46,coupl:0,couple:[2,3,4],cours:[5,67,74,81,131,149],cov:147,coval:[2,14,113,134,147],cover:[2,4,59,68,113],cpp:[1,2,3,4,33,76],cpu:[1,4,5],cpuinfo:5,cpus:4,cr2:44,cr3:44,crash:4,creat:[0,1,2,3,4,20,36,40,41,45,58,59,60,61,62,66,69,70,71,72,74,80,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,20,36],create_box:[2,20,36,45,62,69,153],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:[4,45],criteria:[58,61,91],criterion:[4,20,45,60,61,91,92,104,113,118,147],critic:[2,25,26,80,91],cross:[4,5,34,58,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:73,crystal:[2,5,30,31,39,71,79],crystallin:[2,156],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,148],cscl:134,csequ:2,csh:[3,4,5],cshrc:[3,4],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,cu1:44,cu2:44,cu3au:134,cube:[2,82],cubes:[20,60],cubic:[39,68,71,111],cuda:[1,4],cuh:97,cummul:[2,61,120],cumul:[2,69,70,92],currenlti:63,current:[0,1,2,3,4,5,20,31,33,43,58,59,60,61,62,63,64,69,74,75,76,77,80,81,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[2,45],curvatur:[117,145,161],custom:[0,2,3,4,34,35,36,43,58,61,62,69,70,73,91,94,116,120],cut:[1,2,4,5,20],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:[2,5,22,23,29,30,31,33,37,39,42,61,66,71,73,81,82,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvar:63,cvff:5,cwiggl:81,cyan:58,cycl:[69,70],cyclic:46,cygwin:4,cylind:[58,82],cylindr:2,cyrot:97,d3q15:68,d3q19:68,d_e:80,daan:79,dai:4,daili:4,damp:[2,69,70,73,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:[4,109],darden:108,darken:58,dash:118,dat:[2,36,59],data2xmovi:0,data:1,databas:0,datafil:4,date:[0,2,4],datum:2,davenport:133,davi:81,david:[155,157],daw:[111,144],dcd:[2,58,72],deactiv:130,debug:[2,3,4,41,44,45,72],decai:[37,105,161],decid:[2,4,5,162],decod:58,decompos:[33,148],decomposit:[59,72],decoupl:2,decreas:[5,61,64],dedic:5,def:4,defect:[2,30,137],defin:[2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,4,42,63,65,70,81,97,103,110,113,144,148],deform:[2,43,62,69,131,132],deg2theta:44,degre:[2,6,7,9,13,14,17,18,19,37,39,40,44,45,46,47,49,50,55,56,58,61,69,70,72,74,76,79,83,84,88,89,90,91,108,111,120],delai:[2,4],delet:[4,29,61,69,153,162],delete_atom:45,delete_bond:[21,22,23,24,25,26,27,28,29],delete_el:59,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:[41,64,105,119],dens:[61,75,113],densiti:[2,20,42,45,59,60,68,80,81,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:73,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,37,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,66,68,69,70,71,75,76,78,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:2,depflags:4,deposit:[69,76],depth:[27,58,80,115,117,145],der:[33,103,104,130,160],deriv:[2,33,42,62,63,64,69,70,71,78,79,80,81,82,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:71,descib:58,describ:[0,1,2,3,4,5,20,30,31,41,42,43,44,45,51,54,60,61,62,63,66,67,68,69,70,71,72,73,75,78,79,81,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3,4],descriptor:42,design:[0,2,3,41,44,59,61,69,71,80,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,5,36,40,43,45,62,63,67,69,76,91,92,109,111,120,131,132,154,155,157],desktop:[2,4,58],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,5,20,35,36,40,42,43,45,57,58,59,60,61,62,63,64,67,68,69,70,73,76,79,80,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[4,37,92,104,120,121],determin:[1,2,4,5,27,33,40,41,43,44,45,58,60,62,66,69,71,72,73,74,75,81,82,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,5,63,70,73,94,97,113,136,137,147,158],deviat:[70,71,116],devic:[1,4],devin:104,devis:136,dfactor:58,dfft_fftw2:4,dfft_fftw3:4,dfft_fftw:4,dfft_none:4,dfft_single:4,dfft_xxx:4,dfftw:4,dfftw_size:4,dft:137,dhug:73,dhugoniot:73,dia:134,diag:75,diagnost:[4,5,61,75],diagon:[2,42,43,62,69],diagonalstyl:148,diagram:[20,41,44,57,60,72],diallo:120,diam:58,diamet:[2,45,58,103,117,118,124,145,160],diamond:[113,134],dick:2,dicken:63,did:[4,91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4,5],differ:[1,2,3,4,5,20,29,30,33,37,42,45,57,58,60,61,62,63,64,67,68,69,71,72,73,76,77,78,79,80,81,82,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,2,14,75,105,144,156],difficult:[62,63,72,120],difficulti:[37,39,76],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:137,dihedr:[0,4,5,29,37,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,74,84,85,86,88,91,94,97,101],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:12,dihedral_styl:[0,2,43],dihydrid:113,dij:76,dilat:[62,69,70],dim:[45,134],dimens:[1,2,4,20,36,43,45,58,60,62,68,69,70,73,81,92],dimension:[37,40,41,42,44,80,92,144],dimensionless:[38,42,63,80,148,160],dimer:[2,134],dimstr:[20,60],dintel_offload_noaffinity:5,dipol:0,dipolar:14,dipole:108,dir:[1,3,4,71,73,144],dirac:42,direc:144,direct:[2,4,5,14,30,39,41,42,44,45,46,58,68,70,71,73,78,79,80,81,82,91,92,109,110,118,132],directli:[2,3,4,33,42,45,58,63,68,75,82,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,5,63,78,79,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,5,80,121],disadvantag:[2,60],disallow:69,discard:[20,60,82],discontinu:[91,128],discourag:134,discret:[2,58,63,68],discuss:[0,1],disk:[2,37],disloc:[30,137],disord:[30,137],disp:0,dispar:145,disperion:[108,126],dispers:[2,100,108,126,131,158],displac:[2,4,38,62,69,71,118],displai:[3,57,58],disregard:137,dissip:[2,32,65,67,78,79,109,110,118,131,132],dist:[2,36,72,74,153],distanc:[2,4,6,7,21,22,23,24,25,26,27,28,29,31,34,35,37,38,39,41,42,45,47,58,61,62,64,68,69,70,71,73,74,76,77,79,80,81,82,83],distinct:[2,145],distinguish:[2,42,113],distort:93,distrbut:93,distribut:[0,2,3],distro:144,ditto:[4,161],div:5,diverg:[4,79,94],divid:[2,5,20,36,40,43,57,60,71,91,92,114,147,158],divis:[2,56,68,97,130],dl_poly:2,dlammps_bigbig:4,dlammps_exceptions:4,dlammps_ffmpeg:[4,58],dlammps_gzip:[4,58],dlammps_jpeg:[4,58],dlammps_longlong_to_long:4,dlammps_memalign:[4,5],dlammps_png:[4,58],dlammps_smallbig:4,dlammps_smallsmall:4,dlammps_xdr:4,dlm:69,dlmp_intel_offload:5,dlopen:2,dlvo:[103,160],dm_lb:68,doc:[0,1,2,3,4,33,35,38,40,43,45,57,58,63,69,82,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,4,20,29,30,33,36,41,44,45,46,57,58,59,60,61,62,63,64,66,67,68,69,80,81,82,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[4,45,94,104,112,154,155,156,157,158],dof:40,doi:[2,71],domain:[2,4,20,41,44,58,60,62,68,69,72,80,81,92],domin:[1,113],don:[0,4,5,82,134,147,162],done:[1,2,4,20,45,56,58,59,60,61,62,63,66,69,72,76,78,79,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:43,doti:[97,144],doubl:[1,2,3,4,5,33,46,62,82,97,114,119,137],dover:59,down:[2,3,62,113,147],download:[3,4],downsid:2,dozen:4,dpack_array:4,dpack_memcpy:4,dpack_pointer:4,dpd:2,dpdtheta:[32,110],dpdtheta_i:[65,66],dr_ewald:41,drag:[2,36,69,70,77],dragforc:68,drai:[58,73],drain:91,dramat:[61,62,69,147],drautz:97,draw:58,drawn:[58,67],drayleigh:73,dreid:2,dreiding:0,drfourth:38,drho:[93,111,140,141],drift:[2,38,64,67],drive:[3,4,62,69,71,92],driven:[2,51],driver:[2,4],drop:109,drsquar:38,drude:0,dt_collis:68,dt_lb:68,dt_md:68,dtqm:73,dudarev:44,due:[1,2,4,5,29,30,34,35,38,41,42,43,44,45,58,61,62,67,68,69,70,71,74,78,79,80,81,82,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:80,dullweb:69,dummi:[4,14,156],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,6,46,101],duplic:[20,60,71],durat:[57,80,118],dure:[2,4,5,20,33,46,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:2,dx_lb:68,dy3:44,dyamic:4,dyanam:2,dynam:[0,2,3,4,5,20,32,38,45,58,59,60,61,63,65,67,69,70,72,73,74,78,79,80,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:14,e_1:97,e_2:97,e_a:75,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:[63,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,33,34,35,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,72,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161],eacn:[20,60],eam:[0,4,93,105],earli:[20,60],earlier:[4,92,118,134],earth:113,easi:[2,3,33,43,81],easier:[5,58],easili:[3,58,92],eat:47,eaxmpl:2,eba:7,ebb13:47,ebb:7,ebt:47,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,4,41,44],ecp:113,edg:[2,20,41,44,58,81,82],edge:81,edit:[4,5,162],edition:5,edu:[3,111,131],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,34,35,38,40,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,64,67,69,70,71,72,73,74,76,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161],effici:[0,1,2,4,5,40,56,58,62,69,72,76,97,103,105,122,126,137,140,141,145],efficienc:5,efield:[76,91],eggebrecht:[105,147],ehex:2,eigenvalu:72,einstein:[2,79],either:[1,2,3,4,5,20,30,41,42,43,44,45,58,60,61,62,63,64,68,69,70,71,75,76,82,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaps:[81,149],elast:[2,22,23,92,118,156],elastic:0,elba:14,electr:[2,59,114,161],electric:5,electrolyt:160,electron:[2,41,59,80,93,104,108,111,113,114,134,137,144,147,157,158,161],electron_integr:59,electron_temperatur:59,electron_unit:113,electroneg:[2,104,114,147],electroneg_compon:147,electrostat:[2,5,103,108,113,122,130,132,147,160],elem1:[114,134,148],elem2:[114,134,148],elem:147,element1:[93,111,147],element2:[93,111,147],element:[2,4,34,38,40,42,43,58,59,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158],elementn:[93,111],elementset:59,elif:42,elig:120,elimin:[2,67,76,78,79],elj:108,ellips:2,ellipsoid:[2,45,91,117,132,145],els:[4,58,63,69,80],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:82,emb_lin_neg:134,embed:[3,4,14,80,93,111,114,130,134,135,136,144],embt:47,emin:62,emphas:118,empir:[59,113],empiric:94,emploi:[64,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,32,33,38,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,4,134,147],encod:58,encompass:2,encount:[4,39],encourag:[75,77],end:[1,2,3,4,5,20,47,58,61,62,64,67,69,74,75,80,92,109,111,117,133,137,145,148,149],endbondtors:47,energet:[61,94],energi:[0,1,2,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,32,33,36,40,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:147,enforc:[2,58,61,69,76,122],enforce2d:[2,91],eng:[3,104,136],engineer:[59,78,111],enginer:135,enhanc:[59,64],enlarg:58,enough:[45,60,73,81,82,105],enpub:111,ensembl:[2,33,36,69,72,73,109,147],ensight:2,ensur:[2,42,62,67,69,97,130,154,158],enter:[114,137,158],enthalpi:[75,111],entir:[0,2,3,20,32,40,41,43,44,45,60,61,64,67,69,70,71,72,75,77,80,108,126],entiti:2,entri:[4,41,66,73,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,5,58,71,93,97,104,112,113,144,155],eos:66,epair:[94,116,120],epp:108,epq:108,eps0:160,eps14:130,epsilon0:157,epsilon:[2,19,22,23,28,29,33,46,81,82,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,143,145,146,154,159,160],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:[2,3,4,20,29,33,36,43,45,58,60,62,63,67,68,70,71,72,73,74,75,78,79,80,81,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161],equat:[2,36,39,40,41,44,57,62,63,64,65,66,68,69,70,71,72,73,75,76,80,81,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[71,89],equilibr:[2,36,45,61,62,69,73,78,79,104,105],equilibrium:[1,2,7,9,11,12,13,14,17,18,19,21,24,25,26,27,28,47,48,62,67,68,69,70,73,74,76,79,83,84,88,89,104,134,142,147],equilibrium_start:59,equival:[2,4,14,62,69,74,94,109,113,147,155,157],equlibrium:2,er3:44,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:[0,1,2,3,4,12,48,58,62,63,64,66,69,75,80,81,82,91,105,122,145,153,155,157],erta:118,especi:[5,45,60,73,74],essenti:[3,4,12,48,94,105,122,157],essential:70,essex:14,establish:33,estim:[1,2,4,20,30,36,43,59,60,75],esub:134,eta:[2,68,69,73,112,114,117,144,156,158],eta_dot:69,eta_ij:144,eta_ji:114,etap:69,etap_dot:69,etc:[1,2,3,4,5,29,34,35,36,43,45,58,59,67,69,80,82,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:73,etot:[2,43,73],eu2:44,eu3:44,euler:[75,91,92],eulerian:59,europhi:68,evalu:[3,4,33,36,42,45,46,58,59,63,67,75,81,91,137,140,141,144,147],evanseck:[2,6,46,101],evaul:91,even:[2,4,5,20,30,56,60,62,64,69,80,81,82,91,92,96,113,114,118,145,158],evenli:[20,43,60,68],event:[2,69,80],eventu:[2,4],ever:29,everaer:[103,117,145],everi:[0,1,2,3,4,5,20,36,58,59,60,61,62,63,64,68,69,70,71,73,75,76,80,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[64,68,72],evolv:[68,72],ewald:[2,4,41,43,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[20,60,61,67,80],exactli:[2,4,20,36,45,60,67,73,109,111,118,131,140,141],examin:[2,61,75],exampl:[0,1],exce:[2,5,20,60,62,69,91],exceed:[20,60,69],excel:113,except:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,34,35,40,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,69,70,72,76,80,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,59,64,80,113],excit:113,excite:113,exclud:[2,4,5,40,42,91,118,131,132,153],exclus:[1,4,5,33,46,104,137],excurs:69,exectubl:4,execut:[1,2,3,4,58],exempl:147,exemplari:67,exemplifi:113,exert:[2,82],exhaust:59,exhibit:[37,64,69,113],exist:[2,3,4,30,45,57,58,62,83,84,85,86,88,110,153,162],exit:[3,4,20,60],expans:[4,42,56],expect:[1,4,5,20,60,71,73,134,137],expens:[2,71,80],experi:[2,74,92,109],experienc:[2,4,5],expert:4,explain:[1,2,3,4,20,31,58,60,62,69,71,92,96,111,147,149,162],explan:[2,42,71],explic:138,explicit:[2,3,33,75,94,97,101,111,113,121,131,162],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,40,45,46,47,48,49,50,51,52,53,54,55,62,67,69,70,73,76,80,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:5,exploit:72,explor:[41,44],expon:[75,111,115,117,120,130,138,146],exponenti:[33,75,115,144,154,158,161],expos:3,exposit:[59,109],express:[2,42,45,62,71,75,80,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,5,22,23,28,33,36,63,64,69,70,71,74,78,79,80,81,82,117,134,137,145,148],extent:[1,20,22,60,94],exterior:[2,82],extern:[4,33,58,62,67,68,69,70,80,91,135,136],extra:[2,3,4,5,20,23,40,41,43,44,45,60,69,73,91,108,118,134],extract:[2,3,19,33,92,105,114,134,148],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extramake:4,extrapol:1,extrem:[1,2,58,62,69,79,113,156],extrema:130,extreme:113,extrins:59,f77:4,f90:4,f_1:[2,62],f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:73,f_harm:79,f_i:[14,144],f_id:[2,63],f_ij:144,f_int:78,f_j:14,f_jj:36,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:[0,4],facilit:2,fact:[2,5,79,118,147],factor:[1,2,4,9,13,17,18,19,20,23,24,33,36,41,42,44,46,54,58,60,62,64,68,69,70,72,74,75,76,81,82,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[3,4,62,91,92,107],fairli:[3,162],faken:31,fall:2,fals:147,famili:158,familiar:[0,3,162],fan:144,far:[2,4,60,62,69,71,74,81,84,88,92],farrel:[155,157],fashion:[2,20,45,60,63,69,70,73,79,80,81,92,131],fast:[2,4,5,63,73,75,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,38,40,46,47,48,49,50,51,52,53,54,55,60,69,70,76,78,80,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,80],fault:30,faulti:4,fava:117,favor:61,fcc:[2,30,31,36,39],fcold:64,fdt:[65,66,75],fdti:33,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,4,42,58,61,67,72,82,91,162],fecr:111,feedback:63,feel:[71,82,92],fehlberg:75,felling:136,felt:82,fene:[2,5],fennel:[105,122],fep:0,ferguson:[2,46],fermi:[1,4,157],fermion:113,fernando:133,few:[1,2,3,4,64,69,76,91,92,94,147],fewer:[1,3,5],feynman:72,ffield:[104,114,147],fflag1:58,fflag2:58,ffmpeg:[4,58],ffplai: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0],reset:[2,3,4,34,35,45,62,69,70,76,80,91,132],reset_atomic_reference_posit:59,reset_tim:59,reset_timestep:[2,36],resist:2,resolut:147,resolv:[62,72,132,162],resourc:[93,111],respa:[5,69,71,74,77,81,82,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],respecifi:137,respect:[1,2,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,33,34,40,41,44,46,47,48,49,50,51,52,53,54,55,58,61,62,64,68,69,70,76,80,81,83,84,85,87,88,89,90,91,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,142,143,145,146,147,148,149,154,155,156,157,158,159,160,161],respond:[2,63,113],respons:[2,63],resquar:[2,117],rest:[2,4,74,97,132,134],restart1:72,restart2:72,restart2data:[0,4],restart:[0,1],restartfil:4,restrain:14,restraint:[74,121],restratin:74,restrict:[1,2,4],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,33,35,36,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,58,60,61,62,63,64,67,68,69,70,72,75,76,78,79,80,81,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,134,135,137,139,140,141,142,143,145,146,149,154,155,156,157,158,159,160,161],retain:[94,97,137],retriev:[2,135,136],rev:[2,30,37,39,42,43,69,70,78,79,97,103,104,105,108,111,112,113,117,118,124,131,132,133,134,136,140,141,144,145,148,154,155,156,157,158],revers:[2,33,50,61,69,71,78,92,130],review:[42,137,148,162],rewrit:4,rfac0:[42,148],rg0:77,rh3:44,rh4:44,rheolog:2,rhi:[140,141],rho0:[134,151,152],rho0_meam:134,rho:[68,93,98,99,100,111,133,134,135,136,140,141,145,150],rho_0:[151,152],rho_alpha_beta:111,rho_bkgd:134,rho_colloid:81,rho_e:80,rho_i:[135,136],rho_ref_meam:134,rho_wal:81,rhodopsin:[1,5],rhosum:[150,151,152],rhot:64,rhs:75,rick:[104,147],right:[2,3,4,20,30,45,55,57,60,61,68,71,75,105,162],rightmost:[20,60],rii:[34,35],rij:[37,39,71,109,110,140,141,153],rin:[120,127,128],ring:[2,46,72],rino:[31,158],rirj:118,risi:[42,148],risk:74,rix:[34,35],rk4:75,rkf45:75,rlo:[140,141],rmin0:[42,148],rmin:124,rms:75,rnemd:2,robust:91,rock:134,rockett:144,rodata:4,role:2,roll:4,ronchetti:39,root:[3,33,34,35,111],rose:134,ross:134,rosski:72,rot:[2,36,72,74],rotat:[2,42,45,82,91,108,117,145],rotation:39,rough:[2,45,58],roughli:[4,20,58,69,92],round:[1,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,40,46,47,48,49,50,51,52,53,54,55,69,70,76,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,140,141,142,143,145,146,149,154,155,156,157,158,159,160,161],rous:67,rout:[33,120,130],routin:[2,3,5,68,137],roux:2,row:[2,35,44,80,113],rozero:134,rpm:4,rrespa:[1,5,69,93,94,95,96,98,99,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rsq:[140,141],rsurfac:80,ru3:44,ru4:44,rub:6,rubia:[135,136],rule:[0,2,4,14,30,45,61,69,82,93,95,96,102,103,108,120,125,134,138,149,153,154,155,157,161],run1:2,run2:2,run3:2,run4:2,run5:2,run6:2,run7:2,run8:2,run:[0,1],run_styl:[4,5,69,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rung:75,runtim:[4,58],rutherford:80,rutuparna:[155,157],rxn:75,ryckaert:[76,89],rydberg:137,s0st:2,s2050:1,s2629:111,s319:59,s_i:[2,113],s_ij:2,saddl:92,sadigh:[111,135,136],saed_vtk:41,safe:[4,58,162],safran:160,sagui:108,sai:[1,4,162],said:91,sakai:156,sall:147,salt:[106,116,134],salter:147,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,33,34,35,36,37,38,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,67,68,69,70,71,72,73,74,76,78,79,80,82,83,84,85,87,88,89,90,92,93,94,95,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,138,139,142,143,144,145,146,147,149,153,154,155,156,157,158,159,160,161,162],sampl:[1,2,3,4,36,58,69,72,77,79,97],sample_frequ:59,sandia:[0,30,114,134],saniti:74,satellit:2,satisfi:[4,31,41,42,44,62,64,68,70,76,91,118],satur:106,save:[2,4,58,61,67,75,80,97],sb3:44,sb5:44,sc3:44,scalabl:[0,1,5],scale:[0,1,2,5,36,42,46,58,59,62,68,69,70,72,73,78,79,80,93,94,106,113,115,118,131,132,134,137],scalegamma:68,scalexi:[62,69,70],scalexz:[62,69,70],scaleyz:[62,69,70],scatter:[3,41,44],scatter_atom:3,scatter_coord:3,scenario:[2,61,82],schaik:130,schell:156,schemat:61,scheme:[2,63,67,69,72,76,80],schmid:109,schroding:113,schroeder:39,sci:[31,1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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","2. Getting Started","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 controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[30,33,37,38,39,41,42,44,45,57,58,59,62,67,68,69,70,72,73,78,79,81,97,113,131,132,137,153],"long":[98,99,100,101,102,105,107,108,122,126,130,143,146],"static":4,acceler:1,addition:4,adiabat:2,adp:93,airebo:94,alloi:111,amber:2,angle_styl:[6,7,8,9,10,11,12,13,14,15,16,17,18,19],arrai:2,aspher:2,atc:59,atom:[2,30,31,37,39,42,43],aug:0,balanc:[20,60],barostat:2,bcc:71,beck:95,between:2,bodi:[2,96],bond:61,bond_styl:[21,22,23,24,25,26,27,28,29],bop:97,born:[98,107],box:[2,62],buck:[99,100,107,133],build:[3,4],calcul:2,call:4,centro:30,charmm:[2,6,46,101,130],chunk:[2,35],class2:[7,21,47,83,102],cna:31,code:2,coeffici:2,colloid:[81,103,160],comb3:104,comb:104,command:[2,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],comparison:1,compos:2,comput:[2,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,control:63,core:2,cosin:[8,9,10,11,12,13,48],cossq:84,coul:[98,99,100,101,102,105,106,107,119,122,126,130,143,146],coupl:2,create_atom:45,cubic:124,cut:[26,99,102,105,108,113,116,122,123,130,138,143],cvff:85,data:2,deby:[105,122],delta:9,descript:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],diel:106,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,14,108],discuss:2,disp:2,distanc:86,distribut:4,document:0,dpd:[32,109,110],dreid:120,dreiding:2,drude:2,dsf:[105,122],dump:[2,58],eam:111,edip:112,eff:113,ehex:64,eim:114,elastic:2,energi:110,exampl:[2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],exp6:115,exp:[12,48],expand:[23,125],extend:3,fcc:71,fdt:110,fene:[22,23],fep:33,field:2,file:2,finit:2,fix:[2,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82],fix_modifi:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],flow:2,fluid:68,flux:36,forc:2,fourier:[15,16,49,87],from:[2,3],gauss:116,gaybern:117,gener:[1,2],get:4,github:162,gld:67,global:2,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,139,145,146,149,154,155,156,157,159,160,161],gran:118,granular:2,gromac:119,gyrat:[34,35],harmon:[17,24,25,26,50,52,81,88,142],hbond:120,heat:36,helix:51,hertz:118,hexord:37,histori:118,hook:118,how:2,idealga:150,imag:58,implicit:101,improper_styl:[83,84,85,86,87,88,89,90],indice:0,induc:2,info:[0,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],input:2,install:3,integr:2,intel:[5,6,17,22,24,46,50,54,69,85,88,99,101,117,122,154,155],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,4,162],lennard:133,librari:[2,3,4],line:4,linear:[129,139],list:121,lj1043:81,lj126:81,lj93:81,lj96:123,local:2,lubric:131,lubricateu:132,luci:[140,141],make:4,mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82,91],mod:[80,156],model:2,morri:152,mors:[27,94,120,139],movi:58,mpi:3,msd:38,msm:[98,99,101,105,122],multi:[2,52,140,141],multipl:2,nb3b:142,neb:92,nemd:2,nharmon:53,non:2,nongauss:38,nonlinear:28,nph:69,nphug:70,npt:69,nvt:69,omp:[6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,46,47,48,49,50,51,52,53,54,55,69,70,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,139,142,143,145,146,149,154,155,156,157,158,159,160,161],opl:54,opt:[101,111,122,126,139],optim:1,option:[2,4],orient:71,orientord:39,orthogon:2,other:2,output:[2,4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],overview:3,packag:[1,4,5],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:10,pimd:72,polariz:2,poli:[131,132],polymorph:144,potenti:2,pppm:2,pressur:40,previou:4,process:2,properti:2,python:3,qbmsst:73,quadrat:55,quantiti:2,quartic:[18,29],rattl:76,rebo:94,region:82,relat:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],relax:62,replica:2,requir:4,resquar:145,restart:[2,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],restrain:74,restrict:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rigid:2,ring:89,run:[2,3,4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],scalar:2,screen:4,script:[2,3],sdk:[19,146],serial:3,set:2,shake:76,share:[3,4],shell:2,shift:[11,12,25,26,48],simpl:16,simul:2,size:2,smooth:[128,129,139],smtbq:147,sna:42,snad:42,snap:148,snapshot:2,snav:42,soft:[130,139,149],spc:2,sph:[150,151,152],spheric:[2,56],spline:[135,136],spring:[77,79],squar:13,srp:153,start:[4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],stop:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:43,style:[1,2],summari:2,swap:61,syntax:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],system:2,tabl:[0,2,66,155],taitwat:[151,152],temperatur:2,tersoff:[155,156,157],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,105,122,126,130],tip:4,tool:4,triclin:2,tstat:109,ttm:80,tutori:162,umbrella:90,user:[4,5],using:[2,3],valu:2,variabl:2,variou:1,vashishta:158,vector:2,version:[0,4],via:4,viscos:2,visual:2,wall:[2,81,82],water:2,what:4,wolf:[98,105],wrapper:3,write:2,xrd:44,yukawa:[159,160],zbl:[157,161]}})
\ No newline at end of file
diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/search.html b/doc/utils/sphinx-config/_themes/lammps_theme/search.html
index e3aa9b5c6e..285d27e0d7 100644
--- a/doc/utils/sphinx-config/_themes/lammps_theme/search.html
+++ b/doc/utils/sphinx-config/_themes/lammps_theme/search.html
@@ -1,50 +1,20 @@
-{#
- basic/search.html
- ~~~~~~~~~~~~~~~~~
-
- Template for the search page.
-
- :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
- :license: BSD, see LICENSE for details.
-#}
{%- extends "layout.html" %}
{% set title = _('Search') %}
-{% set script_files = script_files + ['_static/searchtools.js'] %}
{% block footer %}
- <script type="text/javascript">
- jQuery(function() { Search.loadIndex("{{ pathto('searchindex.js', 1) }}"); });
- </script>
- {# this is used when loading the search index using $.ajax fails,
- such as on Chrome for documents on localhost #}
- <script type="text/javascript" id="searchindexloader"></script>
- {{ super() }}
{% endblock %}
{% block body %}
- <noscript>
- <div id="fallback" class="admonition warning">
- <p class="last">
- {% trans %}Please activate JavaScript to enable the search
- functionality.{% endtrans %}
- </p>
- </div>
- </noscript>
-
- {% if search_performed %}
- <h2>{{ _('Search Results') }}</h2>
- {% if not search_results %}
- <p>{{ _('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.') }}</p>
- {% endif %}
- {% endif %}
<div id="search-results">
- {% if search_results %}
- <ul>
- {% for href, caption, context in search_results %}
- <li>
- <a href="{{ pathto(item.href) }}">{{ caption }}</a>
- <p class="context">{{ context|e }}</p>
- </li>
- {% endfor %}
- </ul>
- {% endif %}
+<script>
+ (function() {
+ var cx = '012685039201307511604:um7if1hinba';
+ var gcse = document.createElement('script');
+ gcse.type = 'text/javascript';
+ gcse.async = true;
+ gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
+ var s = document.getElementsByTagName('script')[0];
+ s.parentNode.insertBefore(gcse, s);
+ })();
+</script>
+<gcse:searchresults-only></gcse:searchresults-only>
</div>
{% endblock %}
diff --git a/python/lammps.py b/python/lammps.py
index e1c25cb840..7926fa5e4a 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -309,6 +309,9 @@ class OutputCapture(object):
def __exit__(self, type, value, tracebac):
os.dup2(self.stdout, self.stdout_fd)
+ os.close(self.stdout)
+ os.close(self.stdout_pipe_read)
+ os.close(self.stdout_pipe_write)
# check if we have more to read from the pipe
def more_data(self, pipe):
@@ -350,8 +353,11 @@ class AtomList(object):
def __init__(self, lammps_wrapper_instance):
self.lmp = lammps_wrapper_instance
self.natoms = self.lmp.system.natoms
+ self.dimensions = self.lmp.system.dimensions
def __getitem__(self, index):
+ if self.dimensions == 2:
+ return Atom2D(self.lmp, index + 1)
return Atom(self.lmp, index + 1)
@@ -382,6 +388,12 @@ class Atom(object):
self.lmp.eval("y[%d]" % self.index),
self.lmp.eval("z[%d]" % self.index))
+ @position.setter
+ def position(self, value):
+ self.lmp.set("atom", self.index, "x", value[0])
+ self.lmp.set("atom", self.index, "y", value[1])
+ self.lmp.set("atom", self.index, "z", value[2])
+
@property
def velocity(self):
return (self.lmp.eval("vx[%d]" % self.index),
@@ -399,6 +411,31 @@ class Atom(object):
return self.lmp.eval("q[%d]" % self.index)
+class Atom2D(Atom):
+ def __init__(self, lammps_wrapper_instance, index):
+ super(Atom2D, self).__init__(lammps_wrapper_instance, index)
+
+ @property
+ def position(self):
+ return (self.lmp.eval("x[%d]" % self.index),
+ self.lmp.eval("y[%d]" % self.index))
+
+ @position.setter
+ def position(self, value):
+ self.lmp.set("atom", self.index, "x", value[0])
+ self.lmp.set("atom", self.index, "y", value[1])
+
+ @property
+ def velocity(self):
+ return (self.lmp.eval("vx[%d]" % self.index),
+ self.lmp.eval("vy[%d]" % self.index))
+
+ @property
+ def force(self):
+ return (self.lmp.eval("fx[%d]" % self.index),
+ self.lmp.eval("fy[%d]" % self.index))
+
+
class PyLammps(object):
"""
More Python-like wrapper for LAMMPS (e.g., for iPython)
@@ -608,6 +645,10 @@ class PyLammps(object):
with OutputCapture() as capture:
self.lmp.command(' '.join(cmd_args))
output = capture.output
+
+ if 'verbose' in kwargs and kwargs['verbose']:
+ print(output)
+
lines = output.splitlines()
if len(lines) > 1:
@@ -662,3 +703,7 @@ class IPyLammps(PyLammps):
self.write_dump(*cmd_args)
from IPython.core.display import Image
return Image('snapshot.png')
+
+ def video(self, filename):
+ from IPython.display import HTML
+ return HTML("<video controls><source src=\"" + filename + "\"></video>")
--
GitLab