From 7541033246634ccee92041abd9c07dda3d379165 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 5 Aug 2016 15:50:41 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15445 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Manual.html | 2 +- doc/html/_sources/Manual.txt | 2 +- doc/html/_sources/fix_controller.txt | 24 ++++++++++++------------ doc/html/fix_controller.html | 24 ++++++++++++------------ doc/html/searchindex.js | 2 +- doc/src/Manual.txt | 4 ++-- doc/src/fix_controller.txt | 24 ++++++++++++------------ 7 files changed, 41 insertions(+), 41 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 09c02ecbee..f38909c44f 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -135,7 +135,7 @@

LAMMPS Documentation

-

3 Aug 2016 version

+

5 Aug 2016 version

Version info:

diff --git a/doc/html/_sources/Manual.txt b/doc/html/_sources/Manual.txt index 2ec8d95b62..8ca22675f8 100644 --- a/doc/html/_sources/Manual.txt +++ b/doc/html/_sources/Manual.txt @@ -5,7 +5,7 @@ LAMMPS Documentation ==================== -3 Aug 2016 version +5 Aug 2016 version ------------------ Version info: diff --git a/doc/html/_sources/fix_controller.txt b/doc/html/_sources/fix_controller.txt index 523b118f49..9162c6f643 100644 --- a/doc/html/_sources/fix_controller.txt +++ b/doc/html/_sources/fix_controller.txt @@ -45,12 +45,12 @@ Description This fix enables control of a LAMMPS simulation using a control loop feedback mechanism known as a proportional-integral-derivative (PID) controller. The basic idea is to define a "process variable" which is -a quantity that can be monitor during a running simulation. A desired -target value is chosen for the process variable. A "control variable" -is also defined which is an adjustable attribute of the simulation -which the process variable will respond to. The PID controller -continuously adjusts the control variable based on the difference -between the process variable and the target. +a quantity that can be monitored during a running simulation. A +desired target value is chosen for the process variable. A "control +variable" is also defined which is an adjustable attribute of the +running simulation, which the process variable will respond to. The +PID controller continuously adjusts the control variable based on the +difference between the process variable and the target. Here are examples of ways in which this fix can be used. The examples/pid directory contains a script that implements the simple @@ -133,12 +133,12 @@ counteracted by increasing *Ki*\ . In the language of Charles Dickens error of the past, and *Kd* the error yet to come. Because this fix updates *cvar*\ , but does not initialize its value, -the initial value is that assigned by the user in the internal-style -variable command. This value is used (by the other LAMMPS command that -used the variable) until this fix performs its first update of *cvar* -after *Nevery* timesteps. On the first update, the value of the -derivative term is set to zero, because the value of *e_n-1* is not -yet defined. +the initial value is that assigned by the user in the input script via +the :doc:`internal-style variable ` command. This value is +used (by the other LAMMPS command that used the variable) until this +fix performs its first update of *cvar* after *Nevery* timesteps. On +the first update, the value of the derivative term is set to zero, +because the value of *e_n-1* is not yet defined. ---------- diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html index f80bc97a82..c60f703729 100644 --- a/doc/html/fix_controller.html +++ b/doc/html/fix_controller.html @@ -166,12 +166,12 @@

This fix enables control of a LAMMPS simulation using a control loop feedback mechanism known as a proportional-integral-derivative (PID) controller. The basic idea is to define a “process variable” which is -a quantity that can be monitor during a running simulation. A desired -target value is chosen for the process variable. A “control variable” -is also defined which is an adjustable attribute of the simulation -which the process variable will respond to. The PID controller -continuously adjusts the control variable based on the difference -between the process variable and the target.

+a quantity that can be monitored during a running simulation. A +desired target value is chosen for the process variable. A “control +variable” is also defined which is an adjustable attribute of the +running simulation, which the process variable will respond to. The +PID controller continuously adjusts the control variable based on the +difference between the process variable and the target.

Here are examples of ways in which this fix can be used. The examples/pid directory contains a script that implements the simple thermostat.

@@ -258,12 +258,12 @@ counteracted by increasing Ki. In the language of Charles Dickens (or Donald Trump), Kp represents the error of the present, Ki the error of the past, and Kd the error yet to come.

Because this fix updates cvar, but does not initialize its value, -the initial value is that assigned by the user in the internal-style -variable command. This value is used (by the other LAMMPS command that -used the variable) until this fix performs its first update of cvar -after Nevery timesteps. On the first update, the value of the -derivative term is set to zero, because the value of e_n-1 is not -yet defined.

+the initial value is that assigned by the user in the input script via +the internal-style variable command. This value is +used (by the other LAMMPS command that used the variable) until this +fix performs its first update of cvar after Nevery timesteps. On +the first update, the value of the derivative term is set to zero, +because the value of e_n-1 is not yet defined.

The process variable pvar can be specified as the output of a compute or fix or the evaluation of a diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 29c727d728..d6965aa595 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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gg:[40,43],branch:[3,161],branicio2009:157,branicio:[30,157],breakdown:[1,93],brennan:[31,64,109,139,140,152],brenner:93,brick:[19,59,162],brief:[1,2,68,93,96],briefli:[2,71,103,146,161],brilliantov:117,broadwel:4,broken:[28,29,68,96],brook:2,brown:[4,40,42],brownian:[2,37,130,131],brows:0,browser:57,bryantsev:119,btype:[104,121,125,129,152],buc:98,buck:[2,4,32,97],buckingham:[97,98,99,106,132],buckplusattr:146,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],bulatov:[134,135],bulk:[2,29,67,70,105,133,136,146],bundl:[57,161],button:161,bypass:2,c11:133,c_0:[79,93,150,151],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_foo:162,c_gauss:115,c_hb:119,c_i:65,c_id:[2,32,62,162],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_mytemp:162,c_n_k:66,c_p:42,c_peratom:42,c_pi:96,c_prop:2,c_sigma:96,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,104],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,93,102,159,161,162],callabl:3,callback:3,caltech:[2,112],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,90,91,98,99,101,110,116,118,121,125,127,129,142,144,145,152,162],canon:[68,71,78,136],cao1:71,cao2:71,cao:71,capabl:[3,4,93,101],capac:[64,79,149],capolungo:[40,43],captur:[2,93,99,112,117,125,133],carbid:104,carbon:[57,88,93,103,133],card:[4,32,119],care:[2,44,55,67,68,95],carefulli:[3,28],carlo:[2,60],caro:110,carri:[4,79,117],carrillo:4,cartesian:[2,92],cascad:79,cast:162,cat:[4,57],cate:67,categori:[0,93,162],cation:[113,146],caus:[1,2,4,44,61,68,70,74,75,80,81,90,91,119,121,127,130,131,162],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,ceil:162,cell:[2,40,43,44,61,68,69,72,79,112,136],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,82,95,111,112,116,117,130,131,133,134,135,153,154,155,156,157,162],centr:63,central:[29,36,38,41,70,75,76,85,136,141,157],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62,162],cfg:[2,57],cg_type:145,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,88,107,108,152],challeng:2,champaign:130,chan:136,chandler:[92,110],chandrasekhar:[2,121],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,90,91,108,112,117,130,131,133,136,146,152,161,162],change_box:2,chapter:71,charact:[2,19,57,59,65,74,112,114,120,139,140,143,146,162],character:[2,29,38,41,147],characterist:77,charg:[1,2,3,32,40,43,44,97,98,103,104,106,107,110,112,113,121,125,129,142,146,156,157,159,160,162],charl:62,charmm:0,cheaper:[116,144],check:[2,3,19,35,59,73,75,78,90,91,120,162],checkout:161,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,82,88,89,91,93,97,100,101,103,104,105,107,108,109,112,115,116,118,119,121,125,126,129,133,137,139,140,142,146,152],chemic:[31,40,43,58,114,140],chemistri:[72,93,96,112],chen:79,cheng:103,chi:[70,113,116],chiral:88,chmod:3,cho:133,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,91,129],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[154,156],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,109,112,117,120,123,145,154],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:146,cl1:43,clarendon:[13,107],clarifi:[154,156],clark:142,classic:[0,2,4,71,72,79,89,112],classifi:157,clean:2,clear:[2,3,62,162],clebsch:41,click:[3,44,56,57,91,161],climb:91,clockwis:45,clone:161,close:[2,3,19,42,60,61,67,68,75,81,91,93,96,104,105,133,139,140,156,161],closer:[19,59,61,77,91],closest:[70,116,144,152],cloud:146,cluster:[2,4,42,63,75],cmax:133,cmd:[3,71],cmdarg:3,cmin:133,cmm:[18,145],cna:29,co2:[43,74,75,114],coars:[13,18,28,50,65,74,114,118,140,145],coarser:162,coarsest:41,code:[0,1],coeff:[6,45,46,55,82,120,148],coeffici:0,coefficienct:108,coefficient0:110,coefficient1:110,coeffieci:[2,94],coeffincientn:110,coexist:112,cohes:[2,113,133],coincid:[81,100,130,131],cold:2,coleman:[40,43],collect:[2,34,44,102],colliex:43,collis:[67,117,160],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,93,115,119,162],colvar:0,com:[2,37,63,95,161],comand:60,combiant:105,combin:[2,3,18,32,55,57,58,63,68,71,81,82,102,104,105,109,112,113,114,128,129,147,153,154,156,157,159,162],come:[0,2,13,61,62,68,77,78,153,154,156,157,161],comit:161,comm:[0,3,30,91,108],comm_modifi:[2,96,102,108,112,117,162],comm_styl:[19,59,162],comm_world:3,command:[0,1],comment:[3,45,65,74,79,91,92,110,111,113,114,120,133,139,140,141,146,147,153,154,155,156,157,161,162],commit:161,commmand:2,common:[0,1,2,3,4,30,61,71,81,82,117,119,153,154,156],commonli:[2,9,37,38,57,89,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,67,68,79,109,162],comp:[75,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,82,101],compat:[3,19,49,59,62,63,80,136,162],compens:[2,112],compil:[4,57,136,162],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,71,91,113,162],complex:[2,3,9,36,38,41,44,67,81,91,112,136,162],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,90,91,108,112,117,130,131,146,147,162],componenet:2,composit:[2,67,110],compound:[103,112,113,157],compress:[2,57,69,72],compris:[81,114,144],compton:[40,43],comput:[0,1],computation:[2,79,96],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,66],concis:3,concurr:[4,162],conden:[79,154,156],condens:[2,79,93,106,110,121,157],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,71,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,73,88,91,112],confus:157,conjuct:108,conjug:112,conjunct:[2,32,44,67,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,75,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,79,120],conserv:[13,60,66,67,68,74,75,91,107,108,109,117,127,146],consid:[2,29,32,59,60,79,112,144,146,152,162],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146,162],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,102,144],constrain:[2,63,66,75,76,90,112],constraint:[19,39,42,59,63,75,76,80,90,131],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,107,136,152,153,162],constructor:3,consult:4,consum:[1,162],contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161,162],context:[2,4,159,162],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,96,108,123,126,144,155,162],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,159],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,147,161,162],convent:[13,49,54,56,73,110,112,162],converg:[2,19,57,59,60,61,69,72,73,75,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,82,83,87,88,91,92,110,136,154,156,160,162],convex:81,cool:63,coord:[2,3,36,38,70,80,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,90,91,92,93,95,111,146,162],coords:146,copi:[0,3,57,79,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,81,161],corpor:4,corr:103,correct:[2,3,32,45,57,63,68,72,80,81,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,68,75,81,91,106,131,136,161],correl:[2,35,36,41,66,71,162],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160,162],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,39,57,59,62,72,79,80,81,90,93,115,119,162],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:[1,2,3,19,35,45,59,68,75,81,90,91,115,119,162],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,130,148,162],cov:146,coval:[2,13,112,133,146],cover:[2,58,67,112],cpp:[1,2,3,32,75],cpu:[1,4,162],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161,162],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90,162],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,79,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,81],cubes:[19,59],cubic:[38,67,70,110],cuda:[1,162],cuh:96,cummul:[2,60,119],cumul:[2,68,69,91],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161,162],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,90,93,115,119,162],cut:[1,2,4,19],cuthi:70,cutinn:[130,131],cutlo:70,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvar:62,cvff:4,cwiggl:[80,162],cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:96,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2,162],datum:2,davenport:132,davi:80,david:[154,156],daw:[110,143],dcd:[2,57,71],deactiv:129,debug:[2,3,40,43,44,71,162],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],definit:[2,41,62,64,69,80,96,102,109,112,143,147,162],deform:[2,42,61,68,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,82,83,87,88,89,90,107,110,119],delai:2,delet:[28,60,68,152,161,162],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:[74,162],dellago:[2,63],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:65,demo:3,demonstr:[72,133],dendrim:119,denniston:67,denot:[40,63,104,118],dens:[60,74,112],densiti:[2,19,41,44,58,59,67,79,80,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160,162],dependend:2,deposit:[68,75],depth:[26,57,79,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161,162],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,62,66,68,75,90,91,108,110,119,130,131,153,154,156,162],desktop:[2,57],destabil:96,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161,162],detect:[36,91,103,119,120,162],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159,162],devan:145,devanathan:156,develop:[0,2,3,4,62,69,72,93,96,112,135,136,146,157],deviat:[69,70,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:72,dhugoniot:72,dia:133,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:147,diagram:[19,40,43,56,59,71],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,dicken:62,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,91,92,93,96,99,100,102,103,108,109,110,112,114,116,117,118,121,122,124,125,132,133,134,135,137,138,139,140,141,143,144,145,146,147,148,153,154,156,157,159,162],differenti:[1,2,13,74,104,143,155],difficult:[61,62,71,119],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:[136,162],dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,83,84,85,87,90,93,96,100,162],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:112,dij:75,dilat:[61,68,69],dim:[44,133,162],dimdim:162,dimens:[1,2,19,35,42,44,57,59,61,67,68,69,72,80,91],dimension:[36,39,40,41,43,79,91,143],dimensionless:[37,41,62,79,147,159],dimer:[2,133],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:107,dir:[1,3,70,72,143,162],dirac:41,direc:143,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,70,72,77,78,79,80,81,90,91,108,109,117,131],directli:[2,3,32,41,44,57,62,67,74,81,92,93,97,98,99,104,107,110,112,121,125,142,145,152,162],directori:[0,1,2,3,4,62,77,78,91,92,93,96,103,104,110,111,113,129,133,134,135,136,141,143,146,147,153,154,155,156,157,162],disabl:[4,79,120,162],disadvantag:[2,59],disallow:68,discard:[19,59,81],discontinu:[90,127],discourag:133,discret:[2,57,62,67],discuss:[0,1],disk:[2,36],disloc:[29,136],disord:[29,136],disp:0,dispar:144,disperion:[107,125],dispers:[2,99,107,125,130,157],displac:[2,37,61,68,70,117,162],displai:[3,56,57],disregard:136,dissip:[2,31,64,66,77,78,108,109,117,130,131],dist:[2,35,71,73,152],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,144],distinguish:[2,41,112,162],distort:92,distrbut:92,distribut:[0,2,3,19,32,41,56,59,66,67,68,92,96,104,110,111,113,133,134,135,141,143,144,153,154,155,156,157],distro:143,ditto:160,div:4,diverg:[78,93],divid:[2,4,19,35,39,42,56,59,70,90,91,113,146,157,162],divis:[2,55,67,96,129,162],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[102,159],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,81,90,91,92,93,95,103,104,110,111,113,119,133,134,135,141,143,147,153,154,156,157,161,162],docuement:144,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,91,92,93,94,95,96,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,120,123,124,126,127,128,130,131,133,134,135,136,139,140,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[44,93,103,111,153,154,155,156,157],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,67,68,71,79,80,91],domin:[1,112],don:[0,4,81,133,146,161],donald:62,done:[1,2,19,44,55,57,58,59,60,61,62,65,68,71,75,77,78,90,91,93,99,110,125,131,132,133,139,140,152,161,162],donor:119,dot:42,doti:[96,143],doubl:[1,2,3,4,32,45,81,96,113,118,136,162],dover:58,down:[2,3,61,112,146],download:3,downsid:2,dpd:2,dpdtheta:[31,109],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,76],dragforc:67,drai:[57,72],drain:90,dramat:[60,61,68,146],drautz:96,draw:57,drawn:[57,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[92,110,139,140],drift:[2,37,63,66],drive:[3,61,68,70,91],driven:[2,50],driver:2,drop:108,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,70,73,77,78,79,80,81,90,91,105,108,109,110,115,116,130,131,143,144,145,152,154,156,159,160,162],duffi:79,dullweb:68,dummi:[13,155],dump:[0,1],dump_modifi:[2,57,162],dunbrack:[2,5,45,100],duplic:[19,59,70],durat:[56,79,117],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,90,91,108,129,136,138,139,140,162],dvlo:159,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,71,72,73,77,78,79,90,91,108,109,112,130,131,151],dynamo:[92,110,133],dyre:126,e28637:13,e_1:96,e_2:96,e_a:74,e_b:113,e_ee:112,e_hbond:119,e_i:[2,96,113],e_j:[2,96],e_k:96,e_ke:112,e_kl:2,e_lj:[93,107],e_n:[62,96],e_ne:112,e_nn:112,e_pr:112,e_rebo:93,e_torsion:93,e_tot:136,e_vol:136,eaa:82,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,162],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:[3,57,91,162],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebond:162,ebt:46,ec_ii:133,ec_ij:133,ec_jj:133,echo:[3,40,43],ecp:112,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,161],edition:4,edu:[3,110,130],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160,162],effici:[0,1,2,4,39,55,57,61,68,71,75,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[75,90],eggebrecht:[104,146],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156,162],ejtehadi:[102,116,144],elaplong:162,elaps:[80,148,162],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:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157,162],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,66,75,77,78],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,62,68,79,162],elsewher:[133,162],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:[63,155],empti:[120,162],enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],enclos:[2,133,146,162],encod:57,encompass:2,encount:[38,162],encourag:[74,76],end:[1,2,3,4,19,46,57,60,63,66,68,73,74,79,91,108,110,116,132,136,144,147,148,162],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,68,75,121,162],enforce2d:[2,90],eng:[3,103,135],engineer:[58,77,110],enginer:134,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,104],enpub:110,ensembl:[2,32,35,68,71,72,108,146],ensight:2,ensur:[2,41,61,66,68,96,129,153,157],enter:[113,136,157],enthalpi:[74,110,162],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,107,125],entiti:2,entri:[40,65,72,96,111,133,139,140,141,147,153,154,155,156,157,162],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,70,92,96,103,111,112,143,154,162],eos:65,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,80,81,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160,162],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[70,88],equilibr:[2,35,44,60,61,68,72,77,78,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,82,83,87,88,103,133,141,146],equilibrium_start:58,equival:[2,13,61,68,73,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:77,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,90,104,121,144,152,154,156,162],erta:117,especi:[4,44,59,72,73],essenti:[3,11,47,93,104,121,156],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:133,eta:[2,67,68,72,111,113,116,143,155,157],eta_dot:68,eta_ij:143,eta_ji:113,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,90,91,110,111,129,131,136,153,154,156,157,162],etol:[90,91],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,90,91],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,90,136,139,140,143,146,162],evaluat:162,evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,63,68,79,80,81,90,91,95,112,113,117,144,157],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,91,108,129,146,161,162],everyth:161,everywher:123,eviri:112,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,66,79,162],exactli:[2,19,35,44,59,66,72,108,110,117,130,139,140,162],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,90,162],exceed:[19,59,68],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160,162],excess:112,exchang:[2,58,63,79,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:68,execut:[1,2,3,57,162],exempl:146,exemplari:66,exemplifi:112,exert:[2,81],exhaust:[58,162],exhibit:[36,63,68,112],exist:[2,3,29,44,56,57,61,82,83,84,85,87,109,152,161,162],exit:[3,19,59,162],expans:[41,55,162],expect:[1,4,19,59,70,72,133,136,162],expens:[2,70,79],experi:[2,73,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,91,95,110,146,148,161,162],explan:[2,41,70],explanatori:162,explic:137,explicit:[2,3,32,74,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,66,68,69,72,75,79,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:71,explor:[40,43],expon:[74,110,114,116,119,129,137,145],exponenti:[32,74,114,143,153,157,160,162],expos:3,exposit:[58,108],express:[2,41,44,61,70,74,79,96,110,112,123,133,146,147,162],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,90,107,117,133,162],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,112,155],extrema:129,extreme:112,extrins:58,f_1:2,f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:72,f_foo:162,f_harm:78,f_i:[13,143],f_id:[2,62,162],f_ij:143,f_int:77,f_j:13,f_jj:35,f_k:143,f_langevin:79,f_max:72,f_r:[154,155,156],f_sigma:96,f_solid:78,f_ss:2,face:[2,80,81,116,133,144],facil:0,facilit:2,fact:[2,4,78,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,87,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153,162],fail:[3,61,90,91,106],failur:162,fairli:[3,161],faken:30,fall:[2,162],fals:[146,162],famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,68,70,73,80,83,87,91],farrel:[154,156],fashion:[2,19,44,59,62,68,69,72,78,79,80,91,130,162],fast:[2,4,62,72,74,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,86,87,88,89,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,79],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcm:162,fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,90,161],fecr:110,feedback:62,feel:[70,81,91],fehlberg:74,felling:135,felt:81,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,63,68,75,90,91,93,146,162],fewer:[1,3,4],feynman:71,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:152,fictiti:[2,71,73,104,121,125,152],field:0,fifth:[2,114,141],figshar:70,figur:[1,4,72,161],fij:107,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157,162],fill:[44,57,79,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,62,65,70,73,90,91,104,121,125,133,139,140,146,161,162],fine:[4,78,161,162],finer:[41,44,162],finger:44,finish:[2,3,19,59,162],finit:0,finni:110,fire:[90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,82,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161,162],fischer:[2,5,45,100],fit:[2,73,93,96,133,139,140,155,161,162],five:[30,72,96,134],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161,162],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,79,80],fld:[80,130,131],flexibl:[2,57,112,155],flip:[2,68],floor:162,fluctuat:[2,32,61,66,67,68,69,70,78,79,88,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,96,136],fmass:71,fmax:90,fmsec:68,fno:4,fnorm:90,fnve:63,focu:75,foil:[41,70,147],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],foo:[3,57,74,162],foo_species:74,foot:2,forc:[0,1],forcefield:[73,119],forcegroup:67,ford:107,forgiv:68,fork:161,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,82,85,88,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159,162],formal:[2,35,66,68,71,146],format:[2,19,57,59,65,74,79,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157,162],formation:65,former:[2,19,59,79,96,162],formul:[1,2,42,68,73,75,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,44,46,56,62,70,76,80,82,84,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159,162],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,63,67,104,107],four:[2,3,28,41,62,79,88,91,136],fourier:2,fourth:[2,4,37,73,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,72,74,91,96,114,117,130,131],frame:[41,58,72,116],framer:57,framework:[92,147],frattl:63,free:[2,13,29,32,70,77,78,79,91,112,129,136,138,143,159],freedom:[2,39,60,68,69,71,75,78,90,107],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,108,112,146,162],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,117],from:[0,1],front:72,frontend:57,frozen:[2,39,66,115],fs2:[2,35],fstr:162,ftol:[90,91],fuction:104,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,96,110,112,113,116],fuller:90,fulli:[2,70,90,91,104,143,161],fulton:110,fumi:97,func:162,funcfl:110,fund:0,funrol:136,further:[2,37,57,67,71,79,90,91,92,95,103,136,146,162],furthermor:[11,47,63,74,109,112],futur:[0,2,59,66,91,134,135],g_jik:143,g_p:79,ga3:43,gaa:96,gai:116,gain:[4,62],galindo:137,gamma0:13,gamma:[2,13,67,72,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:79,gamma_ijk:154,gamma_n:117,gamma_p:79,gamma_t:117,gammaa:137,gammafactor:67,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,66,71,73,108,112,115,162],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:68,gener:0,gentler:80,gentli:111,geom:2,geometr:[2,44,59,68,81,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159,162],geometri:[2,9,19,44,59,61],gerar:162,gerber:129,germann:[69,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,91,104,157,161,162],get_natom:3,get_rank:3,get_siz:3,getenv:162,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,68,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,68,70,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gmask:162,gnu:0,gnuplot:3,goal:62,goddard:[2,9,89,112,119],goe:[28,41,44,63,90,107,111,118,123,126,148,160],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],gove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pact:[1,2,93],impart:2,impei:[2,121],implement:[1,2,11,31,32,38,40,43,44,47,56,62,63,64,67,68,71,72,74,75,79,88,90,91,92,96,103,104,106,108,109,110,111,112,121,125,129,133,144,154,156,162],impli:[2,32,42,57,73],implicit:[2,66,80],implict:105,important:78,impos:[2,39,63,70,77,78,80,81,90,91],imposs:1,improp:[0,4,39,42,44,60,82,83,84,85,86,87,88,89,90,162],improper:[4,88],improper_coeff:[82,83,84,85,86,87,88,89],improper_styl:[0,2],improv:[0,1,4,19,59,63,68,119,121,136,153,155],in3:43,inaccur:[1,2],inaccuraci:81,inact:119,inappropri:44,incid:[40,43],includ:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,32,33,34,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,66,67,68,69,70,71,72,73,74,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,141,142,143,144,145,147,148,153,154,155,156,157,158,159,160,161,162],inclus:[0,32,162],incompat:3,incomplet:3,incompress:112,inconsist:60,incorpor:[55,72,96,105,161],incorrect:133,incorrectli:[117,162],increas:[1,2,4,40,42,57,60,62,63,65,73,74,91,93,112,116,139,140,155,162],increasingli:112,increment:[3,59,68,146,162],incur:79,indefinit:77,indent:[90,162],independ:[2,3,19,35,44,59,60,61,66,67,68,78,79,117,136],index:[0,2,3,65,71,79,139,140,162],indic:[2,3,4,6,28,31,33,35,37,39,42,46,57,61,62,68,79,82,88,103,113,133,136,141,146,154,156,161,162],indirectli:[2,62,162],indium:147,individu:[0,1,2,3,4,32,39,42,44,56,57,61,62,63,67,68,75,90,97,98,100,101,104,110,112,118,120,121,125,142,145,162],induc:0,ineffici:[2,29,30,36,38,41,57,68],inerti:131,inertia:[2,131,162],infer:[59,113],infin:90,infininti:57,infinit:[67,79,112],infinitesim:2,inflect:[105,123],influenc:[19,154,155,156],inform:[0,1,2,3,4,19,40,43,44,45,57,58,59,60,61,62,63,67,70,73,75,76,77,80,81,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],infrequ:[2,68,108],infti:[105,130,131],ingtegr:96,inher:90,inherit:2,inhomogen:79,inidividu:90,init:146,init_fil:79,initi:[2,3,19,32,44,57,58,59,60,61,62,65,66,67,68,69,71,72,73,74,77,78,79,80,90,91,93,107,108,136,139,140,146,162],initial:[2,162],initialt:79,inlclud:3,inner2:[100,118],inner:[4,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],inner_distance_cutoff:119,innner:127,inorgan:[2,157],inp:[147,157],input:[0,1],insert:[44,147,152],insid:[2,3,44,63,67,80,81,162],inside:[67,123],insight:2,instabl:[67,107],instal:[1,2,3,4,57,91,99,100,121,125,129,136,161],install:0,instanc:[2,3,115,143],instantan:[2,60,61,62,66,68,69,72],instanti:[2,3,58],instead:[1,2,3,4,19,29,34,45,59,61,67,98,99,110,120,122,129,133,136,138,162],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,57,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],instruction:3,insuffici:2,insult:68,insur:[2,3,30,44,57,79,80,81,102,116,144,162],integ:[2,3,29,38,41,44,45,48,49,52,55,57,60,62,66,67,72,74,79,86,108,109,133,147,162],integral:[71,139,140],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,66],intens:[1,2,33,34,35,37,39,40,43,59,60,68,69,79],intepol:162,inter:[60,91,96,162],interact:[1,2,3,13,28,32,36,38,39,41,42,45,50,55,56,60,70,71,73,74,79,80,81,83,84,85,87,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,142,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160],interatom:[44,77,78,92,96,110,112,133,136,146,155,162],intercept:40,interchang:[2,62],interconvert:112,interesect:81,interest:[1,3,43,71,78,111,131,162],interf:161,interfac:0,interfer:[68,93],interg:2,interi:131,interior:[2,19,81],interlac:133,interleav:[2,44],intermedi:[2,57,70,88,91],intermolecular:93,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,42,44,46,57,58,62,64,65,68,69,74,82,83,87,88,90,109,114,139,140,149,162],internal:[57,162],internal_element_set:58,internal_quadratur:58,internat:[4,40,43,58],interpenetr:133,interpentr:[149,150],interpol:[2,57,58,65,67,70,91,96,139,140,154],interpret:[2,3,55,57,117,148,162],interrupt:72,intersect:[2,40,81],intersert:81,interspers:90,interstiti:136,interv:[2,35,62,68,72,146,162],intestieti:40,intial:[2,93],intiial:19,intramolecular:13,introduc:[2,36,38,57,63,68,72,88,92,104,112,121,125,129,153,162],introduct:0,inv:[40,43],invalid:[33,91,130,131],invari:[38,41,62],invent:75,invers:[2,26,40,43,72,88,89,97,104,121,158,159],invert:[1,2],invis:81,invoc:60,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,63,66,67,68,69,70,75,76,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,147,148,153,154,155,156,157,158,159,160,162],involv:[2,67,90,91,95,116,153,154,156],ion:[2,79,96,105,113,115,133,136,146,156,160],ionic:[2,97,98,105,112,113,142,146],ioniz:[103,112],ipp:0,ir3:43,ir4:43,irregular:[2,19,59,61,68],irrelev:141,irrespect:[130,131],irrevers:74,is_act:162,is_avail:162,is_defin:162,isbn:159,isenthalp:68,ismail:[99,125],isn:[3,63],iso:[61,68,69],isobar:[68,109],isodem:112,isoenerget:109,isoenthalp:109,isol:117,isomorph:71,isotherm:[68,109],isotrop:[2,36,116,130,131],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,45,46,47,48,49,50,51,52,53,54,57,60,61,63,68,69,71,75,78,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,152,153,154,155,156,157,158,159,160,162],issue:58,item:[2,19,59],iter:[2,19,59,61,75,90,91,146,162],iterat:90,ith:[62,162],itself:[2,3,35,57,79,91,104,113,116,139,140,162],ityp:44,ixx:162,ixy:162,ixz:162,iyi:162,iyz:162,izumi:155,izz:162,j0jt:35,j_m:41,jackson:137,jacs:[2,45],janssen:70,januari:133,jaramillo:112,jcp:80,jeffer:4,jello:68,jeremi:135,jik:96,jmm:41,job:75,jochim:68,join:[2,29,117],joint:119,jon:29,jone:[1,2,21,22,32,45,58,63,80,81,90,93,95,98,99,100,101,102,107,116,118,119,120,121,122,123,125,126,128,129,132,137,143,144,145],jonsson:[30,91,146],jorgensen:[2,53,104,121,125],journal:[50,58,110,136,149,150],jpeg:57,jpg:57,jth:162,judici:2,jump:[2,18,69,162],jun:4,just:[2,3,13,35,42,57,62,79,91,93,95,143,161,162],justo:111,jusufi:[105,115],jut:81,k11:35,k22:35,k33:35,k_2:85,k_4:85,k_sigma:96,k_ub:5,kalia:157,kapfer:38,kappa:[2,35,104,109,121,158,159],kappa_:79,karplu:32,karttunen:67,kate:0,kaufmann:4,kayser:105,kcal2j:35,ke_eta_dot:68,ke_etap_dot:68,ke_omega_dot:68,keblinski:[104,146],keef:40,keep:[54,62,74,78,90,104,129,147,161,162],kei:[2,157],kelchner:29,kemper:103,kepler:1,kept:[2,69,77,78],kernel:[4,58,66,136,149,150,151],keword:57,keyword:[2,4,19,29,32,34,36,37,38,39,40,41,42,43,44,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],keywrod:112,khersonskii:41,khvostov:4,kim:[133,134,135],kind:[1,2,3,19,30,57,59,60,75,91,96,112,162],kinemat:[130,131],kinet:[2,32,35,39,42,61,63,68,69,72,74,90,112,114,140],kjl:88,klein:[2,58,68,121,145],kmax:40,kmp_affinity:4,knight:4,knl:4,knock:79,know:[3,19,90,111,161],knowledg:57,known:[41,57,62,63,77],kokko:[1,162],kokkos:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],kollman:[2,45],kone:[77,78],koning00a:77,koning00b:77,koning96:[77,78],koning97:78,koning99:77,kraker:4,kremer:[21,22],kress:[134,135],kspace:[0,1,2,32,39,42,90,97,98,99,100,104,107,121,125,129,131,145,162],kspace_modifi:[2,4],kspace_styl:0,kstart:73,kstop:73,kth:[66,71],kub:5,kubo:[2,35],kumagai:155,kumar:[130,131],kuronen:143,kutta:74,l12:133,l_box:112,l_skin:79,la3:43,label:[63,71,91,162],laboratori:[0,31,64,72],lack:[4,112],lackmann:96,ladd:78,lafitt:137,lag:[62,79],lagrangian:[2,58,72],lagrangian_posit:72,lagrangian_spe:72,lambda1:[154,155,156,157],lambda2:[154,155,156],lambda3:[154,156],lambda4:157,lambda:[32,40,43,67,77,78,79,92,111,129,138,153],lambda_fin:77,lambda_initi:77,lamda:[27,138],laminar:151,lammp:[0,3,91,133,136,161,162],lammps2pdb:2,lammps_clos:2,lammps_command:2,lammps_extract_atom:2,lammps_extract_comput:2,lammps_extract_fix:2,lammps_extract_glob:2,lammps_extract_vari:2,lammps_fil:2,lammps_get_coord:2,lammps_get_natom:2,lammps_ns:2,lammps_open:2,lammps_potentials:103,lammps_put_coord:2,lammps_quest:2,lammps_rk4:74,lammps_set_vari:2,lammps_sppark:2,lammps_vers:2,lamms:2,lamoureux:2,land:4,landron:146,lane:1,langevin:[2,66,68,69,72,73,78,79,91,107,108],languag:[2,3,62,162],larentzo:[31,64],larg:[0,1,2,4,19,29,42,44,50,57,59,60,61,62,63,67,68,72,73,75,79,80,81,88,90,102,108,112,116,117,120,136,139,140,144],larger:[1,2,3,19,29,44,57,63,67,68,73,79,80,81,90,91,96,102,104,105,112,117,121,125,131,152,162],largest:[2,44,90,139,140,152,162],laser:79,last:[1,2,3,42,55,57,59,74,90,91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i:[13,41],r_ii:41,r_ij:[13,96,112,143,160],r_ik:143,r_j:13,r_jik:143,r_m:132,r_me:105,r_mh:115,r_min:106,r_ub:5,ra2:43,rad2theta:43,radial:[41,90,112,119,139,140],radian:[5,6,8,12,16,17,18,43,46,54,73,82,83,87,88],radiat:[40,43,79],radii:[41,60,102,110,116,117,130,131,136,159],radit:112,radiu:[2,33,34,40,41,57,67,76,80,81,96,102,112,113,117,121,129,130,131,132,133,146,147,156,159,162],rahman:[2,61,68,72],rai:43,ram:156,raman:4,ramp:[2,66,68,72,80,100,108,118,129,130,132,148,160,162],ran:[2,3],random:[2,44,57,60,66,67,68,71,72,79,108,109,162],randomli:44,rang:[1,2,4,38,39,41,42,43,50,57,58,62,90,93,94,96,97,98,99,100,101,102,104,105,106,107,108,110,112,114,116,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,142,143,144,145,146,152,156,158,159,160],rank:[2,3],rankin:69,rapid:[2,3],rapidli:[60,68,104,108],rare:2,rasmol:2,rasmussen:116,raster3d:2,rate:[2,4,58,72,74,77,78,114,130,131,140],rather:[2,19,39,57,59,66,79,112,139,140,162],ratio:[2,32,41,59,116,117,144,149],rattl:63,rattle:[63,75],rattle_debug:75,ravelo:[69,123],raw:4,rayleigh:72,rb1:43,rbb:146,rcb:[19,59],rcm:[33,34],rcmx:[33,34],rcmy:[33,34],rcold:63,rcutfac:[41,147],rd1:91,rdn:91,rdt:91,reach:[2,19,59,61,62,69,74,105,162],reacquaint:161,react:2,reactant:[74,112],reaction:[65,74,76,91,112,114,140],reactiv:93,read:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,60,61,65,68,69,71,74,75,78,79,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],read_data:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,44,45,46,47,48,49,50,51,52,53,54,55,56,57,60,71,73,74,82,83,84,85,86,87,88,89,91,94,95,97,98,99,100,101,102,104,105,107,108,109,112,115,116,118,119,121,122,123,124,125,126,127,128,129,130,131,132,137,138,142,143,144,145,146,148,152,158,159],read_dump:91,read_restart:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,44,45,46,47,48,49,50,51,52,53,54,56,58,61,67,68,69,71,79,82,83,84,85,86,87,88,89,91,94,95,97,98,99,100,101,102,104,105,107,108,109,112,115,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,137,138,142,144,145,148,152,158,159],readabl:57,readi:3,readme:[1,2,3,4,136],real:[2,3,11,14,15,35,36,38,41,44,47,71,72,80,86,104,136,156],realli:[1,39,42,161],reamin:[80,81],rearrang:91,reason:[2,3,44,55,77,78,91,105,112,113,115,131],reax:[0,72],rebal:[19,59],rebalanc:[19,59],rebuild:[3,4,108],rebuilt:57,recalcul:32,receiv:70,recent:[3,4,59,62,133,162],reciproc:[2,40,43,97,98,99,104,107,112,121,125,142,145],recogn:[30,68,74,110,133],recomend:2,recommed:74,recommend:[4,57,63,72,78,112,130,131,136,144,146,161],recompil:[1,75],reconstruct:146,recov:[61,63,68],rectangl:[19,59],rectangular:[19,59],rectilinear:[40,43],rector:27,recurs:[19,59,96],recust:19,red:[57,60,71],redefin:162,reduc:[1,2,11,19,39,40,42,43,57,59,60,70,73,74,90,112,116,143,144,153,154,156,162],reduct:[40,43,72],redund:113,reed:72,ref:[77,78],refactor:2,refer:[2,3,4,13,32,44,58,60,61,62,63,68,69,70,71,72,75,82,89,92,116,133,135,136,144,150,151,154,156],referenc:[2,62,104,119,141,144,162],reflect:[2,40,41,43,56,57,62,80,96,162],refresh:58,regard:[2,75],regardless:[44,68],regim:[2,105],region:[0,2,19,35,43,44,50,57,58,59,63,68,79,80],region_styl:81,regoin:2,regress:162,regspher:44,regul:2,regular:[1,19,57,59,79,105],reigon:162,reinder:4,reinhardt:[77,78],reject:[44,60],rel:[1,2,11,18,19,36,41,44,47,59,63,70,74,79,90,112,116,117,130,131,133,144,159],relat:[1,2],relationship:[2,146,159,162],relax:2,releas:0,relev:[2,19,44,58,59,62,63,66,67,75,76,79,80,90,94,102,104,105,107,108,112,115,116,117,118,119,120,122,123,124,126,127,128,130,131,138,139,140,144,148,152,158,159,160],reli:[112,160],reltol:74,remain:[19,32,55,56,61,68,79,96,112,129,136,161,162],remaina:96,remaind:[44,156],remap:[2,44],remedi:2,rememb:161,remot:161,remov:[2,28,36,38,41,44,68,74,75,91,107,131,136,161,162],remove_molecul:58,remove_sourc:58,remove_speci:58,ren:43,renam:161,render:57,rendon:68,reneighbor:[59,108],repeat:[2,57,60,61,74,96,154,156],replac:[2,3,19,33,34,57,59,60,69,93,104,117,123,139,140,162],replica:0,repons:62,report:[0,1,4,40,43,72,73,74,79,91,107,112,133,162],repositori:161,reprens:79,repres:[1,2,19,29,34,50,57,61,62,65,66,67,68,71,74,79,81,91,92,96,116,129,130,131,133,134,135,142,143,162],represent:[2,66,71,79,96,112,116,136,144],reproduc:[4,68,104,110,117],repul:133,repuls:[2,18,21,22,80,81,93,96,102,104,108,112,114,117,119,129,133,137,146,152,156,157,159,160],request:[2,19,67,161,162],requir:[1,2,3,4,18,19,28,31,32,40,42,43,44,45,55,57,58,59,60,64,65,66,67,68,74,75,79,80,82,90,91,92,93,95,96,100,102,103,104,108,109,110,111,112,113,116,117,119,127,129,130,131,133,134,135,136,138,139,140,141,143,144,145,146,147,152,153,154,155,156,157,159,160,162],rerun:[36,38,41,57],rescal:[2,63,68,69,77,78],research:[31,64,67,136],resembl:161,resepct:2,reservoir:[35,63,79],reset:[2,3,33,34,61,68,69,75,79,90,131,162],reset_atomic_reference_posit:58,reset_tim:58,reset_timestep:[2,35],resist:2,resolut:146,resolv:[61,71,131,161],resourc:[92,110],respa:[4,68,70,73,76,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],respecifi:136,respect:[1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,33,39,40,43,45,46,47,48,49,50,51,52,53,54,57,60,61,63,67,68,69,75,79,80,82,83,84,86,87,88,89,90,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,141,142,144,145,146,147,148,153,154,155,156,157,158,159,160,162],respond:[2,62,112],respons:[2,62],resquar:[2,116],rest:[2,73,96,131,133],restart1:71,restart2:71,restart2data:0,restart:[0,1],restor:44,restrain:13,restraint:[73,120],restratin:73,restrict:[1,2],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,34,35,39,40,42,43,44,45,46,47,48,49,50,51,52,53,54,57,59,60,61,62,63,66,67,68,69,71,74,75,77,78,79,80,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,133,134,136,138,139,140,141,142,144,145,148,153,154,155,156,157,158,159,160,162],resum:162,retain:[93,96,136],retriev:[2,134,135,162],rev:[2,29,36,38,41,42,68,69,77,78,96,102,103,104,107,110,111,112,116,117,123,130,131,132,133,135,139,140,143,144,147,153,154,155,156,157],revers:[2,32,49,60,68,70,77,91,129],review:[41,136,147,161],rfac0:[41,147],rg0:76,rh3:43,rh4:43,rheolog:2,rhi:[139,140],rho0:[133,150,151],rho0_meam:133,rho:[67,92,97,98,99,110,132,133,134,135,139,140,144,149],rho_0:[150,151],rho_alpha_beta:110,rho_bkgd:133,rho_colloid:80,rho_e:79,rho_i:[134,135],rho_ref_meam:133,rho_wal:80,rhodopsin:[1,4],rhosum:[149,150,151],rhot:63,rhs:74,rick:[103,146],right:[2,3,19,29,44,54,56,59,60,67,70,74,104,161,162],rightmost:[19,59],rii:[33,34],rij:[36,38,70,108,109,139,140,152],rin:[119,126,127],ring:[2,45,71],rino:[30,157],rirj:117,risi:[41,147],risk:73,rix:[33,34],rk4:74,rkf45:74,rlo:[139,140],rmask:162,rmin0:[41,147],rmin:123,rms:74,rnemd:2,robust:90,rock:133,rockett:143,role:2,ronchetti:38,root:[3,32,33,34,110],rose:133,ross:133,rosski:71,rot:[2,35,71,73],rotat:[2,41,44,81,90,107,116,144],rotation:38,rough:[2,44,57],roughli:[19,57,68,91],round:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,139,140,141,142,144,145,148,153,154,155,156,157,158,159,160,162],rous:66,rout:[32,119,129],routin:[2,3,4,67,136],roux:2,row:[2,34,43,79,112],rozero:133,rrespa:[1,4,68,92,93,94,95,97,98,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],rsq:[139,140],rsurfac:79,ru3:43,ru4:43,rub:5,rubia:[134,135],rule:[0,2,13,29,44,60,68,81,92,94,95,101,102,107,119,124,133,137,148,152,153,154,156,160,162],run1:[2,162],run2:[2,162],run3:[2,162],run4:[2,162],run5:[2,162],run6:[2,162],run7:[2,162],run8:[2,162],run:[0,1],run_styl:[4,68,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],rung:74,runtim:57,rutherford:79,rutuparna:[154,156],rxn:74,ryckaert:[75,88],rydberg:136,s0st:2,s2050:1,s2629:110,s319:58,s_i:[2,112],s_ij:2,saddl:91,sadigh:[110,134,135],saed_vtk:40,safe:[57,161],safran:159,sagui:107,sai:[1,161],said:90,sakai:155,sall:146,salt:[105,115,133],salter:146,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,35,36,37,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,63,66,67,68,69,70,71,72,73,75,77,78,79,81,82,83,84,86,87,88,89,91,92,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,137,138,141,142,143,144,145,146,148,152,153,154,155,156,157,158,159,160,161,162],sampl:[1,2,3,35,57,68,71,76,78,96],sample_frequ:58,sandia:[0,29,113,133],saniti:73,satellit:2,satifsi:162,satisfi:[30,40,41,43,61,63,67,69,75,90,117],satur:105,save:[2,57,60,66,74,79,96],sb3:43,sb5:43,sc3:43,scalabl:[0,1,4],scale:[0,1,2,4,35,41,45,57,58,61,67,68,69,71,72,77,78,79,92,93,105,112,114,117,130,131,133,136,162],scalegamma:67,scalexi:[61,68,69],scalexz:[61,68,69],scaleyz:[61,68,69],scatter:[3,40,43],scatter_atom:3,sc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,79,91,110,113,120,133,139,140,147,161,162],tfinal:162,tfix:73,tflag:57,th4:43,thakkar:4,thakker:4,than:[1,2,3,4,11,19,36,37,38,39,42,47,59,60,61,66,67,70,72,73,74,76,79,80,81,90,91,93,95,96,97,98,99,100,110,112,116,117,130,131,133,139,140,144,146,148,152,153,156,159,160,162],thank:[154,156],thei:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,32,33,34,35,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,60,61,62,66,67,68,69,73,75,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,140,141,142,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161,162],them:[1,2,3,19,28,35,46,57,59,60,61,62,68,69,70,73,75,79,82,91,92,96,110,113,116,144,148,161,162],themselv:[2,3,59,91,92,96,104,110,129,133,134,135,147,162],theorem:[66,96,109],theoret:[37,72,153],theori:[2,41,58,68,96,136,159],therebi:[130,131],therefor:[2,32,63,67,75,106,153],therein:[2,133],thereof:32,thermal:0,thermo:[0,1],thermo_modifi:[2,61,68,152],thermo_press:[39,61,68,69],thermo_styl:[2,31,35,39,42,44,60,61,68,69,72,80,90,93,115,119,162],thermo_temp:[39,60,61,68,69],thermoberendsen:2,thermochemistri:112,thermodyanm:60,thermodynam:0,thermost:2,thermostat:0,thermostatequ:2,thesi:130,thess:97,theta0:[5,6,8,10,11,12,16,17,18,41,47,73,88],theta0max:41,theta10:96,theta1:[46,55,82,96],theta2:[46,55,82,96],theta3:[82,96],theta4:96,theta5:96,theta6:96,theta7:96,theta8:96,theta9:96,theta:[2,10,11,36,38,41,43,44,47,57,73,79,82,88,119,143,155],theta_0:141,theta_:[88,96],theta_c:119,theta_ijk:96,theta_ijl:82,theta_jik:[134,135],theta_pi:96,theta_sigma:96,thi:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],thick:[40,57],thin:57,thing:[2,3,28,61,68,161,162],think:[2,3,62,83,87,90,162],third:[2,13,29,35,41,42,62,66,76,79,103,113,114,133,141,157],thirumalai:50,tho:111,thole:2,thompson:[0,39,41,42,147],those:[1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,32,35,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,57,61,63,68,69,75,77,78,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,138,141,142,144,145,147,148,153,154,155,156,157,158,159,160,161,162],though:[2,35,44,61,62,91,108,110,112,113,116,117,129,130,157,162],thought:[80,117,120],thread:[1,4],three:[1,2,28,29,32,35,36,37,40,41,43,44,50,60,61,62,63,68,69,74,77,79,85,86,88,92,93,96,110,111,113,116,117,120,133,134,135,136,141,143,144,146,147,153,154,155,156,157,162],threebodi:153,thresh:[19,57,59],threshhold:[19,57,59],threshold:[19,59,70],through:[2,3,44,61,65,67,68,71,74,79,80,81,93,109,111,112,114,117,121,136,140,145,146,148,152],throughout:[2,4,40,136],thru:[2,3,33,34,37,90],thrust:1,thu:[1,2,3,19,29,30,34,35,36,38,41,42,44,45,56,57,59,60,61,63,66,68,69,70,75,76,79,80,81,82,90,91,92,93,95,96,97,98,99,100,101,102,103,104,108,109,110,111,112,113,114,115,116,117,121,125,129,130,131,133,134,135,136,138,139,140,142,143,144,146,147,149,150,151,152,153,154,155,156,157,160,162],thumb:[44,102],ti2:43,ti3:43,ti4:43,tidi:161,tight:[96,146],tij:107,tildeslei:[13,32,107],tile:[2,19,44,59,162],tilt:[2,61,68,70,72,157],time:[0,1],time_integr:58,timer:1,timescal:[72,112],timespan:68,timestep:[1,2,3,19,35,42,57,59,60,61,62,63,66,67,68,69,70,73,74,75,77,78,79,80,90,91,96,108,112,119,130,131,148,162],timesteppnig:75,tin:[103,104],tini:[44,90,96],tio2:146,tio:146,tip3p:0,tip4:2,tip4p:0,tip:0,tirrel:80,titl:161,tji:107,tl1:43,tl3:43,tlbr_msw:143,tloop:[68,69],tm3:43,tmp:[2,19,34,57,59,162],tobia:68,togeth:[2,3,4,19,42,44,59,61,68,115],tol:[75,153],toler:[61,74,75,90,91,153],tolernac:74,too:[1,2,19,29,30,36,38,41,57,59,61,63,68,75,79,91,108,162],took:148,tool:[0,1,2,3,19,57,59,91],toolkit:2,top:[0,3,4,67,91,147,161],topic:162,topolog:[2,32,56],torqu:[2,13,67,90,95,107,116,117,131,162],torsion:[2,46,56,93],torsion_flag:93,tosi:97,tot:146,total:[2,3,4,19,31,33,34,35,37,41,42,59,66,67,68,69,71,72,73,74,77,78,79,80,81,90,91,92,93,95,96,103,110,112,117,133,134,135,136,143,146,147,162],toukmaji:107,toward:[13,57,67,69,70,88,91],toxvaerd:126,tptask:4,trace:112,track:[67,79,162],track_displac:58,tractabl:74,trade:[2,104,121,125],tradit:[2,55],trail:[32,91,113,133,147],trajectori:[2,32,68,71,75,108],tran:[49,50],transfer:[1,2,4,58,79,96,136],transform:[2,32,116,138],transit:[2,4,91,105,129,135,136,156],translat:[2,63,68,71,112],transmit:2,transport:[58,79],trap:[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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 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 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525],"try":[1,3,8,12,16,18,219,252,258,344,345,346,351,496,520,525],"var":[3,11,12,178,359,377,509,525],"void":[4,6,7,8,41,181,225,245,501],"while":[1,3,9,11,12,13,17,74,75,115,152,161,176,189,203,208,217,229,231,232,236,248,249,254,255,256,258,264,272,295,308,309,313,315,319,349,379,387,394,400,411,417,459,460,481,483,486,493,496,507,512,519],__main__:496,__pthread_key_cr:12,_boundingbox:204,_compute_group_group:154,_compute_heat_flux:154,_compute_t:8,_j1m1m1:152,_j2m2m2:152,_manifold_rattl:520,_pair_lj:9,_serial:12,_wirnsberg:239,a10:361,a123:361,a12:461,a2m:[6,99],a_0:[258,348,400],a_0_real:258,a_1:348,a_2:348,a_3:348,a_4:348,a_c:408,a_cc:408,a_f:483,a_ij:400,a_pi:400,a_sigma:400,a_ss:408,aat:185,aatom1:[68,126],aatom2:[68,126],aatom3:[68,126],ab_23_cd:361,abbrevi:12,abc:[3,12,361,496,525],aberdeen:[88,89,241,323],abf:230,abf_integr:13,abi:208,abil:[3,229,272,305,318,419],abl:[3,8,9,11,12,39,94,203,208,228,238,246,288,344,351,394,496,525,529],ablat:348,abort:513,about:[0,1,3,6,8,9,11,12,13,15,16,39,41,42,63,65,82,119,126,127,130,172,178,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,240,244,245,246,247,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,268,271,277,281,282,283,284,285,286,287,288,289,290,291,294,298,299,300,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,318,320,321,322,332,333,334,336,337,339,340,341,342,343,344,345,346,347,348,350,351,352,353,355,356,357,358,359,376,379,383,386,387,389,394,399,405,410,427,456,460,489,496,499,500,505,506,508,513,517,520,525,528,530],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,35,37,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,59,65,66,71,74,75,76,77,80,81,94,95,97,98,99,103,104,106,107,123,125,127,128,130,152,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,176,177,178,180,181,184,185,186,187,188,189,190,191,192,193,195,196,197,199,203,204,205,206,207,210,211,212,213,214,218,219,220,222,223,225,228,229,231,232,233,238,242,245,247,251,253,255,256,257,261,271,272,277,301,304,306,311,317,318,319,324,332,336,339,340,341,342,359,361,362,363,364,365,366,367,368,369,371,373,379,381,384,388,389,393,394,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,451,452,454,456,457,459,460,461,462,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,501,502,505,506,507,508,509,512,513,516,519,520,525,526,529,530],abscissa:[451,452,479,480],absenc:214,absent:519,absolut:[3,207,217,230,232,236,319,324,338,378,379,387,424,432,499],absorb:348,absoult:379,abstol:319,ac3:177,academ:247,acc:343,acceler:0,accelri:[6,13],accept:[7,12,95,176,178,207,228,232,247,319,343,404,436,506,513,520],acceptanc:217,acceptor:426,access:[0,3,6,7,8,9,11,12,15,38,40,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,93,96,97,98,99,100,101,102,103,105,106,109,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,128,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,173,174,175,176,177,200,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,234,237,238,239,240,244,245,246,247,248,249,250,251,252,253,255,257,258,259,260,261,262,263,264,265,266,268,269,270,271,272,277,281,282,283,284,285,286,287,288,289,290,291,294,298,299,300,302,303,304,305,306,307,308,309,310,311,312,314,315,316,317,318,320,321,322,324,329,332,333,334,335,336,337,338,339,340,341,342,344,345,346,347,348,350,351,352,353,354,355,356,357,358,374,378,394,396,422,424,426,427,444,459,460,469,495,496,499,504,516,517,525],accident:520,accidenti:371,accler:[9,12],accommod:215,accomod:272,accompani:8,accomplish:[15,232,259,289],accord:[6,66,75,88,133,139,142,160,206,217,226,227,243,258,272,288,300,308,324,326,345,346,348,353,354,356,357,358,390,419,424,435,438,457,464,466,467,469,471,472,474,475,476,512,525],accordingli:[11,112,156,157,171,176,182,390,441,442,476],account:[3,6,95,130,160,176,177,186,198,220,222,237,239,252,253,255,272,278,279,280,292,293,295,297,299,303,309,318,320,322,332,334,335,336,339,340,341,344,348,351,367,388,410,415,424,432,436,441,442,444,447,467,495,512,520,526],accuml:[3,318,344,351],accumul:[6,8,14,75,88,154,210,220,221,255,318,324,350,376,394,504,524],accur:[1,3,6,9,14,16,37,41,56,161,225,270,313,318,319,322,336,344,351,357,359,379,400,419,423,424,449,461,477,479,480,481,483,512,517,525],accuraci:[1,3,6,12,41,202,203,207,225,239,249,272,310,322,349,359,378,379,386,396,419,449,451,452,459,460,479,480,487,507,512,517,519,525,529],accuractli:517,ach:378,achiev:[1,3,6,9,10,15,16,17,28,41,225,239,247,249,272,273,288,300,301,308,378,427,507],achiv:17,acid:9,ackland1:417,ackland2:417,ackland:2,acknowledg:0,acml:12,aco:525,acolor:[206,207],acoust:300,acquir:[3,6,60,63,64,181,182,227,229,232,272,455,491,503,519],across:[1,2,3,6,9,12,13,14,41,59,63,68,71,73,75,84,102,119,126,128,166,180,182,219,222,225,237,251,318,319,320,325,344,348,351,357,361,389,394,493,498,501,502,506,515,517],act:[3,6,73,119,129,163,236,250,253,254,255,256,258,261,271,318,329,343,345,346,348,357,358,359,387,402,413,423,424,426,461,476],acta:[130,177,395],actinid:[9,447],action:[2,6,11,12,75,248,253,346,519],activ:[5,8,11,12,13,15,55,61,95,176,230,248,252,255,261,267,271,298,318,319,327,347,376,440,477,507,519,522,525],active:[267,492],actual:[1,3,6,8,12,56,64,134,161,203,204,207,211,212,224,226,227,231,236,255,256,295,299,304,305,313,316,324,336,339,340,341,343,349,358,359,378,390,423,425,430,435,441,442,476,495,496,507,508,516,525],actualli:338,adam:[378,379],adapt:[2,3,6,9,95,172,210],adapti:299,adaptiv:[9,230,396],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,40,42,75,95,99,112,125,128,129,131,176,178,179,203,204,205,206,210,211,212,213,214,216,218,219,220,222,223,227,230,231,236,238,239,245,249,250,251,253,255,257,258,262,270,271,272,273,274,275,276,277,278,279,280,292,293,295,296,297,299,307,317,318,321,322,332,333,335,339,341,342,346,347,348,350,352,353,357,359,379,381,386,388,396,401,403,406,410,419,427,432,444,449,450,454,460,462,496,498,499,504,506,508,510,517,519,520],add_molecul:216,add_speci:216,add_to_nodeset:216,added:[499,520],addforc:[2,3,210],adding:[8,213,238,317,520],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,236,238,239,242,243,247,249,250,251,255,258,272,273,274,275,276,277,278,279,280,290,292,293,295,296,297,299,307,318,321,322,323,325,349,352,353,357,363,369,372,374,379,381,389,391,394,395,396,400,401,403,405,407,409,410,413,415,416,417,418,419,420,424,425,427,428,429,431,432,440,442,443,444,445,446,447,449,451,452,453,454,457,459,460,462,467,468,477,478,479,480,481,482,483,486,490,493,498,499,500,505,506,507,510,512,519,520,521,523,525,528,529,530],addition:[0,4,6,8,11],additionali:204,addres:9,address:[7,8,11,206,254,520],addtorqu:2,adequ:[264,336,349,378,389,507],adher:28,adhikari:258,adiabat:0,adiam:[206,207],adjac:[39,176,178,239,389,449,479,480,481,512,513],adjiman:448,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,232,252,255,259,263,268,269,272,273,277,295,299,302,304,305,308,309,310,311,316,318,319,327,336,340,344,349,351,352,353,355,356,358,378,379,387,389,394,396,416,441,442,467,483,508,526],adjust_radiu:327,adjust_radius_factor:327,admiss:277,adof:[158,219],adopt:[317,519],adp:[2,3,7],adri:[9,314,459,460],adust:172,advanc:[3,15,252,400,493,504],advantag:[1,6,8,11,17,39,40,41,225,231,394,418,507,512],advect:[3,6,336],advertis:8,advis:[319,389,458,517],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,232,233,239,245,251,253,255,261,267,269,273,274,275,276,278,279,280,286,292,293,295,297,318,320,334,348,358,371,378,385,386,387,389,390,391,394,419,441,442,449,495,496,498,500,501,503,506,508,517],affin:[15,16,17,232,394,409],affiniti:394,afile:249,aforement:17,afresh:[306,506,525],afshar:414,after:[2,3,5,6,8,11,12,14,20,21,32,39,40,41,44,50,59,60,61,63,65,75,156,157,158,159,160,161,162,165,166,167,168,170,171,178,179,181,182,185,186,191,197,202,203,204,205,206,207,208,210,211,212,216,217,219,220,225,226,227,228,229,231,232,236,247,258,259,260,261,262,268,269,270,272,278,279,280,286,292,293,295,297,300,304,308,316,318,319,322,331,333,337,339,340,341,343,344,345,346,347,351,353,355,359,362,363,369,377,384,385,387,388,390,392,393,394,395,396,400,407,409,417,418,419,420,421,427,428,429,440,441,442,444,445,446,447,451,452,453,457,459,460,467,468,477,478,480,481,482,483,486,493,495,497,498,499,500,501,503,504,506,508,510,512,515,516,517,519,520,524,525,526,528,529,530],afterrun:506,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,232,239,251,304,362,377,389,441,442,493,495,496,498,500,505,512,514,525,528],against:[11,12,13,66,233,389,459,460],aggreg:[6,12,68,71,73,84,102,119,126,251,268,316,318,334,493,526],aggress:[239,251,512],agilio:[9,13],agre:[3,8,199,387,396,429,460],agreement:[5,7],ahd:426,ahead:355,aidan:[0,5,7,9,13,381],aij:13,aim:6,airebo:[2,3,7,226,227,315],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,252],aktulga:[7,9,311,460],al2o3:467,al2o3_001:[130,320],al3:177,ala:[258,467],alain:9,alat:[299,444],albe:[457,481,483],albeit:317,albert:9,alchem:[95,172],alcohol:351,alcu:[395,400],alcu_eam:457,alderton:413,alejandr:[272,273],alessandro:13,algebra:447,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,232,239,251,258,260,261,286,301,309,318,322,323,343,344,348,351,356,385,386,387,391,394,415,419,442,447,464,466,493,495,512],alia:[9,15],alias:[1,379],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,253,381,498,501,519],alkali:419,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,264,265,267,268,270,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,331,332,333,335,336,337,338,339,340,343,344,345,346,347,348,349,350,351,353,354,355,356,357,358,359,360,361,362,363,367,372,374,376,377,378,379,380,381,384,387,388,389,390,391,393,394,395,396,397,399,400,401,403,404,405,406,407,409,410,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,495,496,497,498,499,500,501,502,503,505,506,507,508,509,510,511,512,513,515,516,517,519,520,524,525,526,528,529,530],allen:[28,95,413,423],allentildeslei:95,allign:3,allindex:360,alloc:[3,5,6,8,9,11,12,62,245,350,388,390,394,455,460,498,506],allocat:3,alloi:[2,3,12,13,395,400,410],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,237,238,245,247,248,249,250,252,253,255,258,261,262,267,269,272,273,290,299,303,304,305,306,307,308,310,312,317,318,319,320,321,322,324,326,327,331,332,333,334,335,336,343,344,345,346,348,349,350,351,352,353,357,359,361,363,372,374,378,379,381,387,388,389,390,393,394,396,397,400,401,402,403,404,405,410,417,419,424,425,426,427,432,436,441,442,447,449,457,460,461,464,466,467,476,484,487,489,491,493,496,498,500,501,502,503,504,505,508,510,511,512,515,516,520,525,526],almost:[2,3,12,15,62,253,308,348,379,391,394,476],alo:410,alon:[6,7,228,314,459,460,496],alond:13,along:[6,8,12,28,40,74,75,95,130,176,177,178,202,203,206,219,228,239,253,258,259,263,264,269,271,308,318,322,324,328,332,334,343,347,348,354,357,359,381,383,385,386,387,389,410,413,424,427,430,432,436,444,459,460,479,480,498,501,508,509,525],alonso:[445,446],alpha:[6,12,51,211,231,258,308,309,313,387,395,398,401,410,414,415,417,418,420,421,426,431,432,444,450,456,482,484,516,519],alpha_c:440,alpha_i:468,alpha_lj:440,alphabet:[2,3,21,36,44,55,65,186,198,210,363,372,388,407,477,498],alphanumer:[3,65,210,307,315,361,388,525],alreadi:[3,7,8,9,12,16,17,42,57,178,179,181,205,215,219,225,227,232,262,306,308,336,359,360,388,389,414,425,427,434,442,476,487,490,494,498,499,503,508,524,525],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,28,35,36,37,39,40,41,42,44,54,55,56,60,61,63,65,69,74,75,76,77,79,81,86,87,88,89,95,97,98,100,103,113,114,115,116,117,118,120,121,123,125,127,128,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,198,199,201,202,203,204,205,206,207,208,210,211,212,213,215,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,238,241,242,243,245,246,247,248,249,251,252,255,256,257,258,267,269,270,272,273,274,275,276,277,278,279,280,285,289,290,292,293,295,296,297,299,300,301,303,304,305,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,328,329,332,334,336,339,340,341,342,343,347,348,349,350,352,354,357,359,360,361,363,369,372,376,378,379,381,382,384,387,388,389,390,391,393,394,400,404,405,407,411,412,413,414,417,418,419,423,424,426,427,428,436,440,441,444,447,449,453,455,456,457,458,460,461,462,464,471,472,474,475,477,478,479,480,481,482,483,484,486,493,495,496,497,498,499,500,501,502,503,505,506,507,508,510,511,512,513,515,516,517,518,519,520,521,523,524,525,526,528,530],alter:[3,6,8,9,11,12,41,61,155,156,157,158,159,161,164,165,166,167,170,171,178,182,203,204,206,208,211,212,219,226,227,228,229,231,232,271,272,313,316,318,321,329,336,344,351,358,386,389,427,498,503,505,508,525,526,530],altern:[1,6,8,9,11,12,15,16,17,99,178,203,210,220,232,241,252,256,272,307,318,319,343,344,351,364,368,378,386,387,395,396,410,415,417,418,420,429,432,440,444,445,446,453,457,458,468,478,481,483,486,496,498,499,511,513,516],alternat:[387,519],although:[15,28,42,199,261,272,305,309,318,343,377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,431,451,452,457,459,460,467,479,480,495,496,500,505,506,525,528,529,530],character:[6,70,74,117,127,152,468,493,512],characterist:[256,336,345],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,130,177,178,203,204,208,210,211,212,217,233,238,247,307,309,310,311,315,338,351,378,379,388,401,403,409,410,412,413,417,419,420,427,432,436,440,454,459,460,467,477,483,484,486,487,489,490,498,499,503,508,510,519,524,525],charl:231,charmm2lammp:13,charmm:[0,2,3,5],chartreus:207,cheap:336,cheaper:[237,423,461],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,199,200,217,225,226,227,233,244,247,253,254,304,317,322,336,344,346,351,359,361,374,377,387,388,389,390,391,394,416,428,431,449,460,491,493,495,496,498,506,512,515,516,517,525],checkf:199,checkout:520,checkqeq:460,checku:199,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,221,230,236,239,248,249,256,258,271,272,273,290,295,296,301,305,308,310,318,323,324,336,339,340,343,344,345,346,353,362,371,373,378,379,386,389,396,401,405,406,409,410,411,413,414,415,419,422,423,425,426,432,436,437,440,444,448,449,451,452,454,467,476,484,507,510,512,519],chemic:[9,40,88,89,130,172,177,203,204,216,217,247,309,314,315,343,379,421,452,459,460,472,480],chemistri:[308,309,311,396,400,419,459,460],chen:348,cheng:409,chenoweth:[459,460],chenoweth_2008:[459,460],chi:[102,167,202,299,309,311,374,420,423,526],chiefli:458,child:8,chip:[7,9,16,17,394,511],chipot:230,chiral:371,chmod:[11,12],cho:444,chocol:[7,207],choic:[3,6,9,12,14,15,17,40,41,54,74,95,153,156,157,171,182,197,199,219,225,228,232,233,249,255,258,270,272,301,305,309,318,343,354,372,379,385,386,389,391,394,427,440,449,455,460,498,507,508,511,512,518,519,524],choos:[1,3,6,7,8,9,12,16,17,28,39,54,95,128,168,169,206,226,227,228,229,231,233,244,255,258,270,272,274,275,276,277,278,279,280,304,305,323,336,340,354,378,379,386,487,493,495,507,513],chose:[481,483],chosen:[2,3,6,12,16,152,178,181,190,199,206,212,217,229,231,233,244,247,248,256,258,270,272,277,301,304,315,336,340,343,344,349,351,352,358,379,380,386,394,415,419,424,431,434,462,481,493,507,512,513,519],chri:176,christian:[7,9,16],christoph:7,chunk:[0,2,3],chunkid:[69,79,86,98,103,114,116,125,158,173,175,219,333],chute:[4,9,10,250],ciccotti:322,cieplak:[6,184,510],cii:220,cij:220,circl:[42,75,331],circular:[3,6,156,201],circumst:17,circumv:[100,117,313],citat:0,cite:[3,7,8,12,255,467],civ:9,cl1:177,clarendon:[28,413],clarifi:[7,481,483],clariti:361,clark:454,class2:[2,3],classic:[0,3,5,6,7,8,9,15,245,301,308,313,348,373,419],classifi:[477,486],claus:496,clean:[6,12,14,16,506],cleanli:[497,516,529],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:502,click:[2,11,21,36,44,55,178,186,198,206,252,363,372,389,407,477,520],client:[252,254],climb:[271,389,512],clinic:[7,13],clo:[167,202,526],clock:[12,493,512,517],clockwis:[184,354],clone:520,close:[3,6,11,12,13,39,41,70,75,153,181,203,227,228,229,249,256,258,272,288,295,318,322,354,357,377,379,382,385,386,389,394,396,400,410,411,430,444,449,451,452,459,463,465,479,483,502,508,519,520,522],closer:[3,10,41,127,176,202,203,225,229,234,345,389],closest:[227,299,318,351,423,461,476,487],cloud:[467,519],clovertown:17,clsuter:76,clump1:[303,318],clump2:[303,318],clump3:[303,318],clump:318,cluster:[2,3,6,7,12,15,63,65,75],clutter:3,cmap:498,cmatrix:249,cmax:444,cmd:[11,12,301,509],cmdarg:11,cmin:444,cmm:7,cmoput:145,cn1:220,cn2:220,cna:[2,3,7,65,74],cnn:220,cnr:13,cnrs:9,cnt:[427,502],co2:[40,177,319,322,388,421],coars:[7,9,10,28,35,40,54,190,243,303,318,319,336,421,425,452,462,480,507,510],coarser:[379,525],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,197,362,363,369,407,427,431,449,464,466,469,498,527],coeffcient:498,coeffici:[0,2,3,4],coefficienct:414,coefficient0:417,coefficient1:417,coeffieci:[6,398,430],coeffincientn:417,coexist:[247,419],cohes:[6,420,444],coincid:[134,357,405,441,442,493],colberg:205,cold:[6,163,247,251,390,519],coldest:344,coleman8:9,coleman:[9,130,177,320],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,261,268,303,313,316,318,359,378,388,390,408,498,505,511,517,530],collid:[237,336,358],colliex:177,collinear:[3,303],collis:[3,258,336,354,358,416,424,490],colllis:336,colloid:[2,3,4,6,7],colombo:39,colon:[208,359,499,517],color1:207,color2:207,color:[3,9,41,203,206,207,225,248,308,313],column:[3,6,9,12,13,42,65,68,69,70,71,73,74,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,261,269,270,308,318,337,338,348,358,396,422,426,459,460,499,513,515,516,525],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,14,42,65,75],comamnd:232,comand:228,comannd:394,comb3:[2,3],comb:[2,3,4,7,9,210,309],comb_1:310,comb_2:310,combiant:411,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,239,247,252,261,264,272,288,294,301,307,323,340,349,357,360,362,378,379,381,386,394,408,410,411,415,419,420,421,427,439,440,468,478,481,483,484,486,489,501,506,511,519,525,527],come:[0,2,3],comfort:[12,13],comid:333,comit:520,comm:[0,3,11,12,63,77,205,252,254,255,379,389,394,414,449,456,479,480,500],comm_modifi:[2,3,6,39],comm_modift:63,comm_styl:[2,3,41,63],comm_world:11,command:[0,1],comment:[2,4,7,11,12,37,56,184,199,203,242,243,256,318,319,348,388,389,395,417,418,420,421,431,444,451,452,453,460,467,468,478,479,480,481,482,483,486,495,496,498,519,520,525],commerci:7,commit:[9,520],commmand:[3,6,12,61,118,296,430,492,493,495,512,529],common:[0,1],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,373,425,434,468,481,483,498,501,510],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,232,252,254,258,260,261,262,272,300,307,309,310,311,318,323,336,348,359,376,378,390,391,392,394,415,416,455,491,495,496,507,508,525,528,530],communc:378,comp:[7,205,254,255,288,294,322,379,389,419,449,456,461,475,479,480,482],compact:[65,210,407,477],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,236,309,359,361,378,379,387,389,444,467,493,512,513,519,524],comparison:0,compart:383,compass:[7,9,20,21,36,43,44,55,185,186,198,362,363,372,406,477],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,231,239,300,312,340,343,350,353,356,378,394,428,447,449,479,495,496,525],compens:[6,226,227,316,390,419],compet:347,competit:379,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,207,208,252,347,379,394,447,498,499,503,519,525],compl:16,complain:[11,12,16],complement:444,complementari:[7,410,432],complet:[3,6,9,11,12,14,41,61,75,207,225,230,261,301,304,307,336,347,349,360,361,377,389,394,420,464,466,485,493,498,503,506,510,512,515,519,525],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,258,288,331,357,376,389,419,447,479,480,496,498,501,525],compli:[343,347],complic:[6,7,9,12,13,129,217,247,496],complier:12,compon:[3,6,8,12,63,65,69,70,74,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,233,238,239,245,250,254,255,258,261,263,264,268,269,271,272,273,277,278,279,280,292,293,295,297,298,300,301,302,305,316,318,321,322,324,328,329,332,336,339,340,341,343,350,351,356,357,358,378,381,386,387,388,389,394,414,419,424,441,442,464,466,467,468,498,499,508,516,525,526],componenet:6,componennt:129,composit:[6,217,258,417],compound:[409,419,420,486],compres:[75,125,219],compress:[3,6],compris:[40,357,421,461,485],compton:[130,177],comptu:3,compuat:379,comput:[0,1],computation:[3,6,226,227,348,400],computational:519,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,65],compute_peratom:8,compute_sa:[130,320],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,529],concav:357,concentr:[75,243,319,417,421,452,480],concept:[6,158,168,219,507],conceptu:[3,6,75,166,229,232,389,410,427,444,503],concern:[6,77,95,205,248],concetr:75,concis:[11,347],conclud:12,concret:8,concurr:[15,379,525],conden:[348,481,483],condens:[6,160,348,396,412,417,432,486],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:501,confer:[15,447],confid:[3,512],config:[12,203,495],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,232,233,237,247,254,255,286,301,309,347,376,387,389,396,400,418,444,447,478,481,483,486,493,498,500,501,512,516,520],confin:[498,512],confirm:517,conflict:[3,12,40,204,449,496,520],conform:[3,6,13,61,228,229,271,317,324,347,371,389,419,510],confus:[3,486],conjuct:[9,414],conjug:[7,8,255,386,419,459,460],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,255,258,262,286,304,305,309,310,311,313,318,323,336,344,351,356,378,379,389,401,403,407,410,414,419,426,432,449,454,462,484,498,501,505,519,530],connect:[3,6,9,95,163,181,228,252,303,318,322,332,383,389,411,424,459,460,476,483,495,496,498,502,519],conner:396,connor:396,conput:3,consecut:[3,11,12,39,75,178,207,211,212,233,252,253,410,432,436,493,499,501],consequ:[1,6,217,348,431,512],conserv:[3,9,28,210,217,228,236,237,248,251,255,257,258,262,268,270,272,286,288,290,318,319,322,323,339,340,344,351,352,356,389,413,414,415,424,438,467,507,512],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,233,259,273,300,318,343,344,347,348,351,379,407,419,427,460,461,467,476,493,494,496,499,500,501,503,506,508,516,519,525],consider:[6,8,255,256,339,340,341,394,460,507],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,233,236,238,245,248,255,256,257,269,272,274,275,276,277,278,279,280,281,282,284,285,286,287,290,291,292,293,295,296,297,305,308,313,315,316,317,318,319,339,340,341,342,352,378,379,381,383,388,389,394,396,400,402,408,410,419,423,427,430,441,442,444,447,449,451,452,461,464,466,467,479,480,487,496,498,499,500,501,502,503,510,519,525],consistent_fe_initi:216,consit:318,constant:[0,3,4],constantli:239,constitu:[3,6,261,318,353,357,408,461],constitut:[464,466],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,233,239,247,248,253,261,264,266,288,294,303,304,316,318,322,334,344,351,387,388,419,503,510,519],constraint:[3,5],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,272,300,317,319,357,390,394,413,447,449,476,478,479,480,501,502,517,525],constructor:[8,11],consult:[15,460],consum:[1,313,455,525],consumpt:376,contact:[0,2,3,4,5,8,9,12,13,40,42,65],contact_stiff:[463,465],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,231,233,238,242,243,249,253,254,255,258,270,286,299,300,303,304,306,307,308,311,315,318,319,320,325,336,343,347,348,357,358,361,377,379,388,389,392,393,395,396,397,400,409,410,413,417,418,419,421,427,428,444,447,451,452,453,457,458,459,460,468,478,479,480,481,482,483,484,486,493,494,495,496,498,499,500,501,503,505,507,510,512,513,515,516,519,520,525,528,530],content:[4,8,9,12,17,460,514,516],context:[3,6,8,12,15,16,127,128,207,226,227,233,303,315,352,386,489,498,505,514,524,525,526],contibut:74,contigu:495,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,233,239,247,248,249,251,252,253,255,256,257,263,269,270,272,274,275,276,277,278,279,280,292,293,295,296,297,302,304,307,308,318,320,324,335,336,338,345,346,348,354,357,361,377,393,394,400,414,416,434,437,459,460,461,464,466,482,493,496,498,500,501,506,512,513,515,516,525,528],continuum:[6,7,9,216,348,464,466],contour_integr:216,contract:[61,229,232,272,305,318],contradictori:3,contrain:322,contraint:286,contrari:[249,256],contrast:[1,6,42,55,66,160,163,204,232,359,464,466,489,529],contrib:348,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,247,255,258,261,262,267,273,295,296,303,304,312,315,318,320,322,350,378,387,389,397,414,416,417,419,427,441,442,447,449,459,460,467,510,516,519,520],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230],control_typ:216,controlfil:460,convect:99,conveni:[6,12,28,203,208,223,320,381,468,484,517,520,525],convent:[3,8,28,189,196,198,204,207,317,332,360,417,419,525],converg:[3,6,41,96,203,204,206,208,213,225,228,229,238,245,277,288,294,308,310,313,317,322,385,386,387,389,409,410,432,467,493,505,512,517],convers:[3,8,152,206,207,217,220,305,378,410,411,412,419,432,436,440,454,496,512,524],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,270,304,307,359,362,364,368,371,381,389,395,417,447,481,483,490,496,498,499,500,505,515,519,524,525,528,530],convex:[42,357],convinc:[7,12],cook:9,cooki:7,cool:[7,168,239,251,316],cooordin:[203,204],cooper:[5,7],coord123:125,coord1:[3,125,219],coord2:[3,125,219],coord3:[3,125,219],coord:[2,3,6,7,11,61,65,75,76,80],coordb:467,coordbb:467,coordiat:387,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,232,233,236,238,239,240,245,247,250,251,252,253,254,255,256,269,271,272,274,275,276,278,279,280,295,298,299,300,303,304,305,315,316,318,321,322,324,329,332,333,334,335,336,338,346,347,348,355,356,358,359,381,387,388,389,394,395,396,399,418,467,493,498,499,500,501,503,506,508,512,519,525,526],coordn:[125,219],coords:467,copi:[0,3,4,8,9,11,12,14,16,40,131,206,348,389,407,459,496,520],copper:490,coprocessor:[1,7,9,15,16,394,511],coproprocessor:16,copy_arrai:8,copyright:[7,8,303],coral:207,core:[0,1,3,4],core_shel:160,cores:519,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,510],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,206,357,358,381,485,498,520],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:409,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,232,239,247,249,255,272,273,295,303,305,308,347,353,357,378,389,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,485,486,488,489,490,491,498,513,516,519,520],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,233,238,245,256,266,272,273,311,318,322,332,335,354,357,389,390,394,412,442,447,495,496,498,508,520,524,526],correl:[2,3,6,99,100,152,174,210,219],correpond:[242,243],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,232,239,240,243,245,246,250,255,258,259,268,269,270,272,274,275,276,277,278,279,280,281,282,286,290,292,293,295,297,299,300,301,305,310,311,318,319,321,322,343,353,354,356,357,358,360,362,363,364,365,367,368,371,373,379,384,386,388,389,395,396,398,401,402,403,404,405,406,407,408,409,410,413,414,417,418,419,420,421,422,423,424,425,426,427,430,432,433,434,435,436,437,438,439,440,441,444,445,447,449,450,452,453,454,456,457,459,460,461,462,467,468,469,478,479,480,481,482,483,484,486,488,489,490,493,495,496,498,499,501,511,512,513,515,516,519,525],correspondingli:[441,442,507],corrupt:3,cosin:[2,6,7,21],cosineshift:26,cosmo:[249,254],cossq:2,cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,244,272,290,310,319,348,378,379,392,410,432,436,447,449,478,495,507],costheta0:[478,481,483,486],costheta:457,costli:[11,15,96,249,390],couett:4,coul:[2,3,6,9,15,35,45,46,76,95,118,127,172,184,211,212,349,379,387],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,232,245,254,307,308,309,313,316,318,321,336,337,343,347,348,349,353,357,359,361,369,375,377,385,387,390,394,396,397,422,426,427,430,459,460,494,495,496,498,500,502,505,506,513,514,519,525,526],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,309,311,349,378,379,387,394,401,403,404,405,406,409,410,411,412,413,419,424,425,427,432,436,440,443,449,454,459,460,462,467,477,483,484,486,489,503,510,516,519,524],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,233,238,244,247,253,272,286,304,321,322,339,340,357,379,387,388,389,391,394,422,426,449,516,517,525],counter:[3,354,493,504,506,512],counteract:[231,247],counterbal:[239,251],counterbalanc:28,counterclockwis:184,counterpart:[203,493],counterproduct:17,coupl:[0,3,4],couple:[4,6,11,12],courant:325,cours:[3,8,15,138,140,172,203,211,212,248,317,332,347,353,355,356,358,359,379,441,469,495,498,511,519,525,528],courtesi:381,cov:467,coval:[6,9,28,419,444,467,519],covari:249,cover:[6,12,75,199,207,216,258,419,485],coverag:75,cpc:254,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,245,322],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,236,256,349,376,379,394,407,477,493,511,512,515,516,517,525],cpuinfo:15,cpuremain:516,cpus:12,cr2:177,cr3:177,crack:[4,390],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,390,519],craympi:394,creat:[0,1,2,3,4,6,7,8,9,11,12,13,14,16,37,39,41,42,56,60,61,64,65,75,87,99,113,114,119,120,123,126,128,130,146,155,161,162,174,176,178,179,180,181,199,203,204,205,206,207,210,215,216,218,219,220,222,223,225,226],create_atom:[2,3,6,7,8,40,41,61,99],create_bond:[2,3],create_box:[2,3,6,21,40,41,44,59,60,61,64,75,99,176,178,179],create_elementset:216,create_faceset:216,create_group:205,create_nodeset:216,createatom:0,creation:[3,5],crimson:207,critchlei:303,criteria:[3,127,179,206,207,226,227,228,267,387,456,485,500,503,525],criterion:[12,41,133,178,181,217,225,228,247,286,310,325,354,359,387,389,409,419,424,467,503,512,513],criterioni:512,critic:[6,48,49,270,343,348,387],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,232,269,271,295,318,328,332,335,344,351,363,381,389,405,414,416,417,425,426,427,432,434,436,457,462,464,466,481,483,490,498,502,508,528],crossov:1,crossterm:498,crozier:[0,7,13],crucial:308,crystal:[3,4,6,13,15,74,77,117,299,300,346,381,390,498,502,516,519],crystallin:[6,113,300,381,482,519],crystallis:343,crystallogr:[130,177],crystallograph:[381,516],crystallographi:[130,177,381],cs1:177,cs_chunk:6,cs_im:[40,498],cs_re:[40,498],csanyi:[152,458,468],cscl:444,csequ:6,csh:[11,12,15,407],cshrc:[11,12],csic:[418,478,481,483,486],csinfo:6,csisi:[418,478,481,483,486],csld:[2,3,210],cst:417,cstherm:6,cstyle:495,csvr:[2,3,6,210],ctcm:[395,417],ctemp_core:236,cterm:324,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:444,cube:[6,176,181,236,357,381,519],cubes:[41,225],cubic:[2,3,37,56,117,199,242,258,299,336,379,381,417],cuda:[1,3,7,9,12,14,16,394,511,525],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:400,cummul:[3,6,223,226,227,228,230,244,249,255,257,336,339,340,341,342,344,351,426,516],cumul:[6,217,219,222,237,247,255,270,272,277,286,318,320,389],curli:2,currenlti:231,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,233,237,238,239,245,247,249,252,253,255,261,267,269,272,273,278,279,280,286,288,292,293,294,295,297,303,304,309,310,312,315,316,317,318,319,322,323,324,325,326,327,328,329,331,333,334,335,336,339,340,341,347,348,351,352,353,354,355,356,358,359,361,376,377,378,379,382,383,384,386,387,388,389,394,400,407,409,413,417,419,420,424,427,428,431,441,442,444,445,446,449,457,459,460,463,464,465,466,469,481,483,484,487,493,494,495,496,498,499,500,501,502,504,505,506,508,510,512,513,515,516,520,525,526,527,528,529,530],curv:[6,178,247,288,294,300],curvatur:[423,461,490],custom:[0,2,3,6],cut0:496,cut1:507,cut2:507,cut:[1,2,3,6,9,12,14,15,16,17,18,41],cuthi:[299,311],cutinn:[402,441,442],cutlo:[299,311],cutmax:457,cutoff1:[406,413,432,436,440,443,454,462],cutoff2:[401,403,404,406,412,413,432,436,440,443,454,462,484],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,234,242,243,299,308,309,311,313,315,318,323,336,349,353,357,359,376,378,379,387,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,408,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,459,460,461,462,467,468,469,470,471,472,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,496,500,503,507,519,525],cutoffa:418,cutoffc:418,cuu3:417,cval:177,cvar:231,cvd:343,cvel:324,cvff:[2,7,15,363],cwiggl:[3,269,353,356,358,525],cyan:[2,206,207],cycl:[3,247,270,272,273,277],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,253,294,304,354,357,383,501],cylinder_d:383,cylindr:[6,253,332,354],cypress:394,cyrot:400,cyrstal:300,d3q15:258,d3q19:258,d_double_double:14,d_e:348,d_flag2:307,d_flag:307,d_name:[124,203,307,338,508],d_single_double:14,d_single_single:14,d_sx:307,d_sy:307,d_sz:307,daan:346,dai:12,daili:12,daivi:295,damag:[2,3,9,65],dammak:313,damp:[3,6,210,215,255,256,257,262,272,273,277,294,305,308,309,313,318,339,340,352,354,355,386,387,389,401,403,405,410,413,419,424,432,440,454,462,477,484,512,519],damp_com:256,damp_drud:256,dampen:[318,519],dampflag:[354,424],dan:16,danger:[3,12,247,359,414,516],dangl:181,daniel:9,darden:[379,413],darkblu:207,darkcyan:207,darken:206,darkgoldenrod:207,darkgrai:207,darkgreen:207,darkkhaki:207,darkmagenta:207,darkolivegreen:207,darkorang:207,darkorchid:207,darkr:207,darksalmon:207,darkseagreen:207,darkslateblu:207,darkslategrai:207,darkturquois:207,darkviolet:207,dasgupta:309,dash:[424,515],dat:[6,99,199,216,494],data2xmovi:0,data:[1,2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:0,datafil:[12,13,320],dataset:320,datatyp:3,date:[0,4,6,12,13,202,459,460,525],datom1:[84,126],datom2:[84,126],datom3:[84,126],datom4:[84,126],datum:[3,6,42,68,71,73,84,102,119,126,203,220],davenport:443,davi:353,david:[9,18,378,379,481,483],daw:[417,457],dcd:[3,6,7,203,205,206,207,208,301,499,503],dcs:9,ddim:202,deactiv:440,dealt:254,debug:[6,7,11,12,13,16,57,130,134,177,178,301,306,376,378,428,449,487,496,497,505,508,515,525],deby:[2,3,7,211,212,313],decai:[100,410,490],decid:[3,6,12,15,75,269,307,318,349,513,520],decipher:381,deck:307,declar:205,declin:336,decod:206,decompos:[95,468],decomposit:[3,5,7,17,64,216,301,323],decoupl:[6,519],decreas:[3,15,203,204,213,214,221,228,232,238,239,245,247,255,347,378],decrement:324,dedic:[15,394],deepli:375,deeppink:207,deepskyblu:207,def:[12,13,496],defaul:63,defect:[6,74,176,447],defgrad:2,defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,233,236,237,238,241,243,245,246,247,250,253,254,255,256,257,258,267,269,271,272,273,274,275,276,277,278,279,280,282,283,284,287,290,291,292,293,295,296,297,299,300,301,303,304,305,307,309,311,316,318,319,320,321,322,325,329,333,334,336,338,339,340,341,342,344,345,346,348,350,351,353,354,355,356,357,358,359,361,362,363,364,365,366,367,368,371,372,373,374,376,378,379,381,383,384,386,387,388,389,390,391,392,393,394,396,397,398,399,401,402,403,404,405,406,407,408,410,411,413,414,415,416,418,419,421,422,423,424,425,426,427,428,430,432,433,434,435,436,437,438,439,440,441,442,443,447,448,449,450,451,452,453,454,456,457,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,498,499,501,502,503,504,507,508,509,510,512,513,515,516,519,521,522,523,524,525,526,527],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,232,241,253,277,320,338,350,353,356,358,360,372,376,388,397,400,408,415,419,430,457,464,466,468,485,496,498,500,507,509,524,525],defint:516,deform:[2,3,6,7,8,40,42,59,61,63,65,85,122,134,138,139,153],deg2theta:177,deg:519,degener:[3,303],degrad:[8,17,300,379,507],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,236,247,249,250,255,256,261,272,273,277,278,279,280,292,293,295,297,301,303,317,318,322,339,340,341,346,362,364,368,371,373,387,413,417,426,508,516,519,526],degrees:199,degress:[158,219],del:512,delai:[3,6,12,390,416,516],deleg:427,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,244,247,272,320,339,340,359,361,377,388,390,393,449,476,498,499,500,501,509,510,515,520,521,523,525,526],delete_atom:[2,3,7,178],delete_bond:[2,3,43,45,46,47,48,49,50,51,53,54,55,56,68,73,126,179],delete_el:216,deli:202,delimit:[319,496,525],dellago:[6,239],deloc:[273,419,467],delr:444,delt_lo:512,delta:[2,21],delta_1:400,delta_3:400,delta_7:400,delta_conf:3,delta_ij:[444,457],delta_pi:400,delta_r:457,delta_sigma:400,deltah_f:243,delx:202,delz:202,demand:313,demo:11,demon:298,demonstr:[308,444],den:304,dendrim:426,dendtrit:383,denniston:[9,258,260,261,262,300],denomin:[7,183],denot:[130,236,239,256,300,311,313,410,425,427,460,464,466],dens:[75,228,319,419],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,232,245,258,261,265,266,300,304,305,307,309,348,353,381,384,388,395,396,400,417,444,445,446,451,452,457,461,467,471,473,474,475,498,507,508,516,524],density_continuity:466,density_summation:466,dent:383,depart:[0,7],departur:[270,308],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,232,238,240,243,246,249,250,251,253,255,256,258,260,261,269,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,299,310,311,313,315,318,319,321,322,323,329,336,339,340,341,343,345,347,348,350,353,356,357,358,359,361,362,363,364,365,367,368,371,373,379,381,387,388,390,391,392,394,395,396,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,417,418,419,420,421,422,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,444,445,447,448,450,451,452,453,454,456,457,459,460,461,462,467,468,469,477,478,479,481,482,483,484,486,488,489,490,493,495,498,500,501,504,508,510,512,515,516,518,525,526],dependend:6,depflags:12,dephas:[493,512],depos:233,deposit:[2,3,4,112,180,210,217],deprec:[3,309,459],deprect:219,depth:[51,156,206,348,421,423,461],dequidt:9,der:[95,118,408,409,440,459,460,489],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,232,239,247,255,269,272,274,275,276,277,278,279,280,299,305,309,313,345,346,348,353,354,357,386,388,396,400,408,413,419,420,425,434,438,439,444,447,459,460,477,479,480,489,519],derjagin:489,derlet:299,descend:207,descent:[7,386],descib:[40,206,309],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,233,235,236,242,243,248,249,252,253,254,255,256,257,258,260,261,262,267,271,272,273,277,285,296,299,301,306,307,308,309,310,311,318,319,324,332,336,337,338,339,340,341,342,343,344,345,346,351,353,354,356,361,378,379,381,385,386,387,388,389,393,396,397,399,401,402,403,405,406,407,408,409,410,413,417,419,420,421,423,424,425,427,430,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,451,452,456,457,458,459,460,461,462,467,468,469,476,477,478,479,480,481,482,483,484,486,488,489,490,491,493,495,496,498,499,500,501,502,508,511,512,515,520,525,526,528],descript:[2,3,6,8,9,11,12,13,17],descriptor:[152,203,428],deserno:379,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,235,236,272,273,299,300,320,343,348,397,398,399,402,405,410,412,419,440,441,442,445,446,457,460,479],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,232,245,247,248,255,256,257,261,272,295,303,304,305,306,309,313,318,321,322,336,339,340,341,342,347,354,369,375,378,379,381,385,387,388,389,414,417,426,441,442,478,481,483,494,495,496,498,502,507,512,513,515,516,517,525,526,528],desk:7,desktop:[4,6,7,10,12,206],despit:519,destabil:400,destre:371,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,233,239,245,247,248,249,250,252,253,255,257,258,262,269,270,271,272,273,274,275,276,277,278,279,280,284,286,292,293,295,296,297,300,303,304,305,307,308,310,311,312,318,322,323,336,339,340,341,342,343,344,346,347,348,349,350,351,352,359,361,363,372,378,379,382,383,387,388,390,391,394,395,396,397,399,400,402,404,405,406,407,408,409,410,413,414,419,420,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,442,443,444,448,449,451,452,456,459,460,461,467,468,469,477,485,488,489,491,496,498,499,500,501,503,504,507,508,510,513,516,517,520,525,526,530],detect:[2,3,12,42,63,65,94,100,246,304,347,389,409,426,431,493,495,498,509,512,525],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,119,123,126,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,232,233,236,238,243,247,250,251,253,255,256,261,267,269,270,272,278,279,280,292,293,295,297,299,301,304,305,308,315,316,317,318,319,320,321,325,327,329,336,339,340,341,343,349,350,353,354,355,356,357,358,359,372,378,379,381,388,390,391,394,396,397,404,409,413,416,417,421,422,424,427,428,436,444,447,449,452,460,461,467,476,479,480,484,489,495,498,499,501,503,505,508,512,514,515,517,524,525,526],determinist:323,detil:119,devan:[9,462],devanathan:483,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,231,252,277,303,308,309,312,396,400,419,446,447,467,486,500],devemi:9,deviat:[270,277,299,422],deviator:9,devic:[1,3,12,14,16,252,394],device_typ:394,devin:[310,409],devis:446,dfactor:206,dff:519,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,379],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,312,447],dhi:[61,202,232,304],dhug:[270,308],dhugoniot:[270,308],dia:444,diag:319,diagnost:[2,5],diagon:[3,6,91,129,152,153,154,229,272,305,318,351,464,466],diagonalstyl:468,diagram:[41,84,130,177,198,225,301],diallo:426,diam:[206,207,304,388],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,255,304,307,318,336,338,352,354,388,408,423,424,434,461,485,489,498,499,508],diamond:[381,419,444],diamter:[40,304],dick:6,dicken:231,dicsuss:269,dictat:[217,270],did:[3,12,387,414,416,417,424,449,481,483,506],didn:3,die:17,diel:2,dielectr:2,diff:[3,6,12,15,174,350,378],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,232,236,239,242,246,247,248,249,250,251,252,255,256,258,269,272,273,274,275,276,278,279,280,282,284,287,290,291,292,293,297,299,301,303,305,308,309,310,313,316,318,322,324,332,334,336,339,340,341,344,345,346,348,351,352,353,354,357,361,362,372,375,377,378,379,381,382,385,386,388,389,391,392,393,394,395,396,400,404,405,407,408,409,414,415,417,419,421,423,424,425,427,430,432,433,435,436,443,444,445,446,448,449,450,451,452,453,457,459,460,461,462,463,464,466,467,468,469,477,478,479,480,481,483,485,486,489,492,493,495,496,498,500,501,502,503,506,507,508,510,512,513,515,516,517,519,524,525,526,528],differenti:[1,3,6,28,199,319,378,410,457,482],difficult:[229,231,301,394,426,507,517],difficulti:[100,117,322,459],diffract:[7,9,130,177,320],diffus:[0,4],diffuse:[4,6],digit:[2,3,207,361,447,525],dih_table1:199,dih_table2:199,dihedr:[0,2,3,7],dihedral_coeff:[2,3,184,185],dihedral_cosine_shift_exp:26,dihedral_styl:0,dihedralcoeff:[3,200],dihedraltyp:227,dihydrid:419,dij:322,dilat:[2,3,61,63,65,82],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,232,253,354,381,444,501,524,525,526],dimdim:525,dimems:300,dimens:[1,2,3,6,7,12,41,59,60,61,63,65,75,99,125,129,153,158,165,166,167,178,180],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,271,300,348,381,385,389,457,498,508],dimensionless:[115,133,134,136,139,141,143,148,152,231,348,379,468,489],dimensions:320,diment:3,dimentionless:147,dimer:[6,318,444],dimgrai:207,dimstr:[41,225],dinola:[305,339],dintel_offload_noaffinity:15,dipol:[0,2,3,4],dipolar:[4,28,40,203,204,338,519],dir1:509,dir2:509,dir:[1,3,4,8,10,11,12,270,299,308,335,457,459,460,496,509,525],dirac:152,direc:457,direct:[2,3,6,7,12,13,15,28,59,74,75,117,130,152,176,177,178,184,202,203,206,210,213,214,215,232,233],directli:[3,6,8,9,11,12,95,124,129,152,154,178,203,204,205,206,213,231,238,249,253,258,300,319,320,340,352,354,355,356,357,381,386,394,395,396,401,403,404,410,413,417,419,432,436,449,454,462,476,496,508,509,510,516,525],directori:[0,1,2,3],disabl:[3,12,15,348,394,431,496,511,525],disadvantag:[6,225],disallow:[203,232,272],disappear:500,discard:[2,3,41,75,221,225,349,357,495,500,501],discontinu:[199,387,438],discourag:444,discov:[13,349],discret:[6,8,40,42,206,207,231,255,258,294],discuss:[0,1,2,3],disk:[6,92,93,100,171,201,233,247,304,496],disloc:[74,447],disord:[39,74,447],disp:[0,2,3],dispar:461,disperion:[413,436],dispers:[3,6,7,9,176,300,378,379,404,413,436,441,449,460,479,486],displac:[2,3,6,7,12,42,61,65],displace_atom:[2,3,7,113],displace_box:61,displacemet:501,displai:[11,13,21,36,44,55,186,198,203,206,363,372,407,477],dispters:3,disregard:447,dissip:[6,9,40,88,89,241,248,255,300,323,345,346,402,414,415,424,441,442,477],dissolut:226,dist:[6,73,99,119,128,203,301,317,416,476,493,526],distanc:[2,3,6,7,8,9,12,19,20,39,43,45,46,47,48,49,51,53,54,55,56,57,58,60,61,63,65,66,69,73,75,76,77,78,79,80,81,86,87,94,97,98,100,103,113,114,115,116,117,119,125,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,202,203,204,206,207,215,219,226,227,228,229,232,233,234,237,239,247,253,258,269,270,271,272,277,286,299,300,304,308,309,316,317,318,322,324,328,332,333,334,335,336,343,344,346,347,348,351,353,354,355,356,357,358,362],distinct:[6,236,315,378,461],distinguish:[6,94,152,261,419,497,525],distort:[176,395],distrbut:395,distribut:[0,2,4,5,6],distro:[122,407,456,457],ditto:[8,12,14,16,17,42,126,227,318,490,496],div:[8,15],divd:128,diverg:[3,12,39,318,346,396,500,519,528],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,232,299,344,351,356,378,387,389,420,460,467,486,507,515,525],divis:[6,197,258,400,430,440,495,516,525],dl_poly:[6,7],dlambda:172,dlammps_async_imd:252,dlammps_bigbig:[12,39,207],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,347,498,499,503],dlammps_jpeg:[3,12,206],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,206],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,203],dlen:508,dlm:[272,290],dlmp_intel_offload:[9,15],dlo:[61,202,232,304],dlopen:6,dlvo:[7,408,489],dm_lb:258,dmax:[336,385],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,84,86,95,98,102,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,231,233,247,255,256,267,272,273,278,279,280,284,292,293,295,296,297,304,307,318,332,336,339,340,341,350,354,357,359,361,363,372,377,383,387,388,389,394,395,396,399,407,409,410,417,418,420,426,427,429,430,444,445,446,449,453,456,457,458,468,477,478,481,483,485,486,496,498,499,500,501,503,506,507,508,515,516,520,525,526,528,529],docuement:461,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,232,236,238,239,242,243,244,247,248,251,253,255,256,258,261,268,272,273,274,275,276,278,279,280,292,293,294,295,296,297,305,306,307,311,313,316,318,336,339,341,343,344,348,351,352,353,356,357,358,359,364,365,366,368,369,371,377,378,379,380,381,388,389,390,395,396,397,398,399,400,402,404,405,406,408,409,410,411,413,414,416,417,418,419,421,422,423,424,425,427,428,429,430,431,434,435,437,438,439,441,442,444,445,446,447,449,451,452,457,458,459,460,461,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,498,499,500,501,502,505,506,508,509,510,511,512,515,516,519,520,525,530],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,332,388,390,394,396,409,418,429,459,460,478,481,482,483,486,498,500],dof:[3,8,123,156,157,158,171,219,318,526],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[388,498],doi:[6,230,299],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,232,233,251,254,258,272,273,301,313,318,323,348,353,354,378,379,389,394,416,449,493,495,498,502,515],domin:[1,419,512],don:[0,8,9,12,13,15,127,181,213,238,256,357,444,467,496,498,520],donadio:340,donald:231,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,233,242,243,245,247,252,253,255,256,263,272,278,279,280,292,293,295,297,298,300,301,302,304,307,315,318,320,322,336,339,340,341,343,345,346,359,361,377,378,379,387,389,390,393,394,396,404,417,427,428,429,436,442,443,444,449,451,452,459,476,479,480,485,493,494,495,496,499,502,503,506,516,517,519,520,525,526],donor:426,dot:[153,174,213,238,250,271],doti:[400,457],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,232,245,306,357,361,377,379,393,394,400,420,425,447,459,460,494,498,502,506,511,525,526],dover:216,down:[3,6,7,8,11,39,75,229,247,255,336,352,419,449,467,497,517],downhil:[385,386],download:[5,7,8,9,11,12,13,16,252,428,458],downsid:6,downward:315,dozen:[8,9,12,118,210,459,460],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[2,3,6,7],dpde:265,dpdtheta:[40,88,89,415],dpdtheta_i:[241,242,243],dproduct:397,dr_ewald:[130,320],drag:[2,6,99,210],dragforc:258,drai:[206,270,308],drain:[251,352,387],dramat:[9,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98,500,501,505,506,509,512,514,516,525,526],equat:[3,6,7,8,9,99,117,123,130,177,186,198,210,229,231,236,237,239,241,242,243,249,255,256,258,261,270,271,272,273,277,295,299,301,308,309,313,319,322,323,336,344,348,351,353,354,356,358,378,379,383,408,413,414,415,419,420,421,424,429,441,442,444,449,452,461,464,466,471,472,474,475,480,490,519],equation:[249,299,371],equi:273,equidist:271,equil:[3,309,382,505,530],equilater:508,equilibr:[3,4,5,6,7,9,61,99,178,210,217,220,228,229,247,270,272,273,295,296,305,308,309,310,311,344,345,346,351,409,410,459,460,494,508],equilibria:351,equilibribum:[226,227],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,229,232,247,248,249,256,258,272,277,295,308,309,313,317,322,324,332,336,343,344,346,351,362,364,368,371,409,444,453,467,519],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:216,equival:[6,12,13,28,61,63,128,136,137,145,150,176,180,203,207,218,219,220,222,223,229,232,247,255,272,295,305,317,318,356,396,414,419,467,481,483,484,498,501,506,507,516,519],equlibrium:6,equliibr:[309,311],er3:177,eradiu:[40,124,204,419,498],eras:[321,345],erat:[232,442],erc:410,erfc:[410,432,449],erforc:[124,204],erg:524,erhart:[217,417,481,483],ermscal:397,ernst:9,eror:3,eros:444,erose_form:444,erot:[2,3,6,9,65],errata:[481,483],erratum:353,erron:3,error:[0,1,2],erta:424,ervel:[124,204,498],escap:[233,519],especi:[8,15,166,178,210,217,225,247,308,313,316,317,394,495,517],espresso:[9,312],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,300,352,379,396,410,432,483,503,516],essential:[8,277],essex:28,establish:[95,251],estim:[1,3,6,10,12,37,41,56,74,99,153,216,225,237,270,319,336,343,378,379,385,449,460,479,480,512,516],estimat:3,esu:524,esub:444,eta:[6,258,272,308,309,311,352,418,420,423,457,482,486,524],eta_dot:272,eta_ij:457,eta_ji:420,etag:[40,498],etail:516,etap:272,etap_dot:272,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,232,233,245,247,248,255,272,304,315,320,348,349,357,361,377,378,387,388,389,390,392,417,418,427,440,442,447,455,459,460,478,481,483,486,493,496,498,499,500,505,507,508,512,513,514,515,516,517,519,524,525,528,530],ethernet:17,etol:[387,389,493,512],etot0:308,etot:[6,104,106,107,121,153,164,207,236,256,270,308,515,516],eu2:177,eu3:177,euler:[319,387,389],eulerian:216,euqat:470,europhi:258,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,232,238,248,250,251,253,254,255,256,300,306,309,319,321,325,329,339,340,341,350,353,356,358,359,361,385,387,447,449,451,452,457,463,465,467,479,480,493,494,496,500,501,503,505,506,507,508,512,514,516,525,526],evaluat:[378,379,525],evalut:[361,496],evan:[166,295],evanseck:[6,19,184,405,510],evapor:[2,3,9,59,112,210,217],evaul:[8,387],evdwl:[118,154,459,460,516],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,232,233,236,239,253,256,270,272,273,300,304,313,315,318,320,331,336,344,348,351,353,357,359,370,378,385,387,389,394,399,419,420,424,427,430,449,461,486,487,491,498,499,501,503,504,505,507,508,510,513,515,516,517,519,530],evenli:[3,41,57,153,199,225,258,430,487],event:[2,3,6,8,65],eventu:[3,6,12,14,180,512],eventual:309,ever:[9,54,56,254,336],everaer:[408,423,461,477],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,237,239,244,245,247,249,251,252,253,258,259,268,272,273,277,288,294,298,299,300,304,305,306,307,308,309,310,311,313,315,316,318,319,320,322,324,333,336,338,339,340,341,342,343,344,347,348,349,350,351,359,361,377,379,389,390,391,394,414,416,427,440,459,460,467,473,492,493,494,498,500,502,503,505,506,507,512,513,514,516,517,520,525,530],everyth:[8,118,520],everywher:[127,434],eviri:419,evolut:[239,249,258,301,493],evolv:[258,301,349],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,349,378,379,387,401,403,404,410,413,419,432,436,454,462,477,479,484],ewald_disp:413,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,248,249,255,256,257,304,313,314,336,348,363,378,407,500,505,512,525,528,530],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,232,237,242,248,255,256,257,273,285,286,296,300,307,308,336,341,342,355,394,407,414,417,424,427,441,449,451,452,479,480,500,501,508,512,525],exager:519,examin:[6,8,16,228,300,319],examp:496,exampl:[0,1,2,3],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,232,237,244,272,300,315,320,326,327,336,387,394,498,525],exceed:[3,41,61,225,232,272,336,460,506],excel:419,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,232,240,246,247,250,253,255,257,272,273,274,275,276,277,278,279,280,281,282,285,286,290,292,293,295,296,297,301,310,311,318,321,322,332,336,342,348,356,359,360,361,362,363,364,365,367,368,371,372,373,378,379,381,384,388,389,390,392,393,394,395,396,398,401,402,403,404,405,406,407,408,409,410,412,413,414,417,418,419,420,422,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,442,445,450,453,454,456,459,460,461,462,469,477,478,479,481,482,483,484,486,488,489,490,493,495,496,498,500,501,503,506,507,508,509,510,512,516,519,524,525,526,529],exception:496,excess:[221,419],exchang:[2,3,6,8,63,64,210,216,217,239,247,251,255,310,318,344,348,351,378,394,419,513],exchange:378,excit:419,excite:419,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,259,268,303,316,318,343,354,359,387,388,390,402,424,427,430,441,442,449,476,510],exclude:390,exclus:[1,3,12,15,95,184,409,447,449,507,517],excurs:[272,493],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,252,312,361,377,380,393,494,496,506,509,512,525],exempl:467,exemplari:248,exemplifi:419,exert:[6,253,256,288,313,355,356,357,379],exhaust:[216,393,525],exhibit:[100,239,251,272,386,419,507],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,233,247,303,304,306,307,359,360,362,364,365,366,368,372,382,388,415,427,459,476,487,494,496,498,499,500,509,510,511,520,525,526,528],exit:[2,3,11,12,41,59,203,225,377,393,496,497,506,515,516,517,525],exlanatori:3,exp6:2,exp:2,expand:[2,3,44],expans:[12,152,197,203,509,525],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,238,247,249,269,299,305,307,308,313,318,359,379,390,407,444,447,449,493,496,498,500,503,507,512,525],expens:[6,75,207,299,303,318,348,359,378,379,390,394,496],experi:[6,13,14,224,233,252,261,271,305,317,318,385,389,414,449,507,512],experienc:[6,12,15,260,261],experiment:[16,247,378,394,512],expert:12,expertis:7,expir:[516,517],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,232,272,288,299,307,318,332,359,361,377,378,381,388,389,393,399,417,430,467,469,485,496,499,500,503,505,508,519,520,525,530],explan:[3,6,61,124,129,152,203,204,219,271,299,427,492,495,496,498,507],explanatori:[3,8,128,203,204,218,219,222,318,388,495,525],explantori:[3,314],explic:448,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,232,319,326,327,363,378,384,396,397,400,405,407,417,419,431,441,484,492,495,499,502,520],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,232,240,246,248,250,255,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,307,308,310,311,318,321,322,341,342,348,356,362,364,365,367,368,371,373,388,394,395,396,398,401,402,403,404,405,406,407,408,409,410,411,413,414,416,417,418,420,421,422,423,424,425,426,427,431,432,433,434,435,436,437,438,439,440,441,445,447,449,450,451,452,453,454,456,460,461,462,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,486,488,489,490,498,500,501,507,508,510,511,517,519,520],explictli:[15,511],exploit:[14,16,301],explor:[130,177],expon:[3,309,311,319,417,421,423,426,440,448,462],exponenti:[95,319,421,457,478,486,490,512,525],expos:11,exposit:[216,414,416],express:[6,152,164,178,211,212,229,269,299,309,319,348,354,361,400,417,419,434,444,467,468,477,525],expression:361,expressiont:400,extend:[0,3,6,7],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,231,234,238,239,245,246,247,249,250,251,253,255,257,270,272,277,286,299,300,316,317,318,321,324,329,332,333,335,339,340,341,342,343,345,346,348,350,353,357,358,423,444,447,460,461,468,515,516,524],extensiv:[65,210,516],extent:[1,3,41,42,45,59,75,176,180,203,215,225,253,355,358,378,381,396,463,465,479,480,495,498,501],exterior:[3,6,176,357],extern:[2,3,9,94,95,176,206,210,224,229,238],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,272,306,307,308,318,336,387,388,391,392,394,413,424,427,430,444,449,495,496,498,501,510,519,525],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,311,389,410,420,444,468,496,503,515],extract_atom:11,extract_comput:[11,496],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,232,272,346,419,482,519],extrema:440,extreme:419,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,350],f_a:[481,482,483],f_ave:128,f_c:482,f_f:483,f_fix_id:308,f_foo:525,f_harm:346,f_i:[28,457],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,231,267,338,350,516,525],f_ij:457,f_indent:223,f_int:345,f_j:28,f_jj:99,f_k:457,f_langevin:348,f_max:[308,313],f_msst:270,f_r:[256,481,482,483],f_sigma:400,f_solid:346,f_ss:6,face:[3,6,59,61,75,166,176,180,215,353,355,356,357,358,381,423,444,461,498,501],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,249,304,336,346,424,459,467,510],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,232,233,239,247,252,255,257,258,270,272,273,277,301,305,309,317,319,322,325,327,336,340,344,351,352,353,357,368,379,381,388,394,396,397,400,401,403,405,410,411,412,414,415,419,424,427,431,432,444,447,449,451,452,453,454,460,462,469,478,484,495,498,501,502,507,510,512,513,516,519,524,525],factori:[3,496],factoriz:378,fail:[3,9,11,12,61,182,229,233,378,387,389,412,460,496],failur:[133,464,497,525],fairli:[11,449,507,512,520],faken:77,falcon:252,fall:[3,6,207,222,304,496,525],fals:[94,359,467,525],fame:8,famili:[486,495],familiar:[0,11,520],fan:457,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,233,272,299,317,318,336,353,364,368,385,389,390,485,496,498,503,516],farago:255,farrel:[481,483],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,231,233,247,249,253,269,270,272,274,275,276,277,278,279,280,289,292,293,295,296,297,307,308,310,318,324,328,335,338,346,348,352,353,354,356,358,389,427,441,501,510,525,529],fasolino:429,fast:[6,7,9,12,13,15,16,39,203,204,231,283,308,319,349,378,379,402,441,442,447,477,479,480,500,505,507,516,526,530],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,232,240,246,250,254,255,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,305,309,310,311,318,321,322,336,343,345,348,352,356,362,364,365,367,368,371,373,378,379,391,392,394,395,396,398,400,401,402,403,404,405,406,407,408,409,410,413,414,417,418,420,422,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,445,450,453,454,456,460,461,462,469,477,478,479,481,482,483,484,486,488,489,490,493,501,507,511,519],fastest:[1,6,16,166,348,349,394,495],fatal:[3,515],fault:[74,460],faulti:12,fava:423,favor:228,favorit:7,fbmc:343,fcc:[2,3,6,7,66,74,77,99,117,210],fcm:[289,525],fcold:239,fdirect:236,fdotr:428,fdt:[2,9,241,242,243,319,323],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[0,3,5,6],fecr:417,feedback:[7,231,252],feel:[7,252,253,261,299,357,359,389,449],fehlberg:319,felling:446,felt:357,femtosecond:524,fene:[2,3,6,7,10,15,44],fennel:[410,432],fep:[0,2],ferguson:[6,184,510],fermi:[1,9,10,12,14,164,394,483],fermion:419,fernando:443,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,239,256,272,304,307,309,322,350,378,387,388,389,396,467,495,498,503,507,509,517,525,528],fewer:[1,3,11,14,15,63,261,507],fewest:3,fextern:245,feynman:301,fff:496,ffield:[409,420,459,460,467],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,300,378,379,507],fft_inc:[12,379],fft_lib:12,fft_path:12,fftbench:[378,517],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:239,ficiti:476,fictiti:[6,213,214,238,245,249,301,317,410,432,436,476],field1:[499,503],field2:499,field:[0,2,3,5],fifth:[6,332,421,453],figshar:299,figur:[1,3,8,12,15,308,495,496,520],fij:413,file0:299,file1:[11,13,243,299,347,361,388,503,505,509],file2:[11,13,243,347,361,388,503,505,509],file:[0,1,2,3,4],file_from:205,filen:388,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,242,243,299,303,306,309,310,311,314,315,318,319,320,347,348,375,376,377,388,389,395,396,400,410,417,418,420,421,429,444,445,446,451,452,453,457,458,459,460,467,468,478,479,480,481,482,483,486,494,495,496,499,500,505,509,516,525,528,529,530],filennam:505,filep:[3,203,204,207,500,505,530],filepo:315,fill:[7,9,178,206,304,348,381,390,400,447,460,501,520],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,412],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,231,242,243,244,247,271,299,304,305,313,317,385,387,389,390,410,427,432,436,444,451,452,467,477,479,480,519,520,525],find_custom:8,fine:[15,16,182,213,238,346,390,394,520,525],finer:[152,178,525],finest:378,finger:[178,202,269,501],finish:[6,11,41,225,361,375,377,378,391,393,394,485,503,525,526],finit:[0,3,4],finni:[7,417,477],finverse:236,fiorin:[9,230],fire:[2,3,210],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,74,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,232,242,243,247,248,253,258,269,270,271,272,299,301,306,307,308,310,315,318,322,324,332,333,334,336,337,338,345,346,347,348,350,359,361,362,369,381,387,388,389,390,393,394,395,396,399,400,401,403,405,407,409,410,417,419,420,421,424,425,427,428,429,430,431,432,436,441,442,444,446,447,449,451,452,453,457,459,460,467,468,476,478,479,480,481,482,483,486,490,493,494,495,496,498,499,500,503,505,507,510,511,512,515,516,519,520,525,526,527,528,530],fischer:[6,9,18,19,184,405,510],fit:[3,6,9,12,37,56,199,242,317,336,396,400,429,444,449,451,452,472,479,480,482,506,520,525],five:[77,164,308,388,400,445,498,512],fix:[0,1],fix_deposit:3,fix_flux:216,fix_heat:239,fix_id:[3,229,270,272,274,275,276,277,278,279,280,305,308],fix_manifoldforc:520,fix_modifi:[2,3,6,8,120,121,160,163,210],fix_nh:8,fix_nv:520,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:322,fix_reax_bond:459,fix_saed_vtk:320,fix_setforc:8,fix_shak:322,fix_srd:3,fixedpoint:[229,272],fixextern:245,fixid:[206,216],fji:413,flag1:[235,392],flag2:[235,392],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,235,252,255,259,261,268,269,300,307,318,332,335,336,343,347,356,359,374,376,379,388,392,393,394,396,426,431,444,447,476,491,493,495,496,498,499,500,502,503,504,508,520,525],flag_buck:404,flag_coul:[404,413,436],flag_lj:[413,436],flagfld:[402,441,442],flaghi:[3,402,441,442],flaglog:[402,441,442],flagn:235,flagvf:[402,441,442],flat:[6,15,348,353,354,358],flavor:[2,7,12],fld:[353,441,442],flen:397,flex_press:397,flexibl:[3,6,8,179,206,219,230,249,273,344,351,419,482,516],flip:[3,6,232,272,355,356],floor:525,flop:12,floralwhit:207,flow:[4,5],fluctuat:[6,66,95,229,247,248,255,258,272,277,299,300,305,323,346,348,371,415],fluid:[2,6,7,9,10,40,69,79,86,96,103,116,127,128,158,173,175,229,232,250],fluid_veloc:262,flush:[3,207,515],flux:[2,3,6,65],flv:206,fly:[7,9,12,41,206,210,216,221,233,236,318,322,349,400,447,516,519],fmackai:9,fmag:234,fmass:301,fmax:[387,516],fmomentum:236,fmsec:[2,207,255,256,269,272,305,318,339,340,507,518,524,526],fname:377,fno:[9,15],fnorm:[387,516],fnpt:236,fnve:239,fnvt:236,foce:427,fock:397,focu:322,fogarti:[9,311,460],foil:[152,299,468],fold:[15,334,507],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,233,236,237,241,242,243,245,247,248,249,252,254,255,256,258,261,270,272,277,278,279,280,292,293,295,297,300,301,303,306,307,308,309,311,313,315,317,318,319,320,322,338,339,340,341,344,345,346,347,348,350,351,359,360,364,365,366,367,368,371,373,376,381,384,387,388,389,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,456,457,458,459,460,461,462,464,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,495,496,498,499,501,503,505,506,507,510,512,513,514,519,520,525,526,529],foo:[4,8,11,12,203,206,245,319,496,509,525],foo_species:319,foot:6,footprint:[12,394],fopenmp:[9,17],forc:[0,1,2,3,5],force_uvm:16,forceatom:261,forcefield:[317,426],forcegroup:258,forcezero:385,ford:413,forestgreen:207,forev:75,forget:[256,519],forgiv:272,fork:[12,203,520],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,128,152,153,172,173,182,186,203,207,210,211,212,218,219,220,222,223,227,231,248,249,255,257,261,269,295,300,311,313,317,318,319,348,353,357,362,363,366,371,384,386,388,389,396,397,400,407,415,417,419,422,426,427,431,443,444,446,447,451,452,453,454,457,459,460,461,467,468,469,477,479,481,482,483,489,492,495,496,498,503,508,515,516,519,525],formal:[6,82,85,99,248,249,255,272,301,336,344,467],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,242,243,300,303,307,309,311,314,318,319,320,331,347,348,359,360,363,384,388,389,395,396,400,407,417,420,421,431,444,446,451,452,458,459,460,462,468,479,480,486,487,495,496,498,499,500,503,514,515,516,525,527,528],formation:243,former:[6,12,39,41,207,225,348,352,400,402,504,510,525],formerli:[7,13],formul:[1,6,9,40,66,153,213,238,255,272,295,309,311,317,322,347,378,396,400,417,419,423,444,456],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,232,238,250,251,253,255,256,269,299,300,306,315,321,329,334,336,339,340,341,350,353,354,356,358,359,361,362,363,365,372,381,388,396,397,399,400,405,406,407,408,413,414,417,418,423,424,425,426,428,431,432,434,435,436,438,439,441,442,444,448,449,450,461,462,469,477,478,479,481,482,483,486,488,489,494,498,501,508,515,516,524,525,526],forth:[1,6,11,12,13,14,393,496,501,505],fortran: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99],inconveni:381,incorpor:[197,308,400,411,520],incorrect:[3,161,255,444],incorrectli:[3,381,424,525],increas:[1,3,6,15,17,37,56,59,61,120,130,153,199,203,204,206,207,221,226,227,228,231,232,239,242,243,247,255,305,316,317,318,319,344,347,351,378,379,389,394,396,419,423,451,452,460,479,480,482,496,507,512,525],increasingli:419,increment:[3,11,140,213,214,224,225,233,238,244,272,304,324,325,359,377,393,430,467,493,496,510,512,525],incur:[16,219,244,348,495],inde:161,indefatig:7,indefinit:345,indent:[2,3,4,210,223],independ:[4,6,9,11,12,16,41,61,65,86,99,128,131,164,178,202,210,218,219,220,222,223,225,228,229,230,232,233,248,250,255,256,258,261,272,300,305,309,313,318,320,324,335,346,348,381,424,447,493,496,515,526],indetermin:[203,204,207],index:[0,3,6,8,11,12,37,39,40,56,57,68,71,73,84,102,119,128,129,131,176,199,203,207,218,219,220,222,223,242,243,252,254,301,320,348,359,360,361,384,393,449,451,452,459,460,479,480,487,498,513,516,525],indianr:207,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,199,203,206,211,212,218,219,220,222,223,229,231,272,300,318,348,359,362,371,378,388,390,409,416,420,427,444,447,449,453,459,460,467,481,483,495,497,498,500,516,520,525],indigo:207,indirectli:[6,231,307,525],indistinguish:255,indium:468,individu:[0,1],induc:[0,3],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,152,166,206,232,272,300,378,391],inelig:217,inerti:442,inertia:[2,3,6,40,42,65,90,91,92,93],inertiai:129,inertiax:129,inertiaz:129,inexpens:[249,507],inf:[2,3,12,351,501],infer:[3,104,106,107,172,213,214,225,226,227,238,252,303,336,344,351,381,407,420,498,510,516],infil:[3,13,318,495],infin:[3,387,503,516],infininti:206,infinit:[3,233,246,253,255,258,300,336,348,354,355,379,381,419,498,502,524],infinitesim:6,inflect:[411,434,477],influenc:[3,9,41,85,160,269,304,378,379,449,481,482,483],inform:[0,1,2,3,6,7,8,9,11,12,13,14,15,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,236,237,238,239,240,244,245,246,247,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,268,271,281,282,283,284,285,286,287,288,289,290,291,294,298,299,300,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,318,320,321,322,325,332,333,334,336,337,339,340,341,342,343,344,345,347,350,351,352,353,355,356,357,358,360,376,378,379,382,386,387,388,389,390,392,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,413,414,416,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,454,456,457,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,485,486,488,489,490,491,495,496,498,499,500,502,503,505,510,512,513,515,517,525,527,528,529,530],informat:[8,12,499],infrequ:[6,272,414,493,512,517],infti:[411,441,442],ingtegr:400,inher:[378,387,449],inherit:[6,484],inhomogen:[17,348,449],inidividu:387,init:[3,8,316,467],init_fil:348,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,178,179,180,199,202,203,204,206,207,208,211,212,215,216,220,225,227,228,229,231,232,240,242,243,247,248,252,253,254,255,256,258,263,268,269,270,271,272,277,286,288,300,301,302,307,308,313,316,317,318,319,321,323,333,335,336,338,343,345,346,347,348,349,350,353,354,355,356,358,359,361,378,382,386,387,389,396,397,413,414,416,447,451,452,458,459,460,467,479,480,493,495,496,498,500,501,503,505,506,508,512,513,516,519,525,526,528,530],initial:[2,3,6,87,113,180,525],initial_integr:8,initial_integrate_respa:8,initialis:458,initialt:348,inlclud:11,inlin:496,inner2:[405,425],inner:[3,8,15,57,203,253,361,377,385,386,387,389,393,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,413,414,416,417,418,419,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,456,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,485,486,487,488,489,490,491,507,512,525],inner_distance_cutoff:426,innergroup:261,innermost:[37,56,75,392,479,480,507],innernod:261,innner:438,inordin:349,inorgan:[6,486],inp:[230,361,468,486],input1:[71,124,125,128,129,131,338],input2:[71,124,125,128,129,131,338],input:[0,1],input_doubl:3,inquir:325,insensit:12,insert:[3,5,7,8,9,12,61,178,210,233,247,253,304,378,468,476,496,502,519],insertion:[3,233,247,304],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,233,234,239,244,247,253,258,261,304,318,336,353,355,356,357,358,359,376,381,496,497,498,500,501,508,525],inside:[258,434,496,512],insight:[6,13],instabl:[258,413,466],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,379,389,404,405,428,432,436,440,447,493,499,500,505,513,520,530],install:[0,8],instanc:[6,9,11,211,230,249,355,422,427,449,457,496,519],instantan:[6,65,228,229,231,248,249,272,277,300,305,308,313,315,318,343,504,516],instanti:[6,11,12,216,427,495],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,247,255,258,261,262,300,306,307,316,318,338,356,376,378,379,382,390,394,403,404,417,431,433,440,444,447,450,460,477,484,493,501,505,512,514,519,525],institut:[9,252,303],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,232,240,246,250,255,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,310,311,318,321,322,356,362,364,365,367,368,371,373,379,394,395,396,398,401,402,403,404,405,406,408,409,410,413,414,417,418,420,422,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,445,450,453,454,456,460,461,462,469,478,479,481,482,483,484,486,488,489,490,501,507,519],instruction:11,insuffici:[3,6,12],insult:272,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,233,238,240,244,245,247,250,255,268,306,307,316,318,336,348,353,357,358,359,361,377,388,390,394,408,423,427,455,461,479,491,495,496,498,499,503,506,507,515,516,525,526],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,231,233,235,245,247,248,249,252,255,256,257,258,300,303,304,307,308,313,318,319,336,338,340,343,347,348,367,378,381,402,414,415,416,430,444,459,460,464,466,468,493,495,496,497,498,506,507,508,512,515,525,526],integer:[3,498],integr:[2,3,5],integral:[301,451,452],integrate_ulsph:326,intel:[1,2,3,7],intel_coprocessor:15,intel_cpu:12,intel_cpu_intelmpi:15,intel_cpu_mpich:15,intel_cpu_openpmi:15,intel_phi:12,intend:[3,6,8,12,13,35,221,248,458,498],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,237,244,251,261,270,272,277,315,318,320,336,344,348,350,351,515,516,524],intensiv:[65,210,516],intepol:525,inter:[17,42,63,64,158,181,182,203,228,255,257,271,310,318,378,389,400,508,519,525,528,530],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,246,247,252,253,255,257,261,286,299,301,303,304,309,311,317,318,319,326,327,336,337,343,348,352,353,354,357,358,363,364,365,366,368,370,372,378,379,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,454,455,456,457,460,461,462,464,466,467,468,469,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,493,496,498,500,502,503,507,508,510,515,516,519,528],interatom:[3,4,7,9,10,178,203,271,345,346,395,400,417,419,428,444,447,467,482,525],intercept:130,interchang:[6,231],interconnect:17,interconvert:419,intereract:39,interesect:357,interest:[1,5,7,8,9,11,13,75,177,301,343,346,379,418,442,459,460,496,525],interf:[394,520],interfac:[0,3],interfer:[12,272,396],interg:[6,519],intergr:507,interi:442,interior:[3,6,41,357,501],interlac:444,interleav:[6,178,506],intermedi:[6,12,61,206,271,299,371,389,496,497,506,510],intermix:493,intermolecular:[154,396],intern:[0,2,3,5,6,9,11,15,19,20,23,27,31,34,35,39,40,42,65,88,89,95,109,111,129],internal:[3,206,212,304,525],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:254,interpenetr:444,interpentr:[471,472,474],interpol:[6,14,37,56,110,199,206,207,216,242,243,258,299,378,379,389,400,449,451,452,460,473,479,480,481],interpret:[2,6,11,197,206,222,424,469,493,496,512,525],interrupt:308,intersect:[3,6,130,207,357,359,501],intersert:357,interspers:387,interstiti:[176,447],intertia:[3,103],interv:[3,6,99,205,220,231,255,272,308,313,314,327,467,473,493,512,525],intestieti:130,intial:[6,394,396],intiial:[41,503],intiti:[3,335],intra:318,intra_energi:247,intramolecular:[28,154,247],introduc:[6,9,100,117,206,239,272,308,313,318,371,378,395,410,419,432,436,440,478,512,525],introduct:0,intuit:381,inv:[130,177,320],invalid:[3,12,75,97,181,286,389,441,442,500],invari:[117,145,150,152,231],invent:322,invers:[3,6,51,130,177,207],inverse:519,invert:[1,6,182,300],invis:357,invoc:[176,228,394,464,466,496],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,208,210,211,212,213,214,215,216,2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13,208,499],plum:207,pm3:177,pmb:[2,9],pme:379,pmf:[230,324,332],png:[3,12,203,206],pni:206,poariz:6,poem:[2,3,6,9,12,210],poems:[3,6,7],point1:498,point2:498,point3:498,point:[1,2,3,4,6,7,8,9,11,12,15,17,28,37,40,41,42,56,61,74,75,90,92,93,124,125,130,152,156,157,171,176,177,178,189,199,201,202,203,204,206,207,210,215,219,221,223,225,229,232,233,234,238,242,243,246,247,249,252,253,258,261,269,271,272,274,275,276,278,279,280,282,283,284,287,290,291,292,293,295,297,300,301,307,308],point_data:320,pointer:[3,7,8,9,11,245,496],pois:524,poiseuil:[4,213,250],poisson:[61,232,379,424],poisson_solv:216,polak:386,polar:[6,7,117,152,160,177,216,235,409,410,432,484,519],polar_off:409,polar_on:409,polariz:0,poli:[2,3,176,304,381],politano:[9,467],pollock:[7,379],polya:359,polybond:13,polychain:318,polydispers:[3,388,402,408,424,441,442,477,489],polyethylen:396,polygon:[6,42,176],polyhedron:176,polym:[0,5,6,7,10],polymer:7,polymorph:[2,3,7],polynomi:[9,37,56,199,417,438,449,467,472,479,480],polytechn:303,poor:[16,41,225,295,296,322,394,438],poorli:[386,387],pop:[3,8],popen:12,popul:[12,313,381,416,498],popular:[12,203,418],pore:332,poros:181,porou:[258,261],port:[252,254],portabl:[7,9,12,203,205,230,459,500],portion:[1,3,9,11,12,14,41,54,67,72,75,83,96,99,101,118,119,121,124,153,154,168,203,204,207,218,219,222,223,225,229,239,244,258,272,274,275,276,278,279,280,310,315,316,318,320,361,377,390,394,401,403,404,405,406,410,411,413,414,419,421,422,423,425,426,432,436,440,443,454,461,462,483,487,497,498,503,507,508,517,520,525],poschel:424,posfreq:315,posit:[3,6,26,39,40,41,42,46,59,61,74,75,86,87,97,98,113,114,119,128,130,134,152,153,161,176,177,178,180,181,182,187,189,197,199,202,204,205,206,207,210,211,213,215,217,218,219,222,225,226,227,228,229,230,231,232,233,236,238,239,247,248,249,250,252,253,255,256,257,258,260,261,265,266,269,270,272,273,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,295,296,297,299,300,301,303,304,305,308,309,313,315,316,318,319,322,324,328,331,332,335,336,338,339,340,341,343,345,346,347,348,351,353,354,355,356,357,358,359,362,378,381,389,396,397,399,402,414,415,416,419,422,435,451,452,460,467,476,479,480,485,493,498,501,508,517,519,525,526],posix:252,posix_memalign:12,possibl:[1,3,6,8,9,11,12,14,37,40,41,55,61,65,74,75,95,124,126,129,152,153,156,157,171,202,203,204,205,207,210,212,216,217,225,226,227,228,233,235,241,249,256,267,299,304,312,313,315,318,319,331,336,338,348,349,354,367,377,379,387,390,391,394,416,426,444,460,464,466,467,479,480,486,496,502,511,512,516,519,525,526,529],post:[0,4,6],post_forc:8,post_force_integr:8,post_force_respa:8,post_integrate_respa:8,postit:286,postiv:94,postma:[305,339],postprocess:13,pot:[424,460],potentail:420,potenti:0,potentials:10,potentiel:440,potetni:427,potin:447,potpourri:9,pour:[2,3,4,6,9,112,180,207,210,233],pourtoi:343,pow:232,powderblu:207,power7:16,power8:16,power:[3,9,11,15,115,152,207,313,378,394,400,496],pparam:[95,211,212],ppm:[12,203,206],ppn:[14,15,16,17,394],pppm:[0,1,2,3,5],pppm_disp:3,pppmdisp:3,pproni:[3,248],pr3:177,pr4:177,practic:[3,12,229,272,273,300,307,486,495,520],prb:[481,483],prd:[2,3,4,6,9,94,232,389],pre:[3,6],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec:[15,467],prece:466,preced:[2,6,61,184,204,207,218,219,220,221,222,223,254,315,319,320,361,381,389,394,400,426,512,515,516,525],preceed:[11,12,75,166,220,353,496,525],precipit:176,precis:[1,3,9,12,13,14,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,43,45,46,47,48,49,51,53,54,56,113,123,155,165,178,184,185,187,188,189,190,192,193,195,196,199,203,207,213,219,223,224,229,232,239,240,246,250,255,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,309,310,311,318,321,322,356,362,364,365,367,368,371,373,378,379,387,394,395,396,398,401,402,403,404,405,406,408,409,410,413,414,417,418,420,422,423,424,425,426,432,433,434,435,436,437,438,439,440,441,445,447,450,453,454,456,459,460,461,462,467,469,478,479,481,482,483,484,486,488,489,490,500,501,507,508,511,515,516,519,524,525,526],precv:495,predefin:[196,207,359,419],predict:[1,6,10,12,286,318,394,517],preexponenti:512,prefactor:[23,24,27,31,34,35,172,186,198,211,212,220,353,364,368,371,387,408,422,453,461,462,469,489],prefer:[7,8,12,251,317,349,396,520],prefix:[11,12,206,230,231,300,319,492,495],preliminari:[37,56,199,242,243,451,452,479,480],prematur:387,prepar:[8,9,309,312,336,509,519],prepend:459,preprint:[152,288,294,383,468],preprocessor:252,prerecord:230,prescrib:[6,8,156,157,158,171,210,211,216,219,233,269,289,349],presenc:[203,226,227,258,261,441,442,447,489,528],present:[1,3,9,12,15,17,176,199,205,206,231,233,248,249,254,258,259,261,262,313,331,354,357,360,409,419,431,440,447,460,461,467,495,519],preserv:[3,61,229,232,272,322,336,358,499],press:[2,3,6,9,15,28,95,106,107,121,153,164,210,229,236,247,249,256,267,270,272,274,275,276,277,278,279,280],pressdown:224,pressur:[1,2,3,6,7,8,9,59,65],pressure_with_eviri:419,presum:[77,167,210,211,212,232,389,427,501],prevent:[2,3,6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237,355,356,359,381,459,496,498,502],putenv:[509,525],pvar:231,px1:507,px2:507,pxx:[229,272,305,318,378,379,515,516],pxy:[3,6,516],pxz:[3,6,516],py1:507,py2:507,pydir:11,pyi:[229,272,305,318,378,379,516],pymol:[7,11,13],pymol_aspher:0,pympi:11,pypar:11,python:[0,2,3,4,6,7],pythonpath:11,pyz:[3,6,516],pz1:507,pz2:507,pzz:[229,270,272,305,308,318,378,379,516],q_1:467,q_2:467,q_3:467,q_d:519,q_i:[420,440],q_j:440,qbmsst:[2,9],qcore:309,qdamp:309,qdist:[410,432,436,440],qeq1:309,qeq2:309,qeq:[2,3,4,6,7],qeqall:467,qeqallparallel:467,qfile:[309,410],qin:251,qinitmod:467,qmin:386,qmmm:2,qmol:312,qoffload:15,qopenmp:15,qout:251,qoverrid:15,qstep:309,qtb:2,quad:[12,17,394,495],quadrant:15,quadrat:[2,3],quadratur:[95,216],quadrupl:395,quadruplet:[194,198,200,362,364,365,366,368,370,371,372,374],qualifi:[3,254],qualiti:[7,206,207,396],quantic:467,quantit:[78,87,113,114,115,174,424],quantiti:[1,3,4],quantum:[6,9,152,245,249,301,308,312,313,396,400,419,447,467,477],quantum_temperatur:308,quartic:[2,3,7],quartic_spher:216,quartz:[308,313],quasi:301,quat:[3,508],quaternion:[3,6,40,90,124,129,142,156,157,178,274,275,278,279,282,283,284,292,293,423,498,508],quati:[124,129,498],quatj:[124,129,498],quatk:[124,129,498],quatw:[124,129,498],queen:13,quench:[359,493,512],queri:[3,11,54,289,496,525],quest:[6,245],question:[8,9,12,13,288,299,359,456,520,525],queteschin:9,quick:[0,4,12,14,15,16,17,18],quickli:[3,4,8,12,13,39,100,225,232,247,252,336,386,387,389,396],quickmin:[264,288,294,385,386,387,389,512],quicktim:[4,206],quip:2,quit:[2,258,343,361,468],quot:[2,3,12,205,207,306,361,444,493,494,496,506,515,525],quotat:467,r0m:333,r10:400,r12:423,r_1:152,r_2:152,r_c:[411,413,422,483],r_cut:[400,443],r_d:519,r_e:420,r_ewald:320,r_fu:[441,442],r_i:[28,152],r_ii:152,r_ij:[28,400,419,457,490],r_ik:457,r_j:28,r_jik:457,r_m:443,r_me:411,r_mh:422,r_min:412,r_ub:19,r_x86_64_32:12,ra2:177,rad2theta:177,rad:359,radhi:501,radial:[65,75,106,107,124,127,152,162,164,169,219,257,273,285,296,332,342,387,419,426,449,451,452,498,501],radian:[19,20,23,27,31,34,35,37,129,177,185,196,199,317,362,364,368,371,498,501,508],radians:199,radiat:[130,177,348],radic:[180,498],radii:[75,80,119,126,152,228,233,408,417,423,424,441,442,447,463,465,489,501],radit:419,radiu:[2,3,6,40,42,65,75,80,92,93,97,98,119,124,126,130],radlo:501,rafferti:351,rahman:[6,7,229,270,272,273,308,456],rai:[9,16,177],ram:483,raman:15,ramirez:221,ramp:[2,3,6,9,65,161,162,166],ran:[3,6,11],random:[3,6,39,178,181,202,206,215,217,226,227,228,230,233,244,247,248,249,255,256,257,258,268,272,301,304,308,313,316,318,323,336,340,343,348,352,355,402,414,415,416,493,508,513,519,525,526],random_se:493,randomli:[178,181,217,233,247,255,304,336,358,512,513],rang:[1,3,6,7,8,9,10,12,14,15,17,37,39,56,63,75,76,81,96,117,119,120,121,123,127,128,133,152,153,164,172,177,179,182,183,190,199,203,204,206,207,216,217,227,231,232,233,247,249,267,304,320,336,337,343,344,349,351,378,379,387,390,391,394,396,398,400,401,402,403,404,405,406,408,410,411,412,413,414,416,417,419,421,423,425,426,427,429,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,454,457,460,461,462,467,476,477,479,480,483,484,488,489,490,492,496,507,508,516,529],rank:[6,11,12,252,349,376,495],rankin:277,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,75,228,255,270,272,318,339,340,352,410,414],rapp:[309,310,311],rappe_and_goddard:310,rare:6,rasmol:[6,7],rasmussen:423,raster3d:[6,7],rate:[2,6,12,15,136],rather:[2,6,9,12,40,41,64,123,161,206,225,232,248,249,318,340,348,352,354,355,356,359,419,451,452,459,479,480,499,503,508,510,515,525],ratio:[6,61,95,111,152,217,225,232,255,257,336,344,351,352,378,392,423,424,461,471,485,495,498,508,512],rational:[349,510],rattl:[2,3,9,210,239,264],rattle:[3,9,210,239,249,288,294,322],rattle_debug:322,ravelo:[277,434],raw:15,rayleigh:[270,308],rb1:177,rbb:467,rbg:207,rcb:[3,41,225],rcm:[97,98],rcmx:[97,98],rcmy:[97,98],rcold:239,rcut:63,rcutfac:[152,468],rd1:389,rdc:16,rdf:[2,3,65],rdn:389,rdt:389,rdx:4,reach:[6,12,41,131,221,225,227,229,231,256,277,319,328,336,343,361,377,393,411,517,519,525],reacquaint:520,react:6,reactant:[319,419],reaction:[9,243,319,324,334,347,358,389,419,421,452,480],reactiv:[9,315,396],read:[2,3,6,7,8,9,11,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,58,61,126,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,202,203,204,206,207,208,209,210,216,217,228,229,232,233,242,243,247,249,252,269,270,272,274,275,276,277,278,279,280,292,293,295,296,297,300,301,303,304,306,307,311,318,319,322,324,328,331,335,338,346,347,348,354,360,362,363,364,365,366,367,368,370,371,372,373,374,375,377,384,388,389,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,417,418,419,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,454,456,457,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,477,4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6,358,359,378,383,387,397,398,402,408,410,411,413,414,416,419,422,423,424,425,426,431,433,434,435,437,438,439,441,442,449,450,451,452,456,461,469,476,479,480,488,489,490,495,511,526],reli:[3,12,310,419,460,490,498,508],reloc:12,reltol:319,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,232,255,256,263,272,273,278,279,280,292,293,295,297,302,303,327,336,339,340,341,347,348,359,361,369,372,388,400,419,427,440,447,449,477,493,498,499,503,508,510,512,516,517,519,520,525,526],remaina:400,remaind:[9,178,203,233,304,336,349,483,498],remap:[3,6,12,61,63,75,161,178,202,232,253,269,295,378,498,499,500],remedi:[6,519],rememb:[2,520],remot:520,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,244,255,256,261,264,268,270,272,278,279,280,292,293,295,297,303,309,318,319,320,322,336,339,340,341,343,359,378,389,413,442,447,498,501,509,510,520,525,526],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,360,509,520],render:[12,13,203,206,207],rendon:[272,273],reneighbor:[3,8,12,39,59,75,225,247,336,349,359,414,515,516],renssela:303,renumb:75,reorder:[3,12,39,495],rep:513,repeat:[2,6,206,207,228,229,247,319,328,381,400,481,483,485,493,512],repeatedli:2,repel:253,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,233,255,277,306,307,313,315,354,394,396,410,424,434,451,452,479,499,500,505,506,516,525,526,528,530],replic:[2,3,7,381,495,498],replica:[0,2,3,4],replica_fil:12,repons:231,report:[0,1],repositori:[7,9,12,428,458,459,460,520],reprens:348,repres:[1,3,6,8,9,12,14,40,41,42,61,70,74,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,231,236,243,248,250,255,258,272,301,303,305,313,318,319,320,324,332,333,348,350,357,379,389,395,400,423,430,440,441,442,444,445,446,454,457,459,460,484,485,493,495,498,508,510,513,519,525,528],represent:[3,6,8,9,59,61,146,180,203,248,249,301,348,400,419,423,447,461,498,501,519],reprocess:503,reproduc:[3,15,272,354,410,417,424],repul:444,repuls:[6,7,35,40,45,46,119,253,309,353,354,357,396,400,408,410,414,419,421,424,426,440,444,448,467,476,483,486,489,490,508],reqir:[309,311],request:[3,6,8,12,41,113,181,199,203,252,258,316,323,336,338,376,378,449,459,460,493,503,508,512,517,520,525,526,528],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,76,81,100,117,127,152,203,206,449,499],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,210,217,220,222,223,239,247,249,251,255,256,268,272,277,295,303,305,313,318,336,339,340],research:[5,7,88,89,241,258,262,323,447,493,512],resembl:[313,520],resepct:6,reserv:[12,252,519],reservoir:[99,239,247,251,255,348],reset:[2,3,6,8,11,12,63,69,75,78,79,86,87,97,98,103,113,114,116,173,182,210,211,212,229,232],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[2,6,99,499,503],resid:13,residu:252,residue1:390,resist:[6,252],resolut:[221,467,479,480],resolv:[229,301,336,442,520],resort:3,resourc:[7,395,417],respa:[3,15,213,214,224,234,237,238,250,252,253,267,272,299,310,317,321,324,332,333,334,335,352,353,357,392,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,413,414,416,417,418,419,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,450,451,452,454,456,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,485,486,488,489,490,491,506,507,517,518,525],respecifi:447,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,232,239,240,246,250,253,255,256,258,272,274,275,276,277,278,279,280,281,282,288,290,292,293,295,297,309,310,311,318,320,322,324,332,335,348,353,356,362,364,365,367,368,371,373,376,378,379,384,387,388,393,394,395,396,398,400,401,402,403,404,405,406,408,409,410,413,414,417,418,420,421,422,423,424,425,426,427,432,433,434,435,436,437,438,439,440,441,444,445,447,449,450,453,454,456,460,461,462,466,467,468,469,478,479,481,482,483,484,486,488,489,490,495,499,508,511,517,519,525,527,528,530],respon:9,respond:[6,7,161,231,232,419,456],respons:[6,7,231,270,344,351],resquar:[2,3,6,7,9,423],rest:[6,8,12,38,58,200,307,311,317,374,400,442,444,491,515,516,519],restart1:301,restart2:301,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,62,63,113,178,211,212,267,307,324,332,333,338,360,515,516],restore_bia:8,restore_bias_al:8,restrain:[2,3,28,210,217,247,270],restraint:[9,230,270,317,335,431],restratin:317,restrict:[1,2,3,6,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,1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379,386,387,394,406,408,409,419,489,496,498,499,520,525,527,528,529],yflag:[165,166,259,261,268,318,343],yhi:[6,61,180,203,232,347,353,356,358,498,501,516],yhi_bound:[6,203],yield:[6,99,121,128,153,161,166,207,220,229,236,272,295,309,319,344,350,351,354,359,378,399,414,424,449,456,516,525],yip:345,ylat:[178,232,253,516],ylo:[6,61,180,203,232,347,353,356,358,498,501,516],ylo_bound:[6,203],ymax:[215,525],ymid:233,ymin:525,yorig:75,york:[301,379],yoshida:[272,318],you:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,32,34,37,39,40,41,42,43,45,46,47,48,49,50,51,53,54,56,59,60,61,63,65,67,69,71,72,75,76,77,78,79,81,83,86,87,88,89,95,96,97,98,99,100,101,103,112,113,114,116,117,118,120,121,123,125,127,128,129,152,153,155,156,157,158,161,165,166,171,172,173,174,175,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,198,199,203,204,206,207,208,210,211,212,213,214,217,218,219,220,222,223,224,225,226,227,228,229,231,232,233,236,238,239,240,242,244,245,246,247,248,249,250,251,252,253,255,256,257,267,269,272,274,275,276,277,278,279,280,281,282,286,289,290,292,293,295,296,297,300,301,303,304,305,307,309,310,311,313,316,317,318,321,322,324,332,333,335,336,337,339,340,341,342,344,345,346,347,348,350,351,352,353,354,356,357,358,359,361,362,364,365,367,368,369,371,373,377,378,379,381,384,386,387,388,389,390,393,394,395,396,398,400,401,402,403,404,405,406,407,408,409,410,413,414,416,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,444,445,446,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,486,488,489,490,492,493,494,495,496,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,515,516,517,519,520,524,525,526,527,528,530],young:[424,463,465],your:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,43,45,46,47,48,49,51,53,54,56,61,63,118,123,127,155,156,157,161,165,171,176,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,202,203,204,205,206,213,216,220,222,223,224,226,227,228,229,232,233,240,246,247,250,252,255,269,272,274,275,276,277,278,279,280,281,282,290,292,293,295,297,304,307,310,311,316,318,321,322,324,338,344,348,350,351,353,356,357,358,359,362,364,365,367,368,371,373,379,381,388,389,390,393,394,395,396,398,400,401,402,403,404,405,406,407,408,409,410,413,414,416,417,418,420,422,423,424,425,426,427,428,429,432,433,434,435,436,437,438,439,440,441,444,445,446,447,449,450,453,454,456,457,459,460,461,462,469,476,478,479,480,481,482,483,484,486,488,489,490,492,495,496,498,500,501,502,505,506,507,508,509,510,511,515,516,520,524,525,527,528,530],yourself:[6,8,12,13,229,388,520],yplane:354,ypo:178,ysu:[3,203,204,338,499],yuan:9,yukawa:[2,3,7,9,408,477],yukawa_1_1:487,yxz:495,yzx:495,z_i:[419,483,490],z_j:[483,490],z_meam:444,zachari:13,zannoni:423,zbl:[2,3,444,468,477],zblcut:483,zblcutinn:468,zblcutout:468,zblexpscal:483,zblz:468,zcm:318,zcylind:354,zepeda:217,zero:[2,3,4,6,9,11,12,25,26,33,36],zeta:[3,258,309,420],zfactor:206,zflag:[165,166,259,261,268,318,343],zhang:[318,344,424],zhi:[3,6,180,203,215,347,353,356,358,498,501,516],zhi_bound:[6,203],zhou:[13,400,420,457,481,483],zhu:475,ziegenhain:13,ziegler:[303,444,477,483,490],zimmerman2004:216,zimmerman2010:216,zimmerman:[9,74,216,400],zlat:[232,253,516],zlib:[9,203],zlim:467,zlo:[3,6,180,203,215,347,353,355,356,358,498,501,516],zlo_bound:[6,203],zmax:[215,258,525],zmid:233,zmin:[258,525],zn2:177,zone:[130,320],zoom:[3,203,206,207],zorig:75,zplane:354,zr4:177,zrest:335,zsu:[3,203,204,338,499],zwall:353,zwall_veloc:258,zxy:495,zybin:460,zyx:495},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff 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 hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff 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 hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix controller command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Manifolds (surfacse)","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian 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_coeff 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 dsmc 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 hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":226,"default":[36,39,40,55,59,60,61,63,64,74,75,95,96,100,112,113,115,117,118,119,126,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,232,233,237,244,247,248,253,255,256,257,258,259,261,267,270,272,273,277,295,296,300,301,304,305,306,307,308,310,313,315,316,318,320,336,338,343,344,345,346,349,351,353,355,359,372,376,378,379,381,382,385,386,388,390,391,392,394,397,400,402,419,441,442,447,449,459,460,476,477,493,494,495,498,499,501,503,505,506,507,510,512,514,515,516,517,518,524,526,528,529],"function":525,"long":[221,401,403,404,405,406,410,412,413,432,436,440,454,462,484],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,addition:[12,13],addtorqu:214,adiabat:6,adjust_dt:325,adp:395,airebo:396,alloi:417,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:215,arrai:6,aspher:[6,90,156,274,278,282,283,292],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,307,525],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:224,awpmd:[9,397],balanc:[41,225],barostat:6,basal:70,bcc:299,beck:398,berendsen:[305,339],between:6,binary2txt:13,bodi:[6,8,42,71,157,275,279,284,293,399],body:9,bond:[8,13,72,73,226,227,228,314],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:400,born:[401,412],boundari:[7,59],box:[6,60,229],brownian:402,buck:[403,404,412,443],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,change_box:61,charmm:[6,19,184,405,440],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,333],citat:7,class2:[9,20,43,185,362,406],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,353,408,489],colvar:[13,230],colvars:9,com:[78,79,159],comb3:409,comb:[310,409],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,521,522,523,524,525,526,527,528,529,530],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,525],compute_modifi:112,condit:7,conduct:[6,344],constant:[6,525],constraint:7,contact:[80,132],control:231,coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:364,coul:[401,403,404,405,406,410,411,412,425,432,436,440,454,462],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:340,csvr:340,cubic:434,custom:[8,203,204],cut:[49,397,403,406,410,413,419,422,432,433,440,448,454,484],cvff:365,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[410,432],defgrad:139,deform:[161,162,232],delete_atom:181,delete_bond:182,delta:23,deposit:233,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,521,522,523,524,525,526,527,528,529,530],diagnost:7,diel:411,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199,200],dilat:85,dimens:201,dipol:[6,28,86,413],dipole:9,direct:236,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:202,distanc:366,distribut:[7,12],document:0,dpd:[9,88,89,414,415],drag:234,dreid:426,dreiding:6,drude:[6,9,163,235,236,256,519],dsf:[410,432],dsmc:416,dump:[6,8,203,204,205,206,208],dump_modifi:207,dynam:309,eam:[13,417],echo:209,edip:418,eff:[9,13,106,107,162,164,169,257,273,285,296,342,419],efield:238,ehex:239,eim:420,elastic:6,emac:13,energi:[135,415],enforce2d:240,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:244,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,511,512,513,514,515,516,517,518,521,522,523,524,525,526,527,528,529,530],exp6:421,exp:[26,187],expand:[46,435],extend:[8,11],extern:245,fcc:299,fdt:415,featur:[7,8,525],fene:[45,46],fep:[9,13,95,212],field:[6,7],file:6,finit:6,fire:309,fix:[2,6,8,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,2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\ No newline at end of file diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 2a6836d340..b12e710a9e 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -3 Aug 2016 version :c,h4 +5 Aug 2016 version :c,h4 Version info: :h4 diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index 0e4cd8c82f..a43a1c4e67 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -41,12 +41,12 @@ fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre This fix enables control of a LAMMPS simulation using a control loop feedback mechanism known as a proportional-integral-derivative (PID) controller. The basic idea is to define a "process variable" which is -a quantity that can be monitor during a running simulation. A desired -target value is chosen for the process variable. A "control variable" -is also defined which is an adjustable attribute of the simulation -which the process variable will respond to. The PID controller -continuously adjusts the control variable based on the difference -between the process variable and the target. +a quantity that can be monitored during a running simulation. A +desired target value is chosen for the process variable. A "control +variable" is also defined which is an adjustable attribute of the +running simulation, which the process variable will respond to. The +PID controller continuously adjusts the control variable based on the +difference between the process variable and the target. Here are examples of ways in which this fix can be used. The examples/pid directory contains a script that implements the simple @@ -118,12 +118,12 @@ counteracted by increasing {Ki}. In the language of Charles Dickens error of the past, and {Kd} the error yet to come. Because this fix updates {cvar}, but does not initialize its value, -the initial value is that assigned by the user in the internal-style -variable command. This value is used (by the other LAMMPS command that -used the variable) until this fix performs its first update of {cvar} -after {Nevery} timesteps. On the first update, the value of the -derivative term is set to zero, because the value of {e_n-1} is not -yet defined. +the initial value is that assigned by the user in the input script via +the "internal-style variable"_variable.html command. This value is +used (by the other LAMMPS command that used the variable) until this +fix performs its first update of {cvar} after {Nevery} timesteps. On +the first update, the value of the derivative term is set to zero, +because the value of {e_n-1} is not yet defined. :line