From ccf8cf20b378d1309b4197c6087a220fac31ed2e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 20 Aug 2016 22:42:17 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15482 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/dump.txt | 3 +++ doc/html/_sources/dump_modify.txt | 17 +++++++++++++++++ doc/html/_sources/fix_ave_histo.txt | 5 +++-- doc/html/dump.html | 5 ++++- doc/html/dump_modify.html | 13 +++++++++++++ doc/html/fix_ave_histo.html | 5 +++-- doc/html/searchindex.js | 2 +- doc/src/dump.txt | 4 ++++ doc/src/dump_modify.txt | 15 +++++++++++++++ doc/src/fix_ave_histo.txt | 5 +++-- 10 files changed, 66 insertions(+), 8 deletions(-) diff --git a/doc/html/_sources/dump.txt b/doc/html/_sources/dump.txt index 7cbf12d6fd..151986688e 100644 --- a/doc/html/_sources/dump.txt +++ b/doc/html/_sources/dump.txt @@ -169,6 +169,9 @@ or multiple smaller files). Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. + Re-neighbor timesteps will not typically coincide with the timesteps + dump snapshots are written. See the :doc:`dump_modify pbc ` command if you with to force coordinates to be + strictly inside the simulation box. .. note:: diff --git a/doc/html/_sources/dump_modify.txt b/doc/html/_sources/dump_modify.txt index a0784510e5..2662076320 100644 --- a/doc/html/_sources/dump_modify.txt +++ b/doc/html/_sources/dump_modify.txt @@ -36,6 +36,7 @@ Syntax *nfile* arg = Nf Nf = write this many files, one from each of Nf processors *pad* arg = Nchar = # of characters to convert timestep to + *pbc* arg = *yes* or *no* = remap atoms via periodic boundary conditions *precision* arg = power-of-10 value from 10 to 1000000 *region* arg = region-ID or "none" *scale* arg = *yes* or *no* @@ -428,6 +429,21 @@ timestep order. ---------- +The *pbc* keyword applies to all the dump styles. As explained on the +:doc:`dump ` doc page, atom coordinates in a dump file may be +slightly outside the simulation box. This is because periodic +boundary conditions are enforced only on timesteps when neighbor lists +are rebuilt, which will not typically coincide with the timesteps dump +snapshots are written. If the setting of this keyword is set to +*yes*\ , then all atoms will be remapped to the periodic box before the +snapshot is written, then restored to their original position. If it +is set to *no* they will not be. The *no* setting is the default +because it requires no extra computation. + + +---------- + + The *precision* keyword only applies to the dump *xtc* style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to @@ -846,6 +862,7 @@ The option defaults are * label = ENTRIES * nfile = 1 * pad = 0 +* pbc = no * precision = 1000 * region = none * scale = yes diff --git a/doc/html/_sources/fix_ave_histo.txt b/doc/html/_sources/fix_ave_histo.txt index 9adf1610ef..69e51ce155 100644 --- a/doc/html/_sources/fix_ave_histo.txt +++ b/doc/html/_sources/fix_ave_histo.txt @@ -145,8 +145,9 @@ length. The first value (a scalar or vector) is what is histogrammed into bins, in the same manner the fix ave/histo command operates. The second value (a scalar or vector) is used as a "weight". This means that instead of each value tallying a "1" to its bin, the -corresponding weight is tallied. E.g. the Nth entry in the first -vector tallies the Nth entry (weight) in the second vector. +corresponding weight is tallied. E.g. The Nth entry (weight) in the +second vector is tallied to the bin corresponding to the Nth entry in +the first vector. ---------- diff --git a/doc/html/dump.html b/doc/html/dump.html index d87465df8e..40449d1202 100644 --- a/doc/html/dump.html +++ b/doc/html/dump.html @@ -274,7 +274,10 @@ or multiple smaller files).

Note

Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box.

+written to a dump file may be slightly outside the simulation box. +Re-neighbor timesteps will not typically coincide with the timesteps +dump snapshots are written. See the dump_modify pbc command if you with to force coordinates to be +strictly inside the simulation box.

Note

diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html index 3d7b230e46..492ef0a5f5 100644 --- a/doc/html/dump_modify.html +++ b/doc/html/dump_modify.html @@ -158,6 +158,7 @@ nfile arg = Nf Nf = write this many files, one from each of Nf processors pad arg = Nchar = # of characters to convert timestep to +pbc arg = yes or no = remap atoms via periodic boundary conditions precision arg = power-of-10 value from 10 to 1000000 region arg = region-ID or "none" scale arg = yes or no @@ -468,6 +469,17 @@ yield 0000100, 0012000, 2000000. This can be useful so that post-processing programs can easily read the files in ascending timestep order.

+

The pbc keyword applies to all the dump styles. As explained on the +dump doc page, atom coordinates in a dump file may be +slightly outside the simulation box. This is because periodic +boundary conditions are enforced only on timesteps when neighbor lists +are rebuilt, which will not typically coincide with the timesteps dump +snapshots are written. If the setting of this keyword is set to +yes, then all atoms will be remapped to the periodic box before the +snapshot is written, then restored to their original position. If it +is set to no they will not be. The no setting is the default +because it requires no extra computation.

+

The precision keyword only applies to the dump xtc style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to @@ -790,6 +802,7 @@ images less frequently.

  • label = ENTRIES
  • nfile = 1
  • pad = 0
    • +
  • pbc = no
  • precision = 1000
  • region = none
  • scale = yes
    • diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html index cd54bcef35..e8291ddeb4 100644 --- a/doc/html/fix_ave_histo.html +++ b/doc/html/fix_ave_histo.html @@ -254,8 +254,9 @@ length. The first value (a scalar or vector) is what is histogrammed into bins, in the same manner the fix ave/histo command operates. The second value (a scalar or vector) is used as a “weight”. This means that instead of each value tallying a “1” to its bin, the -corresponding weight is tallied. E.g. the Nth entry in the first -vector tallies the Nth entry (weight) in the second vector.

    +corresponding weight is tallied. E.g. The Nth entry (weight) in the +second vector is tallied to the bin corresponding to the Nth entry in +the first vector.

    The Nevery, Nrepeat, and Nfreq arguments specify on what timesteps the input values will be used in order to contribute to the diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index b86fd4ac62..37935b1680 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],bulatov:[134,135],bulk:[2,29,67,70,105,133,136,146],bundl:[57,161],button:161,bypass:2,c11:133,c_0:[79,93,150,151],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_gauss:115,c_hb:119,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:96,c_prop:2,c_sigma:96,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,104],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,93,102,159,161],callabl:3,callback:3,caltech:[2,112],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,90,91,98,99,101,110,116,118,121,125,127,129,142,144,145,152],canon:[68,71,78,136],cao1:71,cao2:71,cao:71,capabl:[3,4,93,101],capac:[64,79,149],capolungo:[40,43],captur:[2,93,99,112,117,125,133],carbid:104,carbon:[57,88,93,103,133],card:[4,32,119],care:[2,44,55,67,68,95],carefulli:[3,28],carlo:[2,60],caro:110,carri:[4,79,117],carrillo:4,cartesian:[2,92],cascad:79,cat:[4,57],cate:67,categori:[0,93],cation:[113,146],caus:[1,2,4,44,61,68,70,74,75,80,81,90,91,119,121,127,130,131],caution:1,cautious:93,caveat:93,cbecker:[92,110],cc1:[2,34],ccc:[111,153,154,156,157],ccflag:4,ccflags:4,ccm6:110,ccsi:[111,153,154,156,157],ccu:96,cd2:43,cdeam:110,cdll:3,cdof:2,cdte:96,cdte_bop:96,cdtese:96,cdzn:96,cdznte:96,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,72,79,112,136],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,82,95,111,112,116,117,130,131,133,134,135,153,154,155,156,157],centr:63,central:[29,36,38,41,70,75,76,85,136,141,157],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:145,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,88,107,108,152],challeng:2,champaign:130,chan:136,chandler:[92,110],chandrasekhar:[2,121],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,90,91,108,112,117,130,131,133,136,146,152,161],change_box:2,chapter:71,charact:[2,19,57,59,65,74,112,114,120,139,140,143,146],character:[2,29,38,41,147],characterist:77,charg:[1,2,3,32,40,43,44,97,98,103,104,106,107,110,112,113,121,125,129,142,146,156,157,159,160],charl:62,charmm:0,cheaper:[116,144],check:[2,3,19,35,59,73,75,78,90,91,120],checkout:161,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,82,88,89,91,93,97,100,101,103,104,105,107,108,109,112,115,116,118,119,121,125,126,129,133,137,139,140,142,146,152],chemic:[31,40,43,58,114,140],chemistri:[72,93,96,112],chen:79,cheng:103,chi:[70,113,116],chiral:88,chmod:3,cho:133,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,91,129],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[154,156],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,109,112,117,120,123,145,154],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:146,cl1:43,clarendon:[13,107],clarifi:[154,156],clark:142,classic:[0,2,4,71,72,79,89,112],classifi:157,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,91,161],climb:91,clockwis:45,clone:161,close:[2,3,19,42,60,61,67,68,75,81,91,93,96,104,105,133,139,140,156,161],closer:[19,59,61,77,91],closest:[70,116,144,152],cloud:146,cluster:[2,4,42,63,75],cmax:133,cmd:[3,71],cmdarg:3,cmin:133,cmm:[18,145],cna:29,co2:[43,74,75,114],coars:[13,18,28,50,65,74,114,118,140,145],coarsest:41,code:[0,1],coeff:[6,45,46,55,82,120,148],coeffici:0,coefficienct:108,coefficient0:110,coefficient1:110,coeffieci:[2,94],coeffincientn:110,coexist:112,cohes:[2,113,133],coincid:[81,100,130,131],cold:2,coleman:[40,43],collect:[2,34,44,102],colliex:43,collis:[67,117,160],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,93,115,119],colvar:0,com:[2,37,63,95,161],comand:60,combiant:105,combin:[2,3,18,32,55,57,58,63,68,71,81,82,102,104,105,109,112,113,114,128,129,147,153,154,156,157,159],come:[0,2,13,61,62,68,77,78,153,154,156,157,161],comit:161,comm:[0,3,30,91,108],comm_modifi:[2,96,102,108,112,117],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,74,79,91,92,110,111,113,114,120,133,139,140,141,146,147,153,154,155,156,157,161],commit:161,commmand:2,common:[0,1,2,3,4,30,61,71,81,82,117,119,153,154,156],commonli:[2,9,37,38,57,89,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,67,68,79,109],comp:[75,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,82,101],compat:[3,19,49,59,62,63,80,136],compens:[2,112],compil:[4,57,136],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,71,91,113],complex:[2,3,9,36,38,41,44,67,81,91,112,136],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,90,91,108,112,117,130,131,146,147],componenet:2,composit:[2,67,110],compound:[103,112,113,157],compress:[2,57,69,72],compris:[81,114,144],compton:[40,43],comput:[0,1],computation:[2,79,96],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,154,156],condens:[2,79,93,106,110,121,157],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,71,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,73,88,91,112],confus:157,conjuct:108,conjug:112,conjunct:[2,32,44,67,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,75,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,79,120],conserv:[13,60,66,67,68,74,75,91,107,108,109,117,127,146],consid:[2,29,32,59,60,79,112,144,146,152],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,102,144],constrain:[2,63,66,75,76,90,112],constraint:[19,39,42,59,63,75,76,80,90,131],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,107,136,152,153],constructor:3,consult:4,consum:1,contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161],context:[2,4,159],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,96,108,123,126,144,155],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,159],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,147,161],convent:[13,49,54,56,73,110,112],converg:[2,19,57,59,60,61,69,72,73,75,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,82,83,87,88,91,92,110,136,154,156,160],convex:81,cool:63,coord:[2,3,36,38,70,80,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,90,91,92,93,95,111,146],coords:146,copi:[0,3,57,79,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,81,161],corpor:4,corr:103,correct:[2,3,32,45,57,63,68,72,80,81,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,68,75,81,91,106,131,136,161],correl:[2,35,36,41,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,35,39,57,59,62,72,79,80,81,90,93,115,119],coulomb:[2,42,90,97,98,99,100,101,103,104,105,106,107,112,117,118,121,125,129,132,142,145,146,156,157,159],coulommb:2,count:[1,2,3,19,35,45,59,61,68,75,81,90,91,115,119],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,130,148],cov:146,coval:[2,13,112,133,146],cover:[2,58,67,112],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,79,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,81],cubes:[19,59],cubic:[38,67,70,110],cuda:1,cuh:96,cummul:[2,60,119],cumul:[2,68,69,91],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,90,93,115,119],cut:[1,2,4,19],cuthi:70,cutinn:[130,131],cutlo:70,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvar:62,cvff:4,cwiggl:80,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:96,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:132,davi:80,david:[154,156],daw:[110,143],dcd:[2,57,71],deactiv:129,debug:[2,3,40,43,44,71],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160],definit:[2,41,62,64,69,80,96,102,109,112,143,147],deform:[2,42,61,68,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,82,83,87,88,89,90,107,110,119],delai:2,delet:[28,60,68,152,161],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:74,dellago:[2,63],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:65,demo:3,demonstr:[72,133],dendrim:119,denniston:67,denot:[40,63,104,118],dens:[60,74,112],densiti:[2,19,41,44,58,59,67,79,80,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160],dependend:2,deposit:[68,75],depth:[26,57,79,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,62,66,68,75,90,91,108,110,119,130,131,153,154,156],desktop:[2,57],destabil:96,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161],detect:[36,91,103,119,120],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159],devan:145,devanathan:156,develop:[0,2,3,4,62,69,72,93,96,112,135,136,146,157],deviat:[69,70,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:72,dhugoniot:72,dia:133,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:147,diagram:[19,40,43,56,59,71],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,dicken:62,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,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,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160],effici:[0,1,2,4,39,55,57,61,68,71,75,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[75,90],eggebrecht:[104,146],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156],ejtehadi:[102,116,144],elaps:[80,148],elast:[2,21,22,91,117,155],elastic:0,elba:13,electr:[2,58,113,160],electric:4,electrolyt:159,electron:[2,40,58,79,92,103,107,110,112,113,133,136,143,146,156,157,160],electron_integr:58,electron_temperatur:58,electron_unit:112,electroneg:[2,103,113,146],electroneg_compon:146,electrostat:[2,4,102,107,112,121,129,131,146,159],elem1:[113,133,147],elem2:[113,133,147],elem:146,element1:[92,110,146],element2:[92,110,146],element:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,66,75,77,78],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,62,68,79],elsewher:133,elt:133,emac:0,email:[0,3,113],emb:81,emb_lin_neg:133,embed:[3,13,79,92,110,113,129,133,134,135,143],embt:46,emin:61,emphas:117,empir:[58,112],empiric:93,emploi:[63,155],empti:120,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],enclos:[2,133,146],encod:57,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,46,57,60,61,63,66,68,73,74,79,91,108,110,116,132,136,144,147,148],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,68,75,121],enforce2d:[2,90],eng:[3,103,135],engineer:[58,77,110],enginer:134,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,104],enpub:110,ensembl:[2,32,35,68,71,72,108,146],ensight:2,ensur:[2,41,61,66,68,96,129,153,157],enter:[113,136,157],enthalpi:[74,110],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,107,125],entiti:2,entri:[40,65,72,96,111,133,139,140,141,147,153,154,155,156,157],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,70,92,96,103,111,112,143,154],eos:65,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,80,81,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[70,88],equilibr:[2,35,44,60,61,68,72,77,78,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,82,83,87,88,103,133,141,146],equilibrium_start:58,equival:[2,13,61,68,73,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:77,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,90,104,121,144,152,154,156],erta:117,especi:[4,44,59,72,73],essenti:[3,11,47,93,104,121,156],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:133,eta:[2,67,68,72,111,113,116,143,155,157],eta_dot:68,eta_ij:143,eta_ji:113,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,90,91,110,111,129,131,136,153,154,156,157],etol:[90,91],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,90,91],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,90,136,139,140,143,146],evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,63,68,79,80,81,90,91,95,112,113,117,144,157],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,91,108,129,146,161],everyth:161,everywher:123,eviri:112,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,66,79],exactli:[2,19,35,44,59,66,72,108,110,117,130,139,140],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,90],exceed:[19,59,68],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],excess:112,exchang:[2,58,63,79,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:68,execut:[1,2,3,57],exempl:146,exemplari:66,exemplifi:112,exert:[2,81],exhaust:58,exhibit:[36,63,68,112],exist:[2,3,29,44,56,57,61,82,83,84,85,87,109,152,161],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,70,72,133,136],expens:[2,70,79],experi:[2,73,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,91,95,110,146,148,161],explan:[2,41,70],explic:137,explicit:[2,3,32,74,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,72,75,79,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:71,explor:[40,43],expon:[74,110,114,116,119,129,137,145],exponenti:[32,74,114,143,153,157,160],expos:3,exposit:[58,108],express:[2,41,44,61,70,74,79,96,110,112,123,133,146,147],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,90,107,117,133],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,112,155],extrema:129,extreme:112,extrins:58,f_1:[2,61],f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:72,f_harm:78,f_i:[13,143],f_id:[2,62],f_ij:143,f_int:77,f_j:13,f_jj:35,f_k:143,f_langevin:79,f_max:72,f_r:[154,155,156],f_sigma:96,f_solid:78,f_ss:2,face:[2,80,81,116,133,144],facil:0,facilit:2,fact:[2,4,78,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,87,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153],fail:[3,61,90,91,106],fairli:[3,161],faken:30,fall:2,fals:146,famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,68,70,73,80,83,87,91],farrel:[154,156],fashion:[2,19,44,59,62,68,69,72,78,79,80,91,130],fast:[2,4,62,72,74,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,86,87,88,89,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,79],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,90,161],fecr:110,feedback:62,feel:[70,81,91],fehlberg:74,felling:135,felt:81,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,63,68,75,90,91,93,146],fewer:[1,3,4],feynman:71,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:152,fictiti:[2,71,73,104,121,125,152],field:0,fifth:[2,114,141],figshar:70,figur:[1,4,72,161],fij:107,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157],fill:[44,57,79,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,62,65,70,73,90,91,104,121,125,133,139,140,146,161],fine:[4,78,161],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:110,fire:[90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,82,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161],fischer:[2,5,45,100],fit:[2,73,93,96,133,139,140,155,161],five:[30,72,96,134],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,79,80],fld:[80,130,131],flexibl:[2,57,112,155],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,70,78,79,88,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,96,136],fmass:71,fmax:90,fmsec:68,fno:4,fnorm:90,fnve:63,focu:75,foil:[41,70,147],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],foo:[3,57,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,119],forcegroup:67,ford:107,forgiv:68,fork:161,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,82,85,88,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159],formal:[2,35,66,68,71,146],format:[2,19,57,59,65,74,79,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157],formation:65,former:[2,19,59,79,96],formul:[1,2,42,68,73,75,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,70,76,80,82,84,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,63,67,104,107],four:[2,3,28,41,62,79,88,91,136],fourier:2,fourth:[2,4,37,73,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,72,74,91,96,114,117,130,131],frame:[41,58,72,116],framer:57,framework:[92,147],frattl:63,free:[2,13,29,32,70,77,78,79,91,112,129,136,138,143,159],freedom:[2,39,60,68,69,71,75,78,90,107],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,108,112,146],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,117],from:[0,1],front:72,frontend:57,frozen:[2,39,66,115],fs2:[2,35],ftol:[90,91],fuction:104,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,96,110,112,113,116],fuller:90,fulli:[2,70,90,91,104,143,161],fulton:110,fumi:97,funcfl:110,fund:0,funrol:136,further:[2,37,57,67,71,79,90,91,92,95,103,136,146],furthermor:[11,47,63,74,109,112],futur:[0,2,59,66,91,134,135],g_jik:143,g_p:79,ga3:43,gaa:96,gai:116,gain:[4,62],galindo:137,gamma0:13,gamma:[2,13,67,72,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:79,gamma_ijk:154,gamma_n:117,gamma_p:79,gamma_t:117,gammaa:137,gammafactor:67,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,66,71,73,108,112,115],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:68,gener:0,gentler:80,gentli:111,geom:2,geometr:[2,44,59,68,81,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159],geometri:[2,9,19,44,59,61],gerber:129,germann:[69,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,91,104,157,161],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,68,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,68,70,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,89,112,119],goe:[28,41,44,63,90,107,111,118,123,126,148,160],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],govern:67,gpa:93,gpl:0,gpt:136,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,86,87,88,89,92,93],grab:2,grad:2,gradient:[2,61,63,79,91,131,139,140],graft:60,grain:[2,13,18,28,44,50,65,70,74,114,118,136,140,145],gram:110,gran:[2,80,81],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[72,161],greater:[1,61,66,68,70,95,97,98,99],greatli:[40,63],green:[2,35,57,71,96,161],green_kubo:2,grest:[21,22,60,99,117,125],grid:[19,40,43,59,67,79],grigera:2,gromac:90,gromacs:[2,90,118],groot:108,ground:[2,31,64,112],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,91,146,157],group_id:3,grow:[2,68,70,74,117],growth:2,gsmooth_factor:133,guarante:44,guess:161,gui:[3,161],guid:[1,149,150,151],guidelin:1,gullet:133,gulp:2,gunnel:136,gunsteren:129,guo:[2,5,45,50,100],gyrat:2,gzip:[57,91],h12:116,h2o:[114,140],had:[2,3,60,61,66,68,69,79,108,117,152],hafskjold:[2,63],half:[1,2,4,19,57,59,68,79,80,81,96,102,112,136],halfwai:[19,57,161],halperin:36,halsei:117,halt:[19,59,63],halv:57,hamak:[80,81,102,144],hamilton:29,hamiltonian:[68,112],han:110,hand:[2,28,29,44,54,57,67,74,104,112]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6,67,68,78,79,117,136],index:[0,2,3,65,71,79,139,140],indic:[2,3,4,6,28,31,33,35,37,39,42,46,57,61,62,68,79,82,88,103,113,133,136,141,146,154,156,161],indirectli:[2,62],indium:147,individu:[0,1,2,3,4,32,39,42,44,56,57,61,62,63,67,68,75,90,97,98,100,101,104,110,112,118,120,121,125,142,145],induc:0,ineffici:[2,29,30,36,38,41,57,68],inerti:131,inertia:[2,131],infer:[59,113],infin:90,infininti:57,infinit:[67,79,112],infinitesim:2,inflect:[105,123],influenc:[19,154,155,156],inform:[0,1,2,3,4,19,40,43,44,45,57,58,59,60,61,62,63,67,70,73,75,76,77,80,81,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],infrequ:[2,68,108],infti:[105,130,131],ingtegr:96,inher:90,inherit:2,inhomogen:79,inidividu:90,init:146,init_fil:79,initi:[2,3,19,32,44,57,58,59,60,61,62,65,66,67,68,69,71,72,73,74,77,78,79,80,90,91,93,107,108,136,139,140,146],initial:2,initialt:79,inlclud:3,inner2:[100,118],inner:[4,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],inner_distance_cutoff:119,innner:127,inorgan:[2,157],inp:[147,157],input:[0,1],insert:[44,147,152],insid:[2,3,44,63,67,80,81],inside:[67,123],insight:2,instabl:[67,107],instal:[1,2,3,4,57,91,99,100,121,125,129,136,161],install:0,instanc:[2,3,115,143],instantan:[2,60,61,62,66,68,69,72],instanti:[2,3,58],instead:[1,2,3,4,19,29,34,45,59,61,67,98,99,110,120,122,129,133,136,138],instruct:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,57,68,69,75,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],instruction:3,insuffici:2,insult:68,insur:[2,3,30,44,57,79,80,81,102,116,144],integ:[2,3,29,38,41,44,45,48,49,52,55,57,60,62,66,67,72,74,79,86,108,109,133,147],integral:[71,139,140],intel:1,intel_coprocessor:4,intel_cpu_intelmpi:4,intel_cpu_mpich:4,intel_cpu_openpmi:4,intend:[2,18,66],intens:[1,2,33,34,35,37,39,40,43,59,60,68,69,79],inter:[60,91,96],interact:[1,2,3,13,28,32,36,38,39,41,42,45,50,55,56,60,70,71,73,74,79,80,81,83,84,85,87,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,142,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160],interatom:[44,77,78,92,96,110,112,133,136,146,155],intercept:40,interchang:[2,62],interconvert:112,interesect:81,interest:[1,3,43,71,78,111,131],interf:161,interfac:0,interfer:[68,93],interg:2,interi:131,interior:[2,19,81],interlac:133,interleav:[2,44],intermedi:[2,57,70,88,91],intermolecular:93,intern:[0,2,3,4,5,6,8,12,16,17,18,31,32,42,44,46,57,58,62,64,65,68,69,74,82,83,87,88,90,109,114,139,140,149],internal:57,internal_element_set:58,internal_quadratur:58,internat:[4,40,43,58],interpenetr:133,interpentr:[149,150],interpol:[2,57,58,65,67,70,91,96,139,140,154],interpret:[2,3,55,57,117,148],interrupt:72,intersect:[2,40,81],intersert:81,interspers:90,interstiti:136,interv:[2,35,62,68,72,146],intestieti:40,intial:[2,93],intiial:19,intramolecular:13,introduc:[2,36,38,57,63,68,72,88,92,104,112,121,125,129,153],introduct:0,inv:[40,43],invalid:[33,91,130,131],invari:[38,41,62],invent:75,invers:[2,26,40,43,72,88,89,97,104,121,158,159],invert:[1,2],invis:81,invoc:60,invok:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,32,33,34,39,44,45,46,47,48,49,50,51,52,53,54,57,58,59,60,61,62,63,66,67,68,69,70,75,76,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,147,148,153,154,155,156,157,158,159,160],involv:[2,67,90,91,95,116,153,154,156],ion:[2,79,96,105,113,115,133,136,146,156,160],ionic:[2,97,98,105,112,113,142,146],ioniz:[103,112],ipp:0,ir3:43,ir4:43,irregular:[2,19,59,61,68],irrelev:141,irrespect:[130,131],irrevers:74,isbn:159,isenthalp:68,ismail:[99,125],isn:[3,63],iso:[61,68,69],isobar:[68,109],isodem:112,isoenerget:109,isoenthalp:109,isol:117,isomorph:71,isotherm:[68,109],isotrop:[2,36,116,130,131],issu:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,30,39,45,46,47,48,49,50,51,52,53,54,57,60,61,63,68,69,71,75,78,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,152,153,154,155,156,157,158,159,160],issue:58,item:[2,19,59],iter:[2,19,59,61,75,90,91,146],iterat:90,ith:62,itself:[2,3,35,57,79,91,104,113,116,139,140],ityp:44,izumi:155,j0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:[33,44,92,96,110,113,133,134,135,147],unlike:[68,69,110,119,120,134,135],unlimit:143,unnecessari:4,unoccupi:79,unoptim:57,unpack:[0,3],unperturb:32,unphys:[2,68],unpublish:136,unrel:[45,161],unrestrain:73,unset:112,unshift:107,unsmooth:127,unsolv:100,unstabl:67,unstag:161,until:[2,19,57,59,61,62,65,77,96,117,139,140],unus:96,unwant:44,unwrap:[33,34,42,60],up_intern:57,updat:[0,2,4,62,66,67,68,72,79,96,107,136],upenn:3,upon:[2,74,96],upper:[19,37,59,61,67,68,72,80,90,117,146],uppercas:0,upsid:2,upsilon:116,upstream:161,urbana:130,urey_bradlei:5,url:161,usabl:110,usag:[2,70,129],use:[2,57,79,116,133,144,146,161],useful:136,user:[0,1,2,3],user_manifold:161,user_misc:[14,15,17,48,52,54,55,86],usernam:161,using:[0,1],usr:3,usual:[2,8,12,16,17,18,23,32,53,55,57,60,61,69,72,73,79,80,81,87,91,100,102,105,107,116,120,129,130,131,141,147,152,153],util:116,v11:2,v22:2,v33:2,v_0:79,v_2:136,v_3:136,v_4:136,v_avp:62,v_delta:32,v_dhug:72,v_drai:72,v_e_hbond:119,v_ij:143,v_jx:35,v_jy:35,v_jz:35,v_k11:35,v_k22:35,v_k33:35,v_lgr_po:72,v_lgr_vel:72,v_linear:80,v_lj:93,v_mu:130,v_n:[67,136],v_name:[2,32,57,62,80],v_occ:115,v_prefactor:148,v_press:42,v_pxxwall:62,v_pxy:2,v_pxz:2,v_pyz:2,v_ramp:80,v_rebo:93,v_t_qm:72,v_torsion:93,v_v11:2,v_v22:2,v_v33:2,v_valu:57,v_wiggl:80,v_x:[44,80],v_xave:2,v_xmax:2,v_xx:44,v_y:44,v_yi:44,vacanc:[77,136],vacf:2,vacuum:[79,105,156,160],valanc:96,valenc:[96,112],valent:96,valid:[2,3,40,43,61,70,110,112,116,136,143],valon:133,value1:69,value2:69,van:[27,32,102,103,129,133,159],vanadium:136,vanilla:2,vanish:75,vapor:[19,59],vare:79,vari:[1,19,32,40,43,58,59,61,68,73,79,80,100,108,109,118,127,130,148],variabl:0,varianc:108,variant:[1,2,61,68,69,117,134,135,138,154,156],variat:[19,59],varieti:[1,2,57,133,157],variou:0,varshalovich:41,vashishta1990:157,vashishta2007:157,vbia:2,vcm:2,vdisplac:80,vdw:103,vec:70,vector:1,vel:[2,108,109,112,117],veld:[99,125],veloc:[2,35,39,42,44,57,61,63,67,68,69,70,71,72,73,75,78,79,80,90,91,108,112,117,130,131],velocit:[108,109,112,117],velocity_bottom:67,velocity_top:67,verbos:146,veri:[1,2,19,32,57,59,61,62,68,71,75,91,112,117,130,131,139,140,147,148,161],verifi:161,verlet:[1,4,58,63,68,71,75,79],versa:[2,60],versu:[2,19,59,62,75,99,107,117,125],vertic:[4,19,57,59],via:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,67,68,69,71,73,75,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],vibrat:[2,70,72,88,112],vice:[2,60],video:57,view:[2,57,96,112,113,146],viewer:57,viewpoint:57,vij:108,vim:0,virial:[35,39,41,42,61,68,69,75,108,109,112],virtual:[2,153],viscoelast:117,viscos:0,viscosity:2,viscou:[2,66,67,90,91],vision:146,visual:0,viz:3,viz_tool:3,vizplotgui_tool:3,vmax:61,vmd:[2,3],voigt:[2,41],vol:[2,35,42,133,156],volpress:136,volum:[2,19,32,35,39,40,42,43,44,59,61,64,67,68,69,72,79,80,81,130,131,136,150,151,160],voronoi:42,voter:[134,135],voth:71,vri:118,vstream:2,vtk:[2,40],w_1:41,w_2:41,w_i:41,w_ik:143,waal:[32,102,103,129,159],wadlei:96,wagner:[58,67,133],wai:[1,2,3,29,32,34,35,36,38,41,42,44,57,60,61,62,66,67,68,69,71,79,80,83,84,85,87,88,90,91,92,93,104,105,108,110,111,113,116,119,121,133,134,135,141,143,144,146,147,148,152,153,154,156,157,161],wait:[1,4],walk:[66,68],wall:0,wallhi:80,wang:[133,143],want:[0,1,2,3,31,34,39,42,44,57,59,60,70,73,78,80,81,91,92,93,96,102,103,108,110,113,133,139,140,141,143,146,148,153,154,156,157,161],ward:96,warm:[4,112],warmup:4,warn:[0,21,22,30,57,68,69,74,130,131,133,139,140,161],warner:92,warning:133,warp:133,warren:[108,139,140],watanab:[77,78],watch:91,water:0,watkin:53,wave:112,wavefunct:112,wavelength:[40,43],wavepacket:112,weak:36,web:1,webb:58,weber:[111,135,143,153,157],weight:[2,32,41,43,45,56,66,67,74,106,108,109,114,133,139,140,147],well:[1,2,3,11,26,36,38,39,42,44,47,57,59,61,67,68,69,74,78,90,91,95,115,116,119,130,131,133,136,144,148,154,155,156,161],went:3,were:[2,3,4,19,29,38,39,44,57,59,93,112,117,120,161],westview:159,what:[0,1,2,3,44,57,59,60,61,65,68,71,73,75,80,90,91,133,139,140,148,152,161],whatev:[57,61,62,68,90,91,101,102,136],whelan:43,when:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,36,37,38,39,44,45,46,47,48,49,50,51,52,53,54,56,57,59,60,61,62,67,68,69,70,72,73,74,75,76,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,147,148,152,153,154,155,156,157,158,159,160,161],whenev:[0,55,119],where:[1,2,3,4,6,7,8,9,10,11,12,13,16,17,18,19,20,23,24,25,26,29,30,31,32,33,34,36,39,40,42,43,46,47,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83,84,85,86,87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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. 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te:149,cl1:43,clarendon:[13,110],clarifi:[157,159],clark:145,classic:[0,2,4,74,75,82,92,115],classifi:160,clean:2,clear:[2,3,59,65],clebsch:41,click:[3,44,56,58,94,164],climb:94,clockwis:45,clone:164,close:[2,3,19,42,57,63,64,70,71,78,84,94,96,99,107,108,136,142,143,159,164],closer:[19,57,62,64,80,94],closest:[73,119,147,155],cloud:149,cluster:[2,4,42,57,66,78],cmax:136,cmd:[3,74],cmdarg:3,cmin:136,cmm:[18,148],cna:29,co2:[43,77,78,117],coars:[13,18,28,50,68,77,117,121,143,148],coarsest:41,code:[0,1],coeff:[6,45,46,55,85,123,151],coeffici:0,coefficienct:111,coefficient0:113,coefficient1:113,coeffieci:[2,97],coeffincientn:113,coexist:115,cohes:[2,116,136],coincid:[57,59,84,103,133,134],cold:2,coleman:[40,43],collect:[2,34,44,57,59,105],colliex:43,collis:[70,120,163],colloid:2,color1:59,color2:59,color:[19,57,58,59,62,69,75],column:[2,29,34,36,38,41,42,43,57,59,61,75,82,96,118,122],colvar:0,com:[2,37,61,66,98,164],comand:63,combiant:108,combin:[2,3,18,32,55,57,58,60,61,66,71,74,84,85,105,107,108,112,115,116,117,131,132,150,156,157,159,160,162],come:[0,2,13,64,65,71,80,81,156,157,159,160,164],comit:164,comm:[0,3,30,94,111],comm_modifi:[2,99,105,111,115,120],comm_styl:[19,62],comm_world:3,command:[0,1],comment:[3,45,57,68,77,82,94,95,113,114,116,117,123,136,142,143,144,149,150,156,157,158,159,160,164],commit:164,commmand:2,common:[0,1,2,3,4,30,64,74,84,85,120,122,156,157,159],commonli:[2,9,37,38,57,58,92,121,126,150,157,159],commun:[1,2,3,4,19,58,59,62,64,70,71,82,112],comp:[78,94,115,147,154,158],compar:[1,2,4,40,43,56,59,93,94,136,149],comparison:0,compass:[6,20,46,56,85,104],compat:[3,19,49,57,61,62,65,66,83,139],compens:[2,115],compil:[4,57,58,59,139],complain:3,complement:136,complementari:[107,124],complet:[2,3,19,59,62,74,94,116],complex:[2,3,9,36,38,41,44,70,84,94,115,139],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,58,59,61,63,64,65,66,70,71,72,74,78,84,93,94,111,115,120,133,134,149,150],componenet:2,composit:[2,70,113],compound:[106,115,116,160],compress:[2,57,58,59,72,75],compris:[84,117,147],compton:[40,43],comput:[0,1],computation:[2,82,99],compute_modifi:[63,64,71,72],compute_sa:40,compute_xrd:43,concav:84,concentr:[68,77,113,117,143],concept:2,conceptu:[2,64,94,107,136],concern:[2,30,32,69],concis:3,concurr:4,conden:[82,157,159],condens:[2,82,96,109,113,124,160],condit:[2,39,40,42,43,57,58,59,60,70,72,73,75,78,79,82,112,115,121],conducit:2,conduct:0,confer:[4,139],config:57,configur:[1,2,4,57,58,64,74,93,94,96,99,114,136,139,156,157,159,160,164],conflict:164,conform:[2,63,64,76,91,94,115],confus:160,conjuct:111,conjug:115,conjunct:[2,32,44,59,70,94,100,101,107,111,115,122,124,145,148],connect:[2,32,63,78,94,108,120,155,159],conner:96,connor:96,consecut:[3,44,59,107,124,128],consequ:[1,2,82,123],conserv:[13,63,69,70,71,77,78,94,110,111,112,120,130,149],consid:[2,29,32,57,59,62,63,82,115,147,149,155],consider:2,consist:[2,3,39,44,50,65,69,71,72,75,76,77,94,96,99,105,107,115,119,133,134,136,139,142,143,147,149],consistent_fe_initi:60,constant:0,constantli:66,constitu:[2,83,84,105,147],constrain:[2,66,69,78,79,93,115],constraint:[19,39,42,62,66,78,79,83,93,134],construct:[2,28,29,30,36,38,40,41,43,64,71,76,77,84,110,139,155,156],constructor:3,consult:4,consum:1,contact:[0,108,114,116,119,120,147],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,60,61,62,65,68,70,73,75,77,82,84,94,95,96,99,106,107,110,113,114,115,117,136,139,142,143,144,146,150,156,157,158,159,160,164],context:[2,4,59,162],contibut:29,contin:4,continu:[0,2,19,59,61,62,63,64,65,66,69,71,72,75,80,81,82,84,99,111,126,129,147,158],continuum:[2,60,82],contour_integr:60,contract:[64,71],contrain:78,contrast:[1,2,162],contrib:82,contribut:[2,29,32,33,34,35,39,41,42,61,64,70,78,93,94,111,113,115,133,134,139,149,164],control:[2,3,4,11,13,19,32,35,41,47,57,58,60,62,64],control_typ:60,convect:35,conveni:[2,13,57,150,164],convent:[13,49,54,56,59,76,113,115],converg:[2,19,57,58,62,63,64,72,75,76,78,93,94,106,107,124,149],convers:[41,58,59,107,108,109,115,124,128,132,145],convert:[2,5,6,8,12,16,17,18,35,44,46,57,58,59,85,86,90,91,94,95,113,139,157,159,163],convex:84,cool:66,cooordin:57,coord:[2,3,36,38,57,59,61,73,83,94],coordb:149,coordbb:149,coordiat:93,coordin:[1,2,3,19,32,33,34,41,44,57,58,59,61,62,63,64,66,71,73,78,79,81,82,93,94,95,96,98,114,149],coords:149,copi:[0,3,58,82,94,164],copper:163,coprocessor:[1,4],coral:59,core:[0,1],coreshel:2,coreshell:[2,101,107,109],cornel:[2,45],corner:[2,58,84,164],cornflowerblu:59,cornsilk:59,corpor:4,corr:106,correct:[2,3,32,45,58,66,71,75,83,84,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],correction_max_iter:60,correctli:[3,57,59,71,78,84,94,109,134,139,164],correl:[2,35,36,41,61,69,74],correpond:68,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,58,59,61,64,65,66,68,70,71,72,73,74,77,78,83,84,85,86,87,89,90,91,92,94,95,96,97,100,101,102,103,104,105,106,107,110,111,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,136,137,139,141,143,144,145,146,147,148,149,150,151,156,157,158,159,160,161,162,163],correspondingli:[133,134],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,58,59,62,71,77,82,107,124,128,139,156],costheta0:[156,157,159,160],costheta:146,costli:[3,4],coul:[2,4,18,21,22,32,45,93],could:[2,3,19,32,34,35,39,57,58,59,62,65,75,82,83,84,93,96,118,122],coulomb:[2,42,93,100,101,102,103,104,106,107,108,109,110,115,120,121,124,128,132,135,145,148,149,159,160,162],coulommb:2,count:[1,2,3,19,35,45,61,62,64,71,78,84,93,94,118,122],counteract:65,counterbal:66,counterbalanc:13,counterclockwis:45,counterpart:57,coupl:0,couple:[2,3],cours:[4,57,69,76,83,133,151],cov:149,coval:[2,13,115,136,149],cover:[2,59,60,70,115],cpp:[1,2,3,32,57,78],cpu:[1,4,59],cpuinfo:4,cr2:43,cr3:43,crai:57,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,62,63,64,68,71,72,73,74,76,82,94,96,99,106,113,114,132,141,142,143,146,149,156,157,158,159,160,164],create_atom:[2,19,35],create_box:[2,19,35,44,64,71,155],create_elementset:60,create_faceset:60,create_nodeset:60,createatom:0,creation:44,crimson:59,criteria:[58,59,63,93],criterion:[19,44,62,63,93,94,106,115,120,149],critic:[2,24,25,82,93],cross:[4,33,57,58,94,103,111,113,121,122,124,126,128,146,148,157,159,163],crossov:1,crozier:0,crucial:75,crystal:[2,4,29,30,38,73,81],crystallin:[2,158],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,150],cscl:136,csequ:2,csh:[3,4],cshrc:3,csic:[114,156,157,159,160],csinfo:2,csisi:[114,156,157,159,160],cst:113,cstherm:2,csvr:2,ctcm:[95,113],ctype:3,cu1:43,cu2:43,cu3au:136,cube:[2,84],cubes:[19,62],cubic:[38,70,73,113],cuda:1,cuh:99,cummul:[2,63,122],cumul:[2,61,71,72,94],currenlti:65,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,62,63,64,65,66,71,76,77,78,79,82,83,93,94,99,106,110,113,115,116,120,123,133,134,136,137,138,146,151,157,159,164],curv:[2,44],curvatur:[119,147,163],custom:[0,2,3,33,34,35,42],cut:[1,2,4,19],cuthi:73,cutinn:[133,134],cutlo:73,cutmax:146,cutoff1:[104,110,124,128,132,135,145,148],cutoff2:[100,101,102,104,109,110,124,128,132,135,145,148],cutoff:[2,4,21,22,28,29,30,32,36,38,41,63,68,73,75,83,84,93,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cutoffa:114,cutoffc:114,cuu3:113,cval:43,cvar:65,cvff:4,cwiggl:83,cyan:[58,59],cycl:[71,72],cyclic:45,cylind:[58,84],cylindr:2,cyrot:99,d3q15:70,d3q19:70,d_e:82,d_name:57,daan:81,damp:[2,71,72,75,93,94,100,101,103,107,110,115,120,124,132,145,148],dampflag:120,danger:111,darden:110,darkblu:59,darkcyan:59,darken:58,darkgoldenrod:59,darkgrai:59,darkgreen:59,darkkhaki:59,darkmagenta:59,darkolivegreen:59,darkorang:59,darkorchid:59,darkr:59,darksalmon:59,darkseagreen:59,darkslateblu:59,darkslategrai:59,darkturquois:59,darkviolet:59,dash:120,dat:[2,35,60],data2xmovi:0,data:1,databas:0,date:[0,2],datum:[2,57],davenport:135,davi:83,david:[157,159],daw:[113,146],dcd:[2,57,58,59,74],deactiv:132,debug:[2,3,40,43,44,74],decai:[36,107,163],decid:[2,4,164],decod:58,decompos:[32,150],decomposit:[60,74],decoupl:2,decreas:[4,57,63,66],dedic:4,deeppink:59,deepskyblu:59,defect:[2,29,139],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,67,68,70,71,72,73,74,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,96,97,98,100,101,102,103,104,105,107,108,110,111,112,114,115,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],definit:[2,41,59,61,65,67,72,83,99,105,112,115,146,150],deform:[2,42,64,71,133,134],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,58,63,71,72,74,76,78,81,85,86,90,91,92,93,110,113,122],delai:2,delet:[28,61,63,71,155,164],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:60,delimit:77,dellago:[2,66],deloc:[115,149],delr:136,delta_1:99,delta_3:99,delta_7:99,delta_ij:[136,146],delta_pi:99,delta_r:146,delta_sigma:99,deltah_f:68,demo:3,demonstr:[75,136],dendrim:122,denniston:70,denot:[40,66,107,121],dens:[63,77,115],densiti:[2,19,41,44,60,62,70,82,83,95,96,99,113,136,137,138,142,143,146,147,149,152,153,154],depart:0,departur:75,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,58,59,61,62,64,68,70,71,72,73,77,78,80,82,83,84,85,86,87,89,90,91,92,93,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,156,157,158,159,160,161,162,163],dependend:2,deposit:[71,78],depth:[26,58,82,117,119,147],der:[32,105,106,132,162],deriv:[2,32,41,64,65,66,71,72,73,80,81,82,83,84,96,99,105,110,115,116,121,126,130,131,136,139,162],derjagin:162,derlet:73,descend:59,descib:58,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,57,61,62,63,64,65,68,69,70,71,72,73,74,75,77,80,81,83,93,94,96,98,100,101,103,104,105,106,107,110,113,115,116,117,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,139,140,142,143,146,147,148,149,150,151,155,156,157,158,159,160,161,162,163,164],descript:[2,3],descriptor:[41,57],design:[0,2,3,40,43,60,63,71,73,82,97,98,103,107,109,115,132,133,134,137,138,146],desir:[2,3,4,35,39,42,44,64,65,69,71,78,93,94,111,113,122,133,134,156,157,159],desktop:[2,58],destabil:99,destre:91,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,64,65,66,69,70,71,72,75,78,81,82,93,95,96,98,99,102,103,104,105,106,107,110,111,115,116,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,136,140,142,143,147,149,150,151,161,162,164],detect:[36,94,106,122,123],determin:[1,2,4,26,32,39,40,42,43,44,57,58,59,61,62,64,68,71,73,74,75,76,77,83,84,96,102,106,110,113,117,118,120,128,136,139,143,147,149,155,162],devan:148,devanathan:159,develop:[0,2,3,4,65,72,75,96,99,115,138,139,149,160],deviat:[72,73,118],devic:1,devin:106,devis:138,dfactor:58,dft:139,dhug:75,dhugoniot:75,dia:136,diag:77,diagnost:[4,63,77],diagon:[2,41,42,64,71],diagonalstyl:150,diagram:[19,40,43,56,62,74],diallo:122,diam:[58,59],diamet:[2,44,57,58,59,105,119,120,126,147,162],diamond:[115,136],dick:2,dicken:65,did:[93,111,113,120,157,159],dielectr:[103,107,108,109,124,128,132,145],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,58,59,61,62,63,64,65,66,69,70,71,73,74,75,78,79,80,81,82,83,84,85,94,95,96,99,102,103,105,106,111,112,113,115,117,119,120,121,124,125,127,128,135,136,137,138,140,141,142,143,144,146,147,148,149,150,151,156,157,159,160,162],differenti:[1,2,13,77,107,146,158],difficult:[64,65,74,122],difficulti:[36,38,78],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:[59,139],dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,63,76,86,87,88,90,93,96,99,103],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:115,dij:78,dilat:[64,71,72],dim:[44,136],dimens:[1,2,19,35,42,44,57,58,59,62,64,70,71,72,75,83,94],dimension:[36,39,40,41,43,82,94,146],dimensionless:[37,41,65,82,150,162],dimer:[2,136],dimgrai:59,dimstr:[19,62],dintel_offload_noaffinity:4,dipol:0,dipolar:[13,57],dipole:110,dir:[1,3,73,75,146],dirac:41,direc:146,direct:[2,4,13,29,38,40,41,43,44,45,57,58,70,72,73,75,80,81,82,83,84,93,94,111,112,120,134],directli:[2,3,32,41,44,57,58,65,70,77,84,95,96,100,101,102,107,110,113,115,124,128,145,148,155],directori:[0,1,2,3,4,65,80,81,94,95,96,99,106,107,113,114,116,132,136,137,138,139,144,146,149,150,156,157,158,159,160],disabl:[4,82,123],disadvantag:[2,62],disallow:[57,71],discard:[19,62,84],discontinu:[93,130],discourag:136,discret:[2,58,59,65,70],discuss:[0,1],disk:[2,36],disloc:[29,139],disord:[29,139],disp:0,dispar:147,disperion:[110,128],dispers:[2,102,110,128,133,160],displac:[2,37,64,71,73,120],displai:[3,56,57,58],disregard:139,dissip:[2,31,67,69,80,81,111,112,120,133,134],dist:[2,35,57,74,76,155],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,58,59,63,64,66,70,71,72,73,75,76,78,79,81,82,83,84,85],distinct:[2,147],distinguish:[2,41,115],distort:95,distrbut:95,distribut:[0,2,3,19,32,41,56,62,69,70,71,95,99,107,113,114,116,136,137,138,144,146,147,156,157,158,159,160],distro:146,ditto:163,div:4,diverg:[81,96],divid:[2,4,19,35,39,42,56,59,61,62,73,93,94,116,149,160],divis:[2,55,70,99,132],dl_poly:2,dlammps_bigbig:59,dlammps_ffmpeg:58,dlammps_gzip:[57,58],dlammps_jpeg:58,dlammps_memalign:4,dlammps_png:58,dlammps_xdr:57,dlm:71,dlmp_intel_offload:4,dlopen:2,dlvo:[105,162],dm_lb:70,doc:[0,1,2,3,32,34,37,39,42,44,56,57,58,59,61,65,71,84,93,94,95,96,98,106,107,113,114,116,122,136,137,138,144,146,150,156,157,159,160,164],docuement:147,dodgerblu:59,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,62,63,64,65,66,68,69,70,71,82,83,84,86,87,88,90,91,94,95,96,97,98,99,102,103,104,105,106,107,108,110,111,113,114,115,117,118,119,120,121,123,126,127,129,130,131,133,134,136,137,138,139,142,143,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],doesn:[44,57,96,106,114,156,157,158,159,160],dof:39,doi:[2,73],domain:[2,19,40,43,58,59,62,64,70,71,74,82,83,94],domin:[1,115],don:[0,4,84,136,149,164],done:[1,2,19,44,55,57,58,59,60,61,62,63,64,65,68,71,74,78,80,81,93,94,96,102,113,128,134,135,136,142,143,155,164],donor:122,dot:42,doti:[99,146],doubl:[1,2,3,4,32,45,64,84,99,116,121,139],dover:60,down:[2,3,64,115,149],download:3,downsid:2,dpd:2,dpdtheta:[31,112],dpdtheta_i:[67,68],dr_ewald:40,drag:[2,35,71,72,79],dragforc:70,drai:[58,75],drain:93,dramat:[63,64,71,149],drautz:99,draw:58,drawn:[57,58,59,69],drayleigh:75,dreid:2,dreiding:0,drfourth:37,drho:[95,113,142,143],drift:[2,37,66,69],drive:[3,64,71,73,94],driven:[2,50],driver:2,drop:[59,111],drsquar:37,drude:0,dt_collis:70,dt_lb:70,dt_md:70,dtqm:75,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,58,61,63,64,69,70,71,72,73,76,80,81,82,83,84,93,94,108,111,112,113,118,119,133,134,146,147,148,155,157,159,162,163],duffi:82,dullweb:71,dummi:[13,158],dump:[0,1],dump_modifi:[2,57,58],dunbrack:[2,5,45,103],duplic:[19,62,73],durat:[56,59,82,120],dure:[2,4,19,32,45,57,60,61,62,63,64,65,66,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,93,94,111,132,139,141,142,143],dvlo:162,dvx:2,dx_lb:70,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,63,65,67,69,71,72,74,75,76,80,81,82,93,94,111,112,115,133,134,154],dynamo:[95,113,136],dyre:129,e28637:13,e_1:99,e_2:99,e_a:77,e_b:116,e_ee:115,e_hbond:122,e_i:[2,99,116],e_j:[2,99],e_k:99,e_ke:115,e_kl:2,e_lj:[96,110],e_n:[65,99],e_ne:115,e_nn:115,e_pr:115,e_rebo:96,e_torsion:96,e_tot:139,e_vol:139,eaa:85,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,68,69,70,71,72,73,74,77,78,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,159,160,161,162,163],eacn:[19,62],eam:[0,95,107],earli:[19,61,62],earlier:[59,94,120,136],earth:115,easi:[2,3,32,42,57,83],easier:[4,57,58],easili:[3,58,59,94],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:136,ec_ij:136,ec_jj:136,echo:[3,40,43],ecp:115,edg:[2,19,40,43,57,58,83,84],edge:83,edit:[4,164],edition:4,edu:[3,113,133],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,59,60,61,63,64,66,69,71,72,73,74,75,76,78,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,110,111,113,114,115,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,137,139,141,142,143,144,145,147,148,149,151,156,157,158,159,160,161,162,163],effici:[0,1,2,4,39,55,57,58,59,64,71,74,78,99,105,107,124,128,139,142,143,147],efficienc:4,efield:[78,93],eggebrecht:[107,149],ehex:2,eigenvalu:74,einstein:[2,81],either:[1,2,3,4,19,29,40,41,42,43,44,57,58,59,61,62,63,64,65,66,70,71,72,73,77,78,84,93,99,105,113,117,120,133,134,136,139,143,146,155,157,159],ejtehadi:[105,119,147],elaps:[83,151],elast:[2,21,22,94,120,158],elastic:0,elba:13,electr:[2,60,116,163],electric:4,electrolyt:162,electron:[2,40,60,82,95,106,110,113,115,116,136,139,146,149,159,160,163],electron_integr:60,electron_temperatur:60,electron_unit:115,electroneg:[2,106,116,149],electroneg_compon:149,electrostat:[2,4,105,110,115,124,132,134,149,162],elem1:[116,136,150],elem2:[116,136,150],elem:149,element1:[95,113,149],element2:[95,113,149],element:[2,33,37,39,41,42,57,58,59,60,61,95,96,99,106,113,114,115,116,136,137,138,139,144,146,149,150,156,157,158,159,160],elementn:[95,113],elementset:60,elif:41,elig:122,elimin:[2,69,78,80,81],elj:110,ellips:2,ellipsoid:[2,44,57,93,119,134,147],els:[58,59,61,65,71,82],elsewher:136,elt:136,emac:0,email:[0,3,116],emb:84,emb_lin_neg:136,embed:[3,13,82,95,113,116,132,136,137,138,146],embt:46,emin:64,emphas:120,empir:[60,115],empiric:96,emploi:[66,158],empti:123,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,57,59,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,80,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],enclos:[2,57,59,136,149],encod:[57,58,59],encompass:2,encount:[38,61],encourag:[77,79],end:[1,2,3,4,19,46,57,58,59,61,63,64,66,69,71,76,77,82,94,111,113,119,135,139,147,150,151],endbondtors:46,energet:[63,96],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111],energy_compon:149,enforc:[2,57,58,59,63,71,78,124],enforce2d:[2,93],eng:[3,57,106,138],engineer:[60,80,113],enginer:137,enhanc:[60,66],enlarg:58,enough:[44,62,75,83,84,107],enpub:113,ensembl:[2,32,35,71,74,75,111,149],ensight:2,ensur:[2,41,57,64,69,71,99,132,156,160],enter:[116,139,160],enthalpi:[77,113],entir:[0,2,3,19,31,39,40,42,43,44,59,62,63,66,69,71,72,73,74,77,79,82,110,128],entiti:[2,57],entri:[40,59,61,68,75,99,114,136,142,143,144,150,156,157,158,159,160],entries:59,entry1:[59,142,143],entry2:59,entryn:59,enumer:57,enumuer:2,environ:[1,2,3,4,58,73,95,99,106,114,115,146,157],eos:68,epair:[59,96,118,122],epp:110,epq:110,eps0:162,eps14:132,epsilon0:159,epsilon:[2,18,21,22,27,28,32,45,83,84,93,98,103,104,105,107,108,109,110,117,119,121,122,123,124,125,126,127,128,129,130,131,132,135,140,145,147,148,156,161,162],epsilon_0:163,epsilon_14:103,epsilon_:147,epsilon_d:108,epsilon_i:[119,147],epsilon_i_:147,epsilon_i_a:[119,147],epsilon_i_b:[119,147],epsilon_i_c:[119,147],epsilon_j:[119,147],epsilon_j_:147,epsilon_j_a:[119,147],epsilon_j_b:[119,147],epsilon_j_c:[119,147],epsilon_lj:147,eqp:110,eqq:110,equal:[2,3,19,28,32,35,42,44,58,59,61,62,64,65,69,70,72,73,74,75,76,77,80,81,82,83,93,94,96,106,111,112,118,119,122,133,139,140,146,147,149,150,151,160,163],equat:[2,35,38,39,40,43,56,64,65,66,67,68,70,71,72,73,74,75,77,78,82,83,105,110,111,112,115,116,117,120,133,134,136,143,147,152,153,154,163],equation:[73,91],equilibr:[2,35,44,63,64,71,75,80,81,106,107],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,64,69,70,71,72,75,76,78,81,85,86,90,91,106,136,144,149],equilibrium_start:60,equival:[2,13,57,59,61,64,71,76,96,111,115,149,157,159],equlibrium:2,er3:43,eradiu:115,eras:80,erat:134,erc:107,erfc:[107,124],erhart:[113,157,159],eros:136,erose_form:136,erot:2,errata:[157,159],erratum:83,error:[0,1,2,3,11,47,57,58,59,61,64,65,66,68,71,77,82,83,84,93,107,124,147,155,157,159],erta:120,especi:[4,44,62,75,76],essenti:[3,11,47,96,107,124,159],essential:72,essex:13,establish:32,estim:[1,2,19,29,35,42,60,62,77],esub:136,eta:[2,70,71,75,114,116,119,146,158,160],eta_dot:71,eta_ij:146,eta_ji:116,etap:71,etap_dot:71,etc:[1,2,3,4,28,33,34,35,42,44,57,58,59,60,61,69,71,82,84,93,94,113,114,132,134,139,156,157,159,160],etol:[93,94],etot0:75,etot:[2,42,59,75],eu2:43,eu3:43,euler:[77,93,94],eulerian:60,europhi:70,evalu:[3,32,35,41,44,45,57,58,59,60,61,65,69,77,83,93,139,142,143,146,149],evanseck:[2,5,45,103],evaul:93,even:[2,4,19,29,55,57,59,61,62,64,66,71,82,83,84,93,94,98,115,116,120,147,160],evenli:[19,42,62,70],event:[2,71,82],eventu:2,ever:28,everaer:[105,119,147],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,64,65,66,70,71,72,73,75,77,78,82,94,111,132,149,164],everyth:164,everywher:126,eviri:115,evolut:[66,70,74],evolv:[70,74],ewald:[2,40,42,93,100,101,102,107,110,115,124,128,145,148],ewald_disp:110,exact:[19,62,63,69,82],exactli:[2,19,35,44,61,62,69,75,111,113,120,133,142,143],examin:[2,63,77],exampl:[0,1],exce:[2,4,19,61,62,64,71,93],exceed:[19,62,71],excel:115,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,62,64,71,72,74,78,82,85,86,87,89,90,91,92,94,95,96,97,100,101,102,103,104,105,106,107,109,110,111,113,114,115,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,137,141,144,145,147,148,151,156,157,158,159,160,161,162,163],excess:115,exchang:[2,60,66,82,115],excit:115,excite:115,exclud:[2,4,39,41,57,93,120,133,134,155],exclus:[1,4,32,45,106,139],excurs:71,execut:[1,2,3,58],exempl:149,exemplari:69,exemplifi:115,exert:[2,84],exhaust:60,exhibit:[36,66,71,115],exist:[2,3,29,44,56,58,59,64,85,86,87,88,90,112,155,164],exit:[3,19,57,62],expans:[41,55,57],expect:[1,4,19,62,73,75,136,139],expens:[2,59,73,82],experi:[2,76,94,111],experienc:[2,4],explain:[1,2,3,19,30,57,58,59,62,64,71,73,94,98,113,149,151,164],explan:[2,41,57,73],explanatori:[57,61],explic:140,explicit:[2,3,32,77,96,99,103,113,115,123,133,164],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,57,59,64,69,71,72,75,78,82,85,86,87,89,90,91,92,95,96,97,100,101,102,103,104,105,106,107,108,110,111,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,141,142,143,144,145,147,148,151,152,153,154,156,157,158,159,160,161,162,163,164],explictli:4,exploit:74,explor:[40,43],expon:[77,113,117,119,122,132,140,148],exponenti:[32,77,117,146,156,160,163],expos:3,exposit:[60,111],express:[2,41,44,64,73,77,82,99,113,115,126,136,149,150],expressiont:99,extend:[0,2],extens:[2,4,21,22,27,32,35,65,66,71,72,73,76,80,81,82,83,84,119,136,139,147,150],extent:[1,19,21,57,62,96],exterior:[2,84],extern:[32,58,64,69,70,71,72,82,93,137,138],extra:[2,3,4,19,22,39,40,42,43,44,59,61,62,71,75,93,110,120,136],extract:[2,3,18,32,94,107,116,136,150],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,58,64,71,81,115,158],extrema:132,extreme:115,extrins:60,f_1:[2,64],f_a:[157,158,159],f_c:158,f_f:159,f_fix_id:75,f_harm:81,f_i:[13,146],f_id:[2,57,61,65],f_ij:146,f_int:80,f_j:13,f_jj:35,f_k:146,f_langevin:82,f_max:75,f_r:[157,158,159],f_sigma:99,f_solid:81,f_ss:2,face:[2,83,84,119,136,147],facil:0,facilit:2,fact:[2,4,81,120,149],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,58,59,62,64,66,70,71,72,74,76,77,78,83,84,90,96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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 command","dump image command","dump_modify command","fix atc command","fix ave/histo command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,40,41,43,44,56,57,58,59,60,64,69,70,71,72,74,75,80,81,83,99,115,133,134,139,155],"long":[100,101,102,103,104,107,109,110,124,128,132,145,148],acceler:1,adiabat:2,adp:95,airebo:96,alloi:113,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:60,atom:[2,29,30,36,38,41,42],aug:0,balanc:[19,62],barostat:2,bcc:73,beck:97,between:2,bodi:[2,98],bond:63,bond_styl:[20,21,22,23,24,25,26,27,28],bop:99,born:[100,109],box:[2,64],buck:[101,102,109,135],build:3,calcul:2,centro:29,charmm:[2,5,45,103,132],chunk:[2,34],class2:[6,20,46,85,104],cna:30,code:2,coeffici:2,colloid:[83,105,162],comb3:106,comb:106,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,control:65,core:2,cosin:[7,8,9,10,11,12,47],cossq:86,coul:[100,101,102,103,104,107,108,109,121,124,128,132,145,148],coupl:2,create_atom:44,cubic:126,custom:57,cut:[25,101,104,107,110,115,118,124,125,132,140,145],cvff:87,data:2,deby:[107,124],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],diel:108,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,110],discuss:2,disp:2,distanc:88,document:0,dpd:[31,111,112],dreid:122,dreiding:2,drude:2,dsf:[107,124],dump:[2,57,58],dump_modifi:59,eam:113,edip:114,eff:115,ehex:66,eim:116,elastic:2,energi:112,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],exp6:117,exp:[11,47],expand:[22,127],extend:3,fcc:73,fdt:112,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84],fix_modifi:[60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],flow:2,fluid:70,flux:35,forc:2,fourier:[14,15,48,89],from:[2,3],gauss:118,gaybern:119,gener:[1,2],github:164,gld:69,global:2,gpu:[97,100,101,103,104,105,107,110,111,113,118,119,121,124,125,126,127,140,141,147,148,151,156,157,158,159,161,162,163],gran:120,granular:2,gromac:121,gyrat:[33,34],h5md:57,harmon:[16,23,24,25,49,51,83,90,144],hbond:122,heat:35,helix:50,hertz:120,hexord:36,histo:61,histori:120,hook:120,how:2,idealga:152,imag:[57,58],implicit:103,improper_styl:[85,86,87,88,89,90,91,92],indice:0,induc:2,info:[0,60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,71,87,90,101,103,119,124,156,157],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,164],lennard:135,librari:[2,3],linear:[131,141],list:123,lj1043:83,lj126:83,lj93:83,lj96:125,local:2,lubric:133,lubricateu:134,luci:[142,143],mdf:135,meam:[136,137,138],measur:1,mgpt:139,mie:140,minim:[60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84,93],mod:[82,158],model:2,molfil:57,morri:154,mors:[26,96,122,141],movi:[57,58],mpi:3,msd:37,msm:[100,101,103,107,124],multi:[2,51,142,143],multipl:2,nb3b:144,neb:94,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:71,nphug:72,npt:71,nvt:71,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,71,72,85,86,87,89,90,91,92,95,96,97,100,101,102,103,104,105,106,107,108,110,111,113,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,137,138,141,144,145,147,148,151,156,157,158,159,160,161,162,163],opl:53,opt:[103,113,124,128,141],optim:1,option:2,orient:73,orientord:38,orthogon:2,other:2,output:[2,60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],overview:3,packag:[1,4],pair:2,pair_styl:[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],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:74,polariz:2,poli:[133,134],polymorph:146,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:75,quadrat:54,quantiti:2,quartic:[17,28],rattl:78,rebo:96,region:84,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,75,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],relax:64,replica:2,resquar:147,restart:[2,60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],restrain:76,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],rigid:2,ring:91,run:[2,3,60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],scalar:2,script:[2,3],sdk:[18,148],serial:3,set:2,shake:78,share:3,shell:2,shift:[10,11,24,25,47],simpl:15,simul:2,size:2,smooth:[130,131,141],smtbq:149,sna:41,snad:41,snap:150,snapshot:2,snav:41,soft:[132,141,151],spc:2,sph:[152,153,154],spheric:[2,55],spline:[137,138],spring:[79,81],squar:12,srp:155,start:[60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],stop:[60,61,62,64,65,66,70,71,72,73,75,76,78,79,80,81,82,83,84],strategi:1,streitz:107,stress:42,style:[1,2],summari:2,swap:63,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],system:2,tabl:[0,2,68,157],taitwat:[153,154],temperatur:2,tersoff:[157,158,159],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,107,124,128,132],triclin:2,tstat:111,ttm:82,tutori:164,umbrella:92,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:160,vector:2,version:0,viscos:2,visual:2,vtk:57,wall:[2,83,84],water:2,weight:61,wolf:[100,107],wrapper:3,write:2,xrd:43,yukawa:[161,162],zbl:[159,163]}}) \ No newline at end of file diff --git a/doc/src/dump.txt b/doc/src/dump.txt index c6d619bd51..5b3508ed69 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -130,6 +130,10 @@ or multiple smaller files). NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. +Re-neighbor timesteps will not typically coincide with the timesteps +dump snapshots are written. See the "dump_modify +pbc"_dump_modify.html command if you with to force coordinates to be +strictly inside the simulation box. NOTE: Unless the "dump_modify sort"_dump_modify.html option is invoked, the lines of atom information written to dump files diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index c7c670bb6b..00734a5975 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -36,6 +36,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o {nfile} arg = Nf Nf = write this many files, one from each of Nf processors {pad} arg = Nchar = # of characters to convert timestep to + {pbc} arg = {yes} or {no} = remap atoms via periodic boundary conditions {precision} arg = power-of-10 value from 10 to 1000000 {region} arg = region-ID or "none" {scale} arg = {yes} or {no} @@ -377,6 +378,19 @@ timestep order. :line +The {pbc} keyword applies to all the dump styles. As explained on the +"dump"_dump.html doc page, atom coordinates in a dump file may be +slightly outside the simulation box. This is because periodic +boundary conditions are enforced only on timesteps when neighbor lists +are rebuilt, which will not typically coincide with the timesteps dump +snapshots are written. If the setting of this keyword is set to +{yes}, then all atoms will be remapped to the periodic box before the +snapshot is written, then restored to their original position. If it +is set to {no} they will not be. The {no} setting is the default +because it requires no extra computation. + +:line + The {precision} keyword only applies to the dump {xtc} style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to @@ -755,6 +769,7 @@ image = no label = ENTRIES nfile = 1 pad = 0 +pbc = no precision = 1000 region = none scale = yes diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 6f6cdc4a04..f6d812c16e 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -136,8 +136,9 @@ length. The first value (a scalar or vector) is what is histogrammed into bins, in the same manner the fix ave/histo command operates. The second value (a scalar or vector) is used as a "weight". This means that instead of each value tallying a "1" to its bin, the -corresponding weight is tallied. E.g. the Nth entry in the first -vector tallies the Nth entry (weight) in the second vector. +corresponding weight is tallied. E.g. The Nth entry (weight) in the +second vector is tallied to the bin corresponding to the Nth entry in +the first vector. :line