From b4abf2abd2753a7279d8c73c82405f7aca453c40 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 22 Mar 2016 13:42:54 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14774 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/_sources/Manual.txt | 2 +- doc/_sources/units.txt | 9 ++++++--- doc/searchindex.js | 2 +- doc/units.html | 9 ++++++--- doc/units.txt | 9 ++++++--- 5 files changed, 20 insertions(+), 11 deletions(-) diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt index 3a12b7da64..c1f3a1b340 100644 --- a/doc/_sources/Manual.txt +++ b/doc/_sources/Manual.txt @@ -5,7 +5,7 @@ LAMMPS Documentation ==================== -14 Mar 2016 version +22 Mar 2016 version ------------------- Version info: diff --git a/doc/_sources/units.txt b/doc/_sources/units.txt index f23f91c9a6..f82ab37ddd 100644 --- a/doc/_sources/units.txt +++ b/doc/_sources/units.txt @@ -78,9 +78,12 @@ results from a unitless LJ simulation into physical quantities. * density = mass/volume, where rho* = rho sigma^dim Note that for LJ units, the default mode of thermodyamic output via -the :doc:`thermo_style ` command is to normalize energies -by the number of atoms, i.e. energy/atom. This can be changed via the -:doc:`thermo_modify norm ` command. +the :doc:`thermo_style ` command is to normalize all +extensive quantities by the number of atoms. E.g. potential energy is +extensive because it is summed over atoms, so it is output as +energy/atom. Temperature is intensive since it is already normalized +by the number of atoms, so it is output as-is. This behavior can be +changed via the :doc:`thermo_modify norm ` command. 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6,8,11,14,18,40,41,42,221,381,406,491,496],advect:[3,6,324],advertis:8,advis:[376,443],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,74,93,124,148,157,171,177,200,201,206,213,214,216,217,218,219,222,223,224,225,227,228,238,244,246,248,254,261,265,266,267,268,270,271,272,278,283,284,285,287,308,309,322,336,346,359,366,372,373,374,376,377,378,381,407,428,429,436,479,480,482,484,485,487,490,492],affin:[16,17,18,227,381,396],afil:242,aforement:18,afresh:[296,490,509],afshar:401,after:[],afterrun:490,afterward:3,afterword:42,ag1:172,ag2:172,again:[6,11,12,16,17,64,147,153,159,167,197,201,227,244,294,350,365,376,428,429,477,479,480,482,484,489,496,498,509,511],against:[11,12,13,66,228,376,444,445],aggreg:[6,12,67,70,72,82,98,115,122,244,260,306,308,322,477,510],aggress:[244,496],agilio:[9,13],agre:[3,8,193,374,383,416,445],agreement:[5,7],ahd:413,ahead:343,aidan:[0,5,7,9,13,369],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:200,akohlmei:[7,9,13,202,245],aktulga:[7,9,301,445],al2o3:452,al2o3_001:[125,309],al3:172,ala:[251,452],alain:9,alat:[289,431],alb:[442,465,467],albeit:307,albert:9,alchem:[92,167],alcohol:339,alcu:[382,387],alcu_eam:442,alderton:400,alejandr:[264,265],alessandro:13,algebra:434,algorithm:[0,1,6,7,8,9,42,63,201,210,221,224,227,251,253,254,278,291,299,308,311,312,331,332,336,339,344,372,373,374,378,381,403,407,429,434,449,451,477,479,496],alia:[9,12,16],alias:[1,367],aliceblu:201,align:[6,9,12,29,42,74,175,193,217,221,246,369,482,485,503],alkali:407,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,166,167,168,169,170,171,172,173,174,175,176,177,179,181,186,192,193,194,197,198,199,200,201,202,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,257,259,260,262,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,284,285,286,287,288,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,320,321,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,349,350,351,355,360,362,364,365,366,367,368,369,371,374,375,376,377,378,380,381,382,383,384,386,387,388,390,391,392,393,394,396,397,400,401,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,497,499,500,501,503,504,508,509,510,511,512,513],allen:[29,92,400,410],allentildeslei:92,allign:3,allindex:348,alloc:[3,5,6,8,9,11,12,62,238,338,375,377,381,440,445,482,490],allocat:3,alloi:[],allosw:74,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,80,97,113,115,149,151,152,153,166,171,172,173,175,181,192,193,197,198,200,201,202,204,205,207,209,210,211,213,214,215,216,217,218,219,221,223,224,225,226,227,228,232,233,238,240,241,242,243,245,248,251,254,255,259,261,264,265,289,293,294,295,296,297,298,302,308,309,311,313,315,316,320,324,331,332,333,334,336,337,338,339,340,341,347,349,351,360,366,367,369,374,375,376,377,380,381,383,384,387,388,389,390,391,392,397,405,407,411,412,413,414,419,423,428,429,434,436,442,445,446,449,451,452,461,468,471,473,477,480,482,484,485,486,487,488,489,492,494,495,496,499,500,504,509,510],almost:[2,3,12,62,246,298,336,367,378,381,461],alo:397,alon:[6,7,224,304,444,445,480],alond:13,along:[6,8,12,29,41,74,92,125,171,172,173,196,197,200,213,224,246,251,252,256,261,263,298,308,311,313,317,321,322,331,335,336,342,345,347,369,372,373,374,376,397,400,411,414,417,419,423,431,444,445,464,482,485,492,493,509],alonso:[432,433],alpha:[6,12,52,205,251,290,298,299,303,374,382,385,388,397,401,403,405,406,408,413,418,419,431,437,441,466,468,500,503],alpha_:[],alpha_c:427,alpha_i:453,alpha_ialpha_j:[],alpha_lj:427,alphabet:[2,3,22,37,45,56,65,181,192,204,351,360,375,394,462,482],alphanumer:[3,65,204,297,305,349,375,509],alreadi:[3,7,8,9,12,16,17,18,43,173,174,176,199,209,213,217,218,221,223,227,255,296,298,324,347,348,375,376,401,412,414,421,429,461,471,474,478,482,483,487,492,509],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,74,75,76,78,80,84,92,94,95,97,99,109,110,111,112,113,114,119,121,123,124,126,147,148,149,150,151,152,153,154,155,156,157,159,160,161,162,163,165,166,167,168,169,170,173,174,175,176,177,179,181,192,193,195,196,197,198,199,200,201,202,204,205,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469,477,482,487,490,494,496,499,503,509],complex:[4,6,8,11,12,13,25,41,43,64,97,113,147,149,161,173,174,251,320,345,364,376,407,434,464,480,482,485,509],compli:[331,335],complic:[6,7,9,12,13,211,240,480],complier:12,compon:[3,6,8,12,63,65,68,69,76,84,93,94,95,96,97,99,100,103,110,111,112,113,114,115,116,117,119,120,124,134,137,138,139,140,143,144,145,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,168,169,170,196,197,198,200,201,207,208,212,213,214,215,216,217,218,219,220,224,225,227,228,233,238,243,247,248,251,254,256,260,261,263,264,265,269,270,271,272,283,284,285,287,288,290,291,292,295,306,308,310,311,313,317,318,321,324,327,328,329,331,338,339,344,345,346,366,369,373,374,375,376,381,401,407,411,428,429,449,451,452,453,482,483,492,500,509,510],componenet:6,composit:[6,211,251,405],compound:[396,407,408,470],compres:[74,121,213],compress:[],compris:[41,345,446,469],compton:[125,172],comptu:3,compuat:367,comput:[],computation:[3,6,222,223,336,387],computational:503,compute_arrai:8,compute_fep:[206,427],compute_group_group:240,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[125,309],compute_scalar:8,compute_temp:8,compute_ti:206,compute_vector:8,compute_xrd:172,concaten:[2,3,512],concav:345,concentr:[74,405],concept:[6,153,163,213,491],conceptu:[3,6,74,161,225,227,376,397,414,431,487],concern:[6,76,92,199,241],concetr:74,concis:[11,335],conclud:12,concret:8,concurr:[16,367,509],conden:[336,465,467],condens:[6,155,336,383,399,405,419,470],condit:[],conducit:6,conduct:[],cone:485,confer:434,confid:[3,496],config:[12,197,479],configfil:226,configur:[1,2,6,12,15,17,38,61,129,175,193,196,197,200,204,225,226,227,228,232,240,247,248,278,291,299,335,364,374,376,383,387,406,431,434,463,465,467,470,477,482,484,485,496,504],confin:[482,496],conflict:[3,12,41,198,436,480,504],conform:[3,6,13,61,224,225,263,307,313,335,359,376,407,494],confus:[3,470],conjuct:[9,401],conjug:[7,8,248,373,407,444,445],conjunct:[6,7,74,91,92,121,156,161,167,173,177,201,205,206,248,251,255,278,294,295,299,300,301,303,308,312,324,332,339,344,366,367,376,388,390,394,397,401,407,413,419,436,439,447,468,482,485,489,503,513],connect:[3,6,9,92,158,176,224,245,293,308,311,321,376,398,411,461,467,479,480,482,486,503],conner:383,connor:383,conput:3,consecut:[3,11,12,40,74,173,201,205,206,228,245,246,397,419,423,477,483,485],consequ:[1,6,211,336,418,496],conserv:[],consid:[6,73,74,81,92,122,155,158,159,176,197,198,201,205,206,212,214,217,221,223,224,228,252,265,290,308,331,332,335,336,339,367,394,407,414,445,446,452,461,477,478,480,483,484,485,487,490,492,500,503,509],consider:[6,8,248,249,327,328,329,381,491],consist:[3,6,8,9,11,12,41,43,67,72,82,98,110,115,118,119,122,153,156,158,173,185,196,202,207,208,213,227,228,231,233,238,241,248,249,250,261,264,266,267,268,269,270,271,272,273,274,276,277,278,279,281,282,283,284,285,286,287,295,298,303,305,307,308,327,328,329,330,340,366,367,369,375,376,381,383,387,389,395,397,407,410,414,417,428,429,431,434,436,446,449,451,452,464,471,480,482,483,484,485,486,487,494,503,509],consistent_fe_initi:210,consit:308,constant:[],constitu:[3,6,254,308,341,345,395,446],constitut:[449,451],constrain:[3,6,8,150,151,152,153,154,156,159,160,161,162,163,165,166,204,213,228,240,241,246,254,258,293,294,306,308,311,322,332,339,374,375,407,487,494,503],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,73,75,76,80,97,113,125,147,172,225,264,290,307,345,377,381,400,434,436,461,463,464,485,486,501,509],constructor:[8,11],consult:445,consum:[1,303,440,509],consumpt:364,contact:[],contact_stiff:[448,450],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,92,96,123,125,147,149,153,161,171,172,173,175,179,181,192,193,197,198,200,201,202,204,205,206,210,212,213,214,216,217,218,219,221,226,228,233,236,242,246,247,248,251,262,278,289,290,293,294,296,298,301,305,308,309,314,324,331,335,336,345,346,349,365,367,375,376,379,380,382,383,384,387,396,397,400,405,406,407,414,415,431,434,438,442,443,444,445,453,463,464,465,466,467,468,470,477,478,479,480,482,483,484,485,487,489,491,494,496,497,499,500,503,504,509,511,513],content:[4,8,9,12,18,445,498,500],context:[3,6,8,12,17,123,124,201,222,223,228,293,305,340,373,473,482,489,498,508,509,510],contibut:73,contigu:479,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,74,84,109,110,169,201,204,205,206,211,213,214,215,216,217,218,219,221,224,225,226,227,228,240,241,242,244,245,246,248,249,250,256,261,262,264,266,267,268,269,270,271,272,283,284,285,286,287,292,294,297,298,308,309,313,323,324,326,333,334,336,342,345,349,365,380,381,387,401,404,421,424,444,445,446,449,451,466,477,480,482,484,485,490,496,497,499,500,509,511],continuum:[6,7,9,210,336,449,451],contour_integr:210,contract:[61,225,227,264,295,308],contradictori:3,contrain:311,contraint:278,contrari:[242,249],contrast:[1,6,43,56,66,155,158,198,227,347,449,451,473,512],contrib:336,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,71,73,74,77,78,80,83,89,92,93,94,95,96,99,108,110,112,114,115,116,117,119,121,124,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,206,211,212,213,214,216,217,218,219,225,240,248,251,254,255,259,265,285,286,293,294,302,305,308,309,311,338,366,374,376,384,401,404,405,407,414,428,429,434,436,444,445,452,494,500,503,504],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,92,96,129,147,182,197,198,200,204,210,211,221,225,226,227,244,245,248,249,264,266,267,268,269,270,271,272,295,300,308,315,316,327,328,329,336,340,364,366,378,407,410,434,444,445,448,450,463,467,477,479,491,497,498],control_typ:210,controlfil:445,convect:96,conveni:[6,12,29,197,202,219,309,369,453,468,504,509],convent:[3,8,29,184,191,192,198,201,307,321,348,405,407,509],converg:[3,6,42,93,197,198,200,202,207,221,224,225,233,238,269,298,300,303,307,311,372,373,374,376,396,397,419,452,477,489,496],convers:[3,8,147,200,201,211,214,295,366,397,398,399,407,419,423,427,439,480,496,508],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,74,96,173,180,197,200,201,214,219,262,294,347,350,352,356,359,369,376,382,405,434,465,467,474,480,482,483,484,489,499,503,508,509,511,513],convex:[43,345],convinc:[7,12],cook:9,cooki:7,cool:[7,163,244,306],cooordin:[197,198],cooper:[5,7],coord123:121,coord1:[3,121,213,217,218],coord2:[3,121,213,217,218],coord3:[3,121,213,217,218],coord:[],coordb:452,coordbb:452,coordiat:374,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,74,77,78,80,84,92,94,95,99,109,110,112,120,121,123,141,147,156,162,168,170,171,173,177,196,197,198,199,200,201,202,204,207,212,213,216,217,218,221,222,223,224,225,226,227,228,231,233,234,238,240,243,244,245,246,247,248,249,261,263,264,266,267,268,270,271,272,285,288,289,290,293,294,295,305,306,308,310,311,313,318,321,322,323,324,326,334,335,336,343,344,346,347,369,374,375,376,381,382,383,386,406,452,477,482,483,484,485,487,490,492,496,503,509,510],coordn:[121,213],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,126,200,336,376,394,444,480,504],copper:474,coproccesor:16,coprocessor:[1,7,9,16,17,381,495],coproprocessor:17,copy_arrai:8,copyright:[7,8,293],coral:201,core:[],core_shel:155,coreshel:[],cornel:[6,179,494],corner123i:120,corner123x:120,corner123z:120,corner1i:120,corner1x:120,corner1z:120,corner2i:120,corner2x:120,corner2z:120,corner3i:120,corner3x:120,corner3z:120,corner:[3,6,41,120,200,345,346,369,469,482,504],cornflowerblu:201,cornsilk:201,corp:9,corpor:16,corr:396,correct:[3,6,9,11,12,16,17,61,92,93,108,109,114,117,123,155,160,167,198,200,227,240,242,248,264,265,285,293,295,298,335,341,345,366,376,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,469,470,472,473,474,475,482,497,500,503,504],correction_max_iter:210,correctli:[3,8,11,17,74,84,108,109,110,150,151,152,154,156,158,159,160,161,162,165,166,169,197,201,207,228,233,238,249,258,264,265,301,308,311,321,323,342,345,376,377,381,399,429,434,479,480,482,492,504,508,510],correl:[],correpond:236,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,73,74,92,102,103,116,119,120,121,122,125,126,134,137,138,139,140,141,143,144,145,147,150,151,160,167,171,172,179,180,181,182,183,184,185,187,188,190,191,193,196,197,198,200,201,205,206,207,213,215,216,217,218,220,223,225,227,234,238,239,243,248,251,252,260,261,262,264,266,267,268,269,270,271,272,273,274,278,281,283,284,285,287,290,291,295,300,308,310,311,327,329,331,340,341,342,344,345,346,348,350,351,352,353,355,356,359,361,367,371,373,375,376,382,383,385,388,389,390,391,392,393,394,395,396,397,400,401,405,406,407,408,409,410,411,412,413,414,417,419,420,421,422,423,424,425,426,427,428,431,432,434,436,437,438,439,441,442,444,445,446,447,452,453,454,463,464,465,466,467,468,470,472,473,474,477,479,480,482,483,485,495,496,497,499,500,503,509],correspondingli:[428,429,491],corrupt:3,cosin:[],cosineshift:27,cosmo:[242,247],cossq:[],cost:[1,6,10,11,12,17,40,42,74,116,125,148,172,200,201,213,217,218,221,222,223,237,264,300,336,366,367,379,397,419,423,434,436,463,479,491],costheta0:[463,465,467,470],costheta:442,costli:[11,93,242,377],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,74,78,92,95,99,110,112,116,119,121,153,163,168,170,186,197,198,200,201,205,206,213,214,217,221,227,238,247,297,298,299,303,306,308,310,324,325,331,335,336,337,341,345,347,349,357,363,365,372,374,377,381,384,409,413,414,417,444,445,478,479,480,482,484,486,489,490,497,498,503,509,510],coulomb:[3,5,6,7,8,9,10,12,14,15,18,75,93,114,115,123,148,174,178,299,301,337,366,367,374,381,388,390,391,392,393,396,397,398,399,400,407,411,412,414,419,423,427,430,436,439,444,445,447,452,462,467,468,470,473,487,494,500,503,508],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,80,96,121,123,124,161,171,177,207,208,211,213,216,217,218,220,221,228,233,237,240,246,264,278,294,311,327,328,345,367,374,375,376,378,381,409,413,436,500,509],counter:[3,342,477,488,490,496],counteract:240,counterbal:244,counterbalanc:29,counterpart:[197,308,477],counterproduct:18,coupl:[],courant:314,cours:[3,8,133,135,167,197,205,206,241,307,321,335,341,343,344,346,347,367,428,454,479,482,495,503,509,511],courtesi:369,cov:452,coval:[6,9,29,407,431,452,503],covari:242,cover:[6,74,193,201,210,251,407,469],coverag:[74,217],cpc:247,cpp:[1,3,6,8,9,11,12,13,92,197,205,206,238,311],cpu:[1,3,9,10,12,14,15,16,17,18,65,74,201,215,231,249,337,364,367,381,394,462,477,495,496,499,500,501,509],cpuremain:500,cr2:172,cr3:172,crack:[4,377],crada:[5,7],crai:[5,7,13,18,197],crash:[3,12,377,503],craympi:381,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:210,create_faceset:210,create_group:199,create_nodeset:210,createatom:[],creation:[],crimson:201,critchlei:293,criteria:[3,123,174,200,201,222,223,224,259,374,441,469,484,487,509],criterion:[12,42,128,173,176,211,221,224,240,278,300,314,342,347,374,376,396,407,411,452,487,496,497],criterioni:496,critic:[6,49,50,262,331,336,374],crmax:74,crmin:74,cross:[3,12,22,74,94,151,171,181,197,198,200,212,217,223,227,261,263,285,308,317,321,323,332,339,351,369,376,392,401,404,405,412,413,414,419,421,423,442,447,449,451,465,467,474,482,486,492,511],crossov:1,crossterm:482,crozier:[0,7,13],crucial:298,crystal:[3,4,6,13,76,113,289,290,334,369,377,482,486,500,503],crystallin:[6,109,290,369,466,503],crystallis:331,crystallogr:[125,172],crystallograph:[369,500],crystallographi:[125,172,369],cs1:172,cs_chunk:6,cs_im:[41,482],cs_re:[41,482],csanyi:[147,443,453],cscl:431,csequ:6,csh:[11,12,394],cshrc:[11,12],csic:[406,463,465,467,470],csinfo:6,csisi:[406,463,465,467,470],csld:[],cst:405,cstherm:6,cstyle:479,csvr:[],ctcm:[382,405],ctemp_cor:231,cterm:313,ctr:9,ctype:11,cu1:172,cu2:172,cu3au:431,cube:[6,42,171,176,221,231,345,369,503],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:387,cummul:[3,6,219,222,223,224,226,237,242,248,250,324,327,328,329,330,332,339,413,500],cumul:[6,211,213,216,217,218,232,240,248,262,264,269,278,308,309,376],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,74,76,84,92,108,109,115,123,124,137,148,153,161,163,169,171,174,177,196,197,198,199,200,201,202,205,206,210,213,217,218,219,221,222,223,224,225,226,227,228,232,233,238,240,242,245,246,248,254,261,264,265,270,271,272,278,283,284,285,287,293,294,299,300,302,305,306,307,308,311,312,313,314,315,316,317,318,320,322,323,324,327,328,329,335,336,339,340,341,342,343,344,346,347,349,364,365,366,367,370,371,373,374,375,376,381,387,394,396,400,405,407,408,411,414,415,418,428,429,431,432,433,436,442,444,445,448,449,450,451,454,465,467,468,471,477,478,479,480,482,483,484,485,486,488,489,490,492,494,496,497,499,500,504,509,510,511,512,513],curv:[6,173,240,290],curvatur:[410,446,474],custom:[],cut0:480,cut1:491,cut2:491,cut:[],cuthi:[289,301],cutinn:[389,428,429],cutlo:[289,301],cutmax:442,cutoff1:[393,400,419,423,427,430,439,447],cutoff2:[388,390,391,393,399,400,419,423,427,430,439,447,468],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,73,75,76,80,92,97,113,115,122,123,147,171,174,176,177,223,224,229,236,289,298,299,301,303,305,308,312,324,337,341,345,347,364,366,367,374,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,452,453,454,455,456,457,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,480,484,487,491,503,509],cutoff_glob:[],cutoff_inn:[],cutoffa:406,cutoffc:406,cuu3:405,cval:172,cvd:331,cvel:313,cvff:[],cwiggl:[3,261,341,344,346,509],cyan:[2,200,201],cycl:[3,240,262,264,265,269],cyclic:[3,193],cygwin:12,cylind:[3,4,74,200,213,246,294,342,345,485],cylindr:[6,246,321,342],cypress:381,cyrot:387,cyrstal:290,d3q15:251,d3q19:251,d_double_doubl:15,d_e:336,d_flag2:297,d_flag:297,d_name:[120,197,297,326,492],d_single_doubl:15,d_single_singl:15,d_sx:297,d_sy:297,d_sz:297,daan:334,dai:12,daili:12,daivi:285,damag:[],dammak:303,damp:[3,6,204,209,248,249,250,255,264,265,269,295,298,299,303,308,327,328,340,342,343,373,374,376,388,390,392,397,400,407,411,419,427,439,447,462,468,496,503],damp_com:249,damp_drud:249,dampen:[308,503],dampflag:[342,411],dan:17,danger:[3,12,240,347,401,500],dangl:176,daniel:9,darden:[367,400],darkblu:201,darkcyan:201,darken:200,darkgoldenrod:201,darkgrai:201,darkgreen:201,darkkhaki:201,darkmagenta:201,darkolivegreen:201,darkorang:201,darkorchid:201,darkr:201,darksalmon:201,darkseagreen:201,darkslateblu:201,darkslategrai:201,darkturquois:201,darkviolet:201,dasgupta:299,dash:[411,499],dat:[6,96,193,210,478],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,309],dataset:309,datatyp:3,date:[0,4,6,12,13,196,444,445,509],datom1:122,datom2:122,datom3:122,datom4:122,datum:[3,6,43,67,70,72,82,98,115,122,197,214],davenport:430,davi:341,david:[9,19,366,367,465,467],daw:[405,442],dbg:14,dcd:[3,6,7,197,199,200,201,202,291,483,487],ddim:196,deactiv:427,dealt:247,debug:[6,7,11,12,13,14,17,125,129,172,173,291,296,364,366,381,415,436,471,480,481,489,492,499,509],deby:[],decai:[97,397,474],decid:[3,6,12,16,74,261,297,308,337,497,504],decipher:369,declar:199,declin:324,decod:200,decompos:[92,453],decomposit:[3,5,7,18,64,210,291,312],decoupl:[6,503],decreas:[3,197,198,207,208,215,224,227,233,238,240,248,335,366],decrement:313,deepli:363,deeppink:201,deepskyblu:201,def:[12,13,480],defaul:63,defect:[6,73,171,434],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,198,199,200,201,204,205,206,207,208,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,227,228,231,232,233,235,238,239,240,243,246,247,248,249,250,251,259,261,263,264,265,266,267,268,269,270,271,272,274,275,276,279,281,282,283,284,285,286,287,289,290,291,293,294,295,297,299,301,306,308,309,310,311,314,318,322,324,326,327,328,329,330,332,333,334,336,338,339,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,359,360,361,362,364,366,367,369,371,373,374,375,376,377,378,379,380,381,383,384,385,386,388,389,390,391,392,393,394,395,397,398,400,401,402,403,404,406,407,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,434,435,436,437,438,439,441,442,444,445,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,482,483,485,486,487,488,491,492,493,494,496,497,499,500,503,505,506,507,508,509,510],definit:[2,3,6,8,12,13,81,83,123,147,201,213,214,215,216,217,218,219,227,235,246,269,309,326,338,341,344,346,348,360,364,375,384,387,395,402,403,407,417,442,449,451,453,469,480,482,484,491,493,508,509],defint:500,deform:[],deg2theta:172,deg:503,degener:[3,293],degrad:[8,18,290,367,491],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,82,97,98,100,102,103,105,107,108,113,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,172,173,179,180,183,184,191,193,196,200,213,224,231,240,242,243,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,307,308,311,327,328,329,334,350,352,356,359,361,374,400,405,413,492,500,503,510],degress:[153,213],del:496,delai:[3,6,12,377,404,500],deleg:414,delet:[2,3,7,8,12,55,59,62,65,171,176,177,204,213,214,216,217,218,219,222,224,237,240,264,309,327,328,347,349,365,375,377,380,436,461,482,483,484,485,493,494,499,504,505,507,509,510],delete_atom:[],delete_bond:[],delete_el:210,deli:196,delimit:[480,509],deloc:[265,407,452],delr:431,delt_lo:496,delta:[],delta_1:387,delta_3:387,delta_7:387,delta_conf:3,delta_ij:[431,442],delta_mu:[],delta_pi:387,delta_r:442,delta_sigma:387,delta_ua:[],delx:196,delz:196,dem:[],demand:303,demo:11,demon:288,demonstr:[298,431],den:294,dendrim:413,denniston:[9,251,253,254,255,290],denomin:[7,178],denot:[125,231,249,290,301,303,397,412,414,445,449,451],dens:[74,224,407],densiti:[3,6,7,9,18,41,42,61,106,123,133,147,159,171,173,205,206,210,213,217,218,221,227,238,251,254,257,258,290,294,295,299,336,341,369,371,375,382,383,387,405,431,432,433,442,446,452,456,458,459,460,482,491,492,500,508],density_continu:451,density_summ:451,depart:[0,7],departur:[262,298],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,72,73,74,82,97,98,109,115,116,119,120,121,122,126,147,149,150,156,160,161,167,173,174,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,200,201,204,205,206,207,208,211,213,215,216,217,219,220,221,223,225,227,233,234,239,242,243,244,246,248,249,251,253,254,261,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,289,300,303,305,308,310,311,312,318,324,327,328,329,331,333,335,336,338,340,341,344,345,346,347,349,350,351,352,353,355,356,359,361,367,369,374,375,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,431,432,434,435,437,438,439,441,442,444,445,446,447,452,453,454,462,463,464,465,466,467,468,470,472,473,474,477,479,482,484,485,488,492,494,496,499,500,502,509,510],dependend:6,depflag:12,dephas:[477,496],depos:228,deposit:[],deprec:[3,299,444],depth:[52,151,200,336,410,446],dequidt:9,der:[92,114,395,396,427,444,445,473,503],deriv:[6,7,8,9,38,57,65,92,147,167,193,214,225,227,240,248,261,264,266,267,268,269,270,271,272,289,295,299,303,333,334,336,341,342,345,373,375,383,387,395,400,407,408,412,421,425,426,431,434,444,445,462,464,473,503],derjagin:473,derlet:289,descend:201,descent:[7,373],descib:[41,200,299],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,73,74,76,93,117,120,123,125,137,147,148,151,152,153,157,158,161,164,166,167,171,172,173,175,176,185,190,193,197,198,199,204,205,206,213,214,215,216,217,218,219,221,224,225,226,227,228,230,231,236,241,242,245,246,247,248,249,250,251,253,254,255,259,263,264,265,269,277,286,289,291,296,297,298,299,300,301,308,313,321,324,325,326,327,328,329,330,331,332,333,334,339,341,342,344,349,366,367,369,372,373,374,375,376,380,383,384,386,388,389,390,392,393,394,395,396,397,400,405,407,408,410,411,412,414,417,419,420,421,422,423,424,425,426,427,428,429,430,431,434,435,441,442,443,444,445,446,447,452,453,454,461,462,463,464,465,466,467,468,470,472,473,474,475,477,479,480,482,483,484,485,486,492,495,496,499,504,509,510,511],descript:[],descriptor:[147,197,415],deserno:367,design:[0,3,6,7,8,11,13,14,15,17,125,155,158,172,210,224,230,231,264,265,289,290,309,331,336,384,385,386,389,392,397,399,407,427,428,429,432,433,442,445,464],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,74,93,96,119,124,148,155,173,186,196,213,219,225,227,238,240,241,248,249,250,254,264,285,293,294,295,296,299,303,308,311,324,327,328,329,330,335,342,357,363,366,367,369,372,374,375,376,401,405,413,428,429,463,465,467,478,479,480,482,486,491,496,497,499,500,509,510,511],desk:7,desktop:[4,6,7,10,12,200],despit:503,destabil:387,destre:359,destroi:[9,11,40,222,223],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,74,78,81,95,96,99,108,110,112,114,116,118,119,121,124,126,147,148,150,151,152,153,156,166,167,168,170,173,174,177,178,181,192,196,197,198,200,201,204,205,206,210,213,214,215,216,217,219,221,223,224,225,226,227,228,238,240,241,242,243,245,246,248,250,251,255,261,262,263,264,265,266,267,268,269,270,271,272,276,278,283,284,285,286,287,290,293,294,295,297,298,300,301,302,308,311,312,324,327,328,329,330,331,332,334,335,336,337,338,339,340,347,349,351,360,366,367,370,374,375,377,378,381,382,383,384,386,387,389,391,392,393,394,395,396,397,400,401,407,408,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,430,431,435,436,441,444,445,446,452,453,454,462,469,472,473,475,480,482,483,484,485,487,488,491,492,494,497,500,501,504,509,510,513],detect:[2,3,12,43,63,65,91,97,239,294,335,376,396,413,418,477,479,482,493,496,509],determ:381,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,74,92,108,114,116,119,125,126,134,148,161,162,171,172,173,196,197,198,200,201,202,203,207,208,209,212,213,214,215,216,217,218,219,220,221,225,227,228,231,233,240,243,244,246,248,249,254,259,261,262,264,270,271,272,283,284,285,287,289,291,294,295,298,305,306,307,308,309,310,314,316,318,324,327,328,329,331,337,338,341,342,343,344,345,346,347,360,366,367,369,375,377,378,381,383,384,391,396,400,404,405,409,411,414,415,423,431,434,436,445,446,452,461,464,468,473,479,482,483,485,487,489,492,496,498,499,501,508,509,510],determinist:312,detil:115,devan:[9,447],devanathan:467,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,245,269,293,298,299,302,383,387,407,433,434,452,470,484],devemi:9,deviat:[262,269,289,409],deviator:9,devic:[1,3,12,15,17,245,381],device_typ:381,devin:[300,396],devis:433,dfactor:200,dff:503,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,367],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,302,434],dhi:[61,196,227,294],dhug:[262,298],dhugoniot:[262,298],dia:431,diagnost:[],diagon:[3,6,88,147,148,149,225,264,295,308,339,449,451],diagonalstyl:453,diagram:[42,125,172,192,221,291],diallo:413,diam:[200,201,294,375],diamet:[3,6,41,43,120,173,197,198,200,201,205,206,248,294,308,324,326,340,342,375,395,410,411,421,446,469,473,482,483,492],diamond:[369,407,431],diamter:[41,294],dick:6,dicsuss:261,dictat:[211,262],did:[3,12,374,401,404,405,411,436,465,467,490],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,169,338,366],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,73,74,92,97,100,102,103,127,147,149,150,151,152,153,154,156,159,160,161,162,163,165,166,167,173,174,176,181,192,193,196,197,200,201,204,206,209,211,213,216,221,222,223,224,225,226,227,231,236,239,240,241,242,243,244,245,248,249,251,261,264,265,266,267,268,270,271,272,274,276,279,281,282,283,284,287,289,291,293,295,298,299,300,303,306,308,311,313,321,322,324,327,328,329,332,333,334,336,339,340,341,342,345,349,350,360,363,365,366,367,369,370,372,373,375,376,378,379,380,381,382,383,387,391,392,394,395,396,401,402,403,405,407,410,411,412,414,417,419,420,422,423,430,431,432,433,435,436,438,442,444,445,446,447,448,449,451,452,453,454,462,463,464,465,467,469,470,473,476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33,334,339,396,397,444,445,478,492],equilibria:339,equilibribum:[222,223],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,156,157,180,182,225,227,240,241,242,249,251,264,269,285,298,299,303,307,311,313,321,324,331,332,334,339,350,352,356,359,396,431,438,452,503],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:210,equival:[6,12,13,29,61,63,131,132,140,145,171,175,201,216,219,225,227,240,248,264,285,295,307,308,344,383,401,407,452,465,467,468,482,485,490,491,500,503],equlibrium:6,equliibr:[299,301],er3:172,eradiu:[41,120,198,407,482],eras:[310,333],erat:[227,429],erc:397,erfc:[397,419,436],erforc:[120,198],erg:508,erhart:[211,405,465,467],ermscal:384,ernst:9,eror:3,eros:431,erose_form:431,erot:[],errata:[465,467],erratum:341,erron:3,error:[],erta:411,ervel:[120,198,482],escap:[228,503],especi:[8,16,161,173,204,211,221,240,298,303,306,307,381,479],espresso:[9,302],essenti:[8,11,12,27,93,135,154,155,156,159,160,161,162,163,165,182,214,269,290,340,367,383,397,419,467,487,500],essex:29,establish:[92,244],estim:[1,3,6,10,12,38,42,57,96,148,210,221,232,262,324,331,366,367,372,436,445,464,496,500],esu:508,esub:431,eta:[6,251,264,298,299,301,340,406,408,410,442,466,470,508],eta_dot:264,eta_ij:442,eta_ji:408,etag:[41,482],etail:500,etap:264,etap_dot:264,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,94,95,96,100,116,117,120,122,148,150,153,154,155,156,157,159,160,161,162,163,165,167,173,175,176,177,186,197,198,200,201,204,205,210,211,212,213,216,217,218,219,222,223,227,228,238,240,241,248,264,294,305,309,336,337,345,349,365,366,374,375,376,377,379,405,406,414,427,429,434,440,444,445,463,465,467,470,477,480,482,483,484,489,491,492,496,497,498,499,500,501,503,508,509,511,513],ethernet:18,etol:[374,376,477,496],etot0:298,etot:[6,100,102,103,117,148,159,201,231,249,262,298,499,500],eu2:172,eu3:172,euler:[374,376],eulerian:210,euqat:455,europhi:251,ev_tal:8,evalu:[2,3,9,11,12,38,57,71,74,92,93,96,114,124,126,147,149,153,163,171,173,196,197,198,200,201,205,206,207,208,210,212,213,214,215,216,217,218,219,220,227,233,241,243,244,246,247,248,249,290,296,299,310,314,318,327,328,329,338,341,344,346,347,349,366,367,372,374,381,434,436,442,448,450,452,464,477,478,480,484,485,487,489,490,491,492,496,498,500,509,510],evalut:[349,480],evan:[161,285],evanseck:[6,20,179,392,494],evapor:[],evaul:[8,374],evdwl:[114,149,444,445,500],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,73,74,93,114,126,171,174,175,189,193,197,198,201,204,205,206,211,212,213,216,217,218,219,221,222,223,225,227,228,231,246,249,262,264,265,290,294,303,305,308,309,320,324,332,336,339,341,345,347,358,366,372,374,376,381,386,407,408,411,414,417,436,446,470,471,475,482,483,485,487,488,489,491,492,494,497,499,500,501,503,513],evenli:[3,42,148,193,221,251,417,471],event:[],eventu:[3,6,12,15,175,299,496],ever:[9,55,57,247,324],evera:[395,410,446,462],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,74,75,96,120,126,135,161,176,197,198,199,200,201,202,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,232,237,238,240,242,244,245,246,251,252,260,264,265,269,288,289,290,294,295,296,297,298,299,300,301,303,305,306,308,309,311,313,324,326,327,328,329,330,331,332,335,336,337,338,339,347,349,365,367,376,377,378,381,401,404,414,427,444,445,452,458,476,477,478,482,484,486,487,489,490,491,496,497,498,500,504,509,513],everyth:[8,114,504],everywher:[123,421],eviri:407,evolut:[242,251,291,477],evolv:[251,291,337],ewald:[2,3,5,6,7,8,9,12,93,117,125,148,337,366,367,374,388,390,391,397,400,407,419,423,439,447,462,464,468],ewald_disp:400,ewalddisp:3,exact:[22,42,45,74,129,167,176,181,221,224,241,242,248,249,250,294,303,304,324,336,351,366,394,484,489,496,509,511,513],exactli:[3,6,12,14,17,38,42,43,57,61,74,75,96,123,151,157,164,173,193,205,206,216,221,227,232,236,241,248,249,250,265,277,278,286,290,298,324,329,330,343,381,394,401,405,411,414,428,436,464,484,485,492,496,509],exager:503,examin:[6,8,17,224,290],examp:[480,509],exampl:[],exce:[3,6,16,17,18,42,60,74,175,212,213,216,217,218,219,221,225,227,232,237,264,290,305,309,315,316,324,374,381,482,509],exceed:[3,42,61,221,227,264,324,490],excel:407,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,74,94,95,115,116,119,124,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,173,177,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,201,204,207,213,214,216,220,221,225,227,234,239,240,243,246,248,250,264,265,266,267,268,269,270,271,272,273,274,277,278,281,283,284,285,286,287,291,300,301,308,310,311,321,324,327,329,330,336,340,344,347,348,349,350,351,352,353,355,356,359,360,361,366,367,369,371,375,376,377,379,380,381,382,383,385,388,389,390,391,392,393,394,395,396,397,399,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,432,437,438,439,441,444,445,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,479,480,482,484,485,487,490,491,492,493,494,496,500,503,508,509,510,512],excess:[215,407],exchang:[2,3,6,8,63,64,204,210,211,240,248,300,308,332,336,339,366,381,407,497],exchange:366,excit:407,exclud:[3,6,9,12,16,17,65,74,119,147,153,160,161,177,197,213,217,222,223,252,260,293,306,308,331,342,347,374,375,377,389,411,414,417,428,429,436,461,494],exclus:[1,3,12,16,92,381,396,434,436,491,501],excurs:[264,477],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,174,200,245,302,349,365,368,380,478,480,490,493,496,509],exempl:452,exemplari:241,exemplifi:407,exert:[6,246,249,303,343,344,345,367],exhaust:[210,380,509],exhibit:[97,264,373,407,491],exist:[3,6,7,8,11,12,13,16,37,56,61,70,73,129,173,174,192,199,200,201,204,209,220,223,225,228,240,293,294,296,347,348,350,352,353,354,356,360,370,375,381,402,403,414,444,461,471,478,480,482,483,484,493,494,495,504,509,510,511],exit:[2,3,11,12,42,59,197,221,236,365,380,480,481,490,499,509],exlanatori:3,exp:[],expand:[],expans:[12,147,197,493,509],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,74,108,154,165,171,193,221,233,240,242,261,289,295,297,298,303,308,347,367,377,394,431,434,436,477,480,482,484,487,491,496,509],expens:[6,74,201,289,293,308,336,347,366,367,377,381,480],experi:[6,13,15,17,220,228,245,254,263,295,307,308,372,376,401,436,491,496],experienc:[6,12,253,254],experiment:[240,366,381,496],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,72,74,75,76,79,80,82,91,98,153,161,193,197,198,200,201,204,213,214,219,221,223,225,227,264,289,297,308,321,347,349,365,366,369,375,376,380,386,405,417,452,454,469,480,483,484,487,489,492,503,504,509,513],explan:[3,6,61,120,147,197,198,213,263,289,414,476,479,480,482,491],explanatori:[3,8,124,197,198,212,213,216,217,218,308,375,479,509],explantori:[3,304],explic:435,explicit:[6,9,11,22,45,80,92,120,123,167,181,205,206,227,315,316,351,371,383,384,387,392,394,405,407,418,428,468,476,479,483,486,504],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,74,116,119,150,160,163,171,173,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,217,220,227,234,239,241,243,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,297,298,300,308,310,311,327,329,330,336,340,344,350,352,353,355,356,359,361,375,381,382,383,385,388,389,390,391,392,393,394,395,396,397,398,400,401,404,405,406,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,432,434,436,437,438,439,441,446,447,454,455,456,457,458,459,460,462,463,464,465,466,467,468,470,472,473,474,482,484,485,491,492,494,495,501,503,504],explictli:[16,495],exploit:[15,17,291],explor:[125,172],expon:[3,299,301,405,410,413,427,435,447],exponenti:[92,442,463,470,474,496,509],expos:11,exposit:[210,401,404],express:[6,147,159,173,205,206,225,261,289,299,336,342,349,387,405,407,421,431,452,453,462,509],expressiont:387,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,71,87,88,89,92,93,96,100,103,104,114,116,124,126,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,198,204,207,208,211,219,220,226,229,233,238,239,240,242,243,244,246,248,250,262,264,269,278,289,290,306,307,308,310,313,318,321,323,327,328,329,330,331,333,334,336,338,341,345,346,410,431,434,445,446,453,499,500],extent:[1,3,42,43,46,59,74,171,175,197,209,217,221,246,343,346,366,369,383,448,450,464,479,482,485],exterior:[3,6,171,345],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,74,108,116,117,119,125,148,150,151,152,154,156,159,160,161,162,163,165,166,172,173,174,175,179,201,216,221,223,264,296,297,298,308,324,374,375,378,379,400,411,414,417,431,436,479,480,482,485,494,503,509],extract:[3,6,11,13,36,65,71,92,114,122,124,126,205,206,301,376,397,408,431,453,480,487,499],extract_atom:11,extract_comput:[11,480],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,200,215,225,227,264,334,407,466,503],extrema:427,extrins:210,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[169,338],f_a:[465,466,467],f_ave:124,f_c:466,f_f:467,f_fix_id:298,f_foo:509,f_harm:334,f_i:[29,442],f_id:[6,74,124,126,197,198,204,212,213,214,215,216,217,218,219,259,326,338,500,509],f_ij:442,f_indent:219,f_int:333,f_j:29,f_jj:96,f_k:442,f_langevin:336,f_max:[298,303],f_msst:262,f_r:[249,465,466,467],f_sigma:387,f_solid:334,f_ss:6,f_temp:[],face:[3,6,59,61,74,161,171,175,209,217,218,341,343,344,345,346,369,410,431,446,482,485],face_threshold:171,facet:171,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,242,294,324,334,411,452,494],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,75,92,96,108,115,122,123,125,147,167,172,175,179,190,196,197,200,201,205,206,214,221,225,227,228,240,245,248,250,251,262,264,265,269,291,295,299,307,311,314,316,324,328,332,339,340,341,345,356,367,369,375,381,383,384,387,388,390,392,397,398,399,401,402,403,407,411,414,418,419,431,434,436,438,439,445,447,454,463,468,479,482,485,486,491,494,496,497,500,503,508,509],factori:[3,480],factoriz:366,fail:[3,9,11,12,61,177,225,228,366,374,376,399,445,480],failur:[128,449,481,509],fairli:[11,436,491,496,504],faken:76,falcon:245,fall:[3,6,201,216,294,480,509],fals:[91,347,349,452,509],fame:8,famili:[470,479],familiar:[0,11,504],fan:442,far:[3,6,12,17,59,61,63,91,197,198,201,202,221,222,223,225,228,264,289,307,308,324,341,352,356,372,376,377,469,480,482,487,500],farago:248,farrel:[465,467],farther:197,fashion:[6,8,42,74,173,201,204,205,206,211,217,221,223,228,240,242,246,261,262,264,266,267,268,269,270,271,272,280,283,284,285,286,287,297,298,300,308,313,317,323,326,334,336,340,341,342,344,346,376,414,428,485,494,509,512],fasolino:416,fast:[6,7,9,12,13,17,40,197,198,275,298,337,366,367,389,428,429,434,462,464,484,489,491,500,510,513],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,111,116,119,150,160,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,220,221,227,234,239,243,247,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,295,299,300,308,310,311,324,327,329,331,333,336,340,344,350,352,353,355,356,359,361,366,367,378,379,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,400,401,405,406,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,432,437,438,439,441,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,485,491,495,503],fastest:[1,6,14,17,161,217,336,337,381,479],fatal:[3,499],fault:[73,445],faulti:12,fava:410,favor:224,favorit:7,fbmc:331,fcc:[],fcm:[280,509],fdirect:231,fdotr:415,fdt:[],fdti:92,fe2:172,fe3:172,fe_md_boundari:210,featu:8,featur:[],fecr:405,feedback:[7,245],feel:[7,245,246,254,289,345,347,376,436],felling:433,felt:345,femtosecond:508,fene:[],fennel:[397,419],fep:[],ferguson:[6,179,494],fermi:[1,9,10,12,15,159,381,467],fermion:407,fernando:430,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,202,212,213,214,216,217,218,219,249,264,294,297,299,311,338,366,374,375,376,383,452,479,482,487,491,493,501,511],fewer:[1,3,11,15,16,63,254,491],fewest:3,fextern:238,feynman:291,fff:480,ffield:[396,408,444,445,452],ffmpeg:[3,12,200],ffplai:200,fft:[1,3,7,9,11,12,14,15,93,116,117,148,290,366,367,491],fft_inc:[12,367],fft_lib:12,fft_path:12,fftbench:[366,501],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:461,fictiti:[6,207,208,233,238,242,291,307,397,419,423,461],field1:[483,487],field2:483,field:[],fifth:[321,438],figur:[1,3,8,12,298,479,480,504],fij:400,file0:289,file1:[11,13,289,335,349,375,487,489,493],file2:[11,13,335,349,375,487,489,493],file:[],file_from:199,filen:375,filenam:[3,12,13,38,42,57,193,197,198,200,201,202,210,213,214,215,216,217,218,219,221,226,236,289,293,296,299,300,301,304,305,308,309,335,336,363,364,365,375,376,382,383,387,397,405,406,408,416,431,432,433,438,442,443,444,445,452,453,463,464,465,466,467,470,478,479,480,483,484,489,493,500,509,511,512,513],filennam:489,filep:[3,197,198,201,484,489,513],filepo:305,fill:[7,9,173,200,294,336,369,377,387,434,445,485,504],filter:[201,210],final_integr:8,final_integrate_respa:8,finchham:[6,155,399],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,74,76,92,124,176,193,202,211,224,225,236,237,240,263,289,294,295,303,307,372,374,376,377,397,414,419,423,431,452,462,464,503,504,509],find_custom:8,fine:[16,17,177,207,233,334,377,381,504,509],finer:[147,173,509],finest:366,finger:[173,196,261,485],finish:[6,11,42,221,349,363,365,366,378,380,381,469,487,509,510],finit:[],finni:[7,405,462],finvers:231,fiorin:[9,226],fire:[],firebrick:201,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,74,84,93,96,109,110,111,113,119,123,124,134,137,140,141,145,148,158,161,167,169,171,172,174,175,176,180,193,197,198,199,200,201,202,204,205,213,214,216,217,218,219,221,224,227,236,240,241,246,251,261,262,263,264,289,291,296,297,298,300,305,308,311,313,321,322,324,325,326,333,334,335,336,338,342,347,349,350,357,369,374,375,376,377,380,381,382,383,386,387,388,390,392,394,396,397,405,407,408,411,412,414,415,416,417,418,419,423,428,429,431,433,434,436,438,442,444,445,452,453,461,463,464,465,466,467,470,474,477,478,479,480,482,483,484,487,489,491,494,495,496,499,500,503,504,509,510,511,513],fischer:[6,9,19,20,179,392,494],fit:[3,6,9,12,38,57,193,236,307,324,383,387,416,431,436,457,464,466,490,504,509],five:[76,159,298,375,387,432,482,496],fix:[],fix_adapt:[167,206,427],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,211,294],fix_eo:9,fix_evapor:211,fix_flux:210,fix_gcmc:[211,375],fix_gl:242,fix_gld:242,fix_grav:294,fix_id:[3,225,262,264,266,267,268,269,270,271,272,295,298],fix_manifoldforc:504,fix_modifi:[],fix_mov:[196,342],fix_nh:8,fix_npt:242,fix_nv:504,fix_nvt:[211,240],fix_poem:[3,6,9],fix_pour:[3,228],fix_qbmsst:9,fix_qeq:[3,396],fix_rattl:311,fix_reax_bond:444,fix_rigid:[254,386],fix_saed_vtk:309,fix_setforc:8,fix_shak:311,fix_shardlow:9,fix_srd:3,fix_styl:269,fix_temp_rescal:330,fixedpoint:[225,264],fixextern:238,fixid:210,fji:400,flag1:[230,379],flag2:[230,379],flag:[3,8,9,11,12,14,15,16,17,41,68,77,78,84,91,94,95,99,109,110,112,125,168,172,176,197,198,200,201,202,219,224,226,230,245,248,252,254,260,261,290,297,308,321,323,324,331,335,344,347,364,367,375,379,380,381,383,413,418,431,434,461,477,479,480,482,483,484,486,487,488,492,504,509],flag_buck:391,flag_coul:[391,400,423],flag_lj:[400,423],flagfld:[389,428,429],flaghi:[3,389,428,429],flaglog:[389,428,429],flagn:230,flagvf:[389,428,429],flat:[6,336,341,342,346],flavor:[2,7,12],fld:[],flen:384,flex_press:384,flexibl:[3,6,8,174,200,213,217,226,242,265,332,339,407,466,500],flip:[3,6,227,264,343,344],floor:509,flop:12,floralwhit:201,flow:[],fluctuat:[6,66,92,225,240,241,248,251,264,269,289,290,312,334,336,359,403],fluid:[],fluid_veloc:255,flush:[3,201,499],flux:[],flv:200,fly:[7,9,12,42,200,204,210,215,228,231,308,311,337,387,434,500,503],fmackai:9,fmag:229,fmass:291,fmax:[374,500],fmomentum:231,fmsec:[2,201,248,249,261,264,295,308,327,328,491,502,508,510],fname:365,fno:[9,12,16],fnorm:[374,500],fnpt:231,fnvt:231,foce:414,fock:384,focu:311,fogarti:[9,301,445],foil:[147,289,453],fold:[322,491],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,73,74,76,85,96,97,102,103,113,120,123,124,126,147,148,151,152,153,159,161,166,169,171,173,174,179,182,183,184,185,187,188,190,191,193,197,199,200,201,204,210,211,212,213,214,215,216,217,218,219,221,226,227,228,231,232,235,236,238,240,241,242,245,247,248,249,251,254,262,264,269,270,271,272,283,284,285,287,290,291,293,296,297,298,299,301,303,305,307,308,309,311,326,327,328,329,332,333,334,335,336,338,339,347,348,352,353,354,355,356,359,361,364,369,371,374,375,376,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,441,442,443,444,445,446,447,449,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,479,480,482,483,485,487,489,490,491,494,496,497,498,503,504,509,510,512],foo:[4,8,11,12,197,200,238,480,493,509],foot:6,footprint:[12,381],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:254,forcefield:[307,413],forcegroup:251,forcezero:372,ford:400,forestgreen:201,forev:74,forget:[249,503],forgiv:264,fork:[],form:[2,3,6,8,12,19,22,45,55,65,68,77,78,80,84,92,94,95,97,99,109,110,112,123,147,148,167,168,177,181,201,204,205,206,223,241,242,248,250,254,261,285,290,301,303,307,308,336,341,345,350,351,354,359,371,373,375,376,383,384,387,394,402,403,405,407,409,413,414,418,430,431,433,434,438,439,442,444,445,446,452,453,454,462,464,465,466,467,473,476,479,480,482,487,492,499,503,509],formal:[6,81,83,96,241,242,248,264,291,324,332,452],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,80,181,193,197,198,199,200,201,202,213,216,217,218,219,221,223,236,290,293,297,299,301,304,308,309,320,335,336,347,348,351,371,375,376,382,383,387,394,405,408,418,431,433,443,444,445,447,453,464,470,471,479,480,482,483,484,487,498,499,500,509,511],former:[6,12,16,40,42,201,221,336,340,387,389,488,494,509],formerli:[7,13],formul:[1,9,41,66,148,207,233,248,264,285,299,301,307,311,335,366,383,387,405,407,410,431,441],formula:[2,3,6,7,13,21,22,37,45,55,56,73,76,92,94,95,96,100,102,103,112,119,125,126,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,172,173,178,180,181,192,196,197,205,206,207,208,213,214,215,216,219,220,227,233,243,244,246,248,249,261,289,290,296,305,310,318,322,324,327,328,329,338,341,344,346,347,349,350,351,353,360,369,375,383,384,386,387,392,393,394,395,400,401,405,406,410,411,412,413,415,418,419,421,422,423,425,426,428,429,431,435,436,437,446,447,454,462,463,464,465,466,467,470,472,473,478,482,485,492,499,500,508,509,510],forth:[1,6,11,12,13,14,15,380,480,485,489],fortran:[3,6,9,11,12,13,238,405,414,431,444,445],fortun:8,forward:[3,8,92,365,376,381],foster:[387,441,442],foul:176,found:[3,6,9,12,76,167,197,224,226,240,245,251,290,331,337,349,365,377,394,397,400,477,483,484,499],four:[6,11,55,84,109,110,147,169,262,336,359,375,376,434,477],fourier:[],fourth:[6,111,307,321,331,392,438,452],fox:[6,125,179,460,494],fphi:[38,57,464],fpic:12,fplo:[38,57,464],fprime:464,fqdn:247,fqq:400,frac:[],fraction:[1,3,6,8,12,16,40,42,83,116,148,176,196,200,201,211,222,223,224,225,262,294,298,305,306,324,329,330,369,376,381,387,389,411,428,429,487,492],fragment:[43,245,305],fraig:43,frame:[88,147,201,210,262,298,343,410],framer:[200,201],framework:[5,242,382,453],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,73,92,167,205,206,289,324,333,334,335,336,373,376,384,407,427,434,442,473,479],freedom:[3,6,8,100,102,103,105,107,108,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,213,224,231,240,242,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,308,311,327,328,329,334,374,400,500,503,510],freeli:[0,6,7,12,151,152,166,171,200],freez:[],frenkel:[240,334],freq:209,frequenc:[3,6,16,40,109,201,215,278,290,291,298,303,364,401,407,445,452,477,491,496,509,512],frequent:[3,66,69,73,75,76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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.USER-CUDA package","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_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/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/local command","compute dilatation/atom 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/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 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 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/spatial command","fix ave/spatial/sphere 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 deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table 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 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/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body 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 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/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","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/conservative 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 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 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 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","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":222,"default":[37,40,41,56,59,60,61,63,64,71,74,92,93,97,108,109,111,113,114,125,129,130,147,153,161,162,166,172,173,176,178,192,195,196,197,198,200,201,202,203,205,206,207,209,210,211,213,217,218,219,222,223,225,226,227,228,232,237,240,241,246,248,249,250,251,252,254,259,262,264,265,269,285,286,290,291,294,295,296,297,298,300,303,305,306,308,309,324,326,331,332,333,334,337,339,341,343,347,360,364,366,367,369,370,372,373,375,377,378,379,381,384,387,389,407,428,429,434,436,444,445,461,462,477,478,479,482,483,485,487,489,490,491,494,496,498,499,500,501,502,508,510,511,512],"function":509,"long":[215,388,390,391,392,393,397,399,400,419,423,427,439,447,468],"new":8,"static":12,acceler:1,account:504,ackland:66,acknowledg:7,adapt:[205,206],addforc:207,addit:[12,13,504],addtorqu:208,adiabat:6,adjust_dt:314,adp:382,after:504,airebo:383,alloi:405,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:209,arrai:6,aspher:[6,9,87,151,266,270,274,275,283],atc:[9,210],atom:[6,7,8,66,69,73,74,75,76,79,80,81,83,84,86,90,97,101,102,105,106,107,113,117,118,120,147,148,171,209,211,212,297,509],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:220,awpmd:[9,384],balanc:[42,221],barostat:6,basal:69,beck:385,berendsen:[295,327],between:6,binary2txt:13,bodi:[6,8,9,43,70,152,267,271,276,284,386],bond:[8,13,71,72,222,223,224,304],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:387,born:[388,399],boundari:[7,59],box:[6,60,225],branch:504,brownian:389,buck:[390,391,399,430],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:73,ch2lmp:13,chain:13,chang:504,change_box:61,charmm:[6,20,179,392,427],chunk:[6,68,74,78,95,99,110,112,121,153,168,170,213],citat:7,class2:[9,21,44,180,350,393],clear:62,cluster:75,cmm:9,cna:76,code:6,coeffici:6,colloid:[9,341,395,473],colvar:[9,13,226],com:[77,78,154],comb3:396,comb:[300,396],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,509],compute_modifi:108,condit:7,conduct:[6,332],conserv:402,constant:[6,509],constraint:7,contact:[79,127],contact_radiu:[],coord:80,core:6,coreshel:9,correl:[214,215],cosin:[23,24,25,26,27,28,182],cossq:352,coul:[388,390,391,392,393,397,398,399,412,419,423,427,439,447],coupl:6,creat:223,create_atom:173,create_bond:174,create_box:175,createatom:13,creation:7,csld:328,csvr:328,cubic:421,cuda:[9,14,116,119,150,160,207,220,234,239,243,264,273,310,311,327,329,340,388,390,392,393,405,411,412,419,420,422,425,437,463,465],custom:[8,197,198],cut:[50,384,390,393,397,400,407,409,419,420,427,435,439,468],cvff:353,damag:[81,128],data2xmovi:13,data:6,databas:13,deby:[397,419],dec:[],defgrad:134,deform:[156,157,227],delete_atom:176,delete_bond:177,delta:24,deposit:228,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],diagnost:7,diel:398,dielectr:178,diffract:9,diffus:6,dihedr:[8,82],dihedral_coeff:181,dihedral_styl:[2,179,180,182,183,184,185,186,187,188,189,190,191,192,193,194],dilat:83,dimens:195,dipol:[6,9,29,400],direct:231,directori:4,discuss:6,disp:6,displac:[84,91],displace_atom:196,distanc:354,distribut:[7,12],document:0,dpd:[9,85,86,401,402,403],drag:229,dreid:[6,413],drude:[6,9,158,230,231,249],dsf:[397,419],dsmc:404,dump:[6,8,197,198,199,200,202],dump_modifi:201,dynam:299,eam:[13,405],echo:203,edip:406,eff:[9,13,102,103,157,159,164,250,265,277,286,330,407],efield:233,eim:408,elast:6,emac:13,energi:[130,403],enforce2d:234,ensembl:7,erot:[87,88,89,90],error:[3,129],evapor:237,event:91,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],exp:[27,182],expand:[47,422],extend:[8,11],extern:238,fcc:289,fdt:403,featur:[7,8,504,509],feb:[],fene:[46,47],fep:[9,13,92,206],field:[6,7],file:6,finit:6,fire:299,fix:[2,6,8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,2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6,8,11,14,18,40,41,42,221,381,406,491,496],advect:[3,6,324],advertis:8,advis:[376,443],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,74,93,124,148,157,171,177,200,201,206,213,214,216,217,218,219,222,223,224,225,227,228,238,244,246,248,254,261,265,266,267,268,270,271,272,278,283,284,285,287,308,309,322,336,346,359,366,372,373,374,376,377,378,381,407,428,429,436,479,480,482,484,485,487,490,492],affin:[16,17,18,227,381,396],afil:242,aforement:18,afresh:[296,490,509],afshar:401,after:[],afterrun:490,afterward:3,afterword:42,ag1:172,ag2:172,again:[6,11,12,16,17,64,147,153,159,167,197,201,227,244,294,350,365,376,428,429,477,479,480,482,484,489,496,498,509,511],against:[11,12,13,66,228,376,444,445],aggreg:[6,12,67,70,72,82,98,115,122,244,260,306,308,322,477,510],aggress:[244,496],agilio:[9,13],agre:[3,8,193,374,383,416,445],agreement:[5,7],ahd:413,ahead:343,aidan:[0,5,7,9,13,369],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:200,akohlmei:[7,9,13,202,245],aktulga:[7,9,301,445],al2o3:452,al2o3_001:[125,309],al3:172,ala:[251,452],alain:9,alat:[289,431],alb:[442,465,467],albeit:307,albert:9,alchem:[92,167],alcohol:339,alcu:[382,387],alcu_eam:442,alderton:400,alejandr:[264,265],alessandro:13,algebra:434,algorithm:[0,1,6,7,8,9,42,63,201,210,221,224,227,251,253,254,278,291,299,308,311,312,331,332,336,339,344,372,373,374,378,381,403,407,429,434,449,451,477,479,496],alia:[9,12,16],alias:[1,367],aliceblu:201,align:[6,9,12,29,42,74,175,193,217,221,246,369,482,485,503],alkali:407,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,166,167,168,169,170,171,172,173,174,175,176,177,179,181,186,192,193,194,197,198,199,200,201,202,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,257,259,260,262,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,284,285,286,287,288,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,320,321,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,349,350,351,355,360,362,364,365,366,367,368,369,371,374,375,376,377,378,380,381,382,383,384,386,387,388,390,391,392,393,394,396,397,400,401,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,497,499,500,501,503,504,508,509,510,511,512,513],allen:[29,92,400,410],allentildeslei:92,allign:3,allindex:348,alloc:[3,5,6,8,9,11,12,62,238,338,375,377,381,440,445,482,490],allocat:3,alloi:[],allosw:74,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,80,97,113,115,149,151,152,153,166,171,172,173,175,181,192,193,197,198,200,201,202,204,205,207,209,210,211,213,214,215,216,217,218,219,221,223,224,225,226,227,228,232,233,238,240,241,242,243,245,248,251,254,255,259,261,264,265,289,293,294,295,296,297,298,302,308,309,311,313,315,316,320,324,331,332,333,334,336,337,338,339,340,341,347,349,351,360,366,367,369,374,375,376,377,380,381,383,384,387,388,389,390,391,392,397,405,407,411,412,413,414,419,423,428,429,434,436,442,445,446,449,451,452,461,468,471,473,477,480,482,484,485,486,487,488,489,492,494,495,496,499,500,504,509,510],almost:[2,3,12,62,246,298,336,367,378,381,461],alo:397,alon:[6,7,224,304,444,445,480],alond:13,along:[6,8,12,29,41,74,92,125,171,172,173,196,197,200,213,224,246,251,252,256,261,263,298,308,311,313,317,321,322,331,335,336,342,345,347,369,372,373,374,376,397,400,411,414,417,419,423,431,444,445,464,482,485,492,493,509],alonso:[432,433],alpha:[6,12,52,205,251,290,298,299,303,374,382,385,388,397,401,403,405,406,408,413,418,419,431,437,441,466,468,500,503],alpha_:[],alpha_c:427,alpha_i:453,alpha_ialpha_j:[],alpha_lj:427,alphabet:[2,3,22,37,45,56,65,181,192,204,351,360,375,394,462,482],alphanumer:[3,65,204,297,305,349,375,509],alreadi:[3,7,8,9,12,16,17,18,43,173,174,176,199,209,213,217,218,221,223,227,255,296,298,324,347,348,375,376,401,412,414,421,429,461,471,474,478,482,483,487,492,508,509],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,74,75,76,78,80,84,92,94,95,97,99,109,110,111,112,113,114,119,121,123,124,126,147,148,149,150,151,152,153,154,155,156,157,159,160,161,162,163,165,166,167,168,169,170,173,174,175,176,177,179,181,192,193,195,196,197,198,199,200,201,202,204,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201],choic:[3,6,9,12,15,16,18,41,42,55,92,148,151,152,166,177,193,213,217,218,221,224,227,228,242,248,251,262,264,291,299,308,331,360,367,372,373,376,378,381,414,427,436,440,482,491,492,495,496,502,503,508],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,92,124,163,164,200,222,223,224,225,228,237,248,251,262,264,266,267,268,269,270,271,272,294,295,312,324,328,342,366,367,373,471,477,479,491,497],chose:[465,467],chosen:[2,3,6,12,17,147,173,176,185,193,200,206,211,225,228,237,240,241,249,251,262,264,269,291,294,305,324,328,331,332,337,339,340,346,367,368,373,381,402,403,407,411,418,421,447,465,477,491,496,503],chri:171,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,78,95,99,110,112,121,153,168,170,213],chute:[4,9,10,243],ciccotti:311,cieplak:[6,179,494],cii:214,cij:214,ciko:2,circl:[43,74,320],circular:[3,6,151,195],circumst:18,circumv:[97,113,303],citat:[],cite:[3,7,8,12,248,452],civ:9,ckio:2,cko:2,cl1:172,clarendon:[29,400],clarifi:[7,465,467],clariti:349,clark:439,class2:[],classic:[0,3,5,6,7,8,9,238,291,298,303,336,361,407],classifi:[462,470],claus:480,clean:[6,12,14,15,17,490],cleanli:[481,512],clear:[],clearli:7,clebsch:147,clermont:[9,13],clever:486,click:[2,11,22,37,45,56,173,181,192,200,245,351,360,376,394,462,504],client:[245,247],climb:[263,376,496],clinic:[7,13],clo:[162,196,510],clock:[12,477,496],clockwis:342,clone:504,close:[3,6,11,12,13,40,42,69,74,148,176,197,223,224,225,242,249,251,264,285,308,311,342,345,365,367,370,372,373,376,381,383,387,397,398,417,431,436,448,450,464,467,486,492,503,504,506],closer:[3,10,42,123,171,196,197,221,225,229,333,376],closest:[223,289,308,339,410,446,461,471],cloud:[452,503],clovertown:18,clsuter:75,clump1:[293,308],clump2:[293,308],clump3:[293,308],clump:308,cluster:[],clutter:3,cmap:482,cmatrix:242,cmax:431,cmd:[11,12,291,493],cmdarg:11,cmin:431,cmm:[],cmoput:140,cn1:214,cn2:214,cna:[],cnn:214,cnr:[9,13],cnt:[414,486],co2:[41,172,311,375],coars:[7,9,10,29,36,41,55,185,293,308,324,412,447,491,494],coarser:[367,509],coarsest:147,code:[],coeff:[3,7,8,12,21,22,33,45,51,179,180,181,186,350,351,357,394,414,418,436,449,451,454,482],coeffcient:482,coeffici:[],coefficienct:401,coefficient0:405,coefficient1:405,coeffieci:[6,385,417],coeffincientn:405,coexist:[240,407],cohes:[6,408,431],coincid:[129,345,392,428,429,477],colberg:199,cold:[6,158,240,244,377,503],coldest:332,coleman8:9,coleman:[9,125,172,309],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,78,88,95,99,104,110,112,121,153,161,168,170,173,197,198,201,213,226,254,260,293,303,306,308,347,366,375,377,395,482,489,495,501,513],collid:[232,324,346],colliex:172,collinear:[3,293],collis:[3,251,324,342,346,404,411,474],colllis:324,colloid:[],colombo:40,colon:[202,347,483],color1:201,color2:201,color:[3,9,42,197,200,201,221,241,298,303],column:[3,6,9,12,13,43,65,67,68,69,70,72,74,78,80,82,84,86,95,97,98,99,110,112,113,115,117,120,121,122,123,124,126,147,148,153,161,168,170,171,172,193,197,198,201,204,212,213,214,216,217,218,219,254,261,262,298,308,325,326,336,346,409,413,444,445,483,497,499,509],columnar:171,colvar:[],colvarmodul:12,com:[],comamnd:227,comand:224,comannd:381,comb3:[],comb:[],comb_1:300,comb_2:300,combiant:398,combin:[3,6,7,9,11,13,36,41,65,67,72,82,92,98,109,115,122,151,152,166,197,200,210,216,245,254,264,291,297,312,328,337,345,348,350,366,367,369,373,381,395,397,398,403,407,408,414,426,427,453,463,465,467,468,470,473,485,490,495,503,509],come:[],comfort:[12,13],comit:504,comm:[0,3,11,12,63,76,199,245,247,248,367,376,381,401,436,441,464,484],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,179,193,197,236,249,308,336,375,376,382,405,406,408,418,431,438,445,452,453,463,464,465,466,467,470,479,480,482,503,504,509],commerci:7,commit:[9,504],commmand:[3,6,12,61,114,286,417,476,477,479,496,512],common:[],commonli:[3,6,9,12,17,25,59,61,111,113,175,197,200,202,361,412,421,453,465,467,482,485,494],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,74,171,176,177,200,201,221,222,223,225,226,227,245,247,251,253,254,255,264,290,297,299,300,301,308,312,324,336,347,364,366,377,378,379,381,403,404,440,475,479,480,491,492,509,511,513],communc:366,comp:[7,199,247,248,311,367,376,407,436,441,446,460,464,466],compact:[65,204,394,462],compani:[5,7],compar:[1,3,4,6,8,12,17,40,91,117,125,156,172,181,192,201,231,299,347,349,366,367,374,376,431,452,477,496,497,503,508],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,180,181,192,350,351,360,393,462],compat:[3,5,7,8,9,11,12,13,17,18,42,74,124,126,184,197,202,206,212,213,214,216,217,218,219,221,290,302,328,331,338,341,344,366,381,415,434,436,464,479,480,509],compens:[6,222,223,306,377,407],compet:335,competit:367,compil:[3,7,8,9,12,13,14,15,16,17,18,19,171,197,199,200,202,245,335,367,381,434,482,483,487,509],compl:17,complain:[11,12,17],complement:431,complementari:[7,397,419],complet:[3,6,9,11,12,15,42,61,74,201,217,221,226,254,291,294,297,324,335,337,348,349,365,376,381,408,449,451,469,477,482,487,490,494,496,499,503,509],complex:[4,6,8,11,12,13,25,41,43,64,97,113,147,149,161,173,174,251,320,345,364,376,407,434,464,480,482,485,509],compli:[331,335],complic:[6,7,9,12,13,211,240,480],complier:12,compon:[3,6,8,12,63,65,68,69,76,84,93,94,95,96,97,99,100,103,110,111,112,113,114,115,116,117,119,120,124,134,137,138,139,140,143,144,145,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,168,169,170,196,197,198,200,201,207,208,212,213,214,215,216,217,218,219,220,224,225,227,228,233,238,243,247,248,251,254,256,260,261,263,264,265,269,270,271,272,283,284,285,287,288,290,291,292,295,306,308,310,311,313,317,318,321,324,327,328,329,331,338,339,344,345,346,366,369,373,374,375,376,381,401,407,411,428,429,449,451,452,453,482,483,492,500,509,510],componenet:6,composit:[6,211,251,405],compound:[396,407,408,470],compres:[74,121,213],compress:[],compris:[41,345,446,469],compton:[125,172],comptu:3,compuat:367,comput:[],computation:[3,6,222,223,336,387],computational:503,compute_arrai:8,compute_fep:[206,427],compute_group_group:240,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[125,309],compute_scalar:8,compute_temp:8,compute_ti:206,compute_vector:8,compute_xrd:172,concaten:[2,3,512],concav:345,concentr:[74,405],concept:[6,153,163,213,491],conceptu:[3,6,74,161,225,227,376,397,414,431,487],concern:[6,76,92,199,241],concetr:74,concis:[11,335],conclud:12,concret:8,concurr:[16,367,509],conden:[336,465,467],condens:[6,155,336,383,399,405,419,470],condit:[],conducit:6,conduct:[],cone:485,confer:434,confid:[3,496],config:[12,197,479],configfil:226,configur:[1,2,6,12,15,17,38,61,129,175,193,196,197,200,204,225,226,227,228,232,240,247,248,278,291,299,335,364,374,376,383,387,406,431,434,463,465,467,470,477,482,484,485,496,504],confin:[482,496],conflict:[3,12,41,198,436,480,504],conform:[3,6,13,61,224,225,263,307,313,335,359,376,407,494],confus:[3,470],conjuct:[9,401],conjug:[7,8,248,373,407,444,445],conjunct:[6,7,74,91,92,121,156,161,167,173,177,201,205,206,248,251,255,278,294,295,299,300,301,303,308,312,324,332,339,344,366,367,376,388,390,394,397,401,407,413,419,436,439,447,468,482,485,489,503,513],connect:[3,6,9,92,158,176,224,245,293,308,311,321,376,398,411,461,467,479,480,482,486,503],conner:383,connor:383,conput:3,consecut:[3,11,12,40,74,173,201,205,206,228,245,246,397,419,423,477,483,485],consequ:[1,6,211,336,418,496],conserv:[],consid:[6,73,74,81,92,122,155,158,159,176,197,198,201,205,206,212,214,217,221,223,224,228,252,265,290,308,331,332,335,336,339,367,394,407,414,445,446,452,461,477,478,480,483,484,485,487,490,492,500,503,509],consider:[6,8,248,249,327,328,329,381,491],consist:[3,6,8,9,11,12,41,43,67,72,82,98,110,115,118,119,122,153,156,158,173,185,196,202,207,208,213,227,228,231,233,238,241,248,249,250,261,264,266,267,268,269,270,271,272,273,274,276,277,278,279,281,282,283,284,285,286,287,295,298,303,305,307,308,327,328,329,330,340,366,367,369,375,376,381,383,387,389,395,397,407,410,414,417,428,429,431,434,436,446,449,451,452,464,471,480,482,483,484,485,486,487,494,503,509],consistent_fe_initi:210,consit:308,constant:[],constitu:[3,6,254,308,341,345,395,446],constitut:[449,451],constrain:[3,6,8,150,151,152,153,154,156,159,160,161,162,163,165,166,204,213,228,240,241,246,254,258,293,294,306,308,311,322,332,339,374,375,407,487,494,503],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,73,75,76,80,97,113,125,147,172,225,264,290,307,345,377,381,400,434,436,461,463,464,485,486,501,509],constructor:[8,11],consult:445,consum:[1,303,440,509],consumpt:364,contact:[],contact_stiff:[448,450],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,92,96,123,125,147,149,153,161,171,172,173,175,179,181,192,193,197,198,200,201,202,204,205,206,210,212,213,214,216,217,218,219,221,226,228,233,236,242,246,247,248,251,262,278,289,290,293,294,296,298,301,305,308,309,314,324,331,335,336,345,346,349,365,367,375,376,379,380,382,383,384,387,396,397,400,405,406,407,414,415,431,434,438,442,443,444,445,453,463,464,465,466,467,468,470,477,478,479,480,482,483,484,485,487,489,491,494,496,497,499,500,503,504,509,511,513],content:[4,8,9,12,18,445,498,500],context:[3,6,8,12,17,123,124,201,222,223,228,293,305,340,373,473,482,489,498,508,509,510],contibut:73,contigu:479,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,74,84,109,110,169,201,204,205,206,211,213,214,215,216,217,218,219,221,224,225,226,227,228,240,241,242,244,245,246,248,249,250,256,261,262,264,266,267,268,269,270,271,272,283,284,285,286,287,292,294,297,298,308,309,313,323,324,326,333,334,336,342,345,349,365,380,381,387,401,404,421,424,444,445,446,449,451,466,477,480,482,484,485,490,496,497,499,500,509,511],continuum:[6,7,9,210,336,449,451],contour_integr:210,contract:[61,225,227,264,295,308],contradictori:3,contrain:311,contraint:278,contrari:[242,249],contrast:[1,6,43,56,66,155,158,198,227,347,449,451,473,512],contrib:336,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,71,73,74,77,78,80,83,89,92,93,94,95,96,99,108,110,112,114,115,116,117,119,121,124,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,206,211,212,213,214,216,217,218,219,225,240,248,251,254,255,259,265,285,286,293,294,302,305,308,309,311,338,366,374,376,384,401,404,405,407,414,428,429,434,436,444,445,452,494,500,503,504],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,92,96,129,147,182,197,198,200,204,210,211,221,225,226,227,244,245,248,249,264,266,267,268,269,270,271,272,295,300,308,315,316,327,328,329,336,340,364,366,378,407,410,434,444,445,448,450,463,467,477,479,491,497,498],control_typ:210,controlfil:445,convect:96,conveni:[6,12,29,197,202,219,309,369,453,468,504,509],convent:[3,8,29,184,191,192,198,201,307,321,348,405,407,509],converg:[3,6,42,93,197,198,200,202,207,221,224,225,233,238,269,298,300,303,307,311,372,373,374,376,396,397,419,452,477,489,496],convers:[3,8,147,200,201,211,214,295,366,397,398,399,407,419,423,427,439,480,496,508],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,74,96,173,180,197,200,201,214,219,262,294,347,350,352,356,359,369,376,382,405,434,465,467,474,480,482,483,484,489,499,503,508,509,511,513],convex:[43,345],convinc:[7,12],cook:9,cooki:7,cool:[7,163,244,306],cooordin:[197,198],cooper:[5,7],coord123:121,coord1:[3,121,213,217,218],coord2:[3,121,213,217,218],coord3:[3,121,213,217,218],coord:[],coordb:452,coordbb:452,coordiat:374,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,74,77,78,80,84,92,94,95,99,109,110,112,120,121,123,141,147,156,162,168,170,171,173,177,196,197,198,199,200,201,202,204,207,212,213,216,217,218,221,222,223,224,225,226,227,228,231,233,234,238,240,243,244,245,246,247,248,249,261,263,264,266,267,268,270,271,272,285,288,289,290,293,294,295,305,306,308,310,311,313,318,321,322,323,324,326,334,335,336,343,344,346,347,369,374,375,376,381,382,383,386,406,452,477,482,483,484,485,487,490,492,496,503,509,510],coordn:[121,213],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,126,200,336,376,394,444,480,504],copper:474,coproccesor:16,coprocessor:[1,7,9,16,17,381,495],coproprocessor:17,copy_arrai:8,copyright:[7,8,293],coral:201,core:[],core_shel:155,coreshel:[],cornel:[6,179,494],corner123i:120,corner123x:120,corner123z:120,corner1i:120,corner1x:120,corner1z:120,corner2i:120,corner2x:120,corner2z:120,corner3i:120,corner3x:120,corner3z:120,corner:[3,6,41,120,200,345,346,369,469,482,504],cornflowerblu:201,cornsilk:201,corp:9,corpor:16,corr:396,correct:[3,6,9,11,12,16,17,61,92,93,108,109,114,117,123,155,160,167,198,200,227,240,242,248,264,265,285,293,295,298,335,341,345,366,376,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,469,470,472,473,474,475,482,497,500,503,504],correction_max_iter:210,correctli:[3,8,11,17,74,84,108,109,110,150,151,152,154,156,158,159,160,161,162,165,166,169,197,201,207,228,233,238,249,258,264,265,301,308,311,321,323,342,345,376,377,381,399,429,434,479,480,482,492,504,508,510],correl:[],correpond:236,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,73,74,92,102,103,116,119,120,121,122,125,126,134,137,138,139,140,141,143,144,145,147,150,151,160,167,171,172,179,180,181,182,183,184,185,187,188,190,191,193,196,197,198,200,201,205,206,207,213,215,216,217,218,220,223,225,227,234,238,239,243,248,251,252,260,261,262,264,266,267,268,269,270,271,272,273,274,278,281,283,284,285,287,290,291,295,300,308,310,311,327,329,331,340,341,342,344,345,346,348,350,351,352,353,355,356,359,361,367,371,373,375,376,382,383,385,388,389,390,391,392,393,394,395,396,397,400,401,405,406,407,408,409,410,411,412,413,414,417,419,420,421,422,423,424,425,426,427,428,431,432,434,436,437,438,439,441,442,444,445,446,447,452,453,454,463,464,465,466,467,468,470,472,473,474,477,479,480,482,483,485,495,496,497,499,500,503,509],correspondingli:[428,429,491],corrupt:3,cosin:[],cosineshift:27,cosmo:[242,247],cossq:[],cost:[1,6,10,11,12,17,40,42,74,116,125,148,172,200,201,213,217,218,221,222,223,237,264,300,336,366,367,379,397,419,423,434,436,463,479,491],costheta0:[463,465,467,470],costheta:442,costli:[11,93,242,377],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,74,78,92,95,99,110,112,116,119,121,153,163,168,170,186,197,198,200,201,205,206,213,214,217,221,227,238,247,297,298,299,303,306,308,310,324,325,331,335,336,337,341,345,347,349,357,363,365,372,374,377,381,384,409,413,414,417,444,445,478,479,480,482,484,486,489,490,497,498,503,509,510],coulomb:[3,5,6,7,8,9,10,12,14,15,18,75,93,114,115,123,148,174,178,299,301,337,366,367,374,381,388,390,391,392,393,396,397,398,399,400,407,411,412,414,419,423,427,430,436,439,444,445,447,452,462,467,468,470,473,487,494,500,503,508],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,8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bas:[],datafil:[12,13,309],dataset:309,datatyp:3,date:[0,4,6,12,13,196,444,445,509],datom1:122,datom2:122,datom3:122,datom4:122,datum:[3,6,43,67,70,72,82,98,115,122,197,214],davenport:430,davi:341,david:[9,19,366,367,465,467],daw:[405,442],dbg:14,dcd:[3,6,7,197,199,200,201,202,291,483,487],ddim:196,deactiv:427,dealt:247,debug:[6,7,11,12,13,14,17,125,129,172,173,291,296,364,366,381,415,436,471,480,481,489,492,499,509],deby:[],decai:[97,397,474],decid:[3,6,12,16,74,261,297,308,337,497,504],decipher:369,declar:199,declin:324,decod:200,decompos:[92,453],decomposit:[3,5,7,18,64,210,291,312],decoupl:[6,503],decreas:[3,197,198,207,208,215,224,227,233,238,240,248,335,366],decrement:313,deepli:363,deeppink:201,deepskyblu:201,def:[12,13,480],defaul:63,defect:[6,73,171,434],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,198,199,200,201,204,205,206,207,208,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,227,228,231,232,233,235,238,239,240,243,246,247,248,249,250,251,259,261,263,264,265,266,267,268,269,270,271,272,274,275,276,279,281,282,283,284,285,286,287,289,290,291,293,294,295,297,299,301,306,308,309,310,311,314,318,322,324,326,327,328,329,330,332,333,334,336,338,339,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,359,360,361,362,364,366,367,369,371,373,374,375,376,377,378,379,380,381,383,384,385,386,388,389,390,391,392,393,394,395,397,398,400,401,402,403,404,406,407,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,434,435,436,437,438,439,441,442,444,445,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,482,483,485,486,487,488,491,492,493,494,496,497,499,500,503,505,506,507,508,509,510],definit:[2,3,6,8,12,13,81,83,123,147,201,213,214,215,216,217,218,219,227,235,246,269,309,326,338,341,344,346,348,360,364,375,384,387,395,402,403,407,417,442,449,451,453,469,480,482,484,491,493,508,509],defint:500,deform:[],deg2theta:172,deg:503,degener:[3,293],degrad:[8,18,290,367,491],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,82,97,98,100,102,103,105,107,108,113,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,172,173,179,180,183,184,191,193,196,200,213,224,231,240,242,243,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,307,308,311,327,328,329,334,350,352,356,359,361,374,400,405,413,492,500,503,510],degress:[153,213],del:496,delai:[3,6,12,377,404,500],deleg:414,delet:[2,3,7,8,12,55,59,62,65,171,176,177,204,213,214,216,217,218,219,222,224,237,240,264,309,327,328,347,349,365,375,377,380,436,461,482,483,484,485,493,494,499,504,505,507,509,510],delete_atom:[],delete_bond:[],delete_el:210,deli:196,delimit:[480,509],deloc:[265,407,452],delr:431,delt_lo:496,delta:[],delta_1:387,delta_3:387,delta_7:387,delta_conf:3,delta_ij:[431,442],delta_mu:[],delta_pi:387,delta_r:442,delta_sigma:387,delta_ua:[],delx:196,delz:196,dem:[],demand:303,demo:11,demon:288,demonstr:[298,431],den:294,dendrim:413,denniston:[9,251,253,254,255,290],denomin:[7,178],denot:[125,231,249,290,301,303,397,412,414,445,449,451],dens:[74,224,407],densiti:[3,6,7,9,18,41,42,61,106,123,133,147,159,171,173,205,206,210,213,217,218,221,227,238,251,254,257,258,290,294,295,299,336,341,369,371,375,382,383,387,405,431,432,433,442,446,452,456,458,459,460,482,491,492,500,508],density_continu:451,density_summ:451,depart:[0,7],departur:[262,298],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,72,73,74,82,97,98,109,115,116,119,120,121,122,126,147,149,150,156,160,161,167,173,174,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,200,201,204,205,206,207,208,211,213,215,216,217,219,220,221,223,225,227,233,234,239,242,243,244,246,248,249,251,253,254,261,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,289,300,303,305,308,310,311,312,318,324,327,328,329,331,333,335,336,338,340,341,344,345,346,347,349,350,351,352,353,355,356,359,361,367,369,374,375,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,431,432,434,435,437,438,439,441,442,444,445,446,447,452,453,454,462,463,464,465,466,467,468,470,472,473,474,477,479,482,484,485,488,492,494,496,499,500,502,509,510],dependend:6,depflag:12,dephas:[477,496],depos:228,deposit:[],deprec:[3,299,444],depth:[52,151,200,336,410,446],dequidt:9,der:[92,114,395,396,427,444,445,473,503],deriv:[6,7,8,9,38,57,65,92,147,167,193,214,225,227,240,248,261,264,266,267,268,269,270,271,272,289,295,299,303,333,334,336,341,342,345,373,375,383,387,395,400,407,408,412,421,425,426,431,434,444,445,462,464,473,503],derjagin:473,derlet:289,descend:201,descent:[7,373],descib:[41,200,299],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,73,74,76,93,117,120,123,125,137,147,148,151,152,153,157,158,161,164,166,167,171,172,173,175,176,185,190,193,197,198,199,204,205,206,213,214,215,216,217,218,219,221,224,225,226,227,228,230,231,236,241,242,245,246,247,248,249,250,251,253,254,255,259,263,264,265,269,277,286,289,291,296,297,298,299,300,301,308,313,321,324,325,326,327,328,329,330,331,332,333,334,339,341,342,344,349,366,367,369,372,373,374,375,376,380,383,384,386,388,389,390,392,393,394,395,396,397,400,405,407,408,410,411,412,414,417,419,420,421,422,423,424,425,426,427,428,429,430,431,434,435,441,442,443,444,445,446,447,452,453,454,461,462,463,464,465,466,467,468,470,472,473,474,475,477,479,480,482,483,484,485,486,492,495,496,499,504,509,510,511],descript:[],descriptor:[147,197,415],deserno:367,design:[0,3,6,7,8,11,13,14,15,17,125,155,158,172,210,224,230,231,264,265,289,290,309,331,336,384,385,386,389,392,397,399,407,427,428,429,432,433,442,445,464],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,74,93,96,119,124,148,155,173,186,196,213,219,225,227,238,240,241,248,249,250,254,264,285,293,294,295,296,299,303,308,311,324,327,328,329,330,335,342,357,363,366,367,369,372,374,375,376,401,405,413,428,429,463,465,467,478,479,480,482,486,491,496,497,499,500,509,510,511],desk:7,desktop:[4,6,7,10,12,200],despit:503,destabil:387,destre:359,destroi:[9,11,40,222,223],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,74,78,81,95,96,99,108,110,112,114,116,118,119,121,124,126,147,148,150,151,152,153,156,166,167,168,170,173,174,177,178,181,192,196,197,198,200,201,204,205,206,210,213,214,215,216,217,219,221,223,224,225,226,227,228,238,240,241,242,243,245,246,248,250,251,255,261,262,263,264,265,266,267,268,269,270,271,272,276,278,283,284,285,286,287,290,293,294,295,297,298,300,301,302,308,311,312,324,327,328,329,330,331,332,334,335,336,337,338,339,340,347,349,351,360,366,367,370,374,375,377,378,381,382,383,384,386,387,389,391,392,393,394,395,396,397,400,401,407,408,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,430,431,435,436,441,444,445,446,452,453,454,462,469,472,473,475,480,482,483,484,485,487,488,491,492,494,497,500,501,504,509,510,513],detect:[2,3,12,43,63,65,91,97,239,294,335,376,396,413,418,477,479,482,493,496,509],determ:381,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,74,92,108,114,116,119,125,126,134,148,161,162,171,172,173,196,197,198,200,201,202,203,207,208,209,212,213,214,215,216,217,218,219,220,221,225,227,228,231,233,240,243,244,246,248,249,254,259,261,262,264,270,271,272,283,284,285,287,289,291,294,295,298,305,306,307,308,309,310,314,316,318,324,327,328,329,331,337,338,341,342,343,344,345,346,347,360,366,367,369,375,377,378,381,383,384,391,396,400,404,405,409,411,414,415,423,431,434,436,445,446,452,461,464,468,473,479,482,483,485,487,489,492,496,498,499,501,508,509,510],determinist:312,detil:115,devan:[9,447],devanathan:467,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,245,269,293,298,299,302,383,387,407,433,434,452,470,484],devemi:9,deviat:[262,269,289,409],deviator:9,devic:[1,3,12,15,17,245,381],device_typ:381,devin:[300,396],devis:433,dfactor:200,dff:503,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,367],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,302,434],dhi:[61,196,227,294],dhug:[262,298],dhugoniot:[262,298],dia:431,diagnost:[],diagon:[3,6,88,147,148,149,225,264,295,308,339,449,451],diagonalstyl:453,diagram:[42,125,172,192,221,291],diallo:413,diam:[200,201,294,375],diamet:[3,6,41,43,120,173,197,198,200,201,205,206,248,294,308,324,326,340,342,375,395,410,411,421,446,469,473,482,483,492],diamond:[369,407,431],diamter:[41,294],dick:6,dicsuss:261,dictat:[211,262],did:[3,12,374,401,404,405,411,436,465,467,490],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,169,338,366],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,73,74,92,97,100,102,103,127,147,149,150,151,152,153,154,156,159,160,161,162,163,165,166,167,173,174,176,181,192,193,196,197,200,201,204,206,209,211,213,216,221,222,223,224,225,226,227,231,236,239,240,241,242,243,244,245,248,249,251,261,264,265,266,267,268,270,271,272,274,276,279,281,282,283,284,287,289,291,293,295,298,299,300,303,306,308,311,313,321,322,324,327,328,329,332,333,334,336,339,340,341,342,345,349,350,360,363,365,366,367,369,370,372,373,375,376,378,379,380,381,382,383,387,391,392,394,395,396,401,402,403,405,407,410,411,412,414,417,419,420,422,423,430,431,432,433,435,436,438,442,444,445,446,447,448,449,451,452,453,454,462,463,464,465,467,469,470,473,476,477,479,480,482,484,485,486,487,490,491,492,494,496,497,499,500,501,503,508,509,510,511],differenti:[1,3,6,29,193,366,397,442,466],difficult:[225,291,381,413,491],difficulti:[97,113,311,444],diffract:[],diffus:[],digit:[2,3,201,349,434,509],dih_table1:193,dih_table2:193,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:223,dihydrid:407,dij:311,dilat:[],dim1:3,dim2:3,dim:[3,61,74,150,154,155,156,159,160,161,162,163,165,173,196,217,227,246,342,369,431,485,508,509,510],dimdim:509,dimems:290,dimens:[],dimensinon:74,dimension:[3,40,97,119,125,147,150,153,154,155,156,159,160,161,162,163,165,172,195,213,217,263,290,336,369,372,376,442,482,492],dimensionless:[111,128,129,131,134,136,138,143,147,336,367,453,473],diment:3,dimentionless:142,dimer:[6,308,431],dimgrai:201,dimstr:[42,221],dinola:[295,327],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,197,198,326,503],dir1:493,dir2:493,dir:[1,3,4,8,10,11,12,262,289,298,323,442,444,445,480,493,509],dirac:147,direc:442,direct:[],directli:[3,6,8,9,11,12,92,120,147,149,197,198,199,200,207,233,242,246,251,290,309,328,340,342,343,344,345,369,373,381,382,383,388,390,391,397,400,405,407,419,423,436,439,447,461,480,492,493,494,500,509],directoi:14,directori:[],disabl:[3,12,16,336,418,480,495,509],disadvantag:[6,221],disallow:[197,227,264],disappear:484,discard:[2,3,42,74,215,217,221,337,345,479,484,485],discontinu:[193,374,425],discourag:431,discov:[13,337],discret:[6,8,41,43,200,201,248,251],discuss:[],disk:[6,89,90,97,166,195,228,240,294,480],disloc:[73,434],disord:[40,73,434],disp:[],dispar:446,disperion:[400,423],dispers:[3,6,7,9,171,290,366,367,391,400,423,428,436,445,464,470],displac:[],displace_atom:[],displace_box:61,displacemet:485,displai:[11,13,22,37,45,56,181,192,197,200,351,360,394,462],dispters:3,disregard:434,dissip:[6,9,41,85,86,235,241,248,290,312,333,334,389,401,402,403,411,428,429,462],dissolut:222,dist:[6,72,96,115,124,197,291,307,404,461,477,510],distanc:[],distinct:[6,231,305,366,446],distinguish:[6,91,147,254,407,481,509],distort:[171,382],distrbut:382,distribut:[],distro:[118,394,441,442],ditto:[8,12,14,15,16,17,18,43,122,223,474,480],div:8,divd:124,diverg:[3,12,40,308,334,383,484,503,511],divid:[3,6,16,42,96,119,124,133,135,148,170,171,181,192,201,213,214,216,221,227,289,332,339,344,366,374,376,408,445,452,470,491,499,509],divis:[6,251,387,417,427,479,500,509],dl_poli:[6,7],dlambda:167,dlammps_async_imd:245,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,200],dlammps_gzip:[3,12,197,200,335,482,483,487],dlammps_jpeg:[3,12,200],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,200],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,197],dlen:492,dlmp_intel_offload:[9,12,16],dlo:[61,196,227,294],dlopen:6,dlvo:[7,395,473],dm_lb:251,dmax:[324,372],dmpvtk:198,dmpvtp:198,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,78,92,95,99,108,110,111,112,114,116,118,119,121,124,126,148,151,152,153,166,168,170,173,174,175,181,192,196,197,198,199,200,201,202,204,205,206,211,212,213,214,215,216,217,218,219,228,240,248,249,259,264,265,270,271,272,276,283,284,285,286,287,294,297,308,321,324,327,328,329,338,342,345,347,349,351,360,365,374,375,376,381,382,383,386,394,396,397,405,406,408,413,414,416,417,431,432,433,436,438,441,442,443,453,462,463,465,467,469,470,480,482,483,484,485,487,490,491,492,499,500,504,509,510,511,512],docuement:446,dodd:43,dodgerblu:201,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,73,74,75,92,93,96,110,114,117,123,124,125,149,151,153,155,156,161,163,167,172,173,174,175,177,179,181,186,192,193,196,197,198,199,200,201,204,210,211,213,217,220,221,223,224,225,227,231,233,236,237,240,241,244,246,248,249,251,254,260,264,265,266,267,268,270,271,272,283,284,285,286,287,295,296,297,301,303,306,308,324,327,329,331,332,336,339,340,341,344,345,346,347,352,353,354,356,357,359,365,366,367,368,369,375,376,377,382,383,384,385,386,387,389,391,392,393,395,396,397,398,400,401,404,405,406,407,409,410,411,412,414,415,416,417,418,421,422,424,425,426,428,429,431,432,433,434,436,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,478,479,480,482,483,484,485,486,489,490,492,493,494,495,496,499,500,503,504,509,513],doegenomestolif:7,doesn:[3,7,8,12,173,197,198,211,217,218,321,375,377,381,383,396,406,416,444,445,463,465,466,467,470,482,484],dof:[3,8,119,151,152,153,166,213,308,510],dof_per_atom:[153,213],dof_per_chunk:[153,213],doff:[375,482],doi:[6,226],domain:[3,6,7,12,13,18,40,42,43,60,63,64,74,125,162,172,175,196,199,200,201,204,211,221,225,227,228,244,247,251,264,265,291,303,308,312,336,341,342,366,367,376,381,404,436,477,479,482,486,499],domin:[1,407,496],don:[0,8,9,12,13,123,176,207,233,249,297,345,431,452,480,482,504],donadio:328,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,61,64,74,167,170,173,176,193,197,200,201,210,211,213,2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00,301,332,333,334,339,396,397,444,445,478,492],equilibria:339,equilibribum:[222,223],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,156,157,180,182,225,227,240,241,242,249,251,264,269,285,298,299,303,307,311,313,321,324,331,332,334,339,350,352,356,359,396,431,438,452,503],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:210,equival:[6,12,13,29,61,63,131,132,140,145,171,175,201,216,219,225,227,240,248,264,285,295,307,308,344,383,401,407,452,465,467,468,482,485,490,491,500,503],equlibrium:6,equliibr:[299,301],er3:172,eradiu:[41,120,198,407,482],eras:[310,333],erat:[227,429],erc:397,erfc:[397,419,436],erforc:[120,198],erg:508,erhart:[211,405,465,467],ermscal:384,ernst:9,eror:3,eros:431,erose_form:431,erot:[],errata:[465,467],erratum:341,erron:3,error:[],erta:411,ervel:[120,198,482],escap:[228,503],especi:[8,16,161,173,204,211,221,240,298,303,306,307,381,479],espresso:[9,302],essenti:[8,11,12,27,93,135,154,155,156,159,160,161,162,163,165,182,214,269,290,340,367,383,397,419,467,487,500],essex:29,establish:[92,244],estim:[1,3,6,10,12,38,42,57,96,148,210,221,232,262,324,331,366,367,372,436,445,464,496,500],esu:508,esub:431,eta:[6,251,264,298,299,301,340,406,408,410,442,466,470,508],eta_dot:264,eta_ij:442,eta_ji:408,etag:[41,482],etail:500,etap:264,etap_dot:264,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,94,95,96,100,116,117,120,122,148,150,153,154,155,156,157,159,160,161,162,163,165,167,173,175,176,177,186,197,198,200,201,204,205,210,211,212,213,216,217,218,219,222,223,227,228,238,240,241,248,264,294,305,309,336,337,345,349,365,366,374,375,376,377,379,405,406,414,427,429,434,440,444,445,463,465,467,470,477,480,482,483,484,489,491,492,496,497,498,499,500,501,503,508,509,511,513],ethernet:18,etol:[374,376,477,496],etot0:298,etot:[6,100,102,103,117,148,159,201,231,249,262,298,499,500],eu2:172,eu3:172,euler:[374,376],eulerian:210,euqat:455,europhi:251,ev_tal:8,evalu:[2,3,9,11,12,38,57,71,74,92,93,96,114,124,126,147,149,153,163,171,173,196,197,198,200,201,205,206,207,208,210,212,213,214,215,216,217,218,219,220,227,233,241,243,244,246,247,248,249,290,296,299,310,314,318,327,328,329,338,341,344,346,347,349,366,367,372,374,381,434,436,442,448,450,452,464,477,478,480,484,485,487,489,490,491,492,496,498,500,509,510],evalut:[349,480],evan:[161,285],evanseck:[6,20,179,392,494],evapor:[],evaul:[8,374],evdwl:[114,149,444,445,500],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,73,74,93,114,126,171,174,175,189,193,197,198,201,204,205,206,211,212,213,216,217,218,219,221,222,223,225,227,228,231,246,249,262,264,265,290,294,303,305,308,309,320,324,332,336,339,341,345,347,358,366,372,374,376,381,386,407,408,411,414,417,436,446,470,471,475,482,483,485,487,488,489,491,492,494,497,499,500,501,503,513],evenli:[3,42,148,193,221,251,417,471],event:[],eventu:[3,6,12,15,175,299,496],ever:[9,55,57,247,324],evera:[395,410,446,462],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,74,75,96,120,126,135,161,176,197,198,199,200,201,202,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,232,237,238,240,242,244,245,246,251,252,260,264,265,269,288,289,290,294,295,296,297,298,299,300,301,303,305,306,308,309,311,313,324,326,327,328,329,330,331,332,335,336,337,338,339,347,349,365,367,376,377,378,381,401,404,414,427,444,445,452,458,476,477,478,482,484,486,487,489,490,491,496,497,498,500,504,509,513],everyth:[8,114,504],everywher:[123,421],eviri:407,evolut:[242,251,291,477],evolv:[251,291,337],ewald:[2,3,5,6,7,8,9,12,93,117,125,148,337,366,367,374,388,390,391,397,400,407,419,423,439,447,462,464,468],ewald_disp:400,ewalddisp:3,exact:[22,42,45,74,129,167,176,181,221,224,241,242,248,249,250,294,303,304,324,336,351,366,394,484,489,496,509,511,513],exactli:[3,6,12,14,17,38,42,43,57,61,74,75,96,123,151,157,164,173,193,205,206,216,221,227,232,236,241,248,249,250,265,277,278,286,290,298,324,329,330,343,381,394,401,405,411,414,428,436,464,484,485,492,496,509],exager:503,examin:[6,8,17,224,290],examp:[480,509],exampl:[],exce:[3,6,16,17,18,42,60,74,175,212,213,216,217,218,219,221,225,227,232,237,264,290,305,309,315,316,324,374,381,482,509],exceed:[3,42,61,221,227,264,324,490],excel:407,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,74,94,95,115,116,119,124,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,173,177,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,201,204,207,213,214,216,220,221,225,227,234,239,240,243,246,248,250,264,265,266,267,268,269,270,271,272,273,274,277,278,281,283,284,285,286,287,291,300,301,308,310,311,321,324,327,329,330,336,340,344,347,348,349,350,351,352,353,355,356,359,360,361,366,367,369,371,375,376,377,379,380,381,382,383,385,388,389,390,391,392,393,394,395,396,397,399,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,432,437,438,439,441,444,445,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,479,480,482,484,485,487,490,491,492,493,494,496,500,503,508,509,510,512],excess:[215,407],exchang:[2,3,6,8,63,64,204,210,211,240,248,300,308,332,336,339,366,381,407,497],exchange:366,excit:407,exclud:[3,6,9,12,16,17,65,74,119,147,153,160,161,177,197,213,217,222,223,252,260,293,306,308,331,342,347,374,375,377,389,411,414,417,428,429,436,461,494],exclus:[1,3,12,16,92,381,396,434,436,491,501],excurs:[264,477],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,174,200,245,302,349,365,368,380,478,480,490,493,496,509],exempl:452,exemplari:241,exemplifi:407,exert:[6,246,249,303,343,344,345,367],exhaust:[210,380,509],exhibit:[97,264,373,407,491],exist:[3,6,7,8,11,12,13,16,37,56,61,70,73,129,173,174,192,199,200,201,204,209,220,223,225,228,240,293,294,296,347,348,350,352,353,354,356,360,370,375,381,402,403,414,444,461,471,478,480,482,483,484,493,494,495,504,509,510,511],exit:[2,3,11,12,42,59,197,221,236,365,380,480,481,490,499,509],exlanatori:3,exp:[],expand:[],expans:[12,147,197,493,509],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,74,108,154,165,171,193,221,233,240,242,261,289,295,297,298,303,308,347,367,377,394,431,434,436,477,480,482,484,487,491,496,509],expens:[6,74,201,289,293,308,336,347,366,367,377,381,480],experi:[6,13,15,17,220,228,245,254,263,295,307,308,372,376,401,436,491,496],experienc:[6,12,253,254],experiment:[240,366,381,496],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,72,74,75,76,79,80,82,91,98,153,161,193,197,198,200,201,204,213,214,219,221,223,225,227,264,289,297,308,321,347,349,365,366,369,375,376,380,386,405,417,452,454,469,480,483,484,487,489,492,503,504,509,513],explan:[3,6,61,120,147,197,198,213,263,289,414,476,479,480,482,491],explanatori:[3,8,124,197,198,212,213,216,217,218,308,375,479,509],explantori:[3,304],explic:435,explicit:[6,9,11,22,45,80,92,120,123,167,181,205,206,227,315,316,351,371,383,384,387,392,394,405,407,418,428,468,476,479,483,486,504],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,74,116,119,150,160,163,171,173,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,217,220,227,234,239,241,243,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,297,298,300,308,310,311,327,329,330,336,340,344,350,352,353,355,356,359,361,375,381,382,383,385,388,389,390,391,392,393,394,395,396,397,398,400,401,404,405,406,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,432,434,436,437,438,439,441,446,447,454,455,456,457,458,459,460,462,463,464,465,466,467,468,470,472,473,474,482,484,485,491,492,494,495,501,503,504],explictli:[16,495],exploit:[15,17,291],explor:[125,172],expon:[3,299,301,405,410,413,427,435,447],exponenti:[92,442,463,470,474,496,509],expos:11,exposit:[210,401,404],express:[6,147,159,173,205,206,225,261,289,299,336,342,349,387,405,407,421,431,452,453,462,509],expressiont:387,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,71,87,88,89,92,93,96,100,103,104,114,116,124,126,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,198,204,207,208,211,219,220,226,229,233,238,239,240,242,243,244,246,248,250,262,264,269,278,289,290,306,307,308,310,313,318,321,323,327,328,329,330,331,333,334,336,338,341,345,346,410,431,434,445,446,453,499,500,508],extent:[1,3,42,43,46,59,74,171,175,197,209,217,221,246,343,346,366,369,383,448,450,464,479,482,485],exterior:[3,6,171,345],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,74,108,116,117,119,125,148,150,151,152,154,156,159,160,161,162,163,165,166,172,173,174,175,179,201,216,221,223,264,296,297,298,308,324,374,375,378,379,400,411,414,417,431,436,479,480,482,485,494,503,509],extract:[3,6,11,13,36,65,71,92,114,122,124,126,205,206,301,376,397,408,431,453,480,487,499],extract_atom:11,extract_comput:[11,480],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,200,215,225,227,264,334,407,466,503],extrema:427,extrins:210,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[169,338],f_a:[465,466,467],f_ave:124,f_c:466,f_f:467,f_fix_id:298,f_foo:509,f_harm:334,f_i:[29,442],f_id:[6,74,124,126,197,198,204,212,213,214,215,216,217,218,219,259,326,338,500,509],f_ij:442,f_indent:219,f_int:333,f_j:29,f_jj:96,f_k:442,f_langevin:336,f_max:[298,303],f_msst:262,f_r:[249,465,466,467],f_sigma:387,f_solid:334,f_ss:6,f_temp:[],face:[3,6,59,61,74,161,171,175,209,217,218,341,343,344,345,346,369,410,431,446,482,485],face_threshold:171,facet:171,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,242,294,324,334,411,452,494],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,75,92,96,108,115,122,123,125,147,167,172,175,179,190,196,197,200,201,205,206,214,221,225,227,228,240,245,248,250,251,262,264,265,269,291,295,299,307,311,314,316,324,328,332,339,340,341,345,356,367,369,375,381,383,384,387,388,390,392,397,398,399,401,402,403,407,411,414,418,419,431,434,436,438,439,445,447,454,463,468,479,482,485,486,491,494,496,497,500,503,508,509],factori:[3,480],factoriz:366,fail:[3,9,11,12,61,177,225,228,366,374,376,399,445,480],failur:[128,449,481,509],fairli:[11,436,491,496,504],faken:76,falcon:245,fall:[3,6,201,216,294,480,509],fals:[91,347,349,452,509],fame:8,famili:[470,479],familiar:[0,11,504],fan:442,far:[3,6,12,17,59,61,63,91,197,198,201,202,221,222,223,225,228,264,289,307,308,324,341,352,356,372,376,377,469,480,482,487,500],farago:248,farrel:[465,467],farther:197,fashion:[6,8,42,74,173,201,204,205,206,211,217,221,223,228,240,242,246,261,262,264,266,267,268,269,270,271,272,280,283,284,285,286,287,297,298,300,308,313,317,323,326,334,336,340,341,342,344,346,376,414,428,485,494,509,512],fasolino:416,fast:[6,7,9,12,13,17,40,197,198,275,298,337,366,367,389,428,429,434,462,464,484,489,491,500,510,513],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,111,116,119,150,160,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,220,221,227,234,239,243,247,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,295,299,300,308,310,311,324,327,329,331,333,336,340,344,350,352,353,355,356,359,361,366,367,378,379,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,400,401,405,406,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,432,437,438,439,441,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,485,491,495,503],fastest:[1,6,14,17,161,217,336,337,381,479],fatal:[3,499],fault:[73,445],faulti:12,fava:410,favor:224,favorit:7,fbmc:331,fcc:[],fcm:[280,509],fdirect:231,fdotr:415,fdt:[],fdti:92,fe2:172,fe3:172,fe_md_boundari:210,featu:8,featur:[],fecr:405,feedback:[7,245],feel:[7,245,246,254,289,345,347,376,436],felling:433,felt:345,femtosecond:508,fene:[],fennel:[397,419],fep:[],ferguson:[6,179,494],fermi:[1,9,10,12,15,159,381,467],fermion:407,fernando:430,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,202,212,213,214,216,217,218,219,249,264,294,297,299,311,338,366,374,375,376,383,452,479,482,487,491,493,501,511],fewer:[1,3,11,15,16,63,254,491],fewest:3,fextern:238,feynman:291,fff:480,ffield:[396,408,444,445,452],ffmpeg:[3,12,200],ffplai:200,fft:[1,3,7,9,11,12,14,15,93,116,117,148,290,366,367,491],fft_inc:[12,367],fft_lib:12,fft_path:12,fftbench:[366,501],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:461,fictiti:[6,207,208,233,238,242,291,307,397,419,423,461],field1:[483,487],field2:483,field:[],fifth:[321,438],figur:[1,3,8,12,298,479,480,504],fij:400,file0:289,file1:[11,13,289,335,349,375,487,489,493],file2:[11,13,335,349,375,487,489,493],file:[],file_from:199,filen:375,filenam:[3,12,13,38,42,57,193,197,198,200,201,202,210,213,214,215,216,217,218,219,221,226,236,289,293,296,299,300,301,304,305,308,309,335,336,363,364,365,375,376,382,383,387,397,405,406,408,416,431,432,433,438,442,443,444,445,452,453,463,464,465,466,467,470,478,479,480,483,484,489,493,500,509,511,512,513],filennam:489,filep:[3,197,198,201,484,489,513],filepo:305,fill:[7,9,173,200,294,336,369,377,387,434,445,485,504],filter:[201,210],final_integr:8,final_integrate_respa:8,finchham:[6,155,399],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,74,76,92,124,176,193,202,211,224,225,236,237,240,263,289,294,295,303,307,372,374,376,377,397,414,419,423,431,452,462,464,503,504,509],find_custom:8,fine:[16,17,177,207,233,334,377,381,504,509],finer:[147,173,509],finest:366,finger:[173,196,261,485],finish:[6,11,42,221,349,363,365,366,378,380,381,469,487,509,510],finit:[],finni:[7,405,462],finvers:231,fiorin:[9,226],fire:[],firebrick:201,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,74,84,93,96,109,110,111,113,119,123,124,134,137,140,141,145,148,158,161,167,169,171,172,174,175,176,180,193,197,198,199,200,201,202,204,205,213,214,216,217,218,219,221,224,227,236,240,241,246,251,261,262,263,264,289,291,296,297,298,300,305,308,311,313,321,322,324,325,326,333,334,335,336,338,342,347,349,350,357,369,374,375,376,377,380,381,382,383,386,387,388,390,392,394,396,397,405,407,408,411,412,414,415,416,417,418,419,423,428,429,431,433,434,436,438,442,444,445,452,453,461,463,464,465,466,467,470,474,477,478,479,480,482,483,484,487,489,491,494,495,496,499,500,503,504,509,510,511,513],fischer:[6,9,19,20,179,392,494],fit:[3,6,9,12,38,57,193,236,307,324,383,387,416,431,436,457,464,466,490,504,509],five:[76,159,298,375,387,432,482,496],fix:[],fix_adapt:[167,206,427],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,211,294],fix_eo:9,fix_evapor:211,fix_flux:210,fix_gcmc:[211,375],fix_gl:242,fix_gld:242,fix_grav:294,fix_id:[3,225,262,264,266,267,268,269,270,271,272,295,298],fix_manifoldforc:504,fix_modifi:[],fix_mov:[196,342],fix_nh:8,fix_npt:242,fix_nv:504,fix_nvt:[211,240],fix_poem:[3,6,9],fix_pour:[3,228],fix_qbmsst:9,fix_qeq:[3,396],fix_rattl:311,fix_reax_bond:444,fix_rigid:[254,386],fix_saed_vtk:309,fix_setforc:8,fix_shak:311,fix_shardlow:9,fix_srd:3,fix_styl:269,fix_temp_rescal:330,fixedpoint:[225,264],fixextern:238,fixid:210,fji:400,flag1:[230,379],flag2:[230,379],flag:[3,8,9,11,12,14,15,16,17,41,68,77,78,84,91,94,95,99,109,110,112,125,168,172,176,197,198,200,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390,391,397,400,407,419,423,439,447,496],recog:12,recoginz:3,recogn:[3,12,16,76,175,222,223,264,375,405,431,444,480,482,489,490,503],recomend:6,recommend:[7,12,14,16,200,201,298,334,366,407,414,428,429,434,445,446,449,451,452,491,501,504],recompil:[1,3,9,12,202,311],recomput:[108,135,177,232,313,404,494],reconstruct:[3,226,452],record:[202,226,313],recov:[225,264],recreat:348,rectangl:[42,221,369],rectangular:[7,42,64,175,221,240,369,482,484,486],rectilinear:[125,172,198],rector:54,recurs:[42,221,387,469],recust:42,recv:479,red:[2,200,201,224,291],redefin:[3,484,490,509],redirect:12,redo:12,reduc:[],reduct:[18,19,124,125,172,262,298,366],redund:408,ree:457,reed:[262,298],rees:[7,9,13],ref:[333,334,373],refactor:6,refer:[],referenc:[3,6,12,65,70,74,121,126,197,198,204,214,240,297,338,367,397,413,438,446,480,500,509],reflect:[],refman:9,reformat:7,refresh:210,reg:485,regard:[6,61,261,311,312,317,441,445],regardless:[15,74,173,176,196,216,217,227,248,264,266,267,268,270,271,272,295,308,318,324,381,479,485,492],regim:[6,332,339,398,491],region:[],region_spher:8,region_styl:345,regist:[8,123,149,320,444,445],regoin:6,regress:509,regspher:173,regstrip:347,regul:6,regular:[1,3,42,64,93,171,175,197,200,211,221,240,336,367,398,417,479,482,484,486],reigon:509,reinhardt:[333,334],reject:[173,224,444,497],rel:[1,6,14,27,36,42,61,74,97,109,129,137,147,151,155,156,158,173,182,201,204,211,217,221,227,228,231,240,246,249,260,261,285,289,294,303,305,306,313,321,324,326,331,332,336,343,347,366,367,374,407,410,411,428,429,431,446,473,483,491,496,500,503,510],relat:[],relatic:[],relationship:[6,236,299,349,366,452,473,503,509],relax:[],releas:[0,5,7,8,13,222],relect:[3,436],reles:43,relev:[2,6,12,42,81,83,118,135,173,177,201,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,227,228,229,232,234,237,239,240,241,244,245,251,252,253,255,256,257,258,260,261,263,273,274,275,276,277,278,279,280,281,282,288,292,293,294,296,297,300,302,304,305,306,309,310,311,313,318,322,324,325,326,331,332,335,336,337,338,339,340,341,342,343,344,346,347,366,374,384,385,389,395,397,398,400,401,404,407,409,410,411,412,413,418,420,421,422,424,425,426,428,429,436,437,441,446,454,461,464,472,473,474,479,495,510],reli:[3,12,300,407,445,474,482,492],reloc:12,remain:[7,12,33,37,42,51,56,61,74,92,110,153,154,155,156,160,161,162,163,165,176,186,192,193,197,205,206,211,213,214,217,218,225,227,248,249,256,264,265,270,271,272,283,284,285,287,292,293,316,324,327,328,329,335,336,347,349,357,360,375,387,407,414,427,434,436,462,477,482,483,487,492,494,496,500,503,504,509,510],remaina:387,remaind:[9,173,197,228,294,324,337,467,482],remap:[3,6,12,61,63,74,156,173,196,217,227,246,261,285,366,482,483,484],remedi:[6,503],rememb:[2,504],remot:504,remov:[2,3,6,8,13,55,74,75,80,97,113,121,123,147,151,152,153,154,155,156,160,161,162,163,165,166,173,176,177,198,204,213,217,222,237,248,249,254,260,262,264,270,271,272,283,284,285,287,293,299,308,309,311,324,327,328,329,331,347,366,376,400,429,434,482,485,493,494,504,509,510],remove_bia:8,remove_bias_al:8,remove_molecul:210,remove_sourc:210,remove_speci:210,ren:172,renam:[12,348,493,504],render:[12,13,197,200,201],rendon:[264,265],reneighbor:[3,8,12,40,59,74,217,221,240,324,337,347,401,499,500],renssela:293,renumb:74,reorder:[3,12,40,479],rep:497,repeat:[2,6,200,201,217,224,225,240,317,369,387,465,467,469,477,496],repeatedli:2,repel:246,repes:197,replac:[2,3,6,11,12,42,65,94,95,124,150,151,152,153,154,155,156,159,160,161,162,163,165,166,197,198,200,201,202,213,214,216,217,218,219,221,224,228,248,269,296,303,305,383,397,421,464,483,484,489,490,500,509,510,511,513],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:336,repres:[1,3,6,8,9,12,15,41,42,43,61,69,74,95,120,123,185,193,197,198,200,213,214,215,216,217,218,219,225,231,241,243,248,251,264,291,293,295,303,308,309,313,321,336,338,345,367,376,382,387,410,417,427,428,429,431,432,433,439,442,444,445,468,469,477,479,482,492,494,497,503,509,511],represent:[3,6,8,9,59,61,141,175,197,241,242,291,336,387,407,410,434,446,482,485,503],reprocess:487,reproduc:[3,264,342,397,405,411],repul:431,repuls:[6,7,36,41,46,47,115,246,299,341,342,345,383,387,395,397,401,407,411,413,427,431,435,452,461,467,470,473,474,492],reqir:[299,301],request:[3,6,8,12,42,109,176,193,197,245,251,306,312,324,326,364,366,436,444,445,477,487,492,496,504,509,510,511],requir:[],rerun:[],rescal:[],research:[5,7,85,86,235,251,255,312,434,477,496],resembl:[303,504],resepct:6,reserv:[12,245,503],reservoir:[96,240,244,248,336],reset:[],reset_atomic_reference_posit:210,reset_dt:8,reset_target:8,reset_tim:210,reset_timestep:[],resid:13,residu:245,residue1:377,resist:[6,245],resolut:[215,452,464],resolv:[225,291,324,429,504],resort:3,resourc:[7,382,405],respa:[3,16,232,245,264,379,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,437,439,441,443,444,445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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.USER-CUDA package","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_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/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/local command","compute dilatation/atom 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/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 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 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/spatial command","fix ave/spatial/sphere 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 deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table 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 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/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body 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 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/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","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/conservative 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 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 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 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","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":222,"default":[37,40,41,56,59,60,61,63,64,71,74,92,93,97,108,109,111,113,114,125,129,130,147,153,161,162,166,172,173,176,178,192,195,196,197,198,200,201,202,203,205,206,207,209,210,211,213,217,218,219,222,223,225,226,227,228,232,237,240,241,246,248,249,250,251,252,254,259,262,264,265,269,285,286,290,291,294,295,296,297,298,300,303,305,306,308,309,324,326,331,332,333,334,337,339,341,343,347,360,364,366,367,369,370,372,373,375,377,378,379,381,384,387,389,407,428,429,434,436,444,445,461,462,477,478,479,482,483,485,487,489,490,491,494,496,498,499,500,501,502,508,510,511,512],"function":509,"long":[215,388,390,391,392,393,397,399,400,419,423,427,439,447,468],"new":8,"static":12,acceler:1,account:504,ackland:66,acknowledg:7,adapt:[205,206],addforc:207,addit:[12,13,504],addtorqu:208,adiabat:6,adjust_dt:314,adp:382,after:504,airebo:383,alloi:405,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:209,arrai:6,aspher:[6,9,87,151,266,270,274,275,283],atc:[9,210],atom:[6,7,8,66,69,73,74,75,76,79,80,81,83,84,86,90,97,101,102,105,106,107,113,117,118,120,147,148,171,209,211,212,297,509],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:220,awpmd:[9,384],balanc:[42,221],barostat:6,basal:69,beck:385,berendsen:[295,327],between:6,binary2txt:13,bodi:[6,8,9,43,70,152,267,271,276,284,386],bond:[8,13,71,72,222,223,224,304],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:387,born:[388,399],boundari:[7,59],box:[6,60,225],branch:504,brownian:389,buck:[390,391,399,430],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:73,ch2lmp:13,chain:13,chang:504,change_box:61,charmm:[6,20,179,392,427],chunk:[6,68,74,78,95,99,110,112,121,153,168,170,213],citat:7,class2:[9,21,44,180,350,393],clear:62,cluster:75,cmm:9,cna:76,code:6,coeffici:6,colloid:[9,341,395,473],colvar:[9,13,226],com:[77,78,154],comb3:396,comb:[300,396],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,509],compute_modifi:108,condit:7,conduct:[6,332],conserv:402,constant:[6,509],constraint:7,contact:[79,127],contact_radiu:[],coord:80,core:6,coreshel:9,correl:[214,215],cosin:[23,24,25,26,27,28,182],cossq:352,coul:[388,390,391,392,393,397,398,399,412,419,423,427,439,447],coupl:6,creat:223,create_atom:173,create_bond:174,create_box:175,createatom:13,creation:7,csld:328,csvr:328,cubic:421,cuda:[9,14,116,119,150,160,207,220,234,239,243,264,273,310,311,327,329,340,388,390,392,393,405,411,412,419,420,422,425,437,463,465],custom:[8,197,198],cut:[50,384,390,393,397,400,407,409,419,420,427,435,439,468],cvff:353,damag:[81,128],data2xmovi:13,data:6,databas:13,deby:[397,419],dec:[],defgrad:134,deform:[156,157,227],delete_atom:176,delete_bond:177,delta:24,deposit:228,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],diagnost:7,diel:398,dielectr:178,diffract:9,diffus:6,dihedr:[8,82],dihedral_coeff:181,dihedral_styl:[2,179,180,182,183,184,185,186,187,188,189,190,191,192,193,194],dilat:83,dimens:195,dipol:[6,9,29,400],direct:231,directori:4,discuss:6,disp:6,displac:[84,91],displace_atom:196,distanc:354,distribut:[7,12],document:0,dpd:[9,85,86,401,402,403],drag:229,dreid:[6,413],drude:[6,9,158,230,231,249],dsf:[397,419],dsmc:404,dump:[6,8,197,198,199,200,202],dump_modifi:201,dynam:299,eam:[13,405],echo:203,edip:406,eff:[9,13,102,103,157,159,164,250,265,277,286,330,407],efield:233,eim:408,elast:6,emac:13,energi:[130,403],enforce2d:234,ensembl:7,erot:[87,88,89,90],error:[3,129],evapor:237,event:91,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],exp:[27,182],expand:[47,422],extend:[8,11],extern:238,fcc:289,fdt:403,featur:[7,8,504,509],feb:[],fene:[46,47],fep:[9,13,92,206],field:[6,7],file:6,finit:6,fire:299,fix:[2,6,8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,2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\ No newline at end of file diff --git a/doc/units.html b/doc/units.html index 166604650c..e327e14c99 100644 --- a/doc/units.html +++ b/doc/units.html @@ -192,9 +192,12 @@ results from a unitless LJ simulation into physical quantities.

  • density = mass/volume, where rho* = rho sigma^dim

    • Note that for LJ units, the default mode of thermodyamic output via -the thermo_style command is to normalize energies -by the number of atoms, i.e. energy/atom. This can be changed via the -thermo_modify norm command.

    +the thermo_style command is to normalize all +extensive quantities by the number of atoms. E.g. potential energy is +extensive because it is summed over atoms, so it is output as +energy/atom. Temperature is intensive since it is already normalized +by the number of atoms, so it is output as-is. This behavior can be +changed via the thermo_modify norm command.

    For style real, these are the units:

    • mass = grams/mole
      • diff --git a/doc/units.txt b/doc/units.txt index 1cdeb1bd15..253168bdc2 100644 --- a/doc/units.txt +++ b/doc/units.txt @@ -74,9 +74,12 @@ electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma density = mass/volume, where rho* = rho sigma^dim :ul Note that for LJ units, the default mode of thermodyamic output via -the "thermo_style"_thermo_style.html command is to normalize energies -by the number of atoms, i.e. energy/atom. This can be changed via the -"thermo_modify norm"_thermo_modify.html command. +the "thermo_style"_thermo_style.html command is to normalize all +extensive quantities by the number of atoms. E.g. potential energy is +extensive because it is summed over atoms, so it is output as +energy/atom. Temperature is intensive since it is already normalized +by the number of atoms, so it is output as-is. This behavior can be +changed via the "thermo_modify norm"_thermo_modify.html command. For style {real}, these are the units: