From 19ca625699aa287c790edc58e2209332776c1fd6 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 26 Feb 2016 15:53:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14684 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/_sources/fix_adapt.txt | 54 ++++++++++++++++++++++---------------- doc/fix_adapt.html | 16 ++++++++--- doc/fix_adapt.txt | 9 ++++++- doc/searchindex.js | 2 +- 4 files changed, 53 insertions(+), 28 deletions(-) diff --git a/doc/_sources/fix_adapt.txt b/doc/_sources/fix_adapt.txt index d1e7734b6a..d3acbb77b1 100644 --- a/doc/_sources/fix_adapt.txt +++ b/doc/_sources/fix_adapt.txt @@ -112,29 +112,31 @@ styles and parameters that can be varied by this fix. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters: -+-----------------------------------+---------------------+------------+ -| :doc:`born ` | a,b,c | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`buck ` | a,c | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`coul/cut ` | scale | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`coul/debye ` | scale | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`coul/long ` | scale | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`lj/cut ` | epsilon,sigma | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`lubricate ` | mu | global | -+-----------------------------------+---------------------+------------+ -| :doc:`gauss ` | a | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`morse ` | d0,r0,alpha | type pairs | -+-----------------------------------+---------------------+------------+ -| :doc:`soft ` | a | type pairs | -+-----------------------------------+---------------------+------------+ ++-----------------------------------+-------------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`coul/cut ` | scale | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`coul/debye ` | scale | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`coul/long ` | scale | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`lubricate ` | mu | global | ++-----------------------------------+-------------------------+------------+ +| :doc:`gauss ` | a | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`morse ` | d0,r0,alpha | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`soft ` | a | type pairs | ++-----------------------------------+-------------------------+------------+ +| :doc:`kim ` | PARAM_FREE_*:i,j,... | global | ++-----------------------------------+-------------------------+------------+ .. note:: @@ -144,6 +146,12 @@ meaning of these parameters: Some parameters are global settings for the pair style, e.g. the viscosity setting "mu" for :doc:`pair_style lubricate `. +For :doc:`pair_kim `, all free parameters supported by the +KIM Model are available (e.g., PARAM_FREE_sigmas provided by the +LennardJones612_Universal__MO_826355984548_001 Model). If the free +parameter corresponds to an array, then the particular array element +to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to +adapt the tenth entry of the sigmas array). Other parameters apply to atom type pairs within the pair style, e.g. the prefactor "a" for :doc:`pair_style soft `. diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html index de290c18ee..c99171bf9f 100644 --- a/doc/fix_adapt.html +++ b/doc/fix_adapt.html @@ -224,9 +224,9 @@ pages for individual pair styles and their energy formulas for the meaning of these parameters:

---+++ @@ -273,6 +273,10 @@ meaning of these parameters:

+ + + +
born a type pairs
kimPARAM_FREE_*&#58i,j,...global
@@ -283,6 +287,12 @@ pair_*.cpp file associated with the potential.

Some parameters are global settings for the pair style, e.g. the viscosity setting “mu” for pair_style lubricate. +For pair_kim, all free parameters supported by the +KIM Model are available (e.g., PARAM_FREE_sigmas provided by the +LennardJones612_Universal__MO_826355984548_001 Model). If the free +parameter corresponds to an array, then the particular array element +to be adapted must be specified (e.g., “PARAM_FREE_sigmas:10”, to +adapt the tenth entry of the sigmas array). Other parameters apply to atom type pairs within the pair style, e.g. the prefactor “a” for pair_style soft.

Note that for many of the potentials, the parameter that can be varied diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt index 2fca3808ed..e13f877748 100644 --- a/doc/fix_adapt.txt +++ b/doc/fix_adapt.txt @@ -113,7 +113,8 @@ meaning of these parameters: "lubricate"_pair_lubricate.html: mu: global: "gauss"_pair_gauss.html: a: type pairs: "morse"_pair_morse.html: d0,r0,alpha: type pairs: -"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) +"soft"_pair_soft.html: a: type pairs: +"kim"_pair_kim.html: PARAM_FREE_*:i,j,...: global :tb(c=3,s=:) NOTE: It is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to the @@ -121,6 +122,12 @@ pair_*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html. +For "pair_kim"_pair_kim.html, all free parameters supported by the +KIM Model are available (e.g., PARAM_FREE_sigmas provided by the +LennardJones612_Universal__MO_826355984548_001 Model). If the free +parameter corresponds to an array, then the particular array element +to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to +adapt the tenth entry of the sigmas array). Other parameters apply to atom type pairs within the pair style, e.g. the prefactor "a" for "pair_style soft"_pair_soft.html. diff --git a/doc/searchindex.js b/doc/searchindex.js index ff9aadbc79..5287345c19 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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dust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha_c:426,alp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4,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[9,297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[9,461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:[3,9],cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[9,239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,510],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[9,16,366,507],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,6,12,13,195,443,444,507],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat:[210,261],did:[3,12,373,400,403,404,410,435,464,466,489],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,168,337,365],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,72,73,91,96,99,101,102,126,146,149,150,151,152,153,155,158,159,160,161,162,164,165,166,172,173,175,180,191,192,195,196,199,200,203,205,208,210,212,215,220,221,222,223,224,225,226,230,235,238,239,240,241,242,243,244,247,248,250,260,263,264,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,290,292,294,297,298,299,302,305,307,310,312,320,321,323,326,327,328,331,332,333,335,338,339,340,341,344,348,349,359,362,364,365,366,368,369,371,372,374,375,377,378,379,380,381,382,386,390,391,393,394,395,400,401,402,404,406,409,410,411,413,416,418,419,421,422,429,430,431,432,434,435,437,441,443,444,445,446,447,448,450,451,452,453,461,462,463,464,466,468,469,472,475,476,478,479,481,483,484,485,486,489,490,491,493,495,496,498,499,500,502,506,507,508,509],differenti:[1,3,6,29,192,365,396,441,465],difficult:[224,290,380,412,490],difficulti:[96,112,310,443],diffract:[],diffus:[],digit:[2,3,200,348,433],dih_table1:192,dih_table2:192,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:222,dihydrid:406,dij:310,dilat:[],dim1:3,dim2:3,dim:[3,61,73,149,153,154,155,158,159,160,161,162,164,172,195,216,226,245,341,368,430,484,506,507,508],dimdim:507,dimems:289,dimens:[],dimensinon:73,dimension:[3,40,96,118,124,146,149,152,153,154,155,158,159,160,161,162,164,171,194,212,216,262,289,335,368,371,375,441,481,491],dimensionless:[110,127,128,130,133,135,137,142,146,335,366,452,472],diment:3,dimentionless:141,dimer:[6,307,430],dimgrai:200,dimstr:[42,220],dinola:[294,326],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,196,197,325,502],dir1:492,dir2:492,dir:[1,3,4,8,11,12,261,288,297,322,441,443,444,479,492,507],dirac:146,direc:441,direct:[],directli:[3,6,8,9,11,12,91,119,146,148,196,197,198,199,206,232,241,245,250,289,308,327,339,341,342,343,344,368,372,380,381,382,387,389,390,396,399,404,406,418,422,435,438,446,460,479,491,492,493,499,507],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,62,197,201,225,246,292,298,301,311,319,323,332,333,375,379,381,382,386,393,395,396,404,405,407,414,415,426,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,479,481,482,483,492,507],disabl:[3,12,16,335,417,479,494,507],disadvantag:[6,220],disallow:[196,226,263],disappear:483,discard:[2,3,42,73,214,216,220,336,344,478,483,484],discontinu:[9,192,373,424],discourag:430,discov:[13,336],discret:[6,8,41,43,199,200,247,250],discuss:[],disk:[6,88,89,96,165,194,227,239,293,479],disloc:[72,433],disord:[40,72,433],disp:[],dispar:445,disperion:[399,422],dispers:[3,6,7,9,170,289,365,366,390,399,422,427,435,444,463,469],displac:[],displace_atom:[],displace_box:61,displacemet:484,displai:[11,13,22,37,45,56,180,191,196,199,350,359,393,461],dispters:3,disregard:433,dissip:[6,9,41,84,85,234,240,247,289,311,332,333,388,400,401,402,410,427,428,461],dissolut:221,dist:[6,71,95,114,123,196,290,306,403,460,476,508],distanc:[],distinct:[6,230,304,365,445],distinguish:[6,90,146,253,406,480],distort:[170,381],distrbut:381,distribut:[],distro:[117,393,440,441],ditto:[8,12,14,15,16,17,18,43,121,222,473,479],div:8,divd:123,diverg:[3,12,40,307,333,483,502,509],divid:[3,6,16,42,95,118,123,132,134,147,169,170,180,191,200,212,213,215,220,226,288,331,338,343,365,373,375,407,444,451,469,490,498,507],divis:[6,250,386,416,426,478,499,507],dl_poli:[6,7],dlambda:166,dlammps_async_imd:244,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,199],dlammps_gzip:[3,12,196,199,334,481,482,486],dlammps_jpeg:[3,12,199],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,199],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,196],dlen:491,dlmp_intel_offload:[9,12,16],dlo:[61,195,226,293],dlopen:6,dlvo:[7,394,472],dm_lb:250,dmax:[323,371],dmpvtk:197,dmpvtp:197,dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,117,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,440,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,498,499,507,508,509,510],docuement:445,dodd:43,dodgerblu:200,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,72,73,74,91,92,95,109,113,116,122,123,124,148,150,152,154,155,160,162,166,171,172,173,174,176,178,180,185,191,192,195,196,197,198,199,200,203,209,210,212,216,219,220,222,223,224,226,230,232,235,236,239,240,243,245,247,248,250,253,259,263,264,265,266,267,269,270,271,282,283,284,285,286,294,295,296,300,302,305,307,323,326,328,330,331,335,338,339,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_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,511],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:506,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,507],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,507,509],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:507,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier:[],fourth:[6,110,306,320,330,391,437,451],fox:[6,124,178,459,493],fphi:[38,57,46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:[112,139,144,146],invent:310,invers:[],invert:[1,6,176,289],invis:344,invoc:[170,223,380,448,450,479],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,61,65,68,73,76,77,83,91,92,93,94,98,108,109,111,115,116,117,118,123,149,159,166,167,170,172,173,175,176,178,179,181,182,183,184,186,187,189,190,192,196,197,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,231,232,233,236,237,238,239,240,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,307,308,309,310,312,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,349,351,352,354,355,358,360,364,365,366,367,368,373,375,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,431,435,436,437,438,440,445,446,448,450,452,453,462,463,464,465,466,469,470,471,472,473,475,478,479,480,482,484,486,489,490,492,493,495,498,499,502,507,508],invokd:3,involv:[3,6,7,8,12,65,114,121,122,123,152,176,203,210,221,239,250,292,295,300,323,365,372,373,375,385,403,409,416,462,464,466,477,478,484,486,490,495,496],ioff:[374,481],ion:[6,7,9,154,287,320,335,366,386,397,407,408,430,433,451,461,466,473,481,502],ionic:[6,9,387,389,397,406,407,438,451,502],ioniz:[9,395,406],ionocoval:9,iparam:[3,222],ipi:[],ipp:[],ir3:171,ir4:171,irregular:[6,42,60,220,224,226,263,307],irrelev:437,irrespect:[427,428],irrevers:230,is_act:[3,507],is_avail:[3,507],is_defin:[3,507],isbn:472,isel:[365,366],isenthalp:[9,263,264,265,266,267],ismail:[365,366,390,422],isn:[3,8,11,12,243],iso:[3,224,230,248,263,264,265,266,267,268,269,270,271,294,302,307,502],isobar:[9,263,264,269,270,271,311,402],isodem:406,isoenerget:[9,311,402],isoenthalp:[311,402],isol:[3,175,346],isomorph:290,isotherm:[9,239,263,264,269,270,271,294,311,402],isotrop:[6,96,247,294,365,366,388,409,427,428],isovolum:308,isralewitz:312,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,61,73,75,83,108,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,199,206,209,219,223,224,226,227,232,233,238,239,242,247,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,290,294,296,299,307,309,310,322,326,327,328,333,339,343,345,348,349,351,352,354,355,358,360,366,374,375,378,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,460,462,463,464,465,466,469,471,472,473,481,483,484,490,493,498,499,507,508],ital:[443,444],itali:13,item:[6,7,8,42,196,200,220],iter:[3,6,12,40,42,65,198,206,207,219,220,224,230,232,237,245,289,298,299,307,310,330,346,348,364,371,372,373,375,379,451,476,486,490,495,499,507],ith:[73,123,125,211,212,213,214,215,216,217,218,325,337,499,507],itself:[2,3,4,6,7,8,9,11,12,13,18,43,61,95,113,163,196,198,199,200,201,213,214,225,230,248,258,262,301,307,335,346,348,374,375,396,407,409,413,414,463,479,485,488,489,493,507,511],itset:491,ityp:[3,121,122,172,208,222,300,470],itype1:122,itype2:122,itypen:122,ivector:8,ivori:200,ixcm:307,ixi:[43,98,307,374,507],ixx:[43,98,307,374,507],ixz:[43,98,307,374,507],iycm:307,iyi:[43,98,307,374,507],iyz:[43,98,307,374,507],izcm:307,izrailev:312,izumi:465,izz:[43,98,307,374,507],j0jt:95,j20:213,j_m:146,jac:[6,178,493],jackson:434,jacobi:3,jacobsen:372,jagreat:13,jame:[9,19],janssen:288,januari:430,jaramillo:[7,9,13,406],jarzynski:312,jatempl:9,jcc:9,jcp:340,jec:13,jeff:13,jello:263,jensen:[247,365],jeremi:[9,432],jerom:9,jewett:13,jiang:[248,502],jiao:[9,13],jiht:[7,9],jik:386,jim:7,jku:[7,9],jmake:12,jmm:146,joannopoulo:261,job:[12,62,310,489],jochim:[263,264],john:[7,9,13,198],johnson:[9,13],join:[6,484],joint:[3,292,412],jon:[9,72],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,47,66,91,113,116,203,209,294,323,340,344,366,368,373,382,385,389,390,391,392,394,399,409,411,412,413,416,417,418,419,420,422,423,425,426,429,434,435,441,445,446,456,461,468,493,502],jonsson:[75,262,372,375,451],jorgensen:[6,189,396,418,422],joul:506,journal:[166,184,209,300,366,404,433,443,444,455,456,458],jparam:[3,222],jpeg:[3,12,199],jpeglib:12,jpg:[4,8,12,196,199,200,510],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:507,jtype1:122,jtype2:122,jtype:[3,122,222,470],jtypen:122,judg:495,judici:6,julien:9,jump:[],june:201,just:[3,6,8,11,12,13,17,19,22,29,43,45,61,63,95,113,116,122,147,150,151,165,176,180,196,199,212,216,217,226,230,236,253,260,294,296,307,330,335,346,348,350,374,375,380,382,385,393,413,441,468,479,483,485,486,488,489,500,502,507,510,511],justo:405,jusufi:[397,408],jut:344,jzimmer:9,k11:95,k22:95,k33:95,k_2:353,k_4:353,k_b:[],k_d:502,k_n:[],k_na:[],k_sigma:386,k_ub:20,kadiri:69,kalia:469,kamberaj:307,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53,472],prefer:[7,8,12,306,336,382],prefix:[11,12,199,225,289,475,478],preliminari:[38,57,192,235,463],prematur:373,prepar:[9,298,301,323,492,502],prepend:443,preprint:[146,452],preprocessor:244,prerecord:225,prescrib:[6,8,150,151,152,165,203,204,209,212,227,260,279,336],presenc:[196,221,222,250,253,427,428,433,472,509],present:[1,3,12,18,170,192,198,199,227,240,241,246,250,251,253,254,302,319,341,344,347,395,406,417,426,433,444,445,451,478,502],preserv:[3,61,224,226,263,310,323,345,482],press:[],pressdown:219,pressur:[],pressure_with_eviri:406,presum:[75,161,203,204,205,226,375,413,484],prevent:[2,3,6,41,126,227,238,293,323,334,358,365,371,373,375,380,400,413,439,455,456,458,460,479,483,489,491,502,507],previou:[],previouli:227,previous:[3,11,61,63,73,90,107,123,125,161,172,174,176,195,196,197,198,200,208,210,211,212,213,215,216,217,218,226,227,239,245,258,260,293,305,307,309,310,335,337,340,341,342,343,345,346,367,410,461,476,479,483,484,494,496,498,499,503,504,505,507,508],prevoiu:341,price:[6,399],primari:[0,6,9,335],primarili:[5,7,9,17,148],primaritli:[],prime:[230,248,411,433,464,466,478],primit:[3,6,343,344,368],princip:[3,244,451],principl:[6,9,11,244,264,298,406,414,433,462,478],prinicp:[43,307,374],print:[],printabl:2,printflag:414,printfluid:250,prior:[170,194,311,367,510],priori:490,prioriz:380,prism:[3,6,160,174,484],priveleg:3,privileg:[11,12,244],prob:[221,222],probab:453,probabl:[3,8,12,41,73,162,175,176,178,210,220,221,222,223,227,239,248,263,293,340,346,373,435,463,476,495,502],probe:507,problem:[],problemat:239,proc:[1,3,8,11,12,15,119,196,197,364,478],proce:[42,55,176,220,231,375,433,488,496,499],procedur:[6,12,40,42,200,210,220,239,247,248,249,263,265,266,267,268,269,270,271,282,283,284,285,286,289,326,327,328,329,332,333,373,375,382,388,482,502],proceed:[12,433],procesor:[42,478],process:[],processor:[],processsor:[42,220,478],procp1:[196,197],procsessor:500,procssor:490,produc:[1,3,4,6,7,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,46,47,48,49,50,52,54,55,57,65,67,70,71,73,81,97,114,115,116,118,119,120,121,123,125,147,149,159,170,178,179,181,182,183,184,186,187,189,190,192,196,197,200,203,206,211,212,213,215,216,217,218,219,220,223,226,233,237,238,240,241,242,247,248,249,258,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,297,298,299,302,307,308,309,310,324,325,326,328,335,336,337,339,340,343,348,349,351,352,354,355,358,360,366,373,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,441,444,445,446,453,462,463,464,465,466,469,471,472,473,476,478,483,484,486,487,490,495,496,507,508],product:[6,16,17,18,146,170,226,284,298,336,380,383,406,444,478,507],proessor:380,prof:292,profi:161,profil:[],program:[3,4,6,7,9,11,12,13,17,148,196,199,200,201,203,225,237,244,250,301,404,479,480,492,507],programm:[13,17],progress:[1,42,220,244,261,297,372,373,375,499,502],prohibit:491,project:[6,7,13,14,372,461],promis:7,promot:386,prompt:[8,11,12,244,492],proni:[3,240,241],proofread:8,prop:[6,296],propag:[4,9,208,263,297,313,406,413],propens:6,proper:[223,288,430,479],properati:296,properli:[206,232,307,311,319,374,375,402,479,508],properti:[],propoerti:323,proport:[6,40,42,91,108,109,168,220,247,248,249,297,331,338,339,410],proportion:247,propos:[6,146,210,224,239,263,284,302,418,432,465,467],prospect:7,protect:323,protein:[7,10,172,305,307,321,481,489],protocol:244,proton:[466,473,506],prototyp:[10,43,440],prouduc:[218,337],prove:[84,85,234,250,311],proven:284,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,41,43,63,69,72,124,145,148,166,170,171,172,198,199,201,211,212,218,223,224,225,226,237,239,244,246,250,254,261,263,289,297,298,301,302,307,311,312,330,332,333,336,337,348,363,365,366,371,375,380,382,386,388,393,395,396,400,405,406,410,412,415,417,426,427,430,432,433,441,442,443,444,451,452,460,461,462,464,465,466,469,478,483,489,491,494,495,499,500,507],proxim:195,psa:343,pscreen:[3,12,490],pscrozi:[0,7,13],psec:[200,226,243,247,248,263,294,307,326,327,501,506],psend:478,pseudo:[406,476,481,486],pseudodynam:330,pseudopotenti:[9,433],psf:6,psi:[407,472],psi_ij:407,pstart:[3,263,264,268,294,307],pstop:[3,263,264,268,294,307],pstyle:[91,113,204,205],psu:[443,444],psuedo:486,pt2:171,pt4:171,ptarget:224,pthread:[12,17],ptr:[6,11,237,479],ptype1:121,ptype2:121,pu3:171,pu4:171,pu6:171,publicli:5,publish:[7,250,254,298,396,430,433,464,466],pull:[312,320],puls:335,pump:[427,428],punctuat:[2,476,495],purchas:199,purdu:[9,13],pure:[11,323,413,431,432,464,466,490],purg:[3,482],purpl:[2,200],purport:11,purpos:[3,6,7,12,43,63,73,124,134,140,155,156,171,172,174,176,192,196,216,218,223,224,247,288,290,293,295,306,323,365,380,390,416,422,433,435,468,474,481,484,488,491,493,494,507,511],push:[3,8,206,219,226,245,262,288,305,312,373,410,453],pushd:245,put:[3,6,8,11,12,13,40,61,160,172,196,227,231,342,343,346,368,443,479,481,485],putenv:[492,507],px1:490,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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/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>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,airebo:382,alloi:404,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:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:6,constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:0,fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,2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443,444],adust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha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396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[9,297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[9,461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:[3,9],cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[9,239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,510],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[9,16,366,507],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,6,12,13,195,443,444,507],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat:[210,261],did:[3,12,373,400,403,404,410,435,464,466,489],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,168,337,365],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,72,73,91,96,99,101,102,126,146,149,150,151,152,153,155,158,159,160,161,162,164,165,166,172,173,175,180,191,192,195,196,199,200,203,205,208,210,212,215,220,221,222,223,224,225,226,230,235,238,239,240,241,242,243,244,247,248,250,260,263,264,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,290,292,294,297,298,299,302,305,307,310,312,320,321,323,326,327,328,331,332,333,335,338,339,340,341,344,348,349,359,362,364,365,366,368,369,371,372,374,375,377,378,379,380,381,382,386,390,391,393,394,395,400,401,402,404,406,409,410,411,413,416,418,419,421,422,429,430,431,432,434,435,437,441,443,444,445,446,447,448,450,451,452,453,461,462,463,464,466,468,469,472,475,476,478,479,481,483,484,485,486,489,490,491,493,495,496,498,499,500,502,506,507,508,509],differenti:[1,3,6,29,192,365,396,441,465],difficult:[224,290,380,412,490],difficulti:[96,112,310,443],diffract:[],diffus:[],digit:[2,3,200,348,433],dih_table1:192,dih_table2:192,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:222,dihydrid:406,dij:310,dilat:[],dim1:3,dim2:3,dim:[3,61,73,149,153,154,155,158,159,160,161,162,164,172,195,216,226,245,341,368,430,484,506,507,508],dimdim:507,dimems:289,dimens:[],dimensinon:73,dimension:[3,40,96,118,124,146,149,152,153,154,155,158,159,160,161,162,164,171,194,212,216,262,289,335,368,371,375,441,481,491],dimensionless:[110,127,128,130,133,135,137,142,146,335,366,452,472],diment:3,dimentionless:141,dimer:[6,307,430],dimgrai:200,dimstr:[42,220],dinola:[294,326],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,196,197,325,502],dir1:492,dir2:492,dir:[1,3,4,8,11,12,261,288,297,322,441,443,444,479,492,507],dirac:146,direc:441,direct:[],directli:[3,6,8,9,11,12,91,119,146,148,196,197,198,199,206,232,241,245,250,289,308,327,339,341,342,343,344,368,372,380,381,382,387,389,390,396,399,404,406,418,422,435,438,446,460,479,491,492,493,499,507],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,62,197,201,225,246,292,298,301,311,319,323,332,333,375,379,381,382,386,393,395,396,404,405,407,414,415,426,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,479,481,482,483,492,507],disabl:[3,12,16,335,417,479,494,507],disadvantag:[6,220],disallow:[196,226,263],disappear:483,discard:[2,3,42,73,214,216,220,336,344,478,483,484],discontinu:[9,192,373,424],discourag:430,discov:[13,336],discret:[6,8,41,43,199,200,247,250],discuss:[],disk:[6,88,89,96,165,194,227,239,293,479],disloc:[72,433],disord:[40,72,433],disp:[],dispar:445,disperion:[399,422],dispers:[3,6,7,9,170,289,365,366,390,399,422,427,435,444,463,469],displac:[],displace_atom:[],displace_box:61,displacemet:484,displai:[11,13,22,37,45,56,180,191,196,199,350,359,393,461],dispters:3,disregard:433,dissip:[6,9,41,84,85,234,240,247,289,311,332,333,388,400,401,402,410,427,428,461],dissolut:221,dist:[6,71,95,114,123,196,290,306,403,460,476,508],distanc:[],distinct:[6,230,304,365,445],distinguish:[6,90,146,253,406,480],distort:[170,381],distrbut:381,distribut:[],distro:[117,393,440,441],ditto:[8,12,14,15,16,17,18,43,121,222,473,479],div:8,divd:123,diverg:[3,12,40,307,333,483,502,509],divid:[3,6,16,42,95,118,123,132,134,147,169,170,180,191,200,212,213,215,220,226,288,331,338,343,365,373,375,407,444,451,469,490,498,507],divis:[6,250,386,416,426,478,499,507],dl_poli:[6,7],dlambda:166,dlammps_async_imd:244,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,199],dlammps_gzip:[3,12,196,199,334,481,482,486],dlammps_jpeg:[3,12,199],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,199],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,196],dlen:491,dlmp_intel_offload:[9,12,16],dlo:[61,195,226,293],dlopen:6,dlvo:[7,394,472],dm_lb:250,dmax:[323,371],dmpvtk:197,dmpvtp:197,dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,117,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,440,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,498,499,507,508,509,510],docuement:445,dodd:43,dodgerblu:200,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,72,73,74,91,92,95,109,113,116,122,123,124,148,150,152,154,155,160,162,166,171,172,173,174,176,178,180,185,191,192,195,196,197,198,199,200,203,209,210,212,216,219,220,222,223,224,226,230,232,235,236,239,240,243,245,247,248,250,253,259,263,264,265,266,267,269,270,271,282,283,284,285,286,294,295,296,300,302,305,307,323,326,328,330,33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_j_c:[409,445],epsilon_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,511],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:506,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,507],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,507,509],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:507,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier:[],fourth:[6,110,306,320,330,391,437,451],fox:[6,124,178,4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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/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>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,airebo:382,alloi:404,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:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:6,constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:0,fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,2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