lammps/doc/searchindex.js

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55,177,178,189,345,346,355,387,456],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,409,428,430,458,472,473,501],compens:[6,217,218,301,371,401],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,428,475,476,480,501],compl:17,complain:[11,12,17],complement:425,complementari:[7,391,413],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,402,443,445,463,470,475,480,483,487,489,492,496,501],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,401,428,458,473,475,478,501],compli:[326,330],complic:[6,7,9,12,13,206,235,473],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,395,401,405,422,423,443,445,446,447,475,476,485,493,501,502],componenet:6,composit:[6,206,246,399],compound:[390,401,402,464],compres:[71,118,208],compress:[],compris:[40,340,440,463],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,381],computational:496,compute_arrai:8,compute_fep:[201,421],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,504],concav:340,concentr:[71,399],concept:[6,150,160,208,484],conceptu:[3,6,71,158,220,222,370,391,408,425,480],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,501],conden:[331,459,461],condens:[6,152,331,377,393,399,413,464],condit:[],conducit:6,conduct:[],cone:478,confer:428,confid:[3,489],config:[12,193,472],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,381,400,425,428,457,459,461,464,470,475,477,478,489],confin:[475,489],conflict:[3,12,40,430,473],conform:[3,6,13,59,219,220,258,302,308,330,354,370,401,487],confus:[3,464],conjuct:395,conjug:[7,8,243,367,401,438,439],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,382,384,388,391,395,401,407,413,430,433,441,462,475,478,482,496,505],connect:[3,6,89,155,173,219,240,288,303,306,316,370,392,405,455,461,472,473,479,496],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,391,413,417,470,476,478],consequ:[1,6,206,331,412,489],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,388,401,408,439,440,446,455,470,471,473,476,477,478,480,483,485,493,496,501],consider:[6,8,243,244,322,323,324,375,484],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,381,383,389,391,401,404,408,411,422,423,425,428,430,440,443,445,446,458,465,473,475,476,477,478,479,480,487,496,501],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,389,440],constitut:[443,445],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,401,480,487,496],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,394,428,430,455,457,458,478,479,494,501],constructor:[8,11],consult:439,consum:[1,298,434,501],consumpt:358,contact:[],contact_stiff:[442,444],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,381,390,391,394,399,400,401,408,409,425,428,432,436,437,438,439,447,457,458,459,460,461,462,464,470,471,472,473,475,476,477,478,480,482,484,487,489,490,492,493,496,501,503,505],content:[12,18,439,491,493],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,467,475,482,491,500,501,502],contibut:70,contigu:472,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,381,395,398,415,418,438,439,440,443,445,460,470,473,475,477,478,483,489,490,492,493,501,503],continuum:[6,7,9,205,331,443,445],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,443,445,467,504],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,395,398,399,401,408,422,423,428,430,438,439,446,487,493,496],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,401,404,428,438,439,442,444,457,461,470,472,484,490,491],control_typ:205,controlfil:439,convect:93,conveni:[6,12,29,193,197,214,304,363,447,501],convent:[3,8,9,29,181,188,189,196,302,316,343,399,401,501],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,390,391,413,446,470,482,489],convers:[3,8,144,195,196,206,209,290,360,391,392,393,401,413,417,421,433,473,489,500],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,399,428,459,461,468,473,475,476,477,482,492,496,500,501,503,505],convex:[42,340],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:446,coordbb:446,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,400,446,470,475,476,477,478,480,483,485,489,496,501,502],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,388,438,473],copper:468,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,488],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,384,391,393],cornel:[6,176,487],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,463,475],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:390,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,398,399,400,401,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,466,467,468,475,490,493,496],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,393,423,428,472,473,475,485,500,502],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,382,383,384,385,386,387,388,389,390,391,394,395,399,400,401,402,403,404,405,406,407,408,411,413,414,415,416,417,418,419,420,421,422,425,426,428,430,431,432,433,435,436,438,439,440,441,446,447,448,457,458,459,460,461,464,466,467,468,470,472,473,475,476,478,488,489,490,492,493,496,501],correspondingli:[422,423,484],corrupt:3,cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,391,413,417,428,430,457,472,484],costheta0:[457,459,461,464],costheta:436,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,403,407,408,411,438,439,471,472,473,475,477,479,482,483,490,491,496,501,502],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,382,384,385,386,387,390,391,392,393,394,401,405,406,408,413,417,421,424,430,433,438,439,441,446,456,461,462,464,467,480,487,493,496,500],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,403,407,430,493,501],counter:[3,337,470,481,483,489],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,470],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,422,448,472,475,488,496,501,503],courtesi:363,cov:446,coval:[6,29,401,425,446,496],covari:237,cover:[6,71,190,196,205,246,401,463],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,388,456,470,488,489,492,493,494,501],cpuremain:493,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,496],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,435,463,477,480,501],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,390,401,405,446,480,489,490],criterioni:489,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,386,395,398,399,406,407,408,413,415,417,436,441,443,445,459,461,468,475,479,485,503],crossov:1,crossterm:475,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,479,493,496],crystallin:[6,106,285,363,460,496],crystallis:326,crystallogr:[122,169],crystallograph:[363,493],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,475],cs_re:[40,475],csanyi:[144,437,447],cscl:425,csequ:6,csh:[11,12,388],cshrc:[11,12],csic:[400,457,459,461,464],csinfo:6,csisi:[400,457,459,461,464],csld:[],cst:399,cstherm:6,cstyle:472,csvr:[],ctcm:[376,399],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:425,cube:[6,41,168,173,216,226,340,363,496],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:381,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,407,493],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,388,390,394,399,401,402,405,408,409,412,422,423,425,426,427,430,436,438,439,442,443,444,445,448,459,461,462,465,470,471,472,473,475,476,477,478,479,481,482,483,485,487,489,490,492,493,501,502,503,504,505],curv:[6,170,235,285],curvatur:[404,440,468],custom:[],cut0:473,cut1:484,cut2:484,cut:[],cuthi:[284,296],cutinn:[383,422,423],cutlo:[284,296],cutmax:436,cutoff1:[387,394,413,417,421,424,433,441],cutoff2:[382,384,385,387,393,394,413,417,421,424,433,441],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,473,477,480,484,496,501],cutoff_glob:[],cutoff_inn:[],cutoffa:400,cutoffc:400,cuu3:399,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,501],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,478],cylindr:[6,241,316,337],cypress:375,cyrot:381,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,485],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,382,384,386,391,394,401,405,413,421,433,441,456,462,489,496],damp_com:244,damp_drud:244,dampen:[303,496],dampflag:[337,405],dan:17,danger:[3,12,235,342,395,493],dangl:173,daniel:9,darden:[361,394],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[405,492],dat:[6,93,190,205,471],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,438,439,501],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:424,davi:336,david:[9,19,360,361,459,461],daw:[399,436],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,476,480],ddim:192,deactiv:421,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,409,430,465,473,474,482,485,492,501],deby:[],decai:[94,391,468],decid:[3,6,12,16,71,256,292,303,332,490],decipher:363,declar:194,declin:319,decod:195,decompos:[89,447],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,496],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,473],defaul:61,defect:[6,70,168,428],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,388,389,391,392,394,395,396,397,398,400,401,403,404,405,406,407,408,409,411,413,414,415,416,417,418,419,420,421,422,423,424,428,429,430,431,432,433,435,436,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,484,485,486,487,489,490,492,493,496,497,498,499,500,501,502],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,381,389,396,397,401,411,436,443,445,447,463,473,475,477,484,486,500,501],defint:493,deform:[],deg2theta:169,deg:496,degener:[3,288],degrad:[8,18,285,361,484],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,394,399,407,485,493,496,502],degress:[150,208],del:489,delai:[3,6,12,371,398,493],deleg:408,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,430,455,475,476,477,478,486,487,492,497,499,501,502],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[473,501],deloc:[260,401,446],delr:425,delt_lo:489,delta:[],delta_1:381,delta_3:381,delta_7:381,delta_conf:3,delta_ij:[425,436],delta_mu:[],delta_pi:381,delta_r:436,delta_sigma:381,delta_ua:[],delx:192,delz:192,dem:[],demand:298,demo:11,demon:283,demonstr:[293,425],den:289,dendrim:407,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,391,406,408,439,443,445],dens:[71,219,401],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,381,399,425,426,427,436,440,446,450,452,453,454,475,484,485,493,500],density_continu:445,density_summ:445,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,399,400,401,402,403,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,425,426,428,429,431,432,433,435,436,438,439,440,441,446,447,448,456,457,458,459,460,461,462,464,466,467,468,470,472,475,477,478,481,485,487,489,492,493,495,501,502],dependend:6,depflag:12,dephas:[470,489],depos:223,deposit:[],deprec:[3,294,438],depth:[51,148,195,331,404,440],dequidt:9,der:[89,111,389,390,421,438,439,467,496],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,381,389,394,401,402,406,415,419,420,425,428,438,439,456,458,467,496],derjagin:467,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,382,383,384,386,387,388,389,390,391,394,399,401,402,404,405,406,408,411,413,414,415,416,417,418,419,420,421,422,423,424,425,428,429,435,436,437,438,439,440,441,446,447,448,455,456,457,458,459,460,461,462,464,466,467,468,470,472,473,475,476,477,478,479,485,488,489,492,501,502,503],descript:[],descriptor:[144,193,409],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,383,386,391,393,401,421,422,423,426,427,436,439,458],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,395,399,407,422,423,457,459,461,471,472,473,475,479,484,489,490,492,493,501,502,503],desk:7,desktop:[4,6,7,10,12,195],despit:496,destabil:381,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,383,385,386,387,388,389,390,391,394,395,401,402,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,423,424,425,429,430,435,438,439,440,446,447,448,456,463,466,467,473,475,476,477,478,480,481,484,485,487,490,493,494,501,502,505],detect:[2,3,12,42,61,63,88,94,234,289,330,370,390,407,412,470,472,475,486,489,501],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,385,390,394,398,399,403,405,408,409,417,425,428,430,439,440,446,455,458,462,467,472,475,476,478,480,482,485,489,491,492,494,500,501,502],determinist:307,detil:112,devan:[9,441],devanathan:461,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,381,401,427,428,446,464,477],devemi:9,deviat:[257,264,284,403],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,390],devis:427,dfactor:195,dff:496,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,428],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:425,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,443,445],diagonalstyl:447,diagram:[41,122,169,189,216,286],diallo:407,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,389,404,405,415,440,463,467,475,476,485],diamond:[363,401,425],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,395,398,399,405,430,459,461,483],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,306,308,316,317,319,322,323,324,327,328,329,331,334,335,336,337,340,344,345,355,357,359,36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,equil:[3,294,364,482,505],equilater:485,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,390,391,438,439,471,485],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,390,425,432,446,496],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,395,401,446,459,461,475,478,483,484,493,496],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,401,475],eras:[305,328],erat:[222,423],erc:391,erfc:[391,413,430],erforc:117,erg:500,erhart:[206,399,459,461],ermscal:378,ernst:9,eror:3,eros:425,erose_form:425,erot:[],errata:[459,461],erratum:336,erron:3,error:[],erta:405,ervel:[117,475],escap:[223,496],especi:[8,16,158,170,199,206,216,235,293,298,301,302,375,472],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,391,413,461,480,493],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,430,439,458,489,493],esu:500,esub:425,eta:[6,246,259,293,294,296,335,400,402,404,436,460,464,500],eta_dot:259,eta_ij:436,eta_ji:402,etag:[40,475],etail:493,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,399,400,408,421,423,428,434,438,439,457,459,461,464,470,473,475,476,477,482,484,485,489,490,491,492,493,494,496,500,501,503,505],ethernet:18,etol:[368,370,470,489],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,492,493],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:449,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,428,430,436,442,444,446,458,470,471,473,477,478,480,482,483,484,485,489,491,493,501,502],evalut:[344,473],evan:[158,280],evanseck:[6,20,176,386,487],evapor:[],evaul:[8,368],evdwl:[111,438,439,493],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,401,402,405,408,411,430,440,464,465,475,476,478,480,481,482,484,485,487,490,492,493,494,496,505],evenli:[3,41,145,190,216,246,411,465],event:[],eventu:[3,6,12,15,172,294,489],ever:[54,56,242,319],evera:[389,404,440,456],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,395,398,408,421,438,439,446,452,469,470,471,475,477,479,480,482,483,484,489,490,491,493,501,505],everyth:[8,111],everywher:[120,415],eviri:401,evolut:[237,246,286,470],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,382,384,385,391,394,401,413,417,433,441,456,458],ewald_disp:394,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,388,477,482,489,501,503,505],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,388,395,399,405,408,422,430,458,477,478,485,489,501],exager:496,examin:[6,8,9,17,219,285],examp:[473,501],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,475,501],exceed:[3,41,59,216,222,259,319,483],excel:401,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,393,394,395,399,400,401,402,403,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,423,426,431,432,433,435,438,439,440,441,448,456,457,458,459,460,461,464,466,467,468,470,472,473,475,477,478,480,483,484,485,486,487,489,493,496,500,501,502,504],excess:[210,401],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,401,490],exchange:360,excit:[9,401],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,383,405,408,411,422,423,430,455,487],exclus:[1,3,9,12,16,89,375,390,428,430,484,494],excurs:[259,470],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,471,473,483,486,489,501],exempl:446,exemplari:236,exemplifi:401,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,501],exhibit:[94,259,367,401,484],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,396,397,408,438,455,465,471,473,475,476,477,486,487,488,501,502,503],exit:[2,3,11,12,41,57,193,216,231,359,374,473,474,483,492,501],exlanatori:3,exp:[],expand:[],expans:[12,144,193,486,501],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,388,425,428,430,470,473,475,477,480,484,489,501],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,473],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,395,430,484,489],experienc:[6,12,248,249],experiment:[235,360,375,489],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,399,411,446,448,463,473,476,477,480,482,485,496,501,505],explan:[3,6,59,117,144,193,208,258,284,408,469,472,473,475,484],explanatori:[3,8,121,193,207,208,211,212,213,303,369,472,501],explantori:[3,299],explic:429,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,381,386,388,399,401,412,422,462,469,472,476,479],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,394,395,398,399,400,402,403,404,405,406,407,408,412,413,414,415,416,417,418,419,420,421,422,426,428,430,431,432,433,435,440,441,448,449,450,451,452,453,454,456,457,458,459,460,461,462,464,466,467,468,475,477,478,484,485,487,488,494,496],explictli:[16,488],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,399,404,407,421,429,441],exponenti:[89,436,457,464,468,489,501],expos:11,exposit:[205,395,398],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,381,399,401,415,425,446,447,456,501],expressiont:381,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,404,425,428,439,440,447,492,493],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,442,444,458,472,475,478],exterior:[3,6,168,340],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,394,405,408,411,425,430,472,473,475,478,487,496,501],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,391,402,425,447,473,480,492],extract_atom:11,extract_comput:[11,473],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,401,460,496],extrema:421,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[459,460,461],f_ave:121,f_c:460,f_f:461,f_fix_id:293,f_harm:329,f_i:[29,436],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,493,501],f_ij:436,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:436,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,459,460,461],f_sigma:381,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,404,425,440,475,478],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,405,446,487],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,381,382,384,386,391,392,393,395,396,397,401,405,408,412,413,425,428,430,432,433,439,441,448,457,462,472,475,478,479,484,487,489,490,493,496,500,501],factori:[3,473],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,393,439,473],failur:[125,443,474,501],fairli:[11,430,484,489],faken:73,falcon:240,fall:[3,6,196,211,289,473,501],fals:[88,342,344,446,501],fame:8,famili:[464,472],familiar:[0,11],fan:436,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,463,473,475,480,493],farago:243,farrel:[459,461],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,408,422,478,487,501,504],fasolino:410,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,383,422,423,428,456,458,477,482,484,493,502,505],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,381,382,383,384,385,386,387,388,389,390,391,394,395,399,400,402,403,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,426,431,432,433,435,440,441,448,456,457,458,459,460,461,464,466,467,468,470,478,484,488,496],fastest:[1,6,14,17,158,212,331,332,375,472],fatal:[3,492],fault:[70,439],faulti:12,fava:404,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,501],fdirect:226,fdotr:409,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:399,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,430],felling:427,felt:340,femtosecond:500,fene:[],fennel:[391,413],fep:[],ferguson:[6,176,487],fermi:[1,12,15,156,375,461],fermion:[9,401],fernando:424,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,446,472,475,480,484,486,494,501,503],fewer:[1,3,11,15,16,61,249,484],fewest:3,fextern:233,feynman:286,fff:473,ffield:[390,402,438,439,446],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,11,12,14,15,90,113,114,145,285,360,361,484],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,494],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:455,fictiti:[6,202,203,228,233,237,286,302,391,413,417,455],field1:[476,480],field2:476,field:[],fifth:[316,432],figur:[1,3,8,12,293,472,473],fij:394,file0:284,file1:[11,13,284,330,344,369,480,482,486],file2:[11,13,330,344,369,480,482,486],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,381,391,399,400,402,410,425,426,427,432,436,437,438,439,446,447,457,458,459,460,461,464,471,472,473,476,477,482,486,493,501,503,504,505],filennam:482,filep:[3,193,196,477,482,505],filepo:300,fill:[7,9,170,195,289,331,363,371,381,428,439,478],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,393],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,391,408,413,417,425,446,456,458,496,501],find_custom:8,fine:[16,17,174,202,228,329,371,375,501],finer:[144,170,501],finest:360,finger:[170,192,256,478],finish:[6,11,41,216,344,357,359,360,372,374,375,463,480,501,502],finit:[],finni:[7,399,456],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,381,382,384,386,388,390,391,399,401,402,405,406,408,409,410,411,412,413,417,422,423,425,427,428,430,432,436,438,439,446,447,455,457,458,459,460,461,464,468,470,471,472,473,475,476,477,480,482,484,487,488,489,492,493,496,501,502,503,505],fischer:[6,9,19,20,176,386,487],fit:[3,6,9,12,38,56,190,231,302,319,377,381,410,425,430,451,458,460,483,501],five:[73,156,293,369,381,426,475,489],fix:[],fix_adapt:[164,201,421],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,390],fix_rattl:306,fix_reax_bond:438,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:394,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,196,197,214,219,221,225,240,243,247,249,255,256,285,292,303,316,318,319,326,330,339,342,358,361,369,373,374,375,377,407,412,425,428,455,470,472,473,475,476,477,479,480,481,485,501],flag_buck:385,flag_coul:[385,394,417],flag_lj:[394,417],flagfld:[383,422,423],flaghi:[3,383,422,423],flaglog:[383,422,423],flagn:225,flagvf:[383,422,423],flat:[6,331,336,337,341],flavor:[2,7,12],fld:[9,336,383,422,423],flen:378,flex_press:378,flexibl:[3,6,8,171,195,208,212,221,237,260,327,334,401,460,493],flip:[3,6,222,259,338,339],floor:501,flop:12,floralwhit:196,flow:[],fluctuat:[6,64,89,220,235,236,243,246,259,264,284,285,307,329,331,354,397],fluid:[],fluid_veloc:250,flush:[3,196,492],flux:[],flv:195,fly:[7,9,12,41,195,199,205,210,223,226,303,306,332,381,428,493,496],fmackai:9,fmag:224,fmass:286,fmax:[368,493],fmomentum:226,fmsec:[2,196,243,244,256,259,290,303,322,323,484,495,500,502],fname:359,fno:[12,16],fnorm:[368,493],fnpt:226,fnvt:226,foce:408,fock:378,focu:306,fogarti:[9,296,439],foil:[144,284,447],fold:[317,484],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,194,195,196,199,205,206,207,208,209,210,211,212,213,214,216,221,222,223,226,227,230,231,233,235,236,237,240,242,243,244,246,249,257,259,264,265,266,267,278,279,280,282,285,286,288,291,292,293,294,296,298,300,302,303,304,306,321,322,323,324,327,328,329,330,331,333,334,342,343,347,348,349,350,351,354,356,358,363,365,368,369,370,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,435,436,437,438,439,440,441,443,445,446,447,448,449,450,451,452,453,454,455,457,458,459,460,461,462,463,464,466,467,468,470,472,473,475,476,478,480,482,483,484,487,489,490,491,496,501,502,504],foo:[4,8,11,12,193,195,233,473,486,501],foot:6,footprint:[12,375],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:249,forcefield:[302,407],forcegroup:246,forcezero:366,ford:394,forestgreen:196,forev:71,forget:[244,496],forgiv:259,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,196,199,200,201,218,236,237,243,245,249,256,280,285,296,298,302,303,331,336,340,345,346,349,354,365,367,369,370,377,378,381,388,396,397,399,401,403,407,408,412,424,425,427,428,432,433,436,438,439,440,446,447,448,456,458,459,460,461,467,469,472,473,475,480,485,492,496,501],formal:[6,78,80,93,236,237,243,259,286,319,327,446],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,208,211,212,213,214,216,218,231,285,288,292,294,296,299,303,304,315,330,331,342,343,346,365,369,370,376,377,381,388,399,402,412,425,427,437,438,439,441,447,458,464,465,472,473,475,476,477,480,491,492,493,501,503],former:[6,12,16,39,41,196,216,331,335,381,383,481,487,501],formerli:[7,13],formul:[1,40,64,145,202,228,243,259,280,294,296,302,306,330,360,377,381,399,401,404,425,435],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,200,201,202,203,208,209,210,211,214,215,222,228,238,239,241,243,244,256,284,285,291,300,305,313,317,319,322,323,324,333,336,339,341,342,344,345,346,348,355,363,369,377,378,380,381,386,387,388,389,394,395,399,400,404,405,406,407,409,412,413,415,416,417,419,420,422,423,425,429,430,431,440,441,448,456,457,459,460,461,464,466,467,471,475,478,485,492,493,500,501,502],forth:[1,6,11,12,13,14,15,374,473,478,482],fortran:[3,6,9,11,12,13,233,399,408,425,438,439],fortun:8,forward:[3,8,89,359,370,375],foster:[381,435,436],foul:173,found:[3,6,9,12,73,164,193,219,221,235,240,246,285,326,332,344,359,371,388,391,394,470,476,477,492],four:[6,11,54,81,106,107,144,166,257,331,354,369,370,428,470],fourier:[],fourth:[6,108,302,316,326,386,432,446],fox:[6,122,176,454,487],fphi:[38,56,458],fpic:12,fplo:[38,56,458],fprime:458,fqdn:242,fqq:394,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,195,196,206,217,218,219,220,257,289,293,300,301,319,324,325,363,370,375,381,383,405,422,423,480,485],fragment:[42,240,300],fraig:42,frame:[85,144,196,205,257,293,338,404],framer:[195,196],framework:[5,237,376,447],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,89,164,201,284,319,328,329,330,331,367,370,378,401,421,428,436,467,472],freedom:[3,6,8,97,99,100,102,104,105,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,208,219,226,235,237,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,303,306,322,323,324,329,368,394,493,496,502],freeli:[0,6,7,12,148,149,163,168,195],freez:[],frenkel:[235,329],freq:204,frequenc:[3,6,16,39,106,196,210,273,285,286,293,298,358,395,401,439,446,470,484,489,501,504],frequent:[3,64,67,70,72,73,77,90,94,110,144,196,217,218,232,327,334,430,482],fri:[257,293],friction:[4,5,6,10,42,199,237,243,293,298,303,331,335,337,405,4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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","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","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","dimension command","displace_atoms command","dump 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","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","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":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,381,383,401,422,423,428,430,438,439,455,456,470,471,472,475,476,478,480,482,483,484,487,489,491,492,493,494,495,500,502,503,504],"function":501,"long":[210,382,384,385,386,387,391,393,394,413,417,421,433,441],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:399,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,501],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:381,born:[382,393],boundari:[7,57],box:[6,58,220],brownian:383,buck:[384,385,393,424],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,386,421],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,387],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,389,467],colvar:[9,13,221],com:[74,75,151],comb3:390,comb:[295,390],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,497,498,499,500,501,502,503,504,505],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,501],compute_modifi:105,condit:7,conduct:[6,327],conserv:396,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[382,384,385,386,387,391,392,393,406,413,417,421,433,441],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:415,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,382,384,386,387,399,405,406,413,414,416,419,431,457,459],custom:8,cut:[49,378,384,387,391,394,401,403,413,414,421,429,433],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[391,413],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,2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