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i:[9,307,447,448],adust:170,advanc:[3,248,390,480,491],advantag:[1,6,8,11,14,18,40,41,42,224,384,409,494,499],advect:[3,6,327],advertis:8,advis:[379,446],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,75,95,127,151,160,174,180,203,204,209,216,217,219,220,221,222,225,226,227,228,230,231,241,247,249,251,257,264,268,269,270,271,273,274,275,281,286,287,288,290,311,312,325,339,349,362,369,375,376,377,379,380,381,384,410,431,432,439,482,483,485,487,488,490,493,495],affin:[16,17,18,230,384,399],afil:245,aforement:18,afresh:[299,493,512],afshar:404,after:[],afterrun:493,afterward:3,afterword:42,ag1:175,ag2:175,again:[6,11,12,16,17,64,150,156,162,170,200,204,230,247,297,353,368,379,431,432,480,482,483,485,487,492,499,501,512,514],against:[11,12,13,66,231,379,447,448],aggreg:[6,12,68,71,73,84,101,118,125,247,263,309,311,325,480,513],aggress:[247,499],agilio:[9,13],agre:[3,8,196,377,386,419,448],agreement:[5,7],ahd:416,ahead:346,aidan:[0,5,7,9,13,372],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:203,akohlmei:[7,9,13,205,248],aktulga:[7,9,304,448],al2o3:455,al2o3_001:[128,312],al3:175,ala:[254,455],alain:9,alat:[292,434],alb:[445,468,470],albeit:310,albert:9,alchem:[94,170],alcohol:342,alcu:[385,390],alcu_eam:445,alderton:403,alejandr:[267,268],alessandro:13,algebra:437,algorithm:[0,1,6,7,8,9,42,63,204,213,224,227,230,254,256,257,281,294,302,311,314,315,334,335,339,342,347,375,376,377,381,384,406,410,432,437,452,454,480,482,499],alia:[9,12,16],alias:[1,370],aliceblu:204,align:[6,9,12,29,42,75,178,196,220,224,249,372,485,488,506],alkali:410,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,169,170,171,172,173,174,175,176,177,178,179,180,182,184,189,195,196,197,200,201,202,203,204,205,207,208,209,210,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,260,262,263,265,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,293,294,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,323,324,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,352,353,354,358,363,365,367,368,369,370,371,372,374,377,378,379,380,381,383,384,385,386,387,389,390,391,393,394,395,396,397,399,400,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,476,477,479,480,482,483,484,485,486,487,488,489,490,492,493,494,495,496,497,498,499,500,502,503,504,506,507,511,512,513,514,515,516],allen:[29,94,403,413],allentildeslei:94,allign:3,allindex:351,alloc:[3,5,6,8,9,11,12,62,241,341,378,380,384,443,448,485,493],allocat:3,alloi:[],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,81,99,116,118,152,154,155,156,169,174,175,176,178,184,195,196,200,201,203,204,205,207,208,210,212,213,214,216,217,218,219,220,221,222,224,226,227,228,229,230,231,235,236,241,243,244,245,246,248,251,254,257,258,262,264,267,268,292,296,297,298,299,300,301,305,311,312,314,316,318,319,323,327,334,335,336,337,339,340,341,342,343,344,350,352,354,363,369,370,372,377,378,379,380,383,384,386,387,390,391,392,393,394,395,400,408,410,414,415,416,417,422,426,431,432,437,439,445,448,449,452,454,455,464,471,474,476,480,483,485,487,488,489,490,491,492,495,497,498,499,502,503,507,512,513],almost:[2,3,12,62,249,301,339,370,381,384,464],alo:400,alon:[6,7,227,307,447,448,483],alond:13,along:[6,8,12,29,41,75,94,128,174,175,176,199,200,203,216,227,249,254,255,259,264,266,301,311,314,316,320,324,325,334,338,339,345,348,350,372,375,376,377,379,400,403,414,417,420,422,426,434,447,448,467,485,488,495,496,512],alonso:[435,436],alpha:[6,12,52,208,254,293,301,302,306,377,385,388,391,400,404,406,408,409,411,416,421,422,434,440,444,469,471,503,506],alpha_:[],alpha_c:430,alpha_i:456,alpha_ialpha_j:[],alpha_lj:430,alphabet:[2,3,22,37,45,56,65,184,195,207,354,363,378,397,465,485],alphanumer:[3,65,207,300,308,352,378,512],alreadi:[3,7,8,9,12,16,17,18,43,176,177,179,202,212,216,220,221,224,226,230,258,299,301,327,350,351,378,379,404,415,417,424,432,464,474,477,481,485,486,490,495,511,512],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,69,75,76,77,79,81,86,94,96,97,99,102,112,113,114,115,116,117,122,124,126,127,129,150,151,152,153,154,155,156,157,158,159,160,162,163,164,165,166,168,169,170,171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17],complement:434,complementari:[7,400,422],complet:[3,6,9,11,12,15,42,61,75,204,220,224,229,257,294,297,300,327,338,340,351,352,368,379,384,411,452,454,472,480,485,490,493,497,499,502,506,512],complex:[4,6,8,11,12,13,25,41,43,64,99,116,150,152,164,176,177,254,323,348,367,379,410,437,467,483,485,488,512],compli:[334,338],complic:[6,7,9,12,13,214,243,483],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,95,96,97,98,99,102,103,106,113,114,115,116,117,118,119,120,122,123,127,137,140,141,142,143,146,147,148,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,171,172,173,199,200,201,203,204,210,211,215,216,217,218,219,220,221,222,223,227,228,230,231,236,241,246,250,251,254,257,259,263,264,266,267,268,272,273,274,275,286,287,288,290,291,293,294,295,298,309,311,313,314,316,320,321,324,327,330,331,332,334,341,342,347,348,349,369,372,376,377,378,379,384,404,410,414,431,432,452,454,455,456,485,486,495,503,512,513],componenet:6,composit:[6,214,254,408],compound:[399,410,411,473],compres:[75,124,216],compress:[],compris:[41,348,449,472],compton:[128,175],comptu:3,compuat:370,comput:[],computation:[3,6,225,226,339,390],computational:506,compute_arrai:8,compute_fep:[209,430],compute_group_group:243,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[128,312],compute_scalar:8,compute_temp:8,compute_ti:209,compute_vector:8,compute_xrd:175,concaten:[2,3,515],concav:348,concentr:[75,408],concept:[6,156,166,216,494],conceptu:[3,6,75,164,228,230,379,400,417,434,490],concern:[6,77,94,202,244],concetr:75,concis:[11,338],conclud:12,concret:8,concurr:[16,370,512],conden:[339,468,470],condens:[6,158,339,386,402,408,422,473],condit:[],conducit:6,conduct:[],cone:488,confer:437,confid:[3,499],config:[12,200,482],configfil:229,configur:[1,2,6,12,15,17,38,61,132,178,196,199,200,203,207,228,229,230,231,235,243,250,251,281,294,302,338,367,377,379,386,390,409,434,437,466,468,470,473,480,485,487,488,499,507],confin:[485,499],conflict:[3,12,41,201,439,483,507],conform:[3,6,13,61,227,228,266,310,316,338,362,379,410,497],confus:[3,473],conjuct:[9,404],conjug:[7,8,251,376,410,447,448],conjunct:[6,7,75,93,94,124,159,164,170,176,180,204,208,209,251,254,258,281,297,298,302,303,304,306,311,315,327,335,342,347,369,370,379,391,393,397,400,404,410,416,422,439,442,450,471,485,488,492,506,516],connect:[3,6,9,94,161,179,227,248,296,311,314,324,379,401,414,447,448,464,470,482,483,485,489,506],conner:386,connor:386,conput:3,consecut:[3,11,12,40,75,176,204,208,209,231,248,249,400,422,426,480,486,488],consequ:[1,6,214,339,421,499],conserv:[],consid:[6,74,75,82,94,125,158,161,162,179,200,201,204,208,209,215,217,220,224,226,227,231,255,268,293,311,334,335,338,339,342,370,397,410,417,448,449,455,464,480,481,483,486,487,488,490,493,495,503,506,512],consider:[6,8,251,252,330,331,332,384,494],consist:[3,6,8,9,11,12,41,43,68,73,84,101,113,118,121,122,125,156,159,161,176,188,199,205,210,211,216,230,231,234,236,241,244,251,252,253,264,267,269,270,271,272,273,274,275,276,277,279,280,281,282,284,285,286,287,288,289,290,298,301,306,308,310,311,330,331,332,333,343,369,370,372,378,379,384,386,390,392,398,400,410,413,417,420,431,432,434,437,439,449,452,454,455,467,474,483,485,486,487,488,489,490,497,506,512],consistent_fe_initi:213,consit:311,constant:[],constitu:[3,6,257,311,344,348,398,449],constitut:[452,454],constrain:[3,6,8,153,154,155,156,157,159,162,163,164,165,166,168,169,207,216,231,243,244,249,257,261,296,297,309,311,314,325,335,342,377,378,410,490,497,506],constraint:[],construct:[6,8,12,14,38,55,57,63,66,70,74,76,77,81,99,116,128,150,175,228,267,293,310,348,380,384,403,437,439,464,466,467,488,489,504,512],constructor:[8,11],consult:448,consum:[1,306,443,512],consumpt:367,contact:[],contact_stiff:[451,453],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,94,98,126,128,150,152,156,164,174,175,176,178,182,184,195,196,200,201,203,204,205,207,208,209,213,215,216,217,219,220,221,222,224,229,231,236,239,245,249,250,251,254,265,281,292,293,296,297,299,301,304,308,311,312,317,327,334,338,339,348,349,352,368,370,378,379,382,383,385,386,387,390,399,400,403,408,409,410,417,418,434,437,441,445,446,447,448,456,466,467,468,469,470,471,473,480,481,482,483,485,486,487,488,490,492,494,497,499,500,502,503,506,507,512,514,516],content:[4,8,9,12,18,448,501,503],context:[3,6,8,12,17,126,127,204,225,226,231,296,308,343,376,476,485,492,501,511,512,513],contibut:74,contigu:482,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,75,86,112,113,172,204,207,208,209,214,216,217,218,219,220,221,222,224,227,228,229,230,231,243,244,245,247,248,249,251,252,253,259,264,265,267,269,270,271,272,273,274,275,286,287,288,289,290,295,297,300,301,311,312,316,326,327,329,336,337,339,345,348,352,368,383,384,390,404,407,424,427,447,448,449,452,454,469,480,483,485,487,488,493,499,500,502,503,512,514],continuum:[6,7,9,213,339,452,454],contour_integr:213,contract:[61,228,230,267,298,311],contradictori:3,contrain:314,contraint:281,contrari:[245,252],contrast:[1,6,43,56,66,158,161,201,230,350,452,454,476,515],contrib:339,contribut:[3,4,5,6,7,8,9,12,13,17,65,67,69,71,72,74,75,78,79,81,83,85,91,94,95,96,97,98,100,102,111,113,115,117,118,119,120,122,124,127,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,209,214,215,216,217,219,220,221,222,228,243,251,254,257,258,262,268,288,289,296,297,305,308,311,312,314,341,369,377,379,387,404,407,408,410,417,431,432,437,439,447,448,455,497,503,506,507],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,94,98,132,150,185,200,201,203,207,213,214,224,228,229,230,247,248,251,252,267,269,270,271,272,273,274,275,298,303,311,318,319,330,331,332,339,343,367,369,381,410,413,437,447,448,451,453,466,470,480,482,494,500,501],control_typ:213,controlfil:448,convect:98,conveni:[6,12,29,200,205,222,312,372,456,471,507,512],convent:[3,8,29,187,194,195,201,204,310,324,351,408,410,512],converg:[3,6,42,95,200,201,203,205,210,224,227,228,236,241,272,301,303,306,310,314,375,376,377,379,399,400,422,455,480,492,499],convers:[3,8,150,203,204,214,217,298,369,400,401,402,410,422,426,430,442,483,499,511],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,75,98,176,183,200,203,204,217,222,265,297,350,353,355,359,362,372,379,385,408,437,468,470,477,483,485,486,487,492,502,506,511,512,514,516],convex:[43,348],convinc:[7,12],cook:9,cooki:7,cool:[7,166,247,309],cooordin:[200,201],cooper:[5,7],coord123:124,coord1:[3,124,216,220,221],coord2:[3,124,216,220,221],coord3:[3,124,216,220,221],coord:[],coordb:455,coordbb:455,coordiat:377,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,69,71,75,78,79,81,86,94,96,97,102,112,113,115,123,124,126,144,150,159,165,171,173,174,176,180,199,200,201,202,203,204,205,207,210,215,216,219,220,221,224,225,226,227,228,229,230,231,234,236,237,241,243,246,247,248,249,250,251,252,264,266,267,269,270,271,273,274,275,288,291,292,293,296,297,298,308,309,311,313,314,316,321,324,325,326,327,329,337,338,339,346,347,349,350,372,377,378,379,384,385,386,389,409,455,480,485,486,487,488,490,493,495,499,506,512,513],coordn:[124,216],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,129,203,339,379,397,447,483,507],copper:477,coproccesor:16,coprocessor:[1,7,9,16,17,384,498],coproprocessor:17,copy_arrai:8,copyright:[7,8,296],coral:204,core:[],core_shel:158,coreshel:[],cornel:[6,182,497],corner123i:123,corner123x:123,corner123z:123,corner1i:123,corner1x:123,corner1z:123,corner2i:123,corner2x:123,corner2z:123,corner3i:123,corner3x:123,corner3z:123,corner:[3,6,41,123,203,348,349,372,472,485,507],cornflowerblu:204,cornsilk:204,corp:9,corpor:16,corr:399,correct:[3,6,9,11,12,16,17,61,94,95,111,112,117,120,126,158,163,170,201,203,230,243,245,251,267,268,288,296,298,301,338,344,348,369,379,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,477,478,485,500,503,506,507],correction_max_iter:213,correctli:[3,8,11,17,75,86,111,112,113,153,154,155,157,159,161,162,163,164,165,168,169,172,200,204,210,231,236,241,252,261,267,268,304,311,314,324,326,345,348,379,380,384,402,432,437,482,483,485,495,507,511,513],correl:[],correpond:239,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,74,75,94,105,106,119,122,123,124,125,128,129,137,140,141,142,143,144,146,147,148,150,153,154,163,170,174,175,182,183,184,185,186,187,188,190,191,193,194,196,199,200,201,203,204,208,209,210,216,218,219,220,221,223,226,228,230,237,241,242,246,251,254,255,263,264,265,267,269,270,271,272,273,274,275,276,277,281,284,286,287,288,290,293,294,298,303,311,313,314,330,332,334,343,344,345,347,348,349,351,353,354,355,356,358,359,362,364,370,374,376,378,379,385,386,388,391,392,393,394,395,396,397,398,399,400,403,404,408,409,410,411,412,413,414,415,416,417,420,422,423,424,425,426,427,428,429,430,431,434,435,437,439,440,441,442,444,445,447,448,449,450,455,456,457,466,467,468,469,470,471,473,475,476,477,480,482,483,485,486,488,498,499,500,502,503,506,512],correspondingli:[431,432,494],corrupt:3,cosin:[],cosineshift:27,cosmo:[245,250],cossq:[],cost:[1,6,10,11,12,17,40,42,75,119,128,151,175,203,204,216,220,221,224,225,226,240,267,303,339,369,370,382,400,422,426,437,439,466,482,494],costheta0:[466,468,470,473],costheta:445,costli:[11,95,245,380],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,69,75,79,94,97,102,113,115,119,122,124,156,166,171,173,189,200,201,203,204,208,209,216,217,220,224,230,241,250,300,301,302,306,309,311,313,327,328,334,338,339,340,344,348,350,352,360,366,368,375,377,380,384,387,412,416,417,420,447,448,481,482,483,485,487,489,492,493,500,501,506,512,513],coulomb:[3,5,6,7,8,9,10,12,14,15,18,76,95,117,118,126,151,177,181,302,304,340,369,370,377,384,391,393,394,395,396,399,400,401,402,403,410,414,415,417,422,426,430,433,439,442,447,448,450,455,465,470,471,473,476,490,497,503,506,511],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,71,81,98,124,126,127,164,174,180,210,211,214,216,219,220,221,223,224,231,236,240,243,249,267,281,297,314,330,331,348,370,377,378,379,381,384,412,416,439,503,512],counter:[3,345,480,491,493,499],counteract:243,counterbal:247,counterbalanc:29,counterpart:[200,311,480],counterproduct:18,coupl:[],courant:317,cours:[3,8,136,138,170,200,208,209,244,310,324,338,344,346,347,349,350,370,431,457,482,485,498,506,512,514],courtesi:372,cov:455,coval:[6,9,29,410,434,455,506],covari:245,cover:[6,75,196,204,213,254,410,472],coverag:[75,220],cpc:250,cpp:[1,3,6,8,9,11,12,13,94,200,208,209,241,314],cpu:[1,3,9,10,12,14,15,16,17,18,65,75,204,218,234,252,340,367,370,384,397,465,480,498,499,502,503,504,512],cpuremain:503,cr2:175,cr3:175,crack:[4,380],crada:[5,7],crai:[5,7,13,18,200],crash:[3,12,380,506],craympi:384,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:213,create_faceset:213,create_group:202,create_nodeset:213,createatom:[],creation:[],crimson:204,critchlei:296,criteria:[3,126,177,203,204,225,226,227,262,377,444,472,487,490,512],criterion:[12,42,131,176,179,214,224,227,243,281,303,317,345,350,377,379,399,410,414,455,490,499,500],criterioni:499,critic:[6,49,50,265,334,339,377],crmax:75,crmin:75,cross:[3,12,22,75,96,154,174,184,200,201,203,215,220,226,230,264,266,288,311,320,324,326,335,342,354,372,379,395,404,407,408,415,416,417,422,424,426,445,450,452,454,468,470,477,485,489,495,514],crossov:1,crossterm:485,crozier:[0,7,13],crucial:301,crystal:[3,4,6,13,77,116,292,293,337,372,380,485,489,503,506],crystallin:[6,112,293,372,469,506],crystallis:334,crystallogr:[128,175],crystallograph:[372,503],crystallographi:[128,175,372],cs1:175,cs_chunk:6,cs_im:[41,485],cs_re:[41,485],csanyi:[150,446,456],cscl:434,csequ:6,csh:[11,12,397],cshrc:[11,12],csic:[409,466,468,470,473],csinfo:6,csisi:[409,466,468,470,473],csld:[],cst:408,cstherm:6,cstyle:482,csvr:[],ctcm:[385,408],ctemp_cor:234,cterm:316,ctr:9,ctype:11,cu1:175,cu2:175,cu3au:434,cube:[6,42,174,179,224,234,348,372,506],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:390,cummul:[3,6,222,225,226,227,229,240,245,251,253,327,330,331,332,333,335,342,416,503],cumul:[6,214,216,219,220,221,235,243,251,265,267,272,281,311,312,379],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,75,77,86,94,111,112,118,126,127,140,151,156,164,166,172,174,177,180,199,200,201,202,203,204,205,208,209,213,216,220,221,222,224,225,226,227,228,229,230,231,235,236,241,243,245,248,249,251,257,264,267,268,273,274,275,281,286,287,288,290,296,297,302,303,305,308,309,310,311,314,315,316,317,318,319,320,321,323,325,326,327,330,331,332,338,339,342,343,344,345,346,347,349,350,352,367,368,369,370,373,374,376,377,378,379,384,390,397,399,403,408,410,411,414,417,418,421,431,432,434,435,436,439,445,447,448,451,452,453,454,457,468,470,471,474,480,481,482,483,485,486,487,488,489,491,492,493,495,497,499,500,502,503,507,512,513,514,515,516],curv:[6,176,243,293],curvatur:[413,449,477],custom:[],cut0:483,cut1:494,cut2:494,cut:[],cuthi:[292,304],cutinn:[392,431,432],cutlo:[292,304],cutmax:445,cutoff1:[396,403,422,426,430,433,442,450],cutoff2:[391,393,394,396,402,403,422,426,430,433,442,450,471],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,74,76,77,81,94,99,116,118,125,126,150,174,177,179,180,226,227,232,239,292,301,302,304,306,308,311,315,327,340,344,348,350,367,369,370,377,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,483,487,490,494,506,512],cutoff_glob:[],cutoff_inn:[],cutoffa:409,cutoffc:409,cuu3:408,cval:175,cvd:334,cvel:316,cvff:[],cwiggl:[3,264,344,347,349,512],cyan:[2,203,204],cycl:[3,243,265,267,268,272],cyclic:[3,196],cygwin:12,cylind:[3,4,75,203,216,249,297,345,348,488],cylindr:[6,249,324,345],cypress:384,cyrot:390,cyrstal:293,d3q15:254,d3q19:254,d_double_doubl:15,d_e:339,d_flag2:300,d_flag:300,d_name:[123,200,300,329,495],d_single_doubl:15,d_single_singl:15,d_sx:300,d_sy:300,d_sz:300,daan:337,dai:12,daili:12,daivi:288,damag:[],dammak:306,damp:[3,6,207,212,251,252,253,258,267,268,272,298,301,302,306,311,330,331,343,345,346,376,377,379,391,393,395,400,403,410,414,422,430,442,450,465,471,499,506],damp_com:252,damp_drud:252,dampen:[311,506],dampflag:[345,414],dan:17,danger:[3,12,243,350,404,503],dangl:179,daniel:9,darden:[370,403],darkblu:204,darkcyan:204,darken:203,darkgoldenrod:204,darkgrai:204,darkgreen:204,darkkhaki:204,darkmagenta:204,darkolivegreen:204,darkorang:204,darkorchid:204,darkr:204,darksalmon:204,darkseagreen:204,darkslateblu:204,darkslategrai:204,darkturquois:204,darkviolet:204,dasgupta:302,dash:[414,502],dat:[6,98,196,213,481],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,312],dataset:312,datatyp:3,date:[0,4,6,12,13,199,447,448,512],datom1:125,datom2:125,datom3:125,datom4:125,datum:[3,6,43,68,71,73,84,101,118,125,200,217],davenport:433,davi:344,david:[9,19,369,370,468,470],daw:[408,445],dbg:14,dcd:[3,6,7,200,202,203,204,205,294,486,490],ddim:199,deactiv:430,dealt:250,debug:[6,7,11,12,13,14,17,128,132,175,176,294,299,367,369,384,418,439,474,483,484,492,495,502,512],deby:[],decai:[99,400,477],decid:[3,6,12,16,75,264,300,311,340,500,507],decipher:372,declar:202,declin:327,decod:203,decompos:[94,456],decomposit:[3,5,7,18,64,213,294,315],decoupl:[6,506],decreas:[3,200,201,210,211,218,227,230,236,241,243,251,338,369],decrement:316,deepli:366,deeppink:204,deepskyblu:204,def:[12,13,483],defaul:63,defect:[6,74,174,437],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,190,191,193,194,195,196,197,198,199,200,201,202,203,204,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,226,227,228,230,231,234,235,236,238,241,242,243,246,249,250,251,252,253,254,262,264,266,267,268,269,270,271,272,273,274,275,277,278,279,282,284,285,286,287,288,289,290,292,293,294,296,297,298,300,302,304,309,311,312,313,314,317,321,325,327,329,330,331,332,333,335,336,337,339,341,342,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,362,363,364,365,367,369,370,372,374,376,377,378,379,380,381,382,383,384,386,387,388,389,391,392,393,394,395,396,397,398,400,401,403,404,405,406,407,409,410,412,413,414,415,416,417,418,420,422,423,424,425,426,427,428,429,430,431,432,433,437,438,439,440,441,442,444,445,447,448,449,450,451,452,453,454,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,488,489,490,491,494,495,496,497,499,500,502,503,506,508,509,510,511,512,513],definit:[2,3,6,8,12,13,82,85,126,150,204,216,217,218,219,220,221,222,230,238,249,272,312,329,341,344,347,349,351,363,367,378,387,390,398,405,406,410,420,445,452,454,456,472,483,485,487,494,496,511,512],defint:503,deform:[],deg2theta:175,deg:506,degener:[3,296],degrad:[8,18,293,370,494],degre:[3,6,8,20,21,24,28,29,32,35,36,38,68,84,99,101,103,105,106,108,110,111,116,122,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,175,176,182,183,186,187,194,196,199,203,216,227,234,243,245,246,251,252,257,267,268,272,273,274,275,286,287,288,290,294,296,310,311,314,330,331,332,337,353,355,359,362,364,377,403,408,416,495,503,506,513],degress:[156,216],del:499,delai:[3,6,12,380,407,503],deleg:417,delet:[2,3,7,8,12,55,59,62,65,174,179,180,207,216,217,219,220,221,222,225,227,240,243,267,312,330,331,350,352,368,378,380,383,439,464,485,486,487,488,496,497,502,507,508,510,512,513],delete_atom:[],delete_bond:[],delete_el:213,deli:199,delimit:[483,512],deloc:[268,410,455],delr:434,delt_lo:499,delta:[],delta_1:390,delta_3:390,delta_7:390,delta_conf:3,delta_ij:[434,445],delta_mu:[],delta_pi:390,delta_r:445,delta_sigma:390,delta_ua:[],delx:199,delz:199,dem:[],demand:306,demo:11,demon:291,demonstr:[301,434],den:297,dendrim:416,denniston:[9,254,256,257,258,293],denomin:[7,181],denot:[128,234,252,293,304,306,400,415,417,448,452,454],dens:[75,227,410],densiti:[3,6,7,9,18,41,42,61,109,126,136,150,162,174,176,208,209,213,216,220,221,224,230,241,254,257,260,261,293,297,298,302,339,344,372,374,378,385,386,390,408,434,435,436,445,449,455,459,461,462,463,485,494,495,503,511],density_continu:454,density_summ:454,depart:[0,7],departur:[265,301],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,68,71,73,74,75,84,99,101,112,118,119,122,123,124,125,129,150,152,153,159,163,164,170,176,177,182,183,184,185,186,187,188,190,191,193,194,195,196,199,200,201,203,204,207,208,209,210,211,214,216,218,219,220,222,223,224,226,228,230,236,237,242,245,246,247,249,251,252,254,256,257,264,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,292,303,306,308,311,313,314,315,321,327,330,331,332,334,336,338,339,341,343,344,347,348,349,350,352,353,354,355,356,358,359,362,364,370,372,377,378,380,381,382,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,408,409,410,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,434,435,437,438,440,441,442,444,445,447,448,449,450,455,456,457,465,466,467,468,469,470,471,473,475,476,477,480,482,485,487,488,491,495,497,499,502,503,505,512,513],dependend:6,depflag:12,dephas:[480,499],depos:231,deposit:[],deprec:[3,302,447],depth:[52,154,203,339,413,449],dequidt:9,der:[94,117,398,399,430,447,448,476,506],deriv:[6,7,8,9,38,57,65,94,150,170,196,217,228,230,243,251,264,267,269,270,271,272,273,274,275,292,298,302,306,336,337,339,344,345,348,376,378,386,390,398,403,410,411,415,424,428,429,434,437,447,448,465,467,476,506],derjagin:476,derlet:292,descend:204,descent:[7,376],descib:[41,203,302],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,71,74,75,77,95,120,123,126,128,140,150,151,154,155,156,160,161,164,167,169,170,174,175,176,178,179,188,193,196,200,201,202,207,208,209,216,217,218,219,220,221,222,224,227,228,229,230,231,233,234,239,244,245,248,249,250,251,252,253,254,256,257,258,262,266,267,268,272,280,289,292,294,299,300,301,302,303,304,311,316,324,327,328,329,330,331,332,333,334,335,336,337,342,344,345,347,352,369,370,372,375,376,377,378,379,383,386,387,389,391,392,393,395,396,397,398,399,400,403,408,410,411,413,414,415,417,420,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,444,445,446,447,448,449,450,455,456,457,464,465,466,467,468,469,470,471,473,475,476,477,478,480,482,483,485,486,487,488,489,495,498,499,502,507,512,513,514],descript:[],descriptor:[150,200,418],deserno:370,design:[0,3,6,7,8,11,13,14,15,17,128,158,161,175,213,227,233,234,267,268,292,293,312,334,339,387,388,389,392,395,400,402,410,430,431,432,435,436,445,448,467],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,75,95,98,122,127,151,158,176,189,199,216,222,228,230,241,243,244,251,252,253,257,267,288,296,297,298,299,302,306,311,314,327,330,331,332,333,338,345,360,366,369,370,372,375,377,378,379,404,408,416,431,432,466,468,470,481,482,483,485,489,494,499,500,502,503,512,513,514],desk:7,desktop:[4,6,7,10,12,203],despit:506,destabil:390,destre:362,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,69,70,71,75,79,82,97,98,102,111,113,115,117,119,121,122,124,127,129,150,151,153,154,155,156,159,169,170,171,173,176,177,180,181,184,195,199,200,201,203,204,207,208,209,213,216,217,218,219,220,222,224,226,227,228,229,230,231,241,243,244,245,246,248,249,251,253,254,258,264,265,266,267,268,269,270,271,272,273,274,275,279,281,286,287,288,289,290,293,296,297,298,300,301,303,304,305,311,314,315,327,330,331,332,333,334,335,337,338,339,340,341,342,343,350,352,354,363,369,370,373,377,378,380,381,384,385,386,387,389,390,392,394,395,396,397,398,399,400,403,404,410,411,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,432,433,434,438,439,444,447,448,449,455,456,457,465,472,475,476,478,483,485,486,487,488,490,491,494,495,497,500,503,504,507,512,513,516],detect:[2,3,12,43,63,65,93,99,242,297,338,379,399,416,421,480,482,485,496,499,512],determ:384,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,71,75,94,111,117,119,122,128,129,137,151,164,165,174,175,176,199,200,201,203,204,205,206,210,211,212,215,216,217,218,219,220,221,222,223,224,228,230,231,234,236,243,246,247,249,251,252,257,262,264,265,267,273,274,275,286,287,288,290,292,294,297,298,301,308,309,310,311,312,313,317,319,321,327,330,331,332,334,340,341,344,345,346,347,348,349,350,363,369,370,372,378,380,381,384,386,387,394,399,403,407,408,412,414,417,418,426,434,437,439,448,449,455,464,467,471,476,482,485,486,488,490,492,495,499,501,502,504,511,512,513],determinist:315,detil:118,devan:[9,450],devanathan:470,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,248,272,296,301,302,305,386,390,410,436,437,455,473,487],devemi:9,deviat:[265,272,292,412],deviator:9,devic:[1,3,12,15,17,248,384],device_typ:384,devin:[303,399],devis:436,dfactor:203,dff:506,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,370],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,305,437],dhi:[61,199,230,297],dhug:[265,301],dhugoniot:[265,301],dia:434,diagnost:[],diagon:[3,6,90,150,151,152,228,267,298,311,342,452,454],diagonalstyl:456,diagram:[42,128,175,195,224,294],diallo:416,diam:[203,204,297,378],diamet:[3,6,41,43,123,176,200,201,203,204,208,209,251,297,311,327,329,343,345,378,398,413,414,424,449,472,476,485,486,495],diamond:[372,410,434],diamter:[41,297],dick:6,dicsuss:264,dictat:[214,265],did:[3,12,377,404,407,408,414,439,468,470,493],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,172,341,369],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,71,74,75,94,99,103,105,106,130,150,152,153,154,155,156,157,159,162,163,164,165,166,168,169,170,176,177,179,184,195,196,199,200,203,204,207,209,212,214,216,219,224,225,226,227,228,229,230,234,239,242,243,244,245,246,247,248,251,252,254,264,267,268,269,270,271,273,274,275,277,279,282,284,285,286,287,290,292,294,296,298,301,302,303,306,309,311,314,316,324,325,327,330,331,332,335,336,337,339,342,343,344,345,348,352,353,363,366,368,369,370,372,373,375,376,378,379,381,382,383,384,38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99],don:[0,8,9,12,13,126,179,210,236,252,300,348,434,455,483,485,507],donadio:331,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,61,64,75,170,173,176,179,196,200,203,204,213,214,216,218,219,220,221,222,224,225,226,227,228,230,231,239,241,243,248,249,251,252,259,267,273,274,275,286,287,288,290,291,293,294,295,297,300,308,311,312,314,327,330,331,332,334,336,337,350,352,368,369,370,377,379,380,383,384,386,394,408,417,418,419,426,432,433,434,439,447,464,467,472,480,481,482,483,486,489,490,493,503,504,506,507,512,513],donor:416,dot:[151,172,210,236,246,266],doti:[390,445],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,94,230,241,299,348,352,368,370,383,384,390,411,415,437,447,448,481,485,489,493,498,512,513],dover:213,down:[3,6,7,8,11,40,75,228,243,251,327,343,384,410,439,455,484,504],downhil:[375,376],download:[5,7,8,9,11,12,13,17,248,418,446],downsid:6,downward:308,dozen:[8,9,12,117,207,447,448],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:260,dpdtheta:[41,87,88,406],dpdtheta_i:[238,239],dproduct:387,dr_ewald:[128,312],drag:[],dragforc:254,drai:[265,301],drain:[247,343,377],dramat:[9,61,199,225,226,227,228,230,267,327,330,331,370,384,439,455,482],drautz:390,draw:203,drawback:300,drawn:[43,200,203,204,244,480],drayleigh:[265,301],dreid:[],drfourth:114,drho:[123,385,408],drift:[6,112,114,244,245,251,252,263,309,327,494,502,506],drive:[11,12,211,228,230,246,267,292,298,311,346,379],driven:[6,188],driver:[6,12,14,15,207,241,248],drop:[3,204,404],droplet:417,drsquar:114,drude:[],dry:240,dsecriptor:418,dsf:[],dsmc:[],dstyle:297,dt_collis:254,dt_lb:254,dt_md:254,dt_srd:327,dtilt:[61,230],dtneb:499,dtqm:301,dtype:[125,226],dual:[16,17,327,384],dudarev:175,due:[1,3,6,9,12,16,17,19,41,55,59,60,63,69,74,75,78,79,86,93,95,96,97,102,111,112,113,114,115,120,126,128,136,150,151,153,154,155,157,159,162,163,164,165,166,168,169,171,175,176,179,180,200,201,203,207,210,211,219,223,225,226,227,228,229,230,231,236,237,240,241,244,245,248,249,251,252,253,254,257,258,259,263,264,265,266,267,272,281,292,295,297,309,310,311,313,324,326,327,328,330,331,332,333,334,336,337,339,343,344,346,347,348,350,370,375,377,379,380,381,401,404,405,406,408,412,413,417,431,432,439,445,447,449,450,464,467,468,470,474,476,477,480,482,485,486,487,494,499,502,503,504,506,512,513],duffi:339,duin:[9,302,307,447,448],duke:370,dummi:[12,29,469],dump0:201,dump10000:201,dump1:490,dump20000:201,dump2:490,dump2vtk_tri:144,dump:[],dump_0:201,dump_1:201,dump_atom:8,dump_custom:8,dump_h5md:202,dump_modifi:[],dump_p:201,dumpcustom:8,dumptimestep:490,dunbrack:[6,20,182,395,497],dunweg:[251,253],duplic:[2,3,14,15,17,42,43,177,201,224,245,292,485,511],dupont:[5,7,13],durat:[37,56,153,154,155,157,158,159,161,162,163,164,165,168,169,195,204,216,243,306,339,363,414,465],dure:[2,3,6,8,9,12,16,17,38,40,42,57,75,94,136,138,152,158,177,180,196,200,201,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,263,264,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,320,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,370,377,379,383,384,404,430,437,439,448,467,480,481,483,485,488,490,492,493,495,497,499,500,503,504,512,515,516],dvector:8,dvlo:476,dvx:6,dx_lb:254,dy3:175,dyamic:12,dyanam:6,dyanmic:499,dynam:[],dynamo:[5,385,408,434],dyne:511,dyre:427,dysam:488,e28637:29,e_1:390,e_2:390,e_b:411,e_data:201,e_e:410,e_hbond:416,e_i:[6,390,411],e_j:[6,390],e_k:[390,410],e_kl:6,e_lj:[386,403],e_n:[390,410],e_nn:410,e_pr:410,e_rebo:386,e_tors:386,e_tot:437,e_vol:437,eaa:353,eaat:183,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,59,61,63,64,65,66,67,69,70,71,72,74,75,76,77,78,79,80,81,82,83,85,86,88,90,92,94,96,97,99,100,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,119,120,121,122,123,124,125,126,127,128,129,130,144,150,151,152,154,155,156,157,158,159,160,163,164,165,166,168,169,170,171,172,173,174,175,176,179,180,182,183,184,185,186,187,188,189,190,191,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,239,240,241,243,244,245,246,247,248,249,250,251,252,253,254,255,257,258,259,260,261,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,279,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,306,308,311,312,313,314,315,316,320,321,323,324,325,326,327,328,329,330,331,332,334,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,355,356,357,358,359,360,362,363,364,368,369,370,372,376,377,378,379,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397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39,449,452,454,459,460,462,463,477,506],equi:268,equidist:266,equil:[3,302,373,492,516],equilater:495,equilibr:[3,4,5,6,7,9,61,98,176,207,214,217,227,228,243,265,267,268,288,289,301,302,303,304,335,336,337,342,399,400,447,448,481,495],equilibria:342,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,159,160,183,185,228,230,243,244,245,252,254,267,272,288,301,302,306,310,314,316,324,327,334,335,337,342,353,355,359,362,399,434,441,455,506],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:213,equival:[6,12,13,29,61,63,134,135,143,148,174,178,204,219,222,228,230,243,251,267,288,298,310,311,347,386,404,410,455,468,470,471,485,488,493,494,503,506],equlibrium:6,equliibr:[302,304],er3:175,eradiu:[41,123,201,410,485],eras:[313,336],erat:[230,432],erc:400,erfc:[400,422,439],erforc:[123,201],erg:511,erhart:[214,408,468,470],ermscal:387,ernst:9,eror:3,eros:434,erose_form:434,erot:[],errata:[468,470],erratum:344,erron:3,error:[],erta:414,ervel:[123,201,485],escap:[231,506],especi:[8,16,164,176,207,214,224,243,301,306,309,310,384,482],espresso:[9,305],essenti:[8,11,12,27,95,138,157,158,159,162,163,164,165,166,168,185,217,272,293,343,370,386,400,422,470,490,503],essex:29,establish:[94,247],estim:[1,3,6,10,12,38,42,57,98,151,213,224,235,265,327,334,369,370,375,439,448,467,499,503],esu:511,esub:434,eta:[6,254,267,301,302,304,343,409,411,413,445,469,473,511],eta_dot:267,eta_ij:445,eta_ji:411,etag:[41,485],etail:503,etap:267,etap_dot:267,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,71,96,97,98,103,119,120,123,125,151,153,156,157,158,159,160,162,163,164,165,166,168,170,176,178,179,180,189,200,201,203,204,207,208,213,214,215,216,219,220,221,222,225,226,230,231,241,243,244,251,267,297,308,312,339,340,348,352,368,369,377,378,379,380,382,408,409,417,430,432,437,443,447,448,466,468,470,473,480,483,485,486,487,492,494,495,499,500,501,502,503,504,506,511,512,514,516],ethernet:18,etol:[377,379,480,499],etot0:301,etot:[6,103,105,106,120,151,162,204,234,252,265,301,502,503],eu2:175,eu3:175,euler:[377,379],eulerian:213,euqat:458,europhi:254,ev_tal:8,evalu:[2,3,9,11,12,38,57,75,94,95,98,117,127,129,150,152,156,166,174,176,199,200,201,203,204,208,209,210,211,213,215,216,217,218,219,220,221,222,223,230,236,244,246,247,249,250,251,252,293,299,302,313,317,321,330,331,332,341,344,347,349,350,352,369,370,375,377,384,437,439,445,451,453,455,467,480,481,483,487,488,490,492,493,494,495,499,501,503,512,513],evalut:[352,483],evan:[164,288],evanseck:[6,20,182,395,497],evapor:[],evaul:[8,377],evdwl:[117,152,447,448,503],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,74,75,95,117,129,174,177,178,192,196,200,201,204,207,208,209,214,215,216,219,220,221,222,224,225,226,228,230,231,234,249,252,265,267,268,293,297,306,308,311,312,323,327,335,339,342,344,348,350,361,369,375,377,379,384,389,410,411,414,417,420,439,449,473,474,478,485,486,488,490,491,492,494,495,497,500,502,503,504,506,516],evenli:[3,42,151,196,224,254,420,474],event:[],eventu:[3,6,12,15,178,302,499],ever:[9,55,57,250,327],evera:[398,413,449,465],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,75,76,98,123,129,138,164,179,200,201,202,203,204,205,207,208,209,210,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,240,241,243,245,247,248,249,254,255,263,267,268,272,291,292,293,297,298,299,300,301,302,303,304,306,308,309,311,312,314,316,327,329,330,331,332,333,334,335,338,339,340,341,342,350,352,368,370,379,380,381,384,404,407,417,430,447,448,455,461,479,480,481,485,487,489,490,492,493,494,499,500,501,503,507,512,516],everyth:[8,117,507],everywher:[126,424],eviri:410,evolut:[245,254,294,480],evolv:[254,294,340],ewald:[2,3,5,6,7,8,9,12,95,120,128,151,340,369,370,377,391,393,394,400,403,410,422,426,442,450,465,467,471],ewald_disp:403,ewalddisp:3,exact:[22,42,45,75,132,170,179,184,224,227,244,245,251,252,253,297,306,307,327,339,354,369,397,487,492,499,512,514,516],exactli:[3,6,12,14,17,38,42,43,57,61,75,76,98,126,154,160,167,176,196,208,209,219,224,230,235,239,244,251,252,253,268,280,281,289,293,301,327,332,333,346,384,397,404,408,414,417,431,439,467,487,488,495,499,512],exager:506,examin:[6,8,17,227,293],examp:[483,512],exampl:[],exce:[3,6,16,17,18,42,60,75,178,215,216,219,220,221,222,224,228,230,235,240,267,293,308,312,318,319,327,377,384,485,512],exceed:[3,42,61,224,230,267,327,493],excel:410,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,75,96,97,118,119,122,127,151,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,176,180,182,183,184,185,186,187,188,190,191,193,194,195,196,199,200,201,204,207,210,216,217,219,223,224,228,230,237,242,243,246,249,251,253,267,268,269,270,271,272,273,274,275,276,277,280,281,284,286,287,288,289,290,294,303,304,311,313,314,324,327,330,332,333,339,343,347,350,351,352,353,354,355,356,358,359,362,363,364,369,370,372,374,378,379,380,382,383,384,385,386,388,391,392,393,394,395,396,397,398,399,400,402,403,404,408,409,410,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,432,435,440,441,442,444,447,448,449,450,457,465,466,467,468,469,470,471,473,475,476,477,480,482,483,485,487,488,490,493,494,495,496,497,499,503,506,511,512,513,515],excess:[218,410],exchang:[2,3,6,8,63,64,207,213,214,243,251,303,311,335,339,342,369,384,410,500],exchange:369,excit:410,exclud:[3,6,9,12,16,17,65,75,122,150,156,163,164,180,200,216,220,225,226,255,263,296,309,311,334,345,350,377,378,380,392,414,417,420,431,432,439,464,497],exclus:[1,3,12,16,94,384,399,437,439,494,504],excurs:[267,480],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,177,203,248,305,352,368,371,383,481,483,493,496,499,512],exempl:455,exemplari:244,exemplifi:410,exert:[6,249,252,306,346,347,348,370],exhaust:[213,383,512],exhibit:[99,267,376,410,494],exist:[3,6,7,8,11,12,13,16,37,56,61,71,74,132,176,177,195,202,203,204,207,212,223,226,228,231,243,296,297,299,350,351,353,355,356,357,359,363,373,378,384,405,406,417,447,464,474,481,483,485,486,487,496,497,498,507,512,513,514],exit:[2,3,11,12,42,59,200,224,239,368,383,483,484,493,502,512],exlanatori:3,exp:[],expand:[],expans:[12,150,200,496,512],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,75,111,157,168,174,196,224,236,243,245,264,292,298,300,301,306,311,350,370,380,397,434,437,439,480,483,485,487,490,494,499,512],expens:[6,75,204,292,296,311,339,350,369,370,380,384,483],experi:[6,13,15,17,223,231,248,257,266,298,310,311,375,379,404,439,494,499],experienc:[6,12,256,257],experiment:[243,369,384,499],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,68,71,73,75,76,77,80,81,84,93,101,156,164,196,200,201,203,204,207,216,217,222,224,226,228,230,267,292,300,311,324,350,352,368,369,372,378,379,383,389,408,420,455,457,472,483,486,487,490,492,495,506,507,512,516],explan:[3,6,61,123,150,200,201,216,266,292,417,479,482,483,485,494],explanatori:[3,8,127,200,201,215,216,219,220,221,311,378,482,512],explantori:[3,307],explic:438,explicit:[6,9,11,22,45,81,94,123,126,170,184,208,209,230,318,319,354,374,386,387,390,395,397,408,410,421,431,471,479,482,486,489,507],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,75,119,122,153,163,166,174,176,182,183,185,186,187,188,190,191,193,194,196,200,201,204,210,220,223,230,237,242,244,246,251,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,300,301,303,311,313,314,330,332,333,339,343,347,353,355,356,358,359,362,364,378,384,385,386,388,391,392,393,394,395,396,397,398,399,400,401,403,404,407,408,409,411,412,413,414,415,416,417,421,422,423,424,425,426,427,428,429,430,431,435,437,439,440,441,442,444,449,450,457,458,459,460,461,462,463,465,466,467,468,469,470,471,473,475,476,477,485,487,488,494,495,497,498,504,506,507],explictli:[16,498],exploit:[15,17,294],explor:[128,175],expon:[3,302,304,408,413,416,430,438,450],exponenti:[94,445,466,473,477,499,512],expos:11,exposit:[213,404,407],express:[6,150,162,176,208,209,228,264,292,302,339,345,352,390,408,410,424,434,455,456,465,512],expressiont:390,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,67,72,83,89,90,91,94,95,98,100,103,106,107,117,119,127,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,201,207,210,211,214,222,223,229,232,236,241,242,243,245,246,247,249,251,253,265,267,272,281,292,293,309,310,311,313,316,321,324,326,330,331,332,333,334,336,337,339,341,344,348,349,413,434,437,448,449,456,502,503,511],extent:[1,3,42,43,46,59,75,174,178,200,212,220,224,249,346,349,369,372,386,451,453,467,482,485,488],exterior:[3,6,174,348],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,75,111,119,120,122,128,151,153,154,155,157,159,162,163,164,165,166,168,169,175,176,177,178,182,204,219,224,226,267,299,300,301,311,327,377,378,381,382,403,414,417,420,434,439,482,483,485,488,497,506,512],extract:[3,6,11,13,36,65,67,72,83,94,100,117,125,127,129,208,209,304,379,400,411,434,456,483,490,502],extract_atom:11,extract_comput:[11,483],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,203,218,228,230,267,337,410,469,506],extrema:430,extrins:213,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[172,341],f_a:[468,469,470],f_ave:127,f_c:469,f_f:470,f_fix_id:301,f_foo:512,f_harm:337,f_i:[29,445],f_id:[6,75,127,129,200,201,207,215,216,217,218,219,220,221,222,262,329,341,503,512],f_ij:445,f_indent:222,f_int:336,f_j:29,f_jj:98,f_k:445,f_langevin:339,f_max:[301,306],f_msst:265,f_r:[252,468,469,470],f_sigma:390,f_solid:337,f_ss:6,f_temp:[],face:[3,6,59,61,75,164,174,178,212,220,221,344,346,347,348,349,372,413,434,449,485,488],face_threshold:174,facet:174,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,245,297,327,337,414,447,455,497],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,76,94,98,111,118,125,126,128,150,170,175,178,182,193,199,200,203,204,208,209,217,224,228,230,231,243,248,251,253,254,265,267,268,272,294,298,302,310,314,317,319,327,331,335,342,343,344,348,359,370,372,378,384,386,387,390,391,393,395,400,401,402,404,405,406,410,414,417,421,422,434,437,439,441,442,448,450,457,466,471,482,485,488,489,494,497,499,500,503,506,511,512],factori:[3,483],factoriz:369,fail:[3,9,11,12,61,180,228,231,369,377,379,402,448,483],failur:[131,452,484,512],fairli:[11,439,494,499,507],faken:77,falcon:248,fall:[3,6,204,219,297,483,512],fals:[93,350,352,455,512],fame:8,famili:[473,482],familiar:[0,11,507],fan:445,far:[3,6,12,17,59,61,63,93,200,201,204,205,224,225,226,228,231,267,292,310,311,327,344,355,359,375,379,380,472,483,485,490,503],farago:251,farrel:[468,470],farther:200,fashion:[6,8,42,75,176,204,207,208,209,214,220,224,226,231,243,245,249,264,265,267,269,270,271,272,273,274,275,283,286,287,288,289,290,300,301,303,311,316,320,326,329,337,339,343,344,345,347,349,379,417,431,488,497,512,515],fasolino:419,fast:[6,7,9,12,13,17,40,200,201,278,301,340,369,370,392,431,432,437,465,467,487,492,494,503,513,516],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,114,119,122,153,163,182,183,185,186,187,188,190,191,193,194,196,200,201,204,210,223,224,230,237,242,246,250,251,267,269,270,271,272,273,274,275,276,277,284,286,287,288,290,298,302,303,311,313,314,327,330,332,334,336,339,343,347,353,355,356,358,359,362,364,369,370,381,382,384,385,386,388,390,391,392,393,394,395,396,397,398,399,400,403,404,408,409,411,412,413,414,415,416,417,422,423,424,425,426,427,428,429,430,431,435,440,441,442,444,449,450,457,465,466,467,468,469,470,471,473,475,476,477,480,488,494,498,506],fastest:[1,6,14,17,164,220,339,340,384,482],fatal:[3,502],fault:[74,448],faulti:12,fava:413,favor:227,favorit:7,fbmc:334,fcc:[],fcm:[283,512],fdirect:234,fdotr:418,fdt:[],fdti:94,fe2:175,fe3:175,fe_md_boundari:213,featu:8,featur:[],fecr:408,feedback:[7,248],feel:[7,248,249,257,292,348,350,379,439],felling:436,felt:348,femtosecond:511,fene:[],fennel:[400,422],fep:[],ferguson:[6,182,497],fermi:[1,9,10,12,15,162,384,470],fermion:410,fernando:433,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,205,215,216,217,219,220,221,222,252,267,297,300,302,314,341,369,377,378,379,386,455,482,485,490,494,496,504,514],fewer:[1,3,11,15,16,63,257,494],fewest:3,fextern:241,feynman:294,fff:483,ffield:[399,411,447,448,455],ffmpeg:[3,12,203],ffplai:203,fft:[1,3,7,9,11,12,14,15,95,119,120,151,293,369,370,494],fft_inc:[12,370],fft_lib:12,fft_path:12,fftbench:[369,504],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:464,fictiti:[6,210,211,236,241,245,294,310,400,422,426,464],field1:[486,490],field2:486,field:[],fifth:[324,441],figur:[1,3,8,12,301,482,483,507],fij:403,file0:292,file1:[11,13,292,338,352,378,490,492,496],file2:[11,13,338,352,378,490,492,496],file:[],file_from:202,filen:378,filenam:[3,12,13,38,42,57,196,200,201,203,204,205,213,216,217,218,219,220,221,222,224,229,239,292,296,299,302,303,304,307,308,311,312,338,339,366,367,368,378,379,385,386,390,400,408,409,411,419,434,435,436,441,445,446,447,448,455,456,466,467,468,469,470,473,481,482,483,486,487,492,496,503,512,514,515,516],filennam:492,filep:[3,200,201,204,487,492,516],filepo:308,fill:[7,9,176,203,297,339,372,380,390,437,448,488,507],filter:[204,213],final_integr:8,final_integrate_respa:8,finchham:[6,158,402],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,75,77,94,127,179,196,205,214,227,228,239,240,243,266,292,297,298,306,310,375,377,379,380,400,417,422,426,434,455,465,467,506,507,512],find_custom:8,fine:[16,17,180,210,236,337,380,384,507,512],finer:[150,176,512],finest:369,finger:[176,199,264,488],finish:[6,11,42,224,352,366,368,369,381,383,384,472,490,512,513],finit:[],finni:[7,408,465],finvers:234,fiorin:[9,229],fire:[],firebrick:204,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,75,86,95,98,112,113,114,116,122,126,127,137,140,143,144,148,151,161,164,170,172,174,175,177,178,179,183,196,200,201,202,203,204,205,207,208,216,217,219,220,221,222,224,227,230,239,243,244,249,254,264,265,266,267,292,294,299,300,301,303,308,311,314,316,324,325,327,328,329,336,337,338,339,341,345,350,352,353,360,372,377,378,379,380,383,384,385,386,389,390,391,393,395,397,399,400,408,410,411,414,415,417,418,419,420,421,422,426,431,432,434,436,437,439,441,445,447,448,455,456,464,466,467,468,469,470,473,477,480,481,482,483,485,486,487,490,492,494,497,498,499,502,503,506,507,512,513,514,516],fischer:[6,9,19,20,182,395,497],fit:[3,6,9,12,38,57,196,239,310,327,386,390,419,434,439,460,467,469,493,507,512],five:[77,162,301,378,390,435,485,499],fix:[],fix_adapt:[170,209,430],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,214,297],fix_eo:9,fix_evapor:214,fix_flux:213,fix_gcmc:[214,378],fix_gl:245,fix_gld:245,fix_grav:297,fix_id:[3,228,265,267,269,270,271,272,273,274,275,298,301],fix_manifoldforc:507,fix_modifi:[],fix_mov:[199,345],fix_nh:8,fix_npt:245,fix_nv:507,fix_nvt:[214,243],fix_poem:[3,6,9],fix_pour:[3,231],fix_qbmsst:9,fix_qeq:[3,399],fix_rattl:314,fix_reax_bond:447,fix_rigid:[257,389],fix_saed_vtk:312,fix_setforc:8,fix_shak:314,fix_shardlow:9,fix_srd:3,fix_styl:272,fix_temp_rescal:333,fixedpoint:[228,267],fixextern:241,fixid:213,fji:403,flag1:[233,382],flag2:[233,382],flag:[3,8,9,11,12,14,15,16,17,41,69,78,79,86,93,96,97,102,112,113,115,128,171,175,179,200,201,203,204,205,222,227,229,233,248,251,255,257,263,264,293,300,311,324,326,327,334,338,347,350,367,370,378,382,383,384,386,416,421,434,437,464,480,482,483,485,486,487,489,490,491,495,507,512],flag_buck:394,flag_coul:[394,403,426],flag_lj:[403,426],flagfld:[392,431,432],flaghi:[3,392,431,432],flaglog:[392,431,432],flagn:233,flagvf:[392,431,432],flat:[6,339,344,345,349],flavor:[2,7,12],fld:[],flen:387,flex_press:387,flexibl:[3,6,8,177,203,216,220,229,245,268,335,342,410,469,503],flip:[3,6,230,267,346,347],floor:512,flop:12,floralwhit:204,flow:[],fluctuat:[6,66,94,228,243,244,251,254,267,272,292,293,315,337,339,362,406],fluid:[],fluid_veloc:258,flush:[3,204,502],flux:[],flv:203,fly:[7,9,12,42,203,207,213,218,231,234,311,314,340,390,437,503,506],fmackai:9,fmag:232,fmass:294,fmax:[377,503],fmomentum:234,fmsec:[2,204,251,252,264,267,298,311,330,331,494,505,511,513],fname:368,fno:[9,12,16],fnorm:[377,503],fnpt:234,fnvt:234,foce:417,fock:387,focu:314,fogarti:[9,304,448],foil:[150,292,456],fold:[325,494],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,74,75,77,87,98,99,105,106,116,123,126,127,129,150,151,154,155,156,162,164,169,172,174,176,177,182,185,186,187,188,190,191,193,194,196,200,202,203,204,207,213,214,215,216,217,218,219,220,221,222,224,229,230,231,234,235,238,239,241,243,244,245,248,250,251,252,254,257,265,267,272,273,274,275,286,287,288,290,293,294,296,299,300,301,302,304,306,308,310,311,312,314,329,330,331,332,335,336,337,338,339,341,342,350,351,355,356,357,358,359,362,364,367,372,374,377,378,379,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,444,445,446,447,448,449,450,452,454,455,456,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,475,476,477,478,480,482,483,485,486,488,490,492,493,494,497,499,500,501,506,507,512,513,515],foo:[4,8,11,12,200,203,241,483,496,512],foot:6,footprint:[12,384],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:257,forcefield:[310,416],forcegroup:254,forcezero:375,ford:403,forestgreen:204,forev:75,forget:[252,506],forgiv:267,fork:[],form:[2,3,6,8,12,19,22,45,55,65,69,78,79,81,86,94,96,97,99,102,112,113,115,126,150,151,170,171,180,184,204,207,208,209,226,244,245,251,253,257,264,288,293,304,306,310,311,339,344,348,353,354,357,362,374,376,378,379,386,387,390,397,405,406,408,410,412,416,417,421,433,434,436,437,441,442,445,447,448,449,455,456,457,465,467,468,469,470,476,479,482,483,485,490,495,502,506,512],formal:[6,82,85,98,244,245,251,267,294,327,335,455],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,71,81,184,196,200,201,202,203,204,205,216,219,220,221,222,224,226,239,293,296,300,302,304,307,311,312,323,338,339,350,351,354,374,378,379,385,386,390,397,408,411,421,434,436,446,447,448,450,456,467,473,474,482,483,485,486,487,490,501,502,503,512,514],former:[6,12,16,40,42,204,224,339,343,390,392,491,497,512],formerli:[7,13],formul:[1,9,41,66,151,210,236,251,267,288,302,304,310,314,338,369,386,390,408,410,413,434,444],formula:[2,3,6,7,13,21,22,37,45,55,56,74,77,94,96,97,98,103,105,106,115,122,128,129,151,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,175,176,181,183,184,195,199,200,208,209,210,211,216,217,218,219,222,223,230,236,246,247,249,251,252,264,292,293,299,308,313,321,325,327,330,331,332,341,344,347,349,350,352,353,354,356,363,372,378,386,387,389,390,395,396,397,398,403,404,408,409,413,414,415,416,418,421,422,424,425,426,428,429,431,432,434,438,439,440,449,450,457,465,466,467,468,469,470,473,475,476,481,485,488,495,502,503,511,512,513],forth:[1,6,11,12,13,14,15,383,483,488,492],fortran:[3,6,9,11,12,13,241,408,417,434,447,448],fortun:8,forward:[3,8,94,368,379,384],foster:[390,444,445],foul:179,found:[3,6,9,12,77,170,200,227,229,243,248,254,293,334,340,352,368,380,397,400,403,480,486,487,502],four:[6,11,55,86,112,113,150,172,265,339,362,378,379,437,480],fourier:[],fourth:[6,114,310,324,334,395,441,455],fox:[6,128,182,463,497],fphi:[38,57,467],fpic:12,fplo:[38,57,467],fprime:467,fqdn:250,fqq:403,frac:[],fraction:[1,3,6,8,12,16,40,42,85,119,151,179,199,203,204,214,225,226,227,228,265,297,301,308,309,327,332,333,372,379,384,390,392,414,431,432,490,495],fragment:[43,248,308],fraig:43,frame:[90,150,204,213,265,301,346,413],framer:[203,204],framework:[5,245,385,456],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,74,94,170,208,209,292,327,336,337,338,339,376,379,387,410,430,437,445,476,482],freedom:[3,6,8,103,105,106,108,110,111,122,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,216,227,234,243,245,251,252,257,267,268,272,273,274,275,286,287,288,290,294,296,311,314,330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350,378,379,384,397,401,410,411,412,432,439,472,474,489,494,513],reax:[],reax_def:3,reaxc:[],reaxff:[3,4,5,7,9,13,207,302,304,307,308,417,447,448,465,497],rebal:[42,224],rebalanc:[42,224],rebo:[],rebuild:[11,12,14,15,16,243,380,404,503],rebuilt:[3,12,200,201,202,203,205,380,384],recalcul:[75,94,327],receiv:[3,223,248,250,292,482],recent:[],reciproc:[6,12,128,174,175,293,369,391,393,394,400,403,410,422,426,442,450,499],recog:12,recoginz:3,recogn:[3,12,16,77,178,225,226,267,378,408,434,447,483,485,492,493,506],recomend:6,recommend:[7,12,14,16,203,204,301,337,369,410,417,431,432,437,448,449,452,454,455,494,504,507],recompil:[1,3,9,12,205,314],recomput:[111,138,180,235,316,407,497],reconstruct:[3,229,455],record:[205,229,316],recov:[228,267],recreat:351,rectangl:[42,224,372],rectangular:[7,42,64,178,224,243,372,485,487,489],rectilinear:[128,175,201],rector:54,recurs:[42,224,390,472],recust:42,recv:482,red:[2,203,204,227,294],redefin:[3,487,493,512],redirect:12,redo:12,reduc:[],reduct:[18,19,127,128,175,265,301,369],redund:411,ree:460,reed:[265,301],rees:[7,9,13],ref:[336,337,376],refactor:6,refer:[],referenc:[3,6,12,65,71,75,124,129,200,201,207,217,243,300,341,370,400,416,441,449,483,503,512],reflect:[],refman:9,reformat:7,refresh:213,reg:488,regard:[6,61,264,314,315,320,444,448],regardless:[15,75,176,179,199,219,220,230,251,267,269,270,271,273,274,275,298,311,321,327,384,482,488,495],regim:[6,335,342,401,494],region:[],region_spher:8,region_styl:348,regist:[8,126,152,323],regoin:6,regress:512,regspher:176,regstrip:350,regul:6,regular:[1,3,42,64,95,174,178,200,203,214,224,243,339,370,401,420,482,485,487,489],reigon:512,reinhardt:[336,337],reject:[176,227,447,500],rel:[1,6,14,27,36,42,61,75,99,112,132,140,150,154,158,159,161,176,185,204,207,214,220,224,230,231,234,243,249,252,263,264,288,292,297,306,308,309,316,324,327,329,334,335,339,346,350,369,370,377,410,413,414,431,432,434,449,476,486,494,499,503,506,513],relat:[],relatic:[],relationship:[6,239,302,352,369,455,476,506,512],relax:[],releas:[0,5,7,8,13,225],relect:[3,439],reles:43,relev:[2,6,12,42,82,85,121,138,176,180,204,208,209,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,240,242,243,244,247,248,254,255,256,258,259,260,261,263,264,266,276,277,278,279,280,281,282,283,284,285,291,295,296,297,299,300,303,305,307,308,309,312,313,314,316,321,325,327,328,329,334,335,338,339,340,341,342,343,344,345,346,347,349,350,369,377,387,388,392,398,400,401,403,404,407,410,412,413,414,415,416,421,423,424,425,427,428,429,431,432,439,440,444,449,457,464,467,475,476,477,482,498,513],reli:[3,12,303,410,448,477,485,495],reloc:12,remain:[7,12,33,37,42,51,56,61,75,94,113,156,157,158,159,163,164,165,166,168,179,189,195,196,200,208,209,214,216,217,220,221,228,230,251,252,259,267,268,273,274,275,286,287,288,290,295,296,319,327,330,331,332,338,339,350,352,360,363,378,390,410,417,430,437,439,465,480,485,486,490,495,497,499,503,506,507,512,513],remaina:390,remaind:[9,176,200,231,297,327,340,470,485],remap:[3,6,12,61,63,75,159,176,199,220,230,249,264,288,369,485,486,487],remedi:[6,506],rememb:[2,507],remot:507,remov:[2,3,6,8,13,55,75,76,81,99,116,124,126,150,154,155,156,157,158,159,163,164,165,166,168,169,176,179,180,201,207,216,220,225,240,251,252,257,263,265,267,273,274,275,286,287,288,290,296,302,311,312,314,327,330,331,332,334,350,369,379,403,432,437,485,488,496,497,507,512,513],remove_bia:8,remove_bias_al:8,remove_molecul:213,remove_sourc:213,remove_speci:213,ren:175,renam:[12,351,496,507],render:[12,13,200,203,204],rendon:[267,268],reneighbor:[3,8,12,40,59,75,220,224,243,327,340,350,404,502,503],renssela:296,renumb:75,reorder:[3,12,40,482],rep:500,repeat:[2,6,203,204,220,227,228,243,320,372,390,468,470,472,480,499],repeatedli:2,repel:249,repes:200,replac:[2,3,6,11,12,42,65,96,97,127,153,154,155,156,157,158,159,162,163,164,165,166,168,169,200,201,203,204,205,216,217,219,220,221,222,224,227,231,251,272,299,306,308,386,400,424,467,486,487,492,493,503,512,513,514,516],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:339,repres:[1,3,6,8,9,12,15,41,42,43,61,70,75,97,123,126,188,196,200,201,203,216,217,218,219,220,221,222,228,234,244,246,251,254,267,294,296,298,306,311,312,316,324,339,341,348,370,379,385,390,413,420,430,431,432,434,435,436,442,445,447,448,471,472,480,482,485,495,497,500,506,512,514],represent:[3,6,8,9,59,61,144,178,200,244,245,294,339,390,410,413,437,449,485,488,506],reprocess:490,reproduc:[3,267,345,400,408,414],repul:434,repuls:[6,7,36,41,46,47,118,249,302,344,345,348,386,390,398,400,404,410,414,416,430,434,438,455,464,470,473,476,477,495],reqir:[302,304],request:[3,6,8,12,42,112,179,196,200,248,254,309,315,327,329,367,369,439,447,448,480,490,495,499,507,512,513,514],requir:[],rerun:[],rescal:[],research:[5,7,87,88,238,254,258,315,437,480,499],resembl:[306,507],resepct:6,reserv:[12,248,506],reservoir:[98,243,247,251,339],reset:[],reset_atomic_reference_posit:213,reset_dt:8,reset_target:8,reset_tim:213,reset_timestep:[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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 command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[37,40,41,56,59,60,61,63,64,75,94,95,99,111,112,114,116,117,128,132,133,150,156,164,165,169,175,176,179,181,195,198,199,200,201,203,204,205,206,208,209,210,212,213,214,216,220,221,222,225,226,228,229,230,231,235,240,243,244,249,251,252,253,254,255,257,262,265,267,268,272,288,289,293,294,297,298,299,300,301,303,306,308,309,311,312,327,329,334,335,336,337,340,342,344,346,350,363,367,369,370,372,373,375,376,378,380,381,382,384,387,390,392,410,431,432,437,439,447,448,464,465,480,481,482,485,486,488,490,492,493,494,497,499,501,502,503,504,505,511,513,514,515],"function":512,"long":[218,391,393,394,395,396,400,402,403,422,426,430,442,450,471],"new":8,"static":12,acceler:1,account:507,ackland:66,acknowledg:7,adapt:[208,209],addforc:210,addit:[12,13,507],addtorqu:211,adiabat:6,adjust_dt:317,adp:385,after:507,airebo:386,alloi:408,amber2lmp:13,amber:6,angl:[8,67,68],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:69,append:212,arrai:6,aspher:[6,9,89,154,269,273,277,278,286],atc:[9,213],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,86,88,92,99,104,105,108,109,110,116,120,121,123,150,151,174,212,214,215,300,512],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:223,awpmd:[9,387],balanc:[42,224],barostat:6,basal:70,beck:388,berendsen:[298,330],between:6,binary2txt:13,bodi:[6,8,9,43,71,155,270,274,279,287,389],bond:[8,13,72,73,225,226,227,307],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:390,born:[391,402],boundari:[7,59],box:[6,60,228],branch:507,brownian:392,buck:[393,394,402,433],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:507,change_box:61,charmm:[6,20,182,395,430],chunk:[6,69,75,79,97,102,113,115,124,156,171,173,216],citat:7,class2:[9,21,44,183,353,396],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,344,398,476],colvar:[9,13,229],com:[78,79,157],comb3:399,comb:[303,399],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,508,509,510,511,512,513,514,515,516],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,512],compute_modifi:111,condit:7,conduct:[6,335],conserv:405,constant:[6,512],constraint:7,contact:[80,130],contact_radiu:[],coord:81,core:6,coreshel:9,correl:[217,218],cosin:[23,24,25,26,27,28,185],cossq:355,coul:[391,393,394,395,396,400,401,402,415,422,426,430,442,450],coupl:6,creat:226,create_atom:176,create_bond:177,create_box:178,createatom:13,creation:7,csld:331,csvr:331,cubic:424,cuda:[9,14,119,122,153,163,210,223,237,242,246,267,276,313,314,330,332,343,391,393,395,396,408,414,415,422,423,425,428,440,466,468],custom:[8,200,201],cut:[50,387,393,396,400,403,410,412,422,423,430,438,442,471],cvff:356,damag:[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