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ect:[3,6,320],advertis:8,advis:[371,438],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,196,197,202,209,210,212,213,214,215,218,219,220,221,223,224,234,240,242,244,250,257,261,262,263,264,266,267,268,274,279,280,281,283,304,305,318,332,342,355,361,367,368,369,371,372,373,376,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,223,376,391],afil:238,aforement:18,afresh:[292,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,198,200,201,202,206,207,209,210,217,218,219,220,221,223,227,236,247,248,249,250,251,256,257,258,260,266,267,268,274,279,280,281,283,286,290,294,302,304,307,316,321,323,324,325,327,328,329,330,331,335,337,339,343,346,347,353,360,366,367,369,370,372,374,375,376,377,378,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,197,223,240,290,346,360,371,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,224,371,439,440],aggreg:[6,12,65,68,69,79,95,112,119,240,256,302,304,318,471,503],aggress:[240,490],agilio:[9,13],agre:[3,8,190,369,378,411,440],agreement:[5,7],ahd:408,ahead:339,aidan:[0,5,7,9,13,364],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:196,akohlmei:[7,9,13,198,241],aktulga:[7,9,297,440],al2o3:447,al2o3_001:[122,305],al3:169,ala:[247,447],alain:9,alat:[285,426],alb:[437,460,462],albeit:303,albert:9,alchem:[89,164],alcohol:335,alcu:[377,382],alcu_eam:437,alderton:395,alejandr:[260,261],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,197,206,217,220,223,247,249,250,274,287,295,304,307,308,327,328,332,335,340,367,368,369,373,376,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,362],aliceblu:197,align:[6,12,29,41,71,172,190,213,217,242,364,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,198,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,255,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,351,356,359,360,361,362,363,364,366,369,370,371,372,373,375,376,377,378,379,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:344,alloc:[3,5,6,8,9,11,12,60,234,334,370,372,376,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,194,196,197,198,200,201,203,205,206,207,209,210,211,212,213,214,215,217,219,220,221,222,223,224,228,229,234,236,237,238,239,241,244,247,250,251,255,257,260,261,285,289,290,291,292,293,294,298,304,305,307,309,311,312,316,320,327,328,329,330,332,333,334,335,336,337,343,345,347,356,361,362,364,369,370,371,372,375,376,379,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,242,294,332,362,373,376,456],alo:392,alon:[6,7,220,300,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,196,209,220,242,247,248,252,257,259,294,304,307,309,313,317,318,327,331,332,338,341,343,364,367,368,369,371,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,201,247,286,294,295,299,369,377,380,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,200,347,356,370,389,457,476],alphan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,71,93,190,207,213,217,218,219,224,233,236,242,243,290,303,307,320,328,330,335,343,345,360,369,370,371,372,373,376,399,410,413,431,440,471,473,474,476,484,490,493,494,502],checkf:190,checkqeq:440,checku:190,chem:[6,13,20,21,25,39,40,43,45,46,89,90,110,116,145,176,177,187,211,222,227,237,238,245,247,259,260,261,281,282,287,291,294,296,304,308,309,320,323,324,327,328,329,330,337,346,355,357,361,362,368,371,378,383,387,388,391,392,393,395,396,398,402,404,405,407,408,414,418,419,422,426,430,431,434,447,456,463,485,488,490,497],chemic:[9,122,164,169,193,194,206,207,236,295,300,301,327,362,439,440,452],chemistri:[9,294,295,297,382,402,439,440],chen:332,cheng:391,chenoweth:[439,440],chenoweth_2008:[439,440],chi:[95,159,192,285,295,297,403,405,503],chiefli:438,child:8,chip:[7,12,17,18,376,489],chipot:222,chiral:355,chmod:[11,12],cho:426,chocol:[7,197],choic:[3,6,12,15,16,18,40,41,54,89,145,148,149,163,174,190,209,213,214,217,220,223,224,238,244,247,258,260,287,295,304,327,356,362,367,368,371,373,376,409,422,431,435,476,485,486,489,490,496,497,501],choos:[1,3,6,7,8,12,16,17,18,29,39,54,89,121,160,161,196,218,219,220,221,224,233,244,247,258,260,262,263,264,265,266,267,268,290,291,308,320,324,338,361,362,368,466,471,473,485,491],chose:[460,462],chosen:[2,3,6,12,17,144,170,173,182,190,196,202,207,221,224,233,236,237,245,247,258,260,265,287,290,301,320,324,327,328,333,335,336,342,362,363,368,376,397,398,402,406,413,416,442,460,471,485,490,497],chri:168,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,92,96,107,109,118,150,165,167,209],chute:[4,10,239],ciccotti:307,cieplak:[6,176,488],cii:210,cij:210,ciko:2,circl:[42,71,316],circular:[3,6,148,191],circumst:18,circumv:[94,110,299],citat:[],cite:[3,7,8,12,244,447],civ:9,ckio:2,cko:2,cl1:169,clarendon:[29,395],clarifi:[7,460,462],clariti:345,clark:434,class2:[],classic:[0,3,5,6,7,8,9,234,287,294,299,332,357,402],classifi:[9,457,465],claus:474,clean:[6,12,14,15,17,484],cleanli:[475,505],clear:[],clearli:7,clebsch:144,clermont:[9,13],clever:480,click:[2,11,22,37,44,55,170,178,189,196,241,347,356,371,389,457],client:[241,243],climb:[259,371,490],clinic:[7,13],clo:[159,192,503],clock:[12,471,490],clockwis:338,close:[3,6,11,12,13,39,41,67,71,145,173,193,219,220,221,238,245,247,260,281,304,307,338,341,360,362,365,367,368,371,376,378,382,392,393,412,426,431,443,445,462,480,486,497,499],closer:[3,41,120,168,192,193,217,221,225,329,371],closest:[219,285,304,335,405,441,456,466],cloud:[447,497],clovertown:18,clsuter:72,clump1:[289,304],clump2:[289,304],clump3:[289,304],clump:304,cluster:[],clutter:[3,9],cmap:476,cmatrix:238,cmax:426,cmd:[11,12,287,487],cmdarg:11,cmin:426,cmm:[],cmoput:137,cn1:210,cn2:210,cna:[],cnn:210,cnr:[9,13],cnt:[409,480],co2:[40,169,307,370],coars:[7,9,29,36,40,54,182,289,304,320,407,442,485,488],coarser:[362,502],coarsest:144,code:[],coeff:[3,7,8,12,21,22,33,44,50,176,177,178,183,346,347,353,389,409,413,431,444,446,449,476],coeffcient:476,coeffici:[],coefficienct:396,coefficient0:400,coefficient1:400,coeffieci:[6,380,412],coeffincientn:400,coexist:[9,236,402],cohes:[6,403,426],coincid:[126,341,387,423,424,471],colberg:195,cold:[6,155,236,240,372,497],coldest:328,coleman8:9,coleman:[9,122,169,305],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,85,92,96,101,107,109,118,150,158,165,167,170,193,194,197,209,222,250,256,289,299,302,304,343,361,370,372,390,476,483,489,495,506],collid:[228,320,342],colliex:169,collinear:[3,289],collis:[3,247,320,338,342,399,406,469],colllis:320,colloid:[],colombo:39,colon:[198,343,477],color1:197,color2:197,color:[3,9,41,193,196,197,217,237,294,299],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,83,92,94,95,96,107,109,110,112,114,117,118,119,120,121,123,144,145,150,158,165,167,168,169,190,193,194,197,200,208,209,210,212,213,214,215,250,257,258,294,304,321,322,332,342,404,408,439,440,477,491,493,502],columnar:168,colvar:[],colvarmodul:12,com:[],comamnd:223,comand:220,comannd:376,comb3:[],comb:[],comb_1:296,comb_2:296,combiant:393,combin:[3,6,7,9,11,13,36,40,63,65,69,79,89,95,106,112,119,148,149,163,193,196,206,212,241,250,260,287,293,308,324,333,341,344,346,361,362,364,368,376,390,392,393,398,402,403,409,421,422,448,458,460,462,465,468,479,484,489,497,502],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,195,241,243,244,362,371,376,396,431,436,459,478],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,176,190,193,232,245,304,332,370,371,377,400,401,403,413,426,433,440,447,448,458,459,460,461,462,465,473,474,476,497,502],commerci:7,commmand:[3,6,12,59,111,282,412,470,471,473,490,505],common:[],commonli:[3,6,12,17,25,57,59,108,110,172,193,196,198,357,407,416,448,460,462,476,479,488],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,173,174,196,197,217,218,219,221,222,223,241,243,247,249,250,251,260,286,293,295,296,297,304,308,320,332,343,359,361,372,373,374,376,398,399,435,473,474,485,486,502,504,506],communc:361,comp:[7,195,243,244,307,362,371,402,431,436,441,455,459,461],compact:[63,200,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,197,227,295,343,345,361,362,369,371,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,346,347,356,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,198,202,208,209,210,212,213,214,215,217,286,298,324,327,334,337,340,361,376,410,429,431,459,473,474,502],compens:[6,218,219,302,372,402],compet:331,competit:362,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,195,196,198,241,331,362,376,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,197,213,217,222,250,287,290,293,320,331,333,344,345,360,371,376,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,247,316,341,359,371,402,429,459,474,476,479,502],compli:[327,331],complic:[6,7,9,12,13,207,236,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,194,196,197,203,204,208,209,210,211,212,213,214,215,216,220,221,223,224,229,234,239,243,244,247,250,252,256,257,259,260,261,265,266,267,268,279,280,281,283,284,286,287,288,291,302,304,306,307,309,313,314,317,320,323,324,325,327,334,335,340,341,342,361,364,368,369,370,371,376,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,207,247,400],compound:[391,402,403,465],compres:[71,118,209],compress:[],compris:[40,341,441,464],compton:[122,169],comptu:3,compuat:362,comput:[],computation:[3,6,218,219,332,382],computational:497,compute_arrai:8,compute_fep:[202,422],compute_group_group:236,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,305],compute_scalar:8,compute_temp:8,compute_ti:202,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:341,concentr:[71,400],concept:[6,150,160,209,485],conceptu:[3,6,71,158,221,223,371,392,409,426,481],concern:[6,73,89,195,237],concetr:71,concis:[11,331],conclud:12,concret:8,concurr:[9,16,362,502],conden:[332,460,462],condens:[6,152,332,378,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:222,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,196,200,221,222,223,224,228,236,243,244,274,287,295,331,359,369,371,378,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,194,431,474],conform:[3,6,13,59,220,221,259,303,309,331,355,371,402,488],confus:[3,465],conjuct:396,conjug:[7,8,244,368,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,197,201,202,244,247,251,274,290,291,295,296,297,299,304,308,320,328,335,340,361,362,371,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,220,241,289,304,307,317,371,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,197,201,202,224,241,242,392,414,418,471,477,479],consequ:[1,6,207,332,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,194,197,201,202,208,210,213,217,219,220,224,248,261,286,304,327,328,331,332,335,362,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,244,245,323,324,325,376,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,198,203,204,209,223,224,227,229,234,237,244,245,246,257,260,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,291,294,299,301,303,304,323,324,325,326,336,361,362,364,370,371,376,378,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:206,consit:304,constant:[],constitu:[3,6,250,304,337,341,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,200,209,224,236,237,242,250,254,289,290,302,304,307,318,328,335,369,370,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,221,260,286,303,341,372,376,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,299,435,502],consumpt:359,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,194,196,197,198,200,201,202,206,208,209,210,212,213,214,215,217,222,224,229,232,238,242,243,244,247,258,274,285,286,289,290,292,294,297,301,304,305,310,320,327,331,332,341,342,345,360,362,370,371,374,375,377,378,379,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,197,218,219,224,289,301,336,368,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,197,200,201,202,207,209,210,211,212,213,214,215,217,220,221,222,223,224,236,237,238,240,241,242,244,245,246,252,257,258,260,262,263,264,265,266,267,268,279,280,281,282,283,288,290,293,294,304,305,309,319,320,322,329,330,332,338,341,345,360,375,376,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,206,332,444,446],contour_integr:206,contract:[59,221,223,260,291,304],contradictori:3,contrain:307,contraint:274,contrari:[238,245],contrast:[1,6,42,55,64,152,155,194,223,343,444,446,468,505],contrib:332,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,202,207,208,209,210,212,213,214,215,221,236,244,247,250,251,255,261,281,282,289,290,298,301,304,305,307,334,361,369,371,379,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,194,196,200,206,207,217,221,222,223,240,241,244,245,260,262,263,264,265,266,267,268,291,296,304,311,312,323,324,325,332,336,359,361,373,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:206,controlfil:440,convect:93,conveni:[6,12,29,193,198,215,305,364,448,502],convent:[3,8,9,29,181,188,189,194,197,303,317,344,400,402,502],converg:[3,6,41,90,193,194,196,198,203,217,220,221,229,234,265,294,296,299,303,307,367,368,369,371,391,392,414,447,471,483,490],convers:[3,8,144,196,197,207,210,291,361,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,196,197,215,258,290,343,346,348,352,355,364,371,377,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,341],convinc:[7,12],cook:9,cooki:7,cool:[7,160,240,302],cooordin:[193,194],cooper:[5,7],coord123:118,coord1:[3,118,209,213,214],coord2:[3,118,209,213,214],coord3:[3,118,209,213,214],coord:[],coordb:447,coordbb:447,coordiat:369,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,198,200,203,208,209,212,213,214,217,218,219,220,221,222,223,224,227,229,230,234,236,239,240,241,242,243,244,245,257,259,260,262,263,264,266,267,268,281,284,285,286,289,290,291,301,302,304,306,307,309,314,317,318,319,320,322,330,331,332,339,340,342,343,364,369,370,371,376,377,378,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,209],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,196,332,371,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,376,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,289],coral:197,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],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:[3,6,40,117,196,341,342,364,464,476],cornflowerblu:197,cornsilk:197,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,194,196,223,236,238,244,260,261,281,289,291,294,331,337,341,361,371,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:206,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,197,203,224,229,234,245,254,260,261,297,304,307,317,319,338,341,371,372,376,394,424,429,473,474,476,486,501,503],correl:[],correpond:232,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,194,196,197,201,202,203,209,211,212,213,214,216,219,221,223,230,234,235,239,244,247,248,256,257,258,260,262,263,264,265,266,267,268,269,270,274,277,279,280,281,283,286,287,291,296,304,306,307,323,325,327,336,337,338,340,341,342,344,346,347,348,349,351,352,355,357,362,366,368,370,371,377,378,380,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[238,243],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,196,197,209,213,214,217,218,219,233,260,296,332,361,362,374,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,238,372],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,194,196,197,201,202,209,210,213,217,223,234,243,293,294,295,299,302,304,306,320,321,327,331,332,333,337,341,343,345,353,358,360,367,369,372,376,379,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,295,297,333,361,362,369,376,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,203,204,207,209,212,213,214,216,217,224,229,233,236,242,260,274,290,307,323,324,341,362,369,370,371,373,376,404,408,431,494,502],counter:[3,338,471,482,484,490],counteract:236,counterbal:240,counterbalanc:29,counterpart:[193,304,471],counterproduct:18,coupl:[],courant:310,cours:[3,8,130,132,164,193,201,202,237,303,317,331,337,339,340,342,343,362,423,449,473,476,489,497,502,504],courtesi:364,cov:447,coval:[6,29,402,426,447,497],covari:238,cover:[6,71,190,197,206,247,402,464],coverag:[71,213],cpc:243,cpp:[1,3,6,8,9,11,12,13,89,193,201,202,234,307],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,197,211,227,245,333,359,362,376,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,372],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,372,497],craympi:376,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:206,create_faceset:206,create_group:195,create_nodeset:206,createatom:[],creation:[],crimson:197,critchlei:289,criteria:[3,120,171,196,197,218,219,220,255,369,436,464,478,481,502],criterion:[12,41,125,170,173,207,217,220,236,274,296,310,338,343,369,371,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,258,327,332,369],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,194,196,208,213,219,223,257,259,281,304,313,317,319,328,335,347,364,371,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:294,crystal:[4,6,13,73,110,285,286,330,364,372,480,494,497],crystallin:[6,106,286,364,461,497],crystallis:327,crystallogr:[122,169],crystallograph:[364,494],crystallographi:[122,169,364],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[377,400],ctemp_cor:227,cterm:309,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,217,227,341,364,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,215,218,219,220,222,233,238,244,246,320,323,324,325,326,328,335,408,494],cumul:[6,207,209,212,213,214,228,236,244,258,260,265,274,304,305,371],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,198,201,202,206,209,213,214,215,217,218,219,220,221,222,223,224,228,229,234,236,238,241,242,244,250,257,260,261,266,267,268,274,279,280,281,283,289,290,295,296,298,301,302,303,304,307,308,309,310,311,312,313,314,316,318,319,320,323,324,325,331,332,335,336,337,338,339,340,342,343,345,359,360,361,362,365,366,368,369,370,371,376,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,236,286],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[285,297],cutinn:[384,423,424],cutlo:[285,297],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,219,220,225,232,285,294,295,297,299,301,304,308,320,333,337,341,343,359,361,362,369,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:[],cutoff_inn:[],cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:327,cvel:309,cvff:[],cwiggl:[3,257,337,340,342,502],cyan:[2,196,197],cycl:[3,236,258,260,261,265],cyclic:[3,190],cygwin:12,cylind:[3,4,71,196,209,242,290,338,341,479],cylindr:[6,242,317,338],cypress:376,cyrot:382,cyrstal:286,d3q15:247,d3q19:247,d_double_doubl:15,d_e:332,d_flag2:293,d_flag:293,d_name:[117,193,293,322,486],d_single_doubl:15,d_single_singl:15,d_sx:293,d_sy:293,d_sz:293,daan:330,dai:12,daili:12,daivi:281,damag:[],dammak:299,damp:[3,6,200,205,244,245,246,251,260,261,265,291,294,295,299,304,323,324,336,338,339,368,369,371,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:245,damp_drud:245,dampen:[304,497],dampflag:[338,406],dan:17,danger:[3,12,236,343,396,494],dangl:173,daniel:9,darden:[362,395],darkblu:197,darkcyan:197,darken:196,darkgoldenrod:197,darkgrai:197,darkgreen:197,darkkhaki:197,darkmagenta:197,darkolivegreen:197,darkorang:197,darkorchid:197,darkr:197,darksalmon:197,darkseagreen:197,darkslateblu:197,darkslategrai:197,darkturquois:197,darkviolet:197,dasgupta:295,dash:[406,493],dat:[6,93,190,206,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,305],dataset:305,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,210],davenport:425,davi:337,david:[9,19,361,362,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,195,196,197,198,287,477,481],ddim:192,deactiv:422,dealt:243,debug:[6,7,11,12,13,14,17,122,126,169,170,287,292,359,361,376,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,257,293,304,333,491],decipher:364,declar:195,declin:320,decod:196,decompos:[89,448],decomposit:[3,5,7,18,62,206,287,308],decoupl:[6,497],decreas:[3,193,194,203,204,211,220,223,229,234,236,244,331,361],decrement:309,deepli:358,deeppink:197,deepskyblu:197,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,227,228,229,231,234,235,236,239,242,243,244,245,246,247,255,257,259,260,261,262,263,264,265,266,267,268,270,271,272,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,297,302,304,305,306,307,310,314,318,320,322,323,324,325,326,328,329,330,332,334,335,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,373,374,375,376,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,197,209,210,211,212,213,214,215,223,231,242,265,305,322,334,337,340,342,344,356,359,370,379,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,289],degrad:[8,18,286,362,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,196,209,220,227,236,238,239,244,245,250,260,261,265,266,267,268,279,280,281,283,287,289,303,304,307,323,324,325,330,346,348,352,355,357,369,395,400,408,486,494,497,503],degress:[150,209],del:490,delai:[3,6,12,372,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,200,209,210,212,213,214,215,218,220,233,236,260,305,323,324,343,345,360,370,372,375,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:206,deli:192,delimit:[474,502],deloc:[261,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:[],delx:192,delz:192,dem:[],demand:299,demo:11,demon:284,demonstr:[294,426],den:290,dendrim:408,denniston:[9,247,249,250,251,286],denomin:[7,175],denot:[122,227,245,286,297,299,392,407,409,440,444,446],dens:[71,220,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,201,202,206,209,213,214,217,223,234,247,250,253,254,286,290,291,295,332,337,364,366,370,377,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[258,294],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,196,197,200,201,202,203,204,207,209,211,212,213,215,216,217,219,221,223,229,230,235,238,239,240,242,244,245,247,249,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,285,296,299,301,304,306,307,308,314,320,323,324,325,327,329,331,332,334,336,337,340,341,342,343,345,346,347,348,349,351,352,355,357,362,364,369,370,372,373,374,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:224,deposit:[],deprec:[3,295,439],depth:[51,148,196,332,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,210,221,223,236,244,257,260,262,263,264,265,266,267,268,285,291,295,299,329,330,332,337,338,341,368,370,378,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:285,descend:197,descent:[7,368],descib:[40,196,295],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,195,200,201,202,209,210,211,212,213,214,215,217,220,221,222,223,224,226,227,232,237,238,241,242,243,244,245,246,247,249,250,251,255,259,260,261,265,273,282,285,287,292,293,294,295,296,297,304,309,317,320,321,322,323,324,325,326,327,328,329,330,335,337,338,340,345,361,362,364,367,368,369,370,371,375,378,379,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:362,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,206,220,226,227,260,261,285,286,305,327,332,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,209,215,221,223,234,236,237,244,245,246,250,260,281,289,290,291,292,295,299,304,307,320,323,324,325,326,331,338,353,358,361,362,364,367,369,370,371,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,196],despit:497,destabil:382,destre:355,destroi:[11,39,218,219],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,194,196,197,200,201,202,206,209,210,211,212,213,215,217,219,220,221,222,223,224,234,236,237,238,239,241,242,244,246,247,251,257,258,259,260,261,262,263,264,265,266,267,268,272,274,279,280,281,282,283,286,289,290,291,293,294,296,297,298,304,307,308,320,323,324,325,326,327,328,330,331,332,333,334,335,336,343,345,347,356,361,362,365,369,370,372,373,376,377,378,379,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,235,290,331,371,391,408,413,471,473,476,487,490,502],determ:376,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,194,196,197,198,199,203,204,205,208,209,210,211,212,213,214,215,216,217,221,223,224,227,229,236,239,240,242,244,245,250,255,257,258,260,266,267,268,279,280,281,283,285,287,290,291,294,301,302,303,304,305,306,310,312,314,320,323,324,325,327,333,334,337,338,339,340,341,342,343,356,361,362,364,370,372,373,376,378,379,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:308,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,241,265,289,294,295,298,378,382,402,428,429,447,465,478],devemi:9,deviat:[258,265,285,404],deviator:9,devic:[1,3,12,15,17,241,376],device_typ:376,devin:[296,391],devis:428,dfactor:196,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,362],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,298,429],dhi:[59,192,223,290],dhug:[258,294],dhugoniot:[258,294],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,221,260,291,304,335,444,446],diagonalstyl:448,diagram:[41,122,169,189,217,287],diallo:408,diam:[196,197,290,370],diamet:[3,6,40,42,117,170,193,194,196,197,201,202,244,290,304,320,322,336,338,370,390,405,406,416,441,464,468,476,477,486],diamond:[364,402,426],diamter:[40,290],dick:6,dicsuss:257,dictat:[207,258],did:[3,12,369,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,334,361],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,15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:395,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,71,84,148,191],ellipsoid:[3,4,6,7,13,40,42,71,84,117,134,148,170,191,192,193,194,244,257,262,266,270,271,279,304,320,366,369,405,424,441,457,476,486,504],ellipsoidflag:476,elong:[227,245,494],elp:[439,440],els:[3,7,8,12,71,111,120,121,123,195,196,208,209,210,212,213,214,215,236,260,304,320,332,333,334,343,345,361,409,475,487,502,505],elsewher:[8,257,320,426,438,439,440,488,494,502],elt:426,emac:[],email:[0,3,5,7,8,9,11,403],emb:[3,9,341],emb_lin_neg:426,embed:[3,5,7,11,12,13,29,90,146,168,332,377,400,403,422,426,427,428,437,457,466,474],embt:177,emi:[7,9],emil:9,emol:[439,440,494],emphas:406,empir:[206,324,378,402],emploi:[9,286,295,299,461],empti:[3,57,71,168,172,304,361,372,413,476,487,488,502],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,85,89,99,100,101,102,103,104,108,113,115,116,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,152,154,156,157,161,162,164,168,169,176,177,179,180,181,182,183,184,185,187,188,189,190,193,194,195,197,198,200,201,202,203,204,205,207,211,214,216,218,219,220,222,223,224,229,230,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,286,287,289,290,294,295,296,297,298,299,300,301,303,304,306,307,309,310,311,312,313,314,316,317,319,320,323,325,326,327,328,329,330,332,333,335,336,337,338,339,340,341,344,346,348,349,351,352,353,355,356,357,362,369,371,375,376,377,378,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,474,477,478,479,483,485,495,502,506],enclos:[2,6,12,172,193,292,345,426,447,472,474,484,502],encod:[13,39,42,193,196,197,293,409],encompass:[3,6,40,42,57,59,120,171,316,334,457,479],encount:[3,8,12,59,110,212,375,481,502],encourag:[7,8,298,318],end12i:117,end12x:117,end12z:117,end1i:117,end1x:117,end1z:117,end2i:117,end2x:117,end2z:117,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,42,57,59,71,117,173,174,177,192,193,194,196,197,198,201,202,210,212,214,215,220,223,237,242,244,246,259,260,261,274,291,303,304,309,320,323,324,325,326,328,331,332,335,339,342,343,360,361,370,371,375,376,396,400,405,412,425,429,441,444,446,448,449,466,471,474,476,477,478,479,481,483,484,488,492,494,497,502,506],end_of_step:8,endbondtors:[3,177,183,476],endif:8,energet:[220,378,440],energi:[],energy_compon:447,energy_update_freq:440,enforc:[6,57,58,107,192,193,194,195,196,198,200,207,220,223,260,284,286,296,304,307,345,361,414,473,502,503],enforce2d:[],eng:[11,65,69,112,193,234,343,345,391,428],eng_previ:345,engil:9,engilitycorp:9,engin:[206,223,289,309,329,400,427],engr:[439,440],enhanc:[202,206,471],enlarg:[59,196],enough:[3,40,61,88,170,171,173,174,217,245,290,294,299,304,333,337,338,341,372,376,392,435,476,480,481],enpub:400,enrti:[],ensembl:[],ensight:6,ensur:[3,6,144,193,194,207,211,221,236,237,260,310,331,362,382,399,422,458,465],enter:[57,160,403,429,465,490],enthalpi:[127,262,263,264,400,493,494,502],entir:[0,2,3,6,11,14,15,41,42,63,82,83,90,113,114,116,120,122,145,150,169,170,197,200,201,202,209,213,214,217,220,222,233,236,237,240,244,245,256,260,262,263,264,265,266,267,268,285,287,289,302,304,318,332,334,345,376,395,418,431,459,476,484,485],entireti:464,entiti:[6,8,40,42,193,304],entri:[3,8,12,38,42,56,65,69,79,95,112,119,122,131,134,135,136,137,138,140,141,142,168,190,194,197,212,213,214,222,232,294,343,370,382,401,426,433,440,448,458,459,460,461,462,465,502],entropi:490,entry1:[38,56,197,389,459],entry2:197,entryn:197,enumer:[171,193],enumuer:6,env:376,environ:[1,3,6,11,12,16,17,18,196,238,243,285,376,377,382,389,391,401,402,437,460,473,487,502],epair:[111,197,404,408,439,440,494],epen:[439,440],epfl:[238,243],epp:395,epq:395,eps0:468,eps14:422,epsilon0:462,epsilon:[3,6,36,45,46,50,53,54,89,176,201,202,236,304,320,337,341,367,369,381,387,388,390,392,393,394,395,405,407,408,409,412,413,414,415,416,417,418,419,420,421,422,425,430,434,441,442,452,458,464,467,468,485,497,501],epsilon_0:469,epsilon_14:387,epsilon_:441,epsilon_d:393,epsilon_i:[405,431,441],epsilon_i_:441,epsilon_i_a:[405,441],epsilon_i_b:[405,441],epsilon_i_c:[405,441],epsilon_ij:431,epsilon_j:[405,431,441],epsilon_j_:441,epsilon_j_a:[405,441],epsilon_j_b:[405,441],epsilon_j_c:[405,441],epsilon_lj:441,epton:436,eqch:165,eqeq:[439,440],eqp:395,eqq:395,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,71,76,79,88,89,93,95,112,114,119,121,123,145,148,164,166,168,170,192,196,197,200,201,202,203,204,207,210,211,212,215,216,217,221,223,224,229,236,237,239,240,242,244,245,247,250,251,257,258,265,276,285,287,290,292,294,295,296,299,301,303,304,306,309,314,316,323,324,325,328,329,330,332,334,335,337,340,342,343,345,360,364,369,371,372,373,375,376,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,200,221,227,228,231,232,238,244,245,247,250,258,259,260,261,265,281,285,287,294,295,299,307,308,320,328,332,335,337,338,340,342,355,361,362,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:261,equidist:259,equil:[3,295,365,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,200,207,210,220,221,236,258,260,261,281,282,294,295,296,297,328,329,330,335,391,392,439,440,472,486],equilibria:335,equilibribum:[218,219],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,221,223,236,237,238,245,247,260,265,281,294,295,299,303,307,309,317,320,327,328,330,335,346,348,352,355,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:206,equival:[6,12,13,29,59,61,128,129,137,142,168,172,197,212,215,221,223,236,244,260,281,291,303,304,340,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[295,297],er3:169,eradiu:[40,117,194,402,476],eras:[306,329],erat:[223,424],erc:392,erfc:[392,414,431],erforc:[117,194],erg:501,erhart:[207,400,460,462],ermscal:379,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:337,erron:3,error:[],erta:406,ervel:[117,194,476],escap:[224,497],especi:[8,16,158,170,200,207,217,236,294,299,302,303,376,473],espresso:[9,298],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,210,265,286,336,362,378,392,414,462,481,494],essex:29,establish:[89,240],estim:[1,3,6,10,12,38,41,56,93,145,206,217,228,258,320,327,361,362,367,431,440,459,490,494],esu:501,esub:426,eta:[6,247,260,294,295,297,336,401,403,405,437,461,465,501],eta_dot:260,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:260,etap_dot:260,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,194,196,197,200,201,206,207,208,209,212,213,214,215,218,219,223,224,234,236,237,244,260,290,301,305,332,333,341,345,360,361,369,370,371,372,374,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[369,371,471,490],etot0:294,etot:[6,97,99,100,114,145,156,197,227,245,258,294,493,494],eu2:169,eu3:169,euler:[369,371],eulerian:206,euqat:450,europhi:247,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,194,196,197,201,202,203,204,206,208,209,210,211,212,213,214,215,216,223,229,237,239,240,242,243,244,245,286,292,295,306,310,314,323,324,325,334,337,340,342,343,345,361,362,367,369,376,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[345,474],evan:[158,281],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,369],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,194,197,200,201,202,207,208,209,212,213,214,215,217,218,219,221,223,224,227,242,245,258,260,261,286,290,299,301,304,305,316,320,328,332,335,337,341,343,354,361,367,369,371,376,381,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,217,247,412,466],event:[],eventu:[3,6,12,15,172,295,490],ever:[54,56,243,320],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,198,200,201,202,203,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,228,233,234,236,238,240,241,242,247,248,256,260,261,265,284,285,286,290,291,292,293,294,295,296,297,299,301,302,304,305,307,309,320,322,323,324,325,326,327,328,331,332,333,334,335,343,345,360,362,371,372,373,376,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[238,247,287,471],evolv:[247,287,333],ewald:[2,3,5,6,7,8,12,90,114,122,145,333,361,362,369,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,217,220,237,238,244,245,246,290,299,300,320,332,347,361,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,201,202,212,217,223,228,232,237,244,245,246,261,273,274,282,286,294,320,325,326,339,376,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,220,286],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,208,209,212,213,214,215,217,221,223,228,233,260,286,301,305,311,312,320,369,376,476,502],exceed:[3,41,59,217,223,260,320,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[211,402],exchang:[2,3,6,8,9,61,62,200,206,207,236,244,296,304,328,332,335,361,376,402,491],exchange:361,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,209,213,218,219,248,256,289,302,304,327,338,343,369,370,372,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,376,391,429,431,485,495],excurs:[260,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,196,241,298,345,360,363,375,472,474,484,487,490,502],exempl:447,exemplari:237,exemplifi:402,exert:[6,242,245,299,339,340,341,362],exhaust:[206,375,502],exhibit:[94,260,368,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,195,196,197,200,205,216,219,221,224,236,289,290,292,343,344,346,348,349,350,352,356,365,370,376,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,217,232,360,375,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,217,229,236,238,257,285,291,293,294,299,304,343,362,372,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,197,285,289,304,332,343,361,362,372,376,474],experi:[6,13,15,17,216,224,241,250,259,291,303,304,367,371,396,431,485,490],experienc:[6,12,249,250],experiment:[236,361,376,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,194,209,259,285,409,470,473,474,476,485],explanatori:[3,8,121,193,194,208,209,212,213,214,304,370,473,502],explantori:[3,300],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,201,202,223,311,312,347,366,378,379,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,213,216,223,230,235,237,239,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,293,294,296,304,306,307,323,325,326,332,336,340,346,348,349,351,352,355,357,370,376,377,378,380,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,287],explor:[122,169],expon:[3,295,297,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[206,396,399],express:[6,144,156,170,201,202,221,257,285,295,332,338,345,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,194,200,203,204,207,215,216,222,225,229,234,235,236,238,239,240,242,244,246,258,260,265,274,285,286,302,303,304,306,309,314,317,319,323,324,325,326,327,329,330,332,334,337,341,342,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,205,213,217,242,339,342,361,364,378,443,445,459,473,476,479],exterior:[3,6,168,341],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,197,212,217,219,260,292,293,294,304,320,369,370,373,374,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,201,202,297,371,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,196,211,221,223,260,330,402,461,497],extrema:422,extrins:206,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,334],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:294,f_harm:330,f_i:[29,437],f_id:[6,71,121,123,193,194,200,208,209,210,211,212,213,214,215,255,322,334,494,502],f_ij:437,f_indent:215,f_int:329,f_j:29,f_jj:93,f_k:437,f_langevin:332,f_max:[294,299],f_msst:258,f_r:[245,460,461,462],f_sigma:382,f_solid:330,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,205,213,214,337,339,340,341,342,364,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,238,290,320,330,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,196,197,201,202,210,217,221,223,224,236,241,244,246,247,258,260,261,265,287,291,295,303,307,310,312,320,324,328,335,336,337,341,352,362,364,370,376,378,379,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:361,fail:[3,11,12,59,174,221,224,361,369,371,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:241,fall:[3,6,197,212,290,474,502],fals:[88,343,345,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,194,197,198,217,218,219,221,224,260,285,303,304,320,337,348,352,367,371,372,464,474,476,481,494],farago:244,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,197,200,201,202,207,213,217,219,224,236,238,242,257,258,260,262,263,264,265,266,267,268,276,279,280,281,282,283,293,294,296,304,309,313,319,322,330,332,336,337,338,340,342,371,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,194,271,294,333,361,362,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,216,217,223,230,235,239,243,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,291,295,296,304,306,307,320,323,325,327,329,332,336,340,346,348,349,351,352,355,357,361,362,373,374,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,213,332,333,376,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:220,favorit:7,fbmc:327,fcc:[],fcm:[276,502],fdirect:227,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:206,featu:8,featur:[],fecr:400,feedback:[7,241],feel:[7,241,242,250,285,341,343,371,431],felling:428,felt:341,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,250,485],fewest:3,fextern:234,feynman:287,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,196],ffplai:196,fft:[1,3,7,11,12,14,15,90,113,114,145,286,361,362,485],fft_inc:[12,362],fft_lib:12,fft_path:12,fftbench:[361,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,203,204,229,234,238,287,303,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[317,433],figur:[1,3,8,12,294,473,474],fij:395,file0:285,file1:[11,13,285,331,345,370,481,483,487],file2:[11,13,331,345,370,481,483,487],file:[],file_from:195,filen:370,filenam:[3,12,13,38,41,56,190,193,194,196,197,198,206,209,210,211,212,213,214,215,217,222,232,285,289,292,295,296,297,300,301,304,305,331,332,358,359,360,370,371,377,378,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,194,197,478,483,506],filepo:301,fill:[7,9,170,196,290,332,364,372,382,429,440,479],filter:[197,206],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,198,207,220,221,232,233,236,259,285,290,291,299,303,367,369,371,372,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,203,229,330,372,376,502],finer:[144,170,502],finest:361,finger:[170,192,257,479],finish:[6,11,41,217,345,358,360,361,373,375,376,464,481,502,503],finit:[],finni:[7,400,457],finvers:227,fiorin:[9,222],fire:[],firebrick:197,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,198,200,201,209,210,212,213,214,215,217,220,223,232,236,237,242,247,257,258,259,260,285,287,292,293,294,296,301,304,307,309,317,318,320,321,322,329,330,331,332,334,338,343,345,346,353,364,369,370,371,372,375,376,377,378,381,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,232,303,320,378,382,411,426,431,452,459,461,484,502],five:[73,156,294,370,382,427,476,490],fix:[],fix_adapt:[164,202,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,207,290],fix_eo:9,fix_evapor:207,fix_flux:206,fix_gcmc:[207,370],fix_gl:238,fix_gld:238,fix_grav:290,fix_id:[3,221,258,260,262,263,264,265,266,267,268,291,294],fix_modifi:[],fix_mov:[192,338],fix_nh:8,fix_npt:238,fix_nvt:[207,236],fix_poem:[3,6],fix_pour:[3,224],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:307,fix_reax_bond:439,fix_rigid:[250,381],fix_saed_vtk:305,fix_setforc:8,fix_shak:307,fix_shardlow:9,fix_srd:3,fix_styl:265,fix_temp_rescal:326,fixedpoint:[221,260],fixextern:234,fixid:206,fji:395,flag1:[226,374],flag2:[226,374],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:226,flagvf:[384,423,424],flat:[6,332,337,338,342],flavor:[2,7,12],fld:[9,337,384,423,424],flen:379,flex_press:379,flexibl:[3,6,8,171,196,209,213,222,238,261,328,335,402,461,494],flip:[3,6,223,260,339,340],floor:502,flop:12,floralwhit:197,flow:[],fluctuat:[6,64,89,221,236,237,244,247,260,265,285,286,308,330,332,355,398],fluid:[],fluid_veloc:251,flush:[3,197,493],flux:[],flv:196,fly:[7,9,12,41,196,200,206,211,224,227,304,307,333,382,429,494,497],fmackai:9,fmag:225,fmass:287,fmax:[369,494],fmomentum:227,fmsec:[2,197,244,245,257,260,291,304,323,324,485,496,501,503],fname:360,fno:[12,16],fnorm:[369,494],fnpt:227,fnvt:227,foce:409,fock:379,focu:307,fogarti:[9,297,440],foil:[144,285,448],fold:[318,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,195,196,197,200,206,207,208,209,210,211,212,213,214,215,217,222,223,224,227,228,231,232,234,236,237,238,241,243,244,245,247,250,258,260,265,266,267,268,279,280,281,283,286,287,289,292,293,294,295,297,299,301,303,304,305,307,322,323,324,325,328,329,330,331,332,334,335,343,344,348,349,350,351,352,355,357,359,364,366,369,370,371,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,196,234,474,487,502],foot:6,footprint:[12,376],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:250,forcefield:[303,408],forcegroup:247,forcezero:367,ford:395,forestgreen:197,forev:71,forget:[245,497],forgiv:260,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,197,200,201,202,219,237,238,244,246,250,257,281,286,297,299,303,304,332,337,341,346,347,350,355,366,368,370,371,378,379,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,237,238,244,260,287,320,328,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,198,209,212,213,214,215,217,219,232,286,289,293,295,297,300,304,305,316,331,332,343,344,347,366,370,371,377,378,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,197,217,332,336,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,203,229,244,260,281,295,297,303,307,331,361,378,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,201,202,203,204,209,210,211,212,215,216,223,229,239,240,242,244,245,257,285,286,292,301,306,314,318,320,323,324,325,334,337,340,342,343,345,346,347,349,356,364,370,378,379,381,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,375,474,479,483],fortran:[3,6,9,11,12,13,234,400,409,426,439,440],fortun:8,forward:[3,8,89,360,371,376],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,220,222,236,241,247,286,327,333,345,360,372,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,258,332,355,370,371,429,471],fourier:[],fourth:[6,108,303,317,327,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:243,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,196,197,207,218,219,220,221,258,290,294,301,302,320,325,326,364,371,376,382,384,406,423,424,481,486],fragment:[42,241,301],fraig:42,frame:[85,144,197,206,258,294,339,405],framer:[196,197],framework:[5,238,377,448],franc:9,fra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95,297,357,408,488],ijj:465,ijk:[351,355,357,382,437,465,473],ijl:355,ikeshoji:6,ikj:465,iko:2,ill:[150,160,209,295],illeg:3,illinoi:[241,361,362,423],illog:474,illustr:[1,6,8,11,12,16,17,18,19,285,287,371,409,474,502],ilmenau:[7,9,14],ilya:[7,9],imag:[],image2pip:196,imageint:3,imagemagick:[4,196],imagin:[317,331,382,401,409,410,412,427,428,433,437,458,460,461,462,465,488],imaginari:[6,94,236,287,476],imbal:[1,12,41,217,376,495],imbalanc:[41,217],imbu:320,imd:[],img:196,immedi:[0,2,3,8,12,170,218,219,224,307,316,321,322,339,473,474,476,478,490,502,505],immens:3,immers:[247,304],impact:[1,4,6,8,228,327,495],impart:[3,6,239,320,342],impei:[6,414],implement:[1,3,6,8,9,12,17,18,27,78,82,83,89,110,122,152,158,169,170,178,179,189,209,222,226,231,238,241,244,247,249,250,251,258,260,281,284,286,287,293,294,297,298,299,307,308,309,320,327,332,336,355,360,361,362,369,371,376,377,379,382,391,392,394,396,397,398,400,401,402,409,414,418,422,426,436,439,440,441,460,462,473,474,485,490,497,502,504],impli:[3,6,40,59,89,145,192,196,201,202,203,223,229,244,303,323,325,326,361,364,389,474],implicit:[],implicitli:8,implict:393,imporop:370,importannt:[],important:330,important_not:[],impos:[2,6,71,116,159,192,200,203,204,216,229,230,234,239,242,251,252,259,274,285,288,306,314,317,319,320,327,328,329,330,335,336,337,340,341,342,369,371,373,470,484],imposs:1,improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:219,imprort:100,improt:[201,202],improv:[0,1,9,16,39,41,197,217,260,286,376,408,414,429,431,440,458,461],in3:169,inaccur:[1,3,6,173,258,361],inaccuraci:341,inact:408,inappropri:170,incid:[122,169,224],includ:[],includig:[345,360],inclus:[],incom:241,incompat:[3,11,410],incomplet:[3,11,476],incompress:[261,402],inconsist:[3,174,220,477],inconveni:364,incorpor:[294,382,393],incorrect:[3,153,244,426],incorrectli:[3,364,406,502],increas:[1,3,6,10,18,38,56,57,59,113,122,145,190,193,194,196,197,211,218,219,220,223,232,236,244,291,302,303,304,328,331,335,361,362,371,376,402,405,440,459,461,474,485,490,502],increasingli:402,increment:[3,11,132,203,204,216,217,224,229,233,260,290,309,310,343,360,375,412,447,471,474,488,490,502],incur:[14,17,209,213,214,233,332,473],inde:153,indefatig:7,indefinit:329,indent:[],independ:[4,6,9,11,12,16,17,41,59,63,93,121,123,156,170,192,200,208,209,210,212,213,214,215,217,220,221,222,223,224,237,239,244,245,247,250,260,286,291,295,299,304,305,309,319,330,332,364,406,429,471,474,493,503],indetermin:[193,194,197],index:[0,3,6,8,11,12,38,39,40,56,68,69,121,123,168,190,193,197,208,210,232,241,243,287,305,332,343,344,345,366,375,431,439,440,459,466,476,491,502],indianr:197,indigo:197,indirectli:[6,502],indistinguish:244,indium:448,individu:[],induc:[],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,94,110,144,158,196,223,260,286,361,373],inelig:207,inerti:424,inertia:[],inexpens:[238,485],inf:[2,3,12,335,479],infer:[3,97,99,100,164,203,204,217,218,219,229,241,289,320,328,335,364,389,403,476,488,494],infil:[3,13,304,473],infin:[3,369,481,494],infininti:196,infinit:[3,224,235,242,244,247,286,320,332,338,339,362,364,402,480,501],infinitesim:6,inflect:[393,416,457],influenc:[3,9,41,80,152,257,290,361,362,431,460,461,462],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,90,119,121,122,169,170,176,193,194,195,196,197,198,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,229,230,233,234,235,236,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,259,269,270,271,272,273,274,275,276,277,278,284,285,286,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,310,317,318,320,321,323,324,325,326,327,328,329,331,334,335,336,337,339,340,341,342,344,359,361,362,365,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,473,474,476,477,478,480,481,483,488,490,491,493,495,502,504,505,506],infrequ:[6,260,396,471,490],infti:[393,423,424],ingtegr:382,inher:[361,369,431],inherit:[6,463],inhomogen:[18,332,431],inidividu:369,init:[3,8,302,447],init_fil:332,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,88,89,106,107,134,166,171,172,190,192,193,194,196,197,198,201,202,205,206,210,217,219,220,221,223,230,232,236,237,241,242,243,244,245,247,252,256,257,258,259,260,265,274,286,287,288,293,294,299,302,303,304,306,308,319,320,322,327,329,330,331,332,333,334,337,338,339,340,342,343,345,361,365,368,369,371,378,379,395,396,399,429,438,439,440,447,459,471,473,474,476,478,479,481,483,484,486,490,491,494,497,502,503,504,506],initial_integr:8,initial_integrate_respa:8,initialis:438,initialt:332,inlclud:11,inlcud:502,inlin:474,inner2:[387,407],inner:[3,8,16,193,242,345,360,367,368,36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run5:[6,375,502],run6:[6,375,502],run7:[6,375,476,477,481,502],run8:[6,375,502],run:[],run_styl:[],runloop:360,runtim:[12,17,196,376],russia:9,rutherford:332,rutuparna:[460,462],ryan:9,ryckaert:[307,355],rycroft:168,rydberg:429,s00:436,s0st:6,s2050:1,s2629:400,s319:206,s_fact:310,s_i:[6,402],s_ij:6,sack:7,saddl:[259,371],saddlebrown:197,sadigh:[207,400,427,428],saed_vtk:122,safe:[12,196,227,245,376],safe_zon:3,safest:[3,320],safeti:310,safezon:440,safran:468,sagui:[362,395],sai:[1,3,12,13,197,439,440,474],said:369,sakai:461,sall:[9,447],salmon:197,salt:[393,404,426,476],salter:447,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,84,86,87,89,90,91,92,93,94,95,97,100,106,107,108,110,112,113,114,116,117,119,120,121,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,162,163,164,166,168,170,171,172,173,174,176,177,178,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,200,201,202,203,206,207,209,212,213,214,215,216,217,218,219,220,221,223,224,228,229,230,235,236,237,238,239,240,241,242,243,244,245,246,247,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,282,283,285,286,287,289,290,291,294,295,296,297,299,300,301,302,303,304,306,307,309,314,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,334,335,336,338,339,340,341,343,344,345,346,347,348,349,351,352,355,357,361,362,364,365,366,370,371,372,373,374,375,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,422,423,424,426,427,430,431,432,433,434,436,437,441,442,447,449,456,457,458,459,460,461,462,465,467,468,469,471,473,474,476,477,478,479,481,484,485,486,487,488,489,490,494,497,501,502,503,505],sampl:[1,2,4,6,9,10,11,12,14,93,106,148,149,163,168,192,196,200,209,210,213,214,222,224,234,236,238,240,260,261,287,290,299,301,305,317,318,320,324,327,330,342,372,382,399,476,490],sample_frequ:206,san:436,sandia:[0,5,7,9,13,14,17,70,115,403,426,436],sandybrown:197,saniti:[303,372],satellit:[6,152],satifsi:502,satisfi:[3,12,73,122,144,169,221,247,265,307,340,369,372,406,490],satur:393,save:[6,8,12,19,40,59,190,194,196,211,220,237,238,244,245,246,290,299,332,344,362,372,374,382,478,481,488],sb3:169,sb5:169,sc3:169,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,71,72,93,117,120,121,144,156,164,190,192,193,194,196,197,200,201,202,206,207,210,221,223,236,240,241,242,244,246,247,258,260,262,263,264,265,266,267,268,287,291,294,295,304,311,312,320,322,324,327,329,330,332,336,343,361,362,364,370,373,377,378,379,393,399,402,406,409,423,424,426,429,436,443,445,463,477,479,481,485,488,490,493,494,502,503],scale_factor:[443,445],scalegamma:247,scalexi:[3,221,260,265],scalexz:[221,260,265],scaleyz:[221,260,265],scan:[197,219,360,477],scatter:[11,122,169],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,220,293,302,320,333,341,372,480,481,485,493],scf:497,schaik:422,schedul:471,schell:461,schemat:220,scheme:[6,9,18,237,238,260,287,299,307,332,361,463],schlitter1:331,schlitter2:331,schlitter:331,schmid:396,schneider:[244,246],schoen:361,schr:497,schroding:402,schroeder:[110,497],schulten:[245,309,362,497],schunk:320,schwen:9,sci:[73,340,391,428,437,447],scienc:[8,206,220,241,309,329,400,427,447,461],scientif:[144,400],scm:11,scratch:[12,41,217],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:197,seamlessli:293,search:[0,2,3,8,12,94,110,171,173,197,198,320,367,368,369,371,373,471,477,478,490,502],seashel:197,sec:[12,496,501],second:[1,3,6,9,10,11,12,16,54,57,59,61,71,90,93,106,108,110,116,137,138,142,145,146,158,164,168,169,171,172,173,192,193,197,200,201,209,210,212,213,214,215,220,236,237,242,257,259,287,301,303,304,307,309,317,318,320,329,330,332,343,361,364,368,369,371,372,376,381,382,383,385,386,391,392,400,402,403,406,407,409,412,413,416,426,431,433,447,458,461,462,463,465,469,471,472,473,474,476,478,483,485,489,490,494,497,501,502,503,504,506],second_mo:447,secondari:[3,182],sectinn:505,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,82,85,88,89,90,91,92,93,95,96,99,100,101,102,103,104,106,107,108,109,111,112,113,115,116,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,171,176,177,178,179,180,181,182,183,184,185,187,188,189,190,192,193,194,195,196,198,200,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,226,227,229,230,232,233,235,236,237,238,239,241,243,244,245,246,247,248,249,250,251,253,254,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,294,295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54,156,157,158,159,160,161,162,163,221,247,250,260,261,265,289,291,304,335,361,362,370,402,423,424,429,444,446,494,502],tenth:[131,360],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,40,45,46,61,89,90,91,93,114,116,145,146,148,149,158,163,164,177,178,179,190,197,201,202,208,210,212,215,223,229,237,238,239,244,245,246,247,259,260,261,262,263,264,265,266,267,268,279,280,281,283,287,291,294,303,304,318,323,324,325,332,334,336,338,346,347,357,361,369,372,377,378,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,414,418,421,422,423,424,426,427,428,429,431,434,441,447,456,458,460,461,462,465,468,485,486,488,494,497],termin:[122,260,369,371,444,446,475,484],termostat:324,terrel:368,terri:7,tersoff:[],tersoff_1:[460,461,462],tersoff_2:[460,461,462],tersoff_mod:461,tertiari:182,tessel:[9,168],test:[],test_descriptor_str:3,testf:190,testu:190,tether:[6,302,309,317,319,330,404],tetot:[9,447],tex:8,texa:436,texas_holdem:303,text:[2,3,4,6,7,8,12,13,38,41,56,190,193,194,196,197,200,206,209,210,211,212,213,214,215,217,222,232,241,292,331,332,344,362,364,371,400,403,413,426,448,459,472,476,477,493,502,504],textur:17,tfac_insert:236,tfactor:[3,197],tfinal:502,tfix:303,tflag:196,tfmc:[],th4:169,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,39,40,41,42,56,57,58,59,61,63,68,71,76,88,90,94,108,110,112,116,119,120,123,145,168,171,172,173,179,190,192,193,195,197,200,205,207,209,212,213,214,215,217,218,219,220,221,223,224,225,228,232,233,236,237,238,239,242,243,244,247,258,285,286,290,291,292,293,294,295,297,299,302,303,304,305,308,309,310,316,317,318,320,324,325,327,328,332,335,336,337,338,339,340,341,342,343,345,361,362,367,368,369,370,371,372,373,376,381,382,383,385,386,387,400,402,405,406,412,423,424,426,431,439,440,441,447,449,456,457,458,459,462,464,466,468,469,471,472,473,474,476,477,478,479,480,481,484,485,488,490,491,493,502,503,504],thank:[241,460,462],thb:440,thb_cutoff:440,thb_cutoff_sq:440,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,57,59,61,63,64,66,68,70,71,74,75,81,84,86,89,91,92,93,96,106,107,109,112,113,116,118,119,120,121,123,144,147,148,150,152,153,156,157,163,165,167,168,170,172,173,174,176,177,179,180,181,182,184,185,187,188,189,190,193,194,196,197,200,201,202,203,205,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,229,230,235,236,237,239,240,241,244,245,247,250,257,260,262,263,264,265,266,267,268,269,270,271,272,277,279,280,281,283,289,290,291,292,293,295,296,303,304,305,306,307,320,321,323,324,325,327,331,332,334,335,336,338,340,341,343,344,345,346,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,432,433,434,436,437,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,464,465,466,467,468,469,472,474,476,477,478,479,480,481,485,486,488,489,494,497,502,504,505],them:[1,2,3,4,6,7,8,9,11,12,13,14,17,39,40,41,54,59,71,93,106,111,118,121,123,146,172,177,193,196,197,198,208,209,210,212,213,214,215,217,220,221,223,233,241,244,245,256,260,262,263,264,265,266,267,268,279,280,283,285,291,293,301,302,303,304,307,320,323,324,325,327,331,332,334,338,339,340,342,343,346,362,364,370,371,372,376,377,382,389,400,403,405,409,412,431,441,449,464,471,474,476,483,488,491,497,502,503],themselv:[6,11,173,201,202,217,245,361,362,371,373,377,382,392,400,422,426,427,428,448,502],theor:327,theorem:[237,244,308,382,398],theoret:[108,241,294,458],theori:[3,6,9,12,40,144,206,222,238,260,286,361,362,382,429,468,490],thereaft:[71,252,288,304,328,335,474],therebi:[333,423,424],therefor:[3,6,12,64,89,155,227,236,245,247,307,327,362,394,438,440,458,463,485,497],therein:[6,426],thereof:89,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,63,113,474,494],thermo_press:[63,116,221,227,260,262,263,264,265,266,267,268,291,493,494,497],thermo_styl:[],thermo_temp:[63,116,147,220,221,236,260,262,263,264,265,266,267,268,279,280,281,283,286,291,323,324,325,493,494,497],thermoberendsen:6,thermochem:501,thermochemistri:402,thermodyam:[494,501],thermodyanm:[63,220,320,343,485],thermodynam:[],thermophys:431,thermost:[6,152,205,222,227,245,339,497],thermostat:[],thermostatequ:6,thesi:[361,362,423,438],thess:383,theta0:[20,21,24,26,27,28,32,33,35,36,144,179,303,355],theta0max:144,theta10:382,theta1:[177,346,382],theta2:[177,346,382],theta3:[346,382],theta4:382,theta5:382,theta6:382,theta7:382,theta8:382,theta9:382,theta:[3,6,26,27,37,38,63,65,80,94,110,144,169,170,179,192,196,239,299,303,332,346,355,408,437,461,476,479,486],theta_0:433,theta_:[355,382],theta_c:408,theta_ijk:382,theta_ijl:346,theta_jik:[427,428],theta_pi:382,theta_sigma:382,thex:295,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,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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 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","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":218,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,194,196,197,198,199,201,202,203,205,206,207,209,213,214,215,218,219,221,222,223,224,228,233,236,237,242,244,245,246,247,248,250,255,258,260,261,265,281,282,286,287,290,291,292,293,294,296,299,301,302,304,305,320,322,327,328,329,330,333,335,337,339,343,356,359,361,362,364,365,367,368,370,372,373,374,376,379,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[211,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[201,202],addforc:203,addit:[12,13],addtorqu:204,adiabat:6,adjust_dt:310,adp:377,airebo:378,alloi:400,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:205,arrai:6,aspher:[6,84,148,262,266,270,271,279],atc:[9,206],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,205,207,208,293,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:216,awpmd:[9,379],balanc:[41,217],barostat:6,basal:67,beck:380,berendsen:[291,323],between:6,binary2txt:13,bodi:[6,8,42,68,149,263,267,272,280,381],bond:[8,13,69,218,219,220,300],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,221],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,209],citat:7,class2:[21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[337,390,468],colvar:[9,13,222],com:[74,75,151],comb3:391,comb:[296,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,328],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[210,211],cosin:[23,24,25,26,27,28,179],cossq:348,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:219,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:324,csvr:324,cubic:416,cuda:[9,14,113,116,147,157,203,216,230,235,239,260,269,306,307,323,325,336,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:[8,193,194],cut:[49,379,385,388,392,395,402,404,414,415,422,430,434],cvff:349,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,223],delete_atom:173,delete_bond:174,delta:24,deposit:224,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:227,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:350,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:225,dreid:[6,408],drude:[6,9,155,226,227,245],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,196,198],dump_modifi:197,dynam:295,eam:[13,400],echo:199,edip:401,eff:[9,13,99,100,154,156,161,246,261,273,282,326,402],efield:229,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:230,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:233,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:234,fcc:285,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,202],field:[6,7],file:6,finit:6,fire:295,fix:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309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