From 0b92c9f075a1997b48d20ee53b3cd74228c14351 Mon Sep 17 00:00:00 2001
From: sjplimp
At the beginning of the first run or -minimize command after this fix is defined, the -initial COM of each chunk is calculated and stored as R0c, where C is +minimize command after this fix is defined, the +initial COM of each chunk is calculated and stored as R0m, where M is the chunk number. Thereafter, at every timestep (or minimization -iteration), the current COM of each chunk is calculated as Rc. A -restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each +iteration), the current COM of each chunk is calculated as Rm. A +restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each atom in each chunk where K is the specified spring constant, Mi is -the mass of the atom, and Mc is the total mass of all atoms in the +the mass of the atom, and Mm is the total mass of all atoms in the chunk. Note that K thus represents the spring constant for the total force on each chunk of atoms, not for a spring applied to each atom.
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246,ceriotti:[13,246,251],certain:[1,2,3,6,8,12,16,39,75,124,128,130,181,201,202,204,216,217,218,220,221,226,242,243,315,318,334,347,358,366,374,387,424,446,457,481,497,501,516,522],certainli:250,cerutti:376,cfg:[3,6,7,9,13,201,203,204,205,206],cfile:457,cfl:[139,322],cfor:321,cg_type:459,cgiko:[],cgikot:[],cgkio:[],cgko:[],cgkot:[],cgo:[],cgot:[],ch2:319,ch2lmp:[],ch3:319,ch5md:203,chain3:387,chain:[],challeng:[6,321],chalopin:310,champaign:[249,375,376,438],chan:444,chandler:[392,414],chandrasekhar:[6,429],chang:[],change_box:[],changeabl:201,channel:[4,211],chapter:[298,376],charact:[2,3,6,12,37,41,56,65,197,201,202,204,205,206,208,223,239,240,304,312,316,358,385,390,416,418,428,448,449,454,456,457,464,476,477,492,493,497,502,503,522,525,526,527],character:[6,70,74,117,127,151,465,490,509],characterist:[253,333,342],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,129,176,177,201,202,206,208,209,210,215,230,235,244,304,306,307,308,312,335,348,375,376,385,398,400,406,407,409,410,414,416,417,424,429,433,437,451,456,457,464,474,480,481,483,484,486,487,495,496,500,505,507,516,521,522],charmm2lammp:13,charmm:[],chartreus:205,cheap:333,cheaper:[234,420,458],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,197,198,215,223,224,225,230,241,244,250,251,301,314,319,333,341,343,348,356,358,371,374,384,385,386,387,388,391,413,425,428,446,457,488,490,492,493,495,503,509,512,513,522],checkf:197,checkout:517,checkqeq:457,checku:197,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,152,183,184,194,219,228,233,236,245,246,253,255,268,269,270,292,293,298,302,305,307,315,320,321,333,336,337,340,341,342,343,350,359,368,370,375,376,383,386,393,398,402,403,406,407,408,410,411,412,416,419,420,422,423,429,433,434,437,441,445,446,448,449,451,464,473,481,504,507,509,516],chemic:[9,40,88,89,129,171,176,201,202,214,215,244,306,311,312,340,376,418,449,456,457,469,477],chemistri:[305,306,308,393,397,416,456,457],chen:345,cheng:406,chenoweth:[456,457],chenoweth_2008:[456,457],chi:[102,166,200,296,306,308,371,417,420,523],chiefli:455,child:8,chip:[7,9,16,17,391,508],chipot:228,chiral:368,chmod:[11,12],cho:441,chocol:[7,205],choic:[3,6,9,12,14,15,17,40,41,54,95,152,155,156,170,181,197,217,223,226,229,230,246,252,255,267,269,298,302,306,315,340,369,376,382,383,386,388,391,424,437,446,452,495,504,505,508,509,515,516,521],choos:[1,3,6,7,8,9,12,15,16,17,28,39,54,95,128,167,168,204,224,225,226,227,230,241,252,255,267,269,271,272,273,274,275,276,277,301,302,320,333,337,351,375,376,383,484,490,492,504,510],chose:[478,480],chosen:[2,3,6,12,16,151,177,180,189,197,204,210,215,227,230,241,244,245,253,255,267,269,274,298,301,312,333,337,340,341,346,348,349,355,376,377,383,391,412,416,421,428,431,459,478,490,504,509,510,516],chri:175,christian:[7,9,16],christoph:7,chunk:[],chunkid:[69,79,86,98,103,114,116,125,157,172,174,217,330],chute:[4,9,10,247],ciccotti:319,cieplak:[6,183,507],cii:218,cij:218,ciko:[],circl:[42,75,328],circular:[3,6,155,199],circumst:17,circumv:[100,117,310],citat:[],cite:[3,7,8,12,252,464],civ:9,ckio:[],cko:[],cl1:176,clarendon:[28,410],clarifi:[7,478,480],clariti:358,clark:451,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,345,370,416],classifi:[474,483],claus:493,clean:[6,12,14,16,503],cleanli:[494,526],clear:[],clearli:7,clebsch:151,clermont:[9,13],clever:499,click:[2,11,21,36,44,55,177,185,196,204,249,360,369,386,404,474,517],client:[249,251],climb:[268,386,509],clinic:[7,13],clo:[166,200,523],clock:[12,490,509],clockwis:[183,351],clone:517,close:[3,6,11,12,13,39,41,70,75,152,180,201,225,226,227,246,253,255,269,285,292,315,319,351,354,374,376,379,382,383,386,391,393,397,407,408,427,441,446,448,449,456,460,462,476,480,499,505,516,517,519],closer:[3,10,41,127,175,200,201,223,227,231,342,386],closest:[225,296,315,348,420,458,473,484],cloud:[464,516],clovertown:17,clsuter:76,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:495,cmatrix:246,cmax:441,cmd:[11,12,298,506],cmdarg:11,cmin:441,cmm:[],cmoput:144,cn1:218,cn2:218,cna:[],cnn:218,cnr:13,cnrs:9,cnt:[424,499],co2:[40,176,316,319,385,418],coars:[7,9,10,28,35,40,54,189,240,300,315,316,333,418,422,449,459,477,504,507],coarser:[376,522],coarsest:151,code:[],coeff:[3,7,8,12,20,21,32,44,50,183,184,185,190,359,360,366,404,424,428,446,461,463,466,495,524],coeffcient:495,coeffici:[],coefficienct:411,coefficient0:414,coefficient1:414,coeffieci:[6,395,427],coeffincientn:414,coexist:[244,416],cohes:[6,417,441],coincid:[133,354,402,438,439,490],colberg:203,cold:[6,162,244,248,387,516],coldest:341,coleman8:9,coleman:[9,129,176,317],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,157,165,172,174,177,201,202,205,217,228,258,265,300,310,313,315,356,375,385,387,405,495,502,508,514,527],collid:[234,333,355],colliex:176,collinear:[3,300],collis:[3,255,333,351,355,413,421,487],colllis:333,colloid:[],colombo:39,colon:[206,356,496],color1:205,color2:205,color:[3,9,41,201,204,205,223,245,305,310],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,130,151,152,157,165,172,174,175,176,197,201,202,205,208,216,217,218,220,221,258,266,267,305,315,334,335,345,355,393,419,423,456,457,496,510,512,522],columnar:175,colvar:[],colvarmodul:12,com:[],comamnd:229,comand:226,comannd:391,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:408,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,155,156,170,201,204,214,220,236,244,249,258,261,269,285,291,298,304,320,337,346,354,357,359,375,376,378,383,391,405,407,408,412,416,417,418,424,436,437,465,475,478,480,481,483,486,498,503,508,516,522,524],come:[],comfort:[12,13],comid:330,comit:517,comm:[0,3,11,12,63,77,203,249,251,252,376,386,391,411,446,453,476,477,497],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,183,197,201,239,240,253,315,316,345,385,386,392,414,415,417,418,428,441,448,449,450,457,464,465,475,476,477,478,479,480,483,492,493,495,516,517,522],commerci:7,commit:[9,517],commmand:[3,6,12,61,118,293,427,489,490,492,509,526],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,179,201,204,206,370,422,431,465,478,480,495,498,507],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,175,180,181,204,205,223,224,225,227,228,229,249,251,255,257,258,259,269,297,304,306,307,308,315,320,333,345,356,373,375,387,388,389,391,412,413,452,488,492,493,504,505,522,525,527],communc:375,comp:[7,203,251,252,285,291,319,376,386,416,446,453,458,472,476,477,479],compact:[65,208,404,474],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,129,160,176,185,196,205,233,306,356,358,375,376,384,386,441,464,490,509,510,516,521],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:380,compass:[7,9,20,21,36,43,44,55,184,185,196,359,360,369,403,474],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,130,188,201,206,210,216,217,218,220,221,223,236,297,309,337,340,347,350,353,375,391,425,444,446,476,492,493,522],compens:[6,224,225,313,387,416],compet:344,competit:376,compil:[3,7,8,9,12,13,14,15,16,17,18,175,201,203,204,206,249,344,376,391,444,495,496,500,516,522],compl:16,complain:[11,12,16],complement:441,complementari:[7,407,429],complet:[3,6,9,11,12,14,41,61,75,205,223,228,258,298,301,304,333,344,346,357,358,374,386,391,417,461,463,482,490,495,500,503,507,509,512,516,522],complex:[4,6,8,11,12,13,24,40,42,64,100,117,151,153,165,177,178,255,285,328,354,373,386,416,444,476,477,493,495,498,522],compli:[340,344],complic:[6,7,9,12,13,215,244,493],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,138,141,142,143,144,147,148,149,151,152,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,172,173,174,200,201,202,204,205,211,212,216,217,218,219,220,221,222,226,227,229,230,235,236,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,318,319,321,325,326,329,333,336,337,338,340,347,348,353,354,355,375,378,383,384,385,386,391,411,416,421,438,439,461,463,464,465,495,496,505,513,522,523],componenet:6,composit:[6,215,255,414],compound:[406,416,417,483],compres:[75,125,217],compress:[],compris:[40,354,418,458,482],compton:[129,176],comptu:3,compuat:376,comput:[],computation:[3,6,224,225,345,397],computational:516,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[129,317],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:176,concaten:[2,3,526],concav:354,concentr:[75,240,316,414,418,449,477],concept:[6,157,167,217,504],conceptu:[3,6,75,165,227,229,386,407,424,441,500],concern:[6,77,95,203,245],concetr:75,concis:[11,344],conclud:12,concret:8,concurr:[15,376,522],conden:[345,478,480],condens:[6,159,345,393,409,414,429,483],condit:[],conducit:6,conduct:[],cone:498,confer:444,confid:[3,509],config:[12,201,492],configfil:228,configur:[1,2,6,12,14,16,37,61,133,179,197,200,201,204,208,227,228,229,230,234,244,251,252,283,298,306,344,373,384,386,393,397,415,441,444,475,478,480,483,490,495,497,498,509,517],confin:[495,509],conflict:[3,12,40,202,446,493,517],conform:[3,6,13,61,226,227,268,314,321,344,368,386,416,507],confus:[3,483],conjuct:[9,411],conjug:[7,8,252,383,416,456,457],conjunct:[6,7,75,94,95,125,160,165,171,177,181,205,209,210,252,255,259,283,301,302,306,307,308,310,315,320,333,341,348,353,375,376,386,398,400,404,407,411,416,423,429,446,451,459,481,495,498,502,516,527],connect:[3,6,9,95,162,180,226,249,300,315,319,329,380,386,408,421,456,457,473,480,492,493,495,499,516],conner:393,connor:393,conput:3,consecut:[3,11,12,39,75,177,205,209,210,230,249,250,407,429,433,490,496,498],consequ:[1,6,215,345,428,509],conserv:[3,9,28,208,215,226,233,234,245,248,252,254,255,259,265,267,269,283,285,315,319,320,336,337,341,348,349,353,386,410,411,412,421,435,464,504,509],consid:[6,74,75,82,95,126,159,162,163,180,201,202,205,209,210,216,218,223,225,226,230,256,270,297,315,340,341,344,345,348,376,404,416,424,457,458,464,473,490,491,493,496,497,498,500,503,505,513,516,522],consider:[6,8,252,253,336,337,338,391,504],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,157,160,162,177,189,200,206,211,212,217,229,230,233,235,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,313,314,315,316,336,337,338,339,349,375,376,378,380,385,386,391,393,397,399,405,407,416,420,424,427,438,439,441,444,446,448,449,458,461,463,464,476,477,484,493,495,496,497,498,499,500,507,516,522],consistent_fe_initi:214,consit:315,constant:[],constantli:236,constitu:[3,6,258,315,350,354,405,458],constitut:[461,463],constrain:[3,6,8,9,154,155,156,157,158,160,163,164,165,166,167,169,170,208,217,230,236,244,245,250,258,261,263,285,291,300,301,313,315,319,331,341,348,384,385,416,500,507,516],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,129,151,176,227,269,297,314,316,354,387,391,410,444,446,473,475,476,477,498,499,514,522],constructor:[8,11],consult:457,consum:[1,310,452,522],consumpt:373,contact:[],contact_stiff:[460,462],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,129,151,153,157,165,175,176,177,179,183,185,196,197,201,202,204,205,206,208,209,210,214,216,217,218,220,221,223,228,230,235,239,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,317,322,333,340,344,345,354,355,358,374,376,385,386,389,390,392,393,394,397,406,407,410,414,415,416,418,424,425,441,444,448,449,450,454,455,456,457,465,475,476,477,478,479,480,481,483,490,491,492,493,495,496,497,498,500,502,504,507,509,510,512,513,516,517,522,525,527],content:[4,8,9,12,17,457,511,513],context:[3,6,8,12,16,127,128,205,224,225,230,300,312,349,383,486,495,502,511,521,522,523],contibut:74,contigu:492,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,173,205,208,209,210,215,217,218,219,220,221,223,226,227,228,229,230,236,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,317,321,332,333,335,342,343,345,351,354,358,374,390,391,397,411,413,431,434,456,457,458,461,463,479,490,493,495,497,498,503,509,510,512,513,522,525],continuum:[6,7,9,214,345,461,463],contour_integr:214,contract:[61,227,229,269,302,315],contradictori:3,contrain:319,contraint:283,contrari:[246,253],contrast:[1,6,42,55,66,159,162,202,229,356,461,463,486,526],contrib:345,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,210,215,216,217,218,220,221,227,244,252,255,258,259,264,270,292,293,300,301,309,312,315,317,319,347,375,384,386,394,411,413,414,416,424,438,439,444,446,456,457,464,507,513,516,517],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,133,151,186,201,202,204,208,214,215,223,227,228,229,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,316,323,324,336,337,338,345,349,373,375,388,416,420,444,456,457,460,462,475,480,490,492,504,510,511],control_typ:214,controlfil:457,convect:99,conveni:[6,12,28,201,206,221,317,378,465,481,517,522],convent:[3,8,28,188,195,196,202,205,314,329,357,414,416,522],converg:[3,6,41,96,201,202,204,206,211,223,226,227,235,242,274,285,291,305,307,310,314,319,382,383,384,386,406,407,429,464,490,502,509],convers:[3,8,151,204,205,215,218,302,375,407,408,409,416,429,433,437,451,493,509,521],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,177,184,201,204,205,218,221,267,301,304,356,359,361,365,368,378,386,392,414,444,478,480,487,493,495,496,497,502,512,516,521,522,525,527],convex:[42,354],convinc:[7,12],cook:9,cooki:7,cool:[7,167,236,248,313],cooordin:[201,202],cooper:[5,7],coord123:125,coord1:[3,125,217],coord2:[3,125,217],coord3:[3,125,217],coord:[],coordb:464,coordbb:464,coordiat:384,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,145,151,160,166,172,174,175,177,181,200,201,202,203,204,205,206,208,211,216,217,220,223,224,225,226,227,228,229,230,233,235,236,237,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,318,319,321,326,329,330,331,332,333,335,343,344,345,352,353,355,356,378,384,385,386,391,392,393,396,415,464,490,495,496,497,498,500,503,505,509,516,522,523],coordn:[125,217],coords:464,copi:[0,3,4,8,9,11,12,14,16,40,130,204,345,386,404,456,493,517],copper:487,coproccesor:15,coprocessor:[1,7,9,15,16,391,508],coproprocessor:16,copy_arrai:8,copyright:[7,8,300],coral:205,core:[],core_shel:159,cores:516,coreshel:[4,6,9],coreshell:[],cornel:[6,183,507],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,204,354,355,378,482,495,517],cornflowerblu:205,cornsilk:205,corp:9,corpor:15,corr:406,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,159,164,171,183,202,204,229,236,244,246,252,269,270,292,300,302,305,344,350,354,375,386,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,487,488,495,510,513,516,517],correction_max_iter:214,correctli:[3,8,11,16,75,87,112,113,114,154,155,156,158,160,162,163,164,165,166,169,170,173,201,205,211,230,235,242,253,263,269,270,308,315,319,329,332,351,354,386,387,391,409,439,444,492,493,495,505,517,521,523],correl:[],correpond:[239,240],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,138,141,142,143,144,145,147,148,149,151,154,155,164,171,175,176,183,184,185,186,187,188,189,191,192,194,195,197,200,201,202,204,205,209,210,211,217,219,220,222,225,227,229,236,237,240,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,316,318,319,340,350,351,353,354,355,357,359,360,361,362,364,365,368,370,376,381,383,385,386,392,393,395,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,417,418,419,420,421,422,423,424,427,429,430,431,432,433,434,435,436,437,438,441,442,444,446,447,449,450,451,453,454,456,457,458,459,464,465,466,475,476,477,478,479,480,481,483,485,486,487,490,492,493,495,496,498,508,509,510,512,513,516,522],correspondingli:[438,439,504],corrupt:3,cosin:[],cosineshift:26,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,129,152,176,204,205,217,223,224,225,241,269,307,345,375,376,389,407,429,433,444,446,475,492,504],costheta0:[475,478,480,483],costheta:454,costli:[11,96,246,387],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,157,167,172,174,190,201,202,204,205,209,210,217,218,223,229,242,251,304,305,306,310,313,315,318,333,334,340,344,345,346,350,354,356,358,366,372,374,382,384,387,391,393,394,419,423,424,427,456,457,491,492,493,495,497,499,502,503,510,511,516,522,523],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,152,178,182,306,308,346,375,376,384,391,398,400,401,402,403,406,407,408,409,410,416,421,422,424,429,433,437,440,446,451,456,457,459,464,474,480,481,483,486,500,507,513,516,521],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,165,175,181,183,211,212,215,217,220,222,223,230,235,241,244,250,269,283,301,319,336,337,354,376,384,385,386,388,391,419,423,446,513,522],counter:[3,351,490,501,503,509],counteract:244,counterbal:[236,248],counterbalanc:28,counterclockwis:183,counterpart:[201,315,490],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:322,cours:[3,8,137,139,171,201,209,210,245,314,329,344,350,352,353,355,356,376,438,466,492,495,508,516,522,525],courtesi:378,cov:464,coval:[6,9,28,416,441,464,516],covari:246,cover:[6,12,75,197,205,214,255,416,482],coverag:75,cpc:251,cpp:[1,3,6,8,9,11,12,13,95,201,209,210,242,319],cpu:[1,3,9,10,12,14,15,16,17,65,75,205,219,233,253,346,373,376,391,404,474,490,508,509,512,513,514,522],cpuremain:513,cpus:12,cr2:176,cr3:176,crack:[4,387],crada:[5,7],crai:[5,7,13,17,201],crash:[3,12,387,516],craympi:391,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:214,create_faceset:214,create_group:203,create_nodeset:214,createatom:[],creation:[],crimson:205,critchlei:300,criteria:[3,127,178,204,205,224,225,226,264,384,453,482,497,500,522],criterion:[12,41,132,177,180,215,223,226,244,283,307,322,351,356,384,386,406,416,421,464,500,509,510],criterioni:509,critic:[6,48,49,267,340,345,384],crmax:75,crmin:75,cross:[3,12,21,75,97,155,175,185,201,202,204,216,225,229,266,268,292,315,325,329,332,341,348,360,378,386,402,411,413,414,422,423,424,429,431,433,454,459,461,463,478,480,487,495,499,505,525],crossov:1,crossterm:495,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,77,117,296,297,343,378,387,495,499,513,516],crystallin:[6,113,297,378,479,516],crystallis:340,crystallogr:[129,176],crystallograph:[378,513],crystallographi:[129,176,378],cs1:176,cs_chunk:6,cs_im:[40,495],cs_re:[40,495],csanyi:[151,455,465],cscl:441,csequ:6,csh:[11,12,404],cshrc:[11,12],csic:[415,475,478,480,483],csinfo:6,csisi:[415,475,478,480,483],csld:[],cst:414,cstherm:6,cstyle:492,csvr:[],ctcm:[392,414],ctemp_core:233,cterm:321,ctr:9,ctype:11,cu1:176,cu2:176,cu3au:441,cube:[6,175,180,233,354,378,516],cubes:[41,223],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:397,cummul:[3,6,221,224,225,226,228,241,246,252,254,333,336,337,338,339,341,348,423,513],cumul:[6,215,217,220,234,244,252,267,269,274,283,315,317,386],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,141,152,157,165,167,173,175,178,181,200,201,202,203,204,205,206,209,210,214,217,221,223,224,225,226,227,228,229,230,234,235,236,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,316,319,320,321,322,323,324,325,326,328,330,331,332,333,336,337,338,344,345,348,349,350,351,352,353,355,356,358,373,374,375,376,379,380,381,383,384,385,386,391,397,404,406,410,414,416,417,421,424,425,428,438,439,441,442,443,446,454,456,457,460,461,462,463,466,478,480,481,484,490,491,492,493,495,496,497,498,499,501,502,503,505,507,509,510,512,513,517,522,523,524,525,526,527],curv:[6,177,244,285,291,297],curvatur:[420,458,487],custom:[],cut0:493,cut1:504,cut2:504,cut:[],cuthi:[296,308],cutinn:[399,438,439],cutlo:[296,308],cutmax:454,cutoff1:[403,410,429,433,437,440,451,459],cutoff2:[398,400,401,403,409,410,429,433,437,440,451,459,481],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,151,175,178,180,181,225,226,231,239,240,296,305,306,308,310,312,315,320,333,346,350,354,356,373,375,376,384,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,458,459,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,493,497,500,504,516,522],cutoffa:415,cutoffc:415,cuu3:414,cval:176,cvd:340,cvel:321,cvff:[],cwiggl:[3,266,350,353,355,522],cyan:[2,204,205],cycl:[3,244,267,269,270,274],cyclic:[3,183,197],cygwin:12,cylind:[3,4,75,204,217,250,291,301,351,354,380,498],cylinder_d:380,cylindr:[6,250,329,351],cypress:391,cyrot:397,cyrstal:297,d3q15:255,d3q19:255,d_double_double:14,d_e:345,d_flag2:304,d_flag:304,d_name:[124,201,304,335,505],d_single_double:14,d_single_single:14,d_sx:304,d_sy:304,d_sz:304,daan:343,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,208,213,252,253,254,259,269,270,274,291,302,305,306,310,315,336,337,349,351,352,383,384,386,398,400,402,407,410,416,421,429,437,451,459,474,481,509,516],damp_com:253,damp_drud:253,dampen:[315,516],dampflag:[351,421],dan:16,danger:[3,12,244,356,411,513],dangl:180,daniel:9,darden:[376,410],darkblu:205,darkcyan:205,darken:204,darkgoldenrod:205,darkgrai:205,darkgreen:205,darkkhaki:205,darkmagenta:205,darkolivegreen:205,darkorang:205,darkorchid:205,darkr:205,darksalmon:205,darkseagreen:205,darkslateblu:205,darkslategrai:205,darkturquois:205,darkviolet:205,dasgupta:306,dash:[421,512],dat:[6,99,197,214,491],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,317],dataset:317,datatyp:3,date:[0,4,6,12,13,200,456,457,522],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,201,218],davenport:440,davi:350,david:[9,18,375,376,478,480],daw:[414,454],dbg:[],dcd:[3,6,7,201,203,204,205,206,298,496,500],dcs:9,ddim:200,deactiv:437,dealt:251,debug:[6,7,11,12,13,16,57,129,133,176,177,298,303,373,375,425,446,484,493,494,502,505,512,522],deby:[],decai:[100,407,487],decid:[3,6,12,15,75,266,304,315,346,510,517],decipher:378,deck:304,declar:203,declin:333,decod:204,decompos:[95,465],decomposit:[3,5,7,17,64,214,298,320],decoupl:[6,516],decreas:[3,201,202,211,212,219,226,229,235,236,242,244,252,344,375],decrement:321,deepli:372,deeppink:205,deepskyblu:205,def:[12,13,493],defaul:63,defect:[6,74,175,444],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,183,184,185,186,187,188,189,191,192,194,195,196,197,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,233,234,235,238,240,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,319,322,326,330,331,333,335,336,337,338,339,341,342,343,345,347,348,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,368,369,370,371,373,375,376,378,381,383,384,385,386,387,388,389,390,391,393,394,395,396,398,399,400,401,402,403,404,405,407,408,410,411,412,413,415,416,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,444,445,446,447,448,449,450,451,453,454,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,492,493,495,496,498,499,500,501,504,505,506,507,509,510,512,513,516,518,519,520,521,522,523,524],definit:[2,3,6,8,12,13,82,85,127,151,205,217,218,219,220,221,229,238,250,274,317,335,347,350,353,355,357,369,373,385,394,397,405,412,416,427,454,461,463,465,482,493,495,497,504,506,521,522],defint:513,deform:[],deg2theta:176,deg:516,degener:[3,300],degrad:[8,17,297,376,504],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,176,177,183,184,187,188,195,197,200,204,217,226,233,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,319,336,337,338,343,359,361,365,368,370,384,410,414,423,505,513,516,523],degrees:197,degress:[157,217],del:509,delai:[3,6,12,387,413,513],deleg:424,delet:[2,3,7,8,12,54,59,62,65,175,180,181,208,217,218,220,221,224,226,241,244,269,317,336,337,356,358,374,385,387,390,446,473,495,496,497,498,506,507,512,517,518,520,522,523],delete_atom:[],delete_bond:[],delete_el:214,deli:200,delimit:[316,493,522],dellago:[6,236],deloc:[270,416,464],delr:441,delt_lo:509,delta:[],delta_1:397,delta_3:397,delta_7:397,delta_conf:3,delta_ij:[441,454],delta_pi:397,delta_r:454,delta_sigma:397,deltah_f:240,delx:200,delz:200,demand:310,demo:11,demon:295,demonstr:[305,441],den:301,dendrim:423,dendtrit:380,denniston:[9,255,257,258,259,297],denomin:[7,182],denot:[129,233,236,253,297,308,310,407,422,424,457,461,463],dens:[75,226,416],densiti:[3,6,7,9,17,40,41,61,110,127,137,151,163,175,177,209,210,214,217,223,229,242,255,258,262,263,297,301,302,304,306,345,350,378,381,385,392,393,397,414,441,442,443,448,449,454,458,464,468,470,471,472,495,504,505,513,521],density_continuity:463,density_summation:463,dent:380,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,130,151,153,154,160,164,165,171,177,178,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,204,205,208,209,210,211,212,215,217,219,220,221,222,223,225,227,229,235,237,240,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,316,318,319,320,326,333,336,337,338,340,342,344,345,347,350,353,354,355,356,358,359,360,361,362,364,365,368,370,376,378,384,385,387,388,389,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,441,442,444,445,447,448,449,450,451,453,454,456,457,458,459,464,465,466,474,475,476,478,479,480,481,483,485,486,487,490,492,495,497,498,501,505,507,509,512,513,515,522,523],dependend:6,depflags:12,dephas:[490,509],depos:230,deposit:[],deprec:[3,306,456],deprect:217,depth:[51,155,204,345,418,420,458],dequidt:9,der:[95,118,405,406,437,456,457,486],deriv:[6,7,8,9,37,56,65,95,151,171,197,218,227,229,236,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,342,343,345,350,351,354,383,385,393,397,405,410,416,417,422,431,435,436,441,444,456,457,474,476,477,486,516],derjagin:486,derlet:296,descend:205,descent:[7,383],descib:[40,204,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,129,141,151,152,155,156,157,161,162,165,168,170,171,175,176,177,179,180,189,194,197,201,202,203,208,209,210,217,218,219,220,221,223,226,227,228,229,230,232,233,239,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,316,321,329,333,334,335,336,337,338,339,340,341,342,343,348,350,351,353,358,375,376,378,382,383,384,385,386,390,393,394,396,398,399,400,402,403,404,405,406,407,410,414,416,417,418,420,421,422,424,427,429,430,431,432,433,434,435,436,437,438,439,440,441,444,445,448,449,453,454,455,456,457,458,459,464,465,466,473,474,475,476,477,478,479,480,481,483,485,486,487,488,490,492,493,495,496,497,498,499,505,508,509,512,517,522,523,525],descript:[],descriptor:[151,201,425],deserno:376,design:[0,3,6,7,8,11,13,14,16,129,159,162,176,214,226,232,233,269,270,296,297,317,340,345,394,395,396,399,402,407,409,416,437,438,439,442,443,454,457,476],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,152,159,177,190,200,217,221,227,229,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,319,333,336,337,338,339,344,351,366,372,375,376,378,382,384,385,386,411,414,423,438,439,475,478,480,491,492,493,495,499,504,509,510,512,513,522,523,525],desk:7,desktop:[4,6,7,10,12,204],despit:516,destabil:397,destre:368,destroi:[9,11,39,224,225],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,130,151,152,154,155,156,157,160,170,171,172,174,177,178,181,182,185,196,200,201,202,204,205,208,209,210,214,217,218,219,220,221,223,225,226,227,228,229,230,236,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,319,320,333,336,337,338,339,340,341,343,344,345,346,347,348,349,356,358,360,369,375,376,379,384,385,387,388,391,392,393,394,396,397,399,401,402,403,404,405,406,407,410,411,416,417,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,445,446,448,449,453,456,457,458,464,465,466,474,482,485,486,488,493,495,496,497,498,500,501,504,505,507,510,513,514,517,522,523,527],detect:[2,3,12,42,63,65,94,100,243,301,344,386,406,423,428,490,492,495,506,509,522],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,138,152,165,166,175,176,177,200,201,202,204,205,206,207,211,212,213,216,217,218,219,220,221,222,223,227,229,230,233,235,240,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,318,322,324,326,333,336,337,338,340,346,347,350,351,352,353,354,355,356,369,375,376,378,385,387,388,391,393,394,401,406,410,413,414,418,419,421,424,425,433,441,444,446,449,457,458,464,473,476,477,481,486,492,495,496,498,500,502,505,509,511,512,514,521,522,523],determinist:320,detil:119,devan:[9,459],devanathan:480,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,249,274,300,305,306,309,393,397,416,443,444,464,483,497],devemi:9,deviat:[267,274,296,419],deviator:9,devic:[1,3,12,14,16,249,391],device_typ:391,devin:[307,406],devis:443,dfactor:204,dff:516,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,376],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,444],dhi:[61,200,229,301],dhug:[267,305],dhugoniot:[267,305],dia:441,diagnost:[],diagon:[3,6,91,151,152,153,227,269,302,315,348,461,463],diagonalstyl:465,diagram:[41,129,176,196,223,298],diallo:423,diam:[204,205,301,385],diamet:[3,6,40,42,124,177,201,202,204,205,209,210,252,301,304,315,333,335,349,351,385,405,420,421,431,458,482,486,495,496,505],diamond:[378,416,441],diamter:[40,301],dick:6,dicsuss:266,dictat:[215,267],did:[3,12,384,411,413,414,421,446,478,480,503],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,173,347,375],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,131,151,153,154,155,156,157,158,160,163,164,165,166,167,169,170,171,177,178,180,185,196,197,200,201,204,205,208,210,213,215,217,220,223,224,225,226,227,228,229,233,236,239,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,319,321,329,331,333,336,337,338,341,342,343,345,348,349,350,351,354,358,359,369,372,374,375,376,378,379,382,383,385,386,388,389,390,391,392,393,397,401,402,404,405,406,411,412,414,416,418,420,421,422,424,427,429,430,432,433,440,441,442,443,445,446,447,448,449,450,454,456,457,458,459,460,461,463,464,465,466,474,475,476,477,478,480,482,483,486,489,490,492,493,495,497,498,499,500,503,504,505,507,509,510,512,513,514,516,521,522,523,525],differenti:[1,3,6,28,197,316,375,407,454,479],difficult:[227,298,391,423,504],difficulti:[100,117,319,456],diffract:[7,9,129,176,317],diffus:[],diffuse:[4,6],digit:[2,3,205,358,444,522],dih_table1:197,dih_table2:197,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,198],dihedraltyp:225,dihydrid:416,dij:319,dilat:[],dim1:3,dim2:3,dim:[3,61,75,154,158,159,160,163,164,165,166,167,169,177,200,229,250,351,378,441,498,521,522,523],dimdim:522,dimems:297,dimens:[],dimensinon:75,dimension:[3,39,100,123,129,151,154,157,158,159,160,163,164,165,166,167,169,176,199,217,268,297,345,378,382,386,454,495,505],dimensionless:[115,132,133,135,138,140,142,147,151,345,376,465,486],dimensions:317,diment:3,dimentionless:146,dimer:[6,315,441],dimgrai:205,dimstr:[41,223],dinola:[302,336],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,201,202,335,516],dir1:506,dir2:506,dir:[1,3,4,8,10,11,12,267,296,305,332,454,456,457,493,506,522],dirac:151,direc:454,direct:[],directli:[3,6,8,9,11,12,95,124,151,153,201,202,203,204,211,235,246,250,255,297,316,317,337,349,351,352,353,354,378,383,391,392,393,398,400,401,407,410,414,416,429,433,446,451,459,473,493,505,506,507,513,522],directoi:[],directori:[],disabl:[3,12,15,345,428,493,508,522],disadvantag:[6,223],disallow:[201,229,269],disappear:497,discard:[2,3,41,75,219,223,346,354,492,497,498],discontinu:[197,384,435],discourag:441,discov:[13,346],discret:[6,8,40,42,204,205,252,255,291],discuss:[],disk:[6,92,93,100,170,199,230,244,301,493],disloc:[74,444],disord:[39,74,444],disp:[],dispar:458,disperion:[410,433],dispers:[3,6,7,9,175,297,375,376,401,410,433,438,446,457,476,483],displac:[],displace_atom:[],displace_box:61,displacemet:498,displai:[11,13,21,36,44,55,185,196,201,204,360,369,404,474],dispters:3,disregard:444,dissip:[6,9,40,88,89,238,245,252,297,320,342,343,399,411,412,421,438,439,474],dissolut:224,dist:[6,73,99,119,128,201,298,314,413,473,490,523],distanc:[],distinct:[6,233,312,375,458],distinguish:[6,94,151,258,416,494,522],distort:[175,392],distrbut:392,distribut:[],distro:[122,404,453,454],ditto:[8,12,14,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375,384,385,386,387,389,414,415,424,437,439,444,452,456,457,475,478,480,483,490,493,495,496,497,502,504,505,509,510,511,512,513,514,516,521,522,525,527],ethernet:17,etol:[384,386,490,509],etot0:305,etot:[6,104,106,107,121,152,163,205,233,253,267,305,512,513],eu2:176,eu3:176,euler:[384,386],eulerian:214,euqat:467,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,130,151,153,157,167,175,177,183,200,201,202,204,205,209,210,211,212,214,216,217,218,219,220,221,222,229,235,245,247,248,250,251,252,253,297,303,306,318,322,326,336,337,338,347,350,353,355,356,358,382,384,444,446,448,449,454,460,462,464,476,477,490,491,493,497,498,500,502,503,504,505,509,511,513,522,523],evaluat:[375,376,522],evalut:[358,493],evan:[165,292],evanseck:[6,19,183,402,507],evapor:[],evaul:[8,384],evdwl:[118,153,456,457,513],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,130,175,178,179,193,197,201,202,205,208,209,210,215,216,217,220,221,223,224,225,227,229,230,233,236,250,253,267,269,270,297,301,310,312,315,317,328,333,341,345,348,350,354,356,367,375,382,384,386,391,396,416,417,421,424,427,446,458,483,484,488,495,496,498,500,501,502,504,505,507,510,512,513,514,516,527],evenli:[3,41,57,152,197,223,255,427,484],event:[],eventu:[3,6,12,14,179,509],eventual:306,ever:[9,54,56,251,333],everaer:[405,420,458,474],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,130,139,165,180,201,202,203,204,205,206,208,209,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,234,236,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,317,319,321,330,333,335,336,337,338,339,340,341,344,345,346,347,348,356,358,374,376,386,387,388,391,411,413,424,437,456,457,464,470,489,490,491,495,497,499,500,502,503,504,509,510,511,513,517,522,527],everyth:[8,118,517],everywher:[127,431],eviri:416,evolut:[236,246,255,298,490],evolv:[255,298,346],ewald:[2,3,5,6,7,8,9,12,96,121,129,152,346,375,376,384,398,400,401,407,410,416,429,433,451,459,474,476,481],ewald_disp:410,ewalddisp:3,exact:[21,41,44,75,133,171,180,185,223,226,245,246,252,253,254,301,310,311,333,345,360,375,404,497,502,509,522,525,527],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,155,161,168,177,197,209,210,220,223,229,234,239,245,252,253,254,270,282,283,293,297,304,305,333,338,339,352,391,404,411,414,421,424,438,446,448,449,476,477,497,498,505,509,522],exager:516,examin:[6,8,16,226,297],examp:[493,522],exampl:[],exce:[3,6,15,16,17,41,60,75,179,216,217,220,221,223,227,229,234,241,269,297,312,317,323,324,333,384,391,495,522],exceed:[3,41,61,223,229,269,333,503],excel:416,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,177,181,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,205,208,211,217,218,220,222,223,227,229,237,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,318,319,329,333,339,345,353,356,357,358,359,360,361,362,364,365,368,369,370,375,376,378,381,385,386,387,389,390,391,392,393,395,398,399,400,401,402,403,404,405,406,407,409,410,411,414,415,416,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,442,447,450,451,453,456,457,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,492,493,495,497,498,500,503,504,505,506,507,509,513,516,521,522,523,526],exception:493,excess:[219,416],exchang:[2,3,6,8,63,64,208,214,215,236,244,248,252,307,315,341,345,348,375,391,416,510],exchange:375,excit:416,excite:416,exclud:[3,6,9,12,15,16,65,75,112,123,151,157,164,165,181,201,217,224,225,256,265,300,313,315,340,351,356,384,385,387,399,421,424,427,438,439,446,473,507],exclude:387,exclus:[1,3,12,15,95,183,406,444,446,504,514],excurs:[269,490],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,178,204,249,309,358,374,377,390,491,493,503,506,509,522],exempl:464,exemplari:245,exemplifi:416,exert:[6,250,253,285,310,352,353,354,376],exhaust:[214,390,522],exhibit:[100,236,248,269,383,416,504],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,133,177,178,196,203,204,205,208,213,222,225,227,230,244,300,301,303,304,356,357,359,361,362,363,365,369,379,385,412,424,456,473,484,491,493,495,496,497,506,507,508,517,522,523,525],exit:[2,3,11,12,41,59,201,223,374,390,493,494,503,512,522],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,151,201,506,522],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,158,169,175,197,223,235,244,246,266,296,302,304,305,310,315,356,376,387,404,441,444,446,490,493,495,497,500,504,509,522],expens:[6,75,205,296,300,315,345,356,375,376,387,391,493],experi:[6,13,14,222,230,249,258,268,302,314,315,382,386,411,446,504,509],experienc:[6,12,257,258],experiment:[16,244,375,391,509],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,157,165,197,201,202,204,205,208,217,218,221,223,225,227,229,269,285,296,304,315,329,356,358,374,375,378,385,386,390,396,414,427,464,466,482,493,496,497,500,502,505,516,517,522,527],explan:[3,6,61,124,151,201,202,217,268,296,424,489,492,493,495,504],explanatori:[3,8,128,201,202,216,217,220,315,385,492,522],explantori:[3,311],explic:445,explicit:[6,9,11,21,44,81,95,124,127,171,185,209,210,229,316,323,324,360,381,393,394,397,402,404,414,416,428,438,481,489,492,496,499,517],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,154,164,167,175,177,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,229,237,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,318,319,338,339,345,353,359,361,362,364,365,368,370,385,391,392,393,395,398,399,400,401,402,403,404,405,406,407,408,410,411,413,414,415,417,418,419,420,421,422,423,424,428,429,430,431,432,433,434,435,436,437,438,442,444,446,447,448,449,450,451,453,458,459,466,467,468,469,470,471,472,474,475,476,477,478,479,480,481,483,485,486,487,495,497,498,504,505,507,508,514,516,517],explictli:[15,508],exploit:[14,16,298],explor:[129,176],expon:[3,306,308,316,414,418,420,423,437,445,459],exponenti:[95,418,454,475,483,487,509,522],expos:11,exposit:[214,411,413],express:[6,151,163,177,209,210,227,266,296,306,316,345,351,358,397,414,416,431,441,464,465,474,522],expression:358,expressiont:397,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,130,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,202,208,211,212,215,221,222,228,231,235,236,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,318,321,326,329,330,332,336,337,338,339,340,342,343,345,347,350,354,355,420,441,444,457,458,465,512,513,521],extensiv:[65,208,513],extent:[1,3,41,42,45,59,75,175,179,201,213,223,250,352,355,375,378,393,460,462,476,477,492,495,498],exterior:[3,6,175,354],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,129,152,154,155,156,158,160,163,164,165,166,167,169,170,176,177,178,179,205,220,223,225,269,303,304,305,315,333,384,385,388,389,410,421,424,427,441,446,492,493,495,498,507,516,522],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,130,209,210,308,386,407,417,441,465,493,500,512],extract_atom:11,extract_comput:[11,493],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,204,219,227,229,269,343,416,479,516],extrema:437,extreme:416,extrins:214,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[173,347],f_a:[478,479,480],f_ave:128,f_c:479,f_f:480,f_fix_id:305,f_foo:522,f_harm:343,f_i:[28,454],f_id:[6,75,128,130,201,202,208,216,217,218,219,220,221,264,335,347,513,522],f_ij:454,f_indent:221,f_int:342,f_j:28,f_jj:99,f_k:454,f_langevin:345,f_max:[305,310],f_msst:267,f_r:[253,478,479,480],f_sigma:397,f_solid:343,f_ss:6,face:[3,6,59,61,75,165,175,179,213,350,352,353,354,355,378,420,441,458,495,498],face_threshold:175,facet:175,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,246,301,333,343,421,456,464,507],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,129,151,171,176,179,183,194,200,201,204,205,209,210,218,223,227,229,230,236,244,249,252,254,255,267,269,270,274,298,302,306,314,316,319,322,324,333,337,341,348,349,350,354,365,376,378,385,391,393,394,397,398,400,402,407,408,409,411,412,416,421,424,428,429,441,444,446,448,449,450,451,457,459,466,475,481,492,495,498,499,504,507,509,510,513,516,521,522],factori:[3,493],factoriz:375,fail:[3,9,11,12,61,181,227,230,375,384,386,409,457,493],failur:[132,461,494,522],fairli:[11,446,504,509,517],faken:77,falcon:249,fall:[3,6,205,220,301,493,522],fals:[94,356,464,522],fame:8,famili:[483,492],familiar:[0,11,517],fan:454,far:[3,6,12,16,59,61,63,94,201,202,205,206,223,224,225,227,230,269,296,314,315,333,350,361,365,382,386,387,482,493,495,500,513],farago:252,farrel:[478,480],farther:201,fashion:[6,8,41,75,177,205,208,209,210,215,223,225,230,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,321,325,332,335,343,345,349,350,351,353,355,386,424,438,498,507,522,526],fasolino:426,fast:[6,7,9,12,13,16,39,201,202,280,305,346,375,376,399,438,439,444,474,476,477,497,502,504,513,523,527],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,154,164,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,223,229,237,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,318,319,333,340,342,345,349,353,359,361,362,364,365,368,370,375,376,388,389,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,498,504,508,516],fastest:[1,6,16,165,345,346,391,492],fatal:[3,512],fault:[74,457],faulti:12,fava:420,favor:226,favorit:7,fbmc:340,fcc:[],fcm:[286,522],fcold:236,fdirect:233,fdotr:425,fdt:[],fdti:95,fe2:176,fe3:176,fe_md_boundari:214,featu:8,featur:[],fecr:414,feedback:[7,249],feel:[7,249,250,258,296,354,356,386,446],felling:443,felt:354,femtosecond:521,fene:[],fennel:[407,429],fep:[],ferguson:[6,183,507],fermi:[1,9,10,12,14,163,391,480],fermion:416,fernando:440,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,206,216,217,218,220,221,236,253,269,301,304,306,319,347,375,384,385,386,393,464,492,495,500,504,506,514,525],fewer:[1,3,11,14,15,63,258,504],fewest:3,fextern:242,feynman:298,fff:493,ffield:[406,417,456,457,464],ffmpeg:[3,12,204],ffplai:204,fft:[1,3,7,9,11,12,14,96,120,121,152,297,375,376,504],fft_inc:[12,376],fft_lib:12,fft_path:12,fftbench:[375,514],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:236,ficiti:473,fictiti:[6,211,212,235,242,246,298,314,407,429,433,473],field1:[496,500],field2:496,field:[],fifth:[6,329,418,450],figur:[1,3,8,12,305,492,493,517],fij:410,file0:296,file1:[11,13,240,296,344,358,385,500,502,506],file2:[11,13,240,344,358,385,500,502,506],file:[],file_from:203,filen:385,filenam:[3,12,13,37,41,56,197,201,202,204,205,206,214,217,218,219,220,221,223,228,239,240,296,300,303,306,307,308,311,312,315,316,317,344,345,372,373,374,385,386,392,393,397,407,414,415,417,418,426,441,442,443,448,449,450,454,455,456,457,464,465,475,476,477,478,479,480,483,491,492,493,496,497,502,506,513,522,525,526,527],filennam:502,filep:[3,201,202,205,497,502,527],filepo:312,fill:[7,9,177,204,301,345,378,387,397,444,457,498,517],filter:[205,214],final_integr:8,final_integrate_respa:8,finchham:[6,159,409],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,180,197,206,215,226,227,239,240,241,244,268,296,301,302,310,314,382,384,386,387,407,424,429,433,441,448,449,464,474,476,477,516,517,522],find_custom:8,fine:[15,16,181,211,235,343,387,391,517,522],finer:[151,177,522],finest:375,finger:[177,200,266,498],finish:[6,11,41,223,358,372,374,375,388,390,391,482,500,522,523],finit:[],finni:[7,414,474],finverse:233,fiorin:[9,228],fire:[],firebrick:205,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,138,141,144,145,149,152,162,165,171,173,175,176,178,179,180,184,197,201,202,203,204,205,206,208,209,217,218,220,221,223,226,229,239,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,319,321,329,330,331,333,334,335,342,343,344,345,347,351,356,358,359,366,378,384,385,386,387,390,391,392,393,396,397,398,400,402,404,406,407,414,416,417,418,421,422,424,425,426,427,428,429,433,438,439,441,443,444,446,448,449,450,454,456,457,464,465,473,475,476,477,478,479,480,483,487,490,491,492,493,495,496,497,500,502,504,507,508,509,512,513,516,517,522,523,524,525,527],fischer:[6,9,18,19,183,402,507],fit:[3,6,9,12,37,56,197,239,314,333,393,397,426,441,446,448,449,469,476,477,479,503,517,522],five:[77,163,305,385,397,442,495,509],fix:[],fix_deposit:3,fix_ehex07:[],fix_flux:214,fix_heat:236,fix_id:[3,227,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:517,fix_modifi:[],fix_nh:8,fix_nv:517,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:319,fix_reax_bond:456,fix_saed_vtk:317,fix_setforc:8,fix_shak:319,fix_srd:3,fixedpoint:[227,269],fixextern:242,fixid:214,fji:410,flag1:[232,389],flag2:[232,389],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,172,176,180,198,201,202,204,205,206,221,226,228,232,249,252,256,258,265,266,297,304,315,329,332,333,340,344,353,356,371,373,376,385,389,390,391,393,423,428,441,444,473,488,490,492,493,495,496,497,499,500,501,505,517,522],flag_buck:401,flag_coul:[401,410,433],flag_lj:[410,433],flagfld:[399,438,439],flaghi:[3,399,438,439],flaglog:[399,438,439],flagn:232,flagvf:[399,438,439],flat:[6,345,350,351,355],flavor:[2,7,12],fld:[350,438,439],flen:394,flex_press:394,flexibl:[3,6,8,178,204,217,228,246,270,341,348,416,479,513],flip:[3,6,229,269,352,353],floor:522,flop:12,floralwhit:205,flow:[],fluctuat:[6,66,95,227,244,245,252,255,269,274,296,297,302,320,343,345,368,412],fluid:[],fluid_veloc:259,flush:[3,205,512],flux:[],flv:204,fly:[7,9,12,41,204,208,214,219,230,233,315,319,346,397,444,513,516],fmackai:9,fmag:231,fmass:298,fmax:[384,513],fmomentum:233,fmsec:[2,205,252,253,266,269,302,315,336,337,504,515,521,523],fname:374,fno:[9,15],fnorm:[384,513],fnpt:233,fnve:236,fnvt:233,foce:424,fock:394,focu:319,fogarti:[9,308,457],foil:[151,296,465],fold:[331,504],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,130,151,152,155,156,157,163,165,170,173,175,177,178,183,186,187,188,189,191,192,194,195,197,201,203,204,205,208,214,215,216,217,218,219,220,221,223,228,229,230,233,234,238,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,317,319,335,336,337,338,341,342,343,344,345,347,348,356,357,361,362,363,364,365,368,370,373,37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44,301],insid:[2,3,6,8,11,75,140,146,177,201,202,205,216,230,231,236,241,244,250,255,258,301,315,333,350,352,353,354,355,356,373,378,493,494,495,497,498,505,522],inside:[255,431,493,509],insight:[6,13],instabl:[255,410,463],instal:[1,3,6,8,9,11,12,14,15,16,175,201,203,204,206,376,386,401,402,425,429,433,437,444,490,496,497,502,510,517,527],install:[],instanc:[6,9,11,209,228,246,352,419,424,446,454,493,516],instantan:[6,65,226,227,245,246,269,274,297,302,305,310,312,315,340,501,513],instanti:[6,11,12,214,424,492],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,155,159,181,183,197,201,202,210,217,220,221,223,227,228,244,252,255,258,259,297,303,304,313,315,335,353,373,375,376,379,387,391,400,401,414,428,430,437,441,444,447,474,481,490,498,502,509,511,516,522],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,154,164,175,183,184,186,187,188,189,191,192,194,195,197,199,204,211,222,229,237,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,318,319,353,359,361,362,364,365,368,370,376,391,392,393,395,398,399,400,401,402,403,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,475,476,478,479,480,481,483,485,486,487,498,504,516],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,16,39,40,63,77,112,114,177,178,197,201,202,204,205,211,224,225,230,235,237,241,242,244,247,252,265,303,304,313,315,333,345,350,354,355,356,358,374,385,387,391,405,420,424,452,458,476,488,492,493,495,496,500,503,504,512,513,522,523],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,130,151,175,177,180,181,183,187,188,192,197,200,201,204,205,215,217,224,225,226,230,232,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,333,335,337,340,344,345,364,375,378,399,411,412,413,427,441,456,457,461,463,465,490,492,493,494,495,503,504,505,509,512,522,523],integer:[3,495],integr:[],integral:[298,448,449],integrate_ulsph:[],intel:[],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,219,245,455,495],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,129,130,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,172,173,174,176,208,217,218,220,221,223,224,225,226,234,241,248,258,267,269,274,312,315,317,333,341,345,347,348,512,513,521],intensiv:[65,208,513],intepol:522,inter:[17,42,63,64,157,180,181,201,226,252,254,268,307,315,375,386,397,505,516,522,525,527],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,133,134,135,136,138,139,140,141,142,143,144,146,147,148,149,151,152,153,155,156,170,171,175,178,179,180,181,182,183,185,189,190,193,196,201,202,208,209,210,224,225,226,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,316,323,324,333,334,340,345,349,350,351,354,355,360,361,362,363,365,367,369,375,376,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,451,452,453,454,457,458,459,461,463,464,465,466,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,490,493,495,497,499,500,504,505,507,512,513,516,525],interatom:[3,4,7,9,10,177,201,268,342,343,392,397,414,416,425,441,444,464,479,522],intercept:129,interchang:6,interconnect:17,interconvert:416,intereract:39,interesect:354,interest:[1,5,7,8,9,11,13,75,176,298,340,343,376,415,439,456,457,493,522],interf:[391,517],interfac:[],interfer:[12,269,393],interg:[6,516],intergr:504,interi:439,interior:[3,6,41,354,498],interlac:441,interleav:[6,177,503],intermedi:[6,12,61,204,268,296,368,386,493,494,503,507],intermix:490,intermolecular:[153,393],intern:[],internal:[3,204,210,301,522],internal_element_set:214,internal_quadratur:214,internat:[129,176,214],internet:251,interpenetr:441,interpentr:[468,469,471],interpol:[6,14,37,56,110,197,204,205,214,239,240,255,296,375,376,386,397,446,448,449,457,470,476,477,478],interpret:[2,6,11,204,220,421,466,490,493,509,522],interrupt:305,intersect:[3,6,129,205,354,356,498],intersert:354,interspers:384,interstiti:[175,444],intertia:[3,103],interv:[3,6,99,203,218,252,269,305,310,311,324,464,470,490,509,522],intestieti:129,intial:[6,391,393],intiial:[41,500],intiti:[3,332],intra:315,intra_energi:244,intramolecular:[28,153,244],introduc:[6,9,100,117,204,236,269,305,310,315,368,375,392,407,416,429,433,437,475,509,522],introduct:[],intuit:378,inv:[129,176,317],invalid:[3,12,75,97,180,283,386,438,439,497],invari:[117,144,149,151],invent:319,invers:[],inverse:516,invert:[1,6,181,297],invis:354,invoc:[175,226,391,461,463,493],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,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392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,483,485,486,487,489,490,491,492,493,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,512,513,514,516,517,521,522,523,524,525,527],young:[421,460,462],your:[],yourself:[6,8,12,13,227,385,517],yplane:351,ypo:177,ysu:[3,201,202,335,496],yuan:9,yukawa:[],yukawa_1_1:484,yxz:492,yzx:492,z_i:[416,480,487],z_j:[480,487],z_meam:441,zachari:13,zannoni:420,zbl:[],zblcut:480,zblcutinn:465,zblcutout:465,zblexpscal:480,zblz:465,zcm:315,zcylind:351,zepeda:215,zero:[],zeta:[3,255,306,417],zfactor:204,zflag:[164,165,256,258,265,315,340],zhang:[315,341,421],zhi:[3,6,179,201,213,344,350,353,355,495,498,513],zhi_bound:[6,201],zhou:[13,397,417,454,478,480],zhu:472,ziegenhain:13,ziegler:[300,441,474,480,487],zimmerman2004:214,zimmerman2010:214,zimmerman:[9,74,214,397],zlat:[229,250,513],zlib:[9,201],zlim:464,zlo:[3,6,179,201,213,344,350,352,353,355,495,498,513],zlo_bound:[6,201],zmax:[213,255,522],zmin:[255,522],zn2:176,zone:[129,317],zoom:[3,201,204,205],zorig:75,zplane:351,zr4:176,zrest:332,zsu:[3,201,202,335,496],zwall:350,zwall_veloc:255,zxy:492,zybin:457,zyx:492},titles:["LAMMPS 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.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx 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 manifoldforce 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/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle 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 rx 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/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","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/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 exp6/rx 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 multi/lucy command","pair_style multi/lucy/rx 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 table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":224,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,129,133,134,151,157,165,166,170,176,177,180,182,196,199,200,201,202,204,205,206,207,209,210,211,213,214,215,217,221,224,225,227,228,229,230,234,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,317,333,335,340,341,342,343,346,348,350,352,356,369,373,375,376,378,379,382,383,385,387,388,389,391,394,397,399,416,438,439,444,446,456,457,473,474,490,491,492,495,496,498,500,502,503,504,507,509,511,512,513,514,515,521,523,525,526],"function":522,"long":[219,398,400,401,402,403,407,409,410,429,433,437,451,459,481],"new":8,"static":12,acceler:1,account:517,ackland:66,acknowledg:7,adapt:[209,210],addforc:211,adding:517,addition:[12,13,517],addtorqu:212,adiabat:6,adjust_dt:322,adp:392,after:517,airebo:393,alloi:414,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:213,arrai:6,aspher:[6,90,155,271,275,279,280,289],asphere:9,atc:[9,214],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,151,152,175,213,215,216,304,522],atom_modifi:39,atom_styl:40,attract:5,aveforc:222,awpmd:[9,394],axel:517,balanc:[41,223],barostat:6,basal:70,beck:395,berendsen:[302,336],between:6,binary2txt:13,bodi:[6,8,42,71,156,272,276,281,290,396],body:9,bond:[8,13,72,73,224,225,226,311],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:397,born:[398,409],boundari:[7,59],box:[6,60,227],branch:517,brownian:399,buck:[400,401,409,440],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:517,change_box:61,charmm:[6,19,183,402,437],chunk:[6,69,75,79,86,98,103,114,116,125,157,172,174,217,330],citat:7,class2:[9,20,43,184,359,403],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,350,405,486],colvar:[13,228],colvars:9,com:[78,79,158],comb3:406,comb:[307,406],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,522],compute_modifi:112,condit:7,conduct:[6,341],constant:[6,522],constraint:7,contact:[80,131],coord:81,core:6,coreshell:9,correl:[218,219],cosin:[22,23,24,25,26,27,186],cossq:361,coul:[398,400,401,402,403,407,408,409,422,429,433,437,451,459],coupl:6,creat:225,create_atom:177,create_bond:178,create_box:179,createatom:13,creation:7,csld:337,csvr:337,cubic:431,cuda:[],custom:[8,201,202],cut:[49,394,400,403,407,410,416,419,429,430,437,445,451,481],cvff:362,damag:[82,132],data2xmovi:13,data:6,databas:13,deby:[407,429],defgrad:138,deform:[160,161,229],delete_atom:180,delete_bond:181,delta:23,deposit:230,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],diagnost:7,diel:408,dielectr:182,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:185,dihedral_styl:[2,183,184,186,187,188,189,190,191,192,193,194,195,196,197,198],dilat:85,dimens:199,dipol:[6,28,86,410],dipole:9,direct:233,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:200,distanc:363,distribut:[7,12],document:0,dpd:[9,88,89,411,412],drag:231,dreid:423,dreiding:6,drude:[6,9,162,232,233,253,516],dsf:[407,429],dsmc:413,dump:[6,8,201,202,203,204,206],dump_modifi:205,dynam:306,eam:[13,414],echo:207,edip:415,eff:[9,13,106,107,161,163,168,254,270,282,293,339,416],efield:235,ehex:236,eim:417,elastic:6,emac:13,energi:[134,412],enforce2d:237,ensembl:7,erot:[90,91,92,93],error:[3,133],evapor:241,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],exp6:418,exp:[26,186],expand:[46,432],extend:[8,11],extern:242,fcc:296,fdt:412,featur:[7,8,517,522],fene:[45,46],fep:[9,13,95,210],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242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246,ceriotti:[13,246,251],certain:[1,2,3,6,8,12,16,39,75,124,128,130,181,201,202,204,216,217,218,220,221,226,242,243,315,318,334,347,358,366,374,387,424,446,457,481,497,501,516,522],certainli:250,cerutti:376,cfg:[3,6,7,9,13,201,203,204,205,206],cfile:457,cfl:[139,322],cfor:321,cg_type:459,cgiko:[],cgikot:[],cgkio:[],cgko:[],cgkot:[],cgo:[],cgot:[],ch2:319,ch2lmp:[],ch3:319,ch5md:203,chain3:387,chain:[],challeng:[6,321],chalopin:310,champaign:[249,375,376,438],chan:444,chandler:[392,414],chandrasekhar:[6,429],chang:[],change_box:[],changeabl:201,channel:[4,211],chapter:[298,376],charact:[2,3,6,12,37,41,56,65,197,201,202,204,205,206,208,223,239,240,304,312,316,358,385,390,416,418,428,448,449,454,456,457,464,476,477,492,493,497,502,503,522,525,526,527],character:[6,70,74,117,127,151,465,490,509],characterist:[253,333,342],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,129,176,177,201,202,206,208,209,210,215,230,235,244,304,306,307,308,312,335,348,375,376,385,398,400,406,407,409,410,414,416,417,424,429,433,437,451,456,457,464,474,480,481,483,484,486,487,495,496,500,505,507,516,521,522],charmm2lammp:13,charmm:[],chartreus:205,cheap:333,cheaper:[234,420,458],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,197,198,215,223,224,225,230,241,244,250,251,301,314,319,333,341,343,348,356,358,371,374,384,385,386,387,388,391,413,425,428,446,457,488,490,492,493,495,503,509,512,513,522],checkf:197,checkout:517,checkqeq:457,checku:197,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,152,183,184,194,219,228,233,236,245,246,253,255,268,269,270,292,293,298,302,305,307,315,320,321,333,336,337,340,341,342,343,350,359,368,370,375,376,383,386,393,398,402,403,406,407,408,410,411,412,416,419,420,422,423,429,433,434,437,441,445,446,448,449,451,464,473,481,504,507,509,516],chemic:[9,40,88,89,129,171,176,201,202,214,215,244,306,311,312,340,376,418,449,456,457,469,477],chemistri:[305,306,308,393,397,416,456,457],chen:345,cheng:406,chenoweth:[456,457],chenoweth_2008:[456,457],chi:[102,166,200,296,306,308,371,417,420,523],chiefli:455,child:8,chip:[7,9,16,17,391,508],chipot:228,chiral:368,chmod:[11,12],cho:441,chocol:[7,205],choic:[3,6,9,12,14,15,17,40,41,54,95,152,155,156,170,181,197,217,223,226,229,230,246,252,255,267,269,298,302,306,315,340,369,376,382,383,386,388,391,424,437,446,452,495,504,505,508,509,515,516,521],choos:[1,3,6,7,8,9,12,15,16,17,28,39,54,95,128,167,168,204,224,225,226,227,230,241,252,255,267,269,271,272,273,274,275,276,277,301,302,320,333,337,351,375,376,383,484,490,492,504,510],chose:[478,480],chosen:[2,3,6,12,16,151,177,180,189,197,204,210,215,227,230,241,244,245,253,255,267,269,274,298,301,312,333,337,340,341,346,348,349,355,376,377,383,391,412,416,421,428,431,459,478,490,504,509,510,516],chri:175,christian:[7,9,16],christoph:7,chunk:[],chunkid:[69,79,86,98,103,114,116,125,157,172,174,217,330],chute:[4,9,10,247],ciccotti:319,cieplak:[6,183,507],cii:218,cij:218,ciko:[],circl:[42,75,328],circular:[3,6,155,199],circumst:17,circumv:[100,117,310],citat:[],cite:[3,7,8,12,252,464],civ:9,ckio:[],cko:[],cl1:176,clarendon:[28,410],clarifi:[7,478,480],clariti:358,clark:451,class2:[],classic:[0,3,5,6,7,8,9,242,298,305,310,345,370,416],classifi:[474,483],claus:493,clean:[6,12,14,16,503],cleanli:[494,526],clear:[],clearli:7,clebsch:151,clermont:[9,13],clever:499,click:[2,11,21,36,44,55,177,185,196,204,249,360,369,386,404,474,517],client:[249,251],climb:[268,386,509],clinic:[7,13],clo:[166,200,523],clock:[12,490,509],clockwis:[183,351],clone:517,close:[3,6,11,12,13,39,41,70,75,152,180,201,225,226,227,246,253,255,269,285,292,315,319,351,354,374,376,379,382,383,386,391,393,397,407,408,427,441,446,448,449,456,460,462,476,480,499,505,516,517,519],closer:[3,10,41,127,175,200,201,223,227,231,342,386],closest:[225,296,315,348,420,458,473,484],cloud:[464,516],clovertown:17,clsuter:76,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[],clutter:3,cmap:495,cmatrix:246,cmax:441,cmd:[11,12,298,506],cmdarg:11,cmin:441,cmm:[],cmoput:144,cn1:218,cn2:218,cna:[],cnn:218,cnr:13,cnrs:9,cnt:[424,499],co2:[40,176,316,319,385,418],coars:[7,9,10,28,35,40,54,189,240,300,315,316,333,418,422,449,459,477,504,507],coarser:[376,522],coarsest:151,code:[],coeff:[3,7,8,12,20,21,32,44,50,183,184,185,190,359,360,366,404,424,428,446,461,463,466,495,524],coeffcient:495,coeffici:[],coefficienct:411,coefficient0:414,coefficient1:414,coeffieci:[6,395,427],coeffincientn:414,coexist:[244,416],cohes:[6,417,441],coincid:[133,354,402,438,439,490],colberg:203,cold:[6,162,244,248,387,516],coldest:341,coleman8:9,coleman:[9,129,176,317],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,157,165,172,174,177,201,202,205,217,228,258,265,300,310,313,315,356,375,385,387,405,495,502,508,514,527],collid:[234,333,355],colliex:176,collinear:[3,300],collis:[3,255,333,351,355,413,421,487],colllis:333,colloid:[],colombo:39,colon:[206,356,496],color1:205,color2:205,color:[3,9,41,201,204,205,223,245,305,310],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,130,151,152,157,165,172,174,175,176,197,201,202,205,208,216,217,218,220,221,258,266,267,305,315,334,335,345,355,393,419,423,456,457,496,510,512,522],columnar:175,colvar:[],colvarmodul:12,com:[],comamnd:229,comand:226,comannd:391,comb3:[],comb:[],comb_1:307,comb_2:307,combiant:408,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,155,156,170,201,204,214,220,236,244,249,258,261,269,285,291,298,304,320,337,346,354,357,359,375,376,378,383,391,405,407,408,412,416,417,418,424,436,437,465,475,478,480,481,483,486,498,503,508,516,522,524],come:[],comfort:[12,13],comid:330,comit:517,comm:[0,3,11,12,63,77,203,249,251,252,376,386,391,411,446,453,476,477,497],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,183,197,201,239,240,253,315,316,345,385,386,392,414,415,417,418,428,441,448,449,450,457,464,465,475,476,477,478,479,480,483,492,493,495,516,517,522],commerci:7,commit:[9,517],commmand:[3,6,12,61,118,293,427,489,490,492,509,526],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,179,201,204,206,370,422,431,465,478,480,495,498,507],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,175,180,181,204,205,223,224,225,227,228,229,249,251,255,257,258,259,269,297,304,306,307,308,315,320,333,345,356,373,375,387,388,389,391,412,413,452,488,492,493,504,505,522,525,527],communc:375,comp:[7,203,251,252,285,291,319,376,386,416,446,453,458,472,476,477,479],compact:[65,208,404,474],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,129,160,176,185,196,205,233,306,356,358,375,376,384,386,441,464,490,509,510,516,521],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:380,compass:[7,9,20,21,36,43,44,55,184,185,196,359,360,369,403,474],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,130,188,201,206,210,216,217,218,220,221,223,236,297,309,337,340,347,350,353,375,391,425,444,446,476,492,493,522],compens:[6,224,225,313,387,416],compet:344,competit:376,compil:[3,7,8,9,12,13,14,15,16,17,18,175,201,203,204,206,249,344,376,391,444,495,496,500,516,522],compl:16,complain:[11,12,16],complement:441,complementari:[7,407,429],complet:[3,6,9,11,12,14,41,61,75,205,223,228,258,298,301,304,333,344,346,357,358,374,386,391,417,461,463,482,490,495,500,503,507,509,512,516,522],complex:[4,6,8,11,12,13,24,40,42,64,100,117,151,153,165,177,178,255,285,328,354,373,386,416,444,476,477,493,495,498,522],compli:[340,344],complic:[6,7,9,12,13,215,244,493],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,138,141,142,143,144,147,148,149,151,152,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,172,173,174,200,201,202,204,205,211,212,216,217,218,219,220,221,222,226,227,229,230,235,236,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,318,319,321,325,326,329,333,336,337,338,340,347,348,353,354,355,375,378,383,384,385,386,391,411,416,421,438,439,461,463,464,465,495,496,505,513,522,523],componenet:6,composit:[6,215,255,414],compound:[406,416,417,483],compres:[75,125,217],compress:[],compris:[40,354,418,458,482],compton:[129,176],comptu:3,compuat:376,comput:[],computation:[3,6,224,225,345,397],computational:516,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[129,317],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:176,concaten:[2,3,526],concav:354,concentr:[75,240,316,414,418,449,477],concept:[6,157,167,217,504],conceptu:[3,6,75,165,227,229,386,407,424,441,500],concern:[6,77,95,203,245],concetr:75,concis:[11,344],conclud:12,concret:8,concurr:[15,376,522],conden:[345,478,480],condens:[6,159,345,393,409,414,429,483],condit:[],conducit:6,conduct:[],cone:498,confer:444,confid:[3,509],config:[12,201,492],configfil:228,configur:[1,2,6,12,14,16,37,61,133,179,197,200,201,204,208,227,228,229,230,234,244,251,252,283,298,306,344,373,384,386,393,397,415,441,444,475,478,480,483,490,495,497,498,509,517],confin:[495,509],conflict:[3,12,40,202,446,493,517],conform:[3,6,13,61,226,227,268,314,321,344,368,386,416,507],confus:[3,483],conjuct:[9,411],conjug:[7,8,252,383,416,456,457],conjunct:[6,7,75,94,95,125,160,165,171,177,181,205,209,210,252,255,259,283,301,302,306,307,308,310,315,320,333,341,348,353,375,376,386,398,400,404,407,411,416,423,429,446,451,459,481,495,498,502,516,527],connect:[3,6,9,95,162,180,226,249,300,315,319,329,380,386,408,421,456,457,473,480,492,493,495,499,516],conner:393,connor:393,conput:3,consecut:[3,11,12,39,75,177,205,209,210,230,249,250,407,429,433,490,496,498],consequ:[1,6,215,345,428,509],conserv:[3,9,28,208,215,226,233,234,245,248,252,254,255,259,265,267,269,283,285,315,319,320,336,337,341,348,349,353,386,410,411,412,421,435,464,504,509],consid:[6,74,75,82,95,126,159,162,163,180,201,202,205,209,210,216,218,223,225,226,230,256,270,297,315,340,341,344,345,348,376,404,416,424,457,458,464,473,490,491,493,496,497,498,500,503,505,513,516,522],consider:[6,8,252,253,336,337,338,391,504],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,157,160,162,177,189,200,206,211,212,217,229,230,233,235,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,313,314,315,316,336,337,338,339,349,375,376,378,380,385,386,391,393,397,399,405,407,416,420,424,427,438,439,441,444,446,448,449,458,461,463,464,476,477,484,493,495,496,497,498,499,500,507,516,522],consistent_fe_initi:214,consit:315,constant:[],constantli:236,constitu:[3,6,258,315,350,354,405,458],constitut:[461,463],constrain:[3,6,8,9,154,155,156,157,158,160,163,164,165,166,167,169,170,208,217,230,236,244,245,250,258,261,263,285,291,300,301,313,315,319,331,341,348,384,385,416,500,507,516],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,129,151,176,227,269,297,314,316,354,387,391,410,444,446,473,475,476,477,498,499,514,522],constructor:[8,11],consult:457,consum:[1,310,452,522],consumpt:373,contact:[],contact_stiff:[460,462],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,129,151,153,157,165,175,176,177,179,183,185,196,197,201,202,204,205,206,208,209,210,214,216,217,218,220,221,223,228,230,235,239,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,317,322,333,340,344,345,354,355,358,374,376,385,386,389,390,392,393,394,397,406,407,410,414,415,416,418,424,425,441,444,448,449,450,454,455,456,457,465,475,476,477,478,479,480,481,483,490,491,492,493,495,496,497,498,500,502,504,507,509,510,512,513,516,517,522,525,527],content:[4,8,9,12,17,457,511,513],context:[3,6,8,12,16,127,128,205,224,225,230,300,312,349,383,486,495,502,511,521,522,523],contibut:74,contigu:492,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,173,205,208,209,210,215,217,218,219,220,221,223,226,227,228,229,230,236,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,317,321,332,333,335,342,343,345,351,354,358,374,390,391,397,411,413,431,434,456,457,458,461,463,479,490,493,495,497,498,503,509,510,512,513,522,525],continuum:[6,7,9,214,345,461,463],contour_integr:214,contract:[61,227,229,269,302,315],contradictori:3,contrain:319,contraint:283,contrari:[246,253],contrast:[1,6,42,55,66,159,162,202,229,356,461,463,486,526],contrib:345,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,210,215,216,217,218,220,221,227,244,252,255,258,259,264,270,292,293,300,301,309,312,315,317,319,347,375,384,386,394,411,413,414,416,424,438,439,444,446,456,457,464,507,513,516,517],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,133,151,186,201,202,204,208,214,215,223,227,228,229,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,316,323,324,336,337,338,345,349,373,375,388,416,420,444,456,457,460,462,475,480,490,492,504,510,511],control_typ:214,controlfil:457,convect:99,conveni:[6,12,28,201,206,221,317,378,465,481,517,522],convent:[3,8,28,188,195,196,202,205,314,329,357,414,416,522],converg:[3,6,41,96,201,202,204,206,211,223,226,227,235,242,274,285,291,305,307,310,314,319,382,383,384,386,406,407,429,464,490,502,509],convers:[3,8,151,204,205,215,218,302,375,407,408,409,416,429,433,437,451,493,509,521],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,177,184,201,204,205,218,221,267,301,304,356,359,361,365,368,378,386,392,414,444,478,480,487,493,495,496,497,502,512,516,521,522,525,527],convex:[42,354],convinc:[7,12],cook:9,cooki:7,cool:[7,167,236,248,313],cooordin:[201,202],cooper:[5,7],coord123:125,coord1:[3,125,217],coord2:[3,125,217],coord3:[3,125,217],coord:[],coordb:464,coordbb:464,coordiat:384,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,145,151,160,166,172,174,175,177,181,200,201,202,203,204,205,206,208,211,216,217,220,223,224,225,226,227,228,229,230,233,235,236,237,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,318,319,321,326,329,330,331,332,333,335,343,344,345,352,353,355,356,378,384,385,386,391,392,393,396,415,464,490,495,496,497,498,500,503,505,509,516,522,523],coordn:[125,217],coords:464,copi:[0,3,4,8,9,11,12,14,16,40,130,204,345,386,404,456,493,517],copper:487,coproccesor:15,coprocessor:[1,7,9,15,16,391,508],coproprocessor:16,copy_arrai:8,copyright:[7,8,300],coral:205,core:[],core_shel:159,cores:516,coreshel:[4,6,9],coreshell:[],cornel:[6,183,507],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,204,354,355,378,482,495,517],cornflowerblu:205,cornsilk:205,corp:9,corpor:15,corr:406,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,159,164,171,183,202,204,229,236,244,246,252,269,270,292,300,302,305,344,350,354,375,386,392,393,394,395,396,397,398,399,400,401,402,403,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,485,486,487,488,495,510,513,516,517],correction_max_iter:214,correctli:[3,8,11,16,75,87,112,113,114,154,155,156,158,160,162,163,164,165,166,169,170,173,201,205,211,230,235,242,253,263,269,270,308,315,319,329,332,351,354,386,387,391,409,439,444,492,493,495,505,517,521,523],correl:[],correpond:[239,240],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,138,141,142,143,144,145,147,148,149,151,154,155,164,171,175,176,183,184,185,186,187,188,189,191,192,194,195,197,200,201,202,204,205,209,210,211,217,219,220,222,225,227,229,236,237,240,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,316,318,319,340,350,351,353,354,355,357,359,360,361,362,364,365,368,370,376,381,383,385,386,392,393,395,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,417,418,419,420,421,422,423,424,427,429,430,431,432,433,434,435,436,437,438,441,442,444,446,447,449,450,451,453,454,456,457,458,459,464,465,466,475,476,477,478,479,480,481,483,485,486,487,490,492,493,495,496,498,508,509,510,512,513,516,522],correspondingli:[438,439,504],corrupt:3,cosin:[],cosineshift:26,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,129,152,176,204,205,217,223,224,225,241,269,307,345,375,376,389,407,429,433,444,446,475,492,504],costheta0:[475,478,480,483],costheta:454,costli:[11,96,246,387],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,157,167,172,174,190,201,202,204,205,209,210,217,218,223,229,242,251,304,305,306,310,313,315,318,333,334,340,344,345,346,350,354,356,358,366,372,374,382,384,387,391,393,394,419,423,424,427,456,457,491,492,493,495,497,499,502,503,510,511,516,522,523],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,152,178,182,306,308,346,375,376,384,391,398,400,401,402,403,406,407,408,409,410,416,421,422,424,429,433,437,440,446,451,456,457,459,464,474,480,481,483,486,500,507,513,516,521],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,165,175,181,183,211,212,215,217,220,222,223,230,235,241,244,250,269,283,301,319,336,337,354,376,384,385,386,388,391,419,423,446,513,522],counter:[3,351,490,501,503,509],counteract:244,counterbal:[236,248],counterbalanc:28,counterclockwis:183,counterpart:[201,315,490],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:322,cours:[3,8,137,139,171,201,209,210,245,314,329,344,350,352,353,355,356,376,438,466,492,495,508,516,522,525],courtesi:378,cov:464,coval:[6,9,28,416,441,464,516],covari:246,cover:[6,12,75,197,205,214,255,416,482],coverag:75,cpc:251,cpp:[1,3,6,8,9,11,12,13,95,201,209,210,242,319],cpu:[1,3,9,10,12,14,15,16,17,65,75,205,219,233,253,346,373,376,391,404,474,490,508,509,512,513,514,522],cpuremain:513,cpus:12,cr2:176,cr3:176,crack:[4,387],crada:[5,7],crai:[5,7,13,17,201],crash:[3,12,387,516],craympi:391,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:214,create_faceset:214,create_group:203,create_nodeset:214,createatom:[],creation:[],crimson:205,critchlei:300,criteria:[3,127,178,204,205,224,225,226,264,384,453,482,497,500,522],criterion:[12,41,132,177,180,215,223,226,244,283,307,322,351,356,384,386,406,416,421,464,500,509,510],criterioni:509,critic:[6,48,49,267,340,345,384],crmax:75,crmin:75,cross:[3,12,21,75,97,155,175,185,201,202,204,216,225,229,266,268,292,315,325,329,332,341,348,360,378,386,402,411,413,414,422,423,424,429,431,433,454,459,461,463,478,480,487,495,499,505,525],crossov:1,crossterm:495,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,77,117,296,297,343,378,387,495,499,513,516],crystallin:[6,113,297,378,479,516],crystallis:340,crystallogr:[129,176],crystallograph:[378,513],crystallographi:[129,176,378],cs1:176,cs_chunk:6,cs_im:[40,495],cs_re:[40,495],csanyi:[151,455,465],cscl:441,csequ:6,csh:[11,12,404],cshrc:[11,12],csic:[415,475,478,480,483],csinfo:6,csisi:[415,475,478,480,483],csld:[],cst:414,cstherm:6,cstyle:492,csvr:[],ctcm:[392,414],ctemp_core:233,cterm:321,ctr:9,ctype:11,cu1:176,cu2:176,cu3au:441,cube:[6,175,180,233,354,378,516],cubes:[41,223],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:397,cummul:[3,6,221,224,225,226,228,241,246,252,254,333,336,337,338,339,341,348,423,513],cumul:[6,215,217,220,234,244,252,267,269,274,283,315,317,386],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,141,152,157,165,167,173,175,178,181,200,201,202,203,204,205,206,209,210,214,217,221,223,224,225,226,227,228,229,230,234,235,236,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,316,319,320,321,322,323,324,325,326,328,330,331,332,333,336,337,338,344,345,348,349,350,351,352,353,355,356,358,373,374,375,376,379,380,381,383,384,385,386,391,397,404,406,410,414,416,417,421,424,425,428,438,439,441,442,443,446,454,456,457,460,461,462,463,466,478,480,481,484,490,491,492,493,495,496,497,498,499,501,502,503,505,507,509,510,512,513,517,522,523,524,525,526,527],curv:[6,177,244,285,291,297],curvatur:[420,458,487],custom:[],cut0:493,cut1:504,cut2:504,cut:[],cuthi:[296,308],cutinn:[399,438,439],cutlo:[296,308],cutmax:454,cutoff1:[403,410,429,433,437,440,451,459],cutoff2:[398,400,401,403,409,410,429,433,437,440,451,459,481],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,151,175,178,180,181,225,226,231,239,240,296,305,306,308,310,312,315,320,333,346,350,354,356,373,375,376,384,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,457,458,459,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,493,497,500,504,516,522],cutoffa:415,cutoffc:415,cuu3:414,cval:176,cvd:340,cvel:321,cvff:[],cwiggl:[3,266,350,353,355,522],cyan:[2,204,205],cycl:[3,244,267,269,270,274],cyclic:[3,183,197],cygwin:12,cylind:[3,4,75,204,217,250,291,301,351,354,380,498],cylinder_d:380,cylindr:[6,250,329,351],cypress:391,cyrot:397,cyrstal:297,d3q15:255,d3q19:255,d_double_double:14,d_e:345,d_flag2:304,d_flag:304,d_name:[124,201,304,335,505],d_single_double:14,d_single_single:14,d_sx:304,d_sy:304,d_sz:304,daan:343,dai:12,daili:12,daivi:292,damag:[],dammak:310,damp:[3,6,208,213,252,253,254,259,269,270,274,291,302,305,306,310,315,336,337,349,351,352,383,384,386,398,400,402,407,410,416,421,429,437,451,459,474,481,509,516],damp_com:253,damp_drud:253,dampen:[315,516],dampflag:[351,421],dan:16,danger:[3,12,244,356,411,513],dangl:180,daniel:9,darden:[376,410],darkblu:205,darkcyan:205,darken:204,darkgoldenrod:205,darkgrai:205,darkgreen:205,darkkhaki:205,darkmagenta:205,darkolivegreen:205,darkorang:205,darkorchid:205,darkr:205,darksalmon:205,darkseagreen:205,darkslateblu:205,darkslategrai:205,darkturquois:205,darkviolet:205,dasgupta:306,dash:[421,512],dat:[6,99,197,214,491],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,317],dataset:317,datatyp:3,date:[0,4,6,12,13,200,456,457,522],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,201,218],davenport:440,davi:350,david:[9,18,375,376,478,480],daw:[414,454],dbg:[],dcd:[3,6,7,201,203,204,205,206,298,496,500],dcs:9,ddim:200,deactiv:437,dealt:251,debug:[6,7,11,12,13,16,57,129,133,176,177,298,303,373,375,425,446,484,493,494,502,505,512,522],deby:[],decai:[100,407,487],decid:[3,6,12,15,75,266,304,315,346,510,517],decipher:378,deck:304,declar:203,declin:333,decod:204,decompos:[95,465],decomposit:[3,5,7,17,64,214,298,320],decoupl:[6,516],decreas:[3,201,202,211,212,219,226,229,235,236,242,244,252,344,375],decrement:321,deepli:372,deeppink:205,deepskyblu:205,def:[12,13,493],defaul:63,defect:[6,74,175,444],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,183,184,185,186,187,188,189,191,192,194,195,196,197,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,233,234,235,238,240,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,319,322,326,330,331,333,335,336,337,338,339,341,342,343,345,347,348,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,368,369,370,371,373,375,376,378,381,383,384,385,386,387,388,389,390,391,393,394,395,396,398,399,400,401,402,403,404,405,407,408,410,411,412,413,415,416,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,444,445,446,447,448,449,450,451,453,454,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,492,493,495,496,498,499,500,501,504,505,506,507,509,510,512,513,516,518,519,520,521,522,523,524],definit:[2,3,6,8,12,13,82,85,127,151,205,217,218,219,220,221,229,238,250,274,317,335,347,350,353,355,357,369,373,385,394,397,405,412,416,427,454,461,463,465,482,493,495,497,504,506,521,522],defint:513,deform:[],deg2theta:176,deg:516,degener:[3,300],degrad:[8,17,297,376,504],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,176,177,183,184,187,188,195,197,200,204,217,226,233,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,319,336,337,338,343,359,361,365,368,370,384,410,414,423,505,513,516,523],degrees:197,degress:[157,217],del:509,delai:[3,6,12,387,413,513],deleg:424,delet:[2,3,7,8,12,54,59,62,65,175,180,181,208,217,218,220,221,224,226,241,244,269,317,336,337,356,358,374,385,387,390,446,473,495,496,497,498,506,507,512,517,518,520,522,523],delete_atom:[],delete_bond:[],delete_el:214,deli:200,delimit:[316,493,522],dellago:[6,236],deloc:[270,416,464],delr:441,delt_lo:509,delta:[],delta_1:397,delta_3:397,delta_7:397,delta_conf:3,delta_ij:[441,454],delta_pi:397,delta_r:454,delta_sigma:397,deltah_f:240,delx:200,delz:200,demand:310,demo:11,demon:295,demonstr:[305,441],den:301,dendrim:423,dendtrit:380,denniston:[9,255,257,258,259,297],denomin:[7,182],denot:[129,233,236,253,297,308,310,407,422,424,457,461,463],dens:[75,226,416],densiti:[3,6,7,9,17,40,41,61,110,127,137,151,163,175,177,209,210,214,217,223,229,242,255,258,262,263,297,301,302,304,306,345,350,378,381,385,392,393,397,414,441,442,443,448,449,454,458,464,468,470,471,472,495,504,505,513,521],density_continuity:463,density_summation:463,dent:380,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,130,151,153,154,160,164,165,171,177,178,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,204,205,208,209,210,211,212,215,217,219,220,221,222,223,225,227,229,235,237,240,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,316,318,319,320,326,333,336,337,338,340,342,344,345,347,350,353,354,355,356,358,359,360,361,362,364,365,368,370,376,378,384,385,387,388,389,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,441,442,444,445,447,448,449,450,451,453,454,456,457,458,459,464,465,466,474,475,476,478,479,480,481,483,485,486,487,490,492,495,497,498,501,505,507,509,512,513,515,522,523],dependend:6,depflags:12,dephas:[490,509],depos:230,deposit:[],deprec:[3,306,456],deprect:217,depth:[51,155,204,345,418,420,458],dequidt:9,der:[95,118,405,406,437,456,457,486],deriv:[6,7,8,9,37,56,65,95,151,171,197,218,227,229,236,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,342,343,345,350,351,354,383,385,393,397,405,410,416,417,422,431,435,436,441,444,456,457,474,476,477,486,516],derjagin:486,derlet:296,descend:205,descent:[7,383],descib:[40,204,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,129,141,151,152,155,156,157,161,162,165,168,170,171,175,176,177,179,180,189,194,197,201,202,203,208,209,210,217,218,219,220,221,223,226,227,228,229,230,232,233,239,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,316,321,329,333,334,335,336,337,338,339,340,341,342,343,348,350,351,353,358,375,376,378,382,383,384,385,386,390,393,394,396,398,399,400,402,403,404,405,406,407,410,414,416,417,418,420,421,422,424,427,429,430,431,432,433,434,435,436,437,438,439,440,441,444,445,448,449,453,454,455,456,457,458,459,464,465,466,473,474,475,476,477,478,479,480,481,483,485,486,487,488,490,492,493,495,496,497,498,499,505,508,509,512,517,522,523,525],descript:[],descriptor:[151,201,425],deserno:376,design:[0,3,6,7,8,11,13,14,16,129,159,162,176,214,226,232,233,269,270,296,297,317,340,345,394,395,396,399,402,407,409,416,437,438,439,442,443,454,457,476],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,152,159,177,190,200,217,221,227,229,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,319,333,336,337,338,339,344,351,366,372,375,376,378,382,384,385,386,411,414,423,438,439,475,478,480,491,492,493,495,499,504,509,510,512,513,522,523,525],desk:7,desktop:[4,6,7,10,12,204],despit:516,destabil:397,destre:368,destroi:[9,11,39,224,225],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,130,151,152,154,155,156,157,160,170,171,172,174,177,178,181,182,185,196,200,201,202,204,205,208,209,210,214,217,218,219,220,221,223,225,226,227,228,229,230,236,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,319,320,333,336,337,338,339,340,341,343,344,345,346,347,348,349,356,358,360,369,375,376,379,384,385,387,388,391,392,393,394,396,397,399,401,402,403,404,405,406,407,410,411,416,417,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,445,446,448,449,453,456,457,458,464,465,466,474,482,485,486,488,493,495,496,497,498,500,501,504,505,507,510,513,514,517,522,523,527],detect:[2,3,12,42,63,65,94,100,243,301,344,386,406,423,428,490,492,495,506,509,522],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,138,152,165,166,175,176,177,200,201,202,204,205,206,207,211,212,213,216,217,218,219,220,221,222,223,227,229,230,233,235,240,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,318,322,324,326,333,336,337,338,340,346,347,350,351,352,353,354,355,356,369,375,376,378,385,387,388,391,393,394,401,406,410,413,414,418,419,421,424,425,433,441,444,446,449,457,458,464,473,476,477,481,486,492,495,496,498,500,502,505,509,511,512,514,521,522,523],determinist:320,detil:119,devan:[9,459],devanathan:480,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,249,274,300,305,306,309,393,397,416,443,444,464,483,497],devemi:9,deviat:[267,274,296,419],deviator:9,devic:[1,3,12,14,16,249,391],device_typ:391,devin:[307,406],devis:443,dfactor:204,dff:516,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,376],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,444],dhi:[61,200,229,301],dhug:[267,305],dhugoniot:[267,305],dia:441,diagnost:[],diagon:[3,6,91,151,152,153,227,269,302,315,348,461,463],diagonalstyl:465,diagram:[41,129,176,196,223,298],diallo:423,diam:[204,205,301,385],diamet:[3,6,40,42,124,177,201,202,204,205,209,210,252,301,304,315,333,335,349,351,385,405,420,421,431,458,482,486,495,496,505],diamond:[378,416,441],diamter:[40,301],dick:6,dicsuss:266,dictat:[215,267],did:[3,12,384,411,413,414,421,446,478,480,503],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,173,347,375],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,131,151,153,154,155,156,157,158,160,163,164,165,166,167,169,170,171,177,178,180,185,196,197,200,201,204,205,208,210,213,215,217,220,223,224,225,226,227,228,229,233,236,239,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,319,321,329,331,333,336,337,338,341,342,343,345,348,349,350,351,354,358,359,369,372,374,375,376,378,379,382,383,385,386,388,389,390,391,392,393,397,401,402,404,405,406,411,412,414,416,418,420,421,422,424,427,429,430,432,433,440,441,442,443,445,446,447,448,449,450,454,456,457,458,459,460,461,463,464,465,466,474,475,476,477,478,480,482,483,486,489,490,492,493,495,497,498,499,500,503,504,505,507,509,510,512,513,514,516,521,522,523,525],differenti:[1,3,6,28,197,316,375,407,454,479],difficult:[227,298,391,423,504],difficulti:[100,117,319,456],diffract:[7,9,129,176,317],diffus:[],diffuse:[4,6],digit:[2,3,205,358,444,522],dih_table1:197,dih_table2:197,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,198],dihedraltyp:225,dihydrid:416,dij:319,dilat:[],dim1:3,dim2:3,dim:[3,61,75,154,158,159,160,163,164,165,166,167,169,177,200,229,250,351,378,441,498,521,522,523],dimdim:522,dimems:297,dimens:[],dimensinon:75,dimension:[3,39,100,123,129,151,154,157,158,159,160,163,164,165,166,167,169,176,199,217,268,297,345,378,382,386,454,495,505],dimensionless:[115,132,133,135,138,140,142,147,151,345,376,465,486],dimensions:317,diment:3,dimentionless:146,dimer:[6,315,441],dimgrai:205,dimstr:[41,223],dinola:[302,336],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,201,202,335,516],dir1:506,dir2:506,dir:[1,3,4,8,10,11,12,267,296,305,332,454,456,457,493,506,522],dirac:151,direc:454,direct:[],directli:[3,6,8,9,11,12,95,124,151,153,201,202,203,204,211,235,246,250,255,297,316,317,337,349,351,352,353,354,378,383,391,392,393,398,400,401,407,410,414,416,429,433,446,451,459,473,493,505,506,507,513,522],directoi:[],directori:[],disabl:[3,12,15,345,428,493,508,522],disadvantag:[6,223],disallow:[201,229,269],disappear:497,discard:[2,3,41,75,219,223,346,354,492,497,498],discontinu:[197,384,435],discourag:441,discov:[13,346],discret:[6,8,40,42,204,205,252,255,291],discuss:[],disk:[6,92,93,100,170,199,230,244,301,493],disloc:[74,444],disord:[39,74,444],disp:[],dispar:458,disperion:[410,433],dispers:[3,6,7,9,175,297,375,376,401,410,433,438,446,457,476,483],displac:[],displace_atom:[],displace_box:61,displacemet:498,displai:[11,13,21,36,44,55,185,196,201,204,360,369,404,474],dispters:3,disregard:444,dissip:[6,9,40,88,89,238,245,252,297,320,342,343,399,411,412,421,438,439,474],dissolut:224,dist:[6,73,99,119,128,201,298,314,413,473,490,523],distanc:[],distinct:[6,233,312,375,458],distinguish:[6,94,151,258,416,494,522],distort:[175,392],distrbut:392,distribut:[],distro:[122,404,453,454],ditto:[8,12,14,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375,384,385,386,387,389,414,415,424,437,439,444,452,456,457,475,478,480,483,490,493,495,496,497,502,504,505,509,510,511,512,513,514,516,521,522,525,527],ethernet:17,etol:[384,386,490,509],etot0:305,etot:[6,104,106,107,121,152,163,205,233,253,267,305,512,513],eu2:176,eu3:176,euler:[384,386],eulerian:214,euqat:467,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,130,151,153,157,167,175,177,183,200,201,202,204,205,209,210,211,212,214,216,217,218,219,220,221,222,229,235,245,247,248,250,251,252,253,297,303,306,318,322,326,336,337,338,347,350,353,355,356,358,382,384,444,446,448,449,454,460,462,464,476,477,490,491,493,497,498,500,502,503,504,505,509,511,513,522,523],evaluat:[375,376,522],evalut:[358,493],evan:[165,292],evanseck:[6,19,183,402,507],evapor:[],evaul:[8,384],evdwl:[118,153,456,457,513],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,130,175,178,179,193,197,201,202,205,208,209,210,215,216,217,220,221,223,224,225,227,229,230,233,236,250,253,267,269,270,297,301,310,312,315,317,328,333,341,345,348,350,354,356,367,375,382,384,386,391,396,416,417,421,424,427,446,458,483,484,488,495,496,498,500,501,502,504,505,507,510,512,513,514,516,527],evenli:[3,41,57,152,197,223,255,427,484],event:[],eventu:[3,6,12,14,179,509],eventual:306,ever:[9,54,56,251,333],everaer:[405,420,458,474],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,130,139,165,180,201,202,203,204,205,206,208,209,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,234,236,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,317,319,321,330,333,335,336,337,338,339,340,341,344,345,346,347,348,356,358,374,376,386,387,388,391,411,413,424,437,456,457,464,470,489,490,491,495,497,499,500,502,503,504,509,510,511,513,517,522,527],everyth:[8,118,517],everywher:[127,431],eviri:416,evolut:[236,246,255,298,490],evolv:[255,298,346],ewald:[2,3,5,6,7,8,9,12,96,121,129,152,346,375,376,384,398,400,401,407,410,416,429,433,451,459,474,476,481],ewald_disp:410,ewalddisp:3,exact:[21,41,44,75,133,171,180,185,223,226,245,246,252,253,254,301,310,311,333,345,360,375,404,497,502,509,522,525,527],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,155,161,168,177,197,209,210,220,223,229,234,239,245,252,253,254,270,282,283,293,297,304,305,333,338,339,352,391,404,411,414,421,424,438,446,448,449,476,477,497,498,505,509,522],exager:516,examin:[6,8,16,226,297],examp:[493,522],exampl:[],exce:[3,6,15,16,17,41,60,75,179,216,217,220,221,223,227,229,234,241,269,297,312,317,323,324,333,384,391,495,522],exceed:[3,41,61,223,229,269,333,503],excel:416,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,177,181,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,205,208,211,217,218,220,222,223,227,229,237,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,318,319,329,333,339,345,353,356,357,358,359,360,361,362,364,365,368,369,370,375,376,378,381,385,386,387,389,390,391,392,393,395,398,399,400,401,402,403,404,405,406,407,409,410,411,414,415,416,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,442,447,450,451,453,456,457,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,492,493,495,497,498,500,503,504,505,506,507,509,513,516,521,522,523,526],exception:493,excess:[219,416],exchang:[2,3,6,8,63,64,208,214,215,236,244,248,252,307,315,341,345,348,375,391,416,510],exchange:375,excit:416,excite:416,exclud:[3,6,9,12,15,16,65,75,112,123,151,157,164,165,181,201,217,224,225,256,265,300,313,315,340,351,356,384,385,387,399,421,424,427,438,439,446,473,507],exclude:387,exclus:[1,3,12,15,95,183,406,444,446,504,514],excurs:[269,490],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,178,204,249,309,358,374,377,390,491,493,503,506,509,522],exempl:464,exemplari:245,exemplifi:416,exert:[6,250,253,285,310,352,353,354,376],exhaust:[214,390,522],exhibit:[100,236,248,269,383,416,504],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,133,177,178,196,203,204,205,208,213,222,225,227,230,244,300,301,303,304,356,357,359,361,362,363,365,369,379,385,412,424,456,473,484,491,493,495,496,497,506,507,508,517,522,523,525],exit:[2,3,11,12,41,59,201,223,374,390,493,494,503,512,522],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,151,201,506,522],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,158,169,175,197,223,235,244,246,266,296,302,304,305,310,315,356,376,387,404,441,444,446,490,493,495,497,500,504,509,522],expens:[6,75,205,296,300,315,345,356,375,376,387,391,493],experi:[6,13,14,222,230,249,258,268,302,314,315,382,386,411,446,504,509],experienc:[6,12,257,258],experiment:[16,244,375,391,509],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,157,165,197,201,202,204,205,208,217,218,221,223,225,227,229,269,285,296,304,315,329,356,358,374,375,378,385,386,390,396,414,427,464,466,482,493,496,497,500,502,505,516,517,522,527],explan:[3,6,61,124,151,201,202,217,268,296,424,489,492,493,495,504],explanatori:[3,8,128,201,202,216,217,220,315,385,492,522],explantori:[3,311],explic:445,explicit:[6,9,11,21,44,81,95,124,127,171,185,209,210,229,316,323,324,360,381,393,394,397,402,404,414,416,428,438,481,489,492,496,499,517],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,154,164,167,175,177,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,229,237,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,318,319,338,339,345,353,359,361,362,364,365,368,370,385,391,392,393,395,398,399,400,401,402,403,404,405,406,407,408,410,411,413,414,415,417,418,419,420,421,422,423,424,428,429,430,431,432,433,434,435,436,437,438,442,444,446,447,448,449,450,451,453,458,459,466,467,468,469,470,471,472,474,475,476,477,478,479,480,481,483,485,486,487,495,497,498,504,505,507,508,514,516,517],explictli:[15,508],exploit:[14,16,298],explor:[129,176],expon:[3,306,308,316,414,418,420,423,437,445,459],exponenti:[95,418,454,475,483,487,509,522],expos:11,exposit:[214,411,413],express:[6,151,163,177,209,210,227,266,296,306,316,345,351,358,397,414,416,431,441,464,465,474,522],expression:358,expressiont:397,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,130,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,202,208,211,212,215,221,222,228,231,235,236,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,318,321,326,329,330,332,336,337,338,339,340,342,343,345,347,350,354,355,420,441,444,457,458,465,512,513,521],extensiv:[65,208,513],extent:[1,3,41,42,45,59,75,175,179,201,213,223,250,352,355,375,378,393,460,462,476,477,492,495,498],exterior:[3,6,175,354],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,129,152,154,155,156,158,160,163,164,165,166,167,169,170,176,177,178,179,205,220,223,225,269,303,304,305,315,333,384,385,388,389,410,421,424,427,441,446,492,493,495,498,507,516,522],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,130,209,210,308,386,407,417,441,465,493,500,512],extract_atom:11,extract_comput:[11,493],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,204,219,227,229,269,343,416,479,516],extrema:437,extreme:416,extrins:214,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[173,347],f_a:[478,479,480],f_ave:128,f_c:479,f_f:480,f_fix_id:305,f_foo:522,f_harm:343,f_i:[28,454],f_id:[6,75,128,130,201,202,208,216,217,218,219,220,221,264,335,347,513,522],f_ij:454,f_indent:221,f_int:342,f_j:28,f_jj:99,f_k:454,f_langevin:345,f_max:[305,310],f_msst:267,f_r:[253,478,479,480],f_sigma:397,f_solid:343,f_ss:6,face:[3,6,59,61,75,165,175,179,213,350,352,353,354,355,378,420,441,458,495,498],face_threshold:175,facet:175,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,246,301,333,343,421,456,464,507],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,129,151,171,176,179,183,194,200,201,204,205,209,210,218,223,227,229,230,236,244,249,252,254,255,267,269,270,274,298,302,306,314,316,319,322,324,333,337,341,348,349,350,354,365,376,378,385,391,393,394,397,398,400,402,407,408,409,411,412,416,421,424,428,429,441,444,446,448,449,450,451,457,459,466,475,481,492,495,498,499,504,507,509,510,513,516,521,522],factori:[3,493],factoriz:375,fail:[3,9,11,12,61,181,227,230,375,384,386,409,457,493],failur:[132,461,494,522],fairli:[11,446,504,509,517],faken:77,falcon:249,fall:[3,6,205,220,301,493,522],fals:[94,356,464,522],fame:8,famili:[483,492],familiar:[0,11,517],fan:454,far:[3,6,12,16,59,61,63,94,201,202,205,206,223,224,225,227,230,269,296,314,315,333,350,361,365,382,386,387,482,493,495,500,513],farago:252,farrel:[478,480],farther:201,fashion:[6,8,41,75,177,205,208,209,210,215,223,225,230,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,321,325,332,335,343,345,349,350,351,353,355,386,424,438,498,507,522,526],fasolino:426,fast:[6,7,9,12,13,16,39,201,202,280,305,346,375,376,399,438,439,444,474,476,477,497,502,504,513,523,527],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,154,164,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,222,223,229,237,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,318,319,333,340,342,345,349,353,359,361,362,364,365,368,370,375,376,388,389,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,474,475,476,478,479,480,481,483,485,486,487,490,498,504,508,516],fastest:[1,6,16,165,345,346,391,492],fatal:[3,512],fault:[74,457],faulti:12,fava:420,favor:226,favorit:7,fbmc:340,fcc:[],fcm:[286,522],fcold:236,fdirect:233,fdotr:425,fdt:[],fdti:95,fe2:176,fe3:176,fe_md_boundari:214,featu:8,featur:[],fecr:414,feedback:[7,249],feel:[7,249,250,258,296,354,356,386,446],felling:443,felt:354,femtosecond:521,fene:[],fennel:[407,429],fep:[],ferguson:[6,183,507],fermi:[1,9,10,12,14,163,391,480],fermion:416,fernando:440,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,206,216,217,218,220,221,236,253,269,301,304,306,319,347,375,384,385,386,393,464,492,495,500,504,506,514,525],fewer:[1,3,11,14,15,63,258,504],fewest:3,fextern:242,feynman:298,fff:493,ffield:[406,417,456,457,464],ffmpeg:[3,12,204],ffplai:204,fft:[1,3,7,9,11,12,14,96,120,121,152,297,375,376,504],fft_inc:[12,376],fft_lib:12,fft_path:12,fftbench:[375,514],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:236,ficiti:473,fictiti:[6,211,212,235,242,246,298,314,407,429,433,473],field1:[496,500],field2:496,field:[],fifth:[6,329,418,450],figur:[1,3,8,12,305,492,493,517],fij:410,file0:296,file1:[11,13,240,296,344,358,385,500,502,506],file2:[11,13,240,344,358,385,500,502,506],file:[],file_from:203,filen:385,filenam:[3,12,13,37,41,56,197,201,202,204,205,206,214,217,218,219,220,221,223,228,239,240,296,300,303,306,307,308,311,312,315,316,317,344,345,372,373,374,385,386,392,393,397,407,414,415,417,418,426,441,442,443,448,449,450,454,455,456,457,464,465,475,476,477,478,479,480,483,491,492,493,496,497,502,506,513,522,525,526,527],filennam:502,filep:[3,201,202,205,497,502,527],filepo:312,fill:[7,9,177,204,301,345,378,387,397,444,457,498,517],filter:[205,214],final_integr:8,final_integrate_respa:8,finchham:[6,159,409],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,180,197,206,215,226,227,239,240,241,244,268,296,301,302,310,314,382,384,386,387,407,424,429,433,441,448,449,464,474,476,477,516,517,522],find_custom:8,fine:[15,16,181,211,235,343,387,391,517,522],finer:[151,177,522],finest:375,finger:[177,200,266,498],finish:[6,11,41,223,358,372,374,375,388,390,391,482,500,522,523],finit:[],finni:[7,414,474],finverse:233,fiorin:[9,228],fire:[],firebrick:205,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,138,141,144,145,149,152,162,165,171,173,175,176,178,179,180,184,197,201,202,203,204,205,206,208,209,217,218,220,221,223,226,229,239,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,319,321,329,330,331,333,334,335,342,343,344,345,347,351,356,358,359,366,378,384,385,386,387,390,391,392,393,396,397,398,400,402,404,406,407,414,416,417,418,421,422,424,425,426,427,428,429,433,438,439,441,443,444,446,448,449,450,454,456,457,464,465,473,475,476,477,478,479,480,483,487,490,491,492,493,495,496,497,500,502,504,507,508,509,512,513,516,517,522,523,524,525,527],fischer:[6,9,18,19,183,402,507],fit:[3,6,9,12,37,56,197,239,314,333,393,397,426,441,446,448,449,469,476,477,479,503,517,522],five:[77,163,305,385,397,442,495,509],fix:[],fix_deposit:3,fix_ehex07:[],fix_flux:214,fix_heat:236,fix_id:[3,227,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:517,fix_modifi:[],fix_nh:8,fix_nv:517,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:319,fix_reax_bond:456,fix_saed_vtk:317,fix_setforc:8,fix_shak:319,fix_srd:3,fixedpoint:[227,269],fixextern:242,fixid:214,fji:410,flag1:[232,389],flag2:[232,389],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,172,176,180,198,201,202,204,205,206,221,226,228,232,249,252,256,258,265,266,297,304,315,329,332,333,340,344,353,356,371,373,376,385,389,390,391,393,423,428,441,444,473,488,490,492,493,495,496,497,499,500,501,505,517,522],flag_buck:401,flag_coul:[401,410,433],flag_lj:[410,433],flagfld:[399,438,439],flaghi:[3,399,438,439],flaglog:[399,438,439],flagn:232,flagvf:[399,438,439],flat:[6,345,350,351,355],flavor:[2,7,12],fld:[350,438,439],flen:394,flex_press:394,flexibl:[3,6,8,178,204,217,228,246,270,341,348,416,479,513],flip:[3,6,229,269,352,353],floor:522,flop:12,floralwhit:205,flow:[],fluctuat:[6,66,95,227,244,245,252,255,269,274,296,297,302,320,343,345,368,412],fluid:[],fluid_veloc:259,flush:[3,205,512],flux:[],flv:204,fly:[7,9,12,41,204,208,214,219,230,233,315,319,346,397,444,513,516],fmackai:9,fmag:231,fmass:298,fmax:[384,513],fmomentum:233,fmsec:[2,205,252,253,266,269,302,315,336,337,504,515,521,523],fname:374,fno:[9,15],fnorm:[384,513],fnpt:233,fnve:236,fnvt:233,foce:424,fock:394,focu:319,fogarti:[9,308,457],foil:[151,296,465],fold:[331,504],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,130,151,152,155,156,157,163,165,170,173,175,177,178,183,186,187,188,189,191,192,194,195,197,201,203,204,205,208,214,215,216,217,218,219,220,221,223,228,229,230,233,234,238,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,317,319,335,336,337,338,341,342,343,344,345,347,348,356,357,361,362,363,364,365,368,370,373,37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44,301],insid:[2,3,6,8,11,75,140,146,177,201,202,205,216,230,231,236,241,244,250,255,258,301,315,333,350,352,353,354,355,356,373,378,493,494,495,497,498,505,522],inside:[255,431,493,509],insight:[6,13],instabl:[255,410,463],instal:[1,3,6,8,9,11,12,14,15,16,175,201,203,204,206,376,386,401,402,425,429,433,437,444,490,496,497,502,510,517,527],install:[],instanc:[6,9,11,209,228,246,352,419,424,446,454,493,516],instantan:[6,65,226,227,245,246,269,274,297,302,305,310,312,315,340,501,513],instanti:[6,11,12,214,424,492],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,155,159,181,183,197,201,202,210,217,220,221,223,227,228,244,252,255,258,259,297,303,304,313,315,335,353,373,375,376,379,387,391,400,401,414,428,430,437,441,444,447,474,481,490,498,502,509,511,516,522],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,154,164,175,183,184,186,187,188,189,191,192,194,195,197,199,204,211,222,229,237,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,318,319,353,359,361,362,364,365,368,370,376,391,392,393,395,398,399,400,401,402,403,405,406,407,410,411,414,415,417,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,442,447,450,451,453,458,459,466,475,476,478,479,480,481,483,485,486,487,498,504,516],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,16,39,40,63,77,112,114,177,178,197,201,202,204,205,211,224,225,230,235,237,241,242,244,247,252,265,303,304,313,315,333,345,350,354,355,356,358,374,385,387,391,405,420,424,452,458,476,488,492,493,495,496,500,503,504,512,513,522,523],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,130,151,175,177,180,181,183,187,188,192,197,200,201,204,205,215,217,224,225,226,230,232,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,333,335,337,340,344,345,364,375,378,399,411,412,413,427,441,456,457,461,463,465,490,492,493,494,495,503,504,505,509,512,522,523],integer:[3,495],integr:[],integral:[298,448,449],integrate_ulsph:[],intel:[],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,219,245,455,495],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,129,130,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,172,173,174,176,208,217,218,220,221,223,224,225,226,234,241,248,258,267,269,274,312,315,317,333,341,345,347,348,512,513,521],intensiv:[65,208,513],intepol:522,inter:[17,42,63,64,157,180,181,201,226,252,254,268,307,315,375,386,397,505,516,522,525,527],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,133,134,135,136,138,139,140,141,142,143,144,146,147,148,149,151,152,153,155,156,170,171,175,178,179,180,181,182,183,185,189,190,193,196,201,202,208,209,210,224,225,226,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,316,323,324,333,334,340,345,349,350,351,354,355,360,361,362,363,365,367,369,375,376,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,451,452,453,454,457,458,459,461,463,464,465,466,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,490,493,495,497,499,500,504,505,507,512,513,516,525],interatom:[3,4,7,9,10,177,201,268,342,343,392,397,414,416,425,441,444,464,479,522],intercept:129,interchang:6,interconnect:17,interconvert:416,intereract:39,interesect:354,interest:[1,5,7,8,9,11,13,75,176,298,340,343,376,415,439,456,457,493,522],interf:[391,517],interfac:[],interfer:[12,269,393],interg:[6,516],intergr:504,interi:439,interior:[3,6,41,354,498],interlac:441,interleav:[6,177,503],intermedi:[6,12,61,204,268,296,368,386,493,494,503,507],intermix:490,intermolecular:[153,393],intern:[],internal:[3,204,210,301,522],internal_element_set:214,internal_quadratur:214,internat:[129,176,214],internet:251,interpenetr:441,interpentr:[468,469,471],interpol:[6,14,37,56,110,197,204,205,214,239,240,255,296,375,376,386,397,446,448,449,457,470,476,477,478],interpret:[2,6,11,204,220,421,466,490,493,509,522],interrupt:305,intersect:[3,6,129,205,354,356,498],intersert:354,interspers:384,interstiti:[175,444],intertia:[3,103],interv:[3,6,99,203,218,252,269,305,310,311,324,464,470,490,509,522],intestieti:129,intial:[6,391,393],intiial:[41,500],intiti:[3,332],intra:315,intra_energi:244,intramolecular:[28,153,244],introduc:[6,9,100,117,204,236,269,305,310,315,368,375,392,407,416,429,433,437,475,509,522],introduct:[],intuit:378,inv:[129,176,317],invalid:[3,12,75,97,180,283,386,438,439,497],invari:[117,144,149,151],invent:319,invers:[],inverse:516,invert:[1,6,181,297],invis:354,invoc:[175,226,391,461,463,493],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,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90,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,410,411,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,483,485,486,487,489,490,491,492,493,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,512,513,514,516,517,521,522,523,524,525,527],young:[421,460,462],your:[],yourself:[6,8,12,13,227,385,517],yplane:351,ypo:177,ysu:[3,201,202,335,496],yuan:9,yukawa:[],yukawa_1_1:484,yxz:492,yzx:492,z_i:[416,480,487],z_j:[480,487],z_meam:441,zachari:13,zannoni:420,zbl:[],zblcut:480,zblcutinn:465,zblcutout:465,zblexpscal:480,zblz:465,zcm:315,zcylind:351,zepeda:215,zero:[],zeta:[3,255,306,417],zfactor:204,zflag:[164,165,256,258,265,315,340],zhang:[315,341,421],zhi:[3,6,179,201,213,344,350,353,355,495,498,513],zhi_bound:[6,201],zhou:[13,397,417,454,478,480],zhu:472,ziegenhain:13,ziegler:[300,441,474,480,487],zimmerman2004:214,zimmerman2010:214,zimmerman:[9,74,214,397],zlat:[229,250,513],zlib:[9,201],zlim:464,zlo:[3,6,179,201,213,344,350,352,353,355,495,498,513],zlo_bound:[6,201],zmax:[213,255,522],zmin:[255,522],zn2:176,zone:[129,317],zoom:[3,201,204,205],zorig:75,zplane:351,zr4:176,zrest:332,zsu:[3,201,202,335,496],zwall:350,zwall_veloc:255,zxy:492,zybin:457,zyx:492},titles:["LAMMPS 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.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx 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 manifoldforce 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/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle 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 rx 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/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","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/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 exp6/rx 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 multi/lucy command","pair_style multi/lucy/rx 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 table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":224,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,129,133,134,151,157,165,166,170,176,177,180,182,196,199,200,201,202,204,205,206,207,209,210,211,213,214,215,217,221,224,225,227,228,229,230,234,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,317,333,335,340,341,342,343,346,348,350,352,356,369,373,375,376,378,379,382,383,385,387,388,389,391,394,397,399,416,438,439,444,446,456,457,473,474,490,491,492,495,496,498,500,502,503,504,507,509,511,512,513,514,515,521,523,525,526],"function":522,"long":[219,398,400,401,402,403,407,409,410,429,433,437,451,459,481],"new":8,"static":12,acceler:1,account:517,ackland:66,acknowledg:7,adapt:[209,210],addforc:211,adding:517,addition:[12,13,517],addtorqu:212,adiabat:6,adjust_dt:322,adp:392,after:517,airebo:393,alloi:414,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:213,arrai:6,aspher:[6,90,155,271,275,279,280,289],asphere:9,atc:[9,214],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,151,152,175,213,215,216,304,522],atom_modifi:39,atom_styl:40,attract:5,aveforc:222,awpmd:[9,394],axel:517,balanc:[41,223],barostat:6,basal:70,beck:395,berendsen:[302,336],between:6,binary2txt:13,bodi:[6,8,42,71,156,272,276,281,290,396],body:9,bond:[8,13,72,73,224,225,226,311],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:397,born:[398,409],boundari:[7,59],box:[6,60,227],branch:517,brownian:399,buck:[400,401,409,440],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:517,change_box:61,charmm:[6,19,183,402,437],chunk:[6,69,75,79,86,98,103,114,116,125,157,172,174,217,330],citat:7,class2:[9,20,43,184,359,403],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,350,405,486],colvar:[13,228],colvars:9,com:[78,79,158],comb3:406,comb:[307,406],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,522],compute_modifi:112,condit:7,conduct:[6,341],constant:[6,522],constraint:7,contact:[80,131],coord:81,core:6,coreshell:9,correl:[218,219],cosin:[22,23,24,25,26,27,186],cossq:361,coul:[398,400,401,402,403,407,408,409,422,429,433,437,451,459],coupl:6,creat:225,create_atom:177,create_bond:178,create_box:179,createatom:13,creation:7,csld:337,csvr:337,cubic:431,cuda:[],custom:[8,201,202],cut:[49,394,400,403,407,410,416,419,429,430,437,445,451,481],cvff:362,damag:[82,132],data2xmovi:13,data:6,databas:13,deby:[407,429],defgrad:138,deform:[160,161,229],delete_atom:180,delete_bond:181,delta:23,deposit:230,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],diagnost:7,diel:408,dielectr:182,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:185,dihedral_styl:[2,183,184,186,187,188,189,190,191,192,193,194,195,196,197,198],dilat:85,dimens:199,dipol:[6,28,86,410],dipole:9,direct:233,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:200,distanc:363,distribut:[7,12],document:0,dpd:[9,88,89,411,412],drag:231,dreid:423,dreiding:6,drude:[6,9,162,232,233,253,516],dsf:[407,429],dsmc:413,dump:[6,8,201,202,203,204,206],dump_modifi:205,dynam:306,eam:[13,414],echo:207,edip:415,eff:[9,13,106,107,161,163,168,254,270,282,293,339,416],efield:235,ehex:236,eim:417,elastic:6,emac:13,energi:[134,412],enforce2d:237,ensembl:7,erot:[90,91,92,93],error:[3,133],evapor:241,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,518,519,520,521,522,523,524,525,526,527],exp6:418,exp:[26,186],expand:[46,432],extend:[8,11],extern:242,fcc:296,fdt:412,featur:[7,8,517,522],fene:[45,46],fep:[9,13,95,210],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242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\ No newline at end of file diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt index f6e1c53799..295961bce3 100644 --- a/doc/src/fix_spring_chunk.txt +++ b/doc/src/fix_spring_chunk.txt @@ -35,13 +35,13 @@ of a compute com/chunk command defined in the input script. It is used to compute the COMs of each chunk. At the beginning of the first "run"_run.html or -"minimize"_miminize.html command after this fix is defined, the -initial COM of each chunk is calculated and stored as R0c, where C is +"minimize"_minimize.html command after this fix is defined, the +initial COM of each chunk is calculated and stored as R0m, where M is the chunk number. Thereafter, at every timestep (or minimization -iteration), the current COM of each chunk is calculated as Rc. A -restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each +iteration), the current COM of each chunk is calculated as Rm. A +restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each atom in each chunk where {K} is the specified spring constant, Mi is -the mass of the atom, and Mc is the total mass of all atoms in the +the mass of the atom, and Mm is the total mass of all atoms in the chunk. Note that {K} thus represents the spring constant for the total force on each chunk of atoms, not for a spring applied to each atom.