lammps/doc/html/searchindex.js

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7,438,461,476,501,519],adjust_radiu:324,adjust_radius_factor:324,admiss:275,adof:[158,218],adopt:[315,512],adp:[],adri:[9,312,453,454],adust:172,advanc:[3,250,396,486,497],advantag:[1,6,8,11,14,18,40,41,42,226,390,415,500,505],advect:[3,6,332],advertis:8,advis:[385,452],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,223,224,227,228,229,230,232,233,243,249,251,253,259,267,271,272,273,274,276,277,278,284,290,291,293,295,316,317,330,344,354,367,374,381,382,383,385,386,387,390,416,437,438,445,488,489,491,493,494,496,499,501],affin:[16,17,18,232,390,405],afil:247,aforement:18,afresh:[304,499,518],afshar:410,after:[],afterrun:499,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,232,249,302,358,373,385,437,438,486,488,489,491,493,498,505,507,518,521],against:[11,12,13,67,233,385,453,454],aggreg:[6,12,69,72,74,85,103,120,127,249,266,314,316,330,486,519],aggress:[249,505],agilio:[9,13],agre:[3,8,198,383,392,425,454],agreement:[5,7],ahd:422,ahead:351,aidan:[0,5,7,9,13,377],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,250],aktulga:[7,9,309,454],al2o3:461,al2o3_001:[130,317],al3:177,ala:[256,461],alain:9,alat:[297,440],alb:[451,474,476],albeit:315,albert:9,alchem:[96,172],alcohol:347,alcu:[391,396],alcu_eam:451,alderton:409,alejandr:[270,271],alessandro:13,algebra:443,algorithm:[0,1,6,7,8,9,42,64,206,215,226,229,232,256,258,259,284,299,307,316,319,320,339,340,344,347,352,381,382,383,387,390,412,416,438,443,458,460,486,488,505],alia:[9,16],alias:[1,375],aliceblu:206,align:[6,9,12,29,42,76,180,198,222,226,251,377,491,494,512],alkali:416,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,262,263,265,266,268,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,311,312,313,314,315,316,317,318,319,320,321,322,323,324,328,329,331,332,333,334,335,336,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,357,358,359,363,368,370,372,373,374,375,376,377,380,383,384,385,386,387,389,390,391,392,393,395,396,397,399,400,401,402,403,405,406,409,410,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,453,454,455,456,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506,508,509,510,512,513,517,518,519,521,522,523],allen:[29,96,409,419],allentildeslei:96,allign:3,allindex:356,alloc:[3,5,6,8,9,11,12,63,243,346,384,386,390,449,454,491,499],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,42,56,58,59,60,61,62,64,65,66,82,101,118,120,154,156,157,158,171,176,177,178,180,186,197,198,199,202,203,205,206,207,209,210,212,214,215,216,218,219,220,221,222,223,224,226,228,229,230,231,232,233,237,238,243,245,246,247,248,250,253,256,259,260,265,267,270,271,297,301,302,303,304,305,306,310,316,317,319,321,323,324,328,332,339,340,341,342,344,345,346,347,348,349,355,357,359,368,370,374,375,377,383,384,385,386,389,390,392,393,396,397,398,399,400,401,406,414,416,420,421,422,423,428,432,437,438,443,445,451,454,455,458,460,461,470,477,480,482,484,486,489,491,493,494,495,496,497,498,501,503,504,505,508,509,513,518,519],almost:[2,3,12,63,251,306,344,375,387,390,470],alo:406,alon:[6,7,229,312,453,454,489],alond:13,along:[6,8,12,29,41,76,96,130,176,177,178,201,202,205,218,229,251,256,257,261,262,267,269,306,316,319,321,325,329,330,339,343,344,350,353,355,377,379,381,382,383,385,406,409,420,423,426,428,432,440,453,454,473,491,494,501,502,518],alonso:[441,442],alpha:[6,12,52,210,256,306,307,311,383,391,394,397,406,410,412,414,415,417,422,427,428,440,446,450,475,477,509,512],alpha_c:436,alpha_i:462,alpha_lj:436,alphabet:[2,3,22,37,45,56,66,186,197,209,359,368,384,403,471,491],alphanumer:[3,66,209,305,313,357,384,518],alreadi:[3,7,8,9,12,16,17,18,43,58,178,179,181,204,214,218,222,223,226,228,232,260,304,306,332,355,356,384,385,410,421,423,430,438,470,480,483,487,491,492,496,501,517,518],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,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03,306,308,316,320,321,332,335,336,339,340,341,342,349,358,367,369,374,375,382,385,392,397,401,402,405,406,407,409,410,412,416,418,419,421,422,428,432,433,436,440,444,445,448,461,470,477,500,503,505,512],chemic:[9,130,172,177,202,203,215,216,245,307,312,313,339,375,453,454,466],chemistri:[306,307,309,392,396,416,453,454],chen:344,cheng:405,chenoweth:[453,454],chenoweth_2008:[453,454],chi:[103,167,201,297,307,309,370,417,419,519],chiefli:452,child:8,chip:[7,9,17,18,390,504],chipot:231,chiral:367,chmod:[11,12],cho:440,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,222,223,226,229,232,233,247,253,256,268,270,299,303,307,316,339,368,375,381,382,385,387,390,423,436,445,449,491,500,501,504,505,511,512,517],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,227,228,229,230,233,242,253,256,268,270,272,273,274,275,276,277,278,302,303,320,332,336,350,374,375,382,480,486,488,500,506],chose:[474,476],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,230,233,242,245,246,254,256,268,270,275,299,302,313,332,336,339,340,345,347,348,354,375,376,382,390,411,412,416,420,427,430,456,474,486,500,505,506,512],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,248],ciccotti:319,cieplak:[6,184,503],cii:219,cij:219,ciko:2,circl:[43,76,328],circular:[3,6,156,200],circumst:18,circumv:[101,118,311],citat:[],cite:[3,7,8,12,253,461],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,409],clarifi:[7,474,476],clariti:357,clark:448,class2:[],classic:[0,3,5,6,7,8,9,243,299,306,311,344,369,416],classifi:[471,479],claus:489,clean:[6,12,14,15,17,499],cleanli:[490,522],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:495,click:[2,11,22,37,45,56,178,186,197,205,250,359,368,385,403,471,513],client:[250,252],climb:[269,385,505],clinic:[7,13],clo:[167,201,519],clock:[12,486,505],clockwis:350,clone:513,close:[3,6,11,12,13,40,42,71,76,153,181,202,228,229,230,247,254,256,270,286,293,316,319,350,353,373,375,378,381,382,385,390,392,396,406,407,426,440,445,453,457,459,473,476,495,501,512,513,515],closer:[3,10,42,128,176,201,202,226,230,234,341,385],closest:[228,297,316,347,419,455,470,480],cloud:[461,512],clovertown:18,clsuter:77,clump1:[301,316],clump2:[301,316],clump3:[301,316],clump:316,cluster:[],clutter:3,cmap:491,cmatrix:247,cmax:440,cmd:[11,12,299,502],cmdarg:11,cmin:440,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:[9,13],cnt:[423,495],co2:[41,177,319,384],coars:[7,9,10,29,36,41,55,190,301,316,332,421,456,500,503],coarser:[375,518],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,358,359,365,403,423,427,445,458,460,463,491,520],coeffcient:491,coeffici:[],coefficienct:410,coefficient0:414,coefficient1:414,coeffieci:[6,394,426],coeffincientn:414,coexist:[245,416],cohes:[6,417,440],coincid:[134,353,401,437,438,486],colberg:204,cold:[6,163,245,249,386,512],coldest:340,coleman8:9,coleman:[9,130,177,317],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,266,301,311,314,316,355,374,384,386,404,491,498,504,510,523],collid:[237,332,354],colliex:177,collinear:[3,301],collis:[3,256,332,350,354,413,420,483],colllis:332,colloid:[],colombo:40,colon:[207,355,492],color1:206,color2:206,color:[3,9,42,202,205,206,226,246,306,311],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,267,268,306,316,333,334,344,354,418,422,453,454,492,506,508,518],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:390,comb3:[],comb:[],comb_1:308,comb_2:308,combiant:407,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,262,270,286,292,299,305,320,336,345,353,356,358,374,375,377,382,390,404,406,407,412,416,417,423,435,436,462,472,474,476,477,479,482,494,499,504,512,518,520],come:[],comfort:[12,13],comit:513,comm:[0,3,11,12,64,78,204,250,252,253,375,385,390,410,445,450,473,493],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,241,254,316,344,384,385,391,414,415,417,427,440,447,454,461,462,472,473,474,475,476,479,488,489,491,512,513,518],commerci:7,commit:[9,513],commmand:[3,6,12,62,119,294,426,485,486,488,505,522],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,369,421,430,462,474,476,491,494,503],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,270,298,305,307,308,309,316,320,332,344,355,372,374,386,387,388,390,412,413,449,484,488,489,500,501,518,521,523],communc:374,comp:[7,204,252,253,286,292,319,375,385,416,445,450,455,469,473,475],compact:[66,209,403,471],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,236,307,355,357,374,375,383,385,440,461,486,505,506,512,517],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:379,compass:[7,9,21,22,37,44,45,56,185,186,197,358,359,368,402,471],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,298,310,336,339,346,349,352,374,390,424,443,445,473,488,489,518],compens:[6,227,228,314,386,416],compet:343,competit:375,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,343,375,390,443,491,492,496,518],compl:17,complain:[11,12,17],complement:440,complementari:[7,406,428],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,299,302,305,332,343,345,356,357,373,385,390,417,458,460,478,486,491,496,499,503,505,508,512,518],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,286,328,353,372,385,416,443,473,489,491,494,518],compli:[339,343],complic:[6,7,9,12,13,216,245,489],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,298,299,300,303,314,316,318,319,321,325,326,329,332,335,336,337,339,346,347,352,353,354,374,377,382,383,384,385,390,410,416,420,437,438,458,460,461,462,491,492,501,509,518,519],componenet:6,composit:[6,216,256,414],compound:[405,416,417,479],compres:[76,126,218],compress:[],compris:[41,353,455,478],compton:[130,177],comptu:3,compuat:375,comput:[],computation:[3,6,227,228,344,396],computational:512,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,317],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,522],concav:353,concentr:[76,414],concept:[6,158,168,218,500],conceptu:[3,6,76,166,230,232,385,406,423,440,496],concern:[6,78,96,204,246],concetr:76,concis:[11,343],conclud:12,concret:8,concurr:[16,375,518],conden:[344,474,476],condens:[6,160,344,392,408,414,428,479],condit:[],conducit:6,conduct:[],cone:494,confer:443,confid:[3,505],config:[12,202,488],configfil:231,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,230,231,232,233,237,245,252,253,284,299,307,343,372,383,385,392,396,415,440,443,472,474,476,479,486,491,493,494,505,513],confin:[491,505],conflict:[3,12,41,203,445,489,513],conform:[3,6,13,62,229,230,269,315,321,343,367,385,416,503],confus:[3,479],conjuct:[9,410],conjug:[7,8,253,382,416,453,454],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,284,302,303,307,308,309,311,316,320,332,340,347,352,374,375,385,397,399,403,406,410,416,422,428,445,448,456,477,491,494,498,512,523],connect:[3,6,9,96,163,181,229,250,301,316,319,329,379,385,407,420,453,454,470,476,488,489,491,495,512],conner:392,connor:392,conput:3,consecut:[3,11,12,40,76,178,206,210,211,233,250,251,406,428,432,486,492,494],consequ:[1,6,216,344,427,505],conserv:[],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,271,298,316,339,340,343,344,347,375,403,416,423,454,455,461,470,486,487,489,492,493,494,496,499,501,509,512,518],consider:[6,8,253,254,335,336,337,390,500],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,303,306,311,313,315,316,335,336,337,338,348,374,375,377,379,384,385,390,392,396,398,404,406,416,419,423,426,437,438,440,443,445,455,458,460,461,473,480,489,491,492,493,494,495,496,503,512,518],consistent_fe_initi:215,consit:316,constant:[],constitu:[3,6,259,316,349,353,404,455],constitut:[458,460],constrain:[3,6,8,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,233,245,246,251,259,262,264,286,292,301,302,314,316,319,330,340,347,383,384,416,496,503,512],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,270,298,315,353,386,390,409,443,445,470,472,473,494,495,510,518],constructor:[8,11],consult:454,consum:[1,311,449,518],consumpt:372,contact:[],contact_stiff:[457,459],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,268,284,297,298,301,302,304,305,306,309,313,316,317,322,332,339,343,344,353,354,357,373,375,384,385,388,389,391,392,393,396,405,406,409,414,415,416,423,424,440,443,447,451,452,453,454,462,472,473,474,475,476,477,479,486,487,488,489,491,492,493,494,496,498,500,503,505,506,508,509,512,513,518,521,523],content:[4,8,9,12,18,454,507,509],context:[3,6,8,12,17,128,129,206,227,228,233,301,313,348,382,482,491,498,507,517,518,519],contibut:75,contigu:488,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,300,302,305,306,316,317,321,331,332,334,341,342,344,350,353,357,373,389,390,396,410,413,430,433,453,454,455,458,460,475,486,489,491,493,494,499,505,506,508,509,518,521],continuum:[6,7,9,215,344,458,460],contour_integr:215,contract:[62,230,232,270,303,316],contradictori:3,contrain:319,contraint:284,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,232,355,458,460,482,522],contrib:344,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,223,224,230,245,253,256,259,260,265,271,293,294,301,302,310,313,316,317,319,346,374,383,385,393,410,413,414,416,423,437,438,443,445,453,454,461,503,509,512,513],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,226,230,231,232,249,250,253,254,270,272,273,274,275,276,277,278,303,308,316,323,324,335,336,337,344,348,372,374,387,416,419,443,453,454,457,459,472,476,486,488,500,506,507],control_typ:215,controlfil:454,convect:100,conveni:[6,12,29,202,207,224,317,377,462,477,513,518],convent:[3,8,29,189,196,197,203,206,315,329,356,414,416,518],converg:[3,6,42,97,202,203,205,207,212,226,229,230,238,243,275,286,292,306,308,311,315,319,381,382,383,385,405,406,428,461,486,498,505],convers:[3,8,152,205,206,216,219,303,374,406,407,408,416,428,432,436,448,489,505,517],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,268,302,305,355,358,360,364,367,377,385,391,414,443,474,476,483,489,491,492,493,498,508,512,517,518,521,523],convex:[43,353],convinc:[7,12],cook:9,cooki:7,cool:[7,168,249,314],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218,222,223],coord2:[3,126,218,222,223],coord3:[3,126,218,222,223],coord:[],coordb:461,coordbb:461,coordiat:383,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,301,302,303,313,314,316,318,319,321,326,329,330,331,332,334,342,343,344,351,352,354,355,377,383,384,385,390,391,392,395,415,461,486,491,492,493,494,496,499,501,505,512,518,519],coordn:[126,218],copi:[0,3,4,8,9,11,12,15,17,41,131,205,344,385,403,453,489,513],copper:483,coproccesor:16,coprocessor:[1,7,9,16,17,390,504],coproprocessor:17,copy_arrai:8,copyright:[7,8,301],coral:206,core:[],core_shel:160,coreshel:[],cornel:[6,184,503],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,353,354,377,478,491,513],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:405,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,232,245,247,253,270,271,293,301,303,306,343,349,353,374,385,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,483,484,491,506,509,512,513],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,264,270,271,309,316,319,329,331,350,353,385,386,390,408,438,443,488,489,491,501,513,517,519],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,298,299,303,308,316,318,319,335,337,339,348,349,350,352,353,354,356,358,359,360,361,363,364,367,369,375,380,382,384,385,391,392,394,397,398,399,400,401,402,403,404,405,406,409,410,414,415,416,417,418,419,420,421,422,423,426,428,429,430,431,432,433,434,435,436,437,440,441,443,445,446,447,448,450,451,453,454,455,456,461,462,463,472,473,474,475,476,477,479,481,482,483,486,488,489,491,492,494,504,505,506,508,509,512,518],correspondingli:[437,438,500],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,222,223,226,227,228,242,270,308,344,374,375,388,406,428,432,443,445,472,488,500],costheta0:[472,474,476,479],costheta:451,costli:[11,97,247,386],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,305,306,307,311,314,316,318,332,333,339,343,344,345,349,353,355,357,365,371,373,381,383,386,390,393,418,422,423,426,453,454,487,488,489,491,493,495,498,499,506,507,512,518,519],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,307,309,345,374,375,383,390,397,399,400,401,402,405,406,407,408,409,416,420,421,423,428,432,436,439,445,448,453,454,456,461,471,476,477,479,482,496,503,509,512,517],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,270,284,302,319,335,336,353,375,383,384,385,387,390,418,422,445,509,518],counter:[3,350,486,497,499,505],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,316,486],counterproduct:18,coupl:[],courant:322,cours:[3,8,138,140,172,202,210,211,246,315,329,343,349,351,352,354,355,375,437,463,488,491,504,512,518,521],courtesi:377,cov:461,coval:[6,9,29,416,440,461,512],covari:247,cover:[6,12,76,198,206,215,256,416,478],coverag:[76,222],cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,319],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,345,372,375,390,403,471,486,504,505,508,509,510,518],cpuremain:509,cr2:177,cr3:177,crack:[4,386],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,386,512],craympi:390,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:301,criteria:[3,128,179,205,206,227,228,229,265,383,450,478,493,496,518],criterion:[12,42,133,178,181,216,226,229,245,284,308,322,350,355,383,385,405,416,420,461,496,505,506],criterioni:505,critic:[6,49,50,268,339,344,383],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,267,269,293,316,325,329,331,340,347,359,377,385,401,410,413,414,421,422,423,428,430,432,451,456,458,460,474,476,483,491,495,501,521],crossov:1,crossterm:491,crozier:[0,7,13],crucial:306,crystal:[3,4,6,13,78,118,297,298,342,377,386,491,495,509,512],crystallin:[6,114,298,377,475,512],crystallis:339,crystallogr:[130,177],crystallograph:[377,509],crystallographi:[130,177,377],cs1:177,cs_chunk:6,cs_im:[41,491],cs_re:[41,491],csanyi:[152,452,462],cscl:440,csequ:6,csh:[11,12,403],cshrc:[11,12],csic:[415,472,474,476,479],csinfo:6,csisi:[415,472,474,476,479],csld:[],cst:414,cstherm:6,cstyle:488,csvr:[],ctcm:[391,414],ctemp_cor:236,cterm:321,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:440,cube:[6,42,176,181,226,236,353,377,512],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:396,cummul:[3,6,224,227,228,229,231,242,247,253,255,332,335,336,337,338,340,347,422,509],cumul:[6,216,218,221,222,223,237,245,253,268,270,275,284,316,317,385],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,267,270,271,276,277,278,284,286,290,291,292,293,295,301,302,307,308,310,313,314,315,316,319,320,321,322,323,324,325,326,328,330,331,332,335,336,337,343,344,347,348,349,350,351,352,354,355,357,372,373,374,375,378,379,380,382,383,384,385,390,396,403,405,409,414,416,417,420,423,424,427,437,438,440,441,442,445,451,453,454,457,458,459,460,463,474,476,477,480,486,487,488,489,491,492,493,494,495,497,498,499,501,503,505,506,508,509,513,518,519,520,521,522,523],curv:[6,178,245,286,292,298],curvatur:[419,455,483],custom:[],cut0:489,cut1:500,cut2:500,cut:[],cuthi:[297,309],cutinn:[398,437,438],cutlo:[297,309],cutmax:451,cutoff1:[402,409,428,432,436,439,448,456],cutoff2:[397,399,400,402,408,409,428,432,436,439,448,456,477],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,297,306,307,309,311,313,316,320,332,345,349,353,355,372,374,375,383,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,454,455,456,461,462,463,464,465,466,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,489,493,496,500,512,518],cutoffa:415,cutoffc:415,cuu3:414,cval:177,cvd:339,cvel:321,cvff:[],cwiggl:[3,267,349,352,354,518],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,251,292,302,350,353,379,494],cylinder_d:379,cylindr:[6,251,329,350],cypress:390,cyrot:396,cyrstal:298,d3q15:256,d3q19:256,d_double_doubl:15,d_e:344,d_flag2:305,d_flag:305,d_name:[125,202,305,334,501],d_single_doubl:15,d_single_singl:15,d_sx:305,d_sy:305,d_sz:305,daan:342,dai:12,daili:12,daivi:293,damag:[],dammak:311,damp:[3,6,209,214,253,254,255,260,270,271,275,292,303,306,307,311,316,335,336,348,350,351,382,383,385,397,399,401,406,409,416,420,428,436,448,456,471,477,505,512],damp_com:254,damp_drud:254,dampen:[316,512],dampflag:[350,420],dan:17,danger:[3,12,245,355,410,509],dangl:181,daniel:9,darden:[375,409],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:307,dash:[420,508],dat:[6,100,198,215,487],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:[0,4,6,12,13,201,453,454,518],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:439,davi:349,david:[9,19,374,375,474,476],daw:[414,451],dbg:14,dcd:[3,6,7,202,204,205,206,207,299,492,496],ddim:201,deactiv:436,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,299,304,372,374,390,424,445,480,489,490,498,501,508,518],deby:[],decai:[101,406,483],decid:[3,6,12,16,76,267,305,316,345,506,513],decipher:377,deck:305,declar:204,declin:332,decod:205,decompos:[96,462],decomposit:[3,5,7,18,65,215,299,320],decoupl:[6,512],decreas:[3,202,203,212,213,220,229,232,238,243,245,253,343,374],decrement:321,deepli:371,deeppink:206,deepskyblu:206,def:[12,13,489],defaul:64,defect:[6,75,176,443],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,237,238,240,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,301,302,303,305,307,309,314,316,317,318,319,322,326,330,332,334,335,336,337,338,340,341,342,344,346,347,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,372,374,375,377,380,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,406,407,409,410,411,412,413,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,438,439,443,444,445,446,447,448,450,451,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,491,492,494,495,496,497,500,501,502,503,505,506,508,509,512,514,515,516,517,518,519,520],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,223,224,232,240,251,275,317,334,346,349,352,354,356,368,372,384,393,396,404,411,412,416,426,451,458,460,462,478,489,491,493,500,502,517,518],defint:509,deform:[],deg2theta:177,deg:512,degener:[3,301],degrad:[8,18,298,375,500],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,315,316,319,335,336,337,342,358,360,364,367,369,383,409,414,422,501,509,512,519],degress:[158,218],del:505,delai:[3,6,12,386,413,509],deleg:423,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,270,317,335,336,355,357,373,384,386,389,445,470,491,492,493,494,502,503,508,513,514,516,518,519],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[489,518],deloc:[271,416,461],delr:440,delt_lo:505,delta:[],delta_1:396,delta_3:396,delta_7:396,delta_conf:3,delta_ij:[440,451],delta_pi:396,delta_r:451,delta_sigma:396,delx:201,delz:201,demand:311,demo:11,demon:296,demonstr:[306,440],den:302,dendrim:422,dendtrit:379,denniston:[9,256,258,259,260,298],denomin:[7,183],denot:[130,236,254,298,309,311,406,421,423,454,458,460],dens:[76,229,416],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,222,223,226,232,243,256,259,263,264,298,302,303,305,307,344,349,377,380,384,391,392,396,414,440,441,442,451,455,461,465,467,468,469,491,500,501,509,517],density_continu:460,density_summ:460,dent:379,depart:[0,7],departur:[268,306],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,21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5,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,299,301,303,306,307,308,311,314,316,319,321,329,330,332,335,336,337,340,341,342,344,347,348,349,350,353,357,358,368,371,373,374,375,377,378,381,382,384,385,387,388,389,390,391,392,396,400,401,403,404,405,410,411,412,414,416,419,420,421,423,426,428,429,431,432,439,440,441,442,444,445,447,451,453,454,455,456,457,458,460,461,462,463,471,472,473,474,476,478,479,482,485,486,488,489,491,493,494,495,496,499,500,501,503,505,506,508,509,510,512,517,518,519,521],differenti:[1,3,6,29,198,374,406,451,475],difficult:[230,299,390,422,500],difficulti:[101,118,319,453],diffract:[],diffus:[],digit:[2,3,206,357,443,518],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:228,dihydrid:416,dij:319,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,222,232,251,350,377,440,494,517,518,519],dimdim:518,dimems:298,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,222,269,298,344,377,381,385,451,491,501],dimensionless:[116,133,134,136,139,141,143,148,152,344,375,462,482],diment:3,dimentionless:147,dimer:[6,316,440],dimgrai:206,dimstr:[42,226],dinola:[303,335],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,202,203,334,512],dir1:502,dir2:502,dir:[1,3,4,8,10,11,12,268,297,306,331,451,453,454,489,502,518],dirac:152,direc:451,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,238,247,251,256,298,317,336,348,350,351,352,353,377,382,390,391,392,397,399,400,406,409,414,416,428,432,445,448,456,470,489,501,502,503,509,518],directoi:14,directori:[],disabl:[3,12,16,344,427,489,504,518],disadvantag:[6,226],disallow:[202,232,270],disappear:493,discard:[2,3,42,76,220,222,226,345,353,488,493,494],discontinu:[198,383,434],discourag:440,discov:[13,345],discret:[6,8,41,43,205,206,253,256,292],discuss:[],disk:[6,93,94,101,171,200,233,245,302,489],disloc:[75,443],disord:[40,75,443],disp:[],dispar:455,disperion:[409,432],dispers:[3,6,7,9,176,298,374,375,400,409,432,437,445,454,473,479],displac:[],displace_atom:[],displace_box:62,displacemet:494,displai:[11,13,22,37,45,56,186,197,202,205,359,368,403,471],dispters:3,disregard:443,dissip:[6,9,41,89,90,240,246,253,298,320,341,342,398,410,411,412,420,437,438,471],dissolut:227,dist:[6,74,100,120,129,202,299,315,413,470,486,519],distanc:[],distinct:[6,236,313,374,455],distinguish:[6,95,152,259,416,490,518],distort:[176,391],distrbut:391,distribut:[],distro:[123,403,450,451],ditto:[8,12,14,15,16,17,18,43,127,228,483,489],div:8,divd:129,diverg:[3,12,40,316,342,392,493,512,521],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,226,232,297,340,347,352,374,383,385,417,454,461,479,500,508,518],divis:[6,256,396,426,436,488,509,518],dl_poli:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,343,491,492,496],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,202],dlen:501,dlmp_intel_offload:[9,16],dlo:[62,201,232,302],dlopen:6,dlvo:[7,404,482],dm_lb:256,dmax:[332,381],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,223,224,233,245,253,254,265,270,271,276,277,278,282,290,291,293,294,295,302,305,316,329,332,335,336,337,346,350,353,355,357,359,368,373,383,384,385,390,391,392,395,403,405,406,414,415,417,422,423,425,426,440,441,442,445,447,450,451,452,462,471,472,474,476,478,479,489,491,492,493,494,496,499,500,501,508,509,513,518,519,521,522],docuement:455,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,222,225,226,228,229,230,232,236,238,241,242,245,246,249,251,253,254,256,259,266,270,271,272,273,274,276,277,278,290,291,292,293,294,295,303,304,305,309,311,314,316,332,335,337,339,340,344,347,348,349,352,353,354,355,360,361,362,364,365,367,373,374,375,376,377,384,385,386,391,392,393,394,395,396,398,400,401,402,404,405,406,407,409,410,413,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,437,438,440,441,442,443,445,451,452,453,454,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,474,475,476,477,478,479,481,482,483,484,486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6,230,232,233,238,245,246,248,249,251,253,254,256,259,260,267,268,275,286,287,297,299,302,304,306,307,308,311,313,315,316,318,321,326,328,335,336,337,340,341,342,344,346,347,349,352,354,355,357,373,377,383,385,386,387,389,390,405,410,412,418,419,422,426,437,443,444,451,453,454,455,457,458,459,461,462,463,473,478,479,483,487,488,489,491,493,494,498,499,502,505,507,509,518,519],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,230,236,237,240,241,247,253,254,256,259,268,269,270,271,275,293,297,299,306,307,311,319,320,332,340,344,347,349,350,352,354,367,374,375,379,404,409,410,412,416,417,420,425,437,438,440,445,455,458,460,465,466,468,469,483,512],equi:271,equidist:269,equil:[3,307,378,498,523],equilater:501,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,229,230,245,268,270,271,293,294,303,306,307,308,309,340,341,342,347,405,406,453,454,487,501],equilibria:347,equilibribum:[227,228],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,230,232,245,246,247,254,256,270,275,293,306,307,311,315,319,321,329,332,339,340,342,347,358,360,364,367,405,440,447,461,512],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,224,230,232,245,253,270,293,303,315,316,352,392,410,416,461,474,476,477,491,494,499,500,509,512],equlibrium:6,equliibr:[307,309],er3:177,eradiu:[41,125,203,416,491],eras:[318,341],erat:[232,438],erc:406,erfc:[406,428,445],erforc:[125,203],erg:517,erhart:[216,414,474,476],ermscal:393,ernst:9,eror:3,eros:440,erose_form:440,erot:[],errata:[474,476],erratum:349,erron:3,error:[],erta:420,ervel:[125,203,491],escap:[233,512],especi:[8,16,166,178,209,216,226,245,306,311,314,315,390,488],espresso:[9,310],essenti:[8,11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,275,298,348,375,392,406,428,476,496,509],essex:29,establish:[96,249],estim:[1,3,6,10,12,38,42,57,100,153,215,226,237,268,332,339,374,375,381,445,454,473,505,509],esu:517,esub:440,eta:[6,256,270,306,307,309,348,415,417,419,451,475,479,517],eta_dot:270,eta_ij:451,eta_ji:417,etag:[41,491],etail:509,etap:270,etap_dot:270,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,270,302,313,317,344,345,353,357,373,374,383,384,385,386,388,414,415,423,436,438,443,449,453,454,472,474,476,479,486,489,491,492,493,498,500,501,505,506,507,508,509,510,512,517,518,521,523],ethernet:18,etol:[383,385,486,505],etot0:306,etot:[6,105,107,108,122,153,164,206,236,254,268,306,508,509],eu2:177,eu3:177,euler:[383,385],eulerian:215,euqat:464,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,298,304,307,318,322,326,335,336,337,346,349,352,354,355,357,374,375,381,383,390,443,445,451,457,459,461,473,486,487,489,493,494,496,498,499,500,501,505,507,509,518,519],evalut:[357,489],evan:[166,293],evanseck:[6,20,184,401,503],evapor:[],evaul:[8,383],evdwl:[119,154,453,454,509],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,268,270,271,298,302,311,313,316,317,328,332,340,344,347,349,353,355,366,374,381,383,385,390,395,416,417,420,423,426,445,455,479,480,484,491,492,494,496,497,498,500,501,503,506,508,509,510,512,523],evenli:[3,42,58,153,198,226,256,426,480],event:[],eventu:[3,6,12,15,180,307,505],ever:[9,55,57,252,332],evera:[404,419,455,471],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,302,303,304,305,306,307,308,309,311,313,314,316,317,319,321,332,334,335,336,337,338,339,340,343,344,345,346,347,355,357,373,375,385,386,387,390,410,413,423,436,453,454,461,467,485,486,487,491,493,495,496,498,499,500,505,506,507,509,513,518,523],everyth:[8,119,513],everywher:[128,430],eviri:416,evolut:[247,256,299,486],evolv:[256,299,345],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,345,374,375,383,397,399,400,406,409,416,428,432,448,456,471,473,477],ewald_disp:409,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,302,311,312,332,344,359,374,403,493,498,505,518,521,523],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,271,283,284,294,298,305,306,332,337,338,351,390,403,410,414,420,423,437,445,473,493,494,501,505,518],exager:512,examin:[6,8,17,229,298],examp:[489,518],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,270,298,313,317,323,324,332,383,390,491,518],exceed:[3,42,62,226,232,270,332,499],excel:416,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,299,308,309,316,318,319,329,332,335,337,338,344,348,352,355,356,357,358,359,360,361,363,364,367,368,369,374,375,377,380,384,385,386,388,389,390,391,392,394,397,398,399,400,401,402,403,404,405,406,408,409,410,414,415,416,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,441,446,447,448,450,453,454,455,456,463,471,472,473,474,475,476,477,479,481,482,483,486,488,489,491,493,494,496,499,500,501,502,503,505,509,512,517,518,519,522],excess:[220,416],exchang:[2,3,6,8,64,65,209,215,216,245,253,308,316,340,344,347,374,390,416,506],exchange:374,excit:416,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,222,227,228,257,266,301,314,316,339,350,355,383,384,386,398,420,423,426,437,438,445,470,503],exclus:[1,3,12,16,96,390,405,443,445,500,510],excurs:[270,486],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,310,357,373,376,389,487,489,499,502,505,518],exempl:461,exemplari:246,exemplifi:416,exert:[6,251,254,286,311,351,352,353,375],exhaust:[215,389,518],exhibit:[101,270,382,416,500],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,301,302,304,305,355,356,358,360,361,362,364,368,378,384,390,411,412,423,453,470,480,487,489,491,492,493,502,503,504,513,518,519,521],exit:[2,3,11,12,42,60,202,226,241,373,389,489,490,499,508,518],exlanatori:3,exp:[],expand:[],expans:[12,152,202,502,518],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,267,297,303,305,306,311,316,355,375,386,403,440,443,445,486,489,491,493,496,500,505,518],expens:[6,76,206,297,301,316,344,355,374,375,386,390,489],experi:[6,13,15,17,225,233,250,259,269,303,315,316,381,385,410,445,500,505],experienc:[6,12,258,259],experiment:[245,374,390,505],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,270,286,297,305,316,329,355,357,373,374,377,384,385,389,395,414,426,461,463,478,489,492,493,496,498,501,512,513,518,523],explan:[3,6,62,125,152,202,203,218,269,297,423,485,488,489,491,500],explanatori:[3,8,129,202,203,217,218,221,222,223,316,384,488,518],explantori:[3,312],explic:444,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,232,323,324,359,380,392,393,396,401,403,414,416,427,437,477,485,488,492,495,513],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,222,225,232,239,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,305,306,308,316,318,319,335,337,338,344,348,352,358,360,361,363,364,367,369,384,390,391,392,394,397,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,417,418,419,420,421,422,423,427,428,429,430,431,432,433,434,435,436,437,441,443,445,446,447,448,450,455,456,463,464,465,466,467,468,469,471,472,473,474,475,476,477,479,481,482,483,491,493,494,500,501,503,504,510,512,513],explictli:[16,504],exploit:[15,17,299],explor:[130,177],expon:[3,307,309,414,419,422,436,444,456],exponenti:[96,451,472,479,483,505,518],expos:11,exposit:[215,410,413],express:[6,152,164,178,210,211,230,267,297,307,344,350,357,396,414,416,430,440,461,462,471,518],expressiont:396,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,224,225,231,234,238,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,314,315,316,318,321,326,329,331,335,336,337,338,339,341,342,344,346,349,353,354,419,440,443,454,455,462,508,509,517],extent:[1,3,42,43,46,60,76,176,180,202,214,222,226,251,351,354,374,377,392,457,459,473,488,491,494],exterior:[3,6,176,353],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,270,304,305,306,316,332,383,384,387,388,409,420,423,426,440,445,488,489,491,494,503,512,518],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,309,385,406,417,440,462,489,496,508],extract_atom:11,extract_comput:[11,489],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,230,232,270,342,416,475,512],extrema:436,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,346],f_a:[474,475,476],f_ave:129,f_c:475,f_f:476,f_fix_id:306,f_foo:518,f_harm:342,f_i:[29,451],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,265,334,346,509,518],f_ij:451,f_indent:224,f_int:341,f_j:29,f_jj:100,f_k:451,f_langevin:344,f_max:[306,311],f_msst:268,f_r:[254,474,475,476],f_sigma:396,f_solid:342,f_ss:6,face:[3,6,60,62,76,166,176,180,214,222,223,349,351,352,353,354,377,419,440,455,491,494],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,302,332,342,420,453,461,503],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,226,230,232,233,245,250,253,255,256,268,270,271,275,299,303,307,315,319,322,324,332,336,340,347,348,349,353,364,375,377,384,390,392,393,396,397,399,401,406,407,408,410,411,412,416,420,423,427,428,440,443,445,447,448,454,456,463,472,477,488,491,494,495,500,503,505,506,509,512,517,518],factori:[3,489],factoriz:374,fail:[3,9,11,12,62,182,230,233,374,383,385,408,454,489],failur:[133,458,490,518],fairli:[11,445,500,505,513],faken:78,falcon:250,fall:[3,6,206,221,302,489,518],fals:[95,355,357,461,518],fame:8,famili:[479,488],familiar:[0,11,513],fan:451,far:[3,6,12,17,60,62,64,95,202,203,206,207,226,227,228,230,233,270,297,315,316,332,349,360,364,381,385,386,478,489,491,496,509],farago:253,farrel:[474,476],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,305,306,308,316,321,325,331,334,342,344,348,349,350,352,354,385,423,437,494,503,518,522],fasolino:425,fast:[6,7,9,12,13,17,40,202,203,281,306,345,374,375,398,437,438,443,471,473,493,498,500,509,519,523],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,303,307,308,316,318,319,332,335,337,339,341,344,348,352,358,360,361,363,364,367,369,374,375,387,388,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,409,410,414,415,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,441,446,447,448,450,455,456,463,471,472,473,474,475,476,477,479,481,482,483,486,494,500,504,512],fastest:[1,6,14,17,166,222,344,345,390,488],fatal:[3,508],fault:[75,454],faulti:12,fava:419,favor:229,favorit:7,fbmc:339,fcc:[],fcm:[287,518],fdirect:236,fdotr:424,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:414,feedback:[7,250],feel:[7,250,251,259,297,353,355,385,445],felling:442,felt:353,femtosecond:517,fene:[],fennel:[406,428],fep:[],ferguson:[6,184,503],fermi:[1,9,10,12,15,164,390,476],fermion:416,fernando:439,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,270,302,305,307,319,346,374,383,384,385,392,461,488,491,496,500,502,510,521],fewer:[1,3,11,15,16,64,259,500],fewest:3,fextern:243,feynman:299,fff:489,ffield:[405,417,453,454,461],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,298,374,375,500],fft_inc:[12,375],fft_lib:12,fft_path:12,fftbench:[374,510],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:470,fictiti:[6,212,213,238,243,247,299,315,406,428,432,470],field1:[492,496],field2:492,field:[],fifth:[6,329,447],figur:[1,3,8,12,306,488,489,513],fij:409,file0:297,file1:[11,13,297,343,357,384,496,498,502],file2:[11,13,343,357,384,496,498,502],file:[],file_from:204,filen:384,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,297,301,304,307,308,309,312,313,316,317,343,344,371,372,373,384,385,391,392,396,406,414,415,417,425,440,441,442,447,451,452,453,454,461,462,472,473,474,475,476,479,487,488,489,492,493,498,502,509,518,521,522,523],filennam:498,filep:[3,202,203,206,493,498,523],filepo:313,fill:[7,9,178,205,302,344,377,386,396,443,454,494,513],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,408],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,269,297,302,303,311,315,381,383,385,386,406,423,428,432,440,461,471,473,512,513,518],find_custom:8,fine:[16,17,182,212,238,342,386,390,513,518],finer:[152,178,518],finest:374,finger:[178,201,267,494],finish:[6,11,42,226,357,371,373,374,387,389,390,478,496,518,519],finit:[],finni:[7,414,471],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,267,268,269,270,297,299,304,305,306,308,313,316,319,321,329,330,332,333,334,341,342,343,344,346,350,355,357,358,365,377,383,384,385,386,389,390,391,392,395,396,397,399,401,403,405,406,414,416,417,420,421,423,424,425,426,427,428,432,437,438,440,442,443,445,447,451,453,454,461,462,470,472,473,474,475,476,479,483,486,487,488,489,491,492,493,496,498,500,503,504,505,508,509,512,513,518,519,520,521,523],fischer:[6,9,19,20,184,401,503],fit:[3,6,9,12,38,57,198,241,315,332,392,396,425,440,445,466,473,475,499,513,518],five:[78,164,306,384,396,441,491,505],fix:[],fix_deposit:3,fix_flux:215,fix_id:[3,230,268,270,272,273,274,275,276,277,278,303,306],fix_manifoldforc:513,fix_modifi:[],fix_nh:8,fix_nv:513,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:319,fix_reax_bond:453,fix_saed_vtk:317,fix_setforc:8,fix_shak:319,fix_srd:3,fixedpoint:[230,270],fixextern:243,fixid:215,fji:409,flag1:[235,388],flag2:[235,388],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,266,267,298,305,316,329,331,332,339,343,352,355,370,372,375,384,388,389,390,392,422,427,440,443,470,484,486,488,489,491,492,493,495,496,497,501,513,518],flag_buck:400,flag_coul:[400,409,432],flag_lj:[409,432],flagfld:[398,437,438],flaghi:[3,398,437,438],flaglog:[398,437,438],flagn:235,flagvf:[398,437,438],flat:[6,344,349,350,354],flavor:[2,7,12],fld:[349,437,438],flen:393,flex_press:393,flexibl:[3,6,8,179,205,218,222,231,247,271,340,347,416,475,509],flip:[3,6,232,270,351,352],floor:518,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,230,245,246,253,256,270,275,297,298,303,320,342,344,367,412],fluid:[],fluid_veloc:260,flush:[3,206,508],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,233,236,316,319,345,396,443,509,512],fmackai:9,fmag:234,fmass:299,fmax:[383,509],fmomentum:236,fmsec:[2,206,253,254,267,270,303,316,335,336,500,511,517,519],fname:373,fno:[9,16],fnorm:[383,509],fnpt:236,fnvt:236,foce:423,fock:393,focu:319,fogarti:[9,309,454],foil:[152,297,462],fold:[330,500],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,298,299,301,304,305,306,307,309,311,313,315,316,317,319,334,335,336,337,340,341,342,343,344,346,347,355,356,360,361,362,363,364,367,369,372,377,380,383,384,385,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,450,451,452,453,454,455,456,458,460,461,462,463,464,465,466,467,468,469,470,472,473,474,475,476,477,478,479,481,482,483,484,486,488,489,491,492,494,496,498,499,500,503,505,506,507,512,513,518,519,522],foo:[4,8,11,12,202,205,243,489,502,518],foot:6,footprint:[12,390],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[315,422],forcegroup:256,forcezero:381,ford:409,forestgreen:206,forev:76,forget:[254,512],forgiv:270,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,267,293,298,309,311,315,316,344,349,353,358,359,362,367,380,382,384,385,392,393,396,403,411,412,414,416,418,422,423,427,439,440,442,443,447,448,451,453,454,455,461,462,463,471,473,474,475,476,482,485,488,489,491,496,501,508,512,518],formal:[6,83,86,100,246,247,253,270,299,332,340,461],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,298,301,305,307,309,312,316,317,328,343,344,355,356,359,380,384,385,391,392,396,403,414,417,427,440,442,452,453,454,456,462,473,479,480,488,489,491,492,493,496,507,508,509,518,520,521],former:[6,12,16,40,42,206,226,344,348,396,398,497,503,518],formerli:[7,13],formul:[1,6,9,41,67,153,212,238,253,270,293,307,309,315,319,343,374,392,396,414,416,419,440,450],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,224,225,232,238,248,249,251,253,254,267,297,298,304,313,318,326,330,332,335,336,337,346,349,352,354,355,357,358,359,361,368,377,384,392,393,395,396,401,402,403,404,409,410,414,415,419,420,421,422,424,427,428,430,431,432,434,435,437,438,440,444,445,446,455,456,463,471,472,473,474,475,476,479,481,482,487,491,494,501,508,509,517,518,519],forth:[1,6,11,12,13,14,15,389,489,494,498],fortran:[3,6,9,11,12,13,243,414,423,440,453,454],fortun:8,forward:[3,8,96,373,385,390],foster:[396,450,451],foul:181,found:[3,6,9,12,78,172,202,229,231,245,250,256,262,298,339,345,357,373,386,403,406,409,486,492,493,508],four:[6,11,55,88,114,115,152,174,268,344,367,384,385,443,486],fourier:[],fourth:[6,116,315,329,339,401,447,461],fox:[6,130,184,469,503],fphi:[38,57,473],fpic:12,fplo:[38,57,473],fprime:473,fqdn:252,fqq:409,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,227,228,229,230,268,302,306,313,314,332,337,338,377,385,390,396,398,420,437,438,496,501],fragment:[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prefix:[11,12,205,231,298,485,488],preliminari:[38,57,198,241,473],prematur:383,prepar:[8,9,307,310,332,502,512],prepend:453,preprint:[152,286,292,379,462],preprocessor:250,prerecord:231,prescrib:[6,8,156,157,158,171,209,210,215,218,233,267,287,345],presenc:[202,227,228,256,259,437,438,443,482,521],present:[1,3,9,12,18,176,198,204,205,233,246,247,252,256,257,259,260,311,328,350,353,356,405,416,427,436,443,454,455,461,488,512],preserv:[3,62,230,232,270,319,332,354,492],press:[],pressdown:225,pressur:[],pressure_with_eviri:416,presum:[78,167,209,210,211,232,385,423,494],prevent:[2,3,6,41,132,233,244,302,332,343,367,374,381,383,385,390,410,423,449,465,466,468,470,489,493,499,501,512,518],previou:[],previouli:233,previous:[3,9,11,62,64,76,95,113,129,131,167,178,180,182,201,202,203,204,206,214,216,217,218,219,221,222,223,224,232,233,245,251,265,267,302,314,316,318,319,344,346,349,350,351,352,354,355,376,420,471,486,489,493,494,504,506,508,509,514,515,516,518,519],prevoiu:350,price:[6,409],primari:[0,6,344],primarili:[5,7,9,17,154],prime:[236,254,421,443,474,476,488],primit:[3,6,352,353,377],princip:[3,250,461],principl:[6,9,11,250,271,307,416,424,443,472,488,513],prinicp:[43,316,384],print:[],printabl:2,printflag:424,printfluid:256,prior:[176,200,320,376,522],priori:500,prioriz:390,prism:[3,6,166,180,494],priveleg:3,privileg:[11,12,250],prob:[227,228],probab:463,probabl:[3,8,12,41,76,168,181,182,184,216,226,227,228,229,233,245,254,270,302,349,355,383,445,473,486,505,512],probe:518,problem:[],problemat:245,proc:[1,3,8,11,12,15,125,202,203,373,488],proce:[42,55,182,226,237,385,443,498,506,509],procedur:[6,12,40,42,206,216,226,245,253,254,255,270,272,273,274,275,276,277,278,290,291,293,294,295,298,335,336,337,338,341,342,383,385,392,398,492,512],proceed:[12,443],procesor:[42,488],process:[],processor:[],processsor:[42,226,488],procp1:[202,203],procsessor:510,procssor:500,produc:[1,3,4,6,7,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,46,47,48,49,50,52,54,55,57,66,69,72,74,76,85,103,120,121,122,124,125,126,127,129,131,153,155,165,176,184,185,187,188,189,190,192,193,195,196,198,202,203,206,209,212,217,218,219,221,222,223,224,225,226,229,232,239,243,244,246,247,248,253,254,255,265,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,302,306,307,308,311,316,317,318,319,333,334,335,337,344,345,346,348,349,352,357,358,360,361,363,364,367,369,375,383,385,388,390,391,392,394,397,398,399,400,401,402,404,405,406,409,410,414,415,416,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,441,446,447,448,450,451,454,455,456,463,472,473,474,475,476,477,479,481,482,483,486,488,493,494,496,497,500,505,506,509,518,519],product:[6,16,17,18,152,176,232,293,307,345,390,393,416,454,488,518],proessor:390,prof:301,profi:167,profil:[],program:[3,4,6,7,9,11,12,13,17,154,202,205,206,207,209,231,243,250,256,310,414,489,490,502,518],programm:[13,17],progress:[1,42,226,250,268,306,382,383,385,509,512],prohibit:501,project:[6,7,13,14,382,471,513],promis:7,promot:396,prompt:[8,11,12,250,502],proni:[3,246,247],proofread:8,prop:[6,305],propag:[4,9,214,270,306,322,416,423],propens:6,proper:[229,297,440,489,513],properati:305,properli:[212,238,316,320,328,384,385,412,489,519],properti:[],propoerti:332,proport:[6,40,42,96,114,115,174,226,253,254,255,306,340,347,348,420],proportion:253,propos:[6,152,216,230,245,270,293,311,428,442,475,477],prospect:7,protect:332,protein:[7,10,178,314,316,330,491,499],protocol:250,proton:[476,483,517],prototyp:[43,450],prouduc:[224,346],prove:[89,90,240,256,320],proven:293,provid:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,29,41,43,64,71,75,130,151,154,172,176,177,178,204,205,207,210,217,218,224,229,230,231,232,243,245,250,252,256,260,268,270,298,305,306,307,310,311,316,320,321,339,341,342,345,346,357,372,374,375,381,385,390,392,396,398,403,405,406,410,415,416,420,422,425,427,436,437,440,442,443,451,452,453,454,461,462,470,471,472,474,475,476,479,488,493,499,501,504,505,509,510,513,518],proxim:201,psa:352,pscreen:[3,12,500],pscrozi:[0,7,13],psec:[206,232,249,253,254,270,303,316,335,336,511,517],psend:488,pseudo:[416,486,491,496],pseudodynam:339,pseudopotenti:[9,443],psf:6,psi:[417,482],psi_ij:417,pstart:[3,270,271,275,303,316],pstop:[3,270,271,275,303,316],pstyle:[96,119,210,211],psu:[453,454],psuedo:496,pt2:177,pt4:177,ptarget:230,pthread:[12,17],ptr:[6,11,243,489],ptype1:127,ptype2:127,pu3:177,pu4:177,pu6:177,publicli:5,publish:[7,256,260,286,292,307,379,406,440,443,474,476],pull:[321,329,513],puls:344,pump:[437,438],punctuat:[2,486,505],purchas:205,purdu:[9,13],pure:[11,332,423,441,442,474,476,500],purg:[3,492],purpl:[2,206],purport:11,purpos:[3,6,7,9,12,43,64,76,130,140,146,161,162,177,178,180,182,198,202,222,224,229,230,253,297,299,302,304,315,332,374,390,400,426,432,443,445,478,484,491,494,498,501,503,504,518,523],push:[3,8,212,225,232,251,269,297,314,321,383,420,463,513],pushd:251,put:[3,6,8,11,12,13,40,62,166,178,202,233,237,351,352,355,377,453,489,491,495],putenv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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_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/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix 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 saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","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/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,298,299,302,303,304,305,306,308,311,313,314,316,317,332,334,339,340,341,342,345,347,349,351,355,368,372,374,375,377,378,381,382,384,386,387,388,390,393,396,398,416,437,438,443,445,453,454,470,471,486,487,488,491,492,494,496,498,499,500,503,505,507,508,509,510,511,517,519,521,522],"function":518,"long":[220,397,399,400,401,402,406,408,409,428,432,436,448,456,477],"new":8,"static":12,acceler:1,account:513,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,addit:[12,13,513],addtorqu:213,adiabat:6,adjust_dt:322,adp:391,after:513,airebo:392,alloi:414,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,9,91,156,272,276,280,281,290],atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,305,518],atom_modifi:40,atom_styl:41,attract:5,aveforc:225,awpmd:[9,393],balanc:[42,226],barostat:6,basal:71,beck:394,berendsen:[303,335],between:6,binary2txt:13,bodi:[6,8,9,43,72,157,273,277,282,291,395],bond:[8,13,73,74,227,228,229,312],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:396,born:[397,408],boundari:[7,60],box:[6,61,230],branch:513,brownian:398,buck:[399,400,408,439],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:513,change_box:62,charmm:[6,20,184,401,436],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,358,402],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,349,404,482],colvar:[9,13,231],com:[79,80,159],comb3:405,comb:[308,405],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,514,515,516,517,518,519,520,521,522,523],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,518],compute_modifi:113,condit:7,conduct:[6,340],conserv:411,constant:[6,518],constraint:7,contact:[81,132],coord:82,core:6,coreshel:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:360,coul:[397,399,400,401,402,406,407,408,421,428,432,436,448,456],coupl:6,creat:228,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:336,csvr:336,cubic:430,cuda:[9,14,121,124,155,165,212,225,239,244,248,270,279,318,319,335,337,348,397,399,401,402,414,420,421,428,429,431,434,446,472,474],custom:[8,202,203],cut:[50,393,399,402,406,409,416,418,428,429,436,444,448,477],cvf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