lammps/doc/searchindex.js

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t:[311,507],adp:[],adri:[9,308,448,449],adust:171,advanc:[3,249,391,481,492],advantag:[1,6,8,11,14,18,40,41,42,225,385,410,495,500],advect:[3,6,328],advertis:8,advis:[380,447],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,96,128,152,161,175,181,204,205,210,217,218,220,221,222,223,226,227,228,229,231,232,242,248,250,252,258,265,269,270,271,272,274,275,276,282,287,288,289,291,312,313,326,340,350,363,370,376,377,378,380,381,382,385,411,432,433,440,483,484,486,488,489,491,494,496],affin:[16,17,18,231,385,400],afil:246,aforement:18,afresh:[300,494,513],afshar:405,after:[],afterrun:494,afterward:3,afterword:42,ag1:176,ag2:176,again:[6,11,12,16,17,65,151,157,163,171,201,205,231,248,298,354,369,380,432,433,481,483,484,486,488,493,500,502,513,515],against:[11,12,13,67,232,380,448,449],aggreg:[6,12,69,72,74,85,102,119,126,248,264,310,312,326,481,514],aggress:[248,500],agilio:[9,13],agre:[3,8,197,378,387,420,449],agreement:[5,7],ahd:417,ahead:347,aidan:[0,5,7,9,13,373],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:204,akohlmei:[7,9,13,206,249],aktulga:[7,9,305,449],al2o3:456,al2o3_001:[129,313],al3:176,ala:[255,456],alain:9,alat:[293,435],alb:[446,469,471],albeit:311,albert:9,alchem:[95,171],alcohol:343,alcu:[386,391],alcu_eam:446,alderton:404,alejandr:[268,269],alessandro:13,algebra:438,algorithm:[0,1,6,7,8,9,42,64,205,214,225,228,231,255,257,258,282,295,303,312,315,316,335,336,340,343,348,376,377,378,382,385,407,411,433,438,453,455,481,483,500],alia:[9,12,16],alias:[1,371],aliceblu:205,align:[6,9,12,29,42,76,179,197,221,225,250,373,486,489,507],alkali:411,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,170,171,172,173,174,175,176,177,178,179,180,181,183,185,190,196,197,198,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,261,263,264,266,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,297,298,299,300,301,302,303,304,305,307,308,309,310,311,312,313,314,315,316,317,318,319,320,324,325,327,328,329,330,331,332,335,336,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,353,354,355,359,364,366,368,369,370,371,372,373,375,378,379,380,381,382,384,385,386,387,388,390,391,392,394,395,396,397,398,400,401,404,405,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447,448,449,450,451,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,483,484,485,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,503,504,505,507,508,512,513,514,515,516,517],allen:[29,95,404,414],allentildeslei:95,allign:3,allindex:352,alloc:[3,5,6,8,9,11,12,63,242,342,379,381,385,444,449,486,494],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,58,60,61,62,64,65,66,82,100,117,119,153,155,156,157,170,175,176,177,179,185,196,197,201,202,204,205,206,208,209,211,213,214,215,217,218,219,220,221,222,223,225,227,228,229,230,231,232,236,237,242,244,245,246,247,249,252,255,258,259,263,265,268,269,293,297,298,299,300,301,302,306,312,313,315,317,319,320,324,328,335,336,337,338,340,341,342,343,344,345,351,353,355,364,370,371,373,378,379,380,381,384,385,387,388,391,392,393,394,395,396,401,409,411,415,416,417,418,423,427,432,433,438,440,446,449,450,453,455,456,465,472,475,477,481,484,486,488,489,490,491,492,493,496,498,499,500,503,504,508,513,514],almost:[2,3,12,63,250,302,340,371,382,385,465],alo:401,alon:[6,7,228,308,448,449,484],alond:13,along:[6,8,12,29,41,76,95,129,175,176,177,200,201,204,217,228,250,255,256,260,265,267,302,312,315,317,321,325,326,335,339,340,346,349,351,373,376,377,378,380,401,404,415,418,421,423,427,435,448,449,468,486,489,496,497,513],alonso:[436,437],alpha:[6,12,52,209,255,294,302,303,307,378,386,389,392,401,405,407,409,410,412,417,422,423,435,441,445,470,472,504,507],alpha_:[],alpha_c:431,alpha_i:457,alpha_ialpha_j:[],alpha_lj:431,alphabet:[2,3,22,37,45,56,66,185,196,208,355,364,379,398,466,486],alphanumer:[3,66,208,301,309,353,379,513],alreadi:[3,7,8,9,12,16,17,18,43,58,177,178,180,203,213,217,221,222,225,227,231,259,300,302,328,351,352,379,380,405,416,418,425,433,465,475,478,482,486,487,491,496,512,513],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,95,97,98,100,103,113,114,115,116,117,118,123,125,127,128,130,151,152,153,154,155,156,157,158,159,160,161,1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,chenoweth:[448,449],chenoweth_2008:[448,449],chi:[102,166,200,293,303,305,366,412,414,514],chiefli:447,child:8,chip:[7,9,12,17,18,385,499],chipot:230,chiral:363,chmod:[11,12],cho:435,chocol:[7,205],choic:[3,6,9,12,15,16,18,41,42,55,95,152,155,156,170,181,197,217,221,222,225,228,231,232,246,252,255,266,268,295,299,303,312,335,364,371,376,377,380,382,385,418,431,440,444,486,495,496,499,500,506,507,512],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,95,128,167,168,204,226,227,228,229,232,241,252,255,266,268,270,271,272,273,274,275,276,298,299,316,328,332,346,370,371,377,475,481,483,495,501],chose:[469,471],chosen:[2,3,6,12,17,151,177,180,189,197,204,210,215,229,232,241,244,245,253,255,266,268,273,295,298,309,328,332,335,336,341,343,344,350,371,372,377,385,406,407,411,415,422,425,451,469,481,495,500,501,507],chri:175,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,98,103,114,116,125,157,172,174,217],chute:[4,9,10,247],ciccotti:315,cieplak:[6,183,498],cii:218,cij:218,ciko:2,circl:[43,76,324],circular:[3,6,155,199],circumst:18,circumv:[100,117,307],citat:[],cite:[3,7,8,12,252,456],civ:9,ckio:2,cko:2,cl1:176,clarendon:[29,404],clarifi:[7,469,471],clariti:353,clark:443,class2:[],classic:[0,3,5,6,7,8,9,242,295,302,307,340,365,411],classifi:[466,474],claus:484,clean:[6,12,14,15,17,494],cleanli:[485,516],clear:[],clearli:7,clebsch:151,clermont:[9,13],clever:490,click:[2,11,22,37,45,56,177,185,196,204,249,355,364,380,398,466,508],client:[249,251],climb:[267,380,500],clinic:[7,13],clo:[166,200,514],clock:[12,481,500],clockwis:346,clone:508,close:[3,6,11,12,13,40,42,71,76,152,180,201,227,228,229,246,253,255,268,289,312,315,346,349,369,371,374,376,377,380,385,387,391,401,402,421,435,440,448,452,454,468,471,490,496,507,508,510],closer:[3,10,42,127,175,200,201,225,229,233,337,380],closest:[227,293,312,343,414,450,465,475],cloud:[456,507],clovertown:18,clsuter:77,clump1:[297,312],clump2:[297,312],clump3:[297,312],clump:312,cluster:[],clutter:3,cmap:486,cmatrix:246,cmax:435,cmd:[11,12,295,497],cmdarg:11,cmin:435,cmm:[],cmoput:144,cn1:218,cn2:218,cna:[],cnn:218,cnr:[9,13],cnt:[418,490],co2:[41,176,315,379],coars:[7,9,10,29,36,41,55,189,297,312,328,416,451,495,498],coarser:[371,513],coarsest:151,code:[],coeff:[3,7,8,12,21,22,33,45,51,183,184,185,190,354,355,361,398,418,422,440,453,455,458,486],coeffcient:486,coeffici:[],coefficienct:405,coefficient0:409,coefficient1:409,coeffieci:[6,389,421],coeffincientn:409,coexist:[244,411],cohes:[6,412,435],coincid:[133,349,396,432,433,481],colberg:203,cold:[6,162,244,248,381,507],coldest:336,coleman8:9,coleman:[9,129,176,313],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,91,98,103,108,114,116,125,157,165,172,174,177,201,202,205,217,230,258,264,297,307,310,312,351,370,379,381,399,486,493,499,505,517],collid:[236,328,350],colliex:176,collinear:[3,297],collis:[3,255,328,346,350,408,415,478],colllis:328,colloid:[],colombo:40,colon:[206,351,487],color1:205,color2:205,color:[3,9,42,201,204,205,225,245,302,307],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,130,151,152,157,165,172,174,175,176,197,201,202,205,208,216,217,218,220,221,222,223,258,265,266,302,312,329,330,340,350,413,417,448,449,487,501,503,513],columnar:175,colvar:[],colvarmodul:12,com:[],comamnd:231,comand:228,comannd:385,comb3:[],comb:[],comb_1:304,comb_2:304,combiant:402,combin:[3,6,7,9,11,13,36,41,66,69,74,85,95,102,113,119,126,155,156,170,201,204,214,220,249,258,268,295,301,316,332,341,349,352,354,370,371,373,377,385,399,401,402,407,411,412,418,430,431,457,467,469,471,472,474,477,489,494,499,507,513],come:[],comfort:[12,13],comit:508,comm:[0,3,11,12,64,78,203,249,251,252,371,380,385,405,440,445,468,488],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,183,197,201,240,253,312,340,379,380,386,409,410,412,422,435,442,449,456,457,467,468,469,470,471,474,483,484,486,507,508,513],commerci:7,commit:[9,508],commmand:[3,6,12,62,118,290,421,480,481,483,500,516],common:[],commonli:[3,6,9,12,17,25,60,62,115,117,179,201,204,206,365,416,425,457,469,471,486,489,498],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,175,180,181,204,205,225,226,227,229,230,231,249,251,255,257,258,259,268,294,301,303,304,305,312,316,328,340,351,368,370,381,382,383,385,407,408,444,479,483,484,495,496,513,515,517],communc:370,comp:[7,203,251,252,315,371,380,411,440,445,450,464,468,470],compact:[66,208,398,466],compani:[5,7],compar:[1,3,4,6,8,12,17,40,94,121,129,160,176,185,196,205,235,303,351,353,370,371,378,380,435,456,481,500,501,507,512],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,184,185,196,354,355,364,397,466],compat:[3,5,7,8,9,11,12,13,17,18,42,76,128,130,188,201,206,210,216,217,218,220,221,222,223,225,294,306,332,335,342,345,348,370,385,419,438,440,468,483,484,513],compens:[6,226,227,310,381,411],compet:339,competit:371,compil:[3,7,8,9,12,13,14,15,16,17,18,19,175,201,203,204,206,249,339,371,385,438,486,487,491,513],compl:17,complain:[11,12,17],complement:435,complementari:[7,401,423],complet:[3,6,9,11,12,15,42,62,76,205,221,225,230,258,295,298,301,328,339,341,352,353,369,380,385,412,453,455,473,481,486,491,494,498,500,503,507,513],complex:[4,6,8,11,12,13,25,41,43,65,100,117,151,153,165,177,178,255,324,349,368,380,411,438,468,484,486,489,513],compli:[335,339],complic:[6,7,9,12,13,215,244,484],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,96,97,98,99,100,103,104,107,114,115,116,117,118,119,120,121,123,124,128,138,141,142,143,144,147,148,149,151,152,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,172,173,174,200,201,202,204,205,211,212,216,217,218,219,220,221,222,223,224,228,229,231,232,237,242,247,251,252,255,258,260,264,265,267,268,269,273,274,275,276,287,288,289,291,292,294,295,296,299,310,312,314,315,317,321,322,325,328,331,332,333,335,342,343,348,349,350,370,373,377,378,379,380,385,405,411,415,432,433,453,455,456,457,486,487,496,504,513,514],componenet:6,composit:[6,215,255,409],compound:[400,411,412,474],compres:[76,125,217],compress:[],compris:[41,349,450,473],compton:[129,176],comptu:3,compuat:371,comput:[],computation:[3,6,226,227,340,391],computational:507,compute_arrai:8,compute_fep:[210,431],compute_group_group:244,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[129,313],compute_scalar:8,compute_temp:8,compute_ti:210,compute_vector:8,compute_xrd:176,concaten:[2,3,516],concav:349,concentr:[76,409],concept:[6,157,167,217,495],conceptu:[3,6,76,165,229,231,380,401,418,435,491],concern:[6,78,95,203,245],concetr:76,concis:[11,339],conclud:12,concret:8,concurr:[16,371,513],conden:[340,469,471],condens:[6,159,340,387,403,409,423,474],condit:[],conducit:6,conduct:[],cone:489,confer:438,confid:[3,500],config:[12,201,483],configfil:230,configur:[1,2,6,12,15,17,38,62,133,179,197,200,201,204,208,229,230,231,232,236,244,251,252,282,295,303,339,368,378,380,387,391,410,435,438,467,469,471,474,481,486,488,489,500,508],confin:[486,500],conflict:[3,12,41,202,440,484,508],conform:[3,6,13,62,228,229,267,311,317,339,363,380,411,498],confus:[3,474],conjuct:[9,405],conjug:[7,8,252,377,411,448,449],conjunct:[6,7,76,94,95,125,160,165,171,177,181,205,209,210,252,255,259,282,298,299,303,304,305,307,312,316,328,336,343,348,370,371,380,392,394,398,401,405,411,417,423,440,443,451,472,486,489,493,507,517],connect:[3,6,9,95,162,180,228,249,297,312,315,325,380,402,415,448,449,465,471,483,484,486,490,507],conner:387,connor:387,conput:3,consecut:[3,11,12,40,76,177,205,209,210,232,249,250,401,423,427,481,487,489],consequ:[1,6,215,340,422,500],conserv:[],consid:[6,75,76,83,95,126,159,162,163,180,201,202,205,209,210,216,218,221,225,227,228,232,256,269,294,312,335,336,339,340,343,371,398,411,418,449,450,456,465,481,482,484,487,488,489,491,494,496,504,507,513],consider:[6,8,252,253,331,332,333,385,495],consist:[3,6,8,9,11,12,41,43,69,74,85,102,114,119,122,123,126,157,160,162,177,189,200,206,211,212,217,231,232,235,237,242,245,252,253,254,265,268,270,271,272,273,274,275,276,277,278,280,281,282,283,285,286,287,288,289,290,291,299,302,307,309,311,312,331,332,333,334,344,370,371,373,379,380,385,387,391,393,399,401,411,414,418,421,432,433,435,438,440,450,453,455,456,468,475,484,486,487,488,489,490,491,498,507,513],consistent_fe_initi:214,consit:312,constant:[],constitu:[3,6,258,312,345,349,399,450],constitut:[453,455],constrain:[3,6,8,154,155,156,157,158,160,163,164,165,166,167,169,170,208,217,232,244,245,250,258,262,297,298,310,312,315,326,336,343,378,379,411,491,498,507],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,100,117,129,151,176,229,268,294,311,349,381,385,404,438,440,465,467,468,489,490,505,513],constructor:[8,11],consult:449,consum:[1,307,444,513],consumpt:368,contact:[],contact_stiff:[452,454],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,95,99,127,129,151,153,157,165,175,176,177,179,183,185,196,197,201,202,204,205,206,208,209,210,214,216,217,218,220,221,222,223,225,230,232,237,240,246,250,251,252,255,266,282,293,294,297,298,300,302,305,309,312,313,318,328,335,339,340,349,350,353,369,371,379,380,383,384,386,387,388,391,400,401,404,409,410,411,418,419,435,438,442,446,447,448,449,457,467,468,469,470,471,472,474,481,482,483,484,486,487,488,489,491,493,495,498,500,501,503,504,507,508,513,515,517],content:[4,8,9,12,18,449,502,504],context:[3,6,8,12,17,127,128,205,226,227,232,297,309,344,377,477,486,493,502,512,513,514],contibut:75,contigu:483,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,87,113,114,173,205,208,209,210,215,217,218,219,220,221,222,223,225,228,229,230,231,232,244,245,246,248,249,250,252,253,254,260,265,266,268,270,271,272,273,274,275,276,287,288,289,290,291,296,298,301,302,312,313,317,327,328,330,337,338,340,346,349,353,369,384,385,391,405,408,425,428,448,449,450,453,455,470,481,484,486,488,489,494,500,501,503,504,513,515],continuum:[6,7,9,214,340,453,455],contour_integr:214,contract:[62,229,231,268,299,312],contradictori:3,contrain:315,contraint:282,contrari:[246,253],contrast:[1,6,43,56,67,159,162,202,231,351,453,455,477,516],contrib:340,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,210,215,216,217,218,220,221,222,223,229,244,252,255,258,259,263,269,289,290,297,298,306,309,312,313,315,342,370,378,380,388,405,408,409,411,418,432,433,438,440,448,449,456,498,504,507,508],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,95,99,133,151,186,201,202,204,208,214,215,225,229,230,231,248,249,252,253,268,270,271,272,273,274,275,276,299,304,312,319,320,331,332,333,340,344,368,370,382,411,414,438,448,449,452,454,467,471,481,483,495,501,502],control_typ:214,controlfil:449,convect:99,conveni:[6,12,29,201,206,223,313,373,457,472,508,513],convent:[3,8,29,188,195,196,202,205,311,325,352,409,411,513],converg:[3,6,42,96,201,202,204,206,211,225,228,229,237,242,273,302,304,307,311,315,376,377,378,380,400,401,423,456,481,493,500],convers:[3,8,151,204,205,215,218,299,370,401,402,403,411,423,427,431,443,484,500,512],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,99,177,184,201,204,205,218,223,266,298,351,354,356,360,363,373,380,386,409,438,469,471,478,484,486,487,488,493,503,507,512,513,515,517],convex:[43,349],convinc:[7,12],cook:9,cooki:7,cool:[7,167,248,310],cooordin:[201,202],cooper:[5,7],coord123:125,coord1:[3,125,217,221,222],coord2:[3,125,217,221,222],coord3:[3,125,217,221,222],coord:[],coordb:456,coordbb:456,coordiat:378,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,95,97,98,103,113,114,116,124,125,127,145,151,160,166,172,174,175,177,181,200,201,202,203,204,205,206,208,211,216,217,220,221,222,225,226,227,228,229,230,231,232,235,237,238,242,244,247,248,249,250,251,252,253,265,267,268,270,271,272,274,275,276,289,292,293,294,297,298,299,309,310,312,314,315,317,322,325,326,327,328,330,338,339,340,347,348,350,351,373,378,379,380,385,386,387,390,410,456,481,486,487,488,489,491,494,496,500,507,513,514],coordn:[125,217],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,130,204,340,380,398,448,484,508],copper:478,coproccesor:16,coprocessor:[1,7,9,16,17,385,499],coproprocessor:17,copy_arrai:8,copyright:[7,8,297],coral:205,core:[],core_shel:159,coreshel:[],cornel:[6,183,498],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:[3,6,41,124,204,349,350,373,473,486,508],cornflowerblu:205,cornsilk:205,corp:9,corpor:16,corr:400,correct:[3,6,9,11,12,16,17,62,95,96,112,113,118,121,127,159,164,171,202,204,231,244,246,252,268,269,289,297,299,302,339,345,349,370,380,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,478,479,486,501,504,507,508],correction_max_iter:214,correctli:[3,8,11,17,76,87,112,113,114,154,155,156,158,160,162,163,164,165,166,169,170,173,201,205,211,232,237,242,253,262,268,269,305,312,315,325,327,346,349,380,381,385,403,433,438,483,484,486,496,508,512,514],correl:[],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,95,106,107,120,123,124,125,126,129,130,138,141,142,143,144,145,147,148,149,151,154,155,164,171,175,176,183,184,185,186,187,188,189,191,192,194,195,197,200,201,202,204,205,209,210,211,217,219,220,221,222,224,227,229,231,238,242,243,247,252,255,256,264,265,266,268,270,271,272,273,274,275,276,277,278,282,285,287,288,289,291,294,295,299,304,312,314,315,331,333,335,344,345,346,348,349,350,352,354,355,356,357,359,360,363,365,371,375,377,379,380,386,387,389,392,393,394,395,396,397,398,399,400,401,404,405,409,410,411,412,413,414,415,416,417,418,421,423,424,425,426,427,428,429,430,431,432,435,436,438,440,441,442,443,445,446,448,449,450,451,456,457,458,467,468,469,470,471,472,474,476,477,478,481,483,484,486,487,489,499,500,501,503,504,507,513],correspondingli:[432,433,495],corrupt:3,cosin:[],cosineshift:27,cosmo:[246,251],cossq:[],cost:[1,6,10,11,12,17,40,42,76,120,129,152,176,204,205,217,221,222,225,226,227,241,268,304,340,370,371,383,401,423,427,438,440,467,483,495],costheta0:[467,469,471,474],costheta:446,costli:[11,96,246,381],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,95,98,103,114,116,120,123,125,157,167,172,174,190,201,202,204,205,209,210,217,218,221,225,231,242,251,301,302,303,307,310,312,314,328,329,335,339,340,341,345,349,351,353,361,367,369,376,378,381,385,388,413,417,418,421,448,449,482,483,484,486,488,490,493,494,501,502,507,513,514],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,96,118,119,127,152,178,182,303,305,341,370,371,378,385,392,394,395,396,397,400,401,402,403,404,411,415,416,418,423,427,431,434,440,443,448,449,451,456,466,471,472,474,477,491,498,504,507,512],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,99,125,127,128,165,175,181,211,212,215,217,220,221,222,224,225,232,237,241,244,250,268,282,298,315,331,332,349,371,378,379,380,382,385,413,417,440,504,513],counter:[3,346,481,492,494,500],counteract:244,counterbal:248,counterbalanc:29,counterpart:[201,312,481],counterproduct:18,coupl:[],courant:318,cours:[3,8,137,139,171,201,209,210,245,311,325,339,345,347,348,350,351,371,432,458,483,486,499,507,513,515],courtesi:373,cov:456,coval:[6,9,29,411,435,456,507],covari:246,cover:[6,76,197,205,214,255,411,473],coverag:[76,221],cpc:251,cpp:[1,3,6,8,9,11,12,13,95,201,209,210,242,315],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,205,219,235,253,341,368,371,385,398,466,481,499,500,503,504,505,513],cpuremain:504,cr2:176,cr3:176,crack:[4,381],crada:[5,7],crai:[5,7,13,18,201],crash:[3,12,381,507],craympi:385,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:214,create_faceset:214,create_group:203,create_nodeset:214,createatom:[],creation:[],crimson:205,critchlei:297,criteria:[3,127,178,204,205,226,227,228,263,378,445,473,488,491,513],criterion:[12,42,132,177,180,215,225,228,244,282,304,318,346,351,378,380,400,411,415,456,491,500,501],criterioni:500,critic:[6,49,50,266,335,340,378],crmax:76,crmin:76,cross:[3,12,22,76,97,155,175,185,201,202,204,216,221,227,231,265,267,289,312,321,325,327,336,343,355,373,380,396,405,408,409,416,417,418,423,425,427,446,451,453,455,469,471,478,486,490,496,515],crossov:1,crossterm:486,crozier:[0,7,13],crucial:302,crystal:[3,4,6,13,78,117,293,294,338,373,381,486,490,504,507],crystallin:[6,113,294,373,470,507],crystallis:335,crystallogr:[129,176],crystallograph:[373,504],crystallographi:[129,176,373],cs1:176,cs_chunk:6,cs_im:[41,486],cs_re:[41,486],csanyi:[151,447,457],cscl:435,csequ:6,csh:[11,12,398],cshrc:[11,12],csic:[410,467,469,471,474],csinfo:6,csisi:[410,467,469,471,474],csld:[],cst:409,cstherm:6,cstyle:483,csvr:[],ctcm:[386,409],ctemp_cor:235,cterm:317,ctr:9,ctype:11,cu1:176,cu2:176,cu3au:435,cube:[6,42,175,180,225,235,349,373,507],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:391,cummul:[3,6,223,226,227,228,230,241,246,252,254,328,331,332,333,334,336,343,417,504],cumul:[6,215,217,220,221,222,236,244,252,266,268,273,282,312,313,380],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,87,95,112,113,119,127,128,141,152,157,165,167,173,175,178,181,200,201,202,203,204,205,206,209,210,214,217,221,222,223,225,226,227,228,229,230,231,232,236,237,242,244,246,249,250,252,258,265,268,269,274,275,276,282,287,288,289,291,297,298,303,304,306,309,310,311,312,315,316,317,318,319,320,321,322,324,326,327,328,331,332,333,339,340,343,344,345,346,347,348,350,351,353,368,369,370,371,374,375,377,378,379,380,385,391,398,400,404,409,411,412,415,418,419,422,432,433,435,436,437,440,446,448,449,452,453,454,455,458,469,471,472,475,481,482,483,484,486,487,488,489,490,492,493,494,496,498,500,501,503,504,508,513,514,515,516,517],curv:[6,177,244,294],curvatur:[414,450,478],custom:[],cut0:484,cut1:495,cut2:495,cut:[],cuthi:[293,305],cutinn:[393,432,433],cutlo:[293,305],cutmax:446,cutoff1:[397,404,423,427,431,434,443,451],cutoff2:[392,394,395,397,403,404,423,427,431,434,443,451,472],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,95,100,117,119,126,127,151,175,178,180,181,227,228,233,240,293,302,303,305,307,309,312,316,328,341,345,349,351,368,370,371,378,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,484,488,491,495,507,513],cutoff_glob:[],cutoff_inn:[],cutoffa:410,cutoffc:410,cuu3:409,cval:176,cvd:335,cvel:317,cvff:[],cwiggl:[3,265,345,348,350,513],cyan:[2,204,205],cycl:[3,244,266,268,269,273],cyclic:[3,197],cygwin:12,cylind:[3,4,76,204,217,250,298,346,349,489],cylindr:[6,250,325,346],cypress:385,cyrot:391,cyrstal:294,d3q15:255,d3q19:255,d_double_doubl:15,d_e:340,d_flag2:301,d_flag:301,d_name:[124,201,301,330,496],d_single_doubl:15,d_single_singl:15,d_sx:301,d_sy:301,d_sz:301,daan:338,dai:12,daili:12,daivi:289,damag:[],dammak:307,damp:[3,6,208,213,252,253,254,259,268,269,273,299,302,303,307,312,331,332,344,346,347,377,378,380,392,394,396,401,404,411,415,423,431,443,451,466,472,500,507],damp_com:253,damp_drud:253,dampen:[312,507],dampflag:[346,415],dan:17,danger:[3,12,244,351,405,504],dangl:180,daniel:9,darden:[371,404],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:303,dash:[415,503],dat:[6,99,197,214,482],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,313],dataset:313,datatyp:3,date:[0,4,6,12,13,200,448,449,513],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,43,69,72,74,85,102,119,126,201,218],davenport:434,davi:345,david:[9,19,370,371,469,471],daw:[409,446],dbg:14,dcd:[3,6,7,201,203,204,205,206,295,487,491],ddim:200,deactiv:431,dealt:251,debug:[6,7,11,12,13,14,17,58,129,133,176,177,295,300,368,370,385,419,440,475,484,485,493,496,503,513],deby:[],decai:[100,401,478],decid:[3,6,12,16,76,265,301,312,341,501,508],decipher:373,declar:203,declin:328,decod:204,decompos:[95,457],decomposit:[3,5,7,18,65,214,295,316],decoupl:[6,507],decreas:[3,201,202,211,212,219,228,231,237,242,244,252,339,370],decrement:317,deepli:367,deeppink:205,deepskyblu:205,def:[12,13,484],defaul:64,defect:[6,75,175,438],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,183,184,185,186,187,188,189,191,192,194,195,196,197,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,231,232,235,236,237,239,242,243,244,247,250,251,252,253,254,255,263,265,267,268,269,270,271,272,273,274,275,276,278,279,280,283,285,286,287,288,289,290,291,293,294,295,297,298,299,301,303,305,310,312,313,314,315,318,322,326,328,330,331,332,333,334,336,337,338,340,342,343,345,346,347,348,349,350,351,353,354,355,356,357,358,359,360,363,364,365,366,368,370,371,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,397,398,399,401,402,404,405,406,407,408,410,411,413,414,415,416,417,418,419,421,423,424,425,426,427,428,429,430,431,432,433,434,438,439,440,441,442,443,445,446,448,449,450,451,452,453,454,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,486,487,489,490,491,492,495,496,497,498,500,501,503,504,507,509,510,511,512,513,514],definit:[2,3,6,8,12,13,83,86,127,151,205,217,218,219,220,221,222,223,231,239,250,273,313,330,342,345,348,350,352,364,368,379,388,391,399,406,407,411,421,446,453,455,457,473,484,486,488,495,497,512,513],defint:504,deform:[],deg2theta:176,deg:507,degener:[3,297],degrad:[8,18,294,371,495],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,100,102,104,106,107,109,111,112,117,123,154,155,156,157,158,159,160,161,162,163,164,165,166,167,169,170,176,177,183,184,187,188,195,197,200,204,217,228,235,244,246,247,252,253,258,268,269,273,274,275,276,287,288,289,291,295,297,311,312,315,331,332,333,338,354,356,360,363,365,378,404,409,417,496,504,507,514],degress:[157,217],del:500,delai:[3,6,12,381,408,504],deleg:418,delet:[2,3,7,8,12,55,60,63,66,175,180,181,208,217,218,220,221,222,223,226,228,241,244,268,313,331,332,351,353,369,379,381,384,440,465,486,487,488,489,497,498,503,508,509,511,513,514],delete_atom:[],delete_bond:[],delete_el:214,deli:200,delimit:[484,513],deloc:[269,411,456],delr:435,delt_lo:500,delta:[],delta_1:391,delta_3:391,delta_7:391,delta_conf:3,delta_ij:[435,446],delta_mu:[],delta_pi:391,delta_r:446,delta_sigma:391,delta_ua:[],delx:200,delz:200,dem:[],demand:307,demo:11,demon:292,demonstr:[302,435],den:298,dendrim:417,denniston:[9,255,257,258,259,294],denomin:[7,182],denot:[129,235,253,294,305,307,401,416,418,449,453,455],dens:[76,228,411],densiti:[3,6,7,9,18,41,42,62,110,127,137,151,163,175,177,209,210,214,217,221,222,225,231,242,255,258,261,262,294,298,299,303,340,345,373,375,379,386,387,391,409,435,436,437,446,450,456,460,462,463,464,486,495,496,504,512],density_continu:455,density_summ:455,depart:[0,7],departur:[266,302],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,100,102,113,119,120,123,124,125,126,130,151,153,154,160,164,165,171,177,178,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,204,205,208,209,210,211,212,215,217,219,220,221,223,224,225,227,229,231,237,238,243,246,247,248,250,252,253,255,257,258,265,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,293,304,307,309,312,314,315,316,322,328,331,332,333,335,337,339,340,342,344,345,348,349,350,351,353,354,355,356,357,359,360,363,365,371,373,378,379,381,382,383,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,435,436,438,439,441,442,443,445,446,448,449,450,451,456,457,458,466,467,468,469,470,471,472,474,476,477,478,481,483,486,488,489,492,496,498,500,503,504,506,513,514],dependend:6,depflag:12,dephas:[481,500],depos:232,deposit:[],deprec:[3,303,448],depth:[52,155,204,340,414,450],dequidt:9,der:[95,118,399,400,431,448,449,477,507],deriv:[6,7,8,9,38,57,66,95,151,171,197,218,229,231,244,252,265,268,270,271,272,273,274,275,276,293,299,303,307,337,338,340,345,346,349,377,379,387,391,399,404,411,412,416,425,429,430,435,438,448,449,466,468,477,507],derjagin:477,derlet:293,descend:205,descent:[7,377],descib:[41,204,303],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,96,121,124,127,129,141,151,152,155,156,157,161,162,165,168,170,171,175,176,177,179,180,189,194,197,201,202,203,208,209,210,217,218,219,220,221,222,223,225,228,229,230,231,232,234,235,240,245,246,249,250,251,252,253,254,255,257,258,259,263,267,268,269,273,281,290,293,295,300,301,302,303,304,305,312,317,325,328,329,330,331,332,333,334,335,336,337,338,343,345,346,348,353,370,371,373,376,377,378,379,380,384,387,388,390,392,393,394,396,397,398,399,400,401,404,409,411,412,414,415,416,418,421,423,424,425,426,427,428,429,430,431,432,433,434,435,438,439,445,446,447,448,449,450,451,456,457,458,465,466,467,468,469,470,471,472,474,476,477,478,479,481,483,484,486,487,488,489,490,496,499,500,503,508,513,514,515],descript:[],descriptor:[151,201,419],deserno:371,design:[0,3,6,7,8,11,13,14,15,17,129,159,162,176,214,228,234,235,268,269,293,294,313,335,340,388,389,390,393,396,401,403,411,431,432,433,436,437,446,449,468],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,96,99,123,128,152,159,177,190,200,217,223,229,231,242,244,245,252,253,254,258,268,289,297,298,299,300,303,307,312,315,328,331,332,333,334,339,346,361,367,370,371,373,376,378,379,380,405,409,417,432,433,467,469,471,482,483,484,486,490,495,500,501,503,504,513,514,515],desk:7,desktop:[4,6,7,10,12,204],despit:507,destabil:391,destre:363,destroi:[9,11,40,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,98,99,103,112,114,116,118,120,122,123,125,128,130,151,152,154,155,156,157,160,170,171,172,174,177,178,181,182,185,196,200,201,202,204,205,208,209,210,214,217,218,219,220,221,223,225,227,228,229,230,231,232,242,244,245,246,247,249,250,252,254,255,259,265,266,267,268,269,270,271,272,273,274,275,276,280,282,287,288,289,290,291,294,297,298,299,301,302,304,305,306,312,315,316,328,331,332,333,334,335,336,338,339,340,341,342,343,344,351,353,355,364,370,371,374,378,379,381,382,385,386,387,388,390,391,393,395,396,397,398,399,400,401,404,405,411,412,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,434,435,439,440,445,448,449,450,456,457,458,466,473,476,477,479,484,486,487,488,489,491,492,495,496,498,501,504,505,508,513,514,517],detect:[2,3,12,43,64,66,94,100,243,298,339,380,400,417,422,481,483,486,497,500,513],determ:385,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,95,112,118,120,123,129,130,138,152,165,166,175,176,177,200,201,202,204,205,206,207,211,212,213,216,217,218,219,220,221,222,223,224,225,229,231,232,235,237,244,247,248,250,252,253,258,263,265,266,268,274,275,276,287,288,289,291,293,295,298,299,302,309,310,311,312,313,314,318,320,322,328,331,332,333,335,341,342,345,346,347,348,349,350,351,364,370,371,373,379,381,382,385,387,388,395,400,404,408,409,413,415,418,419,427,435,438,440,449,450,456,465,468,472,477,483,486,487,489,491,493,496,500,502,503,505,512,513,514],determinist:316,detil:119,devan:[9,451],devanathan:471,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,273,297,302,303,306,387,391,411,437,438,456,474,488],devemi:9,deviat:[266,273,293,413],deviator:9,devic:[1,3,12,15,17,249,385],device_typ:385,devin:[304,400],devis:437,dfactor:204,dff:507,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,371],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,306,438],dhi:[62,200,231,298],dhug:[266,302],dhugoniot:[266,302],dia:435,diagnost:[],diagon:[3,6,91,151,152,153,229,268,299,312,343,453,455],diagonalstyl:457,diagram:[42,129,176,196,225,295],diallo:417,diam:[204,205,298,379],diamet:[3,6,41,43,124,177,201,202,204,205,209,210,252,298,312,328,330,344,346,379,399,414,415,425,450,473,477,486,487,496],diamond:[373,411,435],diamter:[41,298],dick:6,dicsuss:265,dictat:[215,266],did:[3,12,378,405,408,409,415,440,469,471,494],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,173,342,370],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,95,100,104,106,107,131,151,153,154,155,156,157,158,160,163,164,165,166,167,169,170,171,177,178,180,185,196,197,200,201,204,205,208,210,213,215,217,220,225,226,227,228,229,230,231,235,240,243,244,245,246,247,248,249,252,253,255,265,268,269,270,271,272,274,275,276,278,280,283,285,286,287,288,291,293,295,297,299,302,303,304,307,310,312,315,317,325,326,328,331,332,333,336,337,338,340,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3,307,315,316,328,336,340,343,345,346,348,350,363,370,371,399,404,405,407,411,412,415,420,432,433,435,440,450,453,455,460,461,463,464,478,507],equi:269,equidist:267,equil:[3,303,374,493,517],equilater:496,equilibr:[3,4,5,6,7,9,62,99,177,208,215,218,228,229,244,266,268,269,289,290,299,302,303,304,305,336,337,338,343,400,401,448,449,482,496],equilibria:343,equilibribum:[226,227],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,62,160,161,184,186,229,231,244,245,246,253,255,268,273,289,302,303,307,311,315,317,325,328,335,336,338,343,354,356,360,363,400,435,442,456,507],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:214,equival:[6,12,13,29,62,64,135,136,144,149,175,179,205,220,223,229,231,244,252,268,289,299,311,312,348,387,405,411,456,469,471,472,486,489,494,495,504,507],equlibrium:6,equliibr:[303,305],er3:176,eradiu:[41,124,202,411,486],eras:[314,337],erat:[231,433],erc:401,erfc:[401,423,440],erforc:[124,202],erg:512,erhart:[215,409,469,471],ermscal:388,ernst:9,eror:3,eros:435,erose_form:435,erot:[],errata:[469,471],erratum:345,erron:3,error:[],erta:415,ervel:[124,202,486],escap:[232,507],especi:[8,16,165,177,208,215,225,244,302,307,310,311,385,483],espresso:[9,306],essenti:[8,11,12,27,96,139,158,159,160,163,164,165,166,167,169,186,218,273,294,344,371,387,401,423,471,491,504],essex:29,establish:[95,248],estim:[1,3,6,10,12,38,42,57,99,152,214,225,236,266,328,335,370,371,376,440,449,468,500,504],esu:512,esub:435,eta:[6,255,268,302,303,305,344,410,412,414,446,470,474,512],eta_dot:268,eta_ij:446,eta_ji:412,etag:[41,486],etail:504,etap:268,etap_dot:268,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,97,98,99,104,120,121,124,126,152,154,157,158,159,160,161,163,164,165,166,167,169,171,177,179,180,181,190,201,202,204,205,208,209,214,215,216,217,220,221,222,223,226,227,231,232,242,244,245,252,268,298,309,313,340,341,349,353,369,370,378,379,380,381,383,409,410,418,431,433,438,444,448,449,467,469,471,474,481,484,486,487,488,493,495,496,500,501,502,503,504,505,507,512,513,515,517],ethernet:18,etol:[378,380,481,500],etot0:302,etot:[6,104,106,107,121,152,163,205,235,253,266,302,503,504],eu2:176,eu3:176,euler:[378,380],eulerian:214,euqat:459,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,95,96,99,118,128,130,151,153,157,167,175,177,200,201,202,204,205,209,210,211,212,214,216,217,218,219,220,221,222,223,224,231,237,245,247,248,250,251,252,253,294,300,303,314,318,322,331,332,333,342,345,348,350,351,353,370,371,376,378,385,438,440,446,452,454,456,468,481,482,484,488,489,491,493,494,495,496,500,502,504,513,514],evalut:[353,484],evan:[165,289],evanseck:[6,20,183,396,498],evapor:[],evaul:[8,378],evdwl:[118,153,448,449,504],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,96,118,130,175,178,179,193,197,201,202,205,208,209,210,215,216,217,220,221,222,223,225,226,227,229,231,232,235,250,253,266,268,269,294,298,307,309,312,313,324,328,336,340,343,345,349,351,362,370,376,378,380,385,390,411,412,415,418,421,440,450,474,475,479,486,487,489,491,492,493,495,496,498,501,503,504,505,507,517],evenli:[3,42,58,152,197,225,255,421,475],event:[],eventu:[3,6,12,15,179,303,500],ever:[9,55,57,251,328],evera:[399,414,450,466],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,99,124,130,139,165,180,201,202,203,204,205,206,208,209,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,241,242,244,246,248,249,250,255,256,264,268,269,273,292,293,294,298,299,300,301,302,303,304,305,307,309,310,312,313,315,317,328,330,331,332,333,334,335,336,339,340,341,342,343,351,353,369,371,380,381,382,385,405,408,418,431,448,449,456,462,480,481,482,486,488,490,491,493,494,495,500,501,502,504,508,513,517],everyth:[8,118,508],everywher:[127,425],eviri:411,evolut:[246,255,295,481],evolv:[255,295,341],ewald:[2,3,5,6,7,8,9,12,96,121,129,152,341,370,371,378,392,394,395,401,404,411,423,427,443,451,466,468,472],ewald_disp:404,ewalddisp:3,exact:[22,42,45,76,133,171,180,185,225,228,245,246,252,253,254,298,307,308,328,340,355,370,398,488,493,500,513,515,517],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,99,127,155,161,168,177,197,209,210,220,225,231,236,240,245,252,253,254,269,281,282,290,294,302,328,333,334,347,385,398,405,409,415,418,432,440,468,488,489,496,500,513],exager:507,examin:[6,8,17,228,294],examp:[484,513],exampl:[],exce:[3,6,16,17,18,42,61,76,179,216,217,220,221,222,223,225,229,231,236,241,268,294,309,313,319,320,328,378,385,486,513],exceed:[3,42,62,225,231,268,328,494],excel:411,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,97,98,119,120,123,128,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,177,181,183,184,185,186,187,188,189,191,192,194,195,196,197,200,201,202,205,208,211,217,218,220,224,225,229,231,238,243,244,247,250,252,254,268,269,270,271,272,273,274,275,276,277,278,281,282,285,287,288,289,290,291,295,304,305,312,314,315,325,328,331,333,334,340,344,348,351,352,353,354,355,356,357,359,360,363,364,365,370,371,373,375,379,380,381,383,384,385,386,387,389,392,393,394,395,396,397,398,399,400,401,403,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,436,441,442,443,445,448,449,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,483,484,486,488,489,491,494,495,496,497,498,500,504,507,512,513,514,516],excess:[219,411],exchang:[2,3,6,8,64,65,208,214,215,244,252,304,312,336,340,343,370,385,411,501],exchange:370,excit:411,exclud:[3,6,9,12,16,17,66,76,123,151,157,164,165,181,201,217,221,226,227,256,264,297,310,312,335,346,351,378,379,381,393,415,418,421,432,433,440,465,498],exclus:[1,3,12,16,95,385,400,438,440,495,505],excurs:[268,481],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,178,204,249,306,353,369,372,384,482,484,494,497,500,513],exempl:456,exemplari:245,exemplifi:411,exert:[6,250,253,307,347,348,349,371],exhaust:[214,384,513],exhibit:[100,268,377,411,495],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,133,177,178,196,203,204,205,208,213,224,227,229,232,244,297,298,300,351,352,354,356,357,358,360,364,374,379,385,406,407,418,448,465,475,482,484,486,487,488,497,498,499,508,513,514,515],exit:[2,3,11,12,42,60,201,225,240,369,384,484,485,494,503,513],exlanatori:3,exp:[],expand:[],expans:[12,151,201,497,513],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,112,158,169,175,197,225,237,244,246,265,293,299,301,302,307,312,351,371,381,398,435,438,440,481,484,486,488,491,495,500,513],expens:[6,76,205,293,297,312,340,351,370,371,381,385,484],experi:[6,13,15,17,224,232,249,258,267,299,311,312,376,380,405,440,495,500],experienc:[6,12,257,258],experiment:[244,370,385,500],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,94,102,157,165,197,201,202,204,205,208,217,218,223,225,227,229,231,268,293,301,312,325,351,353,369,370,373,379,380,384,390,409,421,456,458,473,484,487,488,491,493,496,507,508,513,517],explan:[3,6,62,124,151,201,202,217,267,293,418,480,483,484,486,495],explanatori:[3,8,128,201,202,216,217,220,221,222,312,379,483,513],explantori:[3,308],explic:439,explicit:[6,9,11,22,45,82,95,124,127,171,185,209,210,231,319,320,355,375,387,388,391,396,398,409,411,422,432,472,480,483,487,490,508],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,120,123,154,164,167,175,177,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,221,224,231,238,243,245,247,252,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,301,302,304,312,314,315,331,333,334,340,344,348,354,356,357,359,360,363,365,379,385,386,387,389,392,393,394,395,396,397,398,399,400,401,402,404,405,408,409,410,412,413,414,415,416,417,418,422,423,424,425,426,427,428,429,430,431,432,436,438,440,441,442,443,445,450,451,458,459,460,461,462,463,464,466,467,468,469,470,471,472,474,476,477,478,486,488,489,495,496,498,499,505,507,508],explictli:[16,499],exploit:[15,17,295],explor:[129,176],expon:[3,303,305,409,414,417,431,439,451],exponenti:[95,446,467,474,478,500,513],expos:11,exposit:[214,405,408],express:[6,151,163,177,209,210,229,265,293,303,340,346,353,391,409,411,425,435,456,457,466,513],expressiont:391,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,90,91,92,95,96,99,101,104,107,108,118,120,128,130,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,202,208,211,212,215,223,224,230,233,237,242,243,244,246,247,248,250,252,254,266,268,273,282,293,294,310,311,312,314,317,322,325,327,331,332,333,334,335,337,338,340,342,345,349,350,414,435,438,449,450,457,503,504,512],extent:[1,3,42,43,46,60,76,175,179,201,213,221,225,250,347,350,370,373,387,452,454,468,483,486,489],exterior:[3,6,175,349],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,112,120,121,123,129,152,154,155,156,158,160,163,164,165,166,167,169,170,176,177,178,179,183,205,220,225,227,268,300,301,302,312,328,378,379,382,383,404,415,418,421,435,440,483,484,486,489,498,507,513],extract:[3,6,11,13,36,66,68,73,84,95,101,118,126,128,130,209,210,305,380,401,412,435,457,484,491,503],extract_atom:11,extract_comput:[11,484],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,204,219,229,231,268,338,411,470,507],extrema:431,extrins:214,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[173,342],f_a:[469,470,471],f_ave:128,f_c:470,f_f:471,f_fix_id:302,f_foo:513,f_harm:338,f_i:[29,446],f_id:[6,76,128,130,201,202,208,216,217,218,219,220,221,222,223,263,330,342,504,513],f_ij:446,f_indent:223,f_int:337,f_j:29,f_jj:99,f_k:446,f_langevin:340,f_max:[302,307],f_msst:266,f_r:[253,469,470,471],f_sigma:391,f_solid:338,f_ss:6,f_temp:[],face:[3,6,60,62,76,165,175,179,213,221,222,345,347,348,349,350,373,414,435,450,486,489],face_threshold:175,facet:175,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,298,328,338,415,448,456,498],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,95,99,112,119,126,127,129,151,171,176,179,183,194,200,201,204,205,209,210,218,225,229,231,232,244,249,252,254,255,266,268,269,273,295,299,303,311,315,318,320,328,332,336,343,344,345,349,360,371,373,379,385,387,388,391,392,394,396,401,402,403,405,406,407,411,415,418,422,423,435,438,440,442,443,449,451,458,467,472,483,486,489,490,495,498,500,501,504,507,512,513],factori:[3,484],factoriz:370,fail:[3,9,11,12,62,181,229,232,370,378,380,403,449,484],failur:[132,453,485,513],fairli:[11,440,495,500,508],faken:78,falcon:249,fall:[3,6,205,220,298,484,513],fals:[94,351,353,456,513],fame:8,famili:[474,483],familiar:[0,11,508],fan:446,far:[3,6,12,17,60,62,64,94,201,202,205,206,225,226,227,229,232,268,293,311,312,328,345,356,360,376,380,381,473,484,486,491,504],farago:252,farrel:[469,471],farther:201,fashion:[6,8,42,76,177,205,208,209,210,215,221,225,227,232,244,246,250,265,266,268,270,271,272,273,274,275,276,284,287,288,289,290,291,301,302,304,312,317,321,327,330,338,340,344,345,346,348,350,380,418,432,489,498,513,516],fasolino:420,fast:[6,7,9,12,13,17,40,201,202,279,302,341,370,371,393,432,433,438,466,468,488,493,495,504,514,517],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,115,120,123,154,164,183,184,186,187,188,189,191,192,194,195,197,201,202,205,211,224,225,231,238,243,247,251,252,268,270,271,272,273,274,275,276,277,278,285,287,288,289,291,299,303,304,312,314,315,328,331,333,335,337,340,344,348,354,356,357,359,360,363,365,370,371,382,383,385,386,387,389,391,392,393,394,395,396,397,398,399,400,401,404,405,409,410,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,436,441,442,443,445,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,489,495,499,507],fastest:[1,6,14,17,165,221,340,341,385,483],fatal:[3,503],fault:[75,449],faulti:12,fava:414,favor:228,favorit:7,fbmc:335,fcc:[],fcm:[284,513],fdirect:235,fdotr:419,fdt:[],fdti:95,fe2:176,fe3:176,fe_md_boundari:214,featu:8,featur:[],fecr:409,feedback:[7,249],feel:[7,249,250,258,293,349,351,380,440],felling:437,felt:349,femtosecond:512,fene:[],fennel:[401,423],fep:[],ferguson:[6,183,498],fermi:[1,9,10,12,15,163,385,471],fermion:411,fernando:434,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,206,216,217,218,220,221,222,223,253,268,298,301,303,315,342,370,378,379,380,387,456,483,486,491,495,497,505,515],fewer:[1,3,11,15,16,64,258,495],fewest:3,fextern:242,feynman:295,fff:484,ffield:[400,412,448,449,456],ffmpeg:[3,12,204],ffplai:204,fft:[1,3,7,9,11,12,14,15,96,120,121,152,294,370,371,495],fft_inc:[12,371],fft_lib:12,fft_path:12,fftbench:[370,505],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:465,fictiti:[6,211,212,237,242,246,295,311,401,423,427,465],field1:[487,491],field2:487,field:[],fifth:[325,442],figur:[1,3,8,12,302,483,484,508],fij:404,file0:293,file1:[11,13,293,339,353,379,491,493,497],file2:[11,13,339,353,379,491,493,497],file:[],file_from:203,filen:379,filenam:[3,12,13,38,42,57,197,201,202,204,205,206,214,217,218,219,220,221,222,223,225,230,240,293,297,300,303,304,305,308,309,312,313,339,340,367,368,369,379,380,386,387,391,401,409,410,412,420,435,436,437,442,446,447,448,449,456,457,467,468,469,470,471,474,482,483,484,487,488,493,497,504,513,515,516,517],filennam:493,filep:[3,201,202,205,488,493,517],filepo:309,fill:[7,9,177,204,298,340,373,381,391,438,449,489,508],filter:[205,214],final_integr:8,final_integrate_respa:8,finchham:[6,159,403],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,95,128,180,197,206,215,228,229,240,241,244,267,293,298,299,307,311,376,378,380,381,401,418,423,427,435,456,466,468,507,508,513],find_custom:8,fine:[16,17,181,211,237,338,381,385,508,513],finer:[151,177,513],finest:370,finger:[177,200,265,489],finish:[6,11,42,225,353,367,369,370,382,384,385,473,491,513,514],finit:[],finni:[7,409,466],finvers:235,fiorin:[9,230],fire:[],firebrick:205,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,87,96,99,113,114,115,117,123,127,128,138,141,144,145,149,152,162,165,171,173,175,176,178,179,180,184,197,201,202,203,204,205,206,208,209,217,218,220,221,222,223,225,228,231,240,244,245,250,255,265,266,267,268,293,295,300,301,302,304,309,312,315,317,325,326,328,329,330,337,338,339,340,342,346,351,353,354,361,373,378,379,380,381,384,385,386,387,390,391,392,394,396,398,400,401,409,411,412,415,416,418,419,420,421,422,423,427,432,433,435,437,438,440,442,446,448,449,456,457,465,467,468,469,470,471,474,478,481,482,483,484,486,487,488,491,493,495,498,499,500,503,504,507,508,513,514,515,517],fischer:[6,9,19,20,183,396,498],fit:[3,6,9,12,38,57,197,240,311,328,387,391,420,435,440,461,468,470,494,508,513],five:[78,163,302,379,391,436,486,500],fix:[],fix_adapt:[171,210,431],fix_atom_swap:[],fix_bal:65,fix_deposit:[3,215,298],fix_eo:9,fix_evapor:215,fix_flux:214,fix_gcmc:[215,379],fix_gl:246,fix_gld:246,fix_grav:298,fix_id:[3,229,266,268,270,271,272,273,274,275,276,299,302],fix_manifoldforc:508,fix_modifi:[],fix_mov:[200,346],fix_nh:8,fix_npt:246,fix_nv:508,fix_nvt:[215,244],fix_poem:[3,6,9],fix_pour:[3,232],fix_qbmsst:9,fix_qeq:[3,400],fix_rattl:315,fix_reax_bond:448,fix_rigid:[258,390],fix_saed_vtk:313,fix_setforc:8,fix_shak:315,fix_shardlow:9,fix_srd:3,fix_styl:273,fix_temp_rescal:334,fixedpoint:[229,268],fixextern:242,fixid:214,fji:404,flag1:[234,383],flag2:[234,383],flag:[3,8,9,11,12,14,15,16,17,41,70,79,80,87,94,97,98,103,113,114,116,129,172,176,180,201,202,204,205,206,223,228,230,234,249,252,256,258,264,265,294,301,312,325,327,328,335,339,348,351,368,371,379,383,384,385,387,417,422,435,438,465,481,483,484,486,487,488,490,491,492,496,508,513],flag_buck:395,flag_coul:[395,404,427],flag_lj:[404,427],flagfld:[393,432,433],flaghi:[3,393,432,433],flaglog:[393,432,433],flagn:234,flagvf:[393,432,433],flat:[6,340,345,346,350],flavor:[2,7,12],fld:[],flen:388,flex_press:388,flexibl:[3,6,8,178,204,217,221,230,246,269,336,343,411,470,504],flip:[3,6,231,268,347,348],floor:513,flop:12,floralwhit:205,flow:[],fluctuat:[6,67,95,229,244,245,252,255,268,273,293,294,299,316,338,340,363,407],fluid:[],fluid_veloc:259,flush:[3,205,503],flux:[],flv:204,fly:[7,9,12,42,204,208,214,219,232,235,312,315,341,391,438,504,507],fmackai:9,fmag:233,fmass:295,fmax:[378,504],fmomentum:235,fmsec:[2,205,252,253,265,268,299,312,331,332,495,506,512,514],fname:369,fno:[9,12,16],fnorm:[378,504],fnpt:235,fnvt:235,foce:418,fock:388,focu:315,fogarti:[9,305,449],foil:[151,293,457],fold:[326,495],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,88,99,100,106,107,117,124,127,128,130,151,152,155,156,157,163,165,170,173,175,177,178,183,186,187,188,189,191,192,194,195,197,201,203,204,205,208,214,215,216,217,218,219,220,221,222,223,225,230,231,232,235,236,239,240,242,244,245,246,249,251,252,253,255,258,266,268,273,274,275,276,287,288,289,291,294,295,297,300,301,302,303,305,307,309,311,312,313,315,330,331,332,333,336,337,338,339,340,342,343,351,352,356,357,358,359,360,363,365,368,373,375,378,379,380,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,476,477,478,479,481,483,484,486,487,489,491,493,494,495,498,500,501,502,507,508,513,514,516],foo:[4,8,11,12,201,204,242,484,497,513],foot:6,footprint:[12,385],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:258,forcefield:[311,417],forcegroup:255,forcezero:376,ford:404,forestgreen:205,forev:76,forget:[253,507],forgiv:268,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,95,97,98,100,103,113,114,116,127,151,152,171,172,181,185,205,208,209,210,227,245,246,252,254,258,265,289,294,305,307,311,312,340,345,349,354,355,358,363,375,377,379,380,387,388,391,398,406,407,409,411,413,417,418,422,434,435,437,438,442,443,446,448,449,450,456,457,458,466,468,469,470,471,477,480,483,484,486,491,496,503,507,513],formal:[6,83,86,99,245,246,252,268,295,328,336,456],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,185,197,201,202,203,204,205,206,217,220,221,222,223,225,227,240,294,297,301,303,305,308,312,313,324,339,340,351,352,355,375,379,380,386,387,391,398,409,412,422,435,437,447,448,449,451,457,468,474,475,483,484,486,487,488,491,502,503,504,513,515],former:[6,12,16,40,42,205,225,340,344,391,393,492,498,513],formerli:[7,13],formul:[1,9,41,67,152,211,237,252,268,289,303,305,311,315,339,370,387,391,409,411,414,435,445],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,95,97,98,99,104,106,107,116,123,129,130,152,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,176,177,182,184,185,196,200,201,209,210,211,212,217,218,219,220,223,224,231,237,247,248,250,252,253,265,293,294,300,309,314,322,326,328,331,332,333,342,345,348,350,351,353,354,355,357,364,373,379,387,388,390,391,396,397,398,399,404,405,409,410,414,415,416,417,419,422,423,425,426,427,429,430,432,433,435,439,440,441,450,451,458,466,467,468,469,470,471,474,476,477,482,486,489,496,503,504,512,513,514],forth:[1,6,11,12,13,14,15,384,484,489,493],fortran:[3,6,9,11,12,13,242,409,418,435,448,449],fortun:8,forward:[3,8,95,369,380,385],foster:[391,445,446],foul:180,found:[3,6,9,12,78,171,201,228,230,244,249,255,294,335,341,353,369,381,398,401,404,481,487,488,503],four:[6,11,55,87,113,114,151,173,266,340,363,379,380,438,481],fourier:[],fourth:[6,115,311,325,335,396,442,456],fox:[6,129,183,464,498],fphi:[38,57,468],fpic:12,fplo:[38,57,468],fprime:468,fqdn:251,fqq:404,frac:[],fraction:[1,3,6,8,12,16,40,42,86,120,152,180,200,204,205,215,226,227,228,229,266,298,302,309,310,328,333,334,373,380,385,391,393,415,432,433,491,496],fragment:[43,249,309],fraig:43,frame:[91,151,205,214,266,302,347,414],framer:[204,205],framework:[5,246,386,457],franc:9,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,95,171,209,210,293,328,337,338,339,340,377,380,388,411,431,438,446,477,483],freedom:[3,6,8,104,106,107,109,111,112,123,154,155,156,157,158,159,16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au_1:245,tau_k:245,tau_n_k:245,tb3:176,tbead:169,tbp:391,tchain:[268,269,273,289,290,312],tcl:307,tcom:253,tcsh:[11,12,398],tdamp:[252,268,269,273,312,331,332],tdephas:481,tdrude:[162,235,253,507],teal:205,tech:[7,9,13],technic:[6,7,9,255,305,328,449],techniqu:[6,7,9,95,208,229,266,302,312,344,347,371,440,468,507],technolgi:9,technolog:[9,14,19,249],tell:[2,6,11,12,37,56,196,208,294,364,381,448,449,466,484,488,507],telsa:17,temeperatur:11,temp:[],temp_drud:507,temp_eff:107,tempcom:[155,156,170],temper:[],temperar:295,temperatur:[],temperature_definit:214,tempfix:501,templ:[7,9,18],templat:[3,8,13,17,19,41,177,178,180,232,244,298,312,315,379,486],templeton2010:214,templeton2011:214,templeton:[9,214],tempor:245,temporari:[2,3,493],temporarili:[197,311,499,500],ten:14,tend:[29,268,293],tensil:[7,231],tensor:[3,6,8,66,90,91,97,98,99,103,116,123,138,141,142,143,144,147,148,149,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,229,255,258,268,269,273,297,299,312,343,370,371,379,411,432,433,438,453,455,504,513],tenth:[138,209,369],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,64,95,96,97,99,121,123,152,153,155,156,165,170,171,184,185,186,197,205,209,210,216,218,220,223,231,237,245,246,247,252,253,254,255,267,268,269,270,271,272,273,274,275,276,287,288,289,291,295,299,302,311,312,326,331,332,333,340,342,344,346,354,355,365,370,378,381,386,387,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,409,410,411,412,414,415,416,423,427,430,431,432,433,435,436,437,438,440,441,443,450,456,465,467,469,470,471,474,477,495,496,498,504,507],termin:[129,268,378,380,453,455,485,494],termostat:332,terrel:377,terri:7,tersoff:[],tersoff_1:[469,470,471],tersoff_2:[469,470,471],tersoff_mod:470,tertiari:189,tessel:[9,175],test:[],test_descriptor_str:3,testf:197,testu:197,tether:[6,310,317,325,327,338,413],tetot:[9,456],tex:8,texa:445,texas_holdem:311,text:[2,3,4,6,7,8,12,13,38,42,57,197,201,202,204,205,208,214,217,218,219,220,221,222,223,225,230,240,249,300,339,340,352,371,373,380,409,412,422,435,457,468,482,486,487,503,508,513,515],textur:17,tfac_insert:244,tfactor:[3,205],tfinal:513,tfix:311,tflag:204,tfmc:[],th4:176,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,60,61,62,64,66,72,76,81,94,96,100,115,117,119,123,126,127,130,152,175,178,179,180,186,197,200,201,203,205,208,213,215,217,220,221,222,223,225,226,227,228,229,231,232,233,236,240,241,244,245,246,247,250,251,252,255,266,293,294,298,299,300,301,302,303,305,307,310,311,312,313,316,317,318,324,325,326,328,332,333,335,336,340,343,344,345,346,347,348,349,350,351,353,370,371,376,377,378,379,380,381,382,385,387,390,391,392,394,395,396,409,411,414,415,421,432,433,435,440,448,449,450,456,458,465,466,467,468,471,473,475,477,478,481,482,483,484,486,487,488,489,490,491,494,495,498,500,501,503,513,514,515],thank:[249,469,471],thb:449,thb_cutoff:449,thb_cutoff_sq:[448,449],thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,60,62,64,66,67,70,72,75,76,79,80,87,90,92,95,96,97,98,99,103,113,114,116,118,119,120,123,125,126,127,128,130,151,154,155,157,159,160,163,164,170,172,174,175,177,179,180,181,183,184,186,187,188,189,191,192,194,195,196,197,201,202,204,205,208,209,210,211,213,216,217,218,220,221,222,223,224,225,226,227,228,229,231,232,237,238,243,244,245,247,248,249,252,253,255,258,265,268,270,271,272,273,274,275,276,277,278,279,280,285,287,288,289,291,297,298,299,300,301,303,304,311,312,313,314,315,328,329,331,332,333,335,339,340,342,343,344,346,348,349,351,352,353,354,356,357,358,359,360,363,364,365,368,370,371,373,375,377,378,379,380,381,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,410,411,412,413,414,415,416,417,418,419,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,445,446,448,449,450,451,456,457,458,465,466,467,468,469,470,471,472,473,474,475,476,477,478,482,484,486,487,488,489,490,491,495,496,498,499,504,507,508,513,515,516],them:[1,2,3,6,7,8,9,11,12,13,14,17,40,41,42,55,62,76,99,113,118,125,128,130,153,179,184,201,204,205,206,216,217,218,220,221,222,223,225,228,229,231,241,249,252,253,264,268,270,271,272,273,274,275,276,287,288,291,293,299,301,309,310,311,312,315,328,331,332,333,335,339,340,342,346,347,348,350,351,354,371,373,379,380,381,385,386,391,398,409,412,414,418,421,440,450,458,472,473,481,484,486,493,498,501,507,508,513,514],themselv:[6,9,11,180,209,210,225,253,370,371,380,382,386,391,401,409,431,435,436,437,457,513],theor:335,theorem:[245,252,316,391,407],theoret:[115,249,302,467],theori:[3,6,9,12,41,151,214,230,246,268,294,370,371,391,438,477,500],thereaft:[76,260,296,312,336,343,484],therebi:[341,432,433],therefor:[3,6,12,67,95,162,235,244,253,255,315,335,371,403,447,449,467,472,495,507],therein:[6,435],thereof:95,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,66,120,484,504],thermo_press:[66,123,229,235,268,270,271,272,273,274,275,276,299,503,504,507],thermo_styl:[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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 displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":226,"default":[37,40,41,56,60,61,62,64,65,76,95,96,100,112,113,115,117,118,129,133,134,151,157,165,166,170,176,177,180,182,196,199,200,201,202,204,205,206,207,209,210,211,213,214,215,217,221,222,223,226,227,229,230,231,232,236,241,244,245,250,252,253,254,255,256,258,263,266,268,269,273,289,290,294,295,298,299,300,301,302,304,307,309,310,312,313,328,330,335,336,337,338,341,343,345,347,351,364,368,370,371,373,374,376,377,379,381,382,383,385,388,391,393,411,432,433,438,440,448,449,465,466,481,482,483,486,487,489,491,493,494,495,498,500,502,503,504,505,506,512,514,515,516],"function":513,"long":[219,392,394,395,396,397,401,403,404,423,427,431,443,451,472],"new":8,"static":12,acceler:1,account:508,ackland:67,acknowledg:7,adapt:[209,210],addforc:211,addit:[12,13,508],addtorqu:212,adiabat:6,adjust_dt:318,adp:386,after:508,airebo:387,alloi:409,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:213,apr:0,arrai:6,aspher:[6,9,90,155,270,274,278,279,287],atc:[9,214],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,87,89,93,100,105,106,109,110,111,117,121,122,124,151,152,175,213,215,216,301,513],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:224,awpmd:[9,388],balanc:[42,225],barostat:6,basal:71,beck:389,berendsen:[299,331],between:6,binary2txt:13,bodi:[6,8,9,43,72,156,271,275,280,288,390],bond:[8,13,73,74,226,227,228,308],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:391,born:[392,403],boundari:[7,60],box:[6,61,229],branch:508,brownian:393,buck:[394,395,403,434],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:508,change_box:62,charmm:[6,20,183,396,431],chunk:[6,70,76,80,98,103,114,116,125,157,172,174,217],citat:7,class2:[9,21,44,184,354,397],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,345,399,477],colvar:[9,13,230],com:[79,80,158],comb3:400,comb:[304,400],come:5,comm_modifi:64,comm_styl:65,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,513],compute_modifi:112,condit:7,conduct:[6,336],conserv:406,constant:[6,513],constraint:7,contact:[81,131],contact_radiu:[],coord:82,core:6,coreshel:9,correl:[218,219],cosin:[23,24,25,26,27,28,186],cossq:356,coul:[392,394,395,396,397,401,402,403,416,423,427,431,443,451],coupl:6,creat:227,create_atom:177,create_bond:178,create_box:179,createatom:13,creation:7,csld:332,csvr:332,cubic:425,cuda:[9,14,120,123,154,164,211,224,238,243,247,268,277,314,315,331,333,344,392,394,396,397,409,415,416,423,424,426,429,441,467,469],custom:[8,201,202],cut:[50,388,394,397,401,404,411,413,423,424,431,439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