diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 09f86315be4e7081046572eeb184cfefec692ece..655458bf7d4501803f9b0deda02016131d907982 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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63,396,421,426,469,480,498,502,510,527],"try":[1,3,8,12,16,18,219,253,259,345,346,347,352,498,522,527],"var":[3,11,12,178,361,379,511,527],"void":[4,6,7,8,41,181,225,245,503],"while":[1,3,9,11,12,13,17,74,75,115,152,161,176,189,203,208,217,229,231,232,236,249,250,255,256,257,259,265,273,296,309,310,314,316,320,350,381,389,396,402,413,419,461,462,483,485,488,495,498,509,514,521],__main__:498,__pthread_key_cr:12,_boundingbox:204,_compute_group_group:154,_compute_heat_flux:154,_compute_t:8,_j1m1m1:152,_j2m2m2:152,_manifold_rattl:522,_pair_lj:9,_serial:12,_wirnsberg:239,a10:363,a123:363,a12:463,a2m:[6,99],a_0:[259,349,402],a_0_real:259,a_1:349,a_2:349,a_3:349,a_4:349,a_c:410,a_cc:410,a_f:485,a_ij:402,a_pi:402,a_sigma:402,a_ss:410,aat:185,aatom1:[68,126],aatom2:[68,126],aatom3:[68,126],ab_23_cd:363,abbrevi:12,abc:[3,12,363,498,527],aberdeen:[88,89,241,324],abf:230,abf_integr:13,abi:208,abil:[3,229,273,306,319,421],abl:[3,8,9,11,12,39,94,203,208,228,238,247,289,345,352,396,498,527,531],ablat:349,abort:515,about:[0,1,3,6,8,9,11,12,13,15,16,39,41,42,63,65,82,119,126,127,130,172,178,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,240,244,245,246,247,248,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,269,272,278,282,283,284,285,286,287,288,289,290,291,292,295,299,300,301,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,321,322,323,333,334,335,337,338,340,341,342,343,344,345,346,347,348,349,351,352,353,354,356,357,358,359,360,361,378,381,385,388,389,391,396,401,407,412,429,458,462,491,498,501,502,507,508,510,515,519,522,527,530,532],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,35,37,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,59,65,66,71,74,75,76,77,80,81,94,95,97,98,99,103,104,106,107,123,125,127,128,130,152,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,176,177,178,180,181,184,185,186,187,188,189,190,191,192,193,195,196,197,199,203,204,205,206,207,210,211,212,213,214,218,219,220,222,223,225,228,229,231,232,233,238,242,245,246,248,252,254,256,257,258,262,272,273,278,302,305,307,312,318,319,320,325,333,337,340,341,342,343,361,363,364,365,366,367,368,369,370,371,373,375,381,383,386,390,391,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,432,434,435,436,437,438,439,440,441,442,443,444,445,446,449,450,451,452,453,454,456,458,459,461,462,463,464,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488,490,491,492,493,494,495,496,497,498,500,501,502,503,504,507,508,509,510,511,514,515,518,521,522,527,528,531,532],abscissa:[453,454,481,482],absenc:214,absent:521,absolut:[3,207,217,230,232,236,320,325,339,380,381,389,426,434,501],absorb:349,absoult:381,abstol:320,ac3:177,academ:248,acc:344,acceler:0,accelri:[6,13],accept:[7,12,95,176,178,207,228,232,248,320,344,406,438,508,515,522],acceptanc:217,acceptor:428,access:[0,3,6,7,8,9,11,12,15,38,40,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,93,96,97,98,99,100,101,102,103,105,106,109,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,128,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,173,174,175,176,177,200,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,234,237,238,239,240,244,245,246,247,248,249,250,251,252,253,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,272,273,278,282,283,284,285,286,287,288,289,290,291,292,295,299,300,301,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,321,322,323,325,330,333,334,335,336,337,338,339,340,341,342,343,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,376,380,396,398,424,426,428,429,446,461,462,471,497,498,501,506,518,519,527],accident:522,accidenti:373,accler:[9,12],accommod:215,accomod:273,accompani:8,accomplish:[15,232,260,290],accord:[6,66,75,88,133,139,142,160,206,217,226,227,243,259,273,289,301,309,325,327,346,347,349,354,355,357,358,359,392,421,426,437,440,459,466,468,469,471,473,474,476,477,478,514,527],accordingli:[11,112,156,157,171,176,182,392,443,444,478],account:[3,6,95,130,160,176,177,186,198,220,222,237,239,253,254,256,273,279,280,281,293,294,296,298,300,304,310,319,321,323,333,335,336,337,340,341,342,345,349,352,369,390,412,417,426,434,438,443,444,446,449,469,497,514,522,528],accuml:[3,319,345,352],accumul:[6,8,14,75,88,154,210,220,221,256,319,325,351,378,396,506,526],accur:[1,3,6,9,14,16,37,41,56,161,225,246,271,314,319,320,323,337,345,352,358,361,381,402,421,425,426,451,463,479,481,482,483,485,514,519,527],accuraci:[1,3,6,12,41,202,203,207,225,239,250,273,311,323,350,361,380,381,388,398,421,451,453,454,461,462,481,482,489,509,514,519,521,527,531],accuractli:519,ach:380,achiev:[1,3,6,9,10,15,16,17,28,41,225,239,246,248,250,273,274,289,301,302,309,380,429,509],achiv:17,acid:9,ackland1:419,ackland2:419,ackland:2,acknowledg:0,acml:12,aco:527,acolor:[206,207],acoust:301,acquir:[3,6,60,63,64,181,182,227,229,232,273,457,493,505,521],across:[1,2,3,6,9,12,13,14,41,59,63,68,71,73,75,84,102,119,126,128,166,180,182,219,222,225,237,246,252,319,320,321,326,345,349,352,358,363,391,396,495,500,503,504,508,517,519],act:[3,6,73,119,129,163,236,246,251,254,255,256,257,259,262,272,319,330,344,346,347,349,358,359,361,389,404,415,425,426,428,463,478],acta:[130,177,397],actinid:[9,449],action:[2,6,11,12,75,249,254,347,521],activ:[5,8,11,12,13,15,55,61,95,176,230,249,253,256,262,268,272,299,319,320,328,348,378,442,479,509,521,524,527],active:[268,494],actual:[1,3,6,8,12,56,64,134,161,203,204,207,211,212,224,226,227,231,236,256,257,296,300,305,306,314,317,325,337,340,341,342,344,350,359,361,380,392,425,427,432,437,443,444,478,497,498,509,510,518,527],actualli:339,adam:[380,381],adapt:[2,3,6,9,95,172,210],adapti:300,adaptiv:[9,230,398],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,40,42,75,95,99,112,125,128,129,131,176,178,179,203,204,205,206,210,211,212,213,214,216,218,219,220,222,223,227,230,231,236,238,239,245,250,251,252,254,256,258,259,263,271,272,273,274,275,276,277,278,279,280,281,293,294,296,297,298,300,308,318,319,322,323,333,334,336,340,342,343,347,348,349,351,353,354,358,361,381,383,388,390,398,403,405,408,412,421,429,434,446,451,452,456,462,464,498,500,501,506,508,510,512,519,521,522],add_molecul:216,add_speci:216,add_to_nodeset:216,added:[501,522],addforc:[2,3,210],adding:[8,213,238,246,318,522],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,236,238,239,242,243,248,250,251,252,256,259,273,274,275,276,277,278,279,280,281,291,293,294,296,297,298,300,308,319,322,323,324,326,350,353,354,358,365,371,374,376,381,383,391,393,396,397,398,402,403,405,407,409,411,412,415,417,418,419,420,421,422,426,427,429,430,431,433,434,442,444,445,446,447,448,449,451,453,454,455,456,459,461,462,464,469,470,479,480,481,482,483,484,485,488,492,495,500,501,502,507,508,509,512,514,521,522,523,525,527,530,531,532],addition:[0,4,6,8,11],additionali:204,addres:9,address:[7,8,11,206,255,522],addtorqu:2,adequ:[265,337,350,380,391,509],adher:28,adhikari:259,adiabat:0,adiam:[206,207],adjac:[39,176,178,239,391,451,481,482,483,514,515],adjiman:450,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,232,253,256,260,264,269,270,273,274,278,296,300,303,305,306,309,310,311,312,317,319,320,328,337,341,345,350,352,353,354,356,357,359,380,381,389,391,396,398,418,443,444,469,485,510,528],adjust_radiu:328,adjust_radius_factor:328,admiss:278,adof:[158,219],adopt:[318,521],adp:[2,3,7],adri:[9,315,461,462],adust:172,advanc:[3,15,253,402,495,506],advantag:[1,6,8,11,17,39,40,41,225,231,396,420,509,514],advect:[3,6,337],advertis:8,advis:[320,391,460,519],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,232,233,239,245,252,254,256,262,268,270,274,275,276,277,279,280,281,287,293,294,296,298,319,321,335,349,359,373,380,387,388,389,391,392,393,396,421,443,444,451,497,498,500,502,503,505,508,510,519],affin:[15,16,17,232,396,411],affiniti:396,afile:250,aforement:17,afresh:[307,508,527],afshar:416,after:[2,3,5,6,8,11,12,14,20,21,32,39,40,41,44,50,59,60,61,63,65,75,156,157,158,159,160,161,162,165,166,167,168,170,171,179,181,182,185,186,191,197,202,203,204,205,206,207,208,210,211,212,216,217,219,220,225,226,227,228,229,231,232,236,248,259,260,261,262,263,269,270,271,273,279,280,281,287,293,294,296,298,301,305,309,317,319,320,323,332,334,338,340,341,342,344,345,346,347,348,352,354,356,361,364,365,371,379,386,387,389,390,392,394,395,396,397,398,402,409,411,419,420,421,422,423,429,430,431,442,443,444,446,447,448,449,453,454,455,459,461,462,469,470,479,480,482,483,484,485,488,495,497,499,500,501,502,503,505,506,508,510,512,514,517,518,519,521,522,526,527,528,530,531,532],afterrun:508,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,232,239,252,305,364,379,391,443,444,495,497,498,500,502,507,514,516,527,530],against:[11,12,13,66,233,391,461,462],aggreg:[6,12,68,71,73,84,102,119,126,252,269,317,319,335,495,528],aggress:[239,252,514],agilio:[9,13],agre:[3,8,199,389,398,431,462],agreement:[5,7],ahd:428,ahead:356,aidan:[0,5,7,9,13,383],aij:13,aim:6,airebo:[2,3,7,226,227,316],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,253],aktulga:[7,9,312,462],al2o3:469,al2o3_001:[130,321],al3:177,ala:[259,469],alain:9,alat:[300,446],albe:[459,483,485],albeit:318,albert:9,alchem:[95,172],alcohol:352,alcu:[397,402],alcu_eam:459,alderton:415,alejandr:[273,274],alessandro:13,algebra:449,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,232,239,252,259,261,262,287,302,310,319,323,324,344,345,349,352,357,387,388,389,393,396,417,421,444,449,466,468,495,497,514],alia:[9,15],alias:[1,381],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,254,383,500,503,521],alkali:421,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,265,266,268,269,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,332,333,334,336,337,338,339,340,341,344,345,346,347,348,349,350,351,352,354,355,356,357,358,359,360,361,362,363,364,365,369,374,376,378,379,380,381,382,383,386,389,390,391,392,393,395,396,397,398,399,401,402,403,405,406,407,408,409,411,412,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,497,498,499,500,501,502,503,504,505,507,508,509,510,511,512,513,514,515,517,518,519,521,522,526,527,528,530,531,532],allen:[28,95,415,425],allentildeslei:95,allign:3,allindex:362,alloc:[3,5,6,8,9,11,12,62,245,351,390,392,396,457,462,500,508],allocat:3,alloi:[2,3,12,13,397,402,412],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,237,238,245,248,249,250,251,253,254,256,259,262,263,268,270,273,274,291,300,304,305,306,307,308,309,311,313,318,319,320,321,322,323,325,327,328,332,333,334,335,336,337,344,345,346,347,349,350,351,352,353,354,358,361,363,365,374,376,380,381,383,389,390,391,392,395,396,398,399,402,403,404,405,406,407,412,419,421,426,427,428,429,434,438,443,444,449,451,459,462,463,466,468,469,478,486,489,491,493,495,498,500,502,503,504,505,506,507,510,512,513,514,517,518,522,527,528],almost:[2,3,12,15,62,254,309,349,381,393,396,478],alo:412,alon:[6,7,228,315,461,462,498],alond:13,along:[6,8,12,28,40,74,75,95,130,176,177,178,202,203,206,219,228,239,254,259,260,264,265,270,272,309,319,323,325,329,333,335,344,348,349,355,358,361,383,385,387,388,389,391,412,415,426,429,432,434,438,446,461,462,481,482,500,503,510,511,527],alonso:[447,448],alpha:[6,12,51,211,231,259,309,310,314,389,397,400,403,412,416,417,419,420,422,423,428,433,434,446,452,458,484,486,518,521],alpha_c:442,alpha_i:470,alpha_lj:442,alphabet:[2,3,21,36,44,55,65,186,198,210,365,374,390,409,479,500],alphanumer:[3,65,210,308,316,363,390,527],alreadi:[3,7,8,9,12,16,17,42,57,178,179,181,205,215,219,225,227,232,263,307,309,337,361,362,390,391,416,427,429,436,444,478,489,492,496,500,501,505,510,526,527],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,28,35,36,37,39,40,41,42,44,54,55,56,60,61,63,65,69,74,75,76,77,79,81,86,87,88,89,95,97,98,100,103,113,114,115,116,117,118,120,121,123,125,127,128,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,198,199,201,202,203,204,205,206,207,208,210,211,212,213,215,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,238,241,242,243,245,246,247,248,249,250,252,253,256,257,258,259,268,270,271,273,274,275,276,277,278,279,280,281,286,290,291,293,294,296,297,298,300,301,302,304,305,306,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,329,330,333,335,337,340,341,342,343,344,348,349,350,351,353,355,358,361,362,363,365,371,374,378,380,381,383,384,386,389,390,391,392,393,395,396,402,406,407,409,413,414,415,416,419,420,421,425,426,428,429,430,438,442,443,446,449,451,455,457,458,459,460,462,463,464,466,473,474,476,477,479,480,481,482,483,484,485,486,488,495,497,498,499,500,501,502,503,504,505,507,508,509,510,512,513,514,515,517,518,519,520,521,522,523,525,526,527,528,530,532],alter:[3,6,8,9,11,12,41,61,155,156,157,158,159,161,164,165,166,167,170,171,178,182,203,204,206,208,211,212,219,226,227,228,229,231,232,272,273,314,317,319,322,330,337,345,352,359,388,391,429,500,505,507,510,527,528,532],altern:[1,6,8,9,11,12,15,16,17,99,178,203,210,220,232,241,253,257,273,308,319,320,344,345,352,366,370,380,388,389,397,398,412,417,419,420,422,431,434,442,446,447,448,455,459,460,470,480,483,485,488,498,500,501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6,59],changeabl:203,channel:[4,213,246],chapter:[302,381],charact:[2,3,6,12,37,41,56,65,199,203,204,206,207,208,210,225,242,243,308,316,320,363,390,395,421,423,433,453,454,459,461,462,469,481,482,497,498,502,507,508,527,530,531,532],character:[6,70,74,117,127,152,470,495,514],characterist:[257,337,346],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,130,177,178,203,204,208,210,211,212,217,233,238,248,308,310,311,312,316,339,352,380,381,390,403,405,411,412,414,415,419,421,422,429,434,438,442,456,461,462,469,479,485,486,488,489,491,492,500,501,505,510,512,521,526,527],charl:231,charmm2lammp:13,charmm:[0,2,3,5],chartreus:207,cheap:337,cheaper:[237,425,463],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,199,200,217,225,226,227,233,244,246,248,254,255,305,318,323,337,345,347,352,361,363,376,379,389,390,391,392,393,396,418,430,433,451,462,493,495,497,498,500,508,514,517,518,519,527],checkf:199,checkout:522,checkqeq:462,checku:199,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,221,230,236,239,246,249,250,257,259,272,273,274,291,296,297,302,306,309,311,319,324,325,337,340,341,344,345,346,347,354,364,373,375,380,381,388,391,398,403,407,408,411,412,413,415,416,417,421,424,425,427,428,434,438,439,442,446,450,451,453,454,456,469,478,486,509,512,514,521],chemic:[9,40,88,89,130,172,177,203,204,216,217,248,310,315,316,344,381,423,454,461,462,474,482],chemistri:[309,310,312,398,402,421,461,462],chen:349,cheng:411,chenoweth:[461,462],chenoweth_2008:[461,462],chi:[102,167,202,300,310,312,376,422,425,528],chiefli:460,child:8,chip:[7,9,16,17,396,513],chipot:230,chiral:373,chmod:[11,12],cho:446,chocol:[7,207],choic:[3,6,9,12,14,15,17,40,41,54,74,95,153,156,157,171,182,197,199,219,225,228,232,233,250,256,259,271,273,302,306,310,319,344,355,374,381,387,388,391,393,396,429,442,451,457,462,500,509,510,513,514,520,521,526],choos:[1,3,6,7,8,9,12,16,17,28,39,54,95,128,168,169,206,226,227,228,229,231,233,244,256,259,271,273,275,276,277,278,279,280,281,305,306,324,337,341,355,380,381,388,489,495,497,509,515],chose:[483,485],chosen:[2,3,6,12,16,152,178,181,190,199,206,212,217,229,231,233,244,248,249,257,259,271,273,278,302,305,316,337,341,344,345,350,352,353,359,381,382,388,396,417,421,426,433,436,464,483,495,509,514,515,521],chri:176,christian:[7,9,16],christoph:7,chunk:[0,2,3],chunkid:[69,79,86,98,103,114,116,125,158,173,175,219,334],chute:[4,9,10,251],ciccotti:323,cieplak:[6,184,512],cii:220,cij:220,circl:[42,75,332],circular:[3,6,156,201],circumst:17,circumv:[100,117,314],citat:0,cite:[3,7,8,12,256,469],civ:9,cl1:177,clarendon:[28,415],clarifi:[7,483,485],clariti:363,clark:456,class2:[2,3],classic:[0,3,5,6,7,8,9,15,245,302,309,314,349,375,421],classifi:[479,488],claus:498,clean:[6,12,14,16,508],cleanli:[499,518,531],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:504,click:[2,11,21,36,44,55,178,186,198,206,253,365,374,391,409,479,522],client:[253,255],climb:[272,391,514],clinic:[7,13],clo:[167,202,528],clock:[12,495,514,519],clockwis:[184,355],clone:522,close:[3,6,11,12,13,39,41,70,75,153,181,203,227,228,229,250,257,259,273,289,296,319,323,355,358,379,381,384,387,388,391,396,398,402,412,413,432,446,451,453,454,461,465,467,481,485,504,510,521,522,524],closer:[3,10,41,127,176,202,203,225,229,234,346,391],closest:[227,300,319,352,425,463,478,489],cloud:[469,521],clovertown:17,clsuter:76,clump1:[304,319],clump2:[304,319],clump3:[304,319],clump:319,cluster:[2,3,6,7,12,15,63,65,75],clutter:3,cmap:500,cmatrix:250,cmax:446,cmd:[11,12,302,511],cmdarg:11,cmin:446,cmm:7,cmoput:145,cn1:220,cn2:220,cna:[2,3,7,65,74],cnn:220,cnr:13,cnrs:9,cnt:[429,504],co2:[40,177,320,323,390,423],coars:[7,9,10,28,35,40,54,190,243,304,319,320,337,423,427,454,464,482,509,512],coarser:[381,527],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,197,364,365,371,409,429,433,451,466,468,471,500,529],coeffcient:500,coeffici:[0,2,3,4],coefficienct:416,coefficient0:419,coefficient1:419,coeffieci:[6,400,432],coeffincientn:419,coexist:[248,421],cohes:[6,422,446],coincid:[134,203,207,358,407,443,444,495],colberg:205,cold:[6,163,248,252,392,521],coldest:345,coleman8:9,coleman:[9,130,177,321],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,262,269,304,314,317,319,361,380,390,392,410,500,507,513,519,532],collid:[237,337,359],colliex:177,collinear:[3,304],collis:[3,259,337,355,359,418,426,492],colllis:337,colloid:[2,3,4,6,7],colombo:39,colon:[208,361,501,519],color1:207,color2:207,color:[3,9,41,203,206,207,225,249,309,314],column:[3,6,9,12,13,42,65,68,69,70,71,73,74,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,262,270,271,309,319,338,339,349,359,398,424,428,461,462,501,515,517,518,527],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,14,42,65,75],comamnd:232,comand:228,comannd:396,comb3:[2,3],comb:[2,3,4,7,9,210,310],comb_1:311,comb_2:311,combiant:413,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,239,246,248,253,262,265,273,289,295,302,308,324,341,350,358,362,364,380,381,383,388,396,410,412,413,417,421,422,423,429,441,442,470,480,483,485,486,488,491,503,508,513,521,527,529],come:[0,2,3],comfort:[12,13],comid:334,comit:522,comm:[0,3,11,12,63,77,205,253,255,256,381,391,396,416,451,458,481,482,502],comm_modifi:[2,3,6,39],comm_modift:63,comm_styl:[2,3,41,63],comm_world:11,command:[0,1],comment:[2,4,7,11,12,37,56,184,199,203,242,243,257,319,320,349,390,391,397,419,420,422,423,433,446,453,454,455,462,469,470,480,481,482,483,484,485,488,497,498,500,521,522,527],commerci:7,commit:[9,522],commmand:[3,6,12,61,118,297,432,494,495,497,514,531],common:[0,1],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,375,427,436,470,483,485,500,503,512],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,232,253,255,259,261,262,263,273,301,308,310,311,312,319,324,337,349,361,378,380,392,393,394,396,417,418,457,493,497,498,509,510,527,530,532],communc:380,comp:[7,205,255,256,289,295,323,381,391,421,451,458,463,477,481,482,484],compact:[65,210,409,479],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,236,246,310,361,363,380,381,389,391,446,469,495,514,515,521,526],comparison:0,compart:385,compass:[7,9,20,21,36,43,44,55,185,186,198,364,365,374,408,479],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,231,239,301,313,341,344,351,354,357,380,396,430,449,451,481,497,498,527],compens:[6,226,227,317,392,421],compet:348,competit:381,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,207,208,253,348,381,396,449,500,501,505,521,527],compl:16,complain:[11,12,16],complement:446,complementari:[7,412,434],complet:[3,6,9,11,12,14,41,61,75,207,225,230,246,262,302,305,308,337,348,350,362,363,379,391,396,422,466,468,487,495,500,505,508,512,514,517,521,527],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,259,289,332,358,378,391,421,449,481,482,498,500,503,527],compli:[344,348],complic:[6,7,9,12,13,129,217,248,498],complier:12,compon:[3,6,8,12,63,65,69,70,74,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,233,238,239,245,251,255,256,259,262,264,265,269,270,272,273,274,278,279,280,281,293,294,296,298,299,301,302,303,306,317,319,322,323,325,329,330,333,337,340,341,342,344,351,352,357,358,359,380,383,388,389,390,391,396,416,421,426,443,444,466,468,469,470,500,501,510,518,527,528],componenet:6,componennt:129,composit:[6,217,259,419],compound:[411,421,422,488],compres:[75,125,219],compress:[3,6],compris:[40,358,423,463,487],compton:[130,177],comptu:3,compuat:381,comput:[0,1],computation:[3,6,226,227,246,349,402],computational:521,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,65],compute_peratom:8,compute_sa:[130,321],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,531],concav:358,concentr:[75,243,320,419,423,454,482],concept:[6,158,168,219,509],conceptu:[3,6,75,166,229,232,391,412,429,446,505],concern:[6,77,95,205,249],concetr:75,concis:[11,348],conclud:12,concret:8,concurr:[15,381,527],conden:[349,483,485],condens:[6,160,349,398,414,419,434,488],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:503,confer:[15,449],confid:[3,514],config:[12,203,497],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,232,233,237,248,255,256,287,302,310,348,378,389,391,398,402,420,446,449,480,483,485,488,495,500,502,503,514,518,522],confin:[500,514],confirm:519,conflict:[3,12,40,204,451,498,522],conform:[3,6,13,61,228,229,272,318,325,348,373,391,421,512],confus:[3,488],conjuct:[9,416],conjug:[7,8,256,388,421,461,462],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,256,259,263,287,305,306,310,311,312,314,319,324,337,345,352,357,380,381,391,403,405,409,412,416,421,428,434,451,456,464,486,500,503,507,521,532],connect:[3,6,9,95,163,181,228,253,304,319,323,333,385,391,413,426,461,462,478,485,497,498,500,504,521],conner:398,connor:398,conput:3,consecut:[3,11,12,39,75,178,207,211,212,233,253,254,412,434,438,495,501,503],consequ:[1,6,217,349,433,514],conserv:[3,9,28,210,217,228,236,237,246,249,252,256,258,259,263,269,271,273,287,289,291,319,320,323,324,340,341,345,352,353,357,391,415,416,417,426,440,469,509,514],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,233,260,274,301,319,344,345,348,349,352,381,409,421,429,462,463,469,478,495,496,498,501,502,503,505,508,510,518,521,527],consider:[6,8,246,256,257,340,341,342,396,462,509],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,233,236,238,245,249,256,257,258,270,273,275,276,277,278,279,280,281,282,283,285,286,287,288,291,292,293,294,296,297,298,306,309,314,316,317,318,319,320,340,341,342,343,353,360,380,381,383,385,390,391,396,398,402,404,410,412,421,425,429,432,443,444,446,449,451,453,454,463,466,468,469,481,482,489,498,500,501,502,503,504,505,512,521,527],consistent_fe_initi:216,consit:319,constant:[0,3,4],constantli:239,constitu:[3,6,262,319,354,358,410,463],constitut:[466,468],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,233,239,246,248,249,254,262,265,267,289,295,304,305,317,319,323,335,345,352,389,390,421,505,512,521],constraint:[3,5],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,273,301,318,320,358,392,396,415,449,451,478,480,481,482,503,504,519,527],constructor:[8,11],consult:[15,462],consum:[1,314,457,527],consumpt:378,contact:[0,2,3,4,5,8,9,12,13,40,42,65],contact_stiff:[465,467],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,231,233,238,242,243,250,254,255,256,259,271,287,300,301,304,305,307,308,309,312,316,319,320,321,326,337,344,348,349,358,359,363,379,381,390,391,394,395,397,398,399,402,411,412,415,419,420,421,423,429,430,446,449,453,454,455,459,460,461,462,470,480,481,482,483,484,485,486,488,495,496,497,498,500,501,502,503,505,507,509,512,514,515,517,518,521,522,527,530,532],content:[4,8,9,12,17,462,516,518],context:[3,6,8,12,15,16,127,128,207,226,227,233,304,316,353,388,491,500,507,516,526,527,528],contibut:74,contigu:497,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,233,239,248,249,250,252,253,254,256,257,258,264,270,271,273,275,276,277,278,279,280,281,293,294,296,297,298,303,305,308,309,319,321,325,336,337,339,346,347,349,355,358,363,379,395,396,402,416,418,436,439,461,462,463,466,468,484,495,498,500,502,503,508,514,515,517,518,527,530],continuum:[6,7,9,216,349,466,468],contour_integr:216,contract:[61,229,232,273,306,319],contradictori:3,contrain:323,contraint:287,contrari:[250,257],contrast:[1,6,42,55,66,160,163,204,232,361,466,468,491,531],contrib:349,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,248,256,259,262,263,268,274,296,297,304,305,313,316,319,321,323,351,380,389,391,399,416,418,419,421,429,443,444,449,451,461,462,469,512,518,521,522],contributor:12,control:[2,3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230],control_typ:216,controlfil:462,convect:99,conveni:[6,12,28,203,208,223,321,383,470,486,519,522,527],convent:[3,8,28,189,196,198,204,207,318,333,362,419,421,527],converg:[3,6,41,96,203,204,206,208,213,225,228,229,238,245,278,289,295,309,311,314,318,323,387,388,389,391,411,412,434,469,495,507,514,519],convers:[3,8,152,206,207,217,220,306,380,412,413,414,421,434,438,442,456,498,514,526],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,271,305,308,361,364,366,370,373,383,391,397,419,449,483,485,492,498,500,501,502,507,517,521,526,527,530,532],convex:[42,358],convinc:[7,12],cook:9,cooki:7,cool:[7,168,239,252,317],cooordin:[203,204],cooper:[5,7],coord123:125,coord1:[3,125,219],coord2:[3,125,219],coord3:[3,125,219],coord:[2,3,6,7,11,61,65,75,76,80],coordb:469,coordbb:469,coordiat:389,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,232,233,236,238,239,240,245,248,251,252,253,254,255,256,257,270,272,273,275,276,277,279,280,281,296,299,300,301,304,305,306,316,317,319,322,323,325,330,333,334,335,336,337,339,347,348,349,356,357,359,361,383,389,390,391,396,397,398,401,420,469,495,500,501,502,503,505,508,510,514,521,527,528],coordn:[125,219],coords:469,copi:[0,3,4,8,9,11,12,14,16,40,131,206,349,391,409,461,498,522],copper:492,coprocessor:[1,7,9,15,16,396,513],coproprocessor:16,copy_arrai:8,copyright:[7,8,304],coral:207,core:[0,1,3,4],core_shel:160,cores:521,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,512],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,206,358,359,383,487,500,522],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:411,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,232,239,246,248,250,256,273,274,296,304,306,309,348,354,358,380,391,397,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,414,415,416,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,492,493,500,515,518,521,522],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,233,238,245,257,267,273,274,312,319,323,333,336,355,358,391,392,396,414,444,449,497,498,500,510,522,526,528],correl:[2,3,6,99,100,152,174,210,219],correpond:[242,243],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,232,239,240,243,245,247,251,256,259,260,269,270,271,273,275,276,277,278,279,280,281,282,283,287,291,293,294,296,298,300,301,302,306,311,312,319,320,322,323,344,354,355,357,358,359,360,362,364,365,366,367,369,370,373,375,381,386,388,390,391,397,398,400,403,404,405,406,407,408,409,410,411,412,415,416,419,420,421,422,423,424,425,426,427,428,429,432,434,435,436,437,438,439,440,441,442,443,446,447,449,451,452,454,455,456,458,459,461,462,463,464,469,470,471,480,481,482,483,484,485,486,488,490,491,492,495,497,498,500,501,503,513,514,515,517,518,521,527],correspondingli:[443,444,509],corrupt:3,cosin:[2,6,7,21],cosineshift:26,cosmo:[250,255],cossq:2,cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,244,273,291,311,320,349,380,381,394,412,434,438,449,451,480,497,509],costheta0:[480,483,485,488],costheta:459,costli:[11,15,96,250,392],couett:4,coul:[2,3,6,9,15,35,45,46,76,95,118,127,172,184,211,212,350,381,389],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,99,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,232,245,255,308,309,310,314,317,319,322,337,338,344,348,349,350,354,358,361,363,371,377,379,387,389,392,396,398,399,424,428,429,432,461,462,496,497,498,500,502,504,507,508,515,516,521,527,528],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,310,312,350,380,381,389,396,403,405,406,407,408,411,412,413,414,415,421,426,427,429,434,438,442,445,451,456,461,462,464,469,479,485,486,488,491,505,512,518,521,526],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,229,233,238,244,248,254,273,287,305,322,323,340,341,358,381,389,390,391,393,396,424,428,451,518,519,527],counter:[3,355,495,506,508,514],counteract:[231,248],counterbal:[239,252],counterbalanc:28,counterclockwis:184,counterpart:[203,495],counterproduct:17,coupl:[0,3,4],couple:[4,6,11,12],courant:326,cours:[3,8,15,138,140,172,203,211,212,249,318,333,348,354,356,357,359,361,381,443,471,497,500,513,521,527,530],courtesi:383,cov:469,coval:[6,9,28,421,446,469,521],covari:250,cover:[6,12,75,199,207,216,259,421,487],coverag:75,cpc:255,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,245,323],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,236,257,350,378,381,396,409,479,495,513,514,517,518,519,527],cpuinfo:15,cpuremain:518,cpus:12,cr2:177,cr3:177,crack:[4,392],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,392,521],craympi:396,creat:[0,1,2,3,4,6,7,8,9,11,12,13,14,16,37,39,41,42,56,60,61,64,65,75,87,99,113,114,119,120,123,126,128,130,146,155,161,162,174,176,178,179,180,181,199,203,204,205,206,207,210,215,216,218,219,220,222,223,225,226],create_atom:[2,3,6,7,8,40,41,61,99],create_bond:[2,3],create_box:[2,3,6,21,40,41,44,59,60,61,64,75,99,176,178,179],create_elementset:216,create_faceset:216,create_group:205,create_nodeset:216,createatom:0,creation:[3,5],crimson:207,critchlei:304,criteria:[3,127,179,206,207,226,227,228,268,389,458,487,502,505,527],criterion:[12,41,133,178,181,217,225,228,248,287,311,326,355,361,389,391,411,421,426,469,505,514,515],criterioni:514,critic:[6,48,49,271,344,349,389],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,232,270,272,296,319,329,333,336,345,352,365,383,391,407,416,418,419,427,428,429,434,436,438,459,464,466,468,483,485,492,500,504,510,530],crossov:1,crossterm:500,crozier:[0,7,13],crucial:309,crystal:[3,4,6,13,15,74,77,117,300,301,347,383,392,500,504,518,521],crystallin:[6,113,301,383,484,521],crystallis:344,crystallogr:[130,177],crystallograph:[383,518],crystallographi:[130,177,383],cs1:177,cs_chunk:6,cs_im:[40,500],cs_re:[40,500],csanyi:[152,460,470],cscl:446,csequ:6,csh:[11,12,15,409],cshrc:[11,12],csic:[420,480,483,485,488],csinfo:6,csisi:[420,480,483,485,488],csld:[2,3,210],cst:419,cstherm:6,cstyle:497,csvr:[2,3,6,210],ctcm:[397,419],ctemp_core:236,cterm:325,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:446,cube:[6,176,181,236,358,383,521],cubes:[41,225],cubic:[2,3,37,56,117,199,242,259,300,337,381,383,419],cuda:[1,3,7,9,12,14,16,396,513,527],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:402,cummul:[3,6,223,226,227,228,230,244,250,256,258,337,340,341,342,343,345,352,428,518],cumul:[6,217,219,222,237,248,256,271,273,278,287,319,321,391],curli:2,currenlti:231,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,233,237,238,239,245,246,248,250,253,254,256,262,268,270,273,274,279,280,281,287,289,293,294,295,296,298,304,305,310,311,313,316,317,318,319,320,323,324,325,326,327,328,329,330,332,334,335,336,337,340,341,342,348,349,352,353,354,355,356,357,359,361,363,378,379,380,381,384,385,386,388,389,390,391,396,402,409,411,415,419,421,422,426,429,430,433,443,444,446,447,448,451,459,461,462,465,466,467,468,471,483,485,486,489,495,496,497,498,500,501,502,503,504,506,507,508,510,512,514,515,517,518,522,527,528,529,530,531,532],curv:[6,178,248,289,295,301],curvatur:[425,463,492],custom:[0,2,3,6],cut0:498,cut1:509,cut2:509,cut:[1,2,3,6,9,12,14,15,16,17,18,41],cuthi:[300,312],cutinn:[404,443,444],cutlo:[300,312],cutmax:459,cutoff1:[408,415,434,438,442,445,456,464],cutoff2:[403,405,406,408,414,415,434,438,442,445,456,464,486],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,234,242,243,300,309,310,312,314,316,319,324,337,350,354,358,361,378,380,381,389,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,498,502,505,509,521,527],cutoffa:420,cutoffc:420,cuu3:419,cval:177,cvar:231,cvd:344,cvel:325,cvff:[2,7,15,365],cwiggl:[3,270,354,357,359,527],cyan:[2,206,207],cycl:[3,248,271,273,274,278],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,254,295,305,355,358,385,503],cylinder_d:385,cylindr:[6,254,333,355],cypress:396,cyrot:402,cyrstal:301,d3q15:259,d3q19:259,d_double_double:14,d_e:349,d_flag2:308,d_flag:308,d_name:[124,203,308,339,510],d_single_double:14,d_single_single:14,d_sx:308,d_sy:308,d_sz:308,daan:347,dai:12,daili:12,daivi:296,damag:[2,3,9,65],dammak:314,damp:[3,6,210,215,256,257,258,263,273,274,278,295,306,309,310,314,319,340,341,353,355,356,388,389,391,403,405,407,412,415,421,426,434,442,456,464,479,486,514,521],damp_com:257,damp_drud:257,dampen:[319,521],dampflag:[355,426],dan:16,danger:[3,12,248,361,416,518],dangl:181,daniel:9,darden:[381,415],darkblu:207,darkcyan:207,darken:206,darkgoldenrod:207,darkgrai:207,darkgreen:207,darkkhaki:207,darkmagenta:207,darkolivegreen:207,darkorang:207,darkorchid:207,darkr:207,darksalmon:207,darkseagreen:207,darkslateblu:207,darkslategrai:207,darkturquois:207,darkviolet:207,dasgupta:310,dash:[426,517],dat:[6,99,199,216,496],data2xmovi:0,data:[1,2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:0,datafil:[12,13,321],dataset:321,datatyp:3,date:[0,4,6,12,13,202,461,462,527],datom1:[84,126],datom2:[84,126],datom3:[84,126],datom4:[84,126],datum:[3,6,42,68,71,73,84,102,119,126,203,220],davenport:445,davi:354,david:[9,18,380,381,483,485],daw:[419,459],dcd:[3,6,7,203,205,206,207,208,302,501,505],dcs:9,ddim:202,deactiv:442,dealt:255,debug:[6,7,11,12,13,16,57,130,134,177,178,302,307,378,380,430,451,489,498,499,507,510,517,527],deby:[2,3,7,211,212,314],decai:[100,412,492],decid:[3,6,12,15,75,270,308,319,350,515,522],decipher:383,deck:308,declar:[205,246],declin:337,decod:206,decompos:[95,470],decomposit:[3,5,7,17,64,216,302,324],decoupl:[6,521],decreas:[3,15,203,204,213,214,221,228,232,238,239,245,248,256,348,380],decrement:325,dedic:[15,396],deepli:377,deeppink:207,deepskyblu:207,def:[12,13,498],defaul:63,defect:[6,74,176,449],defgrad:2,defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,233,236,237,238,241,243,245,247,248,251,254,255,256,257,258,259,268,270,272,273,274,275,276,277,278,279,280,281,283,284,285,288,291,292,293,294,296,297,298,300,301,302,304,305,306,308,310,312,317,319,320,321,322,323,326,330,334,335,337,339,340,341,342,343,345,346,347,349,351,352,354,355,356,357,358,359,361,363,364,365,366,367,368,369,370,373,374,375,376,378,380,381,383,385,386,388,389,390,391,392,393,394,395,396,398,399,400,401,403,404,405,406,407,408,409,410,412,413,415,416,417,418,420,421,423,424,425,426,427,428,429,430,432,434,435,436,437,438,439,440,441,442,443,444,445,449,450,451,452,453,454,455,456,458,459,461,462,463,464,465,466,467,468,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,497,498,500,501,503,504,505,506,509,510,511,512,514,515,517,518,521,523,524,525,526,527,528,529],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,232,241,254,278,321,339,351,354,357,359,362,374,378,390,399,402,410,417,421,432,459,466,468,470,487,498,500,502,509,511,526,527],defint:518,deform:[2,3,6,7,8,40,42,59,61,63,65,85,122,134,138,139,153],deg2theta:177,deg:521,degener:[3,304],degrad:[8,17,301,381,509],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,236,248,250,251,256,257,262,273,274,278,279,280,281,293,294,296,298,302,304,318,319,323,340,341,342,347,364,366,370,373,375,389,415,419,428,510,518,521,528],degrees:199,degress:[158,219],del:514,delai:[3,6,12,392,418,518],deleg:429,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,244,248,273,321,340,341,361,363,379,390,392,395,451,478,500,501,502,503,511,512,517,522,523,525,527,528],delete_atom:[2,3,7,178],delete_bond:[2,3,43,45,46,47,48,49,50,51,53,54,55,56,68,73,126,179],delete_el:216,deli:202,delimit:[320,498,527],dellago:[6,239],deloc:[274,421,469],delr:446,delt_lo:514,delta:[2,21],delta_1:402,delta_3:402,delta_7:402,delta_conf:3,delta_ij:[446,459],delta_pi:402,delta_r:459,delta_sigma:402,deltah_f:243,delx:202,delz:202,demand:314,demo:11,demon:299,demonstr:[309,446],den:305,dendrim:428,dendtrit:385,denniston:[9,259,261,262,263,301],denomin:[7,183],denot:[130,236,239,257,301,312,314,412,427,429,462,466,468],dens:[75,228,320,421],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,232,245,259,262,266,267,301,305,306,308,310,349,354,383,386,390,397,398,402,419,446,447,448,453,454,459,463,469,473,475,476,477,500,509,510,518,526],density_continuity:468,density_summation:468,dent:385,depart:[0,7],departur:[271,309],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,232,238,240,243,247,250,251,252,254,256,257,259,261,262,270,273,275,276,277,278,279,280,281,282,283,291,293,294,296,298,300,311,312,314,316,319,320,322,323,324,330,337,340,341,342,344,346,348,349,351,354,357,358,359,360,361,363,364,365,366,367,369,370,373,375,381,383,389,390,392,393,394,396,397,398,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,419,420,421,422,423,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,446,447,449,450,452,453,454,455,456,458,459,461,462,463,464,469,470,471,479,480,481,483,484,485,486,488,490,491,492,495,497,500,502,503,506,510,512,514,517,518,520,527,528],dependend:6,depflags:12,dephas:[495,514],depos:233,deposit:[2,3,4,112,180,210,217],deprec:[3,310,461],deprect:219,depth:[51,156,206,349,423,425,463],dequidt:9,der:[95,118,410,411,442,461,462,491],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,232,239,248,256,270,273,275,276,277,278,279,280,281,300,306,310,314,346,347,349,354,355,358,388,390,398,402,410,415,421,422,427,436,440,441,446,449,461,462,479,481,482,491,521],derjagin:491,derlet:300,descend:207,descent:[7,388],descib:[40,206,310],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,233,235,236,242,243,246,249,250,253,254,255,256,257,258,259,261,262,263,268,272,273,274,278,286,297,300,302,307,308,309,310,311,312,319,320,325,333,337,338,339,340,341,342,343,344,345,346,347,352,354,355,357,363,380,381,383,387,388,389,390,391,395,398,399,401,403,404,405,407,408,409,410,411,412,415,419,421,422,423,425,426,427,429,432,434,435,436,437,438,439,440,441,442,443,444,445,446,449,450,453,454,458,459,460,461,462,463,464,469,470,471,478,479,480,481,482,483,484,485,486,488,490,491,492,493,495,497,498,500,501,502,503,504,510,513,514,517,522,527,528,530],descript:[2,3,6,8,9,11,12,13,17],descriptor:[152,203,430],deserno:381,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,235,236,273,274,300,301,321,344,349,399,400,401,404,407,412,414,421,442,443,444,447,448,459,462,481],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,232,245,248,249,256,257,258,262,273,296,304,305,306,307,310,314,319,322,323,337,340,341,342,343,348,355,371,377,380,381,383,387,389,390,391,416,419,428,443,444,480,483,485,496,497,498,500,504,509,514,515,517,518,519,527,528,530],desk:7,desktop:[4,6,7,10,12,206],despit:521,destabil:402,destre:373,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,233,239,245,248,249,250,251,253,254,256,258,259,263,270,271,272,273,274,275,276,277,278,279,280,281,285,287,293,294,296,297,298,301,304,305,306,308,309,311,312,313,319,323,324,337,340,341,342,343,344,345,347,348,349,350,351,352,353,361,363,365,374,380,381,384,385,389,390,392,393,396,397,398,399,401,402,404,406,407,408,409,410,411,412,415,416,421,422,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,444,445,446,450,451,453,454,458,461,462,463,469,470,471,479,487,490,491,493,498,500,501,502,503,505,506,509,510,512,515,518,519,522,527,528,532],detect:[2,3,12,42,63,65,94,100,247,305,348,391,411,428,433,495,497,500,511,514,527],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,119,123,126,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,232,233,236,238,243,248,251,252,254,256,257,262,268,270,271,273,279,280,281,293,294,296,298,300,302,305,306,309,316,317,318,319,320,321,322,326,328,330,337,340,341,342,344,350,351,354,355,356,357,358,359,361,374,380,381,383,390,392,393,396,398,399,406,411,415,418,419,423,424,426,429,430,438,446,449,451,454,462,463,469,478,481,482,486,491,497,500,501,503,505,507,510,514,516,517,519,526,527,528],determinist:324,detil:119,devan:[9,464],devanathan:485,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,231,253,278,304,309,310,313,398,402,421,448,449,469,488,502],devemi:9,deviat:[271,278,300,424],deviator:9,devic:[1,3,12,14,16,253,396],device_typ:396,devin:[311,411],devis:448,dfactor:206,dff:521,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,381],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,313,449],dhi:[61,202,232,305],dhug:[271,309],dhugoniot:[271,309],dia:446,diag:320,diagnost:[2,5],diagon:[3,6,91,129,152,153,154,229,273,306,319,352,466,468],diagonalstyl:470,diagram:[41,84,130,177,198,225,302],diallo:428,diam:[206,207,305,390],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,256,305,308,319,337,339,353,355,390,410,425,426,436,463,487,491,500,501,510],diamond:[383,421,446],diamter:[40,305],dick:6,dicken:231,dicsuss:270,dictat:[217,271],did:[3,12,389,416,418,419,426,451,483,485,508],didn:3,die:17,diel:2,dielectr:2,diff:[3,6,12,15,174,351,380],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,232,236,239,242,247,248,249,250,251,252,253,256,257,259,270,273,274,275,276,277,279,280,281,283,285,288,291,292,293,294,298,300,302,304,306,309,310,311,314,317,319,323,325,333,335,337,340,341,342,345,346,347,349,352,353,354,355,358,363,364,374,377,379,380,381,383,384,387,388,390,391,393,394,395,396,397,398,402,406,407,409,410,411,416,417,419,421,423,425,426,427,429,432,434,435,437,438,445,446,447,448,450,451,452,453,454,455,459,461,462,463,464,465,466,468,469,470,471,479,480,481,482,483,485,487,488,491,494,495,497,498,500,502,503,504,505,508,509,510,512,514,515,517,518,519,521,526,527,528,530],differenti:[1,3,6,28,199,320,380,412,459,484],difficult:[229,231,302,396,428,509,519],difficulti:[100,117,323,461],diffract:[7,9,130,177,321],diffus:[0,4],diffuse:[4,6],digit:[2,3,207,363,449,527],dih_table1:199,dih_table2:199,dihedr:[0,2,3,7],dihedral_coeff:[2,3,184,185],dihedral_cosine_shift_exp:26,dihedral_styl:0,dihedralcoeff:[3,200],dihedraltyp:227,dihydrid:421,dij:323,dilat:[2,3,61,63,65,82],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,232,254,355,383,446,503,526,527,528],dimdim:527,dimems:301,dimens:[1,2,3,6,7,12,41,59,60,61,63,65,75,99,125,129,153,158,165,166,167,178,180],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,272,301,349,383,387,391,459,500,510],dimensionless:[115,133,134,136,139,141,143,148,152,231,349,381,470,491],dimensions:321,diment:3,dimentionless:147,dimer:[6,319,446],dimgrai:207,dimstr:[41,225],dinola:[306,340],dintel_offload_noaffinity:15,dipol:[0,2,3,4],dipolar:[4,28,40,203,204,339,521],dir1:511,dir2:511,dir:[1,3,4,8,10,11,12,271,300,309,336,459,461,462,498,511,527],dirac:152,direc:459,direct:[2,3,6,7,12,13,15,28,59,74,75,117,130,152,176,177,178,184,202,203,206,210,213,214,215,232,233],directli:[3,6,8,9,11,12,95,124,129,152,154,178,203,204,205,206,213,231,238,250,254,259,301,320,321,341,353,355,356,357,358,383,388,396,397,398,403,405,406,412,415,419,421,434,438,451,456,464,478,498,510,511,512,518,527],directori:[0,1,2,3],disabl:[3,12,15,349,396,433,498,513,527],disadvantag:[6,225],disallow:[203,232,273],disappear:502,discard:[2,3,41,75,221,225,350,358,497,502,503],discontinu:[199,389,440],discourag:446,discov:[13,350],discret:[6,8,40,42,206,207,231,256,259,295],discuss:[0,1,2,3],disk:[6,92,93,100,171,201,233,248,305,498],disloc:[74,449],disord:[39,74,449],disp:[0,2,3],dispar:463,disperion:[415,438],dispers:[3,6,7,9,176,301,380,381,406,415,438,443,451,462,481,488],displac:[2,3,6,7,12,42,61,65],displace_atom:[2,3,7,113],displace_box:61,displacemet:503,displai:[11,13,21,36,44,55,186,198,203,206,365,374,409,479],dispters:3,disregard:449,dissip:[6,9,40,88,89,241,246,249,256,301,324,346,347,404,416,417,426,443,444,479],dissolut:226,dist:[6,73,99,119,128,203,302,318,418,478,495,528],distanc:[2,3,6,7,8,9,12,19,20,39,43,45,46,47,48,49,51,53,54,55,56,57,58,60,61,63,65,66,69,73,75,76,77,78,79,80,81,86,87,94,97,98,100,103,113,114,115,116,117,119,125,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,202,203,204,206,207,215,219,226,227,228,229,232,233,234,237,239,248,254,259,270,271,272,273,278,287,300,301,305,309,310,317,318,319,323,325,329,333,334,335,336,337,344,345,347,348,349,352,354,355,356,357,358,359,364],distinct:[6,236,316,380,463],distinguish:[6,94,152,262,421,499,527],distort:[176,397],distrbut:397,distribut:[0,2,4,5,6],distro:[122,409,458,459],ditto:[8,12,14,16,17,42,126,227,319,492,498],div:[8,15],divd:128,diverg:[3,12,39,319,347,398,502,521,530],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,232,300,345,352,357,380,389,391,422,462,469,488,509,517,527],divis:[6,197,259,402,432,442,497,518,527],dl_poly:[6,7],dlambda:172,dlammps_async_imd:253,dlammps_bigbig:[12,39,207],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,348,500,501,505],dlammps_jpeg:[3,12,206],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,206],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,203],dlen:510,dlm:[273,291],dlmp_intel_offload:[9,15],dlo:[61,202,232,305],dlopen:6,dlvo:[7,410,491],dm_lb:259,dmax:[337,387],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,84,86,95,98,102,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,231,233,248,256,257,268,273,274,279,280,281,285,293,294,296,297,298,305,308,319,333,337,340,341,342,351,355,358,361,363,365,374,379,385,389,390,391,396,397,398,401,409,411,412,419,420,422,428,429,431,432,446,447,448,451,455,458,459,460,470,479,480,483,485,487,488,498,500,501,502,503,505,508,509,510,517,518,522,527,528,530,531],docuement:463,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,232,236,238,239,242,243,244,246,248,249,252,254,256,257,259,262,269,273,274,275,276,277,279,280,281,293,294,295,296,297,298,306,307,308,312,314,317,319,337,340,342,344,345,349,352,353,354,357,358,359,361,366,367,368,370,371,373,379,380,381,382,383,390,391,392,397,398,399,400,401,402,404,406,407,408,410,411,412,413,415,416,418,419,420,421,423,424,425,426,427,429,430,431,432,433,436,437,439,440,441,443,444,446,447,448,449,451,453,454,459,460,461,462,463,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488,490,491,492,493,495,496,497,498,500,501,502,503,504,507,508,510,511,512,513,514,517,518,521,522,527,532],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,333,390,392,396,398,411,420,431,461,462,480,483,484,485,488,500,502],dof:[3,8,123,156,157,158,171,219,319,528],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[390,500],doi:[6,230,300],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,232,233,252,255,259,273,274,302,314,319,324,349,354,355,380,381,391,396,418,451,495,497,500,504,517],domin:[1,421,514],don:[0,8,9,12,13,15,127,181,213,238,257,358,446,469,498,500,522],donadio:341,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,233,242,243,245,246,248,253,254,256,257,264,273,279,280,281,293,294,296,298,299,301,302,303,305,308,316,319,321,323,337,340,341,342,344,346,347,361,363,379,380,381,389,391,392,395,396,398,406,419,429,430,431,438,444,445,446,451,453,454,461,478,481,482,487,495,496,497,498,501,504,505,508,518,519,521,522,527,528],donor:428,dot:[153,174,213,238,251,272],doti:[402,459],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,229,232,245,307,358,363,379,381,395,396,402,422,427,449,461,462,496,500,504,508,513,527,528],dover:216,down:[3,6,7,8,11,39,75,229,248,256,337,353,421,451,469,499,519],downhil:[387,388],download:[5,7,8,9,11,12,13,16,253,430,460],downsid:6,downward:316,dozen:[8,9,12,11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61,462,512,518,527],elt:446,emac:0,email:[0,3,5,7,8,9,11,422],emb:[3,9,358],emb_lin_neg:446,embed:[3,4,5,7,9,11,12,13,28,96,154,176,349,397,419,422,442,446,447,448,459,479,489,498],embt:185,emi:[7,9],emile:9,emin:229,emol:[461,462,518],emphas:426,empir:[9,216,341,421],empiric:398,emploi:[239,301,310,314,484],empti:[3,59,75,176,180,319,380,392,433,500,511,512,527],empty:3,enabl:[3,6,8,9,11,12,13,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,32,34,36,37,39,40,43,45,46,47,48,49,50,51,53,54,55,56,62,63,64,66,70,82,85,88,89,91,95,96,106,107,108,109,110,111,115,118,122,123,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,160,162,164,165,169,170,172,176,177,184,185,187,188,189,190,191,192,193,195,196,198,199,203,204,205,207,208,210,211,212,213,214,215,217,221,224,226,227,228,230,231,232,233,238,239,240,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,288,289,291,292,293,294,295,296,297,298,300,301,302,304,305,309,310,311,312,313,314,315,316,318,319,320,322,323,324,325,326,327,328,329,330,332,333,334,336,337,343,344,345,346,347,349,350,352,354,355,356,357,358,360,362,364,366,367,369,370,371,373,374,375,381,389,391,395,396,397,398,400,401,402,403,404,405,406,407,408,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,490,491,492,498,501,502,503,507,509,519,527,532],enclos:[2,6,12,180,203,207,307,363,446,469,496,498,508,517,527],encod:[13,39,42,203,206,207,308,429],encompass:[3,6,40,42,59,61,127,179,332,351,479,503],encount:[3,8,12,61,117,222,395,505,527],encourag:[7,8,313,320,335],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,181,182,185,202,203,204,206,207,208,211,212,220,222,223,228,229,232,239,249,254,256,258,272,273,274,287,295,306,318,319,320,325,337,340,341,342,343,345,348,349,352,356,359,361,379,380,390,391,395,396,416,419,425,432,445,449,463,466,468,470,471,489,495,498,500,501,502,503,505,507,508,512,516,518,521,527,532],end_of_step:8,endbondtors:[3,185,191,500],endif:8,energet:[228,398,462],energi:[0,1,2,3,4,5,6,7,8,9,12,13,19,20,22,23,24,25,26,27,28,29,30,31,33,34,35,37,38,40,43,45,46,47,48,49,51,52,53,54,56,57,58,65,67,68,72,73,83,88,89,90,91,92,93,94,95,96,99,101,104,105,106,107,108,109,111,118,119,120,121,123],energy_compon:469,energy_update_freq:462,enforc:[6,9,59,60,114,202,203,204,205,206,207,208,210,217,228,232,273,299,301,311,319,323,363,380,434,497,527,528],enforce2d:[2,3,6,201,210],eng:[11,68,73,119,203,245,361,363,411,448],eng_previ:363,engiliti:9,engilitycorp:9,engin:232,engineer:[216,304,325,346,419],enginer:447,enhanc:[212,216,239,495],enlarg:[61,206],enough:[3,40,63,94,178,179,181,182,225,246,257,305,309,314,319,350,354,355,358,392,396,412,457,500,504,505],enpub:419,ensembl:6,ensight:6,ensur:[3,6,152,203,204,217,221,229,248,249,273,326,348,381,402,418,442,480,488],enter:[59,168,422,449,488,514],enthalpi:[135,275,276,277,320,419,517,518,527],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,130,153,158,177,178,207,210,211,212,219,225,228,230,239,244,248,249,252,256,257,269,273,275,276,277,278,279,280,281,300,302,304,317,319,320,335,349,351,363,396,415,438,451,481,482,500,508,509,517],entireti:487,entiti:[6,8,40,42,203,319],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,130,139,142,143,144,145,146,148,149,150,176,199,204,207,211,222,230,242,243,309,361,390,402,420,446,453,454,455,462,470,480,481,482,483,484,485,488,527],entries:207,entropi:514,entry1:[37,56,207,409,453,454,481,482],entry2:207,entryn:207,enumer:[179,203,493],enumuer:6,env:396,environ:[1,3,6,11,12,15,16,17,206,250,255,300,396,397,402,409,411,420,421,459,483,497,511,527],eos:[9,242,243],epair:[118,207,398,424,428,461,462,518],epen:[461,462],epfl:[250,255],epp:415,epq:415,eps0:491,eps14:442,eps:[458,479],epsilon0:485,epsilon:[3,6,35,45,46,50,53,54,95,184,211,212,248,319,337,354,358,387,389,401,407,408,410,412,413,414,415,423,425,427,428,429,432,433,434,435,436,437,438,439,440,441,442,445,450,456,463,464,474,480,486,487,490,491,509,521,526],epsilon_0:492,epsilon_14:407,epsilon_:463,epsilon_d:413,epsilon_i:[425,451,463],epsilon_i_:463,epsilon_i_a:[425,463],epsilon_i_b:[425,463],epsilon_i_c:[425,463],epsilon_ij:451,epsilon_j:[425,451,463],epsilon_j_:463,epsilon_j_a:[425,463],epsilon_j_b:[425,463],epsilon_j_c:[425,463],epsilon_lj:463,epton:458,eqch:173,eqeq:[461,462],eqp:415,eqq:415,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,131,153,156,172,174,176,178,202,206,207,210,211,212,213,214,217,220,221,222,223,224,225,229,231,232,233,238,248,249,251,252,254,256,257,259,262,263,270,271,278,289,290,300,302,305,307,309,310,311,314,316,318,319,320,322,325,330,332,340,341,342,345,346,347,349,351,352,354,357,359,361,363,379,383,389,391,392,393,395,396,398,411,416,417,424,425,428,432,443,449,450,459,461,462,463,465,466,467,469,470,471,481,482,487,488,492,496,497,498,500,502,503,507,508,511,514,516,518,527,528],equat:[3,6,7,8,9,99,117,123,130,177,186,198,210,229,231,236,237,239,241,242,243,250,256,257,259,262,271,272,273,274,278,296,300,302,309,310,314,320,323,324,337,345,349,352,354,355,357,359,380,381,385,410,415,416,417,421,422,423,426,431,443,444,446,451,454,463,466,468,473,474,476,477,482,492,521],equation:[250,300,373],equi:274,equidist:272,equil:[3,310,384,507,532],equilater:510,equilibr:[3,4,5,6,7,9,61,99,178,210,217,220,228,229,248,271,273,274,296,297,306,309,310,311,312,345,346,347,352,411,412,461,462,496,510],equilibria:352,equilibribum:[226,227],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,229,232,246,248,249,250,257,259,273,278,296,309,310,314,318,323,325,333,337,344,345,347,352,364,366,370,373,411,446,455,469,521],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:216,equival:[6,12,13,28,61,63,128,136,137,145,150,176,180,203,207,218,219,220,222,223,229,232,248,256,273,296,306,318,319,357,398,416,421,469,483,485,486,500,503,508,509,518,521],equlibrium:6,equliibr:[310,312],er3:177,eradiu:[40,124,204,421,500],eras:[322,346],erat:[232,444],erc:412,erfc:[412,434,451],erforc:[124,204],erg:526,erhart:[217,419,483,485],ermscal:399,ernst:9,eror:3,eros:446,erose_form:446,erot:[2,3,6,9,65],errata:[483,485],erratum:354,erron:3,error:[0,1,2],erta:426,ervel:[124,204,500],escap:[233,521],especi:[8,15,166,178,210,217,225,248,309,314,317,318,396,497,519],espresso:[9,313],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,301,353,381,398,412,434,485,505,518],essential:[8,278],essex:28,establish:[95,252],estim:[1,3,6,10,12,37,41,56,74,99,153,216,225,237,271,320,337,344,380,381,387,451,462,481,482,514,518],estimat:3,esu:526,esub:446,eta:[6,259,273,309,310,312,353,420,422,425,459,484,488,526],eta_dot:273,eta_ij:459,eta_ji:422,etag:[40,500],etail:518,etap:273,etap_dot:273,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,232,233,245,248,249,256,273,305,316,321,349,350,358,363,379,380,389,390,391,392,394,419,420,429,442,444,449,457,461,462,480,483,485,488,495,498,500,501,502,507,509,510,514,515,516,517,518,519,521,526,527,530,532],ethernet:17,etol:[389,391,495,514],etot0:309,etot:[6,104,106,107,121,153,164,207,236,257,271,309,517,518],eu2:177,eu3:177,euler:[320,389,391],eulerian:216,euqat:472,europhi:259,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,232,238,249,251,252,254,255,256,257,301,307,310,320,322,326,330,340,341,342,351,354,357,359,361,363,387,389,449,451,453,454,459,465,467,469,481,482,495,496,498,502,503,505,507,508,509,510,514,516,518,527,528],evaluat:[380,381,527],evalut:[363,498],evan:[166,246,296],evanseck:[6,19,184,407,512],evapor:[2,3,9,59,112,210,217],evaul:[8,389],evdwl:[118,154,461,462,518],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,232,233,236,239,254,257,271,273,274,301,305,314,316,319,321,332,337,345,349,352,354,358,361,372,380,387,389,391,396,401,421,422,426,429,432,451,463,488,489,493,500,501,503,505,506,507,509,510,512,515,517,518,519,521,532],evenli:[3,41,57,153,199,225,259,432,489],event:[2,3,6,8,65],eventu:[3,6,12,14,180,514],eventual:310,ever:[9,54,56,255,337],everaer:[410,425,463,479],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,237,239,244,245,248,250,252,253,254,259,260,269,273,274,278,289,295,299,300,301,305,306,307,308,309,310,311,312,314,316,317,319,320,321,323,325,334,337,339,340,341,342,343,344,345,348,349,350,351,352,361,363,379,381,391,392,393,396,416,418,429,442,461,462,469,475,494,495,496,500,502,504,505,507,508,509,514,515,516,518,519,522,527,532],everyth:[8,118,522],everywher:[127,436],eviri:421,evolut:[239,250,259,302,495],evolv:[259,302,350],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,350,380,381,389,403,405,406,412,415,421,434,438,456,464,479,481,486],ewald_disp:415,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,249,250,256,257,258,305,314,315,337,349,365,380,409,502,507,514,527,530,532],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,232,237,242,249,256,257,258,274,286,287,297,301,308,309,337,342,343,356,396,409,416,419,426,429,443,451,453,454,481,482,502,503,510,514,527],exager:521,examin:[6,8,16,228,301,320],examp:498,exampl:[0,1,2,3],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,232,237,244,273,301,316,321,327,328,337,389,396,500,527],exceed:[3,41,61,225,232,273,337,462,508],excel:421,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,232,240,247,248,251,254,256,258,273,274,275,276,277,278,279,280,281,282,283,286,287,291,293,294,296,297,298,302,311,312,319,322,323,333,337,343,349,357,360,361,362,363,364,365,366,367,369,370,373,374,375,380,381,383,386,390,391,392,394,395,396,397,398,400,403,404,405,406,407,408,409,410,411,412,414,415,416,419,420,421,422,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,444,447,452,455,456,458,461,462,463,464,471,479,480,481,483,484,485,486,488,490,491,492,495,497,498,500,502,503,505,508,509,510,511,512,514,518,521,526,527,528,531],exception:498,excess:[221,421],exchang:[2,3,6,8,63,64,210,216,217,239,248,252,256,311,319,345,349,352,380,396,421,515],exchange:380,excit:421,excite:421,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,260,269,304,317,319,344,355,361,389,390,392,404,426,429,432,443,444,451,478,512],exclude:392,exclus:[1,3,12,15,95,184,411,449,451,509,519],excurs:[273,495],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,253,313,363,379,382,395,496,498,508,511,514,527],exempl:469,exemplari:249,exemplifi:421,exert:[6,254,257,289,314,356,357,358,381],exhaust:[216,395,527],exhibit:[100,239,252,273,388,421,509],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,233,248,304,305,307,308,361,362,364,366,367,368,370,374,384,390,417,429,461,478,489,496,498,500,501,502,511,512,513,522,527,528,530],exit:[2,3,11,12,41,59,203,225,379,395,498,499,508,517,518,519,527],exlanatori:3,exp6:2,exp:2,expand:[2,3,44],expans:[12,152,197,203,511,527],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,238,248,250,270,300,306,308,309,314,319,361,381,392,409,446,449,451,495,498,500,502,505,509,514,527],expens:[6,75,207,246,300,304,319,349,361,380,381,392,396,498],experi:[6,13,14,224,233,253,262,272,306,318,319,387,391,416,451,509,514],experienc:[6,12,15,261,262],experiment:[16,248,380,396,514],expert:12,expertis:7,expir:[518,519],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,232,273,289,300,308,319,333,361,363,379,380,383,390,391,395,401,419,432,469,471,487,498,501,502,505,507,510,521,522,527,532],explan:[3,6,61,124,129,152,203,204,219,272,300,429,494,497,498,500,509],explanatori:[3,8,128,203,204,218,219,222,319,390,497,527],explantori:[3,315],explic:450,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,232,320,327,328,365,380,386,398,399,402,407,409,419,421,433,443,486,494,497,501,504,522],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,229,232,240,247,249,251,256,273,275,276,277,278,279,280,281,282,283,291,293,294,296,298,308,309,311,312,319,322,323,342,343,349,357,360,364,366,367,369,370,373,375,390,396,397,398,400,403,404,405,406,407,408,409,410,411,412,413,415,416,418,419,420,422,423,424,425,426,427,428,429,433,434,435,436,437,438,439,440,441,442,443,447,449,451,452,453,454,455,456,458,462,463,464,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,488,490,491,492,500,502,503,509,510,512,513,519,521,522],explictli:[15,513],exploit:[14,16,302],explor:[130,177],expon:[3,310,312,320,419,423,425,428,442,450,464],exponenti:[95,320,423,459,480,488,492,514,527],expos:11,exposit:[216,416,418],express:[6,152,164,178,211,212,229,270,300,310,320,349,355,363,402,419,421,436,446,469,470,479,527],expression:363,expressiont:402,extend:[0,3,6,7],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,231,234,238,239,245,246,247,248,250,251,252,254,256,258,271,273,278,287,300,301,317,318,319,322,325,330,333,334,336,340,341,342,343,344,346,347,349,351,354,358,359,425,446,449,462,463,470,517,518,526],extensiv:[65,210,518],extent:[1,3,41,42,45,59,75,176,180,203,215,225,254,356,359,380,383,398,465,467,481,482,497,500,503],exterior:[3,6,176,358],extern:[2,3,9,94,95,176,206,210,224,229,238],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,273,307,308,309,319,337,389,390,393,394,396,415,426,429,432,446,451,497,498,500,503,512,521,527],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,312,391,412,422,446,470,498,505,517],extract_atom:11,extract_comput:[11,498],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,232,273,347,421,484,521],extrema:442,extreme:421,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:[6,229],f_5:[174,351],f_a:[483,484,485],f_ave:128,f_c:484,f_f:485,f_fix_id:309,f_foo:527,f_harm:347,f_i:[28,459],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,231,268,339,351,518,527],f_ij:459,f_indent:223,f_int:346,f_j:28,f_jj:99,f_k:459,f_langevin:349,f_max:[309,314],f_msst:271,f_r:[257,483,484,485],f_sigma:402,f_solid:347,f_ss:6,face:[3,6,59,61,75,166,176,180,215,354,356,357,358,359,383,425,446,463,500,503],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,250,305,337,347,426,461,469,512],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,232,233,239,248,253,256,258,259,271,273,274,278,302,306,310,318,320,323,326,328,337,341,345,352,353,354,358,370,381,383,390,396,398,399,402,403,405,407,412,413,414,416,417,421,426,429,433,434,446,449,451,453,454,455,456,462,464,471,480,486,497,500,503,504,509,512,514,515,518,521,526,527],factori:[3,498],factoriz:380,fail:[3,9,11,12,61,182,229,233,380,389,391,414,462,498],failur:[133,466,499,527],fairli:[11,451,509,514,522],faken:77,falcon:253,fall:[3,6,207,222,305,498,527],fals:[94,361,469,527],fame:8,famili:[488,497],familiar:[0,11,522],fan:459,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,233,273,300,318,319,337,354,366,370,387,391,392,487,498,500,505,518],farago:256,farrel:[483,485],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,231,233,248,250,254,270,271,273,275,276,277,278,279,280,281,290,293,294,296,297,298,308,309,311,319,325,329,336,339,347,349,353,354,355,357,359,391,429,443,503,512,527,531],fasolino:431,fast:[6,7,9,12,13,15,16,39,203,204,231,284,309,320,350,380,381,404,443,444,449,479,481,482,502,507,509,518,528,532],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,232,240,247,251,255,256,273,275,276,277,278,279,280,281,282,283,291,293,294,296,298,306,310,311,312,319,322,323,337,344,346,349,353,357,360,364,366,367,369,370,373,375,380,381,393,394,396,397,398,400,402,403,404,405,406,407,408,409,410,411,412,415,416,419,420,422,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,447,452,455,456,458,462,463,464,471,479,480,481,483,484,485,486,488,490,491,492,495,503,509,513,521],fastest:[1,6,16,166,349,350,396,497],fatal:[3,517],fault:[74,462],faulti:12,fava:425,favor:228,favorit:7,fbmc:344,fcc:[2,3,6,7,66,74,77,99,117,210],fcm:[290,527],fcold:239,fdirect:236,fdotr:430,fdt:[2,9,241,242,243,320,324],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[0,3,5,6],fecr:419,feedback:[7,231,253],feel:[7,253,254,262,300,358,361,391,451],fehlberg:320,felling:448,felt:358,femtosecond:526,fene:[2,3,6,7,10,15,44],fennel:[412,434],fep:[0,2],ferguson:[6,184,512],fermi:[1,9,10,12,14,164,396,485],fermion:421,fernando:445,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,239,257,273,305,308,310,323,351,380,389,390,391,398,469,497,500,505,509,511,519,527,530],fewer:[1,3,11,14,15,63,262,509],fewest:3,fextern:245,feynman:302,fff:498,ffield:[411,422,461,462,469],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,301,380,381,509],fft_inc:[12,381],fft_lib:12,fft_path:12,fftbench:[380,519],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:239,ficiti:478,fictiti:[6,213,214,238,245,250,302,318,412,434,438,478],field1:[501,505],field2:501,field:[0,2,3,5],fifth:[6,333,423,455],figshar:300,figur:[1,3,8,12,15,309,497,498,522],fij:415,file0:300,file1:[11,13,243,300,348,363,390,505,507,511],file2:[11,13,243,348,363,390,505,507,511],file:[0,1,2,3,4],file_from:205,filen:390,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,242,243,300,304,307,310,311,312,315,316,319,320,321,348,349,377,378,379,390,391,397,398,402,412,419,420,422,423,431,446,447,448,453,454,455,459,460,461,462,469,470,480,481,482,483,484,485,488,496,497,498,501,502,507,511,518,527,530,531,532],filennam:507,filep:[3,203,204,207,502,507,532],filepo:316,fill:[7,9,178,206,305,349,383,392,402,449,462,503,522],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,414],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,231,242,243,244,248,272,300,305,306,314,318,387,389,391,392,412,429,434,438,446,453,454,469,479,481,482,521,522,527],find_custom:8,fine:[15,16,182,213,238,347,392,396,522,527],finer:[152,178,527],finest:380,finger:[178,202,270,503],finish:[6,11,41,225,363,377,379,380,393,395,396,487,505,527,528],finit:[0,3,4],finni:[7,419,479],finverse:236,fiorin:[9,230],fire:[2,3,210],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,74,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,232,242,243,248,249,254,259,270,271,272,273,300,302,307,308,309,311,316,319,323,325,333,334,335,337,338,339,346,347,348,349,351,361,363,364,371,383,389,390,391,392,395,396,397,398,401,402,403,405,407,409,411,412,419,421,422,423,426,427,429,430,431,432,433,434,438,443,444,446,448,449,451,453,454,455,459,461,462,469,470,478,480,481,482,483,484,485,488,492,495,496,497,498,500,501,502,505,507,509,512,513,514,517,518,521,522,527,528,529,530,532],fischer:[6,9,18,19,184,407,512],fit:[3,6,9,12,37,56,199,242,318,337,398,402,431,446,451,453,454,474,481,482,484,508,522,527],five:[77,164,309,390,402,447,500,514],fix:[0,1],fix_deposit:3,fix_flux:216,fix_heat:239,fix_id:[3,229,271,273,275,276,277,278,279,280,281,306,309],fix_manifoldforc:522,fix_modifi:[2,3,6,8,120,121,160,163,210],fix_nh:8,fix_nv:522,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:323,fix_reax_bond:461,fix_saed_vtk:321,fix_setforc:8,fix_shak:323,fix_srd:3,fixedpoint:[229,273],fixextern:245,fixid:[206,216],fji:415,flag1:[235,394],flag2:[235,394],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,235,253,256,260,262,269,270,301,308,319,333,336,337,344,348,357,361,376,378,381,390,394,395,396,398,428,433,446,449,478,493,495,497,498,500,501,502,504,505,506,510,522,527],flag_buck:406,flag_coul:[406,415,438],flag_lj:[415,438],flagfld:[404,443,444],flaghi:[3,404,443,444],flaglog:[404,443,444],flagn:235,flagvf:[404,443,444],flat:[6,15,349,354,355,359],flavor:[2,7,12],fld:[354,443,444],flen:399,flex_press:399,flexibl:[3,6,8,179,206,219,230,250,274,345,352,421,484,518],flip:[3,6,232,273,356,357],floor:527,flop:12,floralwhit:207,flow:[2,4,5],flow_gauss:246,fluctuat:[6,66,95,229,246,248,249,256,259,273,278,300,301,306,324,347,349,373,417],fluid:[2,6,7,9,10,40,69,79,86,96,103,116,127,128,158,173,175,229,232,246,251],fluid_veloc:263,flush:[3,207,517],flux:[2,3,6,65],flv:206,fly:[7,9,12,41,206,210,216,221,233,236,319,323,350,402,449,518,521],fmackai:9,fmag:234,fmass:302,fmax:[389,518],fmomentum:236,fmsec:[2,207,256,257,270,273,306,319,340,341,509,520,526,528],fname:379,fno:[9,15],fnorm:[389,518],fnpt:236,fnve:239,fnvt:236,foce:429,fock:399,focu:323,fogarti:[9,312,462],foil:[152,300,470],fold:[15,335,509],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,233,236,237,241,242,243,245,248,249,250,253,255,256,257,259,262,271,273,278,279,280,281,293,294,296,298,301,302,304,307,308,309,310,312,314,316,318,319,320,321,323,339,340,341,342,345,346,347,348,349,351,352,361,362,366,367,368,369,370,373,375,378,383,386,389,390,391,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,414,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,453,454,455,456,458,459,460,461,462,463,464,466,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488,490,491,492,493,495,497,498,500,501,503,505,507,508,509,512,514,515,516,521,522,527,528,531],foo:[4,8,11,12,203,206,245,320,498,511,527],foo_species:320,foot:6,footprint:[12,396],fopenmp:[9,17],forc:[0,1,2,3,5],force_uvm:16,forceatom:262,forcefield:[318,428],forcegroup:259,forcezero:387,ford:415,forestgreen:207,forev:75,forget:[257,521],forgiv:273,fork:[12,203,522],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,128,152,153,172,173,182,186,203,207,210,211,212,218,219,220,222,223,227,231,249,250,256,258,262,270,296,301,312,314,318,319,320,349,354,358,364,365,368,373,386,388,390,391,398,399,402,409,417,419,421,424,428,429,433,445,446,448,449,453,454,455,456,459,461,462,463,469,470,471,479,481,483,484,485,491,494,497,498,500,505,510,517,518,521,527],formal:[6,82,85,99,249,250,256,273,302,337,345,469],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,242,243,301,304,308,310,312,315,319,320,321,332,348,349,361,362,365,386,390,391,397,398,402,409,419,422,423,433,446,448,453,454,460,461,462,464,470,481,482,488,489,497,498,500,501,502,505,516,517,518,527,529,530],formation:243,former:[6,12,39,41,207,225,349,353,402,404,506,512,527],formerli:[7,13],formul:[1,6,9,40,66,153,213,238,256,273,296,310,312,318,323,348,380,398,402,419,421,425,446,458],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,232,238,251,252,254,256,257,270,300,301,307,316,322,330,335,337,340,341,342,351,354,355,357,359,361,363,364,365,367,374,383,390,398,399,401,402,407,408,409,410,415,416,419,420,425,426,427,428,430,433,434,436,437,438,440,441,443,444,446,450,451,452,463,464,471,479,480,481,483,484,485,488,490,491,496,500,503,510,517,518,526,527,528],forth:[1,6,11,12,13,14,395,498,503,507],fortran:[3,6,9,11,12,13,245,419,429,446,461,462],fortun:8,forward:[3,8,95,379,391,396],foster:[402,458,459],foul:181,found:[3,6,9,12,77,172,203,228,230,239,248,253,259,265,301,344,350,363,379,392,409,412,415,495,501,502,517],four:[6,11,54,87,113,114,152,174,231,271,349,373,390,391,449,495],fourier:[2,6,12],fourth:[6,15,115,318,333,344,407,423,455,469],fox:[6,130,184,477,512],fphi:[37,56,481,482],fpic:12,fplo:[37,56,481,482],fprime:[481,482],fqdn:255,fqq:415,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,202,206,207,217,226,227,228,229,271,305,309,316,317,320,337,342,343,383,391,396,402,404,423,426,443,444,505,510],fragment:[42,253,316],fraig:42,frame:[91,152,207,216,271,309,356,425],framer:[206,207],framework:[5,250,397,470],franc:9,frattl:239,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,211,212,300,337,346,347,348,349,388,391,399,421,442,449,452,459,491,497],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,219,228,236,248,250,256,257,262,273,274,278,279,280,281,293,294,296,298,302,304,319,323,340,341,342,347,389,415,518,521,528],freeli:[0,6,7,12,156,157,171,176,206],freez:[2,3,6,210,215],frenkel:[6,239,248,347],freq:215,frequenc:[3,6,15,39,113,207,221,287,301,302,309,314,320,378,416,421,462,469,495,509,514,527,531],frequent:[3,66,70,74,76,77,81,96,100,117,152,207,226,227,239,244,345,352,451,486,507,519],fri:[271,309],friction:[4,5,6,9,10,42,210,250,256,309,314,319,349,353,355,426,510],friedrich:326,from:[0,1,2,3,5],front:[271,309,356],frontend:[206,313],frozen:[6,123,182,247,249,257,392,424],fs2:[6,99],fscale:253,fstr:527,fstring:498,fstyle:355,ftol:[389,391,495,514],fuchsia:207,fuction:412,fudg:323,fugac:248,fugacity_coeff:248,fulfil:6,full:[1,2,3,6,9,12,15,16,37,39,40,99,206,220,221,230,239,259,300,320,380,381,396,402,419,421,422,425,462,486,500,502,507,508,512,514,519,521,531],full_energi:[3,248],fuller:389,fulli:[3,6,82,250,255,300,389,391,412,459,460,500,522,529,530],fulton:419,fumi:403,func:[498,527],funcfl:419,functionaliri:230,fund:[0,7],fundament:[337,526],funnel_flow:332,funrol:449,further:[3,4,6,8,12,13,63,65,67,72,75,83,94,101,115,118,127,206,207,210,219,222,223,226,233,237,246,259,263,302,310,321,324,326,337,349,351,361,381,387,389,390,391,392,397,401,411,449,469,495,514,515,527],furthermor:[26,187,239,320,417,421],furthest:63,futher:3,futur:0,g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:459,g_p:349,ga3:177,gaa:402,gahler:388,gai:[3,425,479],gain:[15,231,344],gainsboro:207,galindo:450,game:253,gamma0:28,gamma:[3,6,28,256,259,263,301,309,310,312,314,353,416,417,420,425,446,450,473,476,477,480,483,485,488,518],gamma_:[3,349,355],gamma_ijk:483,gamma_n:[355,426],gamma_p:[3,349],gamma_t:[355,426],gammaa:450,gammafactor:259,gammar:450,gan:[459,480,483,485,488],gan_sw:459,gan_tersoff:459,ganzenmuel:[7,9],ganzenmul:9,gao:[6,19,184,407,512],gap:[199,443,444,460,470],gap_2014_5_8_60_17_10_38_466:460,gap_exampl:460,gaseou:7,gass:248,gather:[11,508],gather_atom:11,gather_scatter_loop_unrol:9,gathert_atom:11,gauch:190,gaug:12,gauss:[2,3,118,172,211,212],gaussian:[6,40,65,99,113,115,233,246,249,250,256,302,318,337,341,359,380,416,418,421,424,460,479,495,527,528],gave:[3,451],gavhan:15,gaybern:[2,3,6,7,9,15,156,389],gcc:16,gcmc:[2,3,7,9,210,217],gcores:236,gd3:177,gdot:444,gdrudes:236,ge4:177,gec:[483,485],gen:[273,274],gener:0,genom:7,gentler:[354,357,359],gentli:420,geom:[6,380,418,495,528],geometr:[3,6,7,8,42,59,61,75,86,129,168,169,178,180,203,207,213,224,225,233,238,252,273,279,280,281,293,294,296,298,319,322,330,340,341,342,358,361,380,383,391,401,404,408,410,412,415,421,423,425,427,434,435,436,437,438,439,440,441,442,443,444,445,450,451,454,463,471,482,486,487,490,491,493,500,503,510,518,527],geometri:[3,6,7,9,13,24,38,41,58,75,86,166,178,200,225,226,227,229,233,254,324,376,383,451,500,503],georg:[7,9],georgia:13,gerar:527,gerber:442,germani:9,germann:[278,436,495,514],germano:425,gerolf:13,get:[0,1,3,6,8,9,11],get_natom:[11,498],get_rank:11,get_siz:11,getenv:527,gettimeofdai:12,gewald:[6,380],gezelt:[412,434],gflop:12,gflp:12,gfortran:9,ghost:[3,6,7,12,15,60,63,64,77,176,181,182,229,232,257,273,308,319,321,378,380,392,396,416,417,418,421,426,433,493,505,510,521],ghostwhit:207,giacomo:9,gif:[4,206],gifsicl:206,gigabit:17,giko:2,gikot:2,gillan:470,gingold:[473,474,476],gio:2,git:[7,12,522],github:[8,13,16,230,250,255,460],give:[0,1,2,3,4,5,6,7,8,9,10,11,12,14,15,16,17,54,75,100,117,124,158,161,165,178,203,204,207,213,215,219,220,222,223,229,232,250,273,291,296,300,301,306,314,316,319,351,380,381,389,392,393,396,398,402,418,421,428,429,446,449,451,463,483,484,485,495,497,498,500,510,514,521,528]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sertion:[3,233,248,305],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,233,234,239,244,248,254,259,262,305,319,337,354,356,357,358,359,361,378,383,498,499,500,502,503,510,527],inside:[259,436,498,514],insight:[6,13],instabl:[259,415,468],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,381,391,406,407,430,434,438,442,449,495,501,502,507,515,522,532],install:[0,8],instanc:[6,9,11,211,230,250,356,424,429,451,459,498,521],instantan:[6,65,228,229,231,249,250,273,278,301,306,309,314,316,319,344,506,518],instanti:[6,11,12,216,429,497],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,248,256,259,262,263,301,307,308,317,319,339,357,378,380,381,384,392,396,405,406,419,433,435,442,446,449,452,462,479,486,495,503,507,514,516,521,527],institut:[9,253,304],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,232,240,247,251,256,273,275,276,277,278,279,280,281,282,283,291,293,294,296,298,311,312,319,322,323,357,360,364,366,367,369,370,373,375,381,396,397,398,400,403,404,405,406,407,408,410,411,412,415,416,419,420,422,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,447,452,455,456,458,462,463,464,471,480,481,483,484,485,486,488,490,491,492,503,509,521],instruction:11,insuffici:[3,6,12],insult:273,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,233,238,240,244,245,248,251,256,269,307,308,317,319,337,349,354,358,359,361,363,379,390,392,396,410,425,429,457,463,481,493,497,498,500,501,505,508,509,517,518,527,528],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,231,233,235,245,248,249,250,253,256,257,258,259,301,304,305,308,309,314,319,320,337,339,341,344,348,349,369,380,383,404,416,417,418,432,446,461,462,466,468,470,495,497,498,499,500,508,509,510,514,517,527,528],integer:[3,500],integr:[2,3,5],integral:[302,453,454],integrate_ulsph:327,intel:[1,2,3,7],intel_coprocessor:15,intel_cpu:12,intel_cpu_intelmpi:15,intel_cpu_mpich:15,intel_cpu_openpmi:15,intel_phi:12,intend:[3,6,8,12,13,35,221,249,460,500],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,237,244,252,262,271,273,278,316,319,321,337,345,349,351,352,517,518,526],intensiv:[65,210,518],intepol:527,inter:[17,42,63,64,158,181,182,203,228,256,258,272,311,319,380,391,402,510,521,527,530,532],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,247,248,253,254,256,258,262,287,300,302,304,305,310,312,318,319,320,327,328,337,338,344,349,353,354,355,358,359,365,366,367,368,370,372,374,380,381,389,390,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,456,457,458,459,462,463,464,466,468,469,470,471,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,495,498,500,502,504,505,509,510,512,517,518,521,530],interatom:[3,4,7,9,10,178,203,272,346,347,397,402,419,421,430,446,449,469,484,527],intercept:130,interchang:[6,231],interconnect:17,interconvert:421,intereract:39,interesect:358,interest:[1,5,7,8,9,11,13,75,177,302,344,347,381,420,444,461,462,498,527],interf:[396,522],interfac:[0,3],interfer:[12,273,398],interg:[6,521],intergr:509,interi:444,interior:[3,6,41,358,503],interlac:446,interleav:[6,178,508],intermedi:[6,12,61,206,272,300,373,391,498,499,508,512],intermix:495,intermolecular:[154,398],intern:[0,2,3,5,6,9,11,15,19,20,23,27,31,34,35,39,40,42,65,88,89,95,109,111,129],internal:[3,206,212,305,527],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:255,interpenetr:446,interpentr:[473,474,476],interpol:[6,14,37,56,110,199,206,207,216,242,243,259,300,380,381,391,402,451,453,454,462,475,481,482,483],interpret:[2,6,11,197,206,222,426,471,495,498,514,527],interrupt:309,intersect:[3,6,130,207,358,361,503],intersert:358,interspers:389,interstiti:[176,449],intertia:[3,103],interv:[3,6,99,205,220,231,256,273,309,314,315,328,469,475,495,514,527],intestieti:130,intial:[6,396,398],intiial:[41,505],intiti:[3,336],intra:319,intra_energi:248,intramolecular:[28,154,248],introduc:[6,9,100,117,206,239,273,309,314,319,373,380,397,412,421,434,438,442,480,514,527],introduct:0,intuit:383,inv:[130,177,321],invalid:[3,12,75,97,181,287,391,443,444,502],invari:[117,145,150,152,231]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ptarget:229,pthread:[12,15,16],ptr:[6,11,245,498],ptype1:126,ptype2:126,pu3:177,pu4:177,pu6:177,publicli:5,publish:[7,259,263,289,295,310,385,412,446,449,483,485],pull:[325,333,522],puls:349,pump:[246,443,444],punctuat:[2,495,514],purchas:206,purdu:[9,13],pure:[11,337,429,447,448,483,485,509],purg:[3,501],purpl:[2,207],purport:11,purpos:[3,6,7,9,12,42,63,75,130,140,146,161,162,177,178,180,182,199,203,223,228,229,256,300,302,305,307,318,337,380,406,432,438,449,451,487,493,500,503,507,510,512,513,527,532],push:[3,8,213,224,232,254,272,300,317,325,389,426,471,522],pushd:254,put:[3,6,8,11,12,13,39,61,166,178,203,233,237,356,357,361,383,461,498,500,504],putenv:[511,527],pvar:231,px1:509,px2:509,pxx:[229,273,306,319,380,381,517,518],pxy:[3,6,518],pxz:[3,6,518],py1:509,py2:509,pydir:11,pyi:[229,273,306,319,380,381,518],pymol:[7,11,13],pymol_aspher:0,pympi:11,pypar:11,python:[0,2,3,4,6,7],pythonpath:11,pyz:[3,6,518],pz1:509,pz2:509,pzz:[229,271,273,306,309,319,380,381,518],q_1:469,q_2:469,q_3:469,q_d:521,q_i:[422,442],q_j:442,qbmsst:[2,9],qcore:310,qdamp:310,qdist:[412,434,438,442],qeq1:310,qeq2:310,qeq:[2,3,4,6,7],qeqall:469,qeqallparallel:469,qfile:[310,412],qin:252,qinitmod:469,qmin:388,qmmm:2,qmol:313,qoffload:15,qopenmp:15,qout:252,qoverrid:15,qstep:310,qtb:2,quad:[12,17,396,497],quadrant:15,quadrat:[2,3],quadratur:[95,216],quadrupl:397,quadruplet:[194,198,200,364,366,367,368,370,372,373,374,376],qualifi:[3,255],qualiti:[7,206,207,398],quantic:469,quantit:[78,87,113,114,115,174,426],quantiti:[1,3,4],quantum:[6,9,152,245,250,302,309,313,314,398,402,421,449,469,479],quantum_temperatur:309,quartic:[2,3,7],quartic_spher:216,quartz:[309,314],quasi:302,quat:[3,510],quaternion:[3,6,40,90,124,129,142,156,157,178,275,276,279,280,283,284,285,293,294,425,500,510],quati:[124,129,500],quatj:[124,129,500],quatk:[124,129,500],quatw:[124,129,500],queen:13,quench:[361,495,514],queri:[3,11,54,290,498,527],quest:[6,245],question:[8,9,12,13,289,300,361,458,522,527],queteschin:9,quick:[0,4,12,14,15,16,17,18],quickli:[3,4,8,12,13,39,100,225,232,248,253,337,388,389,391,398],quickmin:[265,289,295,387,388,389,391,514],quicktim:[4,206],quip:2,quit:[2,259,344,363,470],quot:[2,3,12,205,207,307,363,446,495,496,498,508,517,527],quotat:469,r0m:334,r10:402,r12:425,r_1:152,r_2:152,r_c:[413,415,424,485],r_cut:[402,445],r_d:521,r_e:422,r_ewald:321,r_fu:[443,444],r_i:[28,152],r_ii:152,r_ij:[28,402,421,459,492],r_ik:459,r_j:28,r_jik:459,r_m:445,r_me:413,r_mh:424,r_min:414,r_ub:19,r_x86_64_32:12,ra2:177,rad2theta:177,rad:361,radhi:503,radial:[65,75,106,107,124,127,152,162,164,169,219,258,274,286,297,333,343,389,421,428,451,453,454,500,503],radian:[19,20,23,27,31,34,35,37,129,177,185,196,199,318,364,366,370,373,500,503,510],radians:199,radiat:[130,177,349],radic:[180,500],radii:[75,80,119,126,152,228,233,410,419,425,426,443,444,449,465,467,491,503],radit:421,radiu:[2,3,6,40,42,65,75,80,92,93,97,98,119,124,126,130],radlo:503,rafferti:352,rahman:[6,7,229,271,273,274,309,458],rai:[9,16,177],ram:485,raman:15,ramirez:221,ramp:[2,3,6,9,65,161,162,166],ran:[3,6,11],random:[3,6,39,178,181,202,206,215,217,226,227,228,230,233,244,248,249,250,256,257,258,259,269,273,302,305,309,314,317,319,324,337,341,344,349,353,356,404,416,417,418,495,510,515,521,527,528],random_se:495,randomli:[178,181,217,233,248,256,305,337,359,514,515],rang:[1,3,6,7,8,9,10,12,14,15,17,37,39,56,63,75,76,81,96,117,119,120,121,123,127,128,133,152,153,164,172,177,179,182,183,190,199,203,204,206,207,216,217,227,231,232,233,248,250,268,305,321,337,338,344,345,350,352,380,381,389,392,393,396,398,400,402,403,404,405,406,407,408,410,412,413,414,415,416,418,419,421,423,425,427,428,429,431,434,435,436,437,438,439,440,441,442,443,444,445,446,449,450,451,452,456,459,462,463,464,469,478,479,481,482,485,486,490,491,492,494,498,509,510,518,531],rank:[6,11,12,253,350,378,497],rankin:278,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,75,228,256,271,273,319,340,341,353,412,416],rapp:[310,311,312],rappe_and_goddard:311,rare:6,rasmol:[6,7],rasmussen:425,raster3d:[6,7],rate:[2,6,12,15,136],rather:[2,6,9,12,40,41,64,123,161,206,225,232,249,250,319,341,349,353,355,356,357,361,421,453,454,461,481,482,501,505,510,512,517,527],ratio:[6,61,95,111,152,217,225,232,256,258,337,345,352,353,380,394,425,426,463,473,487,497,500,510,514],rational:[350,512],rattl:[2,3,9,210,239,265],rattle:[3,9,210,239,250,289,295,323],rattle_debug:323,ravelo:[278,436],raw:15,rayleigh:[271,309],rb1:177,rbb:469,rbg:207,rcb:[3,41,225],rcm:[97,98],rcmx:[97,98],rcmy:[97,98],rcold:239,rcut:63,rcutfac:[152,470],rd1:391,rdc:16,rdf:[2,3,65],rdn:391,rdt:391,rdx:4,reach:[6,12,41,131,221,225,227,229,231,257,278,320,329,337,344,363,379,395,413,519,521,527],reacquaint:522,react:6,reactant:[320,421],reaction:[9,243,320,325,335,348,359,391,421,423,454,482],reactiv:[9,316,398],read:[2,3,6,7,8,9,11,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,58,61,126,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,202,203,204,206,207,208,209,210,216,217,228,229,232,233,242,243,248,250,253,270,271,273,275,276,277,278,279,280,281,293,294,296,297,298,301,302,304,305,307,308,312,319,320,323,325,329,332,336,339,347,348,349,355,362,364,365,366,367,368,369,370,372,373,374,375,376,377,379,386,390,391,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,456,458,459,460,461,462,463,464,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,489,490,491,492,493,495,497,500,501,502,504,505,506,507,508,510,511,512,514,527,528,529,530,532],read_data:[2,3,6,7,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,64,69,75,78,79,86,87,90,97,98,103,113,114,116,126,173,176,178,179,180,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,200,201,203,206,227,228,232,270,302,308,318,320,348,364,365,366,367,368,369,370,372,373,374,375,376,386,390,391,394,395,396,399,400,401,403,404,405,406,407,408,409,410,412,413,415,416,417,418,421,424,425,427,428,429,432,434,435,436,437,438,439,440,441,442,443,444,445,450,452,456,458,459,461,462,463,464,469,471,478,479,487,490,491,493,497],read_dump:[2,3,203,391,500],read_restart:[2,3,6,8,9,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,39,40,41,43,44,45,46,47,48,49,51,53,54,55,59,60,61,64,178,184,185,186,187,188,189,190,192,193,195,196,198,210,216,217,229,230,232,233,248,259,270,271,273,275,276,277,278,279,280,281,293,294,296,297,298,302,308,319,325,336,339,349,355,364,365,366,367,368,369,370,373,374,375,386,391,399,400,401,403,404,405,406,407,408,409,410,412,413,415,416,417,418,421,424,425,426,427,429,432,434,435,436,437,438,439,440,441,442,443,444,445,450,452,456,458,463,464,471,478,479,487,490,491,493,497,500,501],read_restart_set:8,readabl:[204,206,390,507,532],reader:[3,13,501],readi:[11,12,179,181,182,253,510,521,530,531,532],readme:[1,4,6,8,9,10,11,12,13,15,176,203,204,208,313,385,430,449,461,462,498],real:[3,6,7,11,26,29,30,61,75,99,100,117,152,167,178,187,202,207,215,232,233,236,253,254,257,270,302,309,314,317,353,354,356,357,359,369,380,381,383,387,393,412,449,451,461,462,485,500,503,509,517,520,526,528],realist:[3,233,504],realiz:[75,210,498],realli:[1,3,8,12,123,134,153,207,254,392,429,512,522],realloc:3,realtim:253,reamin:[354,358],rearrang:[204,391],reason:[3,6,7,11,12,18,39,159,170,178,197,219,256,306,319,346,347,350,361,390,391,396,409,413,421,422,424,444,451,487,489,504,509,528],reax:[0,2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,210,310,312,315,316,429,461,462,479,512],rebal:[41,225],rebalanc:[41,225],rebo:[2,7,9,316],rebuild:[11,12,14,15,248,392,416,518],rebuilt:[3,12,203,204,205,206,207,208,392,396],recalcul:[75,95,337],receiv:[3,224,253,255,300,497],recent:[2,3,11,12,15,210,219,222,223,225,226,227,231,252,269],reciproc:[6,12,130,176,177,301,380,403,405,406,412,415,421,434,438,456,464,514],recog:12,recoginz:3,recogn:[3,12,77,180,226,227,273,320,390,419,446,461,498,500,507,508,521],recomend:6,recommed:320,recommend:[7,12,15,206,207,239,309,347,380,421,429,443,444,449,462,463,466,468,469,509,519,522],recompil:[1,3,9,12,208,323],recomput:[112,140,182,237,325,418,512],reconstruct:[3,230,469],record:[208,230,325],recov:[229,239,273],recreat:362,rectangl:[41,225,383],rectangular:[7,41,64,180,225,248,383,500,502,504],rectilinear:[130,177,204],rector:53,recurs:[41,225,402,487],recust:41,recv:497,red:[2,206,207,228,302],redefin:[3,502,508,527],redirect:12,redo:12,reduc:[1,2,3,6,12,16,17,18,26,41,65,75,96,120,121,123,124,125,126],reduct:[17,18,128,130,177,271,309,380],redund:422,ree:474,reed:[271,309],rees:[7,9,13],ref:[346,347,388],refactor:6,refer:[2,3,6,7,8,9,11,12,14,15,28,65,71,75,85,91,94,95,112,113,114,124,126,128,131,156,157,158,171,178,202,203,204,205,210,216,218,219,220,222,223,228,229,231,232,233,239,247,271,273,274,278,300,302,304,305,307,308,309,319,323,325,344,351,356,363,364,375,380,381,388,392,397,404,418,425,432,446,448,449,463,476,477,483,485,495,496,498,502,505,508,509,510,513,514,518],referenc:[3,6,12,65,71,75,125,131,203,204,210,220,231,248,308,351,381,412,428,455,463,498,518,527],reflect:[2,3,6,75,130,152,177,198,206,210,226,227,231,233,262,271,299,301,319,354,356],refman:9,reformat:7,refresh:216,reg:503,regard:[6,61,270,323,324,329,458,462],regardless:[14,75,178,181,202,222,232,256,273,275,276,277,279,280,281,306,319,330,337,396,497,503,510],regim:[6,345,352,413,509],region:[0,2,3,6,7],region_spher:8,region_styl:358,regist:[8,127,154,332],regoin:6,regress:527,regspher:178,regstrip:361,regul:6,regular:[1,3,41,64,96,176,180,203,206,217,225,248,308,349,381,413,432,497,500,502,504],reigon:527,reinder:15,reinhardt:[346,347],reject:[178,228,461,515],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,207,210,217,225,232,233,236,239,248,254,257,269,270,296,300,305,314,316,317,320,325,333,337,339,344,345,349,356,361,380,381,389,421,425,426,443,444,446,463,491,501,509,514,518,521,528],relat:[1,6,8,9,10,12],relationship:[6,242,310,363,380,469,491,521,527],relax:[2,3,4,6,7,210],releas:[0,5,7,8,13,226],relect:[3,451],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,207,211,212,215,216,217,218,219,220,221,222,223,225,226,227,231,232,233,237,239,240,244,247,248,249,252,253,259,260,261,263,264,265,266,267,269,270,272,282,283,284,285,286,287,288,289,290,291,292,295,299,303,304,305,307,308,313,315,316,317,321,323,330,335,337,338,339,344,345,348,349,350,351,352,353,354,355,356,357,359,360,361,380,385,389,399,400,404,410,412,413,415,416,418,421,424,425,426,427,428,433,435,436,437,439,440,441,443,444,451,452,453,454,458,463,471,478,481,482,490,491,492,497,513,528],reli:[3,12,311,421,462,492,500,510],reloc:12,reltol:320,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,232,256,257,264,273,274,279,280,281,293,294,296,298,303,304,328,337,340,341,342,348,349,361,363,371,374,390,402,421,429,442,449,451,479,495,500,501,505,510,512,514,518,519,521,522,527,528],remaina:402,remaind:[9,178,203,233,305,337,350,485,500],remap:[3,6,12,61,63,75,161,178,202,207,232,254,270,296,380,500,501,502],remedi:[6,521],rememb:[2,522],remot:522,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,244,256,257,262,265,269,271,273,279,280,281,293,294,296,298,304,310,319,320,321,323,337,340,341,342,344,361,380,391,415,444,449,500,503,511,512,522,527,528],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,362,511,522],render:[12,13,203,206,207],rendon:[273,274],reneighbor:[3,8,12,39,59,75,225,248,337,350,361,416,517,518],renssela:304,renumb:75,reorder:[3,12,39,497],rep:515,repeat:[2,6,206,207,228,229,248,320,329,383,402,483,485,487,495,514],repeatedli:2,repel:254,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,233,256,278,307,308,314,316,355,396,398,412,426,436,453,454,481,501,502,507,508,518,527,528,530,532],replic:[2,3,7,383,497,500],replica:[0,2,3,4],replica_fil:12,repons:231,report:[0,1],repositori:[7,9,12,430,460,461,462,522],reprens:349,repres:[1,3,6,8,9,12,14,40,41,42,61,70,74,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,231,236,243,249,251,256,259,273,302,304,306,314,319,320,321,325,333,334,349,351,358,381,391,397,402,425,432,442,443,444,446,447,448,456,459,461,462,486,487,495,497,500,510,512,515,521,527,530],represent:[3,6,8,9,59,61,146,180,203,249,250,302,349,402,421,425,449,463,500,503,521],reprocess:505,reproduc:[3,15,273,355,412,419,426],repul:446,repuls:[6,7,35,40,45,46,119,254,310,354,355,358,398,402,410,412,416,421,423,426,428,442,446,450,469,478,485,488,491,492,510],reqir:[310,312],request:[3,6,8,12,41,113,181,199,203,253,259,317,324,337,339,378,380,451,461,462,495,505,510,514,519,522,527,528,530],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,76,81,100,117,127,152,203,206,451,501],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,210,217,220,222,223,239,248,250,252,256,257,269,273,278,296,304,306,314,319,337,340,341],research:[5,7,88,89,241,259,263,324,449,495,514],resembl:[314,522],resepct:6,reserv:[12,253,521],reservoir:[99,239,248,252,256,349],reset:[2,3,6,8,11,12,63,69,75,78,79,86,87,97,98,103,113,114,116,173,178,182,210,211,212,229,232],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[2,6,99,501,505],resid:13,residu:253,residue1:392,resist:[6,253],resolut:[221,469,481,482],resolv:[229,302,337,444,522],resort:3,resourc:[7,397,419],respa:[3,15,213,214,224,234,237,238,251,253,254,268,273,300,311,318,322,325,333,334,335,336,353,354,358,394,397,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,415,416,418,419,420,421,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,447,448,449,450,452,453,454,456,458,460,461,462,463,464,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,487,488,490,491,492,493,508,509,519,520,527],respecifi:449,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,232,239,240,247,251,254,256,257,259,273,275,276,277,278,279,280,281,282,283,289,291,293,294,296,298,310,311,312,319,321,323,325,333,336,349,354,357,360,364,366,367,369,370,373,375,378,380,381,386,389,390,395,396,397,398,400,402,403,404,405,406,407,408,410,411,412,415,416,419,420,422,423,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,446,447,449,451,452,455,456,458,462,463,464,468,469,470,471,480,481,483,484,485,486,488,490,491,492,497,501,510,513,519,521,527,529,530,532],respon:9,respond:[6,7,161,231,232,421,458],respons:[6,7,231,271,345,352],resquar:[2,3,6,7,9,425],rest:[6,8,12,38,58,200,308,312,318,376,402,444,446,493,517,518,521],restart1:302,restart2:302,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,62,63,113,207,211,212,268,308,325,333,334,339,362,517,518],restore_bia:8,restore_bias_al:8,restrain:[2,3,28,210,217,248,271],restraint:[9,230,271,318,336,433],restratin:318,restrict:[1,2,3,6,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,199,202,203,204,206,207,210,213,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,236,239,240,242,246,247,248,249,251,256,257,259,263,271,273,275,276,277,278,279,280,281,282,283,291,293,294,296,297,298,301,302,310,311,312,316,317,319,320,322,323,337,345,346,347,349,350,351,354,355,357,359,360,363,364,366,367,369,370,373,375,380,381,391,394,397,398,400,403,404,405,406,407,408,410,411,412,415,416,419,420,421,422,424,425,426,427,428,429,434,435,436,437,438,439,440,441,442,443,444,446,447,449,451,452,453,454,455,456,458,462,463,464,471,480,481,482,483,484,485,486,488,490,491,492,495,497,500,502,503,505,509,510,511,512,514,526,527,528],resum:527,retain:[2,226,227,398,402,449,497],retart:[32,50,191,371],retir:[3,461],retreiv:8,retriev:[6,8,245,447,448,527],reus:[3,512],rev:[6,13,66,74,100,117,121,152,153,166,217,246,250,256,258,271,273,274,278,296,301,311,314,319,325,337,341,344,346,347,352,388,402,410,411,412,415,419,420,421,425,426,431,436,443,444,445,446,448,453,454,459,463,470,480,483,484,485,488,495],revers:[2,6,8,95,189,228,254,273,291,299,300,310,329,345,346,352,391,442,509,521],revert:[207,517],review:[152,310,325,344,449,460,470,495,514,521,522],rewind:379,rewrap:203,rewrit:[5,12],rewritten:18,rezwanur:458,rfac0:[152,470],rfactor:337,rfile:319,rg0:335,rgb:207,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[453,454,481,482],rho0:[446,466,468,476,477],rho0_meam:446,rho:[2,3,40],rho_0:[476,477],rho_alpha_beta:419,rho_bkgd:446,rho_colloid:354,rho_e:349,rho_fin:348,rho_i:[447,448],rho_initi:348,rho_ref_meam:446,rho_wal:354,rhodo:[9,10],rhodopsin:[1,10,15],rhohi:305,rholo:305,rhosum:[2,110,472,473,474],rhot:239,rhs:320,ribier:388,richard:9,richardson:319,richi:[9,18],rick:[310,311,411,469],rick_and_stuart:311,ridg:[9,18],right:[3,6,11,12,41,74,154,178,196,198,202,204,225,228,254,259,270,299,300,320,363,383,412,500,503,510,522,527],rightmost:[41,225],rigid:[2,3,4],rigidid:129,rigidifi:319,rii:[97,98],rij:[100,117,226,227,300,416,417,453,454,478],rin:[428,439,440],ring:[2,3,6,127,184,302,304],rino:[77,488],rinv:380,rirj:[355,426],risi:[152,470],risk:[8,318,509],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rk4:320,rkf45:320,rlo:[453,454,481,482],rmask:[3,527],rmass:[3,308],rmax:[75,179,226],rmdir:511,rmin0:[152,470],rmin:[75,179,227,436],rms:[320,380,381],rmsd:348,rnemd:6,robert:9,robin:207,robust:[387,388,389,462],rock:446,rockett:459,rod:319,rodata:12,rodnei:314,roi:7,role:[6,344],roll:12,ronchetti:117,room:[59,61],root:[11,95,97,98,205,344,348,419,507],rosati:39,rose:446,ross:446,rosski:302,rosybrown:207,rot:[6,99,302,318,344,528],rotat:[2,3,4,6,7,9,40,65,90,91,92,93,104,142,152,156,157,158],rotate:329,rotation:117,rotaton:503,rough:[6,178,206,359],roughli:[7,10,12,41,161,206,221,248,256,257,265,272,273,287,306,319,337,340,341,344,381,391,396,465,467,502,509],round:[1,3,12,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,42,43,45,46,47,48,49,51,53,54,56,75,123,155,165,184,185,187,188,189,190,192,193,195,196,199,207,213,224,232,240,247,251,256,273,275,276,277,278,279,280,281,282,283,291,293,294,296,298,311,312,319,322,323,357,360,364,366,367,369,370,373,375,381,394,397,398,400,403,404,405,406,407,408,410,411,412,415,416,419,420,422,424,425,426,427,428,432,434,435,436,437,438,439,440,441,442,443,447,452,453,454,455,456,458,462,463,464,471,480,481,483,484,485,486,488,490,491,492,502,503,509,526,527],rous:249,rout:[95,428,442],routin:[5,6,8,11,14,15,37,39,56,96,182,259,449,460,481,482,513],roux:[6,236,257,486,521],row:[6,68,69,71,73,79,84,86,98,102,103,114,116,119,125,126,127,129,131,158,166,173,175,176,177,219,220,222,223,262,319,349,351,359,421],royalblu:207,rozero:446,rperp:[270,329],rpi:304,rpm:12,rrespa:[1,3,5,7,8,15,211,212,270,273,392,397,398,399,400,401,403,404,405,406,407,408,410,411,412,413,415,416,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,447,448,450,452,453,454,456,458,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,487,488,490,491,492,493,509],rspace:3,rsq:[453,454,481,482,489],rsurfac:349,ru3:177,ru4:177,rub:19,rubia:[447,448],rudd:[451,481,482],rudra:[7,9],rudranarayan:[7,304],ruiz:217,rule:0,run1:[6,395,527],run2:[6,377,379,395,527],run3:[6,395,527],run4:[6,395,527],run5:[6,395,527]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59,160,161,162,164,165,166,167,168,169,170,171,229,259,262,273,274,278,304,306,319,352,380,381,390,421,443,444,449,466,468,518,527],tenth:[139,211,379],term:[0,1,3,5,6,7,8,9,12,19,20,21,26,37,40,45,46,63,95,96,97,99,121,123,153,154,156,157,166,171,172,185,186,187,197,199,207,211,212,218,220,222,223,231,232,238,239,249,250,251,256,257,258,259,272,273,274,275,276,277,278,279,280,281,293,294,296,298,302,306,309,318,319,335,340,341,342,349,351,353,355,364,365,375,380,389,392,397,398,402,403,404,405,406,407,408,410,411,412,413,414,415,416,417,419,420,421,422,423,425,426,427,434,438,441,442,443,444,446,447,448,449,451,452,456,463,469,478,480,483,484,485,488,491,509,510,512,518,521],termin:[130,273,389,391,466,468,499,508,519],termostat:341,terrel:388,terri:7,tersoff:[2,3,5,7,8,9,15,96,121,153,154,226,227,412,420,429,459,479],tersoff_1:[483,484,485],tersoff_2:[483,484,485],tersoff_mod:484,tertiari:190,tessel:[9,176],test:[0,3,4,6,7,9,10],test_descriptor_str:3,testf:199,testu:199,tether:[6,268,317,325,333,334,336,347,424],tetot:[9,469],tex:8,texa:458,texas_holdem:318,text:[2,3,4,6,7,8,12,13,37,41,56,199,203,204,206,207,210,216,219,220,221,222,223,225,230,242,243,253,307,348,349,362,381,383,391,419,422,433,446,453,454,470,481,482,496,500,501,517,522,527,529,530],textur:16,tfac_insert:248,tfactor:[3,207],tfinal:527,tfix:318,tflag:206,tfmc:[2,3,7,210],th4:177,thakkar:15,thakker:15,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,26,37,39,40,41,42,56,59,60,61,63,65,71,75,80,94,96,100,115,117,119,123,126,127,129,131,153,176,179,180,181,187,199,202,203,205,207,210,215,217,219,222,223,225,226,227,228,229,232,233,234,237,242,244,246,248,249,250,251,254,255,256,259,268,271,300,301,305,306,307,309,310,312,314,317,318,319,320,321,324,325,326,332,333,335,337,341,342,344,345,349,352,353,354,355,356,357,358,359,361,363,380,381,387,388,389,390,391,392,393,396,398,401,402,403,405,406,407,419,421,425,426,432,443,444,446,451,453,454,461,462,463,469,471,478,479,480,481,482,485,487,489,491,492,495,496,497,498,500,501,502,503,505,508,509,512,514,515,517,519,527,528,530],thank:[253,483,485],thb:462,thb_cutoff:462,thb_cutoff_sq:[461,462],thei:[0,1,2,3,4,6,7,8,11,12,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,36,37,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,59,61,63,65,66,69,71,74,75,78,79,86,87,90,92,95,96,97,98,99,103,113,114,116,118,119,123,125,126,127,128,129,131,152,155,156,158,160,161,164,165,171,173,175,176,178,180,181,182,184,185,187,188,189,190,192,193,195,196,198,199,203,204,206,207,210,211,212,213,215,218,219,220,222,223,224,225,226,227,228,229,231,232,233,238,240,247,248,249,251,252,253,256,257,259,262,270,273,275,276,277,278,279,280,281,282,283,284,285,291,293,294,296,298,304,305,306,307,308,310,311,312,318,319,321,322,323,337,338,341,344,348,349,351,352,355,357,358,360,361,362,363,364,366,367,368,369,370,373,374,375,378,380,381,383,385,386,388,389,390,391,392,395,396,397,398,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,452,454,455,456,458,459,461,462,463,464,469,470,471,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,496,498,500,501,502,503,504,505,509,510,512,513,518,521,522,527,530,531],them:[1,2,3,6,7,8,9,11,12,13,16,39,40,41,54,61,75,99,113,118,125,128,131,154,180,185,203,206,207,208,218,219,220,222,223,225,228,229,231,232,244,253,256,257,265,269,273,275,276,277,278,279,280,281,293,294,298,300,306,308,316,317,318,319,323,337,340,341,342,344,348,349,351,355,356,357,359,361,364,381,383,385,390,391,392,396,397,402,409,419,422,425,429,432,451,463,471,486,487,495,498,500,507,512,515,521,522,527,528],themselv:[6,9,11,181,211,212,225,257,380,381,391,393,397,402,412,419,442,446,447,448,470,527],theor:344,theorem:[249,256,324,402,417],theoret:[115,253,309,480],theori:[3,6,9,12,40,152,216,230,250,273,301,380,381,402,449,491,514],thereaft:[75,264,303,319,334,345,352,498],therebi:[350,443,444],therefor:[3,6,12,66,95,163,236,239,248,257,259,323,344,381,414,460,462,480,486,509,521],therein:[6,446],thereof:95,thermal:[0,2,3,4],thermo:[0,1,2,3],thermo_modifi:[2,3,6,59,65,106,107,128,155,159,161,162,164,165,166,167,168,169,170,210,229,233,273,478,516],thermo_p:[3,65,120,498,518],thermo_press:[65,123,229,236,273,275,276,277,278,279,280,281,306,517,518,521],thermo_styl:[2,3,6,8,65,88,99,104,106,107,120,121,123,128,153,155,164,174,178,202,203,204,210,211,212,213,214,219,220,223,224,228,229,232,236,237,238,251,252,254,256,257,268,271,273,275,276,277,278,279,280,281,293,294,296,298,306,309,322,330,340,341,342,351,354,357,359,361,389,398,424,428,451,461,462,503,505,510,516,517],thermo_temp:[65,123,155,228,229,248,273,275,276,277,278,279,280,281,293,294,296,298,301,306,340,341,342,517,518,521],thermoberendsen:6,thermochem:526,thermochemistri:421,thermodyam:[518,526],thermodyanm:[65,228,337,361,509],thermodynam:[0,3],thermophys:451,thermost:[6,160,215,230,236,257,356,521],thermostat:[0,3],thermostateq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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.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 rigid/local 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 spherical command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix controller command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix flow/gauss command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","fix nve 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","Manifolds (surfacse)","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":226,"default":[36,39,40,55,59,60,61,63,64,74,75,95,96,100,112,113,115,117,118,119,126,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,232,233,237,244,246,248,249,254,256,257,258,259,260,262,268,271,273,274,278,296,297,301,302,305,306,307,308,309,311,314,316,317,319,321,337,339,344,345,346,347,350,352,354,356,361,374,378,380,381,383,384,387,388,390,392,393,394,396,399,402,404,421,443,444,449,451,461,462,478,479,495,496,497,500,501,503,505,507,508,509,512,514,516,517,518,519,520,526,528,530,531],"function":527,"long":[221,403,405,406,407,408,412,414,415,434,438,442,456,464,486],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,addition:[12,13],addtorqu:214,adiabat:6,adjust_dt:326,adp:397,airebo:398,alloi:419,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:215,arrai:6,aspher:[6,90,156,275,279,283,284,293],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,308,527],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:224,awpmd:[9,399],balanc:[41,225],barostat:6,basal:70,bcc:300,beck:400,berendsen:[306,340],between:6,binary2txt:13,bodi:[6,8,42,71,157,276,280,285,294,401],body:9,bond:[8,13,72,73,226,227,228,315],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:402,born:[403,414],boundari:[7,59],box:[6,60,229],brownian:404,buck:[405,406,414,445],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,change_box:61,charmm:[6,19,184,407,442],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,334],citat:7,class2:[9,20,43,185,364,408],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,354,410,491],colvar:[13,230],colvars:9,com:[78,79,159],comb3:411,comb:[311,411],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,523,524,525,526,527,528,529,530,531,532],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,527],compute_modifi:112,condit:7,conduct:[6,345],constant:[6,527],constraint:7,contact:[80,132],control:231,coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:366,coul:[403,405,406,407,408,412,413,414,427,434,438,442,456,464],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:341,csvr:341,cubic:436,custom:[8,203,204],cut:[49,399,405,408,412,415,421,424,434,435,442,450,456,486],cvff:367,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[412,434],defgrad:139,deform:[161,162,232],delete_atom:181,delete_bond:182,delta:23,deposit:233,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,523,524,525,526,527,528,529,530,531,532],diagnost:7,diel:413,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199,200],dilat:85,dimens:201,dipol:[6,28,86,415],dipole:9,direct:236,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:202,distanc:368,distribut:[7,12],document:0,dpd:[9,88,89,416,417],drag:234,dreid:428,dreiding:6,drude:[6,9,163,235,236,257,521],dsf:[412,434],dsmc:418,dump:[6,8,203,204,205,206,208],dump_modifi:207,dynam:310,eam:[13,419],echo:209,edip:420,eff:[9,13,106,107,162,164,169,258,274,286,297,343,421],efield:238,ehex:239,eim:422,elastic:6,emac:13,energi:[135,417],enforce2d:240,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:244,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,513,514,515,516,517,518,519,520,523,524,525,526,527,528,529,530,531,532],exp6:423,exp:[26,187],expand:[46,437],extend:[8,11],extern:245,fcc:300,fdt:417,featur:[7,8,527],fene:[45,46],fep:[9,13,95,212],field:[6,7],file:6,finit:6,fire:310,fix:[2,6,8,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,2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\ No newline at end of file
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,133],brows:0,browser:57,bryantsev:121,btype:[106,123,127,131,154],buc:100,buck:[2,4,32,99],buckingham:[99,100,101,108,134],buckplusattr:148,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,73,74,76,77,79,80,81,84,85,86,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],bulatov:[136,137],bulk:[2,29,67,72,107,135,138,148],bundl:[57,163],button:163,bypass:2,c11:135,c_0:[81,95,152,153],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:81,c_flux:35,c_gauss:117,c_hb:121,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:98,c_prop:2,c_sigma:98,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:77,calcforc:67,calclat:35,calcluat:[37,39,42,106],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:73,call:[1,2,3,4,73,95,104,161,163],callabl:3,callback:3,caltech:[2,114],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,74,81,82,83,92,93,100,101,103,112,118,120,123,127,129,131,144,146,147,154],canon:[68,71,73,80,138],cao1:73,cao2:73,cao:73,capabl:[3,4,95,103],capac:[64,81,151],capolungo:[40,43],captur:[2,95,101,114,119,127,135],carbid:106,carbon:[57,90,95,105,135],card:[4,32,121],care:[2,44,55,67,68,97],carefulli:[3,28],carlo:[2,60],caro:112,carri:[4,81,119],carrillo:4,cartesian:[2,94],cascad:81,cat:[4,57],cate:67,categori:[0,95],cation:[115,148],caus:[1,2,4,44,61,68,72,76,77,82,83,92,93,121,123,129,132,133],caution:1,cautious:95,caveat:95,cbecker:[94,112],cc1:[2,34],ccc:[113,155,156,158,159],ccflag:4,ccflags:4,ccm6:112,ccsi:[113,155,156,158,159],ccu:98,cd2:43,cdeam:112,cdll:3,cdof:2,cdte:98,cdte_bop:98,cdtese:98,cdzn:98,cdznte:98,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,74,81,114,138],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,78,80,82,83,84,97,113,114,118,119,132,133,135,136,137,155,156,157,158,159],centr:63,central:[29,36,38,41,72,77,78,87,138,143,159],centro:2,centroid:73,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:147,ch2:77,ch2lmp:[0,2],ch3:77,chain:[0,2,13,28,60,68,69,71,73,77,80,90,109,110,154],challeng:2,champaign:132,chan:138,chandler:[94,112],chandrasekhar:[2,123],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,74,75,76,77,79,80,81,83,92,93,110,114,119,132,133,135,138,148,154,163],change_box:2,chapter:73,charact:[2,19,57,59,65,76,114,116,122,141,142,145,148],character:[2,29,38,41,149],characterist:79,charg:[1,2,3,32,40,43,44,99,100,105,106,108,109,112,114,115,123,127,131,144,148,158,159,161,162],charl:62,charmm:0,cheaper:[118,146],check:[2,3,19,35,59,75,77,80,92,93,122],checkout:163,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,73,74,79,80,82,84,90,91,93,95,99,102,103,105,106,107,109,110,111,114,117,118,120,121,123,127,128,131,135,139,141,142,144,148,154],chemic:[31,40,43,58,116,142],chemistri:[74,95,98,114],chen:81,cheng:105,chi:[72,115,118],chiral:90,chmod:3,cho:135,choic:[2,4,19,28,29,32,42,55,59,60,67,68,73,93,131],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[156,158],chosen:[2,41,44,50,57,61,62,66,67,68,69,73,111,114,119,122,125,147,156],chunk:0,chunkid:34,ciccotti:77,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:148,cl1:43,clarendon:[13,109],clarifi:[156,158],clark:144,classic:[0,2,4,73,74,81,91,114],classifi:159,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,93,163],climb:93,clockwis:45,clone:163,close:[2,3,19,42,60,61,67,68,70,77,83,93,95,98,106,107,135,141,142,158,163],closer:[19,59,61,79,93],closest:[72,118,146,154],cloud:148,cluster:[2,4,42,63,77],cmax:135,cmd:[3,73],cmdarg:3,cmin:135,cmm:[18,147],cna:29,co2:[43,76,77,116],coars:[13,18,28,50,65,76,116,120,142,147],coarsest:41,code:[0,1],coeff:[6,45,46,55,84,122,150],coeffici:0,coefficienct:110,coefficient0:112,coefficient1:112,coeffieci:[2,96],coeffincientn:112,coexist:114,cohes:[2,115,135],coincid:[83,102,132,133],cold:2,coleman:[40,43],collect:[2,34,44,104],colliex:43,collis:[67,119,162],colloid:2,color:[19,57,59,66,74],column:[2,29,34,36,38,41,42,43,74,81,95,117,121],colvar:0,com:[2,37,63,97,163],comand:60,combiant:107,combin:[2,3,18,32,55,57,58,63,68,70,71,73,83,84,104,106,107,111,114,115,116,130,131,149,155,156,158,159,161],come:[0,2,13,61,62,68,79,80,155,156,158,159,163],comit:163,comm:[0,3,30,93,110],comm_modifi:[2,98,104,110,114,119],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,76,81,93,94,112,113,115,116,122,135,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,61,73,83,84,119,121,155,156,158],commonli:[2,9,37,38,57,91,120,125,149,156,158],commun:[1,2,3,4,19,57,59,61,67,68,81,111],comp:[70,71,77,93,114,146,153,157],compar:[1,2,4,40,43,56,92,93,135,148],comparison:0,compass:[6,20,46,56,84,103],compat:[3,19,49,59,62,63,82,138],compens:[2,114],compil:[4,57,138],complain:3,complement:135,complementari:[106,123],complet:[2,3,19,59,73,93,115],complex:[2,3,9,36,38,41,44,67,70,83,93,114,138],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,73,77,83,92,93,110,114,119,132,133,148,149],componenet:2,composit:[2,67,112],compound:[105,114,115,159],compress:[2,57,69,74],compris:[83,116,146],compton:[40,43],comput:[0,1],computation:[2,81,98],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:83,concentr:[65,76,112,116,142],concept:2,conceptu:[2,61,93,106,135],concern:[2,30,32,66],concis:3,concurr:4,conden:[81,156,158],condens:[2,81,95,108,112,123,159],condit:[2,39,40,42,43,57,58,67,69,72,74,77,78,81,111,114,120],conducit:2,conduct:0,confer:[4,138],configur:[1,2,4,57,61,73,92,93,95,98,113,135,138,155,156,158,159,163],conflict:163,conform:[2,60,61,75,90,93,114],confus:159,conjuct:110,conjug:114,conjunct:[2,32,44,67,93,99,100,106,110,114,121,123,144,147],connect:[2,32,60,77,93,107,119,154,158],conner:95,connor:95,consecut:[3,44,106,123,127],consequ:[1,2,81,122],conserv:[13,60,66,67,68,70,76,77,93,109,110,111,119,129,148],consid:[2,29,32,59,60,81,114,146,148,154],consider:2,consist:[2,3,39,44,50,62,66,68,69,74,75,76,93,95,98,104,106,114,118,132,133,135,138,141,142,146,148],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,82,83,104,146],constrain:[2,63,66,70,71,77,78,92,114],constraint:[19,39,42,59,63,70,77,78,82,92,133],construct:[2,28,29,30,36,38,40,41,43,61,68,75,76,83,109,138,154,155],constructor:3,consult:4,consum:1,contact:[0,107,113,115,118,119,146],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,72,74,76,81,83,93,94,95,98,105,106,109,112,113,114,116,135,138,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,74,79,80,81,83,98,110,125,128,146,157],continuum:[2,58,81],contour_integr:58,contract:[61,68],contrain:77,contrast:[1,2,161],contrib:81,contribut:[2,29,32,33,34,35,39,41,42,61,67,77,92,93,110,112,114,132,133,138,148,163],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,149,163],convent:[13,49,54,56,75,112,114],converg:[2,19,57,59,60,61,69,70,71,74,75,77,92,93,105,106,123,148],convers:[41,57,106,107,108,114,123,127,131,144],convert:[2,5,6,8,12,16,17,18,35,44,46,57,84,85,89,90,93,94,112,138,156,158,162],convex:83,cool:63,coord:[2,3,36,38,72,82,93],coordb:148,coordbb:148,coordiat:92,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,72,77,78,80,81,92,93,94,95,97,113,148],coords:148,copi:[0,3,57,81,93,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,100,106,108],cornel:[2,45],corner:[2,57,83,163],corpor:4,corr:105,correct:[2,3,32,45,57,63,68,74,82,83,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:58,correctli:[3,68,77,83,93,108,133,138,163],correl:[2,35,36,41,66,73],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,72,73,76,77,82,83,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[132,133],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,76,81,106,123,127,138,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,45,92],could:[2,3,19,32,34,35,39,57,59,62,74,81,82,83,92,95,117,121],coulomb:[2,42,92,99,100,101,102,103,105,106,107,108,109,114,119,120,123,127,131,134,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,45,59,61,68,77,83,92,93,117,121],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,75,82,132,150],cov:148,coval:[2,13,114,135,148],cover:[2,58,67,114],cpp:[1,2,3,32,77],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,72,73,75,81,93,95,98,105,112,113,131,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,154],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,92],criterion:[19,44,59,60,92,93,105,114,119,148],critic:[2,24,25,81,92],cross:[4,33,57,93,102,110,112,120,121,123,125,127,145,147,156,158,162],crossov:1,crozier:0,crucial:74,crystal:[2,4,29,30,38,72,80],crystallin:[2,157],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,149],cscl:135,csequ:2,csh:[3,4],cshrc:3,csic:[113,155,156,158,159],csinfo:2,csisi:[113,155,156,158,159],cst:112,cstherm:2,csvr:2,ctcm:[94,112],ctype:3,cu1:43,cu2:43,cu3au:135,cube:[2,83],cubes:[19,59],cubic:[38,67,72,112],cuda:1,cuh:98,cummul:[2,60,121],cumul:[2,68,69,93],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,70,71,75,76,77,78,81,82,92,93,98,105,109,112,114,115,119,122,132,133,135,136,137,145,150,156,158,163],curv:[2,44,70,71],curvatur:[118,146,162],custom:[0,2,3,33,34,35,42,57,60,61,68,69,74,92,95,117,121],cut:[1,2,4,19],cuthi:72,cutinn:[132,133],cutlo:72,cutmax:145,cutoff1:[103,109,123,127,131,134,144,147],cutoff2:[99,100,101,103,108,109,123,127,131,134,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,72,74,82,83,92,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:113,cutoffc:113,cuu3:112,cval:43,cvar:62,cvff:4,cwiggl:82,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,71,83],cylindr:2,cyrot:98,d3q15:67,d3q19:67,d_e:81,daan:80,damp:[2,68,69,71,74,92,93,99,100,102,106,109,114,119,123,131,144,147],dampflag:119,danger:110,darden:109,darken:57,dash:119,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:134,davi:82,david:[156,158],daw:[112,145],dcd:[2,57,73],deactiv:131,debug:[2,3,40,43,44,73],decai:[36,106,162],decid:[2,4,163],decod:57,decompos:[32,149],decomposit:[58,73],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,138],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,72,73,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,99,100,101,102,103,104,106,107,109,110,111,113,114,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,41,62,64,69,82,98,104,111,114,145,149],deform:[2,42,61,68,132,133],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,73,75,77,80,84,85,89,90,91,92,109,112,121],delai:2,delet:[28,60,68,154,163],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:76,dellago:[2,63],deloc:[114,148],delr:135,delta_1:98,delta_3:98,delta_7:98,delta_ij:[135,145],delta_pi:98,delta_r:145,delta_sigma:98,deltah_f:65,demo:3,demonstr:[74,135],dendrim:121,denniston:67,denot:[40,63,106,120],dens:[60,76,114],densiti:[2,19,41,44,58,59,67,81,82,94,95,98,112,135,136,137,141,142,145,146,148,151,152,153],depart:0,departur:74,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,72,76,77,79,81,82,83,84,85,86,88,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,77],depth:[26,57,81,116,118,146],der:[32,104,105,131,161],deriv:[2,32,41,61,62,63,68,69,72,79,80,81,82,83,95,98,104,109,114,115,120,125,129,130,135,138,161],derjagin:161,derlet:72,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,72,73,74,76,79,80,82,92,93,95,97,99,100,102,103,104,105,106,109,112,114,115,116,118,119,120,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,72,81,96,97,102,106,108,114,131,132,133,136,137,145],desir:[2,3,4,35,39,42,44,61,62,66,68,77,92,93,110,112,121,132,133,155,156,158],desktop:[2,57],destabil:98,destre:90,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,74,77,80,81,92,94,95,97,98,101,102,103,104,105,106,109,110,114,115,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,139,141,142,146,148,149,150,160,161,163],detect:[36,93,105,121,122],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,72,73,74,75,76,82,83,95,101,105,109,112,116,117,119,127,135,138,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,62,69,74,95,98,114,137,138,148,159],deviat:[69,72,117],devic:1,devin:105,devis:137,dfactor:57,dft:138,dhug:74,dhugoniot:74,dia:135,diag:76,diagnost:[4,60,76],diagon:[2,41,42,61,68],diagonalstyl:149,diagram:[19,40,43,56,59,73],diallo:121,diam:57,diamet:[2,44,57,104,118,119,125,146,161],diamond:[114,135],dick:2,dicken:62,did:[92,110,112,119,156,158],dielectr:[102,106,107,108,123,127,131,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,72,73,74,77,78,79,80,81,82,83,84,93,94,95,98,101,102,104,105,110,111,112,114,116,118,119,120,123,124,126,127,134,135,136,137,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,76,106,145,157],difficult:[61,62,73,121],difficulti:[36,38,77],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:138,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,75,85,86,87,89,92,95,98,102],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:114,dij:77,dilat:[61,68,69],dim:[44,135],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,74,82,93],dimension:[36,39,40,41,43,81,93,145],dimensionless:[37,41,62,81,149,161],dimer:[2,135],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:109,dir:[1,3,72,74,145],dirac:41,direc:145,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,72,74,79,80,81,82,83,92,93,110,111,119,133],directli:[2,3,32,41,44,57,62,67,76,83,94,95,99,100,101,106,109,112,114,123,127,144,147,154],directori:[0,1,2,3,4,62,79,80,93,94,95,98,105,106,112,113,115,131,135,136,137,138,143,145,148,149,155,156,157,158,159],disabl:[4,81,122],disadvantag:[2,59],disallow:68,discard:[19,59,83],discontinu:[92,129],discourag:135,discret:[2,57,62,67,71],discuss:[0,1],disk:[2,36],disloc:[29,138],disord:[29,138],disp:0,dispar:146,disperion:[109,127],dispers:[2,101,109,127,132,159],displac:[2,37,61,68,72,119],displai:[3,56,57],disregard:138,dissip:[2,31,64,66,79,80,110,111,119,132,133],dist:[2,35,73,75,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,72,74,75,77,78,80,81,82,83,84],distinct:[2,146],distinguish:[2,41,114],distort:94,distrbut:94,distribut:[0,2,3,19,32,41,56,59,66,67,68,94,98,106,112,113,115,135,136,137,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[80,95],divid:[2,4,19,35,39,42,56,59,72,92,93,115,148,159],divis:[2,55,67,98,131],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[104,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,83,92,93,94,95,97,105,106,112,113,115,121,135,136,137,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,71,81,82,83,85,86,87,89,90,93,94,95,96,97,98,101,102,103,104,105,106,107,109,110,112,113,114,116,117,118,119,120,122,125,126,128,129,130,132,133,135,136,137,138,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[44,95,105,113,155,156,157,158,159],dof:39,doi:[2,72],domain:[2,19,40,43,57,59,61,67,68,73,81,82,93],domin:[1,114],don:[0,4,83,135,148,163],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,73,77,79,80,92,93,95,101,112,127,133,134,135,141,142,154,163],donor:121,dot:42,doti:[98,145],doubl:[1,2,3,4,32,45,61,83,98,115,120,138],dover:58,down:[2,3,61,114,148],download:3,downsid:2,dpd:2,dpdtheta:[31,111],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,78],dragforc:67,drai:[57,74],drain:92,dramat:[60,61,68,148],drautz:98,draw:57,drawn:[57,66],drayleigh:74,dreid:2,dreiding:0,drfourth:37,drho:[94,112,141,142],drift:[2,37,63,66],drive:[3,61,68,72,93],driven:[2,50],driver:2,drop:110,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:74,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,72,75,79,80,81,82,83,92,93,107,110,111,112,117,118,132,133,145,146,147,154,156,158,161,162],duffi:81,dullweb:68,dummi:[13,157],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,102],duplic:[19,59,72],durat:[56,81,119],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,92,93,110,131,138,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,70,73,74,75,79,80,81,92,93,110,111,114,132,133,153],dynamo:[94,112,135],dyre:128,e28637:13,e_1:98,e_2:98,e_a:76,e_b:115,e_ee:114,e_hbond:121,e_i:[2,98,115],e_j:[2,98],e_k:98,e_ke:114,e_kl:2,e_lj:[95,109],e_n:[62,98],e_ne:114,e_nn:114,e_pr:114,e_rebo:95,e_torsion:95,e_tot:138,e_vol:138,eaa:84,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,72,73,76,77,78,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,59],eam:[0,94,106],earli:[19,59],earlier:[93,119,135],earth:114,easi:[2,3,32,42,82],easier:[4,57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lerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,76,82,92,138,141,142,145,148],evanseck:[2,5,45,102],evaul:92,even:[2,4,19,29,55,59,61,63,68,81,82,83,92,93,97,114,115,119,146,159],evenli:[19,42,59,67],event:[2,68,81],eventu:2,ever:28,everaer:[104,118,146],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,71,72,74,76,77,81,93,110,131,148,163],everyth:163,everywher:125,eviri:114,evolut:[63,67,73],evolv:[67,73],ewald:[2,40,42,92,99,100,101,106,109,114,123,127,144,147],ewald_disp:109,exact:[19,59,60,66,81],exactli:[2,19,35,44,59,66,74,110,112,119,132,141,142],examin:[2,60,76],exampl:[0,1],exce:[2,4,19,59,61,68,92],exceed:[19,59,68],excel:114,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,73,77,81,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,108,109,110,112,113,114,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:114,exchang:[2,58,63,81,114],excit:114,excite:114,exclud:[2,4,39,41,92,119,132,133,154],exclus:[1,4,32,45,105,138],excurs:68,execut:[1,2,3,57],exempl:148,exemplari:66,exemplifi:114,exert:[2,70,83],exhaust:58,exhibit:[36,63,68,114],exist:[2,3,29,44,56,57,61,84,85,86,87,89,111,154,163],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,72,74,135,138],expens:[2,72,81],experi:[2,75,93,110],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,72,93,97,112,148,150,163],explan:[2,41,72],explic:139,explicit:[2,3,32,76,95,98,102,112,114,122,132,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,74,77,81,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,136,138,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:73,explor:[40,43],expon:[76,112,116,118,121,131,139,147],exponenti:[32,76,116,145,155,159,162],expos:3,exposit:[58,110],express:[2,41,44,61,72,76,81,98,112,114,125,135,148,149],expressiont:98,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,72,75,79,80,81,82,83,118,135,138,146,149],extent:[1,19,21,59,95],exterior:[2,83],extern:[32,57,61,66,67,68,69,71,81,92,136,137],extra:[2,3,4,19,22,39,40,42,43,44,59,68,74,92,109,119,135],extract:[2,3,18,32,93,106,115,135,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,80,114,157],extrema:131,extreme:114,extrins:58,f_1:[2,61],f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:74,f_harm:80,f_i:[13,145],f_id:[2,62],f_ij:145,f_int:79,f_j:13,f_jj:35,f_k:145,f_langevin:81,f_max:74,f_r:[156,157,158],f_sigma:98,f_solid:80,f_ss:2,face:[2,82,83,118,135,146],facil:0,facilit:2,fact:[2,4,80,119,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,73,75,76,77,82,83,89,95,98,99,100,102,106,107,108,110,111,114,119,122,123,135,138,141,142,143,144,147,150,155],fail:[3,61,92,93,108],fairli:[3,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,59,61,68,72,75,82,85,89,93],farrel:[156,158],fashion:[2,19,44,59,62,68,69,74,80,81,82,93,132],fast:[2,4,62,74,76,132,133,138],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,77,79,81,84,85,86,88,89,90,91,94,95,96,98,99,100,101,102,103,104,105,106,109,110,112,113,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,81],fault:29,fava:118,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,76],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,73,83,92,163],fecr:112,feedback:62,feel:[72,83,93],fehlberg:76,felling:137,felt:83,fene:[2,4],fennel:[106,123],fep:0,ferguson:[2,45],fermi:[1,158],fermion:114,fernando:134,few:[1,2,3,63,68,77,92,93,95,148],fewer:[1,3,4],feynman:73,ffield:[105,115,148],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:154,fictiti:[2,73,75,106,123,127,154],field:0,fifth:[2,116,143],figshar:72,figur:[1,4,74,163],fij:109,file0:72,file1:[3,65,72],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,72,76,81,93,94,95,98,106,112,113,115,116,135,136,137,141,142,143,145,148,149,155,156,157,158,159],fill:[44,57,81,98,138,163],filter:58,finchham:[2,108],find:[0,2,3,4,30,32,60,61,62,65,72,75,92,93,106,123,127,135,141,142,148,163],fine:[4,80,163],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:112,fire:[92,93],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,72,73,74,77,78,79,80,81,84,92,93,94,95,97,98,99,100,102,105,106,112,114,115,116,119,120,122,123,127,132,133,135,137,138,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,45,102],fit:[2,75,95,98,135,141,142,157,163],five:[30,74,98,136],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,74],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:77,fix_shak:77,fixedpoint:[61,68],fixid:[57,58],fji:109,flag:[3,4,33,34,40,43,57,60,95,121,122,135,138,154,163],flag_buck:101,flag_coul:[101,109,127],flag_lj:[109,127],flagfld:[132,133],flaghi:[132,133],flaglog:[132,133],flagvf:[132,133],flat:[2,4,81,82],fld:[82,132,133],flexibl:[2,57,114,157],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,72,80,81,90,111],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,77,98,138],fmass:73,fmax:92,fmsec:68,fno:4,fnorm:92,fnve:63,focu:77,foil:[41,72,149],fold:[4,78],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,73,74,75,76,77,79,80,81,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,57,76],foo_species:76,foot:2,forc:[0,1],forcefield:[75,121],forcegroup:67,ford:109,forgiv:68,fork:163,form:[2,28,32,33,34,36,41,42,62,66,75,76,81,82,83,84,87,90,93,95,98,111,112,114,117,121,122,134,135,137,138,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,73,148],format:[2,19,57,59,65,76,81,93,94,95,98,112,115,116,122,135,137,141,142,147,149,159],formation:65,former:[2,19,59,81,98],formul:[1,2,42,68,75,77,95,98,112,114,118,135],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,72,78,82,84,86,95,97,98,102,103,104,109,110,112,113,118,119,120,121,122,123,125,126,127,129,130,132,133,135,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,112,135],forward:[32,93],foster:[98,145],found:[2,30,60,63,67,106,109],four:[2,3,28,41,62,81,90,93,138],fourier:2,fourth:[2,4,37,75,102,116,143,148],fox:[2,40,45,153],fqq:109,fraction:[1,2,4,19,42,57,60,61,74,76,93,98,116,119,132,133],frame:[41,58,74,118],framer:57,framework:[94,149],frattl:63,free:[2,13,29,32,72,79,80,81,93,114,131,138,140,145,161],freedom:[2,39,60,68,69,73,77,80,92,109],freeli:[0,2,57],freez:2,frenkel:[2,63,80],frequenc:[2,4,73,74,76,110,114,148],frequent:[29,30,36,38,41,63],fri:74,friction:[2,74,81,119],from:[0,1],front:74,frontend:57,frozen:[2,39,66,117],fs2:[2,35],ftol:[92,93],fuction:106,fudg:77,fulfil:2,full:[1,2,4,35,57,63,67,72,76,98,112,114,115,118],fuller:92,fulli:[2,72,92,93,106,145,163],fulton:112,fumi:99,funcfl:112,fund:0,funrol:138,further:[2,37,57,67,73,81,92,93,94,97,105,138,148],furthermor:[11,47,63,76,111,114],futur:[0,2,59,66,93,136,137],g_jik:145,g_p:81,ga3:43,gaa:98,gai:118,gain:[4,62],galindo:139,gamma0:13,gamma:[2,13,67,74,110,111,113,118,135,139,151,152,153,155,156,158,159],gamma_:81,gamma_ijk:156,gamma_n:119,gamma_p:81,gamma_t:119,gammaa:139,gammafactor:67,gammar:139,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,45,102],gap:[132,133,149],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:107,gaussian:[2,35,37,66,73,75,110,114,117],gavhan:4,gaybern:[2,4,92],gd3:43,gdot:133,ge4:43,gec:[156,158],gen:68,gener:0,gentler:82,gentli:113,geom:2,geometr:[2,44,59,68,83,93,97,103,104,106,109,114,116,118,120,123,124,125,126,127,128,129,130,131,132,133,134,139,142,146,150,160,161],geometri:[2,9,19,44,59,61],gerber:131,germann:[69,125],germano:118,get:[0,1,2,3,4,19,35,41,44,57,59,61,83,93,106,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[106,123],ghost:[2,4,30,61,68,110,111,114,119,122],gif:57,gifsicl:57,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,44,61,68,72,92,95,98,114,121,135,138,146,156,157,158],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,72,73,74,75,76,77,78,81,82,83,94,95,98,99,100,101,103,104,105,106,107,110,111,112,114,115,116,118,119,121,123,124,125,127,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:138,glotzer:110,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,91,114,121],goe:[28,41,44,63,92,109,113,120,125,128,150,162],gold:29,goldman:74,good:[1,2,4,19,30,40,43,59,62,68,77,93,94,104,112,138,159,163],gordan:41,gordon:2,got:163,gould:[2,45],gov:[0,94,112,115],govern:67,gpa:95,gpl:0,gpt:138,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,77,84,85,86,88,89,90,91,94,95],grab:2,grad:2,gradient:[2,61,63,81,93,133,141,142],graft:60,grain:[2,13,18,28,44,50,65,72,76,116,120,138,142,147],gram:112,gran:[2,82,83],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[74,163],greater:[1,61,66,68,72,97,99,100,101],greatli:[40,63],green:[2,35,57,73,98,163],green_kubo:2,grest:[21,22,60,101,119,127],grid:[19,40,43,59,67,81],grigera:2,gromac:92,gromacs:[2,92,120],groot:110,ground:[2,31,64,114],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,93,148,159],group_id:3,grow:[2,68,72,76,119],growth:2,gsmooth_factor:135,guarante:44,guess:163,gui:[3,163],guid:[1,151,152,153],gu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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 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 quartic command","angle_style sdk command","balance command","bond_style class2 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 morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix nve/manifold/rattle command","fix nvt/manifold/rattle command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born 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_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style 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_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[29,32,36,37,38,40,41,43,44,56,57,58,61,66,67,68,69,73,74,79,80,82,98,114,132,133,138,154],"long":[99,100,101,102,103,106,108,109,123,127,131,144,147],acceler:1,adiabat:2,adp:94,airebo:95,alloi:112,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:58,atom:[2,29,30,36,38,41,42],aug:0,balanc:[19,59],barostat:2,bcc:72,beck:96,between:2,bodi:[2,97],bond:60,bond_styl:[20,21,22,23,24,25,26,27,28],bop:98,born:[99,108],box:[2,61],buck:[100,101,108,134],build:3,calcul:2,centro:29,charmm:[2,5,45,102,131],chunk:[2,34],class2:[6,20,46,84,103],cna:30,code:2,coeffici:2,colloid:[82,104,161],comb3:105,comb:105,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43],conduct:2,constant:2,control:62,core:2,cosin:[7,8,9,10,11,12,47],cossq:85,coul:[99,100,101,102,103,106,107,108,120,123,127,131,144,147],coupl:2,create_atom:44,cubic:125,cut:[25,100,103,106,109,114,117,123,124,131,139,144],cvff:86,data:2,deby:[106,123],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],diel:107,diffus:2,dihedral_styl:[45,46,47,48,49,50,51,52,53,54,55,56],dipol:[2,13,109],discuss:2,disp:2,distanc:87,document:0,dpd:[31,110,111],dreid:121,dreiding:2,drude:2,dsf:[106,123],dump:[2,57],eam:112,edip:113,eff:114,ehex:63,eim:115,elastic:2,energi:111,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],exp6:116,exp:[11,47],expand:[22,126],extend:3,fcc:72,fdt:111,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83],fix_modifi:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],flow:2,fluid:67,flux:35,forc:2,fourier:[14,15,48,88],from:[2,3],gauss:117,gaybern:118,gener:[1,2],github:163,gld:66,global:2,gpu:[96,99,100,102,103,104,106,109,110,112,117,118,120,123,124,125,126,139,140,146,147,150,155,156,157,158,160,161,162],gran:119,granular:2,gromac:120,gyrat:[33,34],harmon:[16,23,24,25,49,51,82,89,143],hbond:121,heat:35,helix:50,hertz:119,hexord:36,histori:119,hook:119,how:2,idealga:151,imag:57,implicit:102,improper_styl:[84,85,86,87,88,89,90,91],indice:0,induc:2,info:[0,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],input:2,install:3,integr:2,intel:[4,5,16,21,23,45,49,53,68,86,89,100,102,118,123,155,156],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,163],lennard:134,librari:[2,3],linear:[130,140],list:122,lj1043:82,lj126:82,lj93:82,lj96:124,local:2,lubric:132,lubricateu:133,luci:[141,142],manifold:[70,71],mdf:134,meam:[135,136,137],measur:1,mgpt:138,mie:139,minim:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83,92],mod:[81,157],model:2,morri:153,mors:[26,95,121,140],movi:57,mpi:3,msd:37,msm:[99,100,102,106,123],multi:[2,51,141,142],multipl:2,nb3b:143,neb:93,nemd:2,nharmon:52,non:2,nongauss:37,nonlinear:27,nph:68,nphug:69,npt:68,nve:70,nvt:[68,71],omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,45,46,47,48,49,50,51,52,53,54,68,69,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,137,140,143,144,146,147,150,155,156,157,158,159,160,161,162],opl:53,opt:[102,112,123,127,140],optim:1,option:2,orient:72,orientord:38,orthogon:2,other:2,output:[2,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],overview:3,packag:[1,4],pair:2,pair_styl:[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],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:73,polariz:2,poli:[132,133],polymorph:145,potenti:2,pppm:2,pressur:39,process:2,properti:2,python:3,qbmsst:74,quadrat:54,quantiti:2,quartic:[17,28],rattl:[70,71,77],rebo:95,region:83,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,74,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],relax:61,replica:2,resquar:146,restart:[2,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],restrain:75,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],rigid:2,ring:90,run:[2,3,58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],scalar:2,script:[2,3],sdk:[18,147],serial:3,set:2,shake:77,share:3,shell:2,shift:[10,11,24,25,47],simpl:15,simul:2,size:2,smooth:[129,130,140],smtbq:148,sna:41,snad:41,snap:149,snapshot:2,snav:41,soft:[131,140,150],spc:2,sph:[151,152,153],spheric:[2,55],spline:[136,137],spring:[78,80],squar:12,srp:154,start:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],stop:[58,59,61,62,63,67,68,69,70,71,72,74,75,77,78,79,80,81,82,83],strategi:1,streitz:106,stress:42,style:[1,2],summari:2,swap:60,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],system:2,tabl:[0,2,65,156],taitwat:[152,153],temperatur:2,tersoff:[156,157,158],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,106,123,127,131],triclin:2,tstat:110,ttm:81,tutori:163,umbrella:91,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:159,vector:2,version:0,viscos:2,visual:2,wall:[2,82,83],water:2,wolf:[99,106],wrapper:3,write:2,xrd:43,yukawa:[160,161],zbl:[158,162]}})
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